##gff-version 3 ##custom-annotation 03-12-2018 ##original-NCBI-annotation 20-03-2014 ##last-updated 03-12-2018 ##note custom annotation used for analysis ##sequence-region NC_002163.1 1 1641386 NC_002163.1 RefSeq CDS 1 1323 . + 0 ID=cds0;Parent=gene0;gene=dnaA;Name=YP_002343473.1;Dbxref=GOA:Q9PJB0 HSSP:O66659 InterPro:IPR001957 InterPro:IPR003593 InterPro:IPR013159 InterPro:IPR013317 UniProtKB FSwiss-Prot:Q9PJB0 Genbank:YP_002343473.1 GeneID:904342;gbkey=CDS;product=chromosomal replication initiation protein;Note=binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication 3B can also affect transcription of multiple genes including itself. NC_002163.1 RefSeq gene 1 1323 . + . ID=gene0;gene=dnaA;Name=dnaA;locus_tag=Cj0001;Dbxref=GeneID:904342;gbkey=Gene NC_002163.1 RefSeq region 301 1239 . + . ID=id151;gene=dnaA;Name=id151;Dbxref=GeneID:904342;gbkey=misc_feature;Note=HMMPfam hit to PF00308 2C Bacterial dnaA protein 2Cscore 4.2e-124 NC_002163.1 RefSeq region 427 450 . + . ID=id152;gene=dnaA;Name=id152;Dbxref=GeneID:904342;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 UTR_Extractor 5'-UTR 1396 1482 . + . ID=utr0;locus_tag=Cj0002;product=DNA polymerase III subunit beta NC_002163.1 RefSeq region 1483 1839 . + . ID=id153;gene=dnaN;Name=id153;Dbxref=GeneID:904340;gbkey=misc_feature;Note=HMMPfam hit to PF00712 2C DNA polymerase III beta subunit 2C N-te 2C score 1.9e-11 NC_002163.1 RefSeq CDS 1483 2550 . + 0 ID=cds1;Parent=gene1;gene=dnaN;Name=YP_002343474.1;Dbxref=GOA:Q0PCC3 InterPro:IPR001001 UniProtKB FTrEMBL:Q0PCC3 Genbank:YP_002343474.1 GeneID:904340;gbkey=CDS;product=DNA polymerase III subunit beta;Note=binds the polymerase to DNA and acts as a sliding clamp NC_002163.1 RefSeq gene 1483 2550 . + . ID=gene1;gene=dnaN;Name=dnaN;locus_tag=Cj0002;Dbxref=GeneID:904340;gbkey=Gene NC_002163.1 RefSeq region 1864 2196 . + . ID=id154;gene=dnaN;Name=id154;Dbxref=GeneID:904340;gbkey=misc_feature;Note=HMMPfam hit to PF02767 2C DNA polymerase III beta subunit 2C cent 2C score 4e-11 NC_002163.1 RefSeq region 2200 2544 . + . ID=id155;gene=dnaN;Name=id155;Dbxref=GeneID:904340;gbkey=misc_feature;Note=HMMPfam hit to PF02768 2C DNA polymerase III beta subunit 2C C-te 2C score 2.7e-05 ### NC_002163.1 RefSeq CDS 2579 4888 . + 0 ID=cds2;Parent=gene2;gene=gyrB;Name=YP_002343475.1;Dbxref=GOA:O87667 HSSP:P06982 InterPro:IPR001241 InterPro:IPR002288 InterPro:IPR003594 InterPro:IPR006171 InterPro:IPR011557 InterPro:IPR013506 InterPro:IPR013759 InterPro:IPR014721 UniProtKB FSwiss-Prot:O87667 Genbank:YP_002343475.1 GeneID:904343;gbkey=CDS;product=DNA gyrase subunit B;Note=negatively supercoils closed circular double-stranded DNA NC_002163.1 RefSeq gene 2579 4888 . + . ID=gene2;gene=gyrB;Name=gyrB;locus_tag=Cj0003;Dbxref=GeneID:904343;gbkey=Gene NC_002163.1 RefSeq region 2666 3097 . + . ID=id156;gene=gyrB;Name=id156;Dbxref=GeneID:904343;gbkey=misc_feature;Note=HMMPfam hit to PF02518 2C Histidine kinase- 2C DNA gyrase B- 2C and H 2C score 1.1e-30 NC_002163.1 RefSeq region 3233 3739 . + . ID=id157;gene=gyrB;Name=id157;Dbxref=GeneID:904343;gbkey=misc_feature;Note=HMMPfam hit to PF00204 2C DNA gyrase B 2C score 6.7e-81 NC_002163.1 RefSeq region 3818 4153 . + . ID=id158;gene=gyrB;Name=id158;Dbxref=GeneID:904343;gbkey=misc_feature;Note=HMMPfam hit to PF01751 2C Toprim domain 2C score 1e-08 NC_002163.1 RefSeq region 3830 3856 . + . ID=id159;gene=gyrB;Name=id159;Dbxref=GeneID:904343;gbkey=misc_feature;Note=PS00177 DNA topoisomerase II signature NC_002163.1 RefSeq region 3962 3994 . + . ID=id160;gene=gyrB;Name=id160;Dbxref=GeneID:904343;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 4652 4852 . + . ID=id161;gene=gyrB;Name=id161;Dbxref=GeneID:904343;gbkey=misc_feature;Note=HMMPfam hit to PF00986 2C DNA gyrase B subunit 2Ccarboxyl terminus 2C score 3.1e-43 ### NC_002163.1 RefSeq gene 4916 5257 . - . ID=gene3;Name=Cj0004c;locus_tag=Cj0004c;Dbxref=GeneID:904344;gbkey=Gene NC_002163.1 RefSeq CDS 4916 5257 . - 0 ID=cds3;Parent=gene3;Name=YP_002343476.1;Dbxref=GOA:Q0PCC1 UniProtKB FTrEMBL:Q0PCC1 Genbank:YP_002343476.1 GeneID:904344;gbkey=CDS;product=monoheme cytochrome C;Note=Original 282000 29 note: Cj0004c 2C possible periplasmic protein 2C len: 113 aa. No Hp match. Contains possible N-terminal signal sequence 7EUpdated 282006 29 note: NCTC11168 Cj0004c encodes a monohaem cytochrome C 28PMID:15632441 29. Together with Cj0005 28molybdopterin oxidoreductase 29 2C they are homologous to sulphite:cytochrome C oxidoreductase 28SOR 29 of Starkeya novella 28PMID:11557133 29. Cj0004 mutants showed wild-type rates of formate-dependent respiration but were unable to respire with sulphite or metabisulphite as electron donors. Periplasmic extracts of wild-type NCTC11168 showed a symmetrical absorption peak 28552nm 29 after addition of sulphite 2C demonstrating the reduction of cytochrome C. No cytochrome C reduction was observed after addition of sulphite to periplasmic extracts of the Cj0004c mutant 28PMID:15632441 29. Characterised within Campylobacter jejuni 2C so not added to product function. Functional classification - Energy metabolism -Respiration - Electron transport 7EPMID:15632441 NC_002163.1 RefSeq region 5120 5137 . - . ID=id162;Name=id162;Dbxref=GeneID:904344;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature ### NC_002163.1 RefSeq CDS 5260 6498 . - 0 ID=cds4;Parent=gene4;Name=YP_002343477.1;Dbxref=GOA:Q0PCC0 InterPro:IPR000572 InterPro:IPR005066 InterPro:IPR008335 UniProtKB FTrEMBL:Q0PCC0 Genbank:YP_002343477.1 GeneID:904345;gbkey=CDS;product=molydopterin containing oxidoreductase;Note=Original 282000 29 note: Cj0005c 2C possible molybdenum containing oxidoreductase 2C len: 412 aa 3B similar to many eukaryotic oxidoreductases e.g. SUOX_HUMAN sulfite oxidase precursor 28488 aa 29 2C fasta scores 3B opt: 543 z-score: 338.2 E 28 29: 1.4e-11 2C 29.8 25 identity in 372 aa overlap and NIA_PETHY nitrate reductase from Petunia hybrida 28909 aa 29 2Cfasta scores 3B opt: 281 z-score: 312.5 E 28 29: 3.8e-10 2C 28.9 25 identity in 395 aa overlap. No Hp match. Contains Pfam match to entry PF00174 oxidored_molyb 2C Oxidoreductase molybdopterin binding domain 2C score 45.20 2C E-value 1e-12 7EUpdated 282006 29 note: Pfam domain PF03404 Mo-co oxidoreductase dimerisation domain identified within CDS. One probable transmembrane helix predicted by TMHMM2.0. Further support given to product function. Supporting paper identified showing interaction with Cj0004c 28PMID:15632441 29. Product function modified to more specific family member based on characterisation paper. Functional classification - Misc 7EPMID:15632441 NC_002163.1 RefSeq gene 5260 6498 . - . ID=gene4;Name=Cj0005c;locus_tag=Cj0005c;Dbxref=GeneID:904345;gbkey=Gene NC_002163.1 RefSeq region 5263 5628 . - . ID=id163;Name=id163;Dbxref=GeneID:904345;gbkey=misc_feature;Note=HMMPfam hit to PF03404 2C Mo-co oxidoreductase dimerisation doma 2C score 6.8e-19 NC_002163.1 RefSeq region 5707 6375 . - . ID=id164;Name=id164;Dbxref=GeneID:904345;gbkey=misc_feature;Note=HMMPfam hit to PF00174 2C Oxidoreductase molybdopterin binding d 2C score 2.1e-14 NC_002163.1 RefSeq region 6007 6039 . - . ID=id165;Name=id165;Dbxref=GeneID:904345;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 6403 6462 . - . ID=id166;Name=id166;Dbxref=GeneID:904345;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0005c by TMHMM2.0 at aa 13-32 ### NC_002163.1 UTR_Extractor 5'-UTR 6499 6525 . - . ID=utr1;locus_tag=Cj0005c;product=molydopterin containing oxidoreductase NC_002163.1 UTR_Extractor 5'-UTR 6683 6702 . + . ID=utr2;locus_tag=Cj0006;product=putative Na 2B 2FH 2B antiporter family protein NC_002163.1 RefSeq CDS 6703 8010 . + 0 ID=cds5;Parent=gene5;Name=YP_002343478.1;Dbxref=GOA:Q0PCB9 InterPro:IPR004770 UniProtKB FTrEMBL:Q0PCB9 Genbank:YP_002343478.1 GeneID:904346;gbkey=CDS;product=Na 2B 2FH 2B antiporter family protein;Note=Original 282000 29 note: Cj0006 2C probable integral membrane protein 2C len: 435 aa 3B similar to e.g. Y325_HAEIN hypothetical protein HI0325 28450 aa 29 2C fasta scores 3B opt: 757 z-score: 1654.9 E 28 29: 0 2C 44.0 25 identity in 450 aa overlap. 47.2 25 identity to HP0758 7EUpdated 282006 29 note: Pfam domain PF03553 Na 2B 2FH 2B antiporter family identified within CDS. Product modified to more specific family member due to motif match. Also 2Celeven probable transmembrane helices predicted by TMHMM2.0 giving further support to product function. No specific characterisation with acceptable identity score has been carried out yet. Thus 2C kept within product function. Functional classification -Transport 2Fbinding proteins - Cations NC_002163.1 RefSeq gene 6703 8010 . + . ID=gene5;Name=Cj0006;locus_tag=Cj0006;Dbxref=GeneID:904346;gbkey=Gene NC_002163.1 RefSeq region 6730 6834 . + . ID=id167;Name=id167;Dbxref=GeneID:904346;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0006 by TMHMM2.0 at aa 10-44 2C 65-87 2C 115-134 2C 146-168 2C188-210 2C 236-253 2C 257-275 2C 288-305 2C 327-349 2C 361-383 and 412-434 NC_002163.1 RefSeq region 6895 6963 . + . ID=id167;Name=id167;Dbxref=GeneID:904346;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0006 by TMHMM2.0 at aa 10-44 2C 65-87 2C 115-134 2C 146-168 2C188-210 2C 236-253 2C 257-275 2C 288-305 2C 327-349 2C 361-383 and 412-434 NC_002163.1 RefSeq region 7000 7032 . + . ID=id168;Name=id168;Dbxref=GeneID:904346;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 7045 7104 . + . ID=id167;Name=id167;Dbxref=GeneID:904346;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0006 by TMHMM2.0 at aa 10-44 2C 65-87 2C 115-134 2C 146-168 2C188-210 2C 236-253 2C 257-275 2C 288-305 2C 327-349 2C 361-383 and 412-434 NC_002163.1 RefSeq region 7138 7206 . + . ID=id167;Name=id167;Dbxref=GeneID:904346;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0006 by TMHMM2.0 at aa 10-44 2C 65-87 2C 115-134 2C 146-168 2C188-210 2C 236-253 2C 257-275 2C 288-305 2C 327-349 2C 361-383 and 412-434 NC_002163.1 RefSeq region 7141 7989 . + . ID=id169;Name=id169;Dbxref=GeneID:904346;gbkey=misc_feature;Note=HMMPfam hit to PF03553 2C Na 2B 2FH 2B antiporter family 2Cscore 4.4e-90 NC_002163.1 RefSeq region 7264 7332 . + . ID=id167;Name=id167;Dbxref=GeneID:904346;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0006 by TMHMM2.0 at aa 10-44 2C 65-87 2C 115-134 2C 146-168 2C188-210 2C 236-253 2C 257-275 2C 288-305 2C 327-349 2C 361-383 and 412-434 NC_002163.1 RefSeq region 7408 7461 . + . ID=id167;Name=id167;Dbxref=GeneID:904346;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0006 by TMHMM2.0 at aa 10-44 2C 65-87 2C 115-134 2C 146-168 2C188-210 2C 236-253 2C 257-275 2C 288-305 2C 327-349 2C 361-383 and 412-434 NC_002163.1 RefSeq region 7471 7527 . + . ID=id167;Name=id167;Dbxref=GeneID:904346;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0006 by TMHMM2.0 at aa 10-44 2C 65-87 2C 115-134 2C 146-168 2C188-210 2C 236-253 2C 257-275 2C 288-305 2C 327-349 2C 361-383 and 412-434 NC_002163.1 RefSeq region 7564 7617 . + . ID=id167;Name=id167;Dbxref=GeneID:904346;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0006 by TMHMM2.0 at aa 10-44 2C 65-87 2C 115-134 2C 146-168 2C188-210 2C 236-253 2C 257-275 2C 288-305 2C 327-349 2C 361-383 and 412-434 NC_002163.1 RefSeq region 7681 7749 . + . ID=id167;Name=id167;Dbxref=GeneID:904346;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0006 by TMHMM2.0 at aa 10-44 2C 65-87 2C 115-134 2C 146-168 2C188-210 2C 236-253 2C 257-275 2C 288-305 2C 327-349 2C 361-383 and 412-434 NC_002163.1 RefSeq region 7783 7851 . + . ID=id167;Name=id167;Dbxref=GeneID:904346;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0006 by TMHMM2.0 at aa 10-44 2C 65-87 2C 115-134 2C 146-168 2C188-210 2C 236-253 2C 257-275 2C 288-305 2C 327-349 2C 361-383 and 412-434 NC_002163.1 RefSeq region 7936 8004 . + . ID=id167;Name=id167;Dbxref=GeneID:904346;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0006 by TMHMM2.0 at aa 10-44 2C 65-87 2C 115-134 2C 146-168 2C188-210 2C 236-253 2C 257-275 2C 288-305 2C 327-349 2C 361-383 and 412-434 ### NC_002163.1 UTR_Extractor 5'-UTR 8103 8143 . + . ID=utr3;locus_tag=Cj0007;product=glutamate synthase large subunit NC_002163.1 RefSeq CDS 8144 12634 . + 0 ID=cds6;Parent=gene6;gene=gltB;Name=YP_002343479.1;Dbxref=GOA:Q0PCB8 InterPro:IPR000583 InterPro:IPR002489 InterPro:IPR002932 InterPro:IPR006982 InterPro:IPR013785 UniProtKB FTrEMBL:Q0PCB8 Genbank:YP_002343479.1 GeneID:904339;gbkey=CDS;product=glutamate synthase large subunit;Note=Original 282000 29 note: Cj0007 2C gltB 2C probable glutamate synthase 28NADPH 29 large subunit 2C len: 1496 aa 3B similar to many e.g. GLTB_ECOLI glutamate synthase 28NADPH 29 large chain 281517 aa 29 2C fasta scores 3B opt: 3846 z-score: 3828.3 E 28 29: 0 2C 42.5 25 identity in 1488 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domains PF00310 Glutamine amidotransferases class-II 2C PF04898 Glutamate synthase central domain 2C PF01645 Conserved region in glutamate synthase and PF01493 GXGXG motif were all identified within CDS. Further support given to product function. Characterised within Bacillus subtilis with acceptable identity score. Thus 2C not added to product function. Functional classification - Central intermediary metabolism - General 7EPMID:2548995 2C PMID:11029411 NC_002163.1 RefSeq gene 8144 12634 . + . ID=gene6;gene=gltB;Name=gltB;locus_tag=Cj0007;Dbxref=GeneID:904339;gbkey=Gene NC_002163.1 RefSeq region 8216 9310 . + . ID=id170;gene=gltB;Name=id170;Dbxref=GeneID:904339;gbkey=misc_feature;Note=HMMPfam hit to PF00310 2C Glutamine amidotransferases class-II 2C score 5.9e-222 NC_002163.1 RefSeq region 9533 10381 . + . ID=id171;gene=gltB;Name=id171;Dbxref=GeneID:904339;gbkey=misc_feature;Note=HMMPfam hit to PF04898 2C Glutamate synthase central domain 2C score 1.8e-181 NC_002163.1 RefSeq region 10547 11644 . + . ID=id172;gene=gltB;Name=id172;Dbxref=GeneID:904339;gbkey=misc_feature;Note=HMMPfam hit to PF01645 2C Conserved region in glutamate synthas 2C score 1e-224 NC_002163.1 RefSeq region 11450 11482 . + . ID=id173;gene=gltB;Name=id173;Dbxref=GeneID:904339;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 11870 12451 . + . ID=id174;gene=gltB;Name=id174;Dbxref=GeneID:904339;gbkey=misc_feature;Note=HMMPfam hit to PF01493 2C GXGXG motif 2C score 4.1e-72 NC_002163.1 RefSeq region 11987 12043 . + . ID=id175;gene=gltB;Name=id175;Dbxref=GeneID:904339;gbkey=misc_feature;Note=PS00095 C-5 cytosine-specific DNA methylases C-terminal signature ### NC_002163.1 RefSeq gene 12644 14395 . + . ID=gene7;Name=Cj0008;locus_tag=Cj0008;Dbxref=GeneID:904337;gbkey=Gene NC_002163.1 RefSeq CDS 12644 14395 . + 0 ID=cds7;Parent=gene7;Name=YP_002343480.1;Dbxref=InterPro:IPR004919 UniProtKB FTrEMBL:Q0PCB7 Genbank:YP_002343480.1 GeneID:904337;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0008 2C unknown 2C len: 583 aa 3B similar to Y686_METJA hypothetical protein MJ0686 28580 aa 29 2C fasta scores 3B opt: 171 z-score: 228.3 E 28 29: 1.9e-05 2C22.8 25 identity in 609 aa overlap. 37.5 25 identity in N-term to HP0938 2C 30.0 25 identity in C-term to HP0937 7EUpdated 282006 29 note: Pfam PF03235 Protein of unknown function 28DUF262 29 2C was present within CDS. Conserved added to product function as motif was identified. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq region 12668 13450 . + . ID=id176;Name=id176;Dbxref=GeneID:904337;gbkey=misc_feature;Note=HMMPfam hit to PF03235 2C Protein of unknown function DUF262 2C score 0.00029 ### NC_002163.1 RefSeq CDS 14398 15843 . + 0 ID=cds8;Parent=gene8;gene=gltD;Name=YP_002343481.1;Dbxref=GOA:Q0PCB6 InterPro:IPR000759 InterPro:IPR001100 InterPro:IPR001327 InterPro:IPR006005 InterPro:IPR012285 InterPro:IPR013027 UniProtKB FTrEMBL:Q0PCB6 Genbank:YP_002343481.1 GeneID:904336;gbkey=CDS;product=glutamate synthase subunit beta;Note=glutamate synthase is composed of subunits alpha and beta 3B beta subunit is a flavin adenine dinucleotide-NADPH dependent oxidoreductase 3B provides electrons to the alpha subunit 2C which binds L-glutamine and 2-oxoglutarate and forms L-glutamate NC_002163.1 RefSeq gene 14398 15843 . + . ID=gene8;gene=gltD;Name=gltD;locus_tag=Cj0009;Dbxref=GeneID:904336;gbkey=Gene NC_002163.1 RefSeq region 14857 15774 . + . ID=id177;gene=gltD;Name=id177;Dbxref=GeneID:904336;gbkey=misc_feature;Note=HMMPfam hit to PF00070 2C Pyridine nucleotide-disulphide oxidoreducta 2C score 2.4e-23 NC_002163.1 RefSeq region 14866 14898 . + . ID=id178;gene=gltD;Name=id178;Dbxref=GeneID:904336;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 15619 15651 . + . ID=id179;gene=gltD;Name=id179;Dbxref=GeneID:904336;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq CDS 15844 16419 . - 0 ID=cds9;Parent=gene9;gene=rnhB;Name=YP_002343482.1;Dbxref=GOA:Q9PJA1 HSSP:Q57599 InterPro:IPR001352 UniProtKB FSwiss-Prot:Q9PJA1 Genbank:YP_002343482.1 GeneID:904334;gbkey=CDS;product=ribonuclease HII;Note=RNH2 3B RNase HII 3B binds manganese 3B endonuclease which specifically degrades the RNA of RNA-DNA hybrids NC_002163.1 RefSeq gene 15844 16419 . - . ID=gene9;gene=rnhB;Name=rnhB;locus_tag=Cj0010c;Dbxref=GeneID:904334;gbkey=Gene NC_002163.1 RefSeq region 15847 16365 . - . ID=id180;gene=rnhB;Name=id180;Dbxref=GeneID:904334;gbkey=misc_feature;Note=HMMPfam hit to PF01351 2C Ribonuclease HII 2C score 7.2e-39 NC_002163.1 RefSeq region 16306 16338 . - . ID=id181;gene=rnhB;Name=id181;Dbxref=GeneID:904334;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq CDS 16452 16691 . - 0 ID=cds10;Parent=gene10;Name=YP_002343483.1;Dbxref=GOA:Q0PCB4 InterPro:IPR000445 InterPro:IPR003583 InterPro:IPR004509 UniProtKB FTrEMBL:Q0PCB4 Genbank:YP_002343483.1 GeneID:904332;gbkey=CDS;product=non-specific DNA binding protein;Note=Updated 282006 29 note: Characterisation work carried out within Bacillus subtilis 2C however 2C sequence alignment was only partial. kept within product function 7EOriginal 282000 29 note: Cj0011c 2C possible non-specific DNA binding protein 2C len: 79 aa 3B similar to the C-terminus of CME1_BACSU comE operon protein 1 28comeA 29 28205 aa 29 2C fasta scores 3B opt: 223 z-score: 359.5 E 28 29: 9e-13 2C 56.9 25 identity in 65 aa overlap. No Hp match. Contains Pfam match to entry PF00633 HHH 2CHelix-hairpin-helix motif. 2C score 31.80 2C E-value 1.6e-05 7EPMID:7968523 2C PMID:7768800 NC_002163.1 RefSeq gene 16452 16691 . - . ID=gene10;Name=Cj0011c;locus_tag=Cj0011c;Dbxref=GeneID:904332;gbkey=Gene NC_002163.1 RefSeq region 16467 16553 . - . ID=id182;Name=id182;Dbxref=GeneID:904332;gbkey=misc_feature;Note=HMMPfam hit to PF00633 2C Helix-hairpin-helix motif 2Cscore 2.1 NC_002163.1 RefSeq region 16554 16643 . - . ID=id183;Name=id183;Dbxref=GeneID:904332;gbkey=misc_feature;Note=HMMPfam hit to PF00633 2C Helix-hairpin-helix motif 2Cscore 1.5e-06 NC_002163.1 RefSeq region 16614 16682 . - . ID=id184;Name=id184;Dbxref=GeneID:904332;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0011c by TMHMM2.0 at aa 4-26 ### NC_002163.1 UTR_Extractor 5'-UTR 16692 16718 . - . ID=utr4;locus_tag=Cj0011c;product=putative non-specific DNA binding protein NC_002163.1 RefSeq CDS 16756 17403 . - 0 ID=cds11;Parent=gene11;gene=rrc;Name=YP_002343484.1;Dbxref=GOA:Q0PCB3 InterPro:IPR003251 InterPro:IPR004039 InterPro:IPR004462 InterPro:IPR009040 InterPro:IPR012347 UniProtKB FTrEMBL:Q0PCB3 Genbank:YP_002343484.1 GeneID:904330;gbkey=CDS;product=non-heme iron protein;Note=Original 282000 29 note: Cj0012c 2C non-haem iron protein 2C len: 215 aa 3B has three possible iron-binding domains 3B C-terminus is similar to rubrerythrins e.g. RUBY_DESVH rubrerythrin 28191 aa 29 2C fasta scores 3B opt: 454 z-score: 746.8 E 28 29: 0 2C 39.5 25 identity in 190 aa overlap 2Cwith the iron-binding residues of both the rubredoxin-like center non-sulfur oxo-bridged di-iron center conserved. N-terminal 33 aa are simialar to the iron-bindingdomain of desulfoferrodoxins e.g. DESR_DESVH desulfoferrodoxin 28125 aa 29 2C fasta scores 3B opt: 161 z-score: 275.8 E 28 29: 4.2e-08 2C68.8 25 identity in 32 aa overlap 2C with the iron-binding residues conserved. No Hp match 7EUpdated 282006 29 note: Pfam domains PF00301 Rubredoxin 2C PF02915 Rubrerythrin and PF06397 Desulfoferrodoxin 2C N-terminal domain were all identified within CDS. Further support given to product function. Characterisation paper within Campylobacter also identified allowing gene name to be designated as Rrc 28Rbo 2FRbr-like protein of C. jejuni 29 protein. Thus 2C not added to product function. Functional classification - Transport 2Fbinding proteins - Cations 7EPMID:15158262 NC_002163.1 RefSeq gene 16756 17403 . - . ID=gene11;gene=rrc;Name=rrc;locus_tag=Cj0012c;Dbxref=GeneID:904330;gbkey=Gene NC_002163.1 RefSeq region 16777 16872 . - . ID=id185;gene=rrc;Name=id185;Dbxref=GeneID:904330;gbkey=misc_feature;Note=HMMPfam hit to PF00301 2C Rubredoxin 2C score 1.9e-05 NC_002163.1 RefSeq region 16903 17283 . - . ID=id186;gene=rrc;Name=id186;Dbxref=GeneID:904330;gbkey=misc_feature;Note=HMMPfam hit to PF02915 2C Rubrerythrin 2C score 6e-43 NC_002163.1 RefSeq region 17296 17403 . - . ID=id187;gene=rrc;Name=id187;Dbxref=GeneID:904330;gbkey=misc_feature;Note=HMMPfam hit to PF06397 2C Desulfoferrodoxin 2CN-terminal domain 2C score 4.4e-20 ### NC_002163.1 UTR_Extractor 5'-UTR 17404 17425 . - . ID=utr5;locus_tag=Cj0012c;product=non-haem iron protein NC_002163.1 RefSeq CDS 17563 19239 . + 0 ID=cds12;Parent=gene12;gene=ilvD;Name=YP_002343485.1;Dbxref=GOA:Q9PJ98 InterPro:IPR000581 InterPro:IPR004404 UniProtKB FSwiss-Prot:Q9PJ98 Genbank:YP_002343485.1 GeneID:904349;gbkey=CDS;product=dihydroxy-acid dehydratase;Note=catalyzes the dehydration of 2 2C3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis NC_002163.1 RefSeq gene 17563 19239 . + . ID=gene12;gene=ilvD;Name=ilvD;locus_tag=Cj0013;Dbxref=GeneID:904349;gbkey=Gene NC_002163.1 RefSeq region 17653 19230 . + . ID=id188;gene=ilvD;Name=id188;Dbxref=GeneID:904349;gbkey=misc_feature;Note=HMMPfam hit to PF00920 2C Dehydratase family 2C score 0 NC_002163.1 RefSeq region 17917 17949 . + . ID=id189;gene=ilvD;Name=id189;Dbxref=GeneID:904349;gbkey=misc_feature;Note=PS00886 Dihydroxy-acid and 6-phosphogluconate dehydratases signature 1 NC_002163.1 RefSeq region 18952 18987 . + . ID=id190;gene=ilvD;Name=id190;Dbxref=GeneID:904349;gbkey=misc_feature;Note=PS00887 Dihydroxy-acid and 6-phosphogluconate dehydratases signature 2 ### NC_002163.1 RefSeq CDS 19251 19775 . - 0 ID=cds13;Parent=gene13;Name=YP_002343486.1;Dbxref=InterPro:IPR009898 UniProtKB FTrEMBL:Q0PCB1 Genbank:YP_002343486.1 GeneID:904347;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0014c 2C probable integral membrane protein 2C len: 174 aa 3B similar to YAGU_ECOLI hypothetical 23.0 kd protein in intF-eaeH intergenic region 28204 aa 29 2C fasta scores 3B opt: 402 z-score: 821.6 E 28 29: 0 2C 45.1 25 identity in 184 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF07274 Protein of unknown function 28DUF1440 29 identified within CDS. Also 2Cthree probable transmembrane helices identified by TMHMM2.0. Further support given to product function. No specific characterisation has been carried out yet. Thus 2C kept within product function. Functional classification - Central intermediary metabolism -General NC_002163.1 RefSeq gene 19251 19775 . - . ID=gene13;Name=Cj0014c;locus_tag=Cj0014c;Dbxref=GeneID:904347;gbkey=Gene NC_002163.1 RefSeq region 19296 19730 . - . ID=id191;Name=id191;Dbxref=GeneID:904347;gbkey=misc_feature;Note=HMMPfam hit to PF07274 2C Protein of unknown function 28DUF1440 29 2C score 1.1e-96 NC_002163.1 RefSeq region 19386 19445 . - . ID=id1;Name=id1;Dbxref=GeneID:904347;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0014c by TMHMM2.0 at aa 12-34 2C 76-98 and 111-130 NC_002163.1 RefSeq region 19482 19550 . - . ID=id1;Name=id1;Dbxref=GeneID:904347;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0014c by TMHMM2.0 at aa 12-34 2C 76-98 and 111-130 NC_002163.1 RefSeq region 19674 19742 . - . ID=id1;Name=id1;Dbxref=GeneID:904347;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0014c by TMHMM2.0 at aa 12-34 2C 76-98 and 111-130 ### NC_002163.1 UTR_Extractor 5'-UTR 19776 19808 . - . ID=utr6;locus_tag=Cj0014c;product=putative integral membrane protein NC_002163.1 RefSeq gene 19867 21093 . - . ID=gene14;Name=Cj0015c;locus_tag=Cj0015c;Dbxref=GeneID:904352;gbkey=Gene NC_002163.1 RefSeq CDS 19867 21093 . - 0 ID=cds14;Parent=gene14;Name=YP_002343487.1;Dbxref=UniProtKB FTrEMBL:Q0PCB0 Genbank:YP_002343487.1 GeneID:904352;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0015c 2C unknown 2C len: 408 aa 3B 35.4 25 identity to HP0711 7EUpdated 282006 29 note: Literature search identified paper 28PMID:15647906 29 giving potential clues to product functionality. Functional classification - Conserved hypothetical proteins 7EPMID:15647906 NC_002163.1 UTR_Extractor 5'-UTR 21094 21129 . - . ID=utr7;locus_tag=Cj0015c;product=hypothetical protein NC_002163.1 UTR_Extractor 5'-UTR 21135 21158 . + . ID=utr8;locus_tag=Cj0016;product=putative transcriptional regulatory protein NC_002163.1 RefSeq gene 21159 21833 . + . ID=gene15;Name=Cj0016;locus_tag=Cj0016;Dbxref=GeneID:904353;gbkey=Gene NC_002163.1 RefSeq CDS 21159 21833 . + 0 ID=cds15;Parent=gene15;Name=YP_002343488.1;Dbxref=GOA:P0C634 GOA:Q9PJ95 InterPro:IPR004479 UniProtKB FSwiss-Prot:P0C634 Genbank:YP_002343488.1 GeneID:904353;gbkey=CDS;product=transcriptional regulator;Note=Original 282000 29 note: Cj0016 2C possible transcriptional regulatory protein 2C len: 224 aa 3B similar to many hypothetical proteins and to TR:Q52925 28EMBL:Z50189 29 Rhizobium meliloti succinoglycan biosynthesis regulator exsB 28234 aa 29 2C fasta scores 3B opt: 284 z-score: 395.5 E 28 29: 9e-15 2C 33.5 25 identity in 191 aa overlap. 33.9 25 identity to HP0639 conserved hypothetical protein 7EUpdated 282006 29 note: Pfam domain PF06508 ExsB identified within CDS. Further support given to product function. Characterisation work carried out within Pseudomonas aeruginosa 2C however 2C identity scores were not acceptable. Thus 2C kept within product function. Functional classification - Broad regulatory functions 7EPMID:9045825 2C PMID:8544814 NC_002163.1 RefSeq region 21369 21593 . + . ID=id192;Name=id192;Dbxref=GeneID:904353;gbkey=misc_feature;Note=HMMPfam hit to PF06508 2C ExsB 2C score 4.4e-41 ### NC_002163.1 RefSeq CDS 21854 23380 . - 0 ID=cds16;Parent=gene16;gene=dsbI;Name=YP_002343489.1;Dbxref=GOA:Q0PCA8 InterPro:IPR003752 UniProtKB FTrEMBL:Q0PCA8 Genbank:YP_002343489.1 GeneID:904354;gbkey=CDS;product=disulfide bond formation protein;Note=Original 282000 29 note: Cj0017c 2C probable ATP 2FGTP binding protein 2C len: 508 aa 3B 37.4 25 identity to HP0595 hypothetical protein. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 7EUpdated 282006 29 note: Pfam domain PF02600 Disulfide bond formation protein DsbB identified within CDS. Gram negative bacterial cells have disulfide bond formation occuring in the oxidative environment of the periplasm and are catalysed by Dsb 28disulfide bond 29 proteins found in the periplasm and in the inner membrane. Supporting paper 28PMID:15632440 29 demonstrates via deletion and complementation that Cj0017c is part of the DsbB family and has been designated as dsbI. There is also strong evidence that Cj0017c and upstream ORF Cj0018c are co-transcribed 28PMID:15632440 29. This information along with motif identification has led to a new product function designation. In addition 2C this coding sequence has 100 25 amino acid identity with DsbI from C. jejuni 81-176 28CJJ81-176_0044 29. Characterisation paper within Campylobacter jejuni has led to being removed from product function. Functional classification -Synthesis and modification of macromolecules - Protein translation and modification 7EPMID:15632440 NC_002163.1 RefSeq gene 21854 23380 . - . ID=gene16;gene=dsbI;Name=dsbI;locus_tag=Cj0017c;Dbxref=GeneID:904354;gbkey=Gene NC_002163.1 RefSeq region 22082 22105 . - . ID=id193;gene=dsbI;Name=id193;Dbxref=GeneID:904354;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 22853 22921 . - . ID=id2;gene=dsbI;Name=id2;Dbxref=GeneID:904354;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0017c by TMHMM2.0 at aa 13-35 2C 50-67 2C 72-91 2C 111-133 and 154-176 NC_002163.1 RefSeq region 22862 23365 . - . ID=id194;gene=dsbI;Name=id194;Dbxref=GeneID:904354;gbkey=misc_feature;Note=HMMPfam hit to PF02600 2C Disulfide bond formation protein DsbB 2C score 1.9e-17 NC_002163.1 RefSeq region 22982 23050 . - . ID=id2;gene=dsbI;Name=id2;Dbxref=GeneID:904354;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0017c by TMHMM2.0 at aa 13-35 2C 50-67 2C 72-91 2C 111-133 and 154-176 NC_002163.1 RefSeq region 23108 23167 . - . ID=id2;gene=dsbI;Name=id2;Dbxref=GeneID:904354;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0017c by TMHMM2.0 at aa 13-35 2C 50-67 2C 72-91 2C 111-133 and 154-176 NC_002163.1 RefSeq region 23180 23233 . - . ID=id2;gene=dsbI;Name=id2;Dbxref=GeneID:904354;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0017c by TMHMM2.0 at aa 13-35 2C 50-67 2C 72-91 2C 111-133 and 154-176 NC_002163.1 RefSeq region 23276 23344 . - . ID=id2;gene=dsbI;Name=id2;Dbxref=GeneID:904354;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0017c by TMHMM2.0 at aa 13-35 2C 50-67 2C 72-91 2C 111-133 and 154-176 ### NC_002163.1 RefSeq gene 23392 23559 . - . ID=gene17;gene=dba;Name=dba;locus_tag=Cj0018c;Dbxref=GeneID:904356;gbkey=Gene NC_002163.1 RefSeq CDS 23392 23559 . - 0 ID=cds17;Parent=gene17;gene=dba;Name=YP_002343490.1;Dbxref=UniProtKB FTrEMBL:Q0PCA7 Genbank:YP_002343490.1 GeneID:904356;gbkey=CDS;product=disulfide bond formation protein;Note=Original 282000 29 note: Cj0018c 2C small hydrophobic protein 2C len: 55 aa 3B similar to TR:E1314390 28EMBL:AL031184 29 small hydrophobic protein SC2A11.18 from Streptomyces coelicolor 2855 aa 29 2C fasta scores 3B opt: 72 z-score: 141.4 E 28 29: 1.3 2C 32.7 25 identity in 49 aa overlap. 49.1 25 identity to HP0594 hypothetical protein 7EUpdated 282006 29 note: Gram negative bacterial cells have disulfide bond formation occuring in the oxidative environment of the periplasm and are catalysed by Dsb 28disulfide bond 29 proteins found in the periplasm and in the inner membrance. Supporting paper 28PMID:15632440 29 speculates Dba has a supportive role as dba is co-transcribed with dsbI. This information has led to a new product function designation. Dba has 100 25 amino acid identity with Dba from 81-176 28CJJ81176_0045 29. Characterisation paper within Campylobacter jejuni has led to being removed from product function. Functional classification - Synthesis and modification of macromolecules - Protein translation and modification 7EPMID:15632440 NC_002163.1 RefSeq region 23428 23487 . - . ID=id195;gene=dba;Name=id195;Dbxref=GeneID:904356;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0018c by TMHMM2.0 at aa 25-44 ### NC_002163.1 UTR_Extractor 5'-UTR 23560 23582 . - . ID=utr9;locus_tag=Cj0018c;product=disulphide bond formation protein NC_002163.1 RefSeq CDS 23665 25443 . - 0 ID=cds18;Parent=gene18;Name=YP_002343491.1;Dbxref=GOA:Q0PCA6 InterPro:IPR003660 InterPro:IPR004089 InterPro:IPR004090 UniProtKB FTrEMBL:Q0PCA6 Genbank:YP_002343491.1 GeneID:904357;gbkey=CDS;product=MCP-domain signal transduction protein;Note=Original 282000 29 note: Cj0019c 2C probable MCP-domain signal transduction protein 2C len: 592 aa 3B similar to other proteins containing the MCP domain e.g. HLYB_VIBCH hemolysin secretion protein precursor 28548 aa 29 2C fasta scores 3B opt: 418 z-score: 492.5 E 28 29: 3.5e-20 2C 22.7 25 identity in 565 aa overlap 2C and AER_ECOLI aerotaxis receptor 28506 aa 29 2C fasta scores 3B opt: 299 z-score: 391.2 E 28 29: 1.6e-14 2C 25.5 25 identity in 357 aa overlap. 27.5 25 identity to HP0103. Contains N-terminal signal sequence and transmembrane anchor around aa 250. Also contains Pfam match to entry PF00015 MCPsignal 2C Methyl-accepting chemotaxis protein 28MCP 29 signaling domain 2C score 104.90 2CE-value 1.7e-28 7EUpdated 282006 29 note: Pfam domain PF00672 HAMP domain identified within CDS. Two probable transmembrace helices identified by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity scores has yet been carried out. Thus 2C kept within product function. Functional classification - Signal transduction NC_002163.1 RefSeq gene 23665 25443 . - . ID=gene18;Name=Cj0019c;locus_tag=Cj0019c;Dbxref=GeneID:904357;gbkey=Gene NC_002163.1 RefSeq region 23668 24375 . - . ID=id196;Name=id196;Dbxref=GeneID:904357;gbkey=misc_feature;Note=HMMPfam hit to PF00015 2C Methyl-accepting chemotaxis protein 28MCP 29 s 2C score 5.5e-10 NC_002163.1 RefSeq region 24505 24720 . - . ID=id197;Name=id197;Dbxref=GeneID:904357;gbkey=misc_feature;Note=HMMPfam hit to PF00672 2C HAMP domain 2C score 1.8e-06 NC_002163.1 RefSeq region 24661 24729 . - . ID=id3;Name=id3;Dbxref=GeneID:904357;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0019c by TMHMM2.0 at aa 10-32 and 239-261 NC_002163.1 RefSeq region 25348 25416 . - . ID=id3;Name=id3;Dbxref=GeneID:904357;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0019c by TMHMM2.0 at aa 10-32 and 239-261 NC_002163.1 RefSeq gene 25433 26347 . - . ID=gene19;Name=Cj0020c;locus_tag=Cj0020c;Dbxref=GeneID:904360;gbkey=Gene NC_002163.1 RefSeq CDS 25433 26347 . - 0 ID=cds19;Parent=gene19;Name=YP_002343492.1;Dbxref=GOA:Q0PCA5 InterPro:IPR004852 InterPro:IPR009056 UniProtKB FTrEMBL:Q0PCA5 Genbank:YP_002343492.1 GeneID:904360;gbkey=CDS;product=cytochrome C551 peroxidase;Note=Original 282000 29 note: Cj0020c 2C probable cytochrome C551 peroxidase 2C len: 304 aa 3B similar to CCPR_PSEAE cytochrome C551 peroxidase precursor 28EC 1.11.1.5 29 28346 aa 29 2C fasta scores 3B opt: 775 z-score: 1167.7 E 28 29: 0 2C 42.3 25 identity in 298 aa overlap. No Hp ortholog. Contains 2x PS00190 Cytochrome c family heme-binding site signature and probable N-terminal signal sequence 7EUpdated 282006 29 note: Characterisation has been carried out within Pseudomonas aeruginosa with acceptable identity score. Appropriate motifs also identified. not added to product function. Functional classification - Cell processes - Detoxification 7EPMID:7781769 2C PMID:8591033 2C PMID:1657179 NC_002163.1 RefSeq region 25454 25786 . - . ID=id198;Name=id198;Dbxref=GeneID:904360;gbkey=misc_feature;Note=HMMPfam hit to PF00034 2C Cytochrome c 2C score 0.0083 NC_002163.1 RefSeq region 25736 25753 . - . ID=id199;Name=id199;Dbxref=GeneID:904360;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature NC_002163.1 RefSeq region 25799 26311 . - . ID=id200;Name=id200;Dbxref=GeneID:904360;gbkey=misc_feature;Note=HMMPfam hit to PF03150 2C Di-haem cytochrome c peroxidase 2C score 3.8e-69 NC_002163.1 RefSeq region 26165 26182 . - . ID=id201;Name=id201;Dbxref=GeneID:904360;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature ### NC_002163.1 UTR_Extractor 5'-UTR 26348 26381 . - . ID=utr10;locus_tag=Cj0020c;product=cytochrome C551 peroxidase NC_002163.1 RefSeq gene 26411 27289 . - . ID=gene20;Name=Cj0021c;locus_tag=Cj0021c;Dbxref=GeneID:904361;gbkey=Gene NC_002163.1 RefSeq CDS 26411 27289 . - 0 ID=cds20;Parent=gene20;Name=YP_002343493.1;Dbxref=GOA:Q0PCA4 InterPro:IPR002529 InterPro:IPR011234 UniProtKB FTrEMBL:Q0PCA4 Genbank:YP_002343493.1 GeneID:904361;gbkey=CDS;product=fumarylacetoacetate 28FAA 29 hydrolase family protein;Note=Original 282000 29 note: Cj0021c 2C unknown 2C len: 292 aa 3B similar to hypothetical proteins e.g. TR:O06724 28EMBL:Z99109 29 B. subtilis yisK 28301 aa 29 2C fasta scores 3B opt: 665 z-score: 1018.0 E 28 29: 0 2C 43.1 25 identity in 255 aa overlap 2C and to C-terminal half of HPCE_ECOLI 2-hydroxyhepta-2 2C4-diene-1 2C7-dioate isomeraase 2F5-carboxymethyl-2-oxo-hex-3-ene-1 2C7-dioate decarboxylase 28405 aa 29 2C fasta scores 3B opt: 328 z-score: 381.2 E 28 29: 5.6e-14 2C 31.2 25 identity in 199 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF01557 Fumarylacetoacetate 28FAA 29 hydrolase family identified within CDS. Product modified to more specific family member due to motif match. No specific characterisation with acceptable identity score has been carried out yet. Thus 2C kept within product function. Functional classification - Misc NC_002163.1 RefSeq region 26504 27007 . - . ID=id202;Name=id202;Dbxref=GeneID:904361;gbkey=misc_feature;Note=HMMPfam hit to PF01557 2C Fumarylacetoacetate 28FAA 29 hydrolase fam 2C score 1.4e-44 ### NC_002163.1 RefSeq CDS 27402 28304 . - 0 ID=cds21;Parent=gene21;Name=YP_002343494.1;Dbxref=GOA:Q0PCA3 InterPro:IPR002942 InterPro:IPR006145 InterPro:IPR006224 UniProtKB FTrEMBL:Q0PCA3 Genbank:YP_002343494.1 GeneID:904362;gbkey=CDS;product=ribosomal pseudouridine synthase;Note=Original 282000 29 note: Cj0022c 2C possible ribosomal pseudouridine synthase 2C len: 300 aa 3B similar to e.g. RLUD_ECOLI ribosomal large subunit pseudouridine synthase D 28EC 4.2.1.70 29 28326 aa 29 2C fasta scores 3B opt: 344 z-score: 412.1 E 28 29: 1.2e-15 2C 29.6 25 identity in 243 aa overlap. 41.1 25 identity to HP0347. Contains PS01129 Hypothetical yabO 2FyceC 2FsfhB family signature and Pfam match to entry PF00849 YABO 2C Hypothetical yabO 2FyceC 2FsfhB family 2C score 182.90 2C E-value 5e-51. Also similar to Cj1280c 2831.0 25 identity 29 and Cj0708 2828.0 25 identity 29 7EUpdated 282006 29 note: Characterisation has been carried out within Escherichia coli 2C however 2C identity score was marginal. Pfam domain PF00849 RNA pseudouridylate synthase was identified within CDS. This Pfam motif has been updated from the previous designation. Further support given to product function. kept within product function. Functional classification -Synthesis and modification of macromolecules - Ribosome maturation and modification 7EPMID:11453071 2C PMID:11087118 2C PMID:9814761 2CPMID:14501142 NC_002163.1 RefSeq gene 27402 28304 . - . ID=gene21;Name=Cj0022c;locus_tag=Cj0022c;Dbxref=GeneID:904362;gbkey=Gene NC_002163.1 RefSeq region 27624 28076 . - . ID=id203;Name=id203;Dbxref=GeneID:904362;gbkey=misc_feature;Note=HMMPfam hit to PF00849 2C RNA pseudouridylate synthase 2C score 7.1e-43 NC_002163.1 RefSeq region 27918 27962 . - . ID=id204;Name=id204;Dbxref=GeneID:904362;gbkey=misc_feature;Note=PS01129 Rlu family of pseudouridine synthase signature ### NC_002163.1 UTR_Extractor 5'-UTR 28305 28352 . - . ID=utr11;locus_tag=Cj0022c;product=putative ribosomal pseudouridine synthase NC_002163.1 UTR_Extractor 5'-UTR 28342 28381 . + . ID=utr12;locus_tag=Cj0023;product=adenylosuccinate lyase ### NC_002163.1 RefSeq CDS 28382 29710 . + 0 ID=cds22;Parent=gene22;gene=purB;Name=YP_002343495.1;Dbxref=GOA:Q0PCA2 InterPro:IPR000362 InterPro:IPR003031 InterPro:IPR004769 UniProtKB FTrEMBL:Q0PCA2 Genbank:YP_002343495.1 GeneID:904425;gbkey=CDS;product=adenylosuccinate lyase;Note=Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide NC_002163.1 RefSeq gene 28382 29710 . + . ID=gene22;gene=purB;Name=purB;locus_tag=Cj0023;Dbxref=GeneID:904425;gbkey=Gene NC_002163.1 RefSeq region 28388 29239 . + . ID=id205;gene=purB;Name=id205;Dbxref=GeneID:904425;gbkey=misc_feature;Note=HMMPfam hit to PF00206 2C Lyase 2C score 3.7e-45 NC_002163.1 RefSeq region 29048 29080 . + . ID=id206;gene=purB;Name=id206;Dbxref=GeneID:904425;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 29162 29191 . + . ID=id207;gene=purB;Name=id207;Dbxref=GeneID:904425;gbkey=misc_feature;Note=PS00163 Fumarate lyases signature ### NC_002163.1 RefSeq region 29726 29995 . + . ID=id208;gene=nrdA;Name=id208;Dbxref=GeneID:904363;gbkey=misc_feature;Note=HMMPfam hit to PF03477 2C ATP cone domain 2C score 6.2e-18 NC_002163.1 RefSeq CDS 29726 32095 . + 0 ID=cds23;Parent=gene23;gene=nrdA;Name=YP_002343496.1;Dbxref=GOA:Q0PCA1 InterPro:IPR000788 InterPro:IPR005144 InterPro:IPR013346 InterPro:IPR013509 UniProtKB FTrEMBL:Q0PCA1 Genbank:YP_002343496.1 GeneID:904363;gbkey=CDS;product=ribonucleotide-diphosphate reductase subunit alpha;Note=Catalyzes the rate-limiting step in dNTP synthesis NC_002163.1 RefSeq gene 29726 32095 . + . ID=gene23;gene=nrdA;Name=nrdA;locus_tag=Cj0024;Dbxref=GeneID:904363;gbkey=Gene NC_002163.1 RefSeq region 30125 30355 . + . ID=id209;gene=nrdA;Name=id209;Dbxref=GeneID:904363;gbkey=misc_feature;Note=HMMPfam hit to PF00317 2C Ribonucleotide reductase 2Call-alpha d 2C score 3.2e-35 NC_002163.1 RefSeq region 30359 32035 . + . ID=id210;gene=nrdA;Name=id210;Dbxref=GeneID:904363;gbkey=misc_feature;Note=HMMPfam hit to PF02867 2C Ribonucleotide reductase 2Cbarrel doma 2C score 7.5e-129 NC_002163.1 RefSeq region 31637 31705 . + . ID=id211;gene=nrdA;Name=id211;Dbxref=GeneID:904363;gbkey=misc_feature;Note=PS00089 Ribonucleotide reductase large subunit signature ### NC_002163.1 RefSeq CDS 32134 33519 . - 0 ID=cds24;Parent=gene24;Name=YP_002343497.1;Dbxref=GOA:Q0PCA0 InterPro:IPR001991 UniProtKB FTrEMBL:Q0PCA0 Genbank:YP_002343497.1 GeneID:904364;gbkey=CDS;product=sodium:dicarboxylate family transmembrane symporter;Note=Original 282000 29 note: Cj0025c 2C probable transmembrane symporter 28possibly glutamate 29 2C len: 461 aa 3B similar to many e.g. YB54_HAEIN hypothetical symporter HI1154 28440 aa 29 2C fasta scores 3B opt: 650 z-score: 890.6 E 28 29: 0 2C 33.7 25 identity in 454 aa overlap 2C and TR:Q46202 28EMBL:X86516 29 Clostridium perfringens gluT-R gene 28fragment 29 28132 aa 29 2C fasta scores 3B opt: 406 z-score: 569.0 E 28 29: 1.9e-24 2C 49.6 25 identity in 119 aa overlap. No Hp match. Contains Pfam match to entry PF00375 SDF 2CSodium:dicarboxylate symporter family 2C score 142.20 2CE-value 9.4e-39 7EUpdated 282006 29 note: Pfam domain PF00375 Sodium:dicarboxylate symporter family identified within CDS. Eleven probable transmembrane helices predicted by TMHMM2.0. Product modified to more specific family member due to motif match. No specific characterisation with acceptable identity score has been carried out yet. Thus 2C kept within product function. Functional classification - Transport 2Fbinding proteins - Other NC_002163.1 RefSeq gene 32134 33519 . - . ID=gene24;Name=Cj0025c;locus_tag=Cj0025c;Dbxref=GeneID:904364;gbkey=Gene NC_002163.1 RefSeq region 32170 33399 . - . ID=id212;Name=id212;Dbxref=GeneID:904364;gbkey=misc_feature;Note=HMMPfam hit to PF00375 2C Sodium:dicarboxylate symporter family 2C score 2.4e-40 NC_002163.1 RefSeq region 32251 32319 . - . ID=id4;Name=id4;Dbxref=GeneID:904364;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0025c by TMHMM2.0 at aa 10-29 2C 41-63 2C 83-105 2C 126-148 2C182-204 2C 225-247 2C 267-289 2C 302-324 2C 339-361 2C 374-396 and 401-423 NC_002163.1 RefSeq region 32332 32400 . - . ID=id4;Name=id4;Dbxref=GeneID:904364;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0025c by TMHMM2.0 at aa 10-29 2C 41-63 2C 83-105 2C 126-148 2C182-204 2C 225-247 2C 267-289 2C 302-324 2C 339-361 2C 374-396 and 401-423 NC_002163.1 RefSeq region 32437 32505 . - . ID=id4;Name=id4;Dbxref=GeneID:904364;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0025c by TMHMM2.0 at aa 10-29 2C 41-63 2C 83-105 2C 126-148 2C182-204 2C 225-247 2C 267-289 2C 302-324 2C 339-361 2C 374-396 and 401-423 NC_002163.1 RefSeq region 32548 32616 . - . ID=id4;Name=id4;Dbxref=GeneID:904364;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0025c by TMHMM2.0 at aa 10-29 2C 41-63 2C 83-105 2C 126-148 2C182-204 2C 225-247 2C 267-289 2C 302-324 2C 339-361 2C 374-396 and 401-423 NC_002163.1 RefSeq region 32653 32721 . - . ID=id4;Name=id4;Dbxref=GeneID:904364;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0025c by TMHMM2.0 at aa 10-29 2C 41-63 2C 83-105 2C 126-148 2C182-204 2C 225-247 2C 267-289 2C 302-324 2C 339-361 2C 374-396 and 401-423 NC_002163.1 RefSeq region 32779 32847 . - . ID=id4;Name=id4;Dbxref=GeneID:904364;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0025c by TMHMM2.0 at aa 10-29 2C 41-63 2C 83-105 2C 126-148 2C182-204 2C 225-247 2C 267-289 2C 302-324 2C 339-361 2C 374-396 and 401-423 NC_002163.1 RefSeq region 32908 32976 . - . ID=id4;Name=id4;Dbxref=GeneID:904364;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0025c by TMHMM2.0 at aa 10-29 2C 41-63 2C 83-105 2C 126-148 2C182-204 2C 225-247 2C 267-289 2C 302-324 2C 339-361 2C 374-396 and 401-423 NC_002163.1 RefSeq region 33076 33144 . - . ID=id4;Name=id4;Dbxref=GeneID:904364;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0025c by TMHMM2.0 at aa 10-29 2C 41-63 2C 83-105 2C 126-148 2C182-204 2C 225-247 2C 267-289 2C 302-324 2C 339-361 2C 374-396 and 401-423 NC_002163.1 RefSeq region 33205 33273 . - . ID=id4;Name=id4;Dbxref=GeneID:904364;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0025c by TMHMM2.0 at aa 10-29 2C 41-63 2C 83-105 2C 126-148 2C182-204 2C 225-247 2C 267-289 2C 302-324 2C 339-361 2C 374-396 and 401-423 NC_002163.1 RefSeq region 33331 33399 . - . ID=id4;Name=id4;Dbxref=GeneID:904364;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0025c by TMHMM2.0 at aa 10-29 2C 41-63 2C 83-105 2C 126-148 2C182-204 2C 225-247 2C 267-289 2C 302-324 2C 339-361 2C 374-396 and 401-423 NC_002163.1 RefSeq region 33433 33492 . - . ID=id4;Name=id4;Dbxref=GeneID:904364;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0025c by TMHMM2.0 at aa 10-29 2C 41-63 2C 83-105 2C 126-148 2C182-204 2C 225-247 2C 267-289 2C 302-324 2C 339-361 2C 374-396 and 401-423 ### NC_002163.1 UTR_Extractor 5'-UTR 33520 33592 . - . ID=utr13;locus_tag=Cj0025c;product=putative sodium:dicarboxylate family transmembrane symporter NC_002163.1 RefSeq gene 33639 34262 . - . ID=gene25;gene=thyX;Name=thyX;locus_tag=Cj0026c;Dbxref=GeneID:904365;gbkey=Gene NC_002163.1 RefSeq CDS 33639 34262 . - 0 ID=cds25;Parent=gene25;gene=thyX;Name=YP_002343498.1;Dbxref=GOA:Q9PJ85 HSSP:Q9WYT0 InterPro:IPR003669 UniProtKB FSwiss-Prot:Q9PJ85 Genbank:YP_002343498.1 GeneID:904365;gbkey=CDS;product=FAD-dependent thymidylate synthase;Note=flavin dependent thymidylate synthase 3B ThyX 3B thymidylate synthase complementing protein 3B catalyzes the formation of dTMP and tetrahydrofolate from dUMP and methylenetetrahydrofolate 3B the enzyme from Mycobacterium tuberculosis forms homotetramers 3B uses FAD as a cofactor NC_002163.1 RefSeq region 33663 34262 . - . ID=id213;gene=thyX;Name=id213;Dbxref=GeneID:904365;gbkey=misc_feature;Note=HMMPfam hit to PF02511 2C Thymidylate synthase complementing protein 2C score 6.3e-43 ### NC_002163.1 UTR_Extractor 5'-UTR 34360 34381 . + . ID=utr14;locus_tag=Cj0027;product=CTP synthetase NC_002163.1 RefSeq CDS 34382 36013 . + 0 ID=cds26;Parent=gene26;gene=pyrG;Name=YP_002343499.1;Dbxref=GOA:Q9PJ84 InterPro:IPR000991 InterPro:IPR004468 InterPro:IPR012998 InterPro:IPR017456 UniProtKB FSwiss-Prot:Q9PJ84 Genbank:YP_002343499.1 GeneID:904367;gbkey=CDS;product=CTP synthetase;Note=CTP synthase 3B cytidine triphosphate synthetase 3B catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen 3B in Escherichia coli this enzyme forms a homotetramer NC_002163.1 RefSeq gene 34382 36013 . + . ID=gene26;gene=pyrG;Name=pyrG;locus_tag=Cj0027;Dbxref=GeneID:904367;gbkey=Gene NC_002163.1 RefSeq region 34391 35218 . + . ID=id214;gene=pyrG;Name=id214;Dbxref=GeneID:904367;gbkey=misc_feature;Note=HMMPfam hit to PF06418 2C CTP synthase N-terminus 2Cscore 4.3e-204 NC_002163.1 RefSeq region 34400 34468 . + . ID=id215;gene=pyrG;Name=id215;Dbxref=GeneID:904367;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0027 by TMHMM2.0 at aa 7-29 NC_002163.1 RefSeq region 35282 35989 . + . ID=id216;gene=pyrG;Name=id216;Dbxref=GeneID:904367;gbkey=misc_feature;Note=HMMPfam hit to PF00117 2C Glutamine amidotransferase class-I 2C score 3.5e-57 NC_002163.1 RefSeq region 35507 35542 . + . ID=id217;gene=pyrG;Name=id217;Dbxref=GeneID:904367;gbkey=misc_feature;Note=PS00442 Glutamine amidotransferases class-I active site NC_002163.1 RefSeq gene 36000 37571 . + . ID=gene27;gene=recJ;Name=recJ;locus_tag=Cj0028;Dbxref=GeneID:904450;gbkey=Gene NC_002163.1 RefSeq CDS 36000 37571 . + 0 ID=cds27;Parent=gene27;gene=recJ;Name=YP_002343500.1;Dbxref=GOA:Q0PC97 InterPro:IPR001667 InterPro:IPR003156 InterPro:IPR004610 UniProtKB FTrEMBL:Q0PC97 Genbank:YP_002343500.1 GeneID:904450;gbkey=CDS;product=single-stranded-DNA-specific exonuclease;Note=Original 282000 29 note: Cj0028 2C recJ 2C probable single-stranded-DNA-specific exonuclease 2C len: 523 aa 3B similar to e.g. RECJ_ECOLI single-stranded-DNA-specific exonuclease 28EC 3.1.-.- 29 28577 aa 29 2C fasta scores 3B opt: 385 z-score: 861.6 E 28 29: 0 2C 29.8 25 identity in 526 aa overlap. 39.0 25 identity to HP0348 7EUpdated 282006 29 note: Pfam domain HMMPfam PF01368 DHH family and HMMPfam PF02272 DHHA1 domain were identified within CDS. Further support given to product function. Characterised within Escherichia coli 2C however 2Cmarginal identity score was obtained. kept within product function. Functional classification - Synthesis and modification of macromolecules - DNA replication 2Crestriction 2Fmodification 2C recombination and repair 7EPMID:2649886 NC_002163.1 RefSeq region 36138 36599 . + . ID=id218;gene=recJ;Name=id218;Dbxref=GeneID:904450;gbkey=misc_feature;Note=HMMPfam hit to PF01368 2C DHH family 2C score 1e-48 NC_002163.1 RefSeq region 37011 37205 . + . ID=id219;gene=recJ;Name=id219;Dbxref=GeneID:904450;gbkey=misc_feature;Note=HMMPfam hit to PF02272 2C DHHA1 domain 2C score 1.5e-16 ### NC_002163.1 UTR_Extractor 5'-UTR 37596 37666 . + . ID=utr15;locus_tag=Cj0029;product=cytoplasmic L-asparaginase NC_002163.1 RefSeq CDS 37667 38662 . + 0 ID=cds28;Parent=gene28;gene=ansA;Name=YP_002343501.1;Dbxref=GOA:Q0PC96 InterPro:IPR004550 InterPro:IPR006034 UniProtKB FTrEMBL:Q0PC96 Genbank:YP_002343501.1 GeneID:904872;gbkey=CDS;product=L-asparaginase;Note=Original 282000 29 note: Cj0029 2C ansA 2C probable cytoplasmic L-asparaginase 2C len: 331 aa 3B similar to many e.g. ASG2_ECOLI L-asparaginase II precursor 28EC 3.5.1.1 29 28348 aa 29 2C fasta scores 3B opt: 1044 z-score: 1510.6 E 28 29: 0 2C52.0 25 identity in 327 aa overlap 2C but with no signal sequence. 45.8 25 identity to HP0723. Contains PS00144 and PS00917 Asparaginase 2Fglutaminase active site signatures 1 and 2 and Pfam match to entry PF00710 Asparaginase 2CAsparaginase 2C score 449.90 2C E-value 2.2e-131 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. Thus 2C not added to product function. Functional classification - Degradation - Amino acids 7EPMID:2407723 2C PMID:1287659 2C PMID:8706862 NC_002163.1 RefSeq gene 37667 38662 . + . ID=gene28;gene=ansA;Name=ansA;locus_tag=Cj0029;Dbxref=GeneID:904872;gbkey=Gene NC_002163.1 RefSeq region 37694 37720 . + . ID=id220;gene=ansA;Name=id220;Dbxref=GeneID:904872;gbkey=misc_feature;Note=PS00144 Asparaginase 2F glutaminase active site signature 1 NC_002163.1 RefSeq region 37712 38644 . + . ID=id221;gene=ansA;Name=id221;Dbxref=GeneID:904872;gbkey=misc_feature;Note=HMMPfam hit to PF00710 2C Asparaginase 2C score 1.5e-132 NC_002163.1 RefSeq region 37928 37960 . + . ID=id222;gene=ansA;Name=id222;Dbxref=GeneID:904872;gbkey=misc_feature;Note=PS00917 Asparaginase 2F glutaminase active site signature 2 ### NC_002163.1 RefSeq gene 39249 40761 . + . ID=gene29;Name=Cjr01;locus_tag=Cjr01;Dbxref=GeneID:3245054;gbkey=Gene NC_002163.1 RefSeq rRNA 39249 40761 . + . ID=rna0;Parent=gene29;Name=rna0;Dbxref=GeneID:3245054;gbkey=rRNA;product=16S ribosomal RNA NC_002163.1 RefSeq exon 39249 40761 . + . ID=id223;Parent=rna0;Name=id223;Dbxref=GeneID:3245054;gbkey=rRNA;product=16S ribosomal RNA NC_002163.1 RefSeq gene 40866 40941 . + . ID=gene30;gene=tRNAAla;Name=tRNAAla;locus_tag=Cjp01;Dbxref=GeneID:904368;gbkey=Gene NC_002163.1 RefSeq tRNA 40866 40941 . + . ID=rna1;Parent=gene30;gene=tRNAAla;Name=rna1;Dbxref=GeneID:904368;gbkey=tRNA;product=tRNA-Ala;Note=tRNA Ala anticodon TGC 2C Cove score 92.14 NC_002163.1 RefSeq exon 40866 40941 . + . ID=id224;Parent=rna1;gene=tRNAAla;Name=id224;Dbxref=GeneID:904368;gbkey=tRNA;product=tRNA-Ala;Note=tRNA Ala anticodon TGC 2C Cove score 92.14 NC_002163.1 RefSeq gene 40950 41026 . + . ID=gene31;gene=tRNAIle;Name=tRNAIle;locus_tag=Cjp02;Dbxref=GeneID:904458;gbkey=Gene NC_002163.1 RefSeq tRNA 40950 41026 . + . ID=rna2;Parent=gene31;gene=tRNAIle;Name=rna2;Dbxref=GeneID:904458;gbkey=tRNA;product=tRNA-Ile;Note=tRNA Ile anticodon GAT 2C Cove score 93.24 NC_002163.1 RefSeq exon 40950 41026 . + . ID=id225;Parent=rna2;gene=tRNAIle;Name=id225;Dbxref=GeneID:904458;gbkey=tRNA;product=tRNA-Ile;Note=tRNA Ile anticodon GAT 2C Cove score 93.24 NC_002163.1 RefSeq gene 41568 44457 . + . ID=gene32;Name=Cjr02;locus_tag=Cjr02;Dbxref=GeneID:3245050;gbkey=Gene NC_002163.1 RefSeq rRNA 41568 44457 . + . ID=rna3;Parent=gene32;Name=rna3;Dbxref=GeneID:3245050;gbkey=rRNA;product=23S ribosomal RNA NC_002163.1 RefSeq exon 41568 44457 . + . ID=id226;Parent=rna3;Name=id226;Dbxref=GeneID:3245050;gbkey=rRNA;product=23S ribosomal RNA NC_002163.1 RefSeq gene 44741 44860 . + . ID=gene33;Name=Cjr03;locus_tag=Cjr03;Dbxref=GeneID:3245045;gbkey=Gene NC_002163.1 RefSeq rRNA 44741 44860 . + . ID=rna4;Parent=gene33;Name=rna4;Dbxref=GeneID:3245045;gbkey=rRNA;product=5S ribosomal RNA NC_002163.1 RefSeq exon 44741 44860 . + . ID=id227;Parent=rna4;Name=id227;Dbxref=GeneID:3245045;gbkey=rRNA;product=5S ribosomal RNA NC_002163.1 RefSeq gene 44966 46363 . + . ID=gene34;Name=Cj0030;locus_tag=Cj0030;Dbxref=GeneID:904369;gbkey=Gene NC_002163.1 RefSeq CDS 44966 46363 . + 0 ID=cds29;Parent=gene34;Name=YP_002343502.1;Dbxref=UniProtKB FTrEMBL:Q0PC95 Genbank:YP_002343502.1 GeneID:904369;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0030 2C unknown 2C len: 465 aa. No Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 UTR_Extractor 5'-UTR 46402 46423 . + . ID=utr16;locus_tag=Cj0031;product=putative type IIS restriction 2Fmodification enzyme NC_002163.1 RefSeq CDS 46424 49000 . + 0 ID=cds30a;Parent=gene35;Name=YP_002343503.1;Dbxref=GOA:Q0PC94 InterPro:IPR002052 InterPro:IPR002296 UniProtKB FTrEMBL:Q0PC94 Genbank:YP_002343503.1 GeneID:904370;gbkey=CDS;product=type IIS restriction 2Fmodification enzyme;Note=Original 282000 29 note: Cj0031 2C probable DNA restriction 2Fmodification enzyme 2C N-terminal half 2C len: 867 aa 3B similar to N-terminus of T257_ECOLI type IIS restriction enzyme Eco57I 28which contains an adenine-specific methyltransferase activity 29 28997 aa 29 2Cfasta scores 3B opt: 126 z-score: 218.0 E 28 29: 6.9e-05 2C 24.0 25 identity in 516 aa overlap. 40.9 25 identity to N-terminus of HP1517. Some similarity to N-terminus of Cj0690c 2824.8 25 identity in 858 aa overlap 29. Contains PS00092 N-6 Adenine-specific DNA methylases signature. Note that there is a polymorphic poly-G tract at the C-terminus of this ORF with 8 2C 9 2C or 10 bases. G10 28the most common in our shotgun 29 causes a termination here 2C G9 causes a termination 6 aa earlier. G8 allows translation to continue into Cj0032 7EOriginal 282000 29 note: Cj0032 2C probable DNA restriction 2Fmodification enzyme 2C C-terminal half 2C len: 867 aa 3B similar to C-terminus of MTB3_BACAR modification methylase BanIII 28580 aa 29 2C fasta scores 3B opt: 132 z-score: 220.8 E 28 29: 4.9e-05 2C 24.6 25 identity in 402 aa overlap. 47.4 25 identity to C-terminus of HP1517. Note that there is a polymorphic poly-G tract at the N-terminus of this ORF with 8 2C 9 2C or 10 bases. G10 28the most common in our shotgun 29 or G9 will not allow translation into this ORF 2CG8 allows translation to continue from Cj0031. Alternative downstram start at 49059 7EUpdated 282006 29 note: Coding sequences have been merged to reflect the complete amino acid sequence for this gene regardless of phase. Previous annotation gave N-terminal and C-terminal portions as seperate CDS. Merging of these CDSs has lead to loss of the downstream CDS. Functional classification - Synthesis and modification of macromolecules - DNA replication 2Crestriction 2Fmodification 2C recombination and repair NC_002163.1 RefSeq gene 46424 50156 . + . ID=gene35;Name=Cj0031;locus_tag=Cj0031;Dbxref=GeneID:904370;gbkey=Gene NC_002163.1 RefSeq CDS 49002 50156 . + 0 ID=cds30b;Parent=gene35;Name=YP_002343503.1;Dbxref=GOA:Q0PC94 InterPro:IPR002052 InterPro:IPR002296 UniProtKB FTrEMBL:Q0PC94 Genbank:YP_002343503.1 GeneID:904370;gbkey=CDS;product=type IIS restriction 2Fmodification enzyme;Note=Original 282000 29 note: Cj0031 2C probable DNA restriction 2Fmodification enzyme 2C N-terminal half 2C len: 867 aa 3B similar to N-terminus of T257_ECOLI type IIS restriction enzyme Eco57I 28which contains an adenine-specific methyltransferase activity 29 28997 aa 29 2Cfasta scores 3B opt: 126 z-score: 218.0 E 28 29: 6.9e-05 2C 24.0 25 identity in 516 aa overlap. 40.9 25 identity to N-terminus of HP1517. Some similarity to N-terminus of Cj0690c 2824.8 25 identity in 858 aa overlap 29. Contains PS00092 N-6 Adenine-specific DNA methylases signature. Note that there is a polymorphic poly-G tract at the C-terminus of this ORF with 8 2C 9 2C or 10 bases. G10 28the most common in our shotgun 29 causes a termination here 2C G9 causes a termination 6 aa earlier. G8 allows translation to continue into Cj0032 7EOriginal 282000 29 note: Cj0032 2C probable DNA restriction 2Fmodification enzyme 2C C-terminal half 2C len: 867 aa 3B similar to C-terminus of MTB3_BACAR modification methylase BanIII 28580 aa 29 2C fasta scores 3B opt: 132 z-score: 220.8 E 28 29: 4.9e-05 2C 24.6 25 identity in 402 aa overlap. 47.4 25 identity to C-terminus of HP1517. Note that there is a polymorphic poly-G tract at the N-terminus of this ORF with 8 2C 9 2C or 10 bases. G10 28the most common in our shotgun 29 or G9 will not allow translation into this ORF 2CG8 allows translation to continue from Cj0031. Alternative downstram start at 49059 7EUpdated 282006 29 note: Coding sequences have been merged to reflect the complete amino acid sequence for this gene regardless of phase. Previous annotation gave N-terminal and C-terminal portions as seperate CDS. Merging of these CDSs has lead to loss of the downstream CDS. Functional classification - Synthesis and modification of macromolecules - DNA replication 2Crestriction 2Fmodification 2C recombination and repair NC_002163.1 RefSeq gene 50156 51937 . + . ID=gene36;Name=Cj0033;locus_tag=Cj0033;Dbxref=GeneID:904331;gbkey=Gene NC_002163.1 RefSeq CDS 50156 51937 . + 0 ID=cds31;Parent=gene36;Name=YP_002343504.1;Dbxref=UniProtKB FTrEMBL:Q0PC93 Genbank:YP_002343504.1 GeneID:904331;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0033 2C probable integral membrane protein 2C len: 593 aa 3B contains 6 possible transmembrane domains in C-terminal half. No Hp match. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 51266 51334 . + . ID=id228;Name=id228;Dbxref=GeneID:904331;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0033 by TMHMM2.0 at aa 371-393 2C 415-434 2C 467-489 2C494-513 2C 518-537 and 557-579 NC_002163.1 RefSeq region 51398 51457 . + . ID=id228;Name=id228;Dbxref=GeneID:904331;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0033 by TMHMM2.0 at aa 371-393 2C 415-434 2C 467-489 2C494-513 2C 518-537 and 557-579 NC_002163.1 RefSeq region 51410 51442 . + . ID=id229;Name=id229;Dbxref=GeneID:904331;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 51554 51622 . + . ID=id228;Name=id228;Dbxref=GeneID:904331;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0033 by TMHMM2.0 at aa 371-393 2C 415-434 2C 467-489 2C494-513 2C 518-537 and 557-579 NC_002163.1 RefSeq region 51635 51694 . + . ID=id228;Name=id228;Dbxref=GeneID:904331;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0033 by TMHMM2.0 at aa 371-393 2C 415-434 2C 467-489 2C494-513 2C 518-537 and 557-579 NC_002163.1 RefSeq region 51707 51766 . + . ID=id228;Name=id228;Dbxref=GeneID:904331;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0033 by TMHMM2.0 at aa 371-393 2C 415-434 2C 467-489 2C494-513 2C 518-537 and 557-579 NC_002163.1 RefSeq region 51824 51892 . + . ID=id228;Name=id228;Dbxref=GeneID:904331;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0033 by TMHMM2.0 at aa 371-393 2C 415-434 2C 467-489 2C494-513 2C 518-537 and 557-579 ### NC_002163.1 RefSeq CDS 51967 52668 . - 0 ID=cds32;Parent=gene37;Name=YP_002343505.1;Dbxref=GOA:Q0PC92 InterPro:IPR007497 InterPro:IPR016907 UniProtKB FTrEMBL:Q0PC92 Genbank:YP_002343505.1 GeneID:904372;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0034c 2C probable periplasmic protein 2C len: 233 aa 3B similar to e.g. TR:O50817 28EMBL:AE000788 29 Borrelia burgdorferi conserved hypothetical protein BBK13 28238 aa 29 2C fasta scores 3B opt: 306 z-score: 257.5 E 28 29: 4.4e-07 2C 28.1 25 identity in 231 aa overlap. No Hp match. Contains possible N-terminal signal sequence. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 51967 52668 . - . ID=gene37;Name=Cj0034c;locus_tag=Cj0034c;Dbxref=GeneID:904372;gbkey=Gene NC_002163.1 RefSeq region 51973 52572 . - . ID=id230;Name=id230;Dbxref=GeneID:904372;gbkey=misc_feature;Note=HMMPfam hit to PF04402 2C Protein of unknown function 28DUF541 29 2C score 2.4e-60 NC_002163.1 RefSeq region 52600 52656 . - . ID=id231;Name=id231;Dbxref=GeneID:904372;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0034c by TMHMM2.0 at aa 5-23 NC_002163.1 RefSeq gene 52665 53867 . - . ID=gene38;Name=Cj0035c;locus_tag=Cj0035c;Dbxref=GeneID:904517;gbkey=Gene NC_002163.1 RefSeq CDS 52665 53867 . - 0 ID=cds33;Parent=gene38;Name=YP_002343506.1;Dbxref=GOA:Q0PC91 InterPro:IPR004812 InterPro:IPR007114 InterPro:IPR011701 UniProtKB FTrEMBL:Q0PC91 Genbank:YP_002343506.1 GeneID:904517;gbkey=CDS;product=efflux protein;Note=Original 282000 29 note: Cj0035c 2C possible efflux protein 2C len: 400 aa 3B similar to many members of the bcr 2FcmlA subfamily of the major facilitator family e.g. BCR_ECOLI bicyclomycin resistance protein 28396 aa 29 2C fasta scores 3B opt: 717 z-score: 1046.3 E 28 29: 0 2C 28.1 25 identity in 398 aa overlap. No Hp ortholog. Contains 12 possible transmembrane domains. Also similar to Cj1375 2825.5 25 identity in 373 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF07690 Major Facilitator Superfamily was identified within CDS. Further support given to product function. Some characterisation work within different bacteria 2C however 2C identity scores were marginal. Thus 2C kept within product function. Functional classification - Antibiotic resistance 7EPMID:2694948 2C PMID:8486276 NC_002163.1 UTR_Extractor 5'-UTR 52669 52688 . - . ID=utr17;locus_tag=Cj0034c;product=putative periplasmic protein NC_002163.1 RefSeq region 52686 52754 . - . ID=id5;Name=id5;Dbxref=GeneID:904517;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0035c by TMHMM2.0 at aa 13-35 2C 50-72 2C 84-106 2C 110-127 2C140-162 2C 167-189 2C 219-241 2C 256-278 2C 285-307 2C 317-339 2C346-368 and 372-394 NC_002163.1 RefSeq region 52719 52751 . - . ID=id232;Name=id232;Dbxref=GeneID:904517;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 52758 53813 . - . ID=id233;Name=id233;Dbxref=GeneID:904517;gbkey=misc_feature;Note=HMMPfam hit to PF07690 2C Major Facilitator Superfamily 2C score 4.8e-52 NC_002163.1 RefSeq region 52764 52832 . - . ID=id5;Name=id5;Dbxref=GeneID:904517;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0035c by TMHMM2.0 at aa 13-35 2C 50-72 2C 84-106 2C 110-127 2C140-162 2C 167-189 2C 219-241 2C 256-278 2C 285-307 2C 317-339 2C346-368 and 372-394 NC_002163.1 RefSeq region 52851 52919 . - . ID=id5;Name=id5;Dbxref=GeneID:904517;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0035c by TMHMM2.0 at aa 13-35 2C 50-72 2C 84-106 2C 110-127 2C140-162 2C 167-189 2C 219-241 2C 256-278 2C 285-307 2C 317-339 2C346-368 and 372-394 NC_002163.1 RefSeq region 52947 53015 . - . ID=id5;Name=id5;Dbxref=GeneID:904517;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0035c by TMHMM2.0 at aa 13-35 2C 50-72 2C 84-106 2C 110-127 2C140-162 2C 167-189 2C 219-241 2C 256-278 2C 285-307 2C 317-339 2C346-368 and 372-394 NC_002163.1 RefSeq region 53034 53102 . - . ID=id5;Name=id5;Dbxref=GeneID:904517;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0035c by TMHMM2.0 at aa 13-35 2C 50-72 2C 84-106 2C 110-127 2C140-162 2C 167-189 2C 219-241 2C 256-278 2C 285-307 2C 317-339 2C346-368 and 372-394 NC_002163.1 RefSeq region 53145 53213 . - . ID=id5;Name=id5;Dbxref=GeneID:904517;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0035c by TMHMM2.0 at aa 13-35 2C 50-72 2C 84-106 2C 110-127 2C140-162 2C 167-189 2C 219-241 2C 256-278 2C 285-307 2C 317-339 2C346-368 and 372-394 NC_002163.1 RefSeq region 53301 53369 . - . ID=id5;Name=id5;Dbxref=GeneID:904517;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0035c by TMHMM2.0 at aa 13-35 2C 50-72 2C 84-106 2C 110-127 2C140-162 2C 167-189 2C 219-241 2C 256-278 2C 285-307 2C 317-339 2C346-368 and 372-394 NC_002163.1 RefSeq region 53382 53450 . - . ID=id5;Name=id5;Dbxref=GeneID:904517;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0035c by TMHMM2.0 at aa 13-35 2C 50-72 2C 84-106 2C 110-127 2C140-162 2C 167-189 2C 219-241 2C 256-278 2C 285-307 2C 317-339 2C346-368 and 372-394 NC_002163.1 RefSeq region 53487 53540 . - . ID=id5;Name=id5;Dbxref=GeneID:904517;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0035c by TMHMM2.0 at aa 13-35 2C 50-72 2C 84-106 2C 110-127 2C140-162 2C 167-189 2C 219-241 2C 256-278 2C 285-307 2C 317-339 2C346-368 and 372-394 NC_002163.1 RefSeq region 53550 53618 . - . ID=id5;Name=id5;Dbxref=GeneID:904517;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0035c by TMHMM2.0 at aa 13-35 2C 50-72 2C 84-106 2C 110-127 2C140-162 2C 167-189 2C 219-241 2C 256-278 2C 285-307 2C 317-339 2C346-368 and 372-394 NC_002163.1 RefSeq region 53652 53720 . - . ID=id5;Name=id5;Dbxref=GeneID:904517;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0035c by TMHMM2.0 at aa 13-35 2C 50-72 2C 84-106 2C 110-127 2C140-162 2C 167-189 2C 219-241 2C 256-278 2C 285-307 2C 317-339 2C346-368 and 372-394 NC_002163.1 RefSeq region 53763 53831 . - . ID=id5;Name=id5;Dbxref=GeneID:904517;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0035c by TMHMM2.0 at aa 13-35 2C 50-72 2C 84-106 2C 110-127 2C140-162 2C 167-189 2C 219-241 2C 256-278 2C 285-307 2C 317-339 2C346-368 and 372-394 ### NC_002163.1 RefSeq gene 53970 55319 . + . ID=gene39;Name=Cj0036;locus_tag=Cj0036;Dbxref=GeneID:904813;gbkey=Gene NC_002163.1 RefSeq CDS 53970 55319 . + 0 ID=cds34;Parent=gene39;Name=YP_002343507.1;Dbxref=UniProtKB FTrEMBL:Q0PC90 Genbank:YP_002343507.1 GeneID:904813;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0036 2C unknown 2C len: 449 aa 3B 37.8 25 identity to HP1143 hypothetical protein. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq CDS 55343 56386 . - 0 ID=cds35;Parent=gene40;Name=YP_002343508.1;Dbxref=GOA:Q0PC89 InterPro:IPR003088 InterPro:IPR009056 InterPro:IPR011031 UniProtKB FTrEMBL:Q0PC89 Genbank:YP_002343508.1 GeneID:904547;gbkey=CDS;product=cytochrome C;Note=Original 282000 29 note: Cj0037c 2C possible cytochrome C 2C len: 347 aa 3B weak simlarity to e.g. TR:O69780 28EMBL:U76906 29 di-heme cytochrome c 28fixP 29 from Rhizobium etli 28287 aa 29 2C fasta scores 3B opt: 97 z-score: 205.7 E 28 29: 0.00034 2C 27.2 25 identity in 151 aa overlap. No Hp match. Contains 2x PS00190 Cytochrome c family heme-binding site signature and Pfam match to entry PF00034 cytochrome_c 2CCytochrome c 2C score 5.90 2C E-value 0.11 7EUpdated 282006 29 note: No specific characterisation with acceptable identity scores has been carried out yet. Thus 2C kept within product function. Functional classification - Energy metabolism - Respiration -Electron transport NC_002163.1 RefSeq gene 55343 56386 . - . ID=gene40;Name=Cj0037c;locus_tag=Cj0037c;Dbxref=GeneID:904547;gbkey=Gene NC_002163.1 RefSeq region 55520 55783 . - . ID=id234;Name=id234;Dbxref=GeneID:904547;gbkey=misc_feature;Note=HMMPfam hit to PF00034 2C Cytochrome c 2C score 0.0012 NC_002163.1 RefSeq region 55736 55753 . - . ID=id235;Name=id235;Dbxref=GeneID:904547;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature NC_002163.1 RefSeq region 56078 56095 . - . ID=id236;Name=id236;Dbxref=GeneID:904547;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature ### NC_002163.1 RefSeq CDS 56564 57211 . - 0 ID=cds36;Parent=gene41;Name=YP_002343509.1;Dbxref=GOA:Q0PC88 UniProtKB FTrEMBL:Q0PC88 Genbank:YP_002343509.1 GeneID:904373;gbkey=CDS;product=poly 28A 29 polymerase family protein;Note=Original 282000 29 note: Cj0038c 2C possible membrane protein 2C len: 215 aa 3B no HP match. Contains two possible transmembrane domains at the N-terminus 7EUpdated 282006 29 note: Pfam domain PF01743 Poly A polymerase family identified within CDS by carrying out own Pfam search. This family includes nucleic acid independent RNA polymerases 2C such as Poly 28A 29 polymerase 2Cwhich adds the poly 28A 29 tail to mRNA 28EC:2.7.7.19 29. This family also includes the tRNA nucleotidyltransferase that adds the CCA to the 3 27 of the tRNA 28EC:2.7.7.25 29. Product modified to more specific family member due to motif match. No specific characterisation has been carried out yet. Thus 2C kept within product function. Functional classification - Synthesis and modification of macromolecules - DNA replication 2Crestriction 2Fmodification 2C recombination and repair NC_002163.1 RefSeq gene 56564 57211 . - . ID=gene41;Name=Cj0038c;locus_tag=Cj0038c;Dbxref=GeneID:904373;gbkey=Gene NC_002163.1 RefSeq region 57032 57085 . - . ID=id6;Name=id6;Dbxref=GeneID:904373;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0038c by TMHMM2.0 at aa 17-39 and 43-60 NC_002163.1 RefSeq region 57095 57163 . - . ID=id6;Name=id6;Dbxref=GeneID:904373;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0038c by TMHMM2.0 at aa 17-39 and 43-60 NC_002163.1 RefSeq gene 57211 59019 . - . ID=gene42;gene=typA;Name=typA;locus_tag=Cj0039c;Dbxref=GeneID:904374;gbkey=Gene NC_002163.1 RefSeq CDS 57211 59019 . - 0 ID=cds37;Parent=gene42;gene=typA;Name=YP_002343510.1;Dbxref=GOA:Q0PC87 InterPro:IPR000640 InterPro:IPR000795 InterPro:IPR004161 InterPro:IPR005225 InterPro:IPR006298 UniProtKB FTrEMBL:Q0PC87 Genbank:YP_002343510.1 GeneID:904374;gbkey=CDS;product=GTP-binding protein TypA;Note=Original 282000 29 note: Cj0039c 2C typA 2C GTP-binding protein typA homolog 2C len: 602 aa 3B similar to TYPA_ECOLI GTP-binding protein typA 2FbipA 28591 aa 29 2C fasta scores 3B opt: 2145 z-score: 2659.1 E 28 29: 0 2C 54.2 25 identity in 592 aa overlap 2C and to many EF-G proteins e.g. EFG_AGRTU elongation factor G 28EF-G 29 28699 aa 29 2C fasta scores 3B opt: 344 z-score: 797.3 E 28 29: 0 2C 26.2 25 identity in 715 aa overlap. 77.3 25 identity to HP0480. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00301 GTP-binding elongation factors signature and Pfam match to entry PF00009 GTP_EFTU 2C Elongation factor Tu family 28contains ATP 2FGTP binding P-loop 29 2C score 282.90 2C E-value 4e-81 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. Thus 2C not added to product function. Homolog designation kept within product function. Functional classification - Synthesis and modification of macromolecules - Protein translation and modification 7EPMID:7783627 2C PMID:9642082 2C PMID:14560797 NC_002163.1 UTR_Extractor 5'-UTR 57212 57453 . - . ID=utr18;locus_tag=Cj0038c;product=putative poly 28A 29 polymerase family protein NC_002163.1 RefSeq region 57580 57843 . - . ID=id237;gene=typA;Name=id237;Dbxref=GeneID:904374;gbkey=misc_feature;Note=HMMPfam hit to PF00679 2C Elongation factor G C-terminus 2C score 7.8e-30 NC_002163.1 RefSeq region 58156 58368 . - . ID=id238;gene=typA;Name=id238;Dbxref=GeneID:904374;gbkey=misc_feature;Note=HMMPfam hit to PF03144 2C Elongation factor Tu domain 2C score 6.7e-12 NC_002163.1 RefSeq region 58429 59016 . - . ID=id239;gene=typA;Name=id239;Dbxref=GeneID:904374;gbkey=misc_feature;Note=HMMPfam hit to PF00009 2C Elongation factor Tu GTP binding domain 2C score 6.7e-70 NC_002163.1 RefSeq region 58846 58893 . - . ID=id240;gene=typA;Name=id240;Dbxref=GeneID:904374;gbkey=misc_feature;Note=PS00301 GTP-binding elongation factors signature NC_002163.1 RefSeq region 58966 58989 . - . ID=id241;gene=typA;Name=id241;Dbxref=GeneID:904374;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 UTR_Extractor 5'-UTR 59020 59050 . - . ID=utr19;locus_tag=Cj0039c;product=GTP-binding protein TypA NC_002163.1 UTR_Extractor 5'-UTR 59125 59153 . + . ID=utr20;locus_tag=Cj0040;product=hypothetical protein NC_002163.1 RefSeq gene 59154 59477 . + . ID=gene43;Name=Cj0040;locus_tag=Cj0040;Dbxref=GeneID:904375;gbkey=Gene NC_002163.1 RefSeq CDS 59154 59477 . + 0 ID=cds38;Parent=gene43;Name=YP_002343511.1;Dbxref=UniProtKB FTrEMBL:Q0PC86 Genbank:YP_002343511.1 GeneID:904375;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0040 2C unknown 2C len: 107 aa 3B no Hp match 7EUpdated 282006 29 note: Literature search identified paper giving clues to product function. Functional classification - Unknown 7EPMID:14985343 NC_002163.1 RefSeq gene 59493 61289 . + . ID=gene44;gene=fliK;Name=fliK;locus_tag=Cj0041;Dbxref=GeneID:904378;gbkey=Gene NC_002163.1 RefSeq CDS 59493 61289 . + 0 ID=cds39;Parent=gene44;gene=fliK;Name=YP_002343512.1;Dbxref=GOA:Q0PC85 UniProtKB FTrEMBL:Q0PC85 Genbank:YP_002343512.1 GeneID:904378;gbkey=CDS;product=flagellar hook-length control protein;Note=Original 282000 29 note: Cj0041 2C unknown 2C len: 598 aa 3B 25.2 25 identity to HP0906 2C but shorter at N-term 7EUpdated 282006 29 note: Literature search identified papers linking product function to be involved in motility and invasion. Unpublished observation by N.Kamal 26 C. Penn have predicted this CDS to be fliK. Literature search identified work carried out in Campylobacter jejuni 2CHelicobacter pylori and Escherichia coli. Product function modified to more specific family member. was kept in product function as not fully characterised. Functional classification - Surface structures 7EPMID:12379703 2C PMID:14985343 2C PMID:15812042 2CPMID:11895937 2C PMID:16077121 2C PMID:15276839 NC_002163.1 RefSeq gene 61343 62227 . + . ID=gene45;gene=flgD;Name=flgD;locus_tag=Cj0042;Dbxref=GeneID:904379;gbkey=Gene NC_002163.1 RefSeq CDS 61343 62227 . + 0 ID=cds40;Parent=gene45;gene=flgD;Name=YP_002343513.1;Dbxref=GOA:Q0PC84 InterPro:IPR005648 UniProtKB FTrEMBL:Q0PC84 Genbank:YP_002343513.1 GeneID:904379;gbkey=CDS;product=flagellar basal body rod modification protein;Note=acts as a scaffold for the assembly of hook proteins onto the flagellar basal body rod NC_002163.1 RefSeq region 61382 61852 . + . ID=id242;gene=flgD;Name=id242;Dbxref=GeneID:904379;gbkey=misc_feature;Note=HMMPfam hit to PF03963 2C Flagellar hook capping protein 2C score 1.4e-60 ### NC_002163.1 RefSeq CDS 62231 63868 . + 0 ID=cds41;Parent=gene46;gene=flgE;Name=YP_002343514.1;Dbxref=GOA:Q0PC83 InterPro:IPR001444 InterPro:IPR010930 InterPro:IPR011491 UniProtKB FTrEMBL:Q0PC83 Genbank:YP_002343514.1 GeneID:906016;gbkey=CDS;product=flagellar hook protein;Note=Original 282000 29 note: Cj0043 2C flgE 2C probable flagellar hook protein 2C len: 545 aa 3B similar to e.g. FLGE_BORBU flagellar hook protein flgE 28442 aa 29 2C fasta scores 3B opt: 350 z-score: 665.8 E 28 29: 7.9e-30 2C 27.5 25 identity in 553 aa overlap. 24.5 25 identity to HP0908. Contains PS00588 Flagella basal body rod proteins signature and Pfam match to entry PF00460 flg_bb_rod 2CFlagella basal body rod proteins 2C score 37.00 2C E-value 6.7e-08 7EUpdated 282006 29 note: Characterised within Borrilia burgdorferi and also some work within Campylobacter jejuni. Identity scores were marginal. Appropriate motifs were present and alignments covered full length of sequence. Thus 2C not added to product function. Functional classification - Surface structures 7EPMID:9658019 2C PMID:9244248 2C PMID:9079915 NC_002163.1 RefSeq gene 62231 63868 . + . ID=gene46;gene=flgE;Name=flgE;locus_tag=Cj0043;Dbxref=GeneID:906016;gbkey=Gene NC_002163.1 RefSeq region 62243 62335 . + . ID=id243;gene=flgE;Name=id243;Dbxref=GeneID:906016;gbkey=misc_feature;Note=HMMPfam hit to PF00460 2C Flagella basal body rod protein 2C score 1.4e-08 NC_002163.1 RefSeq region 62261 62323 . + . ID=id244;gene=flgE;Name=id244;Dbxref=GeneID:906016;gbkey=misc_feature;Note=PS00588 Flagella basal body rod proteins signature NC_002163.1 RefSeq region 63140 63439 . + . ID=id245;gene=flgE;Name=id245;Dbxref=GeneID:906016;gbkey=misc_feature;Note=HMMPfam hit to PF07559 2C Flagellar basal body protein FlaE 2C score 1.9e-29 NC_002163.1 RefSeq region 63743 63859 . + . ID=id246;gene=flgE;Name=id246;Dbxref=GeneID:906016;gbkey=misc_feature;Note=HMMPfam hit to PF06429 2C Domain of unknown function 28DUF1078 29 2C score 8.8e-18 ### NC_002163.1 RefSeq gene 63872 65743 . - . ID=gene47;Name=Cj0044c;locus_tag=Cj0044c;Dbxref=GeneID:904380;gbkey=Gene NC_002163.1 RefSeq CDS 63872 65743 . - 0 ID=cds42;Parent=gene47;Name=YP_002343515.1;Dbxref=UniProtKB FTrEMBL:Q0PC82 Genbank:YP_002343515.1 GeneID:904380;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0044c 2C unknown 2C len: 623 aa 3B no Hp ortholog 2C Also similar to Cj0800c 2828.5 25 identity in 625 aa overlap 29. Preceeded by a C 289-11 29 polymorphic region 3B C11 would allow the translation of Cj0045c to extend by another 15aa 2C overlapping the start of this CDS 3B C9 and C10 28consensus 29 have no effect 7EUpdated 282006 29 note: Literature search identified paper giving further clues to product function. Functional classification - Conserved hypothetical proteins 7EPMID:14985343 NC_002163.1 RefSeq CDS 65744 66466 . - 0 ID=cds43;Parent=gene48;Name=YP_002343516.1;Dbxref=GOA:Q0PC81 InterPro:IPR012312 InterPro:IPR012827 InterPro:IPR016131 UniProtKB FTrEMBL:Q0PC81 Genbank:YP_002343516.1 GeneID:904381;gbkey=CDS;product=iron-binding protein;Note=Original 282000 29 note: Cj0045c 2C possible iron-binding protein 2C len: 240 aa 3B weak similarity to members of the eukaryotic iron-binding hemerythrin family 2Ce.g. HEMT_LINUN hemerythrin alpha chain 28117 aa 29 2C fasta scores 3B opt: 105 z-score: 137.1 E 28 29: 2.5 2C 23.8 25 identity in 122 aa overlap. Note that all of the iron-binding residues are conserved. No Hp match 2C similar to Cj0072c 28pseudogene 29 2C Cj0241c 2830.9 25 identity in 123 aa overlap 29 and Cj1224 2827.7 25 identity in 202 aa overlap 29. Contains a C 289-11 29 polymorphic region at the N-terminus 3B C11 would allow the translation of this CDS to extend by another 15aa 2C overlapping the start of Cj0044c 3B C9 and C10 28consensus 29 have little effect 7EUpdated 282006 29 note: Pfam domain PF01814 Hemerythrin HHE cation binding domain identified within CDS. No specific characterisation with acceptable identity score has been carried out yet. Thus 2C kept within product function. Literature search identified paper giving further clues to product function. Functional classification - Transport 2Fbinding proteins - Cations 7EPMID:14985343 NC_002163.1 RefSeq gene 65744 66466 . - . ID=gene48;Name=Cj0045c;locus_tag=Cj0045c;Dbxref=GeneID:904381;gbkey=Gene NC_002163.1 RefSeq region 66074 66238 . - . ID=id247;Name=id247;Dbxref=GeneID:904381;gbkey=misc_feature;Note=HMMPfam hit to PF01814 2C Hemerythrin HHE cation binding domain 2C score 0.0046 NC_002163.1 RefSeq region 66248 66433 . - . ID=id248;Name=id248;Dbxref=GeneID:904381;gbkey=misc_feature;Note=HMMPfam hit to PF01814 2C Hemerythrin HHE cation binding domain 2C score 0.0029 ### NC_002163.1 UTR_Extractor 5'-UTR 66467 66492 . - . ID=utr21;locus_tag=Cj0045c;product=putative iron-binding protein NC_002163.1 RefSeq gene 66646 66744 . + . ID=gene49;Name=Cjs03;locus_tag=Cjs03;Dbxref=GeneID:7133895;gbkey=Gene NC_002163.1 RefSeq transcript 66646 66744 . + . ID=rna5;Parent=gene49;Name=SRP RNA;Dbxref=GeneID:7133895;gbkey=misc_RNA;Note=Bacterial signal recognition particle RNA 7EUpdated 282006 29 note: Running Rfam search revealed new non-coding RNA families within Campylobacter jejuni. Rfam RF00169 2C Bacterial signal recognition particle RNA was identified within CDS. This SRP is a univerally conserved ribonucleoprotein involved in the co-translational targeting of proteins to membranes NC_002163.1 RefSeq exon 66646 66744 . + . ID=id249;Parent=rna5;Name=id249;Dbxref=GeneID:7133895;gbkey=misc_RNA;Note=Bacterial signal recognition particle RNA 7EUpdated 282006 29 note: Running Rfam search revealed new non-coding RNA families within Campylobacter jejuni. Rfam RF00169 2C Bacterial signal recognition particle RNA was identified within CDS. This SRP is a univerally conserved ribonucleoprotein involved in the co-translational targeting of proteins to membranes NC_002163.1 RefSeq region 66985 67113 . + . ID=id251;Name=id251;Dbxref=GeneID:904382;gbkey=misc_feature;Note=HMMPfam hit to PF00939 2C Sodium:sulfate symporter transmembrane 2C score 8.5e-118 NC_002163.1 RefSeq pseudogene 66985 68504 . + . ID=gene50;Name=Cj0046;locus_tag=Cj0046;Dbxref=GeneID:904382;gbkey=Gene NC_002163.1 RefSeq region 67012 67080 . + . ID=id252;Name=id252;Dbxref=GeneID:904382;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0046 by TMHMM2.0 at aa 10-32 2C 64-86 2C 208-230 2C 260-282 2C287-309 2C 318-340 2C 355-377 2C 384-406 2C 411-433 and 440-462 NC_002163.1 RefSeq region 67229 67411 . + . ID=id250;Name=id250;Dbxref=GeneID:904382;gbkey=misc_feature;Note=Original 282000 29 note: Cj0046 2C probable transmembrane transport protein pseudogene 2C len: 1559 bp 3B fragmentary similarity in all three reading frames to members of the SODIT1 subfamily of the NADC 2FP 2FPHO87 family of transporters e.g. SOT1_SPIOL 2-oxoglutarate 2Fmalate translocator precursor 28spinach 29 28569 aa 29 2C fasta scores 3B opt: 278 z-score: 498.4 E 28 29: 1.7e-20 2C 45.0 25 identity in 80 aa overlap 2C and YBHI_ECOLI 28477 aa 29 fasta scores 3B opt: 196 z-score: 361.3 E 28 29: 7.2e-13 2C 34.6 25 identity in 78 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF00939 Sodium:sulfate symporter transmembrane identified within CDS. Also 2C ten probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity scores yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Other NC_002163.1 RefSeq region 67229 67940 . + . ID=id251;Name=id251;Dbxref=GeneID:904382;gbkey=misc_feature;Note=HMMPfam hit to PF00939 2C Sodium:sulfate symporter transmembrane 2C score 8.5e-118 NC_002163.1 RefSeq region 67289 67357 . + . ID=id252;Name=id252;Dbxref=GeneID:904382;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0046 by TMHMM2.0 at aa 10-32 2C 64-86 2C 208-230 2C 260-282 2C287-309 2C 318-340 2C 355-377 2C 384-406 2C 411-433 and 440-462 NC_002163.1 RefSeq region 67411 67602 . + . ID=id250;Name=id250;Dbxref=GeneID:904382;gbkey=misc_feature;Note=Original 282000 29 note: Cj0046 2C probable transmembrane transport protein pseudogene 2C len: 1559 bp 3B fragmentary similarity in all three reading frames to members of the SODIT1 subfamily of the NADC 2FP 2FPHO87 family of transporters e.g. SOT1_SPIOL 2-oxoglutarate 2Fmalate translocator precursor 28spinach 29 28569 aa 29 2C fasta scores 3B opt: 278 z-score: 498.4 E 28 29: 1.7e-20 2C 45.0 25 identity in 80 aa overlap 2C and YBHI_ECOLI 28477 aa 29 fasta scores 3B opt: 196 z-score: 361.3 E 28 29: 7.2e-13 2C 34.6 25 identity in 78 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF00939 Sodium:sulfate symporter transmembrane identified within CDS. Also 2C ten probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity scores yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Other NC_002163.1 RefSeq region 67602 67940 . + . ID=id250;Name=id250;Dbxref=GeneID:904382;gbkey=misc_feature;Note=Original 282000 29 note: Cj0046 2C probable transmembrane transport protein pseudogene 2C len: 1559 bp 3B fragmentary similarity in all three reading frames to members of the SODIT1 subfamily of the NADC 2FP 2FPHO87 family of transporters e.g. SOT1_SPIOL 2-oxoglutarate 2Fmalate translocator precursor 28spinach 29 28569 aa 29 2C fasta scores 3B opt: 278 z-score: 498.4 E 28 29: 1.7e-20 2C 45.0 25 identity in 80 aa overlap 2C and YBHI_ECOLI 28477 aa 29 fasta scores 3B opt: 196 z-score: 361.3 E 28 29: 7.2e-13 2C 34.6 25 identity in 78 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF00939 Sodium:sulfate symporter transmembrane identified within CDS. Also 2C ten probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity scores yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Other NC_002163.1 RefSeq region 67719 67787 . + . ID=id252;Name=id252;Dbxref=GeneID:904382;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0046 by TMHMM2.0 at aa 10-32 2C 64-86 2C 208-230 2C 260-282 2C287-309 2C 318-340 2C 355-377 2C 384-406 2C 411-433 and 440-462 NC_002163.1 RefSeq region 67875 67940 . + . ID=id252;Name=id252;Dbxref=GeneID:904382;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0046 by TMHMM2.0 at aa 10-32 2C 64-86 2C 208-230 2C 260-282 2C287-309 2C 318-340 2C 355-377 2C 384-406 2C 411-433 and 440-462 NC_002163.1 RefSeq region 67942 67944 . + . ID=id252;Name=id252;Dbxref=GeneID:904382;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0046 by TMHMM2.0 at aa 10-32 2C 64-86 2C 208-230 2C 260-282 2C287-309 2C 318-340 2C 355-377 2C 384-406 2C 411-433 and 440-462 NC_002163.1 RefSeq region 67942 68203 . + . ID=id251;Name=id251;Dbxref=GeneID:904382;gbkey=misc_feature;Note=HMMPfam hit to PF00939 2C Sodium:sulfate symporter transmembrane 2C score 8.5e-118 NC_002163.1 RefSeq region 67942 68203 . + . ID=id250;Name=id250;Dbxref=GeneID:904382;gbkey=misc_feature;Note=Original 282000 29 note: Cj0046 2C probable transmembrane transport protein pseudogene 2C len: 1559 bp 3B fragmentary similarity in all three reading frames to members of the SODIT1 subfamily of the NADC 2FP 2FPHO87 family of transporters e.g. SOT1_SPIOL 2-oxoglutarate 2Fmalate translocator precursor 28spinach 29 28569 aa 29 2C fasta scores 3B opt: 278 z-score: 498.4 E 28 29: 1.7e-20 2C 45.0 25 identity in 80 aa overlap 2C and YBHI_ECOLI 28477 aa 29 fasta scores 3B opt: 196 z-score: 361.3 E 28 29: 7.2e-13 2C 34.6 25 identity in 78 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF00939 Sodium:sulfate symporter transmembrane identified within CDS. Also 2C ten probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity scores yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Other NC_002163.1 RefSeq region 67957 68025 . + . ID=id252;Name=id252;Dbxref=GeneID:904382;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0046 by TMHMM2.0 at aa 10-32 2C 64-86 2C 208-230 2C 260-282 2C287-309 2C 318-340 2C 355-377 2C 384-406 2C 411-433 and 440-462 NC_002163.1 RefSeq region 68050 68118 . + . ID=id252;Name=id252;Dbxref=GeneID:904382;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0046 by TMHMM2.0 at aa 10-32 2C 64-86 2C 208-230 2C 260-282 2C287-309 2C 318-340 2C 355-377 2C 384-406 2C 411-433 and 440-462 NC_002163.1 RefSeq region 68161 68203 . + . ID=id252;Name=id252;Dbxref=GeneID:904382;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0046 by TMHMM2.0 at aa 10-32 2C 64-86 2C 208-230 2C 260-282 2C287-309 2C 318-340 2C 355-377 2C 384-406 2C 411-433 and 440-462 NC_002163.1 RefSeq region 68205 68230 . + . ID=id252;Name=id252;Dbxref=GeneID:904382;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0046 by TMHMM2.0 at aa 10-32 2C 64-86 2C 208-230 2C 260-282 2C287-309 2C 318-340 2C 355-377 2C 384-406 2C 411-433 and 440-462 NC_002163.1 RefSeq region 68205 68278 . + . ID=id250;Name=id250;Dbxref=GeneID:904382;gbkey=misc_feature;Note=Original 282000 29 note: Cj0046 2C probable transmembrane transport protein pseudogene 2C len: 1559 bp 3B fragmentary similarity in all three reading frames to members of the SODIT1 subfamily of the NADC 2FP 2FPHO87 family of transporters e.g. SOT1_SPIOL 2-oxoglutarate 2Fmalate translocator precursor 28spinach 29 28569 aa 29 2C fasta scores 3B opt: 278 z-score: 498.4 E 28 29: 1.7e-20 2C 45.0 25 identity in 80 aa overlap 2C and YBHI_ECOLI 28477 aa 29 fasta scores 3B opt: 196 z-score: 361.3 E 28 29: 7.2e-13 2C 34.6 25 identity in 78 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF00939 Sodium:sulfate symporter transmembrane identified within CDS. Also 2C ten probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity scores yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Other NC_002163.1 RefSeq region 68205 68492 . + . ID=id251;Name=id251;Dbxref=GeneID:904382;gbkey=misc_feature;Note=HMMPfam hit to PF00939 2C Sodium:sulfate symporter transmembrane 2C score 8.5e-118 NC_002163.1 RefSeq region 68249 68315 . + . ID=id252;Name=id252;Dbxref=GeneID:904382;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0046 by TMHMM2.0 at aa 10-32 2C 64-86 2C 208-230 2C 260-282 2C287-309 2C 318-340 2C 355-377 2C 384-406 2C 411-433 and 440-462 NC_002163.1 RefSeq region 68277 68504 . + . ID=id250;Name=id250;Dbxref=GeneID:904382;gbkey=misc_feature;Note=Original 282000 29 note: Cj0046 2C probable transmembrane transport protein pseudogene 2C len: 1559 bp 3B fragmentary similarity in all three reading frames to members of the SODIT1 subfamily of the NADC 2FP 2FPHO87 family of transporters e.g. SOT1_SPIOL 2-oxoglutarate 2Fmalate translocator precursor 28spinach 29 28569 aa 29 2C fasta scores 3B opt: 278 z-score: 498.4 E 28 29: 1.7e-20 2C 45.0 25 identity in 80 aa overlap 2C and YBHI_ECOLI 28477 aa 29 fasta scores 3B opt: 196 z-score: 361.3 E 28 29: 7.2e-13 2C 34.6 25 identity in 78 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF00939 Sodium:sulfate symporter transmembrane identified within CDS. Also 2C ten probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity scores yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Other NC_002163.1 RefSeq region 68328 68396 . + . ID=id252;Name=id252;Dbxref=GeneID:904382;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0046 by TMHMM2.0 at aa 10-32 2C 64-86 2C 208-230 2C 260-282 2C287-309 2C 318-340 2C 355-377 2C 384-406 2C 411-433 and 440-462 NC_002163.1 RefSeq region 68415 68483 . + . ID=id252;Name=id252;Dbxref=GeneID:904382;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0046 by TMHMM2.0 at aa 10-32 2C 64-86 2C 208-230 2C 260-282 2C287-309 2C 318-340 2C 355-377 2C 384-406 2C 411-433 and 440-462 NC_002163.1 RefSeq stem_loop 68496 68544 . + . ID=id253;Name=id253;gbkey=stem_loop NC_002163.1 RefSeq CDS 68532 69548 . - 0 ID=cds44;Parent=gene51;gene=mnmA;Name=YP_002343517.1;Dbxref=GOA:Q9PJ66 InterPro:IPR004506 InterPro:IPR014729 UniProtKB FSwiss-Prot:Q9PJ66 Genbank:YP_002343517.1 GeneID:904383;gbkey=CDS;product=tRNA-specific 2-thiouridylase MnmA;Note=catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs NC_002163.1 RefSeq gene 68532 69548 . - . ID=gene51;gene=mnmA;Name=mnmA;locus_tag=Cj0053c;Dbxref=GeneID:904383;gbkey=Gene NC_002163.1 RefSeq region 68538 69548 . - . ID=id254;gene=mnmA;Name=id254;Dbxref=GeneID:904383;gbkey=misc_feature;Note=HMMPfam hit to PF03054 2C tRNA methyl transferase 2Cscore 1.3e-132 NC_002163.1 RefSeq gene 69548 70153 . - . ID=gene52;gene=Cj0054c;Name=Cj0054c;locus_tag=Cj0054c;Dbxref=GeneID:904384;gbkey=Gene NC_002163.1 RefSeq CDS 69548 70153 . - 0 ID=cds45;Parent=gene52;Name=YP_002343518.1;Dbxref=InterPro:IPR005269 UniProtKB FTrEMBL:Q0PC79 Genbank:YP_002343518.1 GeneID:904384;gbkey=CDS;product=lysine decarboxylase family protein;Note=Original 282000 29 note: Cj0054c 2C unknown 2C len: 201 aa 3B similar to hypothetical proteins e.g. TR:Q46063 28EMBL:X81379 29 Corynebacterium glutamicum hypothetucal protein 28211 aa 29 2C fasta scores 3B opt: 426 z-score: 696.2 E 28 29: 1.6e-31 2C 44.2 25 identity in 156 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF03641 possible lysine decarboxylase family identified within CDS. Product modified to more specific family member due to motif match. No specific characterisation with acceptable identity score has been carried out yet. Thus 2C kept within product function. Functional classification -Misc NC_002163.1 RefSeq region 69551 69967 . - . ID=id255;Name=id255;Dbxref=GeneID:904384;gbkey=misc_feature;Note=HMMPfam hit to PF03641 2C Possible lysine decarboxylase 2C score 2.2e-53 ### NC_002163.1 UTR_Extractor 5'-UTR 70154 70175 . - . ID=utr22;locus_tag=Cj0054c;product=putative lysine decarboxylase family protein NC_002163.1 RefSeq gene 70274 71098 . - . ID=gene53;Name=Cj0055c;locus_tag=Cj0055c;Dbxref=GeneID:904386;gbkey=Gene NC_002163.1 RefSeq CDS 70274 71098 . - 0 ID=cds46;Parent=gene53;Name=YP_002343519.1;Dbxref=InterPro:IPR000269 UniProtKB FTrEMBL:Q0PC78 Genbank:YP_002343519.1 GeneID:904386;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0055c 2C unknown 2C len: 274 aa 3B no Hp match 2C similar in C-terminus to Cj0122 2846.6 25 identity in 148 aa overlap 29 7EUpdated 282006 29 note: Contains Prosite match PS01164 COPPER_AMINE_OXID 2C Copper amine oxidase. Amine oxidases are enzymes that catalyze the oxidation of different biogenic amines e.g. neurotransmitters. Copper-containing amine oxidases are found in bacteria. This particular form binds one copper ion per subunit as well as a 2 2C4 2C5-trihydroxyphenylalanine quinone 28or topaquinone 29 28TPQ 29 cofactor 28PMID:8591028 29. Functional classification -Unknown 7EPMID:8591028 NC_002163.1 RefSeq region 71024 71065 . - . ID=id256;Name=id256;Dbxref=GeneID:904386;gbkey=misc_feature;Note=PS01164 Copper amine oxidase topaquinone signature ### NC_002163.1 UTR_Extractor 5'-UTR 71099 71274 . - . ID=utr23;locus_tag=Cj0055c;product=hypothetical protein NC_002163.1 UTR_Extractor 5'-UTR 71572 71756 . - . ID=utr24;locus_tag=Cj0056c;product=hypothetical protein NC_002163.1 UTR_Extractor 5'-UTR 71935 72004 . + . ID=utr25;locus_tag=Cj0057;product=putative periplasmic protein NC_002163.1 RefSeq CDS 72005 72859 . + 0 ID=cds47;Parent=gene54;Name=YP_002343521.1;Dbxref=UniProtKB FTrEMBL:Q0PC76 Genbank:YP_002343521.1 GeneID:904388;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0057 2C possible periplasmic protein 2C len: 284 aa 3B no Hp match. Contains possible N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 72005 72859 . + . ID=gene54;Name=Cj0057;locus_tag=Cj0057;Dbxref=GeneID:904388;gbkey=Gene NC_002163.1 RefSeq gene 72844 73443 . + . ID=gene55;Name=Cj0058;locus_tag=Cj0058;Dbxref=GeneID:904390;gbkey=Gene NC_002163.1 RefSeq CDS 72844 73443 . + 0 ID=cds48;Parent=gene55;Name=YP_002343522.1;Dbxref=GOA:Q0PC75 InterPro:IPR005074 UniProtKB FTrEMBL:Q0PC75 Genbank:YP_002343522.1 GeneID:904390;gbkey=CDS;product=peptidase C39 family protein;Note=Original 282000 29 note: Cj0058 2C possible periplasmic protein 2C len: 199 aa 3B no Hp match. Contains possible N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF03412 Peptidase C39 family identified within CDS. Product modified to more specific family member based on motif match. No specific characterisation with acceptable identity scores carried out yet. Thus 2C kept within product function. Functional classification - Degradation of macromolecules - Proteins 2C peptides and glycopeptides NC_002163.1 RefSeq region 72949 73374 . + . ID=id257;Name=id257;Dbxref=GeneID:904390;gbkey=misc_feature;Note=HMMPfam hit to PF03412 2C Peptidase C39 family 2C score 4.5e-11 ### NC_002163.1 RefSeq CDS 73492 74334 . - 0 ID=cds49;Parent=gene56;gene=fliY;Name=YP_002343523.1;Dbxref=GOA:Q0PC74 InterPro:IPR001172 InterPro:IPR001543 InterPro:IPR012826 UniProtKB FTrEMBL:Q0PC74 Genbank:YP_002343523.1 GeneID:904391;gbkey=CDS;product=flagellar motor switch protein FliY;Note=One of three proteins involved in switching the direction of the flagellar rotation NC_002163.1 RefSeq gene 73492 74334 . - . ID=gene56;gene=fliY;Name=fliY;locus_tag=Cj0059c;Dbxref=GeneID:904391;gbkey=Gene NC_002163.1 RefSeq region 73516 73746 . - . ID=id258;gene=fliY;Name=id258;Dbxref=GeneID:904391;gbkey=misc_feature;Note=HMMPfam hit to PF01052 2C Surface presentation of antigens 28SPOA 29 prot 2C score 6.1e-24 NC_002163.1 RefSeq gene 74331 75410 . - . ID=gene57;gene=fliM;Name=fliM;locus_tag=Cj0060c;Dbxref=GeneID:904392;gbkey=Gene NC_002163.1 RefSeq CDS 74331 75410 . - 0 ID=cds50;Parent=gene57;gene=fliM;Name=YP_002343524.1;Dbxref=GOA:Q0PC73 InterPro:IPR001543 InterPro:IPR001689 UniProtKB FTrEMBL:Q0PC73 Genbank:YP_002343524.1 GeneID:904392;gbkey=CDS;product=flagellar motor switch protein FliM;Note=with FliG and FliN makes up the switch complex which is involved in switching the direction of the flagella rotation NC_002163.1 UTR_Extractor 5'-UTR 74335 74445 . - . ID=utr26;locus_tag=Cj0059c;product=flagellar motor switch protein FliY NC_002163.1 RefSeq region 74430 74660 . - . ID=id259;gene=fliM;Name=id259;Dbxref=GeneID:904392;gbkey=misc_feature;Note=HMMPfam hit to PF01052 2C Surface presentation of antigens 28SPOA 29 prot 2C score 0.00022 NC_002163.1 RefSeq region 74718 75290 . - . ID=id260;gene=fliM;Name=id260;Dbxref=GeneID:904392;gbkey=misc_feature;Note=HMMPfam hit to PF02154 2C Flagellar motor switch protein FliM 2C score 8.3e-105 NC_002163.1 RefSeq gene 75410 76126 . - . ID=gene58;gene=fliA;Name=fliA;locus_tag=Cj0061c;Dbxref=GeneID:904393;gbkey=Gene NC_002163.1 RefSeq CDS 75410 76126 . - 0 ID=cds51;Parent=gene58;gene=fliA;Name=YP_002343525.1;Dbxref=GOA:Q0PC72 InterPro:IPR000943 InterPro:IPR007627 InterPro:IPR007630 InterPro:IPR011991 InterPro:IPR012845 InterPro:IPR014284 UniProtKB FTrEMBL:Q0PC72 Genbank:YP_002343525.1 GeneID:904393;gbkey=CDS;product=flagellar biosynthesis sigma factor;Note=sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released 3B this sigma factor directs late flagellar biosynthesis genes NC_002163.1 RefSeq region 75422 75571 . - . ID=id261;gene=fliA;Name=id261;Dbxref=GeneID:904393;gbkey=misc_feature;Note=HMMPfam hit to PF04545 2C Sigma-70 2C region 2C score 5.8e-19 NC_002163.1 RefSeq region 75428 75508 . - . ID=id262;gene=fliA;Name=id262;Dbxref=GeneID:904393;gbkey=misc_feature;Note=PS00716 Sigma-70 factors family signature 2 NC_002163.1 RefSeq region 75827 76045 . - . ID=id263;gene=fliA;Name=id263;Dbxref=GeneID:904393;gbkey=misc_feature;Note=HMMPfam hit to PF04542 2C Sigma-70 region 2C score 3.3e-12 NC_002163.1 RefSeq CDS 76083 76439 . - 0 ID=cds52;Parent=gene59;Name=YP_002343526.1;Dbxref=UniProtKB FTrEMBL:Q0PC71 Genbank:YP_002343526.1 GeneID:904394;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0062c 2C probable integral membrane protein 2C len: 118 aa 3B no Hp match. Contains two possible transmembrane domains. Functional classification - Cell envelope - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 76083 76439 . - . ID=gene59;Name=Cj0062c;locus_tag=Cj0062c;Dbxref=GeneID:904394;gbkey=Gene NC_002163.1 RefSeq region 76278 76346 . - . ID=id7;Name=id7;Dbxref=GeneID:904394;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0062c by TMHMM2.0 at aa 7-26 and 32-54 NC_002163.1 RefSeq region 76362 76421 . - . ID=id7;Name=id7;Dbxref=GeneID:904394;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0062c by TMHMM2.0 at aa 7-26 and 32-54 ### NC_002163.1 RefSeq CDS 76458 77324 . - 0 ID=cds53;Parent=gene60;Name=YP_002343527.1;Dbxref=GOA:Q0PC70 InterPro:IPR002586 UniProtKB FTrEMBL:Q0PC70 Genbank:YP_002343527.1 GeneID:904395;gbkey=CDS;product=ATP-binding protein;Note=Original 282000 29 note: Cj0063c 2C probable ATP-binding protein 2C len: 288 aa 3B similar to hypothetical proteins in other flagellar operons e.g. YLXH_BACSU hypothetical 33.2 kd protein in flhF-cheB intergenic region 28298 aa 29 2C fasta scores 3B opt: 390 z-score: 493.5 E 28 29: 3.1e-20 2C 29.0 25 identity in 293 aa overlap 2C and to cell division proteins e.g. MIND_BACSU septum site-determining protein minD 28268 aa 29 2C fasta scores 3B opt: 323 z-score: 417.6 E 28 29: 5.3e-16 2C32.9 25 identity in 249 aa overlap. 45.7 25 identity to HP1034. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 and Pfam match to entry PF00991 ParA 2C ParA family ATPase 2C score 34.80 2C E-value 1.3e-06 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score carried out yet. Thus 2C kept within product function. Functional classification - Cell envelope - Surface structures NC_002163.1 RefSeq gene 76458 77324 . - . ID=gene60;Name=Cj0063c;locus_tag=Cj0063c;Dbxref=GeneID:904395;gbkey=Gene NC_002163.1 RefSeq region 76623 77249 . - . ID=id264;Name=id264;Dbxref=GeneID:904395;gbkey=misc_feature;Note=HMMPfam hit to PF01656 2C CobQ 2FCobB 2FMinD 2FParA nucleotide binding domai 2C score 5.8e-21 NC_002163.1 RefSeq region 77211 77234 . - . ID=id265;Name=id265;Dbxref=GeneID:904395;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq gene 77317 78771 . - . ID=gene61;gene=flhF;Name=flhF;locus_tag=Cj0064c;Dbxref=GeneID:904464;gbkey=Gene NC_002163.1 RefSeq CDS 77317 78771 . - 0 ID=cds54;Parent=gene61;gene=flhF;Name=YP_002343528.1;Dbxref=GOA:O52908 HSSP:P70722 InterPro:IPR000897 InterPro:IPR003593 UniProtKB FSwiss-Prot:O52908 Genbank:YP_002343528.1 GeneID:904464;gbkey=CDS;product=flagellar biosynthesis regulator FlhF;Note=positive regulator of class III flagellar genes NC_002163.1 RefSeq region 77347 77931 . - . ID=id266;gene=flhF;Name=id266;Dbxref=GeneID:904464;gbkey=misc_feature;Note=HMMPfam hit to PF00448 2C SRP54-type protein 2C GTPase domain 2C score 1.9e-40 NC_002163.1 RefSeq region 77884 77907 . - . ID=id267;gene=flhF;Name=id267;Dbxref=GeneID:904464;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 RefSeq CDS 78781 79254 . - 0 ID=cds55;Parent=gene62;gene=folK;Name=YP_002343529.1;Dbxref=GOA:Q9PJ54 InterPro:IPR000550 UniProtKB FSwiss-Prot:Q9PJ54 Genbank:YP_002343529.1 GeneID:904396;gbkey=CDS;product=2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase;Note=Original 282000 29 note: Cj0065c 2C folK 2C possible 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase 2C len: 157 aa 2C similar to e.g. HPPK_BACSU 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase 28EC 2.7.6.3 29 28167 aa 29 2C fasta scores 3B opt: 194 z-score: 370.0 E 28 29: 2.4e-13 2C 28.7 25 identity in 129 aa overlap. 35.6 25 identity to HP1036. Contains Pfam match to entry PF01288 HPPK 2C7 2C8-dihydro-6-hydroxymethylpterin-pyrophosphokinase 28HPPK 29 2C score 4.10 2C E-value 1.1e-06 7EUpdated 282006 29 note: Characterised within Bacillus subtilis and Escherichia coli 2C however 2C identity scores were marginal. Thus 2C kept within product function. Functional classification - Biosynthesis of cofactors 2C prosthetic groups and carriers - Folic acid 7EPMID:1325970 NC_002163.1 RefSeq gene 78781 79254 . - . ID=gene62;gene=folK;Name=folK;locus_tag=Cj0065c;Dbxref=GeneID:904396;gbkey=Gene NC_002163.1 RefSeq region 78784 79164 . - . ID=id268;gene=folK;Name=id268;Dbxref=GeneID:904396;gbkey=misc_feature;Note=HMMPfam hit to PF01288 2C7 2C8-dihydro-6-hydroxymethylpterin-pyrophosph 2C score 3.1e-25 NC_002163.1 RefSeq region 78880 78915 . - . ID=id269;gene=folK;Name=id269;Dbxref=GeneID:904396;gbkey=misc_feature;Note=PS00794 7 2C8-dihydro-6-hydroxymethylpterin-pyrophosphokinase signature ### NC_002163.1 RefSeq gene 79257 79736 . - . ID=gene63;gene=aroQ;Name=aroQ;locus_tag=Cj0066c;Dbxref=GeneID:904397;gbkey=Gene NC_002163.1 RefSeq CDS 79257 79736 . - 0 ID=cds56;Parent=gene63;gene=aroQ;Name=YP_002343530.1;Dbxref=GOA:Q9PJ53 HSSP:Q48255 InterPro:IPR001874 UniProtKB FSwiss-Prot:Q9PJ53 Genbank:YP_002343530.1 GeneID:904397;gbkey=CDS;product=3-dehydroquinate dehydratase;Note=catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis NC_002163.1 RefSeq region 79305 79730 . - . ID=id270;gene=aroQ;Name=id270;Dbxref=GeneID:904397;gbkey=misc_feature;Note=HMMPfam hit to PF01220 2C Dehydroquinase class II 2Cscore 1.4e-74 ### NC_002163.1 UTR_Extractor 5'-UTR 79737 79765 . - . ID=utr27;locus_tag=Cj0066c;product=3-dehydroquinate dehydratase NC_002163.1 UTR_Extractor 5'-UTR 79810 79826 . + . ID=utr28;locus_tag=Cj0067;product=chlorohydrolase NC_002163.1 RefSeq CDS 79827 81056 . + 0 ID=cds57;Parent=gene64;Name=YP_002343531.1;Dbxref=GOA:Q0PC66 InterPro:IPR006680 UniProtKB FTrEMBL:Q0PC66 Genbank:YP_002343531.1 GeneID:904398;gbkey=CDS;product=chlorohydrolase;Note=Catalyzes the hydrolytic cleavage of a carbon-halogen bond in N-ethylammeline NC_002163.1 RefSeq gene 79827 81056 . + . ID=gene64;Name=Cj0067;locus_tag=Cj0067;Dbxref=GeneID:904398;gbkey=Gene NC_002163.1 RefSeq region 79992 80957 . + . ID=id271;Name=id271;Dbxref=GeneID:904398;gbkey=misc_feature;Note=HMMPfam hit to PF01979 2C Amidohydrolase family 2Cscore 1.8e-68 NC_002163.1 RefSeq CDS 81044 81940 . + 0 ID=cds58;Parent=gene65;gene=pspA;Name=YP_002343532.1;Dbxref=GOA:Q0PC65 InterPro:IPR002142 InterPro:IPR004635 UniProtKB FTrEMBL:Q0PC65 Genbank:YP_002343532.1 GeneID:905251;gbkey=CDS;product=protease;Note=Original 282000 29 note: Cj0068 2C pspA 2C probable protease required for pilus-like appendage formation 2C len: 298 aa 3B almost identical to TR:P71127 28EMBL:U38524 29 pspA 28298 aa 29 2899.0 25 identity in 298 aa overlap 29 and similar to the C-terminus of e.g. SPPA_ECOLI protease IV 28618 aa 29 2Cfasta scores 3B opt: 285 z-score: 266.8 E 28 29: 1.3e-07 2C 24.7 25 identity in 251 aa overlap. 42.0 25 identity to HP1435 7EUpdated 282006 29 note: Pfam domain PF01343 Peptidase family S49 identified within CDS. Product function based on direct submission with paper 28PMID:8793884 29. not added to product function due to characterisation work within Campylobacter jejuni. Functional classification -Degradation of macromolecules - Surface structures 7EPMID:8793884 2C PMID:3522590 NC_002163.1 RefSeq gene 81044 81940 . + . ID=gene65;gene=pspA;Name=pspA;locus_tag=Cj0068;Dbxref=GeneID:905251;gbkey=Gene NC_002163.1 RefSeq region 81080 81148 . + . ID=id272;gene=pspA;Name=id272;Dbxref=GeneID:905251;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0068 by TMHMM2.0 at aa 13-35 NC_002163.1 RefSeq region 81344 81805 . + . ID=id273;gene=pspA;Name=id273;Dbxref=GeneID:905251;gbkey=misc_feature;Note=HMMPfam hit to PF01343 2C Peptidase family S49 2C score 1.4e-74 ### NC_002163.1 UTR_Extractor 5'-UTR 81995 82018 . + . ID=utr29;locus_tag=Cj0069;product=hypothetical protein NC_002163.1 RefSeq gene 82019 83050 . + . ID=gene66;Name=Cj0069;locus_tag=Cj0069;Dbxref=GeneID:905192;gbkey=Gene NC_002163.1 RefSeq CDS 82019 83050 . + 0 ID=cds59;Parent=gene66;Name=YP_002343533.1;Dbxref=UniProtKB FTrEMBL:Q0PC64 Genbank:YP_002343533.1 GeneID:905192;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0069 2C unknown 2C len: 343 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Literature search identified paper giving further clues to product function. Functional classification - Unknown 7EPMID:14702320 NC_002163.1 RefSeq region 83292 83654 . - . ID=id274;Name=id274;Dbxref=GeneID:904399;gbkey=misc_feature;Note=Original 282000 29 note: Cj0072c 2C possible iron-binding protein pseudogene 2C len: 98 aa 3B Weak similarity to members of the eukaryotic iron-binding hemerythrin family 2C e.g. HEMM_THEZO myohemerythrin 28118 aa 29. Note that all of the iron-binding residues are conserved. No Hp match. Also similar to N-terminus of Cj1224 2850.5 25 identity in 91 aa overlap 29 2C Cj0241c 2840.5 25 identity in 79 aa overlap 29 and Cj0045c 2832.5 25 identity in 83 aa overlap 29. Contains one frameshift 7EUpdated 282006 29 note: Pfam domains x2 PF01814 Hemerythrin HHE cation binding domain identified within CDS. Further support given to product function. Similar to many Campylobacter species designated as methy-accepting chemotaxis protein and also iron-binding proteins. No specific characterisation with acceptable identity score has been carried out yet. Thus 2C kept within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification -Transport 2Fbinding proteins - Cations NC_002163.1 RefSeq pseudogene 83292 83893 . - . ID=gene67;Name=Cj0072c;locus_tag=Cj0072c;Dbxref=GeneID:904399;gbkey=Gene NC_002163.1 RefSeq region 83523 83654 . - . ID=id275;Name=id275;Dbxref=GeneID:904399;gbkey=misc_feature;Note=HMMPfam hit to PF01814 2C Hemerythrin HHE cation binding domain 2C score 2.9 NC_002163.1 RefSeq region 83654 83686 . - . ID=id275;Name=id275;Dbxref=GeneID:904399;gbkey=misc_feature;Note=HMMPfam hit to PF01814 2C Hemerythrin HHE cation binding domain 2C score 2.9 NC_002163.1 RefSeq region 83654 83893 . - . ID=id274;Name=id274;Dbxref=GeneID:904399;gbkey=misc_feature;Note=Original 282000 29 note: Cj0072c 2C possible iron-binding protein pseudogene 2C len: 98 aa 3B Weak similarity to members of the eukaryotic iron-binding hemerythrin family 2C e.g. HEMM_THEZO myohemerythrin 28118 aa 29. Note that all of the iron-binding residues are conserved. No Hp match. Also similar to N-terminus of Cj1224 2850.5 25 identity in 91 aa overlap 29 2C Cj0241c 2840.5 25 identity in 79 aa overlap 29 and Cj0045c 2832.5 25 identity in 83 aa overlap 29. Contains one frameshift 7EUpdated 282006 29 note: Pfam domains x2 PF01814 Hemerythrin HHE cation binding domain identified within CDS. Further support given to product function. Similar to many Campylobacter species designated as methy-accepting chemotaxis protein and also iron-binding proteins. No specific characterisation with acceptable identity score has been carried out yet. Thus 2C kept within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification -Transport 2Fbinding proteins - Cations NC_002163.1 RefSeq region 83696 83866 . - . ID=id276;Name=id276;Dbxref=GeneID:904399;gbkey=misc_feature;Note=HMMPfam hit to PF01814 2C Hemerythrin HHE cation binding domain 2C score 0.007 ### NC_002163.1 RefSeq CDS 84087 84743 . - 0 ID=cds60;Parent=gene68;Name=YP_002343535.1;Dbxref=InterPro:IPR003741 UniProtKB FTrEMBL:Q0PC62 Genbank:YP_002343535.1 GeneID:904400;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0073c 2C unknown 2C len: 218 aa 3B similar to hypothetical proteins e.g. YKGG_ECOLI 28282 aa 29 2C fasta scores 3B opt: 215 z-score: 231.0 E 28 29: 1.3e-05 2C32.2 25 identity in 146 aa overlap. 41.8 25 identity to HP0137 7EUpdated 282006 29 note: Pfam domain PF02589 Uncharacterized ACR 2C YkgG family COG1556 identified within CDS. Conserved added to product function. Literature search identified paper giving further clues to product function. Functional classification - Conserved hypothetical proteins 7EPMID:15773975 NC_002163.1 RefSeq gene 84087 84743 . - . ID=gene68;Name=Cj0073c;locus_tag=Cj0073c;Dbxref=GeneID:904400;gbkey=Gene NC_002163.1 RefSeq region 84090 84470 . - . ID=id277;Name=id277;Dbxref=GeneID:904400;gbkey=misc_feature;Note=HMMPfam hit to PF02589 2C Uncharacterized ACR 2C YkgG family COG1556 2C score 1.2e-29 NC_002163.1 RefSeq gene 84736 86175 . - . ID=gene69;Name=Cj0074c;locus_tag=Cj0074c;Dbxref=GeneID:904401;gbkey=Gene NC_002163.1 RefSeq CDS 84736 86175 . - 0 ID=cds61;Parent=gene69;Name=YP_002343536.1;Dbxref=GOA:Q0PC61 InterPro:IPR001450 InterPro:IPR002048 InterPro:IPR003741 InterPro:IPR004452 InterPro:IPR012285 UniProtKB FTrEMBL:Q0PC61 Genbank:YP_002343536.1 GeneID:904401;gbkey=CDS;product=iron-sulfur protein;Note=Original 282000 29 note: Cj0074c 2C probable iron-sulfur protein 2C len: 479 aa 3B similar to hypothetical proteins e.g. YKGF_ECOLI 28475 aa 29 2C fasta scores 3B opt: 1142 z-score: 1335.9 E 28 29: 0 2C 38.3 25 identity in 462 aa overlap. 58.1 25 identity to HP0138. Contains 2x PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature and 2x Pfam match to entry PF00037 fer4 2C 4Fe-4S ferredoxins and related iron-sulfur cluster binding domains. 2C scores 13.80 2C E-value 0.0095 2C and 12.30 2C E-value 0.026 7EUpdated 282006 29 note: No specific characterisation with acceptable identity scores. Thus 2C kept within product function. Functional classification -Energy metabolism - Electron transport 7EPMID:15773975 NC_002163.1 RefSeq region 85042 85113 . - . ID=id278;Name=id278;Dbxref=GeneID:904401;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 0.00065 NC_002163.1 RefSeq region 85057 85092 . - . ID=id279;Name=id279;Dbxref=GeneID:904401;gbkey=misc_feature;Note=PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature NC_002163.1 RefSeq region 85192 85263 . - . ID=id280;Name=id280;Dbxref=GeneID:904401;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 0.0015 NC_002163.1 RefSeq region 85207 85242 . - . ID=id281;Name=id281;Dbxref=GeneID:904401;gbkey=misc_feature;Note=PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature NC_002163.1 RefSeq region 85258 85296 . - . ID=id282;Name=id282;Dbxref=GeneID:904401;gbkey=misc_feature;Note=PS00018 EF-hand calcium-binding domain NC_002163.1 RefSeq CDS 86172 86912 . - 0 ID=cds62;Parent=gene70;Name=YP_002343537.1;Dbxref=InterPro:IPR004017 UniProtKB FTrEMBL:Q0PC60 Genbank:YP_002343537.1 GeneID:904402;gbkey=CDS;product=oxidoreductase iron-sulfur subunit;Note=Original 282000 29 note: Cj0075c 2C possible oxidoreductase iron-sulfur subunit 2C len: 246 aa 3B similar to hypothetical proteins and to the C-terminus of e.g. TR:O53142 28EMBL:AJ000942 29 Methanobacterium thermoautotrophicum strain Marburg 2C Thiol:fumarate reductase subunit B 28488 aa 29 2C fasta scores 3B opt: 217 z-score: 476.0 E 28 29: 3e-1 2C 24.3 25 identity in 235 aa overlap. 60.7 25 identity to HP0139 7EUpdated 282006 29 note: Pfam domain x2 PF02754 Cysteine-rich domain identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score. Thus 2C kept within product function. Functional classification - Energy metabolism - Electron transport 7EPMID:15773975 NC_002163.1 RefSeq gene 86172 86912 . - . ID=gene70;Name=Cj0075c;locus_tag=Cj0075c;Dbxref=GeneID:904402;gbkey=Gene NC_002163.1 RefSeq region 86259 86447 . - . ID=id283;Name=id283;Dbxref=GeneID:904402;gbkey=misc_feature;Note=HMMPfam hit to PF02754 2C Cysteine-rich domain 2C score 7.2e-19 NC_002163.1 RefSeq region 86655 86831 . - . ID=id284;Name=id284;Dbxref=GeneID:904402;gbkey=misc_feature;Note=HMMPfam hit to PF02754 2C Cysteine-rich domain 2C score 5.1e-12 ### NC_002163.1 RefSeq CDS 87036 88718 . - 0 ID=cds63;Parent=gene71;gene=lctP;Name=YP_002343538.1;Dbxref=GOA:Q0PC59 InterPro:IPR003804 UniProtKB FTrEMBL:Q0PC59 Genbank:YP_002343538.1 GeneID:904403;gbkey=CDS;product=L-lactate permease;Note=Original 282000 29 note: Cj0076c 2C lctP 2C probable L-lactate permease 2C len: 560 aa 3B highly similar to many e.g. LLDP_ECOLI L-lactate permease 28551 aa 29 2C fasta scores 3B opt: 1957 z-score: 2614.5 E 28 29: 0 2C 54.0 25 identity in 556 aa overlap. 61.2 25 identity to HP0141 and 60.6 25 identity to HP0140 7EUpdated 282006 29 note: Pfam domain PF02652 L-lactate permease identified within CDS. Thirteen probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. Thus 2C not added to product function. Functional classification - Transport 2Fbinding proteins -Carbohydrates 2C organic acids and alcohols 7EPMID:8407843 2C PMID:11283302 2C PMID:11785976 NC_002163.1 RefSeq gene 87036 88718 . - . ID=gene71;gene=lctP;Name=lctP;locus_tag=Cj0076c;Dbxref=GeneID:904403;gbkey=Gene NC_002163.1 RefSeq region 87057 87125 . - . ID=id8;gene=lctP;Name=id8;Dbxref=GeneID:904403;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0076c by TMHMM2.0 at aa 15-37 2C 42-61 2C 76-98 2C 119-150 2C165-187 2C 194-216 2C 255-272 2C 297-319 2C 372-391 2C 403-425 2C452-474 2C 495-517 and 532-554 NC_002163.1 RefSeq region 87081 88664 . - . ID=id285;gene=lctP;Name=id285;Dbxref=GeneID:904403;gbkey=misc_feature;Note=HMMPfam hit to PF02652 2C L-lactate permease 2C score 1.2e-268 NC_002163.1 RefSeq region 87168 87236 . - . ID=id8;gene=lctP;Name=id8;Dbxref=GeneID:904403;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0076c by TMHMM2.0 at aa 15-37 2C 42-61 2C 76-98 2C 119-150 2C165-187 2C 194-216 2C 255-272 2C 297-319 2C 372-391 2C 403-425 2C452-474 2C 495-517 and 532-554 NC_002163.1 RefSeq region 87183 87215 . - . ID=id286;gene=lctP;Name=id286;Dbxref=GeneID:904403;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 87297 87365 . - . ID=id8;gene=lctP;Name=id8;Dbxref=GeneID:904403;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0076c by TMHMM2.0 at aa 15-37 2C 42-61 2C 76-98 2C 119-150 2C165-187 2C 194-216 2C 255-272 2C 297-319 2C 372-391 2C 403-425 2C452-474 2C 495-517 and 532-554 NC_002163.1 RefSeq region 87444 87512 . - . ID=id8;gene=lctP;Name=id8;Dbxref=GeneID:904403;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0076c by TMHMM2.0 at aa 15-37 2C 42-61 2C 76-98 2C 119-150 2C165-187 2C 194-216 2C 255-272 2C 297-319 2C 372-391 2C 403-425 2C452-474 2C 495-517 and 532-554 NC_002163.1 RefSeq region 87546 87605 . - . ID=id8;gene=lctP;Name=id8;Dbxref=GeneID:904403;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0076c by TMHMM2.0 at aa 15-37 2C 42-61 2C 76-98 2C 119-150 2C165-187 2C 194-216 2C 255-272 2C 297-319 2C 372-391 2C 403-425 2C452-474 2C 495-517 and 532-554 NC_002163.1 RefSeq region 87762 87830 . - . ID=id8;gene=lctP;Name=id8;Dbxref=GeneID:904403;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0076c by TMHMM2.0 at aa 15-37 2C 42-61 2C 76-98 2C 119-150 2C165-187 2C 194-216 2C 255-272 2C 297-319 2C 372-391 2C 403-425 2C452-474 2C 495-517 and 532-554 NC_002163.1 RefSeq region 87903 87956 . - . ID=id8;gene=lctP;Name=id8;Dbxref=GeneID:904403;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0076c by TMHMM2.0 at aa 15-37 2C 42-61 2C 76-98 2C 119-150 2C165-187 2C 194-216 2C 255-272 2C 297-319 2C 372-391 2C 403-425 2C452-474 2C 495-517 and 532-554 NC_002163.1 RefSeq region 88071 88139 . - . ID=id8;gene=lctP;Name=id8;Dbxref=GeneID:904403;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0076c by TMHMM2.0 at aa 15-37 2C 42-61 2C 76-98 2C 119-150 2C165-187 2C 194-216 2C 255-272 2C 297-319 2C 372-391 2C 403-425 2C452-474 2C 495-517 and 532-554 NC_002163.1 RefSeq region 88158 88226 . - . ID=id8;gene=lctP;Name=id8;Dbxref=GeneID:904403;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0076c by TMHMM2.0 at aa 15-37 2C 42-61 2C 76-98 2C 119-150 2C165-187 2C 194-216 2C 255-272 2C 297-319 2C 372-391 2C 403-425 2C452-474 2C 495-517 and 532-554 NC_002163.1 RefSeq region 88269 88364 . - . ID=id8;gene=lctP;Name=id8;Dbxref=GeneID:904403;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0076c by TMHMM2.0 at aa 15-37 2C 42-61 2C 76-98 2C 119-150 2C165-187 2C 194-216 2C 255-272 2C 297-319 2C 372-391 2C 403-425 2C452-474 2C 495-517 and 532-554 NC_002163.1 RefSeq region 88425 88493 . - . ID=id8;gene=lctP;Name=id8;Dbxref=GeneID:904403;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0076c by TMHMM2.0 at aa 15-37 2C 42-61 2C 76-98 2C 119-150 2C165-187 2C 194-216 2C 255-272 2C 297-319 2C 372-391 2C 403-425 2C452-474 2C 495-517 and 532-554 NC_002163.1 RefSeq region 88536 88595 . - . ID=id8;gene=lctP;Name=id8;Dbxref=GeneID:904403;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0076c by TMHMM2.0 at aa 15-37 2C 42-61 2C 76-98 2C 119-150 2C165-187 2C 194-216 2C 255-272 2C 297-319 2C 372-391 2C 403-425 2C452-474 2C 495-517 and 532-554 NC_002163.1 RefSeq region 88608 88676 . - . ID=id8;gene=lctP;Name=id8;Dbxref=GeneID:904403;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0076c by TMHMM2.0 at aa 15-37 2C 42-61 2C 76-98 2C 119-150 2C165-187 2C 194-216 2C 255-272 2C 297-319 2C 372-391 2C 403-425 2C452-474 2C 495-517 and 532-554 ### NC_002163.1 UTR_Extractor 5'-UTR 88719 88746 . - . ID=utr30;locus_tag=Cj0076c;product=L-lactate permease NC_002163.1 RefSeq gene 88890 89459 . - . ID=gene72;gene=cdtC;Name=cdtC;locus_tag=Cj0077c;Dbxref=GeneID:904404;gbkey=Gene NC_002163.1 RefSeq CDS 88890 89459 . - 0 ID=cds64;Parent=gene72;gene=cdtC;Name=YP_002343539.1;Dbxref=GOA:Q46102 InterPro:IPR003558 UniProtKB FTrEMBL:Q46102 Genbank:YP_002343539.1 GeneID:904404;gbkey=CDS;product=cytolethal distending toxin C;Note=Original 282000 29 note: Cj0077c 2C cdtC 2C cytolethal distending toxin 2C len: 189 aa 2C identical to TR:Q46102 28EMBL:U51121 29 cdtC 28189 aa 29. No Hp match. Contains N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF03499 Cytolethal distending toxin C identified within CDS. Product modified to more specific family member due to motif match. Characterised within Campylobacter jejuni 2C so not added to product function. Functional classification -Pathogenicity 7EPMID:10688204 2C PMID:8675309 2C PMID:11083762 NC_002163.1 RefSeq region 89040 89438 . - . ID=id287;gene=cdtC;Name=id287;Dbxref=GeneID:904404;gbkey=misc_feature;Note=HMMPfam hit to PF03499 2C Cytolethal distending toxin C 2C score 3.6e-81 ### NC_002163.1 RefSeq CDS 89470 90267 . - 0 ID=cds65;Parent=gene73;gene=cdtB;Name=YP_002343540.1;Dbxref=GOA:Q46101 InterPro:IPR003539 InterPro:IPR005135 UniProtKB FTrEMBL:Q46101 Genbank:YP_002343540.1 GeneID:904405;gbkey=CDS;product=cytolethal distending toxin B;Note=Original 282000 29 note: Cj0078c 2C cdtB 2C cytolethal distending toxin 2C len: 265 aa 3B identical toTR:Q46101 28EMBL:U51121 29 cdtB 28265 aa 29 and similar to e.g. TR:Q47089 28EMBL:U03293 29 Escherichia coli cdtB 28273 aa 29 2C fasta scores 3B opt: 946 z-score: 1533.6 E 28 29: 0 2C 55.2 25 identity in 268 aa overlap. No Hp match. Contains N-terminal signal sequence 7EUpdated 282006 29 note: Prosite domain PRO1388 CDTOXINB 2C Cytolethal distending toxin B signature identified within CDS. Product modified to more specific family member due to motif match. Characterised within Campylobacter jejuni 2C so not added to product function. Functional classification - Pathogenicity 7EPMID:10688204 2C PMID:8675309 2C PMID:11083762 NC_002163.1 RefSeq gene 89470 90267 . - . ID=gene73;gene=cdtB;Name=cdtB;locus_tag=Cj0078c;Dbxref=GeneID:904405;gbkey=Gene NC_002163.1 RefSeq region 89476 90207 . - . ID=id288;gene=cdtB;Name=id288;Dbxref=GeneID:904405;gbkey=misc_feature;Note=HMMPfam hit to PF03372 2CEndonuclease 2FExonuclease 2Fphosphatase fa 2C score 7.8e-23 NC_002163.1 RefSeq gene 90264 91070 . - . ID=gene74;gene=cdtA;Name=cdtA;locus_tag=Cj0079c;Dbxref=GeneID:904406;gbkey=Gene NC_002163.1 RefSeq CDS 90264 91070 . - 0 ID=cds66;Parent=gene74;gene=cdtA;Name=YP_002343541.1;Dbxref=GOA:Q0PC56 InterPro:IPR000772 InterPro:IPR003558 InterPro:IPR015957 UniProtKB FSwiss-Prot:Q0PC56 Genbank:YP_002343541.1 GeneID:904406;gbkey=CDS;product=cytolethal distending toxin A;Note=Original 282000 29 note: Cj0079c 2C cdtA 2C cytolethal distending toxin 2C len: 268 aa 3B identical to TR:Q46100 28EMBL:U51121 29 cdtB 28268 aa 29 and similar to e.g. TR:Q47088 28EMBL:U03293 29 Escherichia coli cdtA 28237 aa 29 2C fasta scores 3B opt: 310 z-score: 408.0 E 28 29: 1.8e-15 2C 32.7 25 identity in 159 aa overlap. No Hp match. Contains N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site 7EUpdated 282006 29 note: Pfam domain PF03498 Cytolethal distending toxin A identified within CDS. Product modified to more specific family member due to motif match. Characterised within Campylobacter jejuni 2C so not added to product function. Functional classification -Pathogenicity 7EPMID:10688204 2C PMID:8675309 2C PMID:11083762 NC_002163.1 RefSeq region 90420 90704 . - . ID=id289;gene=cdtA;Name=id289;Dbxref=GeneID:904406;gbkey=misc_feature;Note=HMMPfam hit to PF03498 2C Cytolethal distending toxin A 2C score 1.6e-33 NC_002163.1 RefSeq region 91005 91058 . - . ID=id290;gene=cdtA;Name=id290;Dbxref=GeneID:904406;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0079c by TMHMM2.0 at aa 5-22 NC_002163.1 RefSeq region 91011 91043 . - . ID=id291;gene=cdtA;Name=id291;Dbxref=GeneID:904406;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 UTR_Extractor 5'-UTR 91071 91100 . - . ID=utr31;locus_tag=Cj0079c;product=cytolethal distending toxin A NC_002163.1 UTR_Extractor 5'-UTR 91136 91146 . + . ID=utr32;locus_tag=Cj0080;product=hypothetical protein NC_002163.1 RefSeq gene 91147 91416 . + . ID=gene75;Name=Cj0080;locus_tag=Cj0080;Dbxref=GeneID:904407;gbkey=Gene NC_002163.1 RefSeq CDS 91147 91416 . + 0 ID=cds67;Parent=gene75;Name=YP_002343542.1;Dbxref=GOA:Q0PC55 UniProtKB FTrEMBL:Q0PC55 Genbank:YP_002343542.1 GeneID:904407;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0080 2C possible membrane protein 2C len: 267 aa 3B no Hp match 3B Contains one possible transmembrane domain 7EUpdated 282006 29 note: Two probable transmembrane helices predicted by TMHMM2.0 NC_002163.1 RefSeq region 91174 91233 . + . ID=id292;Name=id292;Dbxref=GeneID:904407;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0080 by TMHMM2.0 at aa 10-29 and 42-64 NC_002163.1 RefSeq region 91270 91338 . + . ID=id292;Name=id292;Dbxref=GeneID:904407;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0080 by TMHMM2.0 at aa 10-29 and 42-64 ### NC_002163.1 RefSeq CDS 91417 92979 . + 0 ID=cds68;Parent=gene76;gene=cydA;Name=YP_002343543.1;Dbxref=GOA:Q0PC54 InterPro:IPR002585 UniProtKB FTrEMBL:Q0PC54 Genbank:YP_002343543.1 GeneID:904408;gbkey=CDS;product=cytochrome bd oxidase subunit I;Note=Original 282000 29 note: Cj0081 2C cydA 2C probable cytochrome bd oxidase subunit I 2C len: 520 aa 3Bsimilar to many e.g. APPC_ECOLI cytochrome bd-ii oxidase subunit I 28EC 1.10.3.- 29 28514 aa 29 2C fasta scores 3B opt: 1412 z-score: 1888.2 E 28 29: 0 2C 45.7 25 identity in 530 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF01654 Bacterial Cytochrome Ubiquinol Oxidase identified within CDS. Also 2Cnine probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. Thus 2C not added to product function. Functional classification - Energy metabolism - Electron transport 7EPMID:8626304 2C PMID:9068659 2C PMID:9852001 NC_002163.1 RefSeq gene 91417 92979 . + . ID=gene76;gene=cydA;Name=cydA;locus_tag=Cj0081;Dbxref=GeneID:904408;gbkey=Gene NC_002163.1 RefSeq region 91441 92952 . + . ID=id293;gene=cydA;Name=id293;Dbxref=GeneID:904408;gbkey=misc_feature;Note=HMMPfam hit to PF01654 2C Bacterial Cytochrome Ubiquinol Oxidase 2C score 3.3e-191 NC_002163.1 RefSeq region 91459 91527 . + . ID=id294;gene=cydA;Name=id294;Dbxref=GeneID:904408;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0081 by TMHMM2.0 at aa 15-37 2C 56-78 2C 98-120 2C 127-149 2C186-208 2C 221-240 2C 391-413 2C 426-448 and 477-499 NC_002163.1 RefSeq region 91582 91650 . + . ID=id294;gene=cydA;Name=id294;Dbxref=GeneID:904408;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0081 by TMHMM2.0 at aa 15-37 2C 56-78 2C 98-120 2C 127-149 2C186-208 2C 221-240 2C 391-413 2C 426-448 and 477-499 NC_002163.1 RefSeq region 91708 91776 . + . ID=id294;gene=cydA;Name=id294;Dbxref=GeneID:904408;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0081 by TMHMM2.0 at aa 15-37 2C 56-78 2C 98-120 2C 127-149 2C186-208 2C 221-240 2C 391-413 2C 426-448 and 477-499 NC_002163.1 RefSeq region 91795 91863 . + . ID=id294;gene=cydA;Name=id294;Dbxref=GeneID:904408;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0081 by TMHMM2.0 at aa 15-37 2C 56-78 2C 98-120 2C 127-149 2C186-208 2C 221-240 2C 391-413 2C 426-448 and 477-499 NC_002163.1 RefSeq region 91972 92040 . + . ID=id294;gene=cydA;Name=id294;Dbxref=GeneID:904408;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0081 by TMHMM2.0 at aa 15-37 2C 56-78 2C 98-120 2C 127-149 2C186-208 2C 221-240 2C 391-413 2C 426-448 and 477-499 NC_002163.1 RefSeq region 92077 92136 . + . ID=id294;gene=cydA;Name=id294;Dbxref=GeneID:904408;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0081 by TMHMM2.0 at aa 15-37 2C 56-78 2C 98-120 2C 127-149 2C186-208 2C 221-240 2C 391-413 2C 426-448 and 477-499 NC_002163.1 RefSeq region 92587 92655 . + . ID=id294;gene=cydA;Name=id294;Dbxref=GeneID:904408;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0081 by TMHMM2.0 at aa 15-37 2C 56-78 2C 98-120 2C 127-149 2C186-208 2C 221-240 2C 391-413 2C 426-448 and 477-499 NC_002163.1 RefSeq region 92692 92760 . + . ID=id294;gene=cydA;Name=id294;Dbxref=GeneID:904408;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0081 by TMHMM2.0 at aa 15-37 2C 56-78 2C 98-120 2C 127-149 2C186-208 2C 221-240 2C 391-413 2C 426-448 and 477-499 NC_002163.1 RefSeq region 92845 92913 . + . ID=id294;gene=cydA;Name=id294;Dbxref=GeneID:904408;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0081 by TMHMM2.0 at aa 15-37 2C 56-78 2C 98-120 2C 127-149 2C186-208 2C 221-240 2C 391-413 2C 426-448 and 477-499 NC_002163.1 RefSeq gene 92979 94103 . + . ID=gene77;gene=cydB;Name=cydB;locus_tag=Cj0082;Dbxref=GeneID:904409;gbkey=Gene NC_002163.1 RefSeq CDS 92979 94103 . + 0 ID=cds69;Parent=gene77;gene=cydB;Name=YP_002343544.1;Dbxref=GOA:Q0PC53 InterPro:IPR003317 UniProtKB FTrEMBL:Q0PC53 Genbank:YP_002343544.1 GeneID:904409;gbkey=CDS;product=cytochrome bd oxidase subunit II;Note=Original 282000 29 note: Cj0082 2C cydB 2C probable cytochrome bd oxidase subunit II 2C len: 520 aa 3Bsimilar to many e.g. CYDB_ECOLI cytochrome d ubiquinol oxidase subunit II 28EC 1.10.3.- 29 28379 aa 29 2C fasta scores 3B opt: 466 z-score: 449.6 E 28 29: 8.7e-18 2C 27.7 25 identity in 386 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02322 Cytochrome oxidase subunit II identified within CDS. Also 2C nine probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli with marginal identity score. not added to product function. Functional classification - Energy metabolism - Electron transport 7EPMID:8626304 2C PMID:9068659 2C PMID:9852001 2CPMID:15470119 NC_002163.1 RefSeq region 93000 94061 . + . ID=id295;gene=cydB;Name=id295;Dbxref=GeneID:904409;gbkey=misc_feature;Note=HMMPfam hit to PF02322 2C Cytochrome oxidase subunit II 2C score 3.5e-13 NC_002163.1 RefSeq region 93006 93071 . + . ID=id296;gene=cydB;Name=id296;Dbxref=GeneID:904409;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0082 by TMHMM2.0 at aa 10-31 2C 59-81 2C 86-108 2C 129-151 2C175-197 2C 210-229 2C 249-271 2C 284-306 and 332-354 NC_002163.1 RefSeq region 93153 93221 . + . ID=id296;gene=cydB;Name=id296;Dbxref=GeneID:904409;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0082 by TMHMM2.0 at aa 10-31 2C 59-81 2C 86-108 2C 129-151 2C175-197 2C 210-229 2C 249-271 2C 284-306 and 332-354 NC_002163.1 RefSeq region 93234 93302 . + . ID=id296;gene=cydB;Name=id296;Dbxref=GeneID:904409;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0082 by TMHMM2.0 at aa 10-31 2C 59-81 2C 86-108 2C 129-151 2C175-197 2C 210-229 2C 249-271 2C 284-306 and 332-354 NC_002163.1 RefSeq region 93363 93431 . + . ID=id296;gene=cydB;Name=id296;Dbxref=GeneID:904409;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0082 by TMHMM2.0 at aa 10-31 2C 59-81 2C 86-108 2C 129-151 2C175-197 2C 210-229 2C 249-271 2C 284-306 and 332-354 NC_002163.1 RefSeq region 93501 93569 . + . ID=id296;gene=cydB;Name=id296;Dbxref=GeneID:904409;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0082 by TMHMM2.0 at aa 10-31 2C 59-81 2C 86-108 2C 129-151 2C175-197 2C 210-229 2C 249-271 2C 284-306 and 332-354 NC_002163.1 RefSeq region 93606 93665 . + . ID=id296;gene=cydB;Name=id296;Dbxref=GeneID:904409;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0082 by TMHMM2.0 at aa 10-31 2C 59-81 2C 86-108 2C 129-151 2C175-197 2C 210-229 2C 249-271 2C 284-306 and 332-354 NC_002163.1 RefSeq region 93723 93791 . + . ID=id296;gene=cydB;Name=id296;Dbxref=GeneID:904409;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0082 by TMHMM2.0 at aa 10-31 2C 59-81 2C 86-108 2C 129-151 2C175-197 2C 210-229 2C 249-271 2C 284-306 and 332-354 NC_002163.1 RefSeq region 93828 93896 . + . ID=id296;gene=cydB;Name=id296;Dbxref=GeneID:904409;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0082 by TMHMM2.0 at aa 10-31 2C 59-81 2C 86-108 2C 129-151 2C175-197 2C 210-229 2C 249-271 2C 284-306 and 332-354 NC_002163.1 RefSeq region 93972 94040 . + . ID=id296;gene=cydB;Name=id296;Dbxref=GeneID:904409;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0082 by TMHMM2.0 at aa 10-31 2C 59-81 2C 86-108 2C 129-151 2C175-197 2C 210-229 2C 249-271 2C 284-306 and 332-354 ### NC_002163.1 RefSeq sRNA 94249 94344 . + . ID=NC_002163.1:CJnc10:unknown_transcript_1;Parent=NC_002163.1:CJnc10;Name=NC_002163.1:CJnc10:unknown_transcript_1;locus_tag=CJnc10;gbkey=misc_RNA;product=CJnc10 NC_002163.1 RefSeq gene 94249 94344 . + . ID=NC_002163.1:CJnc10;Name=NC_002163.1:CJnc10;locus_tag=CJnc10 NC_002163.1 RefSeq CDS 94297 94992 . - 0 ID=cds70;Parent=gene78;Name=YP_002343545.1;Dbxref=GOA:Q0PC52 InterPro:IPR001920 InterPro:IPR004380 InterPro:IPR015942 UniProtKB FTrEMBL:Q0PC52 Genbank:YP_002343545.1 GeneID:904410;gbkey=CDS;product=amino acid recemase;Note=Original 282000 29 note: Cj0085c 2C probable amino acid recemase 2C len: 231 aa 3B similar to members of the aspartate 2Fglutamate racemases family e.g. YGEA_ECOLI 28230 aa 29 2C fasta scores 3B opt: 667 z-score: 1155.6 E 28 29: 0 2C 46.7 25 identity in 225 aa overlap 2C and RACD_STRTR aspartate racemase 28243 aa 29 2C fasta scores 3B opt: 254 z-score: 230.9 E 28 29: 1.3e-05 2C 25.4 25 identity in 232 aa overlap. No Hp match. Contains PS00924 Aspartate and glutamate racemases signature 2 andPfam match to entry PF01177 Asp_Glu_race 2CAspartate 2F glutamate racemase 2C score 108.40 2C E-value 1.3e-28 7EUpdated 282006 29 note: Pfam domain PF01177 Asp 2FGlu 2FHydantoin racemase identified within CDS. No specific characterisation with acceptable identity score identified. Thus 2C kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 94297 94992 . - . ID=gene78;Name=Cj0085c;locus_tag=Cj0085c;Dbxref=GeneID:904410;gbkey=Gene NC_002163.1 RefSeq region 94309 94986 . - . ID=id297;Name=id297;Dbxref=GeneID:904410;gbkey=misc_feature;Note=HMMPfam hit to PF01177 2C Asp 2FGlu 2FHydantoin racemase 2Cscore 4.8e-67 NC_002163.1 RefSeq region 94387 94419 . - . ID=id298;Name=id298;Dbxref=GeneID:904410;gbkey=misc_feature;Note=PS00924 Aspartate and glutamate racemases signature 2 ### NC_002163.1 RefSeq CDS 95108 95803 . - 0 ID=cds71;Parent=gene79;gene=ung;Name=YP_002343546.1;Dbxref=GOA:Q9PJ40 HSSP:P13051 InterPro:IPR002043 InterPro:IPR005122 UniProtKB FSwiss-Prot:Q9PJ40 Genbank:YP_002343546.1 GeneID:904411;gbkey=CDS;product=uracil-DNA glycosylase;Note=Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine NC_002163.1 RefSeq gene 95108 95803 . - . ID=gene79;gene=ung;Name=ung;locus_tag=Cj0086c;Dbxref=GeneID:904411;gbkey=Gene NC_002163.1 RefSeq region 95147 95623 . - . ID=id299;gene=ung;Name=id299;Dbxref=GeneID:904411;gbkey=misc_feature;Note=HMMPfam hit to PF03167 2C Uracil DNA glycosylase superfamily 2C score 1.6e-73 NC_002163.1 RefSeq region 95576 95605 . - . ID=id300;gene=ung;Name=id300;Dbxref=GeneID:904411;gbkey=misc_feature;Note=PS00130 Uracil-DNA glycosylase signature ### NC_002163.1 UTR_Extractor 5'-UTR 95804 95834 . - . ID=utr33;locus_tag=Cj0086c;product=uracil-DNA glycosylase NC_002163.1 UTR_Extractor 5'-UTR 96016 96073 . + . ID=utr34;locus_tag=Cj0087;product=aspartate ammonia-lyase NC_002163.1 RefSeq CDS 96074 97480 . + 0 ID=cds72;Parent=gene80;gene=aspA;Name=YP_002343547.1;Dbxref=GOA:Q0PC50 InterPro:IPR000362 InterPro:IPR003031 InterPro:IPR004708 UniProtKB FTrEMBL:Q0PC50 Genbank:YP_002343547.1 GeneID:904412;gbkey=CDS;product=aspartate ammonia-lyase;Note=catalyzes the formation of fumarate from aspartate NC_002163.1 RefSeq gene 96074 97480 . + . ID=gene80;gene=aspA;Name=aspA;locus_tag=Cj0087;Dbxref=GeneID:904412;gbkey=Gene NC_002163.1 RefSeq region 96104 97099 . + . ID=id301;gene=aspA;Name=id301;Dbxref=GeneID:904412;gbkey=misc_feature;Note=HMMPfam hit to PF00206 2C Lyase 2C score 1.2e-151 NC_002163.1 RefSeq region 97022 97051 . + . ID=id302;gene=aspA;Name=id302;Dbxref=GeneID:904412;gbkey=misc_feature;Note=PS00163 Fumarate lyases signature ### NC_002163.1 RefSeq CDS 97496 98833 . + 0 ID=cds73;Parent=gene81;gene=dcuA;Name=YP_002343548.1;Dbxref=GOA:Q0PC49 InterPro:IPR004668 UniProtKB FTrEMBL:Q0PC49 Genbank:YP_002343548.1 GeneID:904413;gbkey=CDS;product=anaerobic C4-dicarboxylate transporter;Note=functions in anaerobic transport of C4-dicarboxylate compounds such as fumarate 3B similar to dcuB NC_002163.1 RefSeq gene 97496 98833 . + . ID=gene81;gene=dcuA;Name=dcuA;locus_tag=Cj0088;Dbxref=GeneID:904413;gbkey=Gene NC_002163.1 RefSeq region 97502 97555 . + . ID=id303;gene=dcuA;Name=id303;Dbxref=GeneID:904413;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0088 by TMHMM2.0 at aa 3-20 2C 25-42 2C 49-71 2C 91-113 2C134-156 2C 171-193 2C 230-249 2C 259-281 2C 301-323 2C 338-360 2C380-402 and 422-444 NC_002163.1 RefSeq region 97517 98608 . + . ID=id304;gene=dcuA;Name=id304;Dbxref=GeneID:904413;gbkey=misc_feature;Note=HMMPfam hit to PF03605 2C Anaerobic c4-dicarboxylate membrane transpo 2C score 3.9e-245 NC_002163.1 RefSeq region 97568 97621 . + . ID=id303;gene=dcuA;Name=id303;Dbxref=GeneID:904413;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0088 by TMHMM2.0 at aa 3-20 2C 25-42 2C 49-71 2C 91-113 2C134-156 2C 171-193 2C 230-249 2C 259-281 2C 301-323 2C 338-360 2C380-402 and 422-444 NC_002163.1 RefSeq region 97640 97708 . + . ID=id303;gene=dcuA;Name=id303;Dbxref=GeneID:904413;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0088 by TMHMM2.0 at aa 3-20 2C 25-42 2C 49-71 2C 91-113 2C134-156 2C 171-193 2C 230-249 2C 259-281 2C 301-323 2C 338-360 2C380-402 and 422-444 NC_002163.1 RefSeq region 97766 97834 . + . ID=id303;gene=dcuA;Name=id303;Dbxref=GeneID:904413;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0088 by TMHMM2.0 at aa 3-20 2C 25-42 2C 49-71 2C 91-113 2C134-156 2C 171-193 2C 230-249 2C 259-281 2C 301-323 2C 338-360 2C380-402 and 422-444 NC_002163.1 RefSeq region 97895 97963 . + . ID=id303;gene=dcuA;Name=id303;Dbxref=GeneID:904413;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0088 by TMHMM2.0 at aa 3-20 2C 25-42 2C 49-71 2C 91-113 2C134-156 2C 171-193 2C 230-249 2C 259-281 2C 301-323 2C 338-360 2C380-402 and 422-444 NC_002163.1 RefSeq region 98006 98074 . + . ID=id303;gene=dcuA;Name=id303;Dbxref=GeneID:904413;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0088 by TMHMM2.0 at aa 3-20 2C 25-42 2C 49-71 2C 91-113 2C134-156 2C 171-193 2C 230-249 2C 259-281 2C 301-323 2C 338-360 2C380-402 and 422-444 NC_002163.1 RefSeq region 98012 98044 . + . ID=id305;gene=dcuA;Name=id305;Dbxref=GeneID:904413;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 98183 98242 . + . ID=id303;gene=dcuA;Name=id303;Dbxref=GeneID:904413;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0088 by TMHMM2.0 at aa 3-20 2C 25-42 2C 49-71 2C 91-113 2C134-156 2C 171-193 2C 230-249 2C 259-281 2C 301-323 2C 338-360 2C380-402 and 422-444 NC_002163.1 RefSeq region 98270 98338 . + . ID=id303;gene=dcuA;Name=id303;Dbxref=GeneID:904413;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0088 by TMHMM2.0 at aa 3-20 2C 25-42 2C 49-71 2C 91-113 2C134-156 2C 171-193 2C 230-249 2C 259-281 2C 301-323 2C 338-360 2C380-402 and 422-444 NC_002163.1 RefSeq region 98396 98464 . + . ID=id303;gene=dcuA;Name=id303;Dbxref=GeneID:904413;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0088 by TMHMM2.0 at aa 3-20 2C 25-42 2C 49-71 2C 91-113 2C134-156 2C 171-193 2C 230-249 2C 259-281 2C 301-323 2C 338-360 2C380-402 and 422-444 NC_002163.1 RefSeq region 98507 98575 . + . ID=id303;gene=dcuA;Name=id303;Dbxref=GeneID:904413;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0088 by TMHMM2.0 at aa 3-20 2C 25-42 2C 49-71 2C 91-113 2C134-156 2C 171-193 2C 230-249 2C 259-281 2C 301-323 2C 338-360 2C380-402 and 422-444 NC_002163.1 RefSeq region 98633 98701 . + . ID=id303;gene=dcuA;Name=id303;Dbxref=GeneID:904413;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0088 by TMHMM2.0 at aa 3-20 2C 25-42 2C 49-71 2C 91-113 2C134-156 2C 171-193 2C 230-249 2C 259-281 2C 301-323 2C 338-360 2C380-402 and 422-444 NC_002163.1 RefSeq region 98759 98827 . + . ID=id303;gene=dcuA;Name=id303;Dbxref=GeneID:904413;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0088 by TMHMM2.0 at aa 3-20 2C 25-42 2C 49-71 2C 91-113 2C134-156 2C 171-193 2C 230-249 2C 259-281 2C 301-323 2C 338-360 2C380-402 and 422-444 ### NC_002163.1 UTR_Extractor 5'-UTR 98912 98940 . + . ID=utr35;locus_tag=Cj0089;product=putative lipoprotein NC_002163.1 RefSeq CDS 98941 100302 . + 0 ID=cds74;Parent=gene82;Name=YP_002343549.1;Dbxref=UniProtKB FTrEMBL:Q0PC48 Genbank:YP_002343549.1 GeneID:904416;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj0089 2C probable lipoprotein 2Clen: 453 aa 3B 27.4 25 identity to HP0018. Contains N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 98941 100302 . + . ID=gene82;Name=Cj0089;locus_tag=Cj0089;Dbxref=GeneID:904416;gbkey=Gene NC_002163.1 RefSeq region 98968 99000 . + . ID=id306;Name=id306;Dbxref=GeneID:904416;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 99313 99414 . + . ID=id307;Name=id307;Dbxref=GeneID:904416;gbkey=misc_feature;Note=HMMPfam hit to PF07719 2C Tetratricopeptide repeat 2Cscore 1.4 NC_002163.1 RefSeq region 99577 99678 . + . ID=id308;Name=id308;Dbxref=GeneID:904416;gbkey=misc_feature;Note=HMMPfam hit to PF07719 2C Tetratricopeptide repeat 2Cscore 0.12 ### NC_002163.1 RefSeq gene 100312 100680 . + . ID=gene83;Name=Cj0090;locus_tag=Cj0090;Dbxref=GeneID:904418;gbkey=Gene NC_002163.1 RefSeq CDS 100312 100680 . + 0 ID=cds75;Parent=gene83;Name=YP_002343550.1;Dbxref=UniProtKB FTrEMBL:Q0PC47 Genbank:YP_002343550.1 GeneID:904418;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj0090 2C probable lipoprotein 2Clen: 122 aa 3B no Hp match. Contains N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 100327 100359 . + . ID=id309;Name=id309;Dbxref=GeneID:904418;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq CDS 100704 101327 . + 0 ID=cds76;Parent=gene84;Name=YP_002343551.1;Dbxref=GOA:Q0PC46 InterPro:IPR014094 UniProtKB FTrEMBL:Q0PC46 Genbank:YP_002343551.1 GeneID:904419;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj0091 2C probable lipoprotein 2Clen: 207 aa 3B 33.5 25 identity to HP1457. Contains N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 100704 101327 . + . ID=gene84;Name=Cj0091;locus_tag=Cj0091;Dbxref=GeneID:904419;gbkey=Gene NC_002163.1 RefSeq region 100722 100781 . + . ID=id310;Name=id310;Dbxref=GeneID:904419;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0091 by TMHMM2.0 at aa 7-26 NC_002163.1 RefSeq region 100731 100763 . + . ID=id311;Name=id311;Dbxref=GeneID:904419;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq CDS 101410 102747 . + 0 ID=cds77;Parent=gene85;Name=YP_002343552.1;Dbxref=GOA:Q0PC45 UniProtKB FTrEMBL:Q0PC45 Genbank:YP_002343552.1 GeneID:904420;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0092 2C probable periplasmic protein 2C len: 445 aa 3B no Hp match. Contains probable N-terminal signal sequence and PS00017 ATP 2FGTP-binding site motif A 28P-loop 29. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 101410 102747 . + . ID=gene85;Name=Cj0092;locus_tag=Cj0092;Dbxref=GeneID:904420;gbkey=Gene NC_002163.1 RefSeq region 101605 101628 . + . ID=id312;Name=id312;Dbxref=GeneID:904420;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 UTR_Extractor 5'-UTR 102522 102756 . + . ID=utr36;locus_tag=Cj0093;product=putative periplasmic protein ### NC_002163.1 RefSeq gene 102757 103959 . + . ID=gene86;Name=Cj0093;locus_tag=Cj0093;Dbxref=GeneID:904421;gbkey=Gene NC_002163.1 RefSeq CDS 102757 103959 . + 0 ID=cds78;Parent=gene86;Name=YP_002343553.1;Dbxref=GOA:Q0PC44 UniProtKB FTrEMBL:Q0PC44 Genbank:YP_002343553.1 GeneID:904421;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0093 2C probable periplasmic protein 2C len: 400 aa 3B no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 UTR_Extractor 5'-UTR 104043 104117 . + . ID=utr37;locus_tag=Cj0094;product=50S ribosomal protein L21 NC_002163.1 RefSeq region 104118 104402 . + . ID=id313;gene=rplU;Name=id313;Dbxref=GeneID:904422;gbkey=misc_feature;Note=HMMPfam hit to PF00829 2C Ribosomal prokaryotic L21 protein 2C score 3.6e-48 NC_002163.1 RefSeq gene 104118 104426 . + . ID=gene87;gene=rplU;Name=rplU;locus_tag=Cj0094;Dbxref=GeneID:904422;gbkey=Gene NC_002163.1 RefSeq CDS 104118 104426 . + 0 ID=cds79;Parent=gene87;gene=rplU;Name=YP_002343554.1;Dbxref=GOA:Q0PC43 InterPro:IPR001787 UniProtKB FSwiss-Prot:Q0PC43 Genbank:YP_002343554.1 GeneID:904422;gbkey=CDS;product=50S ribosomal protein L21;Note=Original 282000 29 note: Cj0094 2C rplU 2C 50S ribosomal protein L21 2C len: 102 aa 3B similar to many e.g. RL21_ECOLI 50S ribosomal protein L21 28103 aa 29 2C fasta scores 3B opt: 268 z-score: 457.7 E 28 29: 3.1e-18 2C 40.8 25 identity in 103 aa overlap. 58.8 25 identity to HP0296. Contains PS01169 Ribosomal protein L21 signature and Pfam match to entry PF00829 Ribosomal_L21p 2C Ribosomal prokaryotic L21 protein 2Cscore 152.80 2C E-value 5.7e-42 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. Thus 2C not added to product function. Functional classification - Ribosomal protein synthesis and modification 7EPMID:378941 2C 8312607 NC_002163.1 RefSeq region 104328 104396 . + . ID=id314;gene=rplU;Name=id314;Dbxref=GeneID:904422;gbkey=misc_feature;Note=PS01169 Ribosomal protein L21 signature ### NC_002163.1 RefSeq CDS 104437 104691 . + 0 ID=cds80;Parent=gene88;gene=rpmA;Name=YP_002343555.1;Dbxref=GOA:Q9PJ31 InterPro:IPR001684 UniProtKB FSwiss-Prot:Q9PJ31 Genbank:YP_002343555.1 GeneID:904423;gbkey=CDS;product=50S ribosomal protein L27;Note=involved in the peptidyltransferase reaction during translation NC_002163.1 RefSeq gene 104437 104691 . + . ID=gene88;gene=rpmA;Name=rpmA;locus_tag=Cj0095;Dbxref=GeneID:904423;gbkey=Gene NC_002163.1 RefSeq region 104440 104682 . + . ID=id315;gene=rpmA;Name=id315;Dbxref=GeneID:904423;gbkey=misc_feature;Note=HMMPfam hit to PF01016 2C Ribosomal L27 protein 2Cscore 3.7e-54 NC_002163.1 RefSeq region 104536 104580 . + . ID=id316;gene=rpmA;Name=id316;Dbxref=GeneID:904423;gbkey=misc_feature;Note=PS00831 Ribosomal protein L27 signature ### NC_002163.1 RefSeq stem_loop 104722 104783 . + . ID=id317;Name=id317;gbkey=stem_loop NC_002163.1 RefSeq CDS 104798 105850 . + 0 ID=cds81;Parent=gene89;gene=obgE;Name=YP_002343556.1;Dbxref=GOA:Q0PC41 InterPro:IPR002917 InterPro:IPR006073 InterPro:IPR006074 InterPro:IPR006169 InterPro:IPR014100 UniProtKB FTrEMBL:Q0PC41 Genbank:YP_002343556.1 GeneID:905891;gbkey=CDS;product=GTPase ObgE;Note=essential GTPase 3B exhibits high exchange rate for GTP 2FGDP 3B associates with 50S ribosomal subunit 3B involved in regulation of chromosomal replication NC_002163.1 RefSeq gene 104798 105850 . + . ID=gene89;gene=obgE;Name=obgE;locus_tag=Cj0096;Dbxref=GeneID:905891;gbkey=Gene NC_002163.1 RefSeq region 104801 105268 . + . ID=id318;gene=obgE;Name=id318;Dbxref=GeneID:905891;gbkey=misc_feature;Note=HMMPfam hit to PF01018 2C GTP1 2FOBG 2C score 2.7e-75 NC_002163.1 RefSeq region 105272 105646 . + . ID=id319;gene=obgE;Name=id319;Dbxref=GeneID:905891;gbkey=misc_feature;Note=HMMPfam hit to PF01926 2C GTPase of unknown function 2Cscore 2.7e-33 NC_002163.1 RefSeq region 105290 105313 . + . ID=id320;gene=obgE;Name=id320;Dbxref=GeneID:905891;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 105431 105472 . + . ID=id321;gene=obgE;Name=id321;Dbxref=GeneID:905891;gbkey=misc_feature;Note=PS00905 GTP1 2FOBG family signature ### NC_002163.1 RefSeq gene 105955 106710 . + . ID=gene90;gene=proB;Name=proB;locus_tag=Cj0097;Dbxref=GeneID:904426;gbkey=Gene NC_002163.1 RefSeq CDS 105955 106710 . + 0 ID=cds82;Parent=gene90;gene=proB;Name=YP_002343557.1;Dbxref=GOA:Q9PJ29 InterPro:IPR001048 InterPro:IPR001057 InterPro:IPR005715 InterPro:IPR011529 PDB:2AKO UniProtKB FSwiss-Prot:Q9PJ29 Genbank:YP_002343557.1 GeneID:904426;gbkey=CDS;product=gamma-glutamyl kinase;Note=catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis NC_002163.1 RefSeq region 105958 106638 . + . ID=id322;gene=proB;Name=id322;Dbxref=GeneID:904426;gbkey=misc_feature;Note=HMMPfam hit to PF00696 2C Amino acid kinase family 2Cscore 1e-41 ### NC_002163.1 UTR_Extractor 5'-UTR 106759 106783 . + . ID=utr38;locus_tag=Cj0098;product=methionyl-tRNA formyltransferase NC_002163.1 RefSeq CDS 106784 107701 . + 0 ID=cds83;Parent=gene91;gene=fmt;Name=YP_002343558.1;Dbxref=GOA:Q9PJ28 HSSP:P23882 InterPro:IPR001555 InterPro:IPR002376 InterPro:IPR005793 InterPro:IPR005794 InterPro:IPR015518 UniProtKB FSwiss-Prot:Q9PJ28 Genbank:YP_002343558.1 GeneID:904427;gbkey=CDS;product=methionyl-tRNA formyltransferase;Note=modifies the free amino group of the aminoacyl moiety of methionyl-tRNA 28fMet 29 which is important in translation initiation 3B inactivation of this gene in Escherichia coli severely impairs growth NC_002163.1 RefSeq gene 106784 107701 . + . ID=gene91;gene=fmt;Name=fmt;locus_tag=Cj0098;Dbxref=GeneID:904427;gbkey=Gene NC_002163.1 RefSeq region 106787 107326 . + . ID=id323;gene=fmt;Name=id323;Dbxref=GeneID:904427;gbkey=misc_feature;Note=HMMPfam hit to PF00551 2C Formyl transferase 2C score 4.4e-36 NC_002163.1 RefSeq region 107393 107674 . + . ID=id324;gene=fmt;Name=id324;Dbxref=GeneID:904427;gbkey=misc_feature;Note=HMMPfam hit to PF02911 2C Formyl transferase 2CC-terminal domain 2C score 8e-24 NC_002163.1 RefSeq CDS 107664 108317 . + 0 ID=cds84;Parent=gene92;gene=birA;Name=YP_002343559.1;Dbxref=GOA:Q0PC38 InterPro:IPR004143 InterPro:IPR004408 UniProtKB FTrEMBL:Q0PC38 Genbank:YP_002343559.1 GeneID:904428;gbkey=CDS;product=biotin--protein ligase;Note=catalyzes the formation of biotinyl-5 27-AMP 2C also acts as a transcriptional repressor of the biotin operon NC_002163.1 RefSeq gene 107664 108317 . + . ID=gene92;gene=birA;Name=birA;locus_tag=Cj0099;Dbxref=GeneID:904428;gbkey=Gene NC_002163.1 RefSeq region 107694 108083 . + . ID=id325;gene=birA;Name=id325;Dbxref=GeneID:904428;gbkey=misc_feature;Note=HMMPfam hit to PF03099 2C Biotin 2Flipoate A 2FB protein ligase famil 2C score 2e-13 NC_002163.1 UTR_Extractor 5'-UTR 108199 108313 . + . ID=utr39;locus_tag=Cj0100;product=parA family protein NC_002163.1 RefSeq CDS 108314 109099 . + 0 ID=cds85;Parent=gene93;Name=YP_002343560.1;Dbxref=GOA:Q0PC37 InterPro:IPR002586 UniProtKB FTrEMBL:Q0PC37 Genbank:YP_002343560.1 GeneID:904430;gbkey=CDS;product=ParA family protein;Note=Original 282000 29 note: Cj0100 2C parA family protein 2C len: 261 aa 3B similar to members of the parA family e.g. SOJ_BACSU soj protein 28253 aa 29 fasta scores 3B opt: 762 z-score: 1251.6 E 28 29: 0 2C 46.3 25 identity in 259 aa overlap. 61.1 25 identity to HP1139. Contains Pfam match to entry PF00991 ParA 2C ParA family ATPase 2C score 118.40 2CE-value 1.3e-31 7EUpdated 282006 29 note: Pfam domain PF01656 CobQ 2FCobB 2FMinD 2FParA nucleotide binding domain identified within CDS. This family consists of cobyrinic acid a 2Cc-diamide synthases family protein. Some characterisation work within Bacillus subtilis with acceptable identity score. not added to product function. Functional classification - Cell division 7EPMID:8071208 NC_002163.1 RefSeq gene 108314 109099 . + . ID=gene93;gene=Cj0100;Name=Cj0100;locus_tag=Cj0100;Dbxref=GeneID:904430;gbkey=Gene NC_002163.1 RefSeq region 108326 109006 . + . ID=id326;Name=id326;Dbxref=GeneID:904430;gbkey=misc_feature;Note=HMMPfam hit to PF01656 2C CobQ 2FCobB 2FMinD 2FParA nucleotide binding domai 2C score 9.4e-53 ### NC_002163.1 RefSeq gene 109105 109941 . + . ID=gene94;Name=Cj0101;locus_tag=Cj0101;Dbxref=GeneID:904366;gbkey=Gene NC_002163.1 RefSeq CDS 109105 109941 . + 0 ID=cds86;Parent=gene94;Name=YP_002343561.1;Dbxref=GOA:Q9PJ25 InterPro:IPR003115 InterPro:IPR004437 UniProtKB FSwiss-Prot:Q9PJ25 Genbank:YP_002343561.1 GeneID:904366;gbkey=CDS;product=parB family protein;Note=Original 282000 29 note: Cj0101 2C parB family protein 2C len: 278 aa 3B similar to members of the parB family e.g.SP0J_BACSU stage 0 sporulation protein J 28282 aa 29 2C fasta scores 3B opt: 563 z-score: 842.8 E 28 29: 0 2C 36.1 25 identity in 288 aa overlap. 41.7 25 identity to HP1138 plasmid replication-partition related protein. Contains helix-turn-helix motif 28Score 1486 2C 2B4.25 SD 29 7EUpdated 282006 29 note: Pfam domain PF02195 ParB-like nuclease domain identified within CDS. Some characterisation within Bacillus subtilis with acceptable identity score. not added to product function. Functional classification - Cell division 7EPMID:1900505 2C PMID:8071208 NC_002163.1 RefSeq region 109198 109467 . + . ID=id327;Name=id327;Dbxref=GeneID:904366;gbkey=misc_feature;Note=HMMPfam hit to PF02195 2C ParB-like nuclease domain 2Cscore 2.7e-34 ### NC_002163.1 UTR_Extractor 5'-UTR 109977 110001 . + . ID=utr40;locus_tag=Cj0102;product=F0F1 ATP synthase subunit B 27 NC_002163.1 RefSeq CDS 110002 110427 . + 0 ID=cds87;Parent=gene95;gene=atpF';Name=YP_002343562.1;Dbxref=GOA:Q0PC35 InterPro:IPR002146 UniProtKB FTrEMBL:Q0PC35 Genbank:YP_002343562.1 GeneID:904431;gbkey=CDS;product=F0F1 ATP synthase subunit B 27;Note=Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B 27 is part of the membrane proton channel. NC_002163.1 RefSeq gene 110002 110427 . + . ID=gene95;gene=atpF';Name=atpF';locus_tag=Cj0102;Dbxref=GeneID:904431;gbkey=Gene NC_002163.1 RefSeq region 110026 110418 . + . ID=id328;gene=atpF';Name=id328;Dbxref=GeneID:904431;gbkey=misc_feature;Note=HMMPfam hit to PF00430 2C ATP synthase B 2FB 27 CF 280 29 2Cscore 1.5e-06 NC_002163.1 RefSeq region 110029 110088 . + . ID=id329;gene=atpF';Name=id329;Dbxref=GeneID:904431;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0102 by TMHMM2.0 at aa 10-29 ### NC_002163.1 RefSeq CDS 110438 110950 . + 0 ID=cds88;Parent=gene96;gene=atpF;Name=YP_002343563.1;Dbxref=GOA:Q0PC34 InterPro:IPR002146 UniProtKB FTrEMBL:Q0PC34 Genbank:YP_002343563.1 GeneID:904432;gbkey=CDS;product=F0F1 ATP synthase subunit B;Note=Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel. NC_002163.1 RefSeq gene 110438 110950 . + . ID=gene96;gene=atpF;Name=atpF;locus_tag=Cj0103;Dbxref=GeneID:904432;gbkey=Gene NC_002163.1 RefSeq region 110450 110503 . + . ID=id330;gene=atpF;Name=id330;Dbxref=GeneID:904432;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0103 by TMHMM2.0 at aa 5-22 and 27-49 NC_002163.1 RefSeq region 110513 110923 . + . ID=id331;gene=atpF;Name=id331;Dbxref=GeneID:904432;gbkey=misc_feature;Note=HMMPfam hit to PF00430 2C ATP synthase B 2FB 27 CF 280 29 2Cscore 0.00034 NC_002163.1 RefSeq region 110516 110584 . + . ID=id330;gene=atpF;Name=id330;Dbxref=GeneID:904432;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0103 by TMHMM2.0 at aa 5-22 and 27-49 ### NC_002163.1 RefSeq gene 110953 111474 . + . ID=gene97;gene=atpH;Name=atpH;locus_tag=Cj0104;Dbxref=GeneID:904434;gbkey=Gene NC_002163.1 RefSeq CDS 110953 111474 . + 0 ID=cds89;Parent=gene97;gene=atpH;Name=YP_002343564.1;Dbxref=GOA:Q0PC33 InterPro:IPR000711 UniProtKB FTrEMBL:Q0PC33 Genbank:YP_002343564.1 GeneID:904434;gbkey=CDS;product=F0F1 ATP synthase subunit delta;Note=Produces ATP from ADP in the presence of a proton gradient across the membrane. The delta subunit is part of the catalytic core of the ATP synthase complex NC_002163.1 RefSeq region 110965 111414 . + . ID=id332;gene=atpH;Name=id332;Dbxref=GeneID:904434;gbkey=misc_feature;Note=HMMPfam hit to PF00213 2C ATP synthase delta 28OSCP 29 subunit 2C score 1.1e-07 ### NC_002163.1 RefSeq CDS 111488 112993 . + 0 ID=cds90;Parent=gene98;gene=atpA;Name=YP_002343565.1;Dbxref=GOA:Q9PJ21 HSSP:P09219 InterPro:IPR000194 InterPro:IPR000793 InterPro:IPR004100 InterPro:IPR005294 InterPro:IPR017458 UniProtKB FSwiss-Prot:Q9PJ21 Genbank:YP_002343565.1 GeneID:904435;gbkey=CDS;product=F0F1 ATP synthase subunit alpha;Note=produces ATP from ADP in the presence of a proton gradient across the membrane 3B the alpha chain is a catalytic subunit NC_002163.1 RefSeq gene 111488 112993 . + . ID=gene98;gene=atpA;Name=atpA;locus_tag=Cj0105;Dbxref=GeneID:904435;gbkey=Gene NC_002163.1 RefSeq region 111557 111763 . + . ID=id333;gene=atpA;Name=id333;Dbxref=GeneID:904435;gbkey=misc_feature;Note=HMMPfam hit to PF02874 2C ATP synthase alpha 2Fbeta family 2C beta-ba 2C score 7.9e-19 NC_002163.1 RefSeq region 111929 112579 . + . ID=id334;gene=atpA;Name=id334;Dbxref=GeneID:904435;gbkey=misc_feature;Note=HMMPfam hit to PF00006 2C ATP synthase alpha 2Fbeta family 2C nucleot 2C score 3.4e-115 NC_002163.1 RefSeq region 111992 112015 . + . ID=id335;gene=atpA;Name=id335;Dbxref=GeneID:904435;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 112550 112579 . + . ID=id336;gene=atpA;Name=id336;Dbxref=GeneID:904435;gbkey=misc_feature;Note=PS00152 ATP synthase alpha and beta subunits signature NC_002163.1 RefSeq region 112613 112927 . + . ID=id337;gene=atpA;Name=id337;Dbxref=GeneID:904435;gbkey=misc_feature;Note=HMMPfam hit to PF00306 2C ATP synthase alpha 2Fbeta chain 2C C termin 2C score 2.5e-36 ### NC_002163.1 RefSeq CDS 113002 113886 . + 0 ID=cds91;Parent=gene99;gene=atpG;Name=YP_002343566.1;Dbxref=GOA:Q9PJ20 InterPro:IPR000131 UniProtKB FSwiss-Prot:Q9PJ20 Genbank:YP_002343566.1 GeneID:904436;gbkey=CDS;product=F0F1 ATP synthase subunit gamma;Note=Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit NC_002163.1 RefSeq gene 113002 113886 . + . ID=gene99;gene=atpG;Name=atpG;locus_tag=Cj0106;Dbxref=GeneID:904436;gbkey=Gene NC_002163.1 RefSeq region 113005 113880 . + . ID=id338;gene=atpG;Name=id338;Dbxref=GeneID:904436;gbkey=misc_feature;Note=HMMPfam hit to PF00231 2C ATP synthase 2C score 2.8e-83 NC_002163.1 UTR_Extractor 5'-UTR 113705 113911 . + . ID=utr41;locus_tag=Cj0107;product=F0F1 ATP synthase subunit beta ### NC_002163.1 RefSeq CDS 113912 115309 . + 0 ID=cds92;Parent=gene100;gene=atpD;Name=YP_002343567.1;Dbxref=GOA:Q0PC30 InterPro:IPR000194 InterPro:IPR000793 InterPro:IPR003593 InterPro:IPR004100 InterPro:IPR005722 UniProtKB FSwiss-Prot:Q0PC30 Genbank:YP_002343567.1 GeneID:904437;gbkey=CDS;product=F0F1 ATP synthase subunit beta;Note=Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit NC_002163.1 RefSeq gene 113912 115309 . + . ID=gene100;gene=atpD;Name=atpD;locus_tag=Cj0107;Dbxref=GeneID:904437;gbkey=Gene NC_002163.1 RefSeq region 113924 114136 . + . ID=id339;gene=atpD;Name=id339;Dbxref=GeneID:904437;gbkey=misc_feature;Note=HMMPfam hit to PF02874 2C ATP synthase alpha 2Fbeta family 2C beta-ba 2C score 4.3e-21 NC_002163.1 RefSeq region 114302 114946 . + . ID=id340;gene=atpD;Name=id340;Dbxref=GeneID:904437;gbkey=misc_feature;Note=HMMPfam hit to PF00006 2C ATP synthase alpha 2Fbeta family 2C nucleot 2C score 1e-94 NC_002163.1 RefSeq region 114365 114388 . + . ID=id341;gene=atpD;Name=id341;Dbxref=GeneID:904437;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 114917 114946 . + . ID=id342;gene=atpD;Name=id342;Dbxref=GeneID:904437;gbkey=misc_feature;Note=PS00152 ATP synthase alpha and beta subunits signature NC_002163.1 RefSeq region 114983 115306 . + . ID=id343;gene=atpD;Name=id343;Dbxref=GeneID:904437;gbkey=misc_feature;Note=HMMPfam hit to PF00306 2C ATP synthase alpha 2Fbeta chain 2C C termin 2C score 7.2e-55 ### NC_002163.1 RefSeq CDS 115313 115702 . + 0 ID=cds93;Parent=gene101;gene=atpC;Name=YP_002343568.1;Dbxref=GOA:Q9PJ18 HSSP:P00832 InterPro:IPR001469 UniProtKB FSwiss-Prot:Q9PJ18 Genbank:YP_002343568.1 GeneID:904438;gbkey=CDS;product=F0F1 ATP synthase subunit epsilon;Note=part of catalytic core of ATP synthase 3B alpha 283 29beta 283 29gamma 281 29delta 281 29epsilon 281 29 3B involved in producing ATP from ADP in the presence of the proton motive force across the membrane NC_002163.1 RefSeq gene 115313 115702 . + . ID=gene101;gene=atpC;Name=atpC;locus_tag=Cj0108;Dbxref=GeneID:904438;gbkey=Gene NC_002163.1 RefSeq region 115322 115570 . + . ID=id344;gene=atpC;Name=id344;Dbxref=GeneID:904438;gbkey=misc_feature;Note=HMMPfam hit to PF02823 2C ATP synthase 2C Delta 2FEpsilon chain 2C beta 2C score 2.6e-21 NC_002163.1 RefSeq gene 115702 116256 . + . ID=gene102;gene=exbB3;Name=exbB3;locus_tag=Cj0109;Dbxref=GeneID:904439;gbkey=Gene NC_002163.1 RefSeq CDS 115702 116256 . + 0 ID=cds94;Parent=gene102;gene=exbB3;Name=YP_002343569.1;Dbxref=GOA:Q0PC28 InterPro:IPR002898 InterPro:IPR017269 UniProtKB FTrEMBL:Q0PC28 Genbank:YP_002343569.1 GeneID:904439;gbkey=CDS;product=MotA 2FTolQ 2FExbB proton channel family protein;Note=Original 282000 29 note: Cj0109 2C exbB3 2C probable exbB 2FtolQ family transport protein 2C len: 184 aa 3B similar to members of the exbB 2FtolQ family 2C e.g. EXBB_ECOLI biopolymer transport exbB protein 28244 aa 29 2C fasta scores 3B opt: 208 z-score: 287.0 E 28 29: 9.9e-09 2C 33.6 25 identity in 128 aa overlap 2C and TOLQ_ECOLI tolQ protein 28230 aa 29 2Cfasta scores 3B opt: 187 z-score: 280.1 E 28 29: 2.4e-08 2C 48.4 25 identity in 62 aa overlap. 42.6 25 identity to HP1130. Also similar to Cj0179 2830.6 25 identity in 186 aa overlap 29 and Cj1628 2844.4 25 identity in 81 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01618 2CMotA 2FTolQ 2FExbB proton channel family identified within CDS. Product modified to more specific family member due to motif match. No specific characterisation has been carried out yet. Thus 2C kept within product function. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:8437515 2C PMID:9371459 NC_002163.1 RefSeq region 115744 115812 . + . ID=id345;gene=exbB3;Name=id345;Dbxref=GeneID:904439;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0109 by TMHMM2.0 at aa 15-37 2C 96-118 and 138-160 NC_002163.1 RefSeq region 115837 116235 . + . ID=id346;gene=exbB3;Name=id346;Dbxref=GeneID:904439;gbkey=misc_feature;Note=HMMPfam hit to PF01618 2C MotA 2FTolQ 2FExbB proton channel family 2C score 1e-24 NC_002163.1 RefSeq region 115987 116055 . + . ID=id345;gene=exbB3;Name=id345;Dbxref=GeneID:904439;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0109 by TMHMM2.0 at aa 15-37 2C 96-118 and 138-160 NC_002163.1 RefSeq region 116113 116181 . + . ID=id345;gene=exbB3;Name=id345;Dbxref=GeneID:904439;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0109 by TMHMM2.0 at aa 15-37 2C 96-118 and 138-160 ### NC_002163.1 RefSeq CDS 116265 116654 . + 0 ID=cds95;Parent=gene103;gene=exbD3;Name=YP_002343570.1;Dbxref=GOA:Q0PC27 InterPro:IPR003400 InterPro:IPR014168 UniProtKB FTrEMBL:Q0PC27 Genbank:YP_002343570.1 GeneID:904440;gbkey=CDS;product=ExbD 2FTolR family transport protein;Note=Original 282000 29 note: Cj0110 2C exbD3 2C probable exbD 2FtolR family transport protein 2C len: 129 aa 3B similar to members of the exbD 2FtolR family 2C e.g. EXBD_ECOLI biopolymer transport exbD protein 28141 aa 29 2C fasta scores 3B opt: 225 z-score: 240.1 E 28 29: 4e-06 2C 31.1 25 identity in 132 aa overlap 2C and TOLR_ECOLI tolR protein 28142 aa 29 2C fasta scores 3B opt: 191 z-score: 240.1 E 28 29: 4.1e-06 2C 27.7 25 identity in 130 aa overlap. 46.8 25 identity to HP1129. Also similar to Cj0180 2834.1 25 identity in 126 aa overlap 29 and Cj1629 2826.4 25 identity in 121 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF02472 Biopolymer transport protein ExbD 2FTolR identified within CDS. Further support given to product function. No specific characterisation with acceptable identity scores were identified. Thus 2C kept within product function. Functional classification - Transport 2Fbinding proteins -Other 7EPMID:9371459 NC_002163.1 RefSeq gene 116265 116654 . + . ID=gene103;gene=exbD3;Name=exbD3;locus_tag=Cj0110;Dbxref=GeneID:904440;gbkey=Gene NC_002163.1 RefSeq region 116271 116651 . + . ID=id347;gene=exbD3;Name=id347;Dbxref=GeneID:904440;gbkey=misc_feature;Note=HMMPfam hit to PF02472 2C Biopolymer transport protein ExbD 2FTolR 2C score 7.2e-16 NC_002163.1 RefSeq region 116292 116360 . + . ID=id348;gene=exbD3;Name=id348;Dbxref=GeneID:904440;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0110 by TMHMM2.0 at aa 10-32 ### NC_002163.1 RefSeq gene 116657 117436 . + . ID=gene104;Name=Cj0111;locus_tag=Cj0111;Dbxref=GeneID:904442;gbkey=Gene NC_002163.1 RefSeq CDS 116657 117436 . + 0 ID=cds96;Parent=gene104;Name=YP_002343571.1;Dbxref=UniProtKB FTrEMBL:Q0PC26 Genbank:YP_002343571.1 GeneID:904442;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0111 2C possible periplasmic protein 2C len: 259 aa 3B no Hp match. Contains possible N-terminal signal sequence 7EUpdated 282006 29 note: Literature search identified paper 28PMID:15231804 29 suggesting a number of differentially expressed genes 28e.g. Cj0111 29 in microarray experiments may be co-trasncribed. Cj0111 seems to be iron induced and based on RT-PCR seems to be co-transcribed with Cj1658. Functional classification - Miscellaneous periplasmic proteins 7EPMID:15231804 NC_002163.1 RefSeq region 116681 116749 . + . ID=id349;Name=id349;Dbxref=GeneID:904442;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0111 by TMHMM2.0 at aa 9-31 ### NC_002163.1 RefSeq CDS 117446 118654 . + 0 ID=cds97;Parent=gene105;gene=tolB;Name=YP_002343572.1;Dbxref=GOA:Q9PJ14 InterPro:IPR007195 InterPro:IPR011042 InterPro:IPR011659 InterPro:IPR014167 UniProtKB FSwiss-Prot:Q9PJ14 Genbank:YP_002343572.1 GeneID:904443;gbkey=CDS;product=translocation protein TolB;Note=forms dimers 3B may be involved in cell envelope integrity 3B interacts with outer membrane proteins and with the C-terminal domain of inner membrane protein TolA NC_002163.1 RefSeq gene 117446 118654 . + . ID=gene105;gene=tolB;Name=tolB;locus_tag=Cj0112;Dbxref=GeneID:904443;gbkey=Gene NC_002163.1 RefSeq region 117455 117889 . + . ID=id350;gene=tolB;Name=id350;Dbxref=GeneID:904443;gbkey=misc_feature;Note=HMMPfam hit to PF04052 2C TolB amino-terminal domain 2Cscore 4e-51 NC_002163.1 RefSeq region 118589 118621 . + . ID=id351;gene=tolB;Name=id351;Dbxref=GeneID:904443;gbkey=misc_feature;Note=PS00284 Serpins signature ### NC_002163.1 UTR_Extractor 5'-UTR 118705 118730 . + . ID=utr42;locus_tag=Cj0113;product=peptidoglycan associated lipoprotein NC_002163.1 RefSeq CDS 118731 119228 . + 0 ID=cds98;Parent=gene106;gene=pal;Name=YP_002343573.1;Dbxref=GOA:Q46123 HSSP:P07176 InterPro:IPR006664 InterPro:IPR006665 InterPro:IPR014169 UniProtKB FTrEMBL:Q46123 Genbank:YP_002343573.1 GeneID:904444;gbkey=CDS;product=peptidoglycan associated lipoprotein;Note=Original 282000 29 note: Cj0113 2C pal 2C peptidoglycan associated lipoprotein 28omp18 29 2C len: 165 aa 3B identical to TR:Q46123 28EMBL:X83374 29 precursor of peptidoglycan associated lipoprotein 28165 aa 29 2C almost identical to TR:Q46099 omp18 28165 aa 29 2893.9 25 identity 29. Similar to e.g. PAL_ECOLI peptidoglycan-associated lipoprotein precursor 28173 aa 29 2C fasta scores 3B opt: 322 z-score: 491.5 E 28 29: 4e-20 2C 38.5 25 identity in 169 aa overlap. 42.2 25 identity 28in 109 aa overlap 29 to HP1125. Contains N-terminal signal sequence with appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site and Pfam match to entry PF00691 OmpA 2C OmpA family 2C score 100.60 2C E-value 3.2e-26 7EUpdated 282006 29 note: Characterised within Campylobacter jejuni 28PMID:8576327 29. not added to product function. Functional classification - Membranes 2Clipoproteins and porins 7EPMID:8576327 NC_002163.1 RefSeq gene 118731 119228 . + . ID=gene106;gene=pal;Name=pal;locus_tag=Cj0113;Dbxref=GeneID:904444;gbkey=Gene NC_002163.1 RefSeq region 118755 118787 . + . ID=id352;gene=pal;Name=id352;Dbxref=GeneID:904444;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 118911 119201 . + . ID=id353;gene=pal;Name=id353;Dbxref=GeneID:904444;gbkey=misc_feature;Note=HMMPfam hit to PF00691 2C OmpA family 2C score 2.1e-27 ### NC_002163.1 RefSeq gene 119232 120179 . + . ID=gene107;Name=Cj0114;locus_tag=Cj0114;Dbxref=GeneID:904445;gbkey=Gene NC_002163.1 RefSeq CDS 119232 120179 . + 0 ID=cds99;Parent=gene107;Name=YP_002343574.1;Dbxref=GOA:Q0PC23 InterPro:IPR011990 UniProtKB FTrEMBL:Q0PC23 Genbank:YP_002343574.1 GeneID:904445;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0114 2C possible periplasmic protein 2C len: 315 aa 3B similar to hypothetical protein YBGF_ECOLI hypothetical 28.2 kd protein in pal-lysT intergenic region 28263 aa 29 2C fasta scores 3B opt: 144 z-score: 238.8 E 28 29: 4.8e-06 2C 21.3 25 identity in 249 aa overlap. 28.6 25 identity to HP1124. Contains possible N-terminal signal sequence 7EUpdated 282006 29 note: Prosite PS50005 TPR_REPEAT 2CTetratricopeptide region identified within CDS. Supporting paper identifies protein as a glycoprotein. Functional classification - Miscellaneous periplasmic proteins 7EPMID:12186869 NC_002163.1 RefSeq region 119934 120035 . + . ID=id354;Name=id354;Dbxref=GeneID:904445;gbkey=misc_feature;Note=HMMPfam hit to PF07719 2C Tetratricopeptide repeat 2Cscore 0.012 ### NC_002163.1 RefSeq CDS 120194 120763 . + 0 ID=cds100;Parent=gene108;gene=slyD;Name=YP_002343575.1;Dbxref=GOA:Q0PC22 InterPro:IPR001179 UniProtKB FTrEMBL:Q0PC22 Genbank:YP_002343575.1 GeneID:904446;gbkey=CDS;product=FKBP-type peptidyl-prolyl cis-trans isomerase;Note=Original 282000 29 note: Cj0115 2C slyD 2C probable peptidyl-prolyl cis-trans isomerase 2C len: 189 aa 3B similar to many of the FKBP-type e.g. SLYD_ECOLI FKBP-type peptidyl-prolyl cis-trans isomerase 28196 aa 29 2C fasta scores 3B opt: 478 z-score: 296.9 E 28 29: 2.8e-09 2C 38.5 25 identity in 200 aa overlap. 39.2 25 identity to HP1123 7EUpdated 282006 29 note: Prosite PS50059 FKBP_PPIASE 2CPeptidylprolyl isomerase 2C FKBP-type domain identified within CDS. Product modified to more specific family member due to motif match. Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Protein translation and modification 7EPMID:9188461 NC_002163.1 RefSeq gene 120194 120763 . + . ID=gene108;gene=slyD;Name=slyD;locus_tag=Cj0115;Dbxref=GeneID:904446;gbkey=Gene NC_002163.1 RefSeq region 120701 120733 . + . ID=id355;gene=slyD;Name=id355;Dbxref=GeneID:904446;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq gene 120763 121683 . + . ID=gene109;gene=fabD;Name=fabD;locus_tag=Cj0116;Dbxref=GeneID:904447;gbkey=Gene NC_002163.1 RefSeq CDS 120763 121683 . + 0 ID=cds101;Parent=gene109;gene=fabD;Name=YP_002343576.1;Dbxref=GOA:Q0PC21 InterPro:IPR001227 InterPro:IPR004410 InterPro:IPR014043 UniProtKB FTrEMBL:Q0PC21 Genbank:YP_002343576.1 GeneID:904447;gbkey=CDS;product=malonyl CoA-acyl carrier protein transacylase;Note=Original 282000 29 note: Cj0116 2C fabD 2C probable malonyl CoA-acyl carrier protein transacylase 2C len: 306 aa 3B similar to many e.g. FABD_ECOLI malonyl CoA-acyl carrier protein transacylase 28EC 2.3.1.39 29 28308 aa 29 2C fasta scores 3B opt: 555 z-score: 655.2 E 28 29: 3.1e-29 2C 36.1 25 identity in 296 aa overlap. 49.5 25 identity to HP0090. Contains Pfam match to entry PF00698 Acyl_transf 2C Acyl transferase domain 2C score 58.10 2C E-value 1.9e-13 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity scores. Thus 2C not added to product function. Functional classification - Fatty acid biosynthesis 7EPMID:1339356 2C PMID:7768883 2C PMID:8759840 NC_002163.1 RefSeq region 120772 121680 . + . ID=id356;gene=fabD;Name=id356;Dbxref=GeneID:904447;gbkey=misc_feature;Note=HMMPfam hit to PF00698 2C Acyl transferase domain 2Cscore 6.7e-07 NC_002163.1 RefSeq gene 121680 122369 . + . ID=gene110;gene=pfs;Name=pfs;locus_tag=Cj0117;Dbxref=GeneID:904448;gbkey=Gene NC_002163.1 RefSeq CDS 121680 122369 . + 0 ID=cds102;Parent=gene110;gene=pfs;Name=YP_002343577.1;Dbxref=GOA:Q0PC20 InterPro:IPR000845 InterPro:IPR010049 UniProtKB FTrEMBL:Q0PC20 Genbank:YP_002343577.1 GeneID:904448;gbkey=CDS;product=5 27-methylthioadenosine 2FS-adenosylhomocysteine nucleosidase;Note=enables the cleavage of the glycosidic bond in both 5 27-methylthioadenosine and S-adenosylhomocysteine NC_002163.1 RefSeq region 121686 122357 . + . ID=id357;gene=pfs;Name=id357;Dbxref=GeneID:904448;gbkey=misc_feature;Note=HMMPfam hit to PF01048 2C Phosphorylase family 2C score 1.9e-56 NC_002163.1 UTR_Extractor 5'-UTR 122241 122365 . + . ID=utr43;locus_tag=Cj0118;product=hypothetical protein NC_002163.1 RefSeq CDS 122366 123121 . + 0 ID=cds103;Parent=gene111;Name=YP_002343578.1;Dbxref=InterPro:IPR011063 InterPro:IPR012089 InterPro:IPR014729 UniProtKB FTrEMBL:Q0PC19 Genbank:YP_002343578.1 GeneID:904449;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0118 2C unknown 2C len: 251 aa 3B similar to hypothetical proteins from many organisms e.g. YDAO_ECOLI 28311 aa 29 2C fasta scores 3B opt: 447 z-score: 465.6 E 28 29: 1.1e-18 2C 32.5 25 identity in 240 aa overlap. 49.4 25 identity to HP1182. Contains Pfam match to entry PF01171 UPF0021 2C Uncharacterized protein family UPF0021 2C score -88.80 2C E-value 9.9e-05 7EUpdated 282006 29 note: Pfam domain PF01171 PP-loop family identified within CDS. No specific characterisation has been carried out. Thus 2C kept within product function. Conserved added to product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 122366 123121 . + . ID=gene111;gene=Cj0118;Name=Cj0118;locus_tag=Cj0118;Dbxref=GeneID:904449;gbkey=Gene NC_002163.1 RefSeq region 122444 123043 . + . ID=id358;Name=id358;Dbxref=GeneID:904449;gbkey=misc_feature;Note=HMMPfam hit to PF01171 2C PP-loop family 2C score 4e-14 ### NC_002163.1 RefSeq CDS 123126 123647 . + 0 ID=cds104;Parent=gene112;Name=YP_002343579.1;Dbxref=GOA:Q0PC18 InterPro:IPR000868 UniProtKB FTrEMBL:Q0PC18 Genbank:YP_002343579.1 GeneID:904451;gbkey=CDS;product=hydrolase;Note=Original 282000 29 note: Cj0119 2C unknown 2C len: 173 aa 3B similar to a hypothetical protein from B. subtilis TR:O32091 28EMBL:Z99120 29 YUEJ protein 28183 aa 29 2C fasta scores 3B opt: 172 z-score: 282.5 E 28 29: 1.8e-08 2C 29.5 25 identity in 166 aa overlap. No Hp match 7EUpdated 282006 29 note: Motif match 28IPR000868 29 identified link to hydrolase. Product modified to more specific family member based on motif match. No specific characterisation with acceptable identity score has been carried out yet. kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 123126 123647 . + . ID=gene112;Name=Cj0119;locus_tag=Cj0119;Dbxref=GeneID:904451;gbkey=Gene NC_002163.1 RefSeq gene 123647 124261 . + . ID=gene113;Name=Cj0120;locus_tag=Cj0120;Dbxref=GeneID:904452;gbkey=Gene NC_002163.1 RefSeq CDS 123647 124261 . + 0 ID=cds105;Parent=gene113;Name=YP_002343580.1;Dbxref=UniProtKB FTrEMBL:Q0PC17 Genbank:YP_002343580.1 GeneID:904452;gbkey=CDS;product=recombination protein RecO;Note=Original 282000 29 note: Cj0120 2C unknown 2C len: 204 aa 3B 41.7 25 identity to HP0951. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq CDS 124258 124665 . + 0 ID=cds106;Parent=gene114;Name=YP_002343581.1;Dbxref=GOA:Q9PJ06 InterPro:IPR002036 UniProtKB FSwiss-Prot:Q9PJ06 Genbank:YP_002343581.1 GeneID:904453;gbkey=CDS;product=metalloprotease;Note=Original 282000 29 note: Cj0121 2C unknown 2C len: 135 aa 3B similar to hypothetical proteins from many organisms e.g. YBEY_ECOLI 28155 aa 29 fasta scores 3B opt: 218 z-score: 353.9 E 28 29: 1.9e-12 2C 37.8 25 identity in 111 aa overlap. 59.8 25 identity to HP1160 7EUpdated 282006 29 note: Pfam PF02130 Uncharacterized protein family UPF0054 was present within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 124258 124665 . + . ID=gene114;Name=Cj0121;locus_tag=Cj0121;Dbxref=GeneID:904453;gbkey=Gene NC_002163.1 RefSeq region 124339 124602 . + . ID=id359;Name=id359;Dbxref=GeneID:904453;gbkey=misc_feature;Note=HMMPfam hit to PF02130 2C Uncharacterized protein family UPF0054 2C score 6.5e-36 ### NC_002163.1 UTR_Extractor 5'-UTR 124762 124788 . + . ID=utr44;locus_tag=Cj0122;product=hypothetical protein NC_002163.1 RefSeq gene 124789 125478 . + . ID=gene115;Name=Cj0122;locus_tag=Cj0122;Dbxref=GeneID:904454;gbkey=Gene NC_002163.1 RefSeq CDS 124789 125478 . + 0 ID=cds107;Parent=gene115;Name=YP_002343582.1;Dbxref=UniProtKB FTrEMBL:Q0PC15 Genbank:YP_002343582.1 GeneID:904454;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0122 2C unknown 2C len: 229 aa 3B no Hp match. Similar in C-terminus to Cj0055c 2846.6 25 identity in 148 aa overlap 29 2C and in N-terminus to Cj0416 2888.2 25 identity in 34 aa overlap 29 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 RefSeq CDS 125503 126429 . - 0 ID=cds108;Parent=gene116;Name=YP_002343583.1;Dbxref=GOA:Q0PC14 InterPro:IPR001269 InterPro:IPR013785 UniProtKB FTrEMBL:Q0PC14 Genbank:YP_002343583.1 GeneID:904455;gbkey=CDS;product=tRNA-dihydrouridine synthase;Note=Original 282000 29 note: Cj0123c 2C possible transcriptional regulator 2C len: 308 aa 3B similar to hypothetical proteins e.g. YACF_BACSU 28333 aa 29 2C fasta scores 3B opt: 566 z-score: 916.8 E 28 29: 0 2C 37.2 25 identity in 312 aa overlap 2C and to e.g. NIR3_RHOCA nitrogen regulation protein nifR3 28324 aa 29 2C fasta scores 3B opt: 517 z-score: 616.2 E 28 29: 4.6e-27 2C 34.4 25 identity in 317 aa overlap. 49.5 25 identity to HP0727. Contains Pfam match to entry PF01207 UPF0034 2C Uncharacterized protein family UPF0034 2Cscore 260.90 2C E-value 1.7e-74 7EUpdated 282006 29 note: Pfam domain PF01207 Dihydrouridine synthase 28Dus 29 identified within CDS. Product modified to more specific family member due to motif match. No specific characterisation with acceptable identity scores carried out yet. Thus 2C kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 125503 126429 . - . ID=gene116;Name=Cj0123c;locus_tag=Cj0123c;Dbxref=GeneID:904455;gbkey=Gene NC_002163.1 RefSeq region 125515 126402 . - . ID=id360;Name=id360;Dbxref=GeneID:904455;gbkey=misc_feature;Note=HMMPfam hit to PF01207 2C Dihydrouridine synthase 28Dus 29 2C score 3.1e-75 NC_002163.1 RefSeq gene 126426 127412 . - . ID=gene117;Name=Cj0124c;locus_tag=Cj0124c;Dbxref=GeneID:904457;gbkey=Gene NC_002163.1 RefSeq CDS 126426 127412 . - 0 ID=cds109;Parent=gene117;Name=YP_002343584.1;Dbxref=GOA:Q0PC13 UniProtKB FTrEMBL:Q0PC13 Genbank:YP_002343584.1 GeneID:904457;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0124c 2C probable membrane protein 2C len: 328 aa 3B 21.1 25 identity to HP0948. Contains two possible transmembrane domains. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 127221 127289 . - . ID=id9;Name=id9;Dbxref=GeneID:904457;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0124c by TMHMM2.0 at aa 5-27 and 42-64 NC_002163.1 RefSeq region 127332 127400 . - . ID=id9;Name=id9;Dbxref=GeneID:904457;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0124c by TMHMM2.0 at aa 5-27 and 42-64 NC_002163.1 RefSeq CDS 127402 127764 . - 0 ID=cds110;Parent=gene118;Name=YP_002343585.1;Dbxref=GOA:Q0PC12 InterPro:IPR000962 UniProtKB FTrEMBL:Q0PC12 Genbank:YP_002343585.1 GeneID:904459;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0125c 2C unknown 2C len: 120 aa 3B some similarity to e.g. DKSA_ECOLI dnaK suppressor protein 28151 aa 29 2C fasta scores 3B opt: 186 z-score: 276.6 E 28 29: 3.8e-08 2C 26.3 25 identity in 118 aa overlap. No Hp match. Contains PS01102 Prokaryotic dksA 2FtraR C4-type zinc finger and Pfam match to entry PF01258 zf_dskA_traR 2CProkaryotic dksA 2FtraR C4-type zinc finger 2C score 39.20 2CE-value 9.7e-08 7EUpdated 282006 29 note: No specific characterisation has been carried out yet. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 127402 127764 . - . ID=gene118;Name=Cj0125c;locus_tag=Cj0125c;Dbxref=GeneID:904459;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 127413 127532 . - . ID=utr45;locus_tag=Cj0124c;product=hypothetical protein NC_002163.1 RefSeq region 127417 127617 . - . ID=id361;Name=id361;Dbxref=GeneID:904459;gbkey=misc_feature;Note=HMMPfam hit to PF01258 2C Prokaryotic dksA 2FtraR C4-type zinc finge 2C score 6.8e-09 NC_002163.1 RefSeq region 127441 127515 . - . ID=id362;Name=id362;Dbxref=GeneID:904459;gbkey=misc_feature;Note=PS01102 Prokaryotic dksA 2FtraR C4-type zinc finger ### NC_002163.1 RefSeq CDS 127776 128237 . - 0 ID=cds111;Parent=gene119;Name=YP_002343586.1;Dbxref=InterPro:IPR003742 UniProtKB FSwiss-Prot:Q9PJ01 Genbank:YP_002343586.1 GeneID:904460;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0126c 2C unknown 2C len: 153 aa 3B similar to hypotheticals e.g. YBEA_ECOLI 28155 aa 29 2Cfasta scores 3B opt: 189 z-score: 288.6 E 28 29: 8.1e-09 2C 28.1 25 identity in 153 aa overlap. 37.2 25 identity to HP0949 7EUpdated 282006 29 note: Pfam PF02590 Uncharacterized ACR family was present within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 127776 128237 . - . ID=gene119;Name=Cj0126c;locus_tag=Cj0126c;Dbxref=GeneID:904460;gbkey=Gene NC_002163.1 RefSeq region 127782 128225 . - . ID=id363;Name=id363;Dbxref=GeneID:904460;gbkey=misc_feature;Note=HMMPfam hit to PF02590 2C Uncharacterized ACR 2CCOG1576 2C score 9.2e-69 NC_002163.1 RefSeq gene 128227 129069 . - . ID=gene120;gene=accD;Name=accD;locus_tag=Cj0127c;Dbxref=GeneID:904461;gbkey=Gene NC_002163.1 RefSeq CDS 128227 129069 . - 0 ID=cds112;Parent=gene120;gene=accD;Name=YP_002343587.1;Dbxref=GOA:Q0PC10 InterPro:IPR000022 InterPro:IPR000438 InterPro:IPR011762 UniProtKB FTrEMBL:Q0PC10 Genbank:YP_002343587.1 GeneID:904461;gbkey=CDS;product=acetyl-CoA carboxylase subunit beta;Note=catalyzes the carboxylation of acetyl-CoA to malonyl-CoA 3B forms a tetramer of AccA2D2 subunits NC_002163.1 RefSeq region 128974 128991 . - . ID=id364;gene=accD;Name=id364;Dbxref=GeneID:904461;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature ### NC_002163.1 UTR_Extractor 5'-UTR 129070 129097 . - . ID=utr46;locus_tag=Cj0127c;product=acetyl-CoA carboxylase subunit beta NC_002163.1 RefSeq CDS 129078 129800 . - 0 ID=cds113;Parent=gene121;Name=YP_002343588.1;Dbxref=GOA:Q0PC09 InterPro:IPR000760 UniProtKB FTrEMBL:Q0PC09 Genbank:YP_002343588.1 GeneID:904462;gbkey=CDS;product=inositol monophosphatase family protein;Note=Original 282000 29 note: Cj0128c 2C unknown 2C len: 240 aa 3B some similarity to e.g. SUHB_ECOLI extragenic suppressor protein suhB 28267 aa 29 2C fasta scores 3B opt: 168 z-score: 229.0 E 28 29: 1.7e-05 2C 29.9 25 identity in 134 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF00459 Inositol monophosphatase family identified within CDS. Product modified to more specific family member due to motif match. Characterised within Escherichia coli 2C however 2Cidentity scores were not acceptable. Functional classification - Misc 7EPMID:10747806 2C PMID:8002619 NC_002163.1 RefSeq gene 129078 129800 . - . ID=gene121;Name=Cj0128c;locus_tag=Cj0128c;Dbxref=GeneID:904462;gbkey=Gene NC_002163.1 RefSeq region 129096 129800 . - . ID=id365;Name=id365;Dbxref=GeneID:904462;gbkey=misc_feature;Note=HMMPfam hit to PF00459 2C Inositol monophosphatase family 2C score 1.2e-06 NC_002163.1 RefSeq region 129219 129287 . - . ID=id366;Name=id366;Dbxref=GeneID:904462;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0128c by TMHMM2.0 at aa 172-194 NC_002163.1 RefSeq gene 129800 132019 . - . ID=gene122;Name=Cj0129c;locus_tag=Cj0129c;Dbxref=GeneID:904463;gbkey=Gene NC_002163.1 RefSeq CDS 129800 132019 . - 0 ID=cds114;Parent=gene122;Name=YP_002343589.1;Dbxref=GOA:Q0PC08 InterPro:IPR000184 InterPro:IPR010827 InterPro:IPR016474 UniProtKB FTrEMBL:Q0PC08 Genbank:YP_002343589.1 GeneID:904463;gbkey=CDS;product=outer membrane protein;Note=Original 282000 29 note: Cj0129c 2C probable outer membrane protein 2C len: 739 aa 3B similar to e.g. TR:O30912 28EMBL:AF021245 29 Neisseria meningitidis outer membrane protein omp85 28797 aa 29 2C fasta scores 3B opt: 643 z-score: 886.3 E 28 29: 0 2C 25.3 25 identity in 782 aa overlap 2C and D152_HAEIN protective surface antigen d15 precursor 28795 aa 29 2C fasta scores 3B opt: 523 z-score: 548.2 E 28 29: 2.8e-23 2C24.3 25 identity in 807 aa overlap. 34.2 25 identity to HP0655. Contains N-terminbal signal sequence and Pfam match to entry PF01103 Bac_suface_Ag 2C Bacterial surface antigen 2C score 404.10 2C E-value 1.3e-117 7EUpdated 282006 29 note: Pfam domains PF01103 Surface antigen and x5 PF07244 Surface antigen variable number repeat were identified within CDS. Further support given to product function. Literature search identified papers giving further clues to product function. Characterisation has been carried out within Escherichia coli 2C however 2Cidentity scores were marginal. Appropriate motifs were present. not added to product function. Functional classification - Membranes 2C lipoproteins and porins 7EPMID:11422558 2C PMID:16102012 NC_002163.1 UTR_Extractor 5'-UTR 129801 129995 . - . ID=utr47;locus_tag=Cj0128c;product=putative inositol monophosphatase family protein NC_002163.1 RefSeq region 129803 130726 . - . ID=id367;Name=id367;Dbxref=GeneID:904463;gbkey=misc_feature;Note=HMMPfam hit to PF01103 2C Surface antigen 2C score 3e-78 NC_002163.1 RefSeq region 130760 130921 . - . ID=id368;Name=id368;Dbxref=GeneID:904463;gbkey=misc_feature;Note=HMMPfam hit to PF07244 2C Surface antigen variable number repeat 2C score 5.9e-08 NC_002163.1 RefSeq region 130991 131164 . - . ID=id369;Name=id369;Dbxref=GeneID:904463;gbkey=misc_feature;Note=HMMPfam hit to PF07244 2C Surface antigen variable number repeat 2C score 3e-07 NC_002163.1 RefSeq region 131234 131416 . - . ID=id370;Name=id370;Dbxref=GeneID:904463;gbkey=misc_feature;Note=HMMPfam hit to PF07244 2C Surface antigen variable number repeat 2C score 1.7e-07 NC_002163.1 RefSeq region 131519 131692 . - . ID=id371;Name=id371;Dbxref=GeneID:904463;gbkey=misc_feature;Note=HMMPfam hit to PF07244 2C Surface antigen variable number repeat 2C score 1.3e-07 NC_002163.1 RefSeq region 131756 131896 . - . ID=id372;Name=id372;Dbxref=GeneID:904463;gbkey=misc_feature;Note=HMMPfam hit to PF07244 2C Surface antigen variable number repeat 2C score 3.7e-07 ### NC_002163.1 UTR_Extractor 5'-UTR 132020 132048 . - . ID=utr48;locus_tag=Cj0129c;product=outer membrane protein NC_002163.1 RefSeq gene 132096 132923 . + . ID=gene123;gene=tyrA;Name=tyrA;locus_tag=Cj0130;Dbxref=GeneID:904465;gbkey=Gene NC_002163.1 RefSeq CDS 132096 132923 . + 0 ID=cds115;Parent=gene123;gene=tyrA;Name=YP_002343590.1;Dbxref=GOA:Q0PC07 InterPro:IPR003099 UniProtKB FTrEMBL:Q0PC07 Genbank:YP_002343590.1 GeneID:904465;gbkey=CDS;product=prephenate dehydrogenase;Note=catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate NC_002163.1 RefSeq region 132108 132911 . + . ID=id373;gene=tyrA;Name=id373;Dbxref=GeneID:904465;gbkey=misc_feature;Note=HMMPfam hit to PF02153 2C Prephenate dehydrogenase 2Cscore 1.2e-83 ### NC_002163.1 UTR_Extractor 5'-UTR 132965 133002 . + . ID=utr49;locus_tag=Cj0131;product=putative peptidase M23 family protein NC_002163.1 RefSeq CDS 133003 134376 . + 0 ID=cds116;Parent=gene124;Name=YP_002343591.1;Dbxref=GOA:Q0PC06 InterPro:IPR002886 InterPro:IPR016047 UniProtKB FTrEMBL:Q0PC06 Genbank:YP_002343591.1 GeneID:904466;gbkey=CDS;product=peptidase M23 family protein;Note=Original 282000 29 note: Cj0131 2C probable periplasmic protein 2C len: 457 aa 3B similar to hypothetical proteins e.g.TR:O25694 28EMBL:AE000754 29 Aquifex aeolicus AQ_1743 28422 aa 29 2C fasta scores 3B opt: 401 z-score: 635.2 E 28 29: 4e-28 2C 30.0 25 identity in 420 aa overlap. 30.0 25 identity to HP1054. Contains probable N-terminal signal sequence. Also similar in C-terminus to Cj1235 2830.2 25 identity in 222 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01551 Peptidase family M23 identified within CDS. Product modified to more specific family member due to motif match. No specific characterisation with acceptable identity scores identified yet. Thus 2C kept within product function. Functional classification - Degradation of macromolecules - Proteins 2C peptides and glycopeptides NC_002163.1 RefSeq gene 133003 134376 . + . ID=gene124;Name=Cj0131;locus_tag=Cj0131;Dbxref=GeneID:904466;gbkey=Gene NC_002163.1 RefSeq region 133027 133095 . + . ID=id374;Name=id374;Dbxref=GeneID:904466;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0131 by TMHMM2.0 at aa 9-31 NC_002163.1 RefSeq region 134002 134289 . + . ID=id375;Name=id375;Dbxref=GeneID:904466;gbkey=misc_feature;Note=HMMPfam hit to PF01551 2C Peptidase family M23 2C score 5.2e-27 NC_002163.1 RefSeq region 134376 135197 . + . ID=id376;gene=lpxC;Name=id376;Dbxref=GeneID:904467;gbkey=misc_feature;Note=HMMPfam hit to PF03331 2C UDP-3-O-acyl N-acetylglycosamine deacetylase 2C score 5.5e-135 NC_002163.1 RefSeq gene 134376 135260 . + . ID=gene125;gene=lpxC;Name=lpxC;locus_tag=Cj0132;Dbxref=GeneID:904467;gbkey=Gene NC_002163.1 RefSeq CDS 134376 135260 . + 0 ID=cds117;Parent=gene125;gene=lpxC;Name=YP_002343592.1;Dbxref=GOA:Q9PIZ5 HSSP:O67648 InterPro:IPR004463 InterPro:IPR011334 InterPro:IPR015870 UniProtKB FSwiss-Prot:Q9PIZ5 Genbank:YP_002343592.1 GeneID:904467;gbkey=CDS;product=UDP-3-O- 5B3-hydroxymyristoyl 5D N-acetylglucosamine deacetylase;Note=zinc-dependent 3B catalyzes the deacetylation of UDP- 283-O-acyl 29-N-acetylglucosamine to UDP-3-O- 283-hydroxytetradecanoyl 29-glucosamine in the second step of lipid A biosynthesis ### NC_002163.1 RefSeq CDS 135299 135700 . + 0 ID=cds118;Parent=gene126;Name=YP_002343593.1;Dbxref=GOA:Q0PC04 UniProtKB FTrEMBL:Q0PC04 Genbank:YP_002343593.1 GeneID:904469;gbkey=CDS;product=glycoprotease family protein;Note=Original 282000 29 note: Cj0133 2C unknown 2C len: 133 aa 3B 33.6 25 identity to HP1051 7EUpdated 282006 29 note: Pfam domain PF00814 Glycoprotease family identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification - Degradation of macromolecules - Proteins 2Cpeptides and glycopeptides NC_002163.1 RefSeq gene 135299 135700 . + . ID=gene126;Name=Cj0133;locus_tag=Cj0133;Dbxref=GeneID:904469;gbkey=Gene NC_002163.1 RefSeq region 135323 135550 . + . ID=id377;Name=id377;Dbxref=GeneID:904469;gbkey=misc_feature;Note=HMMPfam hit to PF00814 2C Glycoprotease family 2C score 1e-18 NC_002163.1 UTR_Extractor 5'-UTR 135677 135708 . + . ID=utr50;locus_tag=Cj0134;product=homoserine kinase ### NC_002163.1 RefSeq CDS 135709 136587 . + 0 ID=cds119;Parent=gene127;gene=thrB;Name=YP_002343594.1;Dbxref=GOA:Q9PIZ3 InterPro:IPR000870 InterPro:IPR006203 InterPro:IPR006204 InterPro:IPR014721 UniProtKB FSwiss-Prot:Q9PIZ3 Genbank:YP_002343594.1 GeneID:904490;gbkey=CDS;product=homoserine kinase;Note=catalyzes the formation of O-phospho-L-homoserine from L-homoserine in threonine biosynthesis from asparate NC_002163.1 RefSeq gene 135709 136587 . + . ID=gene127;gene=thrB;Name=thrB;locus_tag=Cj0134;Dbxref=GeneID:904490;gbkey=Gene NC_002163.1 RefSeq region 135928 136494 . + . ID=id378;gene=thrB;Name=id378;Dbxref=GeneID:904490;gbkey=misc_feature;Note=HMMPfam hit to PF00288 2C GHMP kinases ATP-binding protei 2C score 6e-28 NC_002163.1 RefSeq region 135955 135990 . + . ID=id379;gene=thrB;Name=id379;Dbxref=GeneID:904490;gbkey=misc_feature;Note=PS00627 GHMP kinases ATP-binding domain NC_002163.1 RefSeq region 136279 136311 . + . ID=id380;gene=thrB;Name=id380;Dbxref=GeneID:904490;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq CDS 136612 136869 . + 0 ID=cds120;Parent=gene128;Name=YP_002343595.1;Dbxref=InterPro:IPR007393 UniProtKB FTrEMBL:Q0PC02 Genbank:YP_002343595.1 GeneID:904470;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0135 2C unknown 2C len: 85 aa 3B 44.6 25 identity to HP1049 7EUpdated 282006 29 note: Pfam PF04296 Protein of unknown function 28DUF448 29 was present within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 136612 136869 . + . ID=gene128;Name=Cj0135;locus_tag=Cj0135;Dbxref=GeneID:904470;gbkey=Gene NC_002163.1 RefSeq region 136624 136857 . + . ID=id381;Name=id381;Dbxref=GeneID:904470;gbkey=misc_feature;Note=HMMPfam hit to PF04296 2C Protein of unknown function 28DUF448 29 2C score 5.8e-31 NC_002163.1 UTR_Extractor 5'-UTR 136816 136855 . + . ID=utr51;locus_tag=Cj0136;product=translation initiation factor IF-2 NC_002163.1 RefSeq region 136856 137014 . + . ID=id382;gene=infB;Name=id382;Dbxref=GeneID:904471;gbkey=misc_feature;Note=HMMPfam hit to PF04760 2C Translation initiation factor IF-2 2C N-ter 2C score 8.4e-15 NC_002163.1 RefSeq gene 136856 139471 . + . ID=gene129;gene=infB;Name=infB;locus_tag=Cj0136;Dbxref=GeneID:904471;gbkey=Gene NC_002163.1 RefSeq CDS 136856 139471 . + 0 ID=cds121;Parent=gene129;gene=infB;Name=YP_002343596.1;Dbxref=GOA:Q9PIZ1 HSSP:O26359 InterPro:IPR000178 InterPro:IPR000795 InterPro:IPR004161 InterPro:IPR005225 InterPro:IPR006847 InterPro:IPR015760 UniProtKB FSwiss-Prot:Q9PIZ1 Genbank:YP_002343596.1 GeneID:904471;gbkey=CDS;product=translation initiation factor IF-2;Note=Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits during initiation of protein synthesis. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex NC_002163.1 RefSeq region 137729 137884 . + . ID=id383;gene=infB;Name=id383;Dbxref=GeneID:904471;gbkey=misc_feature;Note=HMMPfam hit to PF04760 2C Translation initiation factor IF-2 2C N-ter 2C score 1.2e-20 NC_002163.1 RefSeq region 137963 138466 . + . ID=id384;gene=infB;Name=id384;Dbxref=GeneID:904471;gbkey=misc_feature;Note=HMMPfam hit to PF00009 2C Elongation factor Tu GTP binding domain 2C score 2.5e-54 NC_002163.1 RefSeq region 137972 138301 . + . ID=id385;gene=infB;Name=id385;Dbxref=GeneID:904471;gbkey=misc_feature;Note=HMMPfam hit to PF01926 2C GTPase of unknown function 2Cscore 8.6e-10 NC_002163.1 RefSeq region 137990 138013 . + . ID=id386;gene=infB;Name=id386;Dbxref=GeneID:904471;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 138533 138724 . + . ID=id387;gene=infB;Name=id387;Dbxref=GeneID:904471;gbkey=misc_feature;Note=HMMPfam hit to PF03144 2C Elongation factor Tu domain 2C score 1.3e-08 NC_002163.1 RefSeq region 139229 139435 . + . ID=id388;gene=infB;Name=id388;Dbxref=GeneID:904471;gbkey=misc_feature;Note=HMMPfam hit to PF03144 2C Elongation factor Tu domain 2C score 1.4e-08 NC_002163.1 RefSeq region 139319 139387 . + . ID=id389;gene=infB;Name=id389;Dbxref=GeneID:904471;gbkey=misc_feature;Note=PS01176 Initiation factor 2 signature NC_002163.1 RefSeq CDS 139468 139830 . + 0 ID=cds122;Parent=gene130;gene=rbfA;Name=YP_002343597.1;Dbxref=GOA:Q9PIZ0 InterPro:IPR000238 InterPro:IPR015946 UniProtKB FSwiss-Prot:Q9PIZ0 Genbank:YP_002343597.1 GeneID:904468;gbkey=CDS;product=ribosome-binding factor A;Note=associates with free 30S ribosomal subunits 3B essential for efficient processing of 16S rRNA 3B in Escherichia coli rbfA is induced by cold shock NC_002163.1 RefSeq gene 139468 139830 . + . ID=gene130;gene=rbfA;Name=rbfA;locus_tag=Cj0137;Dbxref=GeneID:904468;gbkey=Gene NC_002163.1 RefSeq gene 139820 140242 . + . ID=gene131;gene=rimP;Name=rimP;locus_tag=Cj0138;Dbxref=GeneID:904546;gbkey=Gene NC_002163.1 RefSeq CDS 139820 140242 . + 0 ID=cds123;Parent=gene131;Name=YP_002343598.1;Dbxref=HSSP:Q97S61 InterPro:IPR003728 UniProtKB FSwiss-Prot:Q9PIY9 Genbank:YP_002343598.1 GeneID:904546;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0138 2C unknown 2C len: 140 aa 3B similar to hypothetical proteins e.g. YHBC_ECOLI 28152 aa 29 2Cfasta scores 3B opt: 272 z-score: 436.7 E 28 29: 4.5e-17 2C 41.4 25 identity in 116 aa overlap. 38.9 25 identity to HP1046 7EUpdated 282006 29 note: Pfam PF02576 Uncharacterised BCR 2C YhbC family was present within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq region 139823 140227 . + . ID=id390;Name=id390;Dbxref=GeneID:904546;gbkey=misc_feature;Note=HMMPfam hit to PF02576 2C Uncharacterised BCR 2C YhbC family COG0779 2C score 1e-62 ### NC_002163.1 RefSeq CDS 140289 142640 . + 0 ID=cds124;Parent=gene132;Name=YP_002343599.1;Dbxref=GOA:Q0PBZ8 InterPro:IPR011704 UniProtKB FTrEMBL:Q0PBZ8 Genbank:YP_002343599.1 GeneID:904929;gbkey=CDS;product=endonuclease;Note=Original 282000 29 note: Cj0139 2C possible endonuclease 2C len: 783 aa 3B similar in part to MCRB_ECOLI 5-methylcytosine-specific restriction enzyme B 28465 aa 29 2Cfasta scores 3B opt: 305 z-score: 505.4 E 28 29: 6.7e-21 2C 40.9 25 identity in 186 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF07728 ATPase family associated with various cellular activities was identified within CDS. Characterised within Eschereichia coli with acceptable identity scores. Sequence alignment was only partial. Thus 2C kept within product function. Functional classification - DNA replication 2Crestriction 2Fmodification 2C recombination and repair 7EPMID:7781618 NC_002163.1 RefSeq gene 140289 142640 . + . ID=gene132;Name=Cj0139;locus_tag=Cj0139;Dbxref=GeneID:904929;gbkey=Gene NC_002163.1 RefSeq region 141279 141302 . + . ID=id391;Name=id391;Dbxref=GeneID:904929;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq gene 142633 143964 . + . ID=gene133;Name=Cj0140;locus_tag=Cj0140;Dbxref=GeneID:904472;gbkey=Gene NC_002163.1 RefSeq CDS 142633 143964 . + 0 ID=cds125;Parent=gene133;Name=YP_002343600.1;Dbxref=UniProtKB FTrEMBL:Q0PBZ7 Genbank:YP_002343600.1 GeneID:904472;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0140 2C unknown 2C len: 443 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 RefSeq gene 143953 144756 . - . ID=gene134;Name=Cj0141c;locus_tag=Cj0141c;Dbxref=GeneID:904473;gbkey=Gene NC_002163.1 RefSeq CDS 143953 144756 . - 0 ID=cds126;Parent=gene134;Name=YP_002343601.1;Dbxref=GOA:Q0PBZ6 InterPro:IPR001626 UniProtKB FTrEMBL:Q0PBZ6 Genbank:YP_002343601.1 GeneID:904473;gbkey=CDS;product=ABC transporter;Note=Original 282000 29 note: Cj0141c 2C ABC transporter integral membrane protein 2C len: 267 aa 3B similar to many e.g. MNTB_SYNY3 manganese transport system membrane protein 28306 aa 29 2C fasta scores 3B opt: 425 z-score: 449.6 E 28 29: 8.7e-18 2C 25.8 25 identity in 264 aa overlap. No Hp match. Contains Pfam match to entry PF00950 ABC-3 2C ABC 3 transport family 2C score 276.20 2C E-value 4.3e-79 7EUpdated 282006 29 note: Seven probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity score identified. Thus 2C added to product function. Functional classification -Transport 2Fbinding proteins - Other NC_002163.1 RefSeq region 143968 144741 . - . ID=id392;Name=id392;Dbxref=GeneID:904473;gbkey=misc_feature;Note=HMMPfam hit to PF00950 2C ABC 3 transport family 2Cscore 7.6e-82 NC_002163.1 RefSeq region 143974 144042 . - . ID=id10;Name=id10;Dbxref=GeneID:904473;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0141c by TMHMM2.0 at aa 13-35 2C 55-77 2C 90-112 2C 132-150 2C171-200 2C 215-237 and 239-261 NC_002163.1 RefSeq region 144016 144048 . - . ID=id393;Name=id393;Dbxref=GeneID:904473;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 144046 144114 . - . ID=id10;Name=id10;Dbxref=GeneID:904473;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0141c by TMHMM2.0 at aa 13-35 2C 55-77 2C 90-112 2C 132-150 2C171-200 2C 215-237 and 239-261 NC_002163.1 RefSeq region 144157 144246 . - . ID=id10;Name=id10;Dbxref=GeneID:904473;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0141c by TMHMM2.0 at aa 13-35 2C 55-77 2C 90-112 2C 132-150 2C171-200 2C 215-237 and 239-261 NC_002163.1 RefSeq region 144307 144363 . - . ID=id10;Name=id10;Dbxref=GeneID:904473;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0141c by TMHMM2.0 at aa 13-35 2C 55-77 2C 90-112 2C 132-150 2C171-200 2C 215-237 and 239-261 NC_002163.1 RefSeq region 144421 144489 . - . ID=id10;Name=id10;Dbxref=GeneID:904473;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0141c by TMHMM2.0 at aa 13-35 2C 55-77 2C 90-112 2C 132-150 2C171-200 2C 215-237 and 239-261 NC_002163.1 RefSeq region 144526 144594 . - . ID=id10;Name=id10;Dbxref=GeneID:904473;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0141c by TMHMM2.0 at aa 13-35 2C 55-77 2C 90-112 2C 132-150 2C171-200 2C 215-237 and 239-261 NC_002163.1 RefSeq region 144652 144720 . - . ID=id10;Name=id10;Dbxref=GeneID:904473;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0141c by TMHMM2.0 at aa 13-35 2C 55-77 2C 90-112 2C 132-150 2C171-200 2C 215-237 and 239-261 NC_002163.1 RefSeq region 144685 144717 . - . ID=id394;Name=id394;Dbxref=GeneID:904473;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq CDS 144749 145603 . - 0 ID=cds127;Parent=gene135;Name=YP_002343602.1;Dbxref=GOA:Q0PBZ5 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FTrEMBL:Q0PBZ5 Genbank:YP_002343602.1 GeneID:904475;gbkey=CDS;product=ABC transporter ATP-binding protein;Note=Original 282000 29 note: Cj0142c 2C ABC transporter ATP-binding protein 2C len: 284 aa 3B simlar to many e.g. MNTA_SYNY3 manganese transport system ATP-binding protein 28260 aa 29 2C fasta scores 3B opt: 417 z-score: 613.7 E 28 29: 6.2e-27 2C 32.9 25 identity in 252 aa overlap. No Hp ortholog but 30.4 25 identity to HP0250 oligopeptide ABC transporter. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2CPS00211 ABC transporters family signature and Pfam match to entry PF00005 ABC_tran 2C ABC transporters 2C score 165.90 2CE-value 6.9e-46 7EUpdated 282006 29 note: Some characterisation within Bacillus subtilis with acceptable identity score. Sequence alignment was only partial. Thus 2C added to product function. Functional classification -Transport 2Fbinding proteins - Other 7EPMID:10760146 NC_002163.1 RefSeq gene 144749 145603 . - . ID=gene135;Name=Cj0142c;locus_tag=Cj0142c;Dbxref=GeneID:904475;gbkey=Gene NC_002163.1 RefSeq region 144986 145519 . - . ID=id395;Name=id395;Dbxref=GeneID:904475;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 7.4e-49 NC_002163.1 RefSeq region 145169 145213 . - . ID=id396;Name=id396;Dbxref=GeneID:904475;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq region 145475 145498 . - . ID=id397;Name=id397;Dbxref=GeneID:904475;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 RefSeq gene 145616 146506 . - . ID=gene136;Name=Cj0143c;locus_tag=Cj0143c;Dbxref=GeneID:904476;gbkey=Gene NC_002163.1 RefSeq CDS 145616 146506 . - 0 ID=cds128;Parent=gene136;Name=YP_002343603.1;Dbxref=GOA:Q0PBZ4 InterPro:IPR006127 UniProtKB FTrEMBL:Q0PBZ4 Genbank:YP_002343603.1 GeneID:904476;gbkey=CDS;product=substrate-binding protein;Note=Original 282000 29 note: Cj0143c 2C probable periplasmic solute binding protein for ABC transport system 2C len: 296 aa 3B similar to e.g. ZNUA_ECOLI high-affinity zinc uptake system protein znuA 28328 aa 29 2C fasta scores 3B opt: 386 z-score: 471.6 E 28 29: 5.2e-19 2C 26.4 25 identity in 288 aa overlap. No Hp match. Contains probable N-terminal signal sequence and Pfam match to entry PF01297 Lipoprotein_4 2Cscore 133.20 2C E-value 4.6e-36 7EUpdated 282006 29 note: Pfam domain PPF01297 Periplasmic solute binding protein identified within CDS. Further support given to product function. Some characterisation within Eschericia coli 2C however 2C identity score was marginal. Thus 2C kept within product function. Paper identified linking protein to glycoprotein 28PMID:12186869 29. Also 2C found to have adhesin family signature. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:9680209 2C PMID:12186869 NC_002163.1 RefSeq region 145628 146494 . - . ID=id398;Name=id398;Dbxref=GeneID:904476;gbkey=misc_feature;Note=HMMPfam hit to PF01297 2C Periplasmic solute binding protein family 2C score 6.1e-62 ### NC_002163.1 UTR_Extractor 5'-UTR 146507 146533 . - . ID=utr52;locus_tag=Cj0143c;product=putative periplasmic solute binding protein NC_002163.1 UTR_Extractor 5'-UTR 146654 146704 . + . ID=utr53;locus_tag=Cj0144;product=putative methyl-accepting chemotaxis signal transduction protein NC_002163.1 RefSeq CDS 146705 148684 . + 0 ID=cds129;Parent=gene137;Name=YP_002343604.1;Dbxref=GOA:Q0PBZ3 InterPro:IPR004010 InterPro:IPR004089 UniProtKB FTrEMBL:Q0PBZ3 Genbank:YP_002343604.1 GeneID:904478;gbkey=CDS;product=methyl-accepting chemotaxis signal transduction protein;Note=Original 282000 29 note: Cj0144 2C probable methyl-accepting chemotaxis signal transduction protein 2Clen: 659 aa 3B similar to mnay e.g. MCPS_ENTAE methyl-accepting chemotaxis serine transducer 28557 aa 29 2Cfasta scores 3B opt: 297 z-score: 493.4 E 28 29: 3.2e-20 2C 28.6 25 identity in 377 aa overlap. No Hp ortholog. C-terminus contains repeat1 2C and is identical to the other repeat 1-containing genes Cj0262c and Cj1564. Contains N-terminal signal sequence and transmembrane anchor around aa 300. Also contains Pfam match to entry PF00015 MCPsignal 2CMethyl-accepting chemotaxis protein 28MCP 29 signaling domain 2C score 110.60 2C E-value 4.1e-30 7EUpdated 282006 29 note: Some characterisation work within Bacillus subtilis and Escherichia coli 2C however 2Cidentity scores were unnacceptable. Thus 2C kept within product function. Functional classification -Chemotaxis and mobility 7EPMID:6213619 2C PMID:7921238 NC_002163.1 RefSeq gene 146705 148684 . + . ID=gene137;Name=Cj0144;locus_tag=Cj0144;Dbxref=GeneID:904478;gbkey=Gene NC_002163.1 RefSeq region 146732 146800 . + . ID=id399;Name=id399;Dbxref=GeneID:904478;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0144 by TMHMM2.0 at aa 10-32 and 287-309 NC_002163.1 RefSeq region 147563 147631 . + . ID=id399;Name=id399;Dbxref=GeneID:904478;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0144 by TMHMM2.0 at aa 10-32 and 287-309 NC_002163.1 RefSeq repeat_region 147606 148684 . + . ID=id400;Name=id400;Dbxref=GeneID:904478;gbkey=repeat_region;Note=repeat 1: identical to complement 28238817..239964 29 and 1492913..1493990 28approximate numbers 29 NC_002163.1 RefSeq region 148184 148678 . + . ID=id401;Name=id401;Dbxref=GeneID:904478;gbkey=misc_feature;Note=HMMPfam hit to PF00015 2C Methyl-accepting chemotaxis protein 28MCP 29 s 2C score 6.4e-21 ### NC_002163.1 RefSeq region 148819 150504 . + . ID=id402;Name=id402;Dbxref=GeneID:904480;gbkey=misc_feature;Note=HMMPfam hit to PF05787 2C Bacterial protein of unknown function 28DUF83 2C score 0 NC_002163.1 RefSeq gene 148819 150600 . + . ID=gene138;Name=Cj0145;locus_tag=Cj0145;Dbxref=GeneID:904480;gbkey=Gene NC_002163.1 RefSeq CDS 148819 150600 . + 0 ID=cds130;Parent=gene138;Name=YP_002343605.1;Dbxref=InterPro:IPR006311 InterPro:IPR008557 UniProtKB FTrEMBL:Q0PBZ2 Genbank:YP_002343605.1 GeneID:904480;gbkey=CDS;product=TAT pathway signal sequence domain-containing protein;Note=Original 282000 29 note: Cj0145 2C unknown 2C len: 593 aa 3B some similarity to a hypothetical protein from Streptomyces coelicolor TR:O69840 28EMBL:AL023517 29 SC1B5.12C 28465 aa 29 2C fasta scores 3B opt: 124 z-score: 327.1 E 28 29: 5.8e-11 2C 23.0 25 identity in 574 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF05787 Bacterial protein of unknown function 28DUF83 29 2C identified within CDS. TIGRFAM TIGR01409 TAT_signal_seq 2C Tat 28twin-arginine translocation 29 pathway signal sequence identified within CDS. Product modified to more specific family member based on motif search results. No specific characterisation with acceptable identity scores carried out yet. Thus 2C kept within product function. Functional classification -Misc 7EPMID:10766774 ### NC_002163.1 RefSeq CDS 150638 151576 . - 0 ID=cds131;Parent=gene139;gene=trxB;Name=YP_002343606.1;Dbxref=GOA:Q0PBZ1 InterPro:IPR000103 InterPro:IPR000759 InterPro:IPR001327 InterPro:IPR005982 InterPro:IPR008255 InterPro:IPR013027 UniProtKB FTrEMBL:Q0PBZ1 Genbank:YP_002343606.1 GeneID:904481;gbkey=CDS;product=thioredoxin reductase;Note=Original 282000 29 note: Cj0146c 2C trxB 2C probable thioredoxin reductase 2C len: 312 aa 3B similar to many e.g. TRXB_LISMO thioredoxin reductase 28EC 1.6.4.5 29 28319 aa 29 2Cfasta scores 3B opt: 749 z-score: 926.7 E 28 29: 0 2C 38.0 25 identity in 313 aa overlap. 64.2 25 identity to HP0825. Contains PS00573 Pyridine nucleotide-disulphide oxidoreductases class-II active site 7EUpdated 282006 29 note: Pfam domain PF00070 Pyridine nucleotide-disulphide oxidoreductase identified within CDS. Further support given to product function. Characterised within Listeria monocytogenes with acceptable identity scores. Appropriate motifs identified. Thus 2C not added to product function. Functional classification - Biosynthesis of cofactors 2C prosthetic groups and carriers - Thioredoxin 7EPMID:2644268 2C PMID:15358361 NC_002163.1 RefSeq gene 150638 151576 . - . ID=gene139;gene=trxB;Name=trxB;locus_tag=Cj0146c;Dbxref=GeneID:904481;gbkey=Gene NC_002163.1 RefSeq region 150716 151570 . - . ID=id403;gene=trxB;Name=id403;Dbxref=GeneID:904481;gbkey=misc_feature;Note=HMMPfam hit to PF00070 2C Pyridine nucleotide-disulphide oxidoreducta 2C score 6e-58 NC_002163.1 RefSeq region 151115 151177 . - . ID=id404;gene=trxB;Name=id404;Dbxref=GeneID:904481;gbkey=misc_feature;Note=PS00573 Pyridine nucleotide-disulphide oxidoreductases class-II active site ### NC_002163.1 UTR_Extractor 5'-UTR 151577 151607 . - . ID=utr54;locus_tag=Cj0146c;product=thioredoxin reductase NC_002163.1 RefSeq CDS 151710 152024 . - 0 ID=cds132;Parent=gene140;gene=trxA;Name=YP_002343607.1;Dbxref=GOA:Q0PBZ0 InterPro:IPR005746 InterPro:IPR006662 InterPro:IPR012335 InterPro:IPR013766 InterPro:IPR015467 UniProtKB FTrEMBL:Q0PBZ0 Genbank:YP_002343607.1 GeneID:904479;gbkey=CDS;product=thioredoxin;Note=Original 282000 29 note: Cj0147c 2C trxA 2C thioredoxin 2Clen: 104 aa 3B highly similar to many e.g. THIO_ECOLI thioredoxin 1 28108 aa 29 2C fasta scores 3B opt: 344 z-score: 590.5 E 28 29: 1.2e-25 2C 45.7 25 identity in 105 aa overlap. 68.6 25 identity to HP0824. Contains PS00194 Thioredoxin family active site and Pfam match to entry PF00085 thiored 2C Thioredoxins 2C score 144.20 2C E-value 3.6e-42 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. Thus 2C not added to product function. Appropiate motifs present. Paper identified linking protein to glycoprotein. Functional classification - Biosynthesis of cofactors 2Cprosthetic groups and carriers - Thioredoxin 7EPMID:12186869 2C PMID:15358361 NC_002163.1 RefSeq gene 151710 152024 . - . ID=gene140;gene=trxA;Name=trxA;locus_tag=Cj0147c;Dbxref=GeneID:904479;gbkey=Gene NC_002163.1 RefSeq region 151713 152018 . - . ID=id405;gene=trxA;Name=id405;Dbxref=GeneID:904479;gbkey=misc_feature;Note=HMMPfam hit to PF00085 2C Thioredoxin 2C score 6.9e-39 NC_002163.1 RefSeq region 151908 151964 . - . ID=id406;gene=trxA;Name=id406;Dbxref=GeneID:904479;gbkey=misc_feature;Note=PS00194 Thioredoxin family active site ### NC_002163.1 RefSeq CDS 152081 152419 . - 0 ID=cds133;Parent=gene141;Name=YP_002343608.1;Dbxref=GOA:Q9PIX9 InterPro:IPR003509 UniProtKB FSwiss-Prot:Q9PIX9 Genbank:YP_002343608.1 GeneID:904489;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0148c 2C unknown 2C len: 112 aa 3B similar to hypothetical proteins e.g. TR:G3323225 28EMBL:AE001259 29 Treponema pallidum TP0913 28126 aa 29 2C fasta scores 3B opt: 156 z-score: 253.1 E 28 29: 7.6e-07 2C 31.0 25 identity in 100 aa overlap. 47.1 25 identity to HP0823 7EUpdated 282006 29 note: Pfam PF02021 Uncharacterised protein family was present within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 152081 152419 . - . ID=gene141;Name=Cj0148c;locus_tag=Cj0148c;Dbxref=GeneID:904489;gbkey=Gene NC_002163.1 RefSeq region 152120 152389 . - . ID=id407;Name=id407;Dbxref=GeneID:904489;gbkey=misc_feature;Note=HMMPfam hit to PF02021 2C Uncharacterised protein family UPF0102 2C score 6e-16 NC_002163.1 RefSeq gene 152419 153666 . - . ID=gene142;gene=hom;Name=hom;locus_tag=Cj0149c;Dbxref=GeneID:904482;gbkey=Gene NC_002163.1 RefSeq CDS 152419 153666 . - 0 ID=cds134;Parent=gene142;gene=hom;Name=YP_002343609.1;Dbxref=GOA:Q0PBY8 InterPro:IPR001342 InterPro:IPR002912 InterPro:IPR005106 InterPro:IPR016204 UniProtKB FTrEMBL:Q0PBY8 Genbank:YP_002343609.1 GeneID:904482;gbkey=CDS;product=homoserine dehydrogenase;Note=catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine NC_002163.1 RefSeq region 152437 152661 . - . ID=id408;gene=hom;Name=id408;Dbxref=GeneID:904482;gbkey=misc_feature;Note=HMMPfam hit to PF01842 2C ACT domain 2C score 2e-10 NC_002163.1 RefSeq region 152755 153291 . - . ID=id409;gene=hom;Name=id409;Dbxref=GeneID:904482;gbkey=misc_feature;Note=HMMPfam hit to PF00742 2C Homoserine dehydrogenase 2Cscore 2.7e-73 NC_002163.1 RefSeq region 153085 153153 . - . ID=id410;gene=hom;Name=id410;Dbxref=GeneID:904482;gbkey=misc_feature;Note=PS01042 Homoserine dehydrogenase signature NC_002163.1 RefSeq region 153295 153666 . - . ID=id411;gene=hom;Name=id411;Dbxref=GeneID:904482;gbkey=misc_feature;Note=HMMPfam hit to PF03447 2C Homoserine dehydrogenase 2CNAD binding d 2C score 3.1e-13 ### NC_002163.1 RefSeq gene 153670 154872 . - . ID=gene143;Name=Cj0150c;locus_tag=Cj0150c;Dbxref=GeneID:904483;gbkey=Gene NC_002163.1 RefSeq CDS 153670 154872 . - 0 ID=cds135;Parent=gene143;Name=YP_002343610.1;Dbxref=GOA:Q0PBY7 InterPro:IPR004839 InterPro:IPR015421 UniProtKB FTrEMBL:Q0PBY7 Genbank:YP_002343610.1 GeneID:904483;gbkey=CDS;product=aspartate aminotransferase;Note=catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate NC_002163.1 RefSeq region 153679 154629 . - . ID=id412;Name=id412;Dbxref=GeneID:904483;gbkey=misc_feature;Note=HMMPfam hit to PF00155 2C Aminotransferase class I and II 2C score 1.3e-29 ### NC_002163.1 RefSeq CDS 154884 155690 . - 0 ID=cds136;Parent=gene144;Name=YP_002343611.1;Dbxref=UniProtKB FTrEMBL:Q0PBY6 Genbank:YP_002343611.1 GeneID:904484;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0151c 2C possible periplasmic protein 2C len: 268 aa 3B 26.0 25 identity to HP0555. Contains possible N-terminal signal sequence. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 154884 155690 . - . ID=gene144;Name=Cj0151c;locus_tag=Cj0151c;Dbxref=GeneID:904484;gbkey=Gene NC_002163.1 RefSeq CDS 155684 156622 . - 0 ID=cds137;Parent=gene145;Name=YP_002343612.1;Dbxref=UniProtKB FTrEMBL:Q0PBY5 Genbank:YP_002343612.1 GeneID:904485;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0152c 2C possible membrane protein 2C len: 312 aa 3B 25.0 25 identity to HP0554. Contains one probable transmembrane domain around aa 110. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 155684 156622 . - . ID=gene145;Name=Cj0152c;locus_tag=Cj0152c;Dbxref=GeneID:904485;gbkey=Gene NC_002163.1 RefSeq region 156275 156343 . - . ID=id413;Name=id413;Dbxref=GeneID:904485;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0152c by TMHMM2.0 at aa 94-116 NC_002163.1 RefSeq CDS 156615 157298 . - 0 ID=cds138;Parent=gene146;Name=YP_002343613.1;Dbxref=GOA:Q0PBY4 InterPro:IPR001537 InterPro:IPR013123 UniProtKB FTrEMBL:Q0PBY4 Genbank:YP_002343613.1 GeneID:904486;gbkey=CDS;product=rRNA methylase;Note=Original 282000 29 note: Cj0153c 2C probable rRNA methylase 2C len: 227 aa 3B similar to members of the spoU family e.g. NHS_STRAS 23S rRNA methyltransferase 28274 aa 29 2C fasta scores 3B opt: 197 z-score: 247.9 E 28 29: 1.5e-06 2C29.9 25 identity in 157 aa overlap. 42.7 25 identity to HP0553. Contains Pfam match to entry PF00588 SpoU_methylase 2C SpoU rRNA Methylase family 2C score 106.90 2CE-value 3.8e-28 7EUpdated 282006 29 note: Characterised within Escherichia coli with marginal identity score. kept within product function. Functional classification -RNA synthesis 2C RNA modification and DNA transcription 7EPMID:11698387 NC_002163.1 RefSeq gene 156615 157298 . - . ID=gene146;Name=Cj0153c;locus_tag=Cj0153c;Dbxref=GeneID:904486;gbkey=Gene NC_002163.1 RefSeq region 156633 157052 . - . ID=id414;Name=id414;Dbxref=GeneID:904486;gbkey=misc_feature;Note=HMMPfam hit to PF00588 2C SpoU rRNA Methylase family 2Cscore 7e-28 NC_002163.1 UTR_Extractor 5'-UTR 157298 157298 . - . ID=utr55;locus_tag=Cj0153c;product=putative rRNA methylase ### NC_002163.1 RefSeq CDS 157312 158136 . - 0 ID=cds139;Parent=gene147;Name=YP_002343614.1;Dbxref=GOA:Q0PBY3 InterPro:IPR000878 InterPro:IPR008189 InterPro:IPR014777 UniProtKB FTrEMBL:Q0PBY3 Genbank:YP_002343614.1 GeneID:904487;gbkey=CDS;product=tetrapyrrole methylase family protein;Note=Original 282000 29 note: Cj0154c 2C possible methylase 2Clen: 274 aa 3B similar to hypotehtical proteins e.g. YABC_BACSU 28292 aa 29 2C fasta scores 3B opt: 453 z-score: 741.0 E 28 29: 0 2C 32.9 25 identity in 289 aa overlap. 42.3 25 identity to HP0552. Contains PS01296 Uncharacterized protein family UPF0011 signature and Pfam match to entry PF00590 TP_methylase 2C Tetrapyrrole 28Corrin 2FPorphyrin 29 Methylases. 2Cscore 81.20 2C E-value 2.2e-20 7EUpdated 282006 29 note: Pfam domain PF00590 Tetrapyrrole 28Corrin 2FPorphyrin 29 Methylase was identified within CDS. Product modified to more specific family member due to motif match. No specific characterisation with acceptable identity score has yet been carried out. Thus 2C kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 157312 158136 . - . ID=gene147;Name=Cj0154c;locus_tag=Cj0154c;Dbxref=GeneID:904487;gbkey=Gene NC_002163.1 RefSeq region 157516 158136 . - . ID=id415;Name=id415;Dbxref=GeneID:904487;gbkey=misc_feature;Note=HMMPfam hit to PF00590 2C Tetrapyrrole 28Corrin 2FPorphyrin 29 Methylas 2C score 9.6e-20 NC_002163.1 RefSeq region 157849 157884 . - . ID=id416;Name=id416;Dbxref=GeneID:904487;gbkey=misc_feature;Note=PS01296 Uncharacterized protein family UPF0011 signature ### NC_002163.1 RefSeq CDS 158139 158339 . - 0 ID=cds140;Parent=gene148;gene=rpmE;Name=YP_002343615.1;Dbxref=GOA:Q9PIX2 InterPro:IPR002150 UniProtKB FSwiss-Prot:Q9PIX2 Genbank:YP_002343615.1 GeneID:904488;gbkey=CDS;product=50S ribosomal protein L31;Note=RpmE 3B there appears to be two types of ribosomal proteins L31 in bacterial genomes 3B some contain a CxxC motif while others do not 3B Bacillus subtilis has both types 3B the proteins in this cluster have the CXXC motif 3B RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth 3B expression of ytiA is controlled by a zinc-specific transcriptional repressor 3B RpmE contains one zinc ion and a CxxC motif is responsible for this binding 3B forms an RNP particle along with proteins L5 2C L18 2C and L25 and 5S rRNA 3B found crosslinked to L2 and L25 and EF-G 3B may be near the peptidyltransferase site of the 50S ribosome NC_002163.1 RefSeq gene 158139 158339 . - . ID=gene148;gene=rpmE;Name=rpmE;locus_tag=Cj0155c;Dbxref=GeneID:904488;gbkey=Gene NC_002163.1 RefSeq region 158142 158339 . - . ID=id417;gene=rpmE;Name=id417;Dbxref=GeneID:904488;gbkey=misc_feature;Note=HMMPfam hit to PF01197 2C Ribosomal protein L31 2Cscore 4.2e-40 NC_002163.1 RefSeq region 158166 158222 . - . ID=id418;gene=rpmE;Name=id418;Dbxref=GeneID:904488;gbkey=misc_feature;Note=PS01143 Ribosomal protein L31 signature NC_002163.1 RefSeq region 158217 158234 . - . ID=id419;gene=rpmE;Name=id419;Dbxref=GeneID:904488;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature ### NC_002163.1 UTR_Extractor 5'-UTR 158340 158367 . - . ID=utr56;locus_tag=Cj0155c;product=50S ribosomal protein L31 NC_002163.1 RefSeq gene 158418 159074 . - . ID=gene149;Name=Cj0156c;locus_tag=Cj0156c;Dbxref=GeneID:904493;gbkey=Gene NC_002163.1 RefSeq CDS 158418 159074 . - 0 ID=cds141;Parent=gene149;Name=YP_002343616.1;Dbxref=InterPro:IPR006700 UniProtKB FTrEMBL:Q0PBY1 Genbank:YP_002343616.1 GeneID:904493;gbkey=CDS;product=16S ribosomal RNA methyltransferase RsmE;Note=in Escherichia coli RsmE methylates the N3 position of the U1498 base in 16S rRNA 3B cells lacking this function can grow 2C but are outcompeted by wild-type 3B SAM-dependent m 283 29U1498 methyltransferase NC_002163.1 RefSeq region 158424 158711 . - . ID=id420;Name=id420;Dbxref=GeneID:904493;gbkey=misc_feature;Note=HMMPfam hit to PF04452 2C Protein of unknown function 28DUF558 29 2C score 1.2e-28 ### NC_002163.1 RefSeq CDS 159076 159483 . - 0 ID=cds142;Parent=gene150;Name=YP_002343617.1;Dbxref=GOA:Q0PBY0 UniProtKB FTrEMBL:Q0PBY0 Genbank:YP_002343617.1 GeneID:904494;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0157c 2C probable integral membrane protein 2C len: 135 aa 3B no Hp match. Contains four probable transmembrane domains. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 159076 159483 . - . ID=gene150;Name=Cj0157c;locus_tag=Cj0157c;Dbxref=GeneID:904494;gbkey=Gene NC_002163.1 RefSeq region 159091 159159 . - . ID=id11;Name=id11;Dbxref=GeneID:904494;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0157c by TMHMM2.0 at aa 10-29 2C 46-68 2C 78-97 and 109-131 NC_002163.1 RefSeq region 159193 159252 . - . ID=id11;Name=id11;Dbxref=GeneID:904494;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0157c by TMHMM2.0 at aa 10-29 2C 46-68 2C 78-97 and 109-131 NC_002163.1 RefSeq region 159280 159348 . - . ID=id11;Name=id11;Dbxref=GeneID:904494;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0157c by TMHMM2.0 at aa 10-29 2C 46-68 2C 78-97 and 109-131 NC_002163.1 RefSeq region 159295 159327 . - . ID=id421;Name=id421;Dbxref=GeneID:904494;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 159397 159456 . - . ID=id11;Name=id11;Dbxref=GeneID:904494;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0157c by TMHMM2.0 at aa 10-29 2C 46-68 2C 78-97 and 109-131 NC_002163.1 RefSeq gene 159483 159908 . - . ID=gene151;Name=Cj0158c;locus_tag=Cj0158c;Dbxref=GeneID:904474;gbkey=Gene NC_002163.1 RefSeq CDS 159483 159908 . - 0 ID=cds143;Parent=gene151;Name=YP_002343618.1;Dbxref=GOA:Q0PBX9 UniProtKB FTrEMBL:Q0PBX9 Genbank:YP_002343618.1 GeneID:904474;gbkey=CDS;product=heme-binding lipoprotein;Note=Original 282000 29 note: Cj0158c 2C possible haem-binding lipoprotein 2C len: 141 aa 3B no Hp match. Contains N-terminal signal sequence with appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site 2C PS00190 Cytochrome c family heme-binding site signature 2C and Pfam match to entry PF00034 cytochrome_c 2C Cytochrome c 2C score -3.00 2C E-value 0.87 7EUpdated 282006 29 note: No specific characterisation with acceptable identity scores identified yet. kept within product function. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 159486 159689 . - . ID=id422;Name=id422;Dbxref=GeneID:904474;gbkey=misc_feature;Note=HMMPfam hit to PF00034 2C Cytochrome c 2C score 0.041 NC_002163.1 RefSeq region 159642 159659 . - . ID=id423;Name=id423;Dbxref=GeneID:904474;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature NC_002163.1 RefSeq region 159849 159881 . - . ID=id424;Name=id424;Dbxref=GeneID:904474;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq CDS 159908 160489 . - 0 ID=cds144;Parent=gene152;Name=YP_002343619.1;Dbxref=GOA:Q0PBX8 InterPro:IPR007115 UniProtKB FTrEMBL:Q0PBX8 Genbank:YP_002343619.1 GeneID:904501;gbkey=CDS;product=6-pyruvoyl-tetrahydropterin synthase;Note=Original 282000 29 note: Cj0159c 2C unknown 2C len: 193 aa 3B similar in N-terminus to hypothetical proteins e.g.TR:O27296 28EMBL:AE000890 29 Methanobacterium thermoautotrophicum MTH1228 28161 aa 29 2C fasta scores 3B opt: 140 z-score: 234.0 E 28 29: 8.9e-06 2C 37.9 25 identity in 66 aa overlap. 35.8 25 identity to HP0933 7EUpdated 282006 29 note: Pfam domain PF01242 6-pyruvoyl tetrahydropterin synthase was identified within CDS. Product modified to more specific family member due to motif match with own search. No specific characterisation with acceptable identity scores carried out yet. Thus 2C kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 159908 160489 . - . ID=gene152;Name=Cj0159c;locus_tag=Cj0159c;Dbxref=GeneID:904501;gbkey=Gene NC_002163.1 RefSeq gene 160486 161229 . - . ID=gene153;Name=Cj0160c;locus_tag=Cj0160c;Dbxref=GeneID:904496;gbkey=Gene NC_002163.1 RefSeq CDS 160486 161229 . - 0 ID=cds145;Parent=gene153;Name=YP_002343620.1;Dbxref=GOA:Q0PBX7 InterPro:IPR007197 UniProtKB FTrEMBL:Q0PBX7 Genbank:YP_002343620.1 GeneID:904496;gbkey=CDS;product=radical SAM domain-containing protein;Note=Original 282000 29 note: Cj0160c 2C unknown 2C len: 247 aa 3B similar to hypothetical proteins e.g. TR:O67826 28EMBL:AE000769 29 Aquifex aeolicus AQ_2035 28219 aa 29 2C fasta scores 3B opt: 130 z-score: 282.9 E 28 29: 1.7e-08 2C 28.8 25 identity in 233 aa overlap. 43.1 25 identity to HP0934 7EUpdated 282006 29 note: Pfam domain PF04055 Radical SAM superfamily was identified within CDS. Product modified to more specific family member due to motif match. No specific characterisation carried out yet 2C so kept within product function. Functional classification - Misc NC_002163.1 UTR_Extractor 5'-UTR 160490 160516 . - . ID=utr57;locus_tag=Cj0159c;product=putative 6-pyruvoyl tetrahydropterin synthase NC_002163.1 RefSeq region 160567 161163 . - . ID=id425;Name=id425;Dbxref=GeneID:904496;gbkey=misc_feature;Note=HMMPfam hit to PF04055 2C Radical SAM superfamily 2Cscore 3.1e-08 ### NC_002163.1 RefSeq CDS 161232 162194 . - 0 ID=cds146;Parent=gene154;gene=moaA;Name=YP_002343621.1;Dbxref=GOA:Q9PIW6 InterPro:IPR000385 InterPro:IPR006638 InterPro:IPR007197 InterPro:IPR010505 InterPro:IPR013483 InterPro:IPR013785 UniProtKB FSwiss-Prot:Q9PIW6 Genbank:YP_002343621.1 GeneID:904499;gbkey=CDS;product=molybdenum cofactor biosynthesis protein A;Note=together with moaC 2C is involved in the conversion of a guanosine derivative 28GXP 29 into molybdopterin precursor Z NC_002163.1 RefSeq gene 161232 162194 . - . ID=gene154;gene=moaA;Name=moaA;locus_tag=Cj0161c;Dbxref=GeneID:904499;gbkey=Gene NC_002163.1 RefSeq region 161286 161654 . - . ID=id426;gene=moaA;Name=id426;Dbxref=GeneID:904499;gbkey=misc_feature;Note=HMMPfam hit to PF06463 2C Molybdenum Cofactor Synthesis C 2C score 1.5e-47 NC_002163.1 RefSeq region 161667 162152 . - . ID=id427;gene=moaA;Name=id427;Dbxref=GeneID:904499;gbkey=misc_feature;Note=HMMPfam hit to PF04055 2C Radical SAM superfamily 2Cscore 5.8e-38 NC_002163.1 RefSeq region 162111 162146 . - . ID=id428;gene=moaA;Name=id428;Dbxref=GeneID:904499;gbkey=misc_feature;Note=PS01305 moaA 2F nifB 2F pqqE family signature ### NC_002163.1 RefSeq CDS 162207 162722 . - 0 ID=cds147;Parent=gene155;Name=YP_002343622.1;Dbxref=GOA:Q0PBX5 UniProtKB FTrEMBL:Q0PBX5 Genbank:YP_002343622.1 GeneID:904500;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0162c 2C probable periplasmic protein 2C len: 171 aa 3B no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 162207 162722 . - . ID=gene155;Name=Cj0162c;locus_tag=Cj0162c;Dbxref=GeneID:904500;gbkey=Gene NC_002163.1 RefSeq region 162651 162710 . - . ID=id429;Name=id429;Dbxref=GeneID:904500;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0162c by TMHMM2.0 at aa 5-24 NC_002163.1 RefSeq gene 162719 163216 . - . ID=gene156;Name=Cj0163c;locus_tag=Cj0163c;Dbxref=GeneID:904502;gbkey=Gene NC_002163.1 RefSeq CDS 162719 163216 . - 0 ID=cds148;Parent=gene156;Name=YP_002343623.1;Dbxref=GOA:Q0PBX4 UniProtKB FTrEMBL:Q0PBX4 Genbank:YP_002343623.1 GeneID:904502;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0163c 2C unknown 2C len: 165 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 RefSeq gene 163207 164091 . - . ID=gene157;gene=ubiA;Name=ubiA;locus_tag=Cj0164c;Dbxref=GeneID:904503;gbkey=Gene NC_002163.1 RefSeq CDS 163207 164091 . - 0 ID=cds149;Parent=gene157;gene=ubiA;Name=YP_002343624.1;Dbxref=GOA:Q0PBX3 InterPro:IPR000537 InterPro:IPR006371 UniProtKB FTrEMBL:Q0PBX3 Genbank:YP_002343624.1 GeneID:904503;gbkey=CDS;product=prenyltransferase;Note=UbiA prenyltransferase family catalyzes the transfer of a prenyl group to various acceptors with hydrophobic ring structures in the biosynthesis of respiratory quinones 2C hemes 2C chlorophylls 2C vitamin E 2C and shikonin NC_002163.1 RefSeq region 163213 163281 . - . ID=id12;gene=ubiA;Name=id12;Dbxref=GeneID:904503;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0164c by TMHMM2.0 at aa 12-34 2C 44-63 2C 96-118 2C 138-160 2C165-187 2C 207-229 2C 234-256 and 271-293 NC_002163.1 RefSeq region 163219 164034 . - . ID=id430;gene=ubiA;Name=id430;Dbxref=GeneID:904503;gbkey=misc_feature;Note=HMMPfam hit to PF01040 2C UbiA prenyltransferase family 2C score 3.1e-52 NC_002163.1 RefSeq region 163324 163392 . - . ID=id12;gene=ubiA;Name=id12;Dbxref=GeneID:904503;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0164c by TMHMM2.0 at aa 12-34 2C 44-63 2C 96-118 2C 138-160 2C165-187 2C 207-229 2C 234-256 and 271-293 NC_002163.1 RefSeq region 163405 163473 . - . ID=id12;gene=ubiA;Name=id12;Dbxref=GeneID:904503;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0164c by TMHMM2.0 at aa 12-34 2C 44-63 2C 96-118 2C 138-160 2C165-187 2C 207-229 2C 234-256 and 271-293 NC_002163.1 RefSeq region 163531 163599 . - . ID=id12;gene=ubiA;Name=id12;Dbxref=GeneID:904503;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0164c by TMHMM2.0 at aa 12-34 2C 44-63 2C 96-118 2C 138-160 2C165-187 2C 207-229 2C 234-256 and 271-293 NC_002163.1 RefSeq region 163612 163680 . - . ID=id12;gene=ubiA;Name=id12;Dbxref=GeneID:904503;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0164c by TMHMM2.0 at aa 12-34 2C 44-63 2C 96-118 2C 138-160 2C165-187 2C 207-229 2C 234-256 and 271-293 NC_002163.1 RefSeq region 163738 163806 . - . ID=id12;gene=ubiA;Name=id12;Dbxref=GeneID:904503;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0164c by TMHMM2.0 at aa 12-34 2C 44-63 2C 96-118 2C 138-160 2C165-187 2C 207-229 2C 234-256 and 271-293 NC_002163.1 RefSeq region 163762 163794 . - . ID=id431;gene=ubiA;Name=id431;Dbxref=GeneID:904503;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 163903 163962 . - . ID=id12;gene=ubiA;Name=id12;Dbxref=GeneID:904503;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0164c by TMHMM2.0 at aa 12-34 2C 44-63 2C 96-118 2C 138-160 2C165-187 2C 207-229 2C 234-256 and 271-293 NC_002163.1 RefSeq region 163990 164058 . - . ID=id12;gene=ubiA;Name=id12;Dbxref=GeneID:904503;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0164c by TMHMM2.0 at aa 12-34 2C 44-63 2C 96-118 2C 138-160 2C165-187 2C 207-229 2C 234-256 and 271-293 ### NC_002163.1 UTR_Extractor 5'-UTR 164092 164117 . - . ID=utr58;locus_tag=Cj0164c;product=prenyltransferase NC_002163.1 RefSeq CDS 164162 165031 . + 0 ID=cds150;Parent=gene158;gene=miaA;Name=YP_002343625.1;Dbxref=GOA:Q9PIW2 InterPro:IPR002627 UniProtKB FSwiss-Prot:Q9PIW2 Genbank:YP_002343625.1 GeneID:904521;gbkey=CDS;product=tRNA delta 282 29-isopentenylpyrophosphate transferase;Note=IPP transferase 3B isopentenyltransferase 3B involved in tRNA modification 3B in Escherichia coli this enzyme catalyzes the addition of a delta2-isopentenyl group from dimethylallyl diphosphate to the N6-nitrogen of adenosine adjacent to the anticodon of tRNA species that read codons starting with uracil 3B further tRNA modifications may occur 3B mutations in miaA result in defects in translation efficiency and fidelity NC_002163.1 RefSeq gene 164162 165031 . + . ID=gene158;gene=miaA;Name=miaA;locus_tag=Cj0166;Dbxref=GeneID:904521;gbkey=Gene NC_002163.1 RefSeq region 164186 164209 . + . ID=id432;gene=miaA;Name=id432;Dbxref=GeneID:904521;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 164267 164986 . + . ID=id433;gene=miaA;Name=id433;Dbxref=GeneID:904521;gbkey=misc_feature;Note=HMMPfam hit to PF01715 2C IPP transferase 2C score 5.9e-46 NC_002163.1 RefSeq gene 165017 165580 . - . ID=gene159;Name=Cj0167c;locus_tag=Cj0167c;Dbxref=GeneID:904504;gbkey=Gene NC_002163.1 RefSeq CDS 165017 165580 . - 0 ID=cds151;Parent=gene159;Name=YP_002343626.1;Dbxref=GOA:Q9PIW1 InterPro:IPR003810 UniProtKB FSwiss-Prot:Q9PIW1 Genbank:YP_002343626.1 GeneID:904504;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0167c 2C probable integral membrane protein 2C len: 187 aa 3B similar to hypothetical proteins e.g. YEBN_ECOLI 28206 aa 29 2C fasta scores 3B opt: 451 z-score: 792.0 E 28 29: 0 2C 38.1 25 identity in 197 aa overlap. No Hp match 7EUpdated 282006 29 note: Six probable transmembrane helices predicted by TMHMM2.0. Also 2C Pfam domains x2 PF02659 Domain of unknown function DUF were identified within CDS. This family consists of hypothetical transmembrane proteins with unknown function. Further support given to product function. No specific characterisation yet 2C so included in product function. Functional classification - Membranes 2Clipoproteins and porins NC_002163.1 RefSeq region 165026 165085 . - . ID=id13;Name=id13;Dbxref=GeneID:904504;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0167c by TMHMM2.0 at aa 4-23 2C 36-58 2C 63-85 2C 105-127 2C131-153 and 166-185 NC_002163.1 RefSeq region 165050 165265 . - . ID=id434;Name=id434;Dbxref=GeneID:904504;gbkey=misc_feature;Note=HMMPfam hit to PF02659 2C Domain of unknown function DUF 2C score 1.5e-17 NC_002163.1 RefSeq region 165122 165190 . - . ID=id13;Name=id13;Dbxref=GeneID:904504;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0167c by TMHMM2.0 at aa 4-23 2C 36-58 2C 63-85 2C 105-127 2C131-153 and 166-185 NC_002163.1 RefSeq region 165200 165268 . - . ID=id13;Name=id13;Dbxref=GeneID:904504;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0167c by TMHMM2.0 at aa 4-23 2C 36-58 2C 63-85 2C 105-127 2C131-153 and 166-185 NC_002163.1 RefSeq region 165326 165394 . - . ID=id13;Name=id13;Dbxref=GeneID:904504;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0167c by TMHMM2.0 at aa 4-23 2C 36-58 2C 63-85 2C 105-127 2C131-153 and 166-185 NC_002163.1 RefSeq region 165335 165565 . - . ID=id435;Name=id435;Dbxref=GeneID:904504;gbkey=misc_feature;Note=HMMPfam hit to PF02659 2C Domain of unknown function DUF 2C score 4.5e-15 NC_002163.1 RefSeq region 165407 165475 . - . ID=id13;Name=id13;Dbxref=GeneID:904504;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0167c by TMHMM2.0 at aa 4-23 2C 36-58 2C 63-85 2C 105-127 2C131-153 and 166-185 NC_002163.1 RefSeq region 165512 165571 . - . ID=id13;Name=id13;Dbxref=GeneID:904504;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0167c by TMHMM2.0 at aa 4-23 2C 36-58 2C 63-85 2C 105-127 2C131-153 and 166-185 ### NC_002163.1 UTR_Extractor 5'-UTR 165581 165611 . - . ID=utr59;locus_tag=Cj0167c;product=putative integral membrane protein NC_002163.1 RefSeq gene 165728 165802 . + . ID=gene160;gene=tRNAGlu;Name=tRNAGlu;locus_tag=Cjp03;Dbxref=GeneID:904506;gbkey=Gene NC_002163.1 RefSeq tRNA 165728 165802 . + . ID=rna6;Parent=gene160;gene=tRNAGlu;Name=rna6;Dbxref=GeneID:904506;gbkey=tRNA;product=tRNA-Glu;Note=tRNA Glu anticodon TTC 2C Cove score 66.15 NC_002163.1 RefSeq exon 165728 165802 . + . ID=id436;Parent=rna6;gene=tRNAGlu;Name=id436;Dbxref=GeneID:904506;gbkey=tRNA;product=tRNA-Glu;Note=tRNA Glu anticodon TTC 2C Cove score 66.15 NC_002163.1 RefSeq gene 165938 166105 . - . ID=gene161;Name=Cj0168c;locus_tag=Cj0168c;Dbxref=GeneID:904507;gbkey=Gene NC_002163.1 RefSeq CDS 165938 166105 . - 0 ID=cds152;Parent=gene161;Name=YP_002343627.1;Dbxref=GOA:Q0PBX0 UniProtKB FTrEMBL:Q0PBX0 Genbank:YP_002343627.1 GeneID:904507;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0168c 2C probable periplasmic protein 2C len: 55 aa 3B No Hp ortholog. Some similarity in C-term to Cj0909 2835.0 25 identity in 40 aa overlap 29. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Literature search identified paper giving further support to product function. N-terminal matches to Yersinia pestis 2C acid shock protein 2 precursor. Functional classification - Miscellaneous periplasmic proteins 7EPMID:15632442 NC_002163.1 RefSeq region 166043 166096 . - . ID=id437;Name=id437;Dbxref=GeneID:904507;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0168c by TMHMM2.0 at aa 4-21 ### NC_002163.1 UTR_Extractor 5'-UTR 166106 166136 . - . ID=utr60;locus_tag=Cj0168c;product=putative periplasmic protein NC_002163.1 UTR_Extractor 5'-UTR 166345 166372 . + . ID=utr61;locus_tag=Cj0169;product=superoxide dismutase NC_002163.1 RefSeq region 166373 166615 . + . ID=id438;gene=sodB;Name=id438;Dbxref=GeneID:904414;gbkey=misc_feature;Note=HMMPfam hit to PF00081 2C Iron 2Fmanganese superoxide dismutases 2C alpha- 2C score 2.8e-30 NC_002163.1 RefSeq CDS 166373 167035 . + 0 ID=cds153;Parent=gene162;gene=sodB;Name=YP_002343628.1;Dbxref=GOA:Q0PBW9 HSSP:P09157 InterPro:IPR001189 UniProtKB FSwiss-Prot:Q0PBW9 Genbank:YP_002343628.1 GeneID:904414;gbkey=CDS;product=superoxide dismutase;Note=Original 282000 29 note: Cj0169 2C sodB 2C superoxide dismutase 28Fe 29 2C len: 220 aa 3B 99.1 25 identical to SODF_CAMJE 2C and highly simlar to many e.g. SODF_ECOLI superoxide dismutase 28Fe 29 28EC 1.15.1.1 29 28192 aa 29 2C fasta scores 3B opt: 740 z-score: 1209.9 E 28 29: 0 2C 57.9 25 identity in 195 aa overlap. 61.6 25 identity to HP0389. Contains PS00088 Manganese and iron superoxide dismutases signature and Pfam match to entry PF00081 sodfe 2C Iron 2Fmanganese superoxide dismutases 28SODM 29 2C score 275.90 2C E-value 5.2e-79 7EUpdated 282006 29 note: Characterised within Campylobacter jejuni 2C so not added. Paper identified linking protein to glycoprotein 28PMID:12186869 29. Functional classification -Detoxification 7EPMID:12186869 2C PMID:8025686 2C PMID:8005660 NC_002163.1 RefSeq gene 166373 167035 . + . ID=gene162;gene=sodB;Name=sodB;locus_tag=Cj0169;Dbxref=GeneID:904414;gbkey=Gene NC_002163.1 RefSeq region 166637 166966 . + . ID=id439;gene=sodB;Name=id439;Dbxref=GeneID:904414;gbkey=misc_feature;Note=HMMPfam hit to PF02777 2C Iron 2Fmanganese superoxide dismutases 2C C-term 2C score 3.3e-45 NC_002163.1 RefSeq region 166862 166885 . + . ID=id440;gene=sodB;Name=id440;Dbxref=GeneID:904414;gbkey=misc_feature;Note=PS00088 Manganese and iron superoxide dismutases signature ### NC_002163.1 RefSeq CDS 167050 167295 . + 0 ID=cds154a;Parent=gene163;Name=YP_002343629.1;Dbxref=UniProtKB FTrEMBL:Q0PBW8 Genbank:YP_002343629.1 GeneID:904508;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0171 2C unknown 2C len: 166 aa 3B no Hp match. Contains polyporphic sequence G 289 2C11 29 at N-terminus 3B G11 allows translation from the upstream CDS Cj0170 2C G9 28consensus 29 would only allow this CDS to start at aa 47. Similar to Cj1326 2851.9 25 identity in 135 aa overlap 29 2C which also contains a polymorphic sequence allowing possible translation from Cj1325 7EOriginal 282000 29 note: Cj0170 2C unknown 2C len: 90 aa 3B no Hp match. Contains polyporphic sequence G 289 2C11 29 at C-terminus 3B G9 28consensus 29 gives this translation stop 2CG11 allows translation into the downstream CDS Cj0171. Similar to Cj1325 2873.8 25 identity in 61 aa overlap 29 2C which also contains a polymorphic sequence allowing possible translation into Cj1326 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Coding sequences have been merged to reflect the complete amino acid sequence for this gene regardless of phase. Previous annotation gave Cj0170 and Cj0171 as seperate CDS. Merging of these CDSs has lead to loss of the downstream CDS. Functional classification - Unknown NC_002163.1 RefSeq gene 167050 167794 . + . ID=gene163;Name=Cj0170;locus_tag=Cj0170;Dbxref=GeneID:904508;gbkey=Gene NC_002163.1 RefSeq CDS 167297 167794 . + 0 ID=cds154b;Parent=gene163;Name=YP_002343629.1;Dbxref=UniProtKB FTrEMBL:Q0PBW8 Genbank:YP_002343629.1 GeneID:904508;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0171 2C unknown 2C len: 166 aa 3B no Hp match. Contains polyporphic sequence G 289 2C11 29 at N-terminus 3B G11 allows translation from the upstream CDS Cj0170 2C G9 28consensus 29 would only allow this CDS to start at aa 47. Similar to Cj1326 2851.9 25 identity in 135 aa overlap 29 2C which also contains a polymorphic sequence allowing possible translation from Cj1325 7EOriginal 282000 29 note: Cj0170 2C unknown 2C len: 90 aa 3B no Hp match. Contains polyporphic sequence G 289 2C11 29 at C-terminus 3B G9 28consensus 29 gives this translation stop 2CG11 allows translation into the downstream CDS Cj0171. Similar to Cj1325 2873.8 25 identity in 61 aa overlap 29 2C which also contains a polymorphic sequence allowing possible translation into Cj1326 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Coding sequences have been merged to reflect the complete amino acid sequence for this gene regardless of phase. Previous annotation gave Cj0170 and Cj0171 as seperate CDS. Merging of these CDSs has lead to loss of the downstream CDS. Functional classification - Unknown NC_002163.1 RefSeq gene 167807 169012 . - . ID=gene164;Name=Cj0172c;locus_tag=Cj0172c;Dbxref=GeneID:904510;gbkey=Gene NC_002163.1 RefSeq CDS 167807 169012 . - 0 ID=cds155;Parent=gene164;Name=YP_002343630.1;Dbxref=GOA:Q0PBW7 InterPro:IPR005097 UniProtKB FTrEMBL:Q0PBW7 Genbank:YP_002343630.1 GeneID:904510;gbkey=CDS;product=saccharopine dehydrogenase;Note=Original 282000 29 note: Cj0172c 2C unknown 2C len: 401 aa 3B similar to hypothetical proteins e.g. TR:Q55131 28EMBL:D64001 29 Synechocystis sp. SLR0049 28398 aa 29 2C fasta scores 3B opt: 1534 z-score: 2324.2 E 28 29: 0 2C 55.7 25 identity in 397 aa overlap. 63.8 25 identity to HP1507 conserved hypothetical ATP-binding protein 7EUpdated 282006 29 note: Pfam domain PF03435 Saccharopine dehydrogenase was identified within CDS. Product modified to more specific family member due to motif match. No specific characterisation has yet been carried out. kept within product function. Functional classification - Misc NC_002163.1 RefSeq region 167837 169003 . - . ID=id441;Name=id441;Dbxref=GeneID:904510;gbkey=misc_feature;Note=HMMPfam hit to PF03435 2C Saccharopine dehydrogenase 2Cscore 2e-236 ### NC_002163.1 UTR_Extractor 5'-UTR 169013 169136 . - . ID=utr62;locus_tag=Cj0172c;product=putative saccharopine dehydrogenase NC_002163.1 RefSeq CDS 169054 169962 . - 0 ID=cds156;Parent=gene165;gene=cfbpC;Name=YP_002343631.1;Dbxref=GOA:Q0PBW6 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FTrEMBL:Q0PBW6 Genbank:YP_002343631.1 GeneID:904511;gbkey=CDS;product=iron-uptake ABC transporter ATP-binding protein;Note=Original 282000 29 note: Cj0173c 2C possible iron-uptake ABC transport system ATP-binding protein 2C len: 302 aa 3B similar to many e.g. HITC_HAEIN iron 28iii 29-transport ATP-binding protein hitC 28356 aa 29 2C fasta scores 3B opt: 389 z-score: 783.2 E 28 29: 0 2C 38.0 25 identity in 250 aa overlap. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2CPS00211 ABC transporters family signature and Pfam match to entry PF00005 ABC_tran 2C ABC transporters 2C score 163.10 2CE-value 4.9e-45. No Hp ortholog 7EUpdated 282006 29 note: Literature search identified many supporting papers within Campylobacter jejuni 28PMID:12069882 29 and also paper carrying out the original work within Serratia marcescens. Designated as Campylobacter ferric binding protein 28Cfbp 29 system. Characterisation with acceptable identity score yet to be carried out. Thus 2C kept within product function. Functional classification - Transport 2Fbinding proteins -Cations 7EPMID:15231804 2C PMID:12069882 2C PMID:15731081 2CPMID:2644190 2C PMID:7927717 NC_002163.1 RefSeq gene 169054 169962 . - . ID=gene165;gene=cfbpC;Name=cfbpC;locus_tag=Cj0173c;Dbxref=GeneID:904511;gbkey=Gene NC_002163.1 RefSeq region 169378 169881 . - . ID=id442;gene=cfbpC;Name=id442;Dbxref=GeneID:904511;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 2.3e-45 NC_002163.1 RefSeq region 169564 169608 . - . ID=id443;gene=cfbpC;Name=id443;Dbxref=GeneID:904511;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq region 169837 169860 . - . ID=id444;gene=cfbpC;Name=id444;Dbxref=GeneID:904511;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 169946 171562 . - 0 ID=cds157;Parent=gene166;gene=cfbpB;Name=YP_002343632.1;Dbxref=GOA:Q0PBW5 InterPro:IPR000515 UniProtKB FTrEMBL:Q0PBW5 Genbank:YP_002343632.1 GeneID:904512;gbkey=CDS;product=iron-uptake ABC transporter permease;Note=Original 282000 29 note: Cj0174c 2C possible iron-uptake ABC transport system permease 2C len: 538 aa 3B similar to e.g. SFUB_SERMA iron 28iii 29-transport system permease 28527 aa 29 2C fasta scores 3B opt: 333 z-score: 335.6 E 28 29: 1.9e-11 2C 21.5 25 identity in 522 aa overlap. No Hp match. Contains Pfam match to entry PF00528 BPD_transp 2CBinding-protein-dependent transport systems inner membrane component 2C score 27.90 2C E-value 0.00024 7EUpdated 282006 29 note: Literature search identified many supporting papers within Campylobacter jejuni 28PMID:12069882 29 and also paper carrying out the original work within Serratia marcescens. Designated as Campylobacter ferric binding protein 28Cfbp 29 system. Characterisation with acceptable identity score yet to be carried out. Thus 2C kept within product function. Functional classification - Transport 2Fbinding proteins -Cations 7EPMID:15231804 2C PMID:12069882 2C PMID:15731081 2CPMID:2644190 2C PMID:7927717 NC_002163.1 RefSeq gene 169946 171562 . - . ID=gene166;gene=cfbpB;Name=cfbpB;locus_tag=Cj0174c;Dbxref=GeneID:904512;gbkey=Gene NC_002163.1 RefSeq region 169982 170050 . - . ID=id14;gene=cfbpB;Name=id14;Dbxref=GeneID:904512;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0174c by TMHMM2.0 at aa 13-35 2C 69-91 2C 104-124 2C 144-166 2C187-209 2C 241-263 2C 292-314 2C 329-351 2C 371-393 2C 408-430 2C451-473 and 505-527 NC_002163.1 RefSeq region 170144 170212 . - . ID=id14;gene=cfbpB;Name=id14;Dbxref=GeneID:904512;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0174c by TMHMM2.0 at aa 13-35 2C 69-91 2C 104-124 2C 144-166 2C187-209 2C 241-263 2C 292-314 2C 329-351 2C 371-393 2C 408-430 2C451-473 and 505-527 NC_002163.1 RefSeq region 170273 170341 . - . ID=id14;gene=cfbpB;Name=id14;Dbxref=GeneID:904512;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0174c by TMHMM2.0 at aa 13-35 2C 69-91 2C 104-124 2C 144-166 2C187-209 2C 241-263 2C 292-314 2C 329-351 2C 371-393 2C 408-430 2C451-473 and 505-527 NC_002163.1 RefSeq region 170384 170452 . - . ID=id14;gene=cfbpB;Name=id14;Dbxref=GeneID:904512;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0174c by TMHMM2.0 at aa 13-35 2C 69-91 2C 104-124 2C 144-166 2C187-209 2C 241-263 2C 292-314 2C 329-351 2C 371-393 2C 408-430 2C451-473 and 505-527 NC_002163.1 RefSeq region 170510 170578 . - . ID=id14;gene=cfbpB;Name=id14;Dbxref=GeneID:904512;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0174c by TMHMM2.0 at aa 13-35 2C 69-91 2C 104-124 2C 144-166 2C187-209 2C 241-263 2C 292-314 2C 329-351 2C 371-393 2C 408-430 2C451-473 and 505-527 NC_002163.1 RefSeq region 170621 170689 . - . ID=id14;gene=cfbpB;Name=id14;Dbxref=GeneID:904512;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0174c by TMHMM2.0 at aa 13-35 2C 69-91 2C 104-124 2C 144-166 2C187-209 2C 241-263 2C 292-314 2C 329-351 2C 371-393 2C 408-430 2C451-473 and 505-527 NC_002163.1 RefSeq region 170753 171382 . - . ID=id445;gene=cfbpB;Name=id445;Dbxref=GeneID:904512;gbkey=misc_feature;Note=HMMPfam hit to PF00528 2C Binding-protein-dependent transport syst 2C score 5.4e-07 NC_002163.1 RefSeq region 170774 170842 . - . ID=id14;gene=cfbpB;Name=id14;Dbxref=GeneID:904512;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0174c by TMHMM2.0 at aa 13-35 2C 69-91 2C 104-124 2C 144-166 2C187-209 2C 241-263 2C 292-314 2C 329-351 2C 371-393 2C 408-430 2C451-473 and 505-527 NC_002163.1 RefSeq region 170936 171004 . - . ID=id14;gene=cfbpB;Name=id14;Dbxref=GeneID:904512;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0174c by TMHMM2.0 at aa 13-35 2C 69-91 2C 104-124 2C 144-166 2C187-209 2C 241-263 2C 292-314 2C 329-351 2C 371-393 2C 408-430 2C451-473 and 505-527 NC_002163.1 RefSeq region 171065 171133 . - . ID=id14;gene=cfbpB;Name=id14;Dbxref=GeneID:904512;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0174c by TMHMM2.0 at aa 13-35 2C 69-91 2C 104-124 2C 144-166 2C187-209 2C 241-263 2C 292-314 2C 329-351 2C 371-393 2C 408-430 2C451-473 and 505-527 NC_002163.1 RefSeq region 171191 171253 . - . ID=id14;gene=cfbpB;Name=id14;Dbxref=GeneID:904512;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0174c by TMHMM2.0 at aa 13-35 2C 69-91 2C 104-124 2C 144-166 2C187-209 2C 241-263 2C 292-314 2C 329-351 2C 371-393 2C 408-430 2C451-473 and 505-527 NC_002163.1 RefSeq region 171290 171358 . - . ID=id14;gene=cfbpB;Name=id14;Dbxref=GeneID:904512;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0174c by TMHMM2.0 at aa 13-35 2C 69-91 2C 104-124 2C 144-166 2C187-209 2C 241-263 2C 292-314 2C 329-351 2C 371-393 2C 408-430 2C451-473 and 505-527 NC_002163.1 RefSeq region 171458 171526 . - . ID=id14;gene=cfbpB;Name=id14;Dbxref=GeneID:904512;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0174c by TMHMM2.0 at aa 13-35 2C 69-91 2C 104-124 2C 144-166 2C187-209 2C 241-263 2C 292-314 2C 329-351 2C 371-393 2C 408-430 2C451-473 and 505-527 NC_002163.1 RefSeq CDS 171562 172566 . - 0 ID=cds158;Parent=gene167;gene=cfbpA;Name=YP_002343633.1;Dbxref=GOA:Q0PBW4 InterPro:IPR006059 PDB:1Y4T UniProtKB FTrEMBL:Q0PBW4 Genbank:YP_002343633.1 GeneID:904513;gbkey=CDS;product=iron-uptake ABC transporter substrate-binding protein;Note=Original 282000 29 note: Cj0175c 2C possible iron-uptake ABC transport system periplasmic iron-binding protein 2Clen: 334 aa 3B similar to e.g. HITA_HAEIN iron-utilization periplasmic protein precursor 28332 aa 29 2C fasta scores 3B opt: 466 z-score: 500.8 E 28 29: 1.2e-20 2C 29.8 25 identity in 332 aa overlap. No Hp match. Contains N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF01547 Bacterial extracellular solute-binding protein identified within CDS. Further support given to product function. Literature search identified many supporting papers within Campylobacter jejuni 28PMID:12069882 29 and also paper carrying out the original work within Serratia marcescens. Designated as Campylobacter ferric binding protein 28Cfbp 29 system. Characterisation with acceptable identity score yet to be carried out. Thus 2C kept within product function. Paper identified linked protein to glycoprotein 28PMID:15231804 29. Functional classification -Transport 2Fbinding proteins - Cations 7EPMID:15613474 2C PMID:15231804 2C PMID:12069882 2CPMID:12186869 2C PMID:2644190 NC_002163.1 RefSeq gene 171562 172566 . - . ID=gene167;gene=cfbpA;Name=cfbpA;locus_tag=Cj0175c;Dbxref=GeneID:904513;gbkey=Gene NC_002163.1 RefSeq region 171727 172566 . - . ID=id446;gene=cfbpA;Name=id446;Dbxref=GeneID:904513;gbkey=misc_feature;Note=HMMPfam hit to PF01547 2C Bacterial extracellular solute-binding prot 2C score 4.7e-14 NC_002163.1 RefSeq CDS 172563 172694 . - 0 ID=cds159;Parent=gene168;Name=YP_002343634.1;Dbxref=UniProtKB FTrEMBL:Q0PBW3 Genbank:YP_002343634.1 GeneID:904515;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj0176c 2C probable lipoprotein 2C len: 43 aa 3B no Hp match. Contains N-terminal signal sequence with appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site 7EUpdated 282006 29 note: Literature search identified papers giving further clues to product function. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 172563 172694 . - . ID=gene168;gene=Cj0176c;Name=Cj0176c;locus_tag=Cj0176c;Dbxref=GeneID:904515;gbkey=Gene NC_002163.1 RefSeq region 172638 172670 . - . ID=id447;Name=id447;Dbxref=GeneID:904515;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 UTR_Extractor 5'-UTR 172695 172717 . - . ID=utr63;locus_tag=Cj0176c;product=putative lipoprotein NC_002163.1 RefSeq region 172916 173764 . + . ID=id448;Name=id448;Dbxref=GeneID:904516;gbkey=misc_feature;Note=HMMPfam hit to PF04187 2C Protein of unknown function 2C DUF399 2C score 5e-164 NC_002163.1 RefSeq CDS 172916 173767 . + 0 ID=cds160;Parent=gene169;Name=YP_002343635.1;Dbxref=InterPro:IPR007314 InterPro:IPR016773 UniProtKB FTrEMBL:Q0PBW2 Genbank:YP_002343635.1 GeneID:904516;gbkey=CDS;product=iron transport protein;Note=Original 282000 29 note: Cj0177 2C probable lipoprotein 2Clen: 283 aa 3B simlar to TR:O68876 28EMBL:AF055999 29 hypothetical protein PhuW from Pseudomonas aeruginosa hemin uptake locus 28295 aa 29 2C fasta scores 3B opt: 375 z-score: 307.6 E 28 29: 7.1e-10 2C 31.3 25 identity in 246 aa overlap. No Hp match. Contains N-terminal signal sequence with appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site 7EUpdated 282006 29 note: Pfam domain PF04187 Protein of unknown function 2C DUF399 identified within CDS. Literature search identified papers giving further clues to product function. Product function modified to iron transport protein based on information from literature. No specific characterisation with acceptable identity scores has been carried out yet. Thus 2C kept within product function. Functional classification -Transport 2Fbinding proteins - Cations 7EPMID:12069882 2C PMID:15231804 2C PMID:15231804 NC_002163.1 RefSeq gene 172916 173767 . + . ID=gene169;Name=Cj0177;locus_tag=Cj0177;Dbxref=GeneID:904516;gbkey=Gene NC_002163.1 RefSeq region 172940 172972 . + . ID=id449;Name=id449;Dbxref=GeneID:904516;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq CDS 173764 176031 . + 0 ID=cds161;Parent=gene170;Name=YP_002343636.1;Dbxref=GOA:Q0PBW1 InterPro:IPR000531 InterPro:IPR012910 UniProtKB FTrEMBL:Q0PBW1 Genbank:YP_002343636.1 GeneID:904518;gbkey=CDS;product=TonB-denpendent outer membrane receptor;Note=Original 282000 29 note: Cj0178 2C possible outer membrane siderophore receptor 2C len: 755 aa 3B similar to e.g. YC17_HAEIN probable tonB-dependent receptor HI1217 28913 aa 29 2C fasta scores 3B opt: 440 z-score: 1818.4 E 28 29: 0 2C32.7 25 identity in 912 aa overlap 2C and TR:O68881 28EMBL:AF055999 29 outer membrane hemin receptor PhuR from Pseudomonas aeruginosa 28764 aa 29 2C fasta scores 3B opt: 145 z-score: 207.4 E 28 29: 0.00027 22.3 25 identity in 806 aa overlap. No Hp match. Contains N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domains PF07715 TonB-dependent Receptor Plug Domain and PF00593 TonB dependent receptor identified within CDS. Literature search identified papers giving further clues to product function. Product function modified to more specific family member. No specific characterisation with acceptable identity scores has been carried out yet. Thus 2C kept within product function. Functional classification - Transport 2Fbinding proteins - Cations 7EPMID:15731081 2C PMID:15632442 2C PMID:15231804 2CPMID:12069882 NC_002163.1 RefSeq gene 173764 176031 . + . ID=gene170;Name=Cj0178;locus_tag=Cj0178;Dbxref=GeneID:904518;gbkey=Gene NC_002163.1 RefSeq region 173881 174234 . + . ID=id450;Name=id450;Dbxref=GeneID:904518;gbkey=misc_feature;Note=HMMPfam hit to PF07715 2C TonB-dependent Receptor Plug Domain 2C score 9.2e-13 NC_002163.1 RefSeq region 175135 176028 . + . ID=id451;Name=id451;Dbxref=GeneID:904518;gbkey=misc_feature;Note=HMMPfam hit to PF00593 2C TonB dependent receptor 2Cscore 1.5e-22 ### NC_002163.1 RefSeq CDS 176043 176804 . + 0 ID=cds162;Parent=gene171;gene=exbB1;Name=YP_002343637.1;Dbxref=GOA:Q0PBW0 InterPro:IPR002898 UniProtKB FTrEMBL:Q0PBW0 Genbank:YP_002343637.1 GeneID:904520;gbkey=CDS;product=biopolymer transport protein;Note=Original 282000 29 note: Cj0179 2C exbB1 2C biopolymer transport protein 2C len: 253 aa 3B highly similar to e.g. EXBB_ECOLI biopolymer transport exbB protein 28244 aa 29 2Cfasta scores 3B opt: 537 z-score: 811.2 E 28 29: 0 2C 46.3 25 identity in 216 aa overlap. No Hp ortholog 7EUpdated 282006 29 note: Pfam domain PF01618 MotA 2FTolQ 2FExbB proton channel family identified within CDS. Also 2C three probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. Thus 2C not added. Cj0179-Cj0181 28exbB1 2C exbD1 2C tonB1 29 function as an outer-membrane energy transducer system. Functional classification -Transport 2Fbinding proteins - Other 7EPMID:7642501 2C PMID:8437515 2C PMID:15632442 2CPMID:12069882 NC_002163.1 RefSeq gene 176043 176804 . + . ID=gene171;gene=exbB1;Name=exbB1;locus_tag=Cj0179;Dbxref=GeneID:904520;gbkey=Gene NC_002163.1 RefSeq region 176211 176264 . + . ID=id452;gene=exbB1;Name=id452;Dbxref=GeneID:904520;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0179 by TMHMM2.0 at aa 57-74 2C 155-177 and 197-219 NC_002163.1 RefSeq region 176322 176756 . + . ID=id453;gene=exbB1;Name=id453;Dbxref=GeneID:904520;gbkey=misc_feature;Note=HMMPfam hit to PF01618 2C MotA 2FTolQ 2FExbB proton channel family 2C score 8.6e-47 NC_002163.1 RefSeq region 176505 176573 . + . ID=id452;gene=exbB1;Name=id452;Dbxref=GeneID:904520;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0179 by TMHMM2.0 at aa 57-74 2C 155-177 and 197-219 NC_002163.1 RefSeq region 176631 176699 . + . ID=id452;gene=exbB1;Name=id452;Dbxref=GeneID:904520;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0179 by TMHMM2.0 at aa 57-74 2C 155-177 and 197-219 NC_002163.1 UTR_Extractor 5'-UTR 176778 176790 . + . ID=utr64;locus_tag=Cj0180;product=biopolymer transport protein NC_002163.1 RefSeq gene 176791 177201 . + . ID=gene172;gene=exbD1;Name=exbD1;locus_tag=Cj0180;Dbxref=GeneID:904523;gbkey=Gene NC_002163.1 RefSeq CDS 176791 177201 . + 0 ID=cds163;Parent=gene172;gene=exbD1;Name=YP_002343638.1;Dbxref=GOA:Q0PBV9 InterPro:IPR003400 UniProtKB FTrEMBL:Q0PBV9 Genbank:YP_002343638.1 GeneID:904523;gbkey=CDS;product=biopolymer transport protein;Note=Original 282000 29 note: Cj0180 2C exbD1 2C biopolymer transport protein 2C len: 136 aa 3B highly similar to e.g. EXBD_ECOLI biopolymer transport exbD protein 28141 aa 29 2Cfasta scores 3B opt: 356 z-score: 629.2 E 28 29: 8.7e-28 2C 42.9 25 identity in 119 aa overlap. No Hp ortholog 7EUpdated 282006 29 note: Pfam domain PF02472 Biopolymer transport protein ExbD 2FTolR identified within CDS. Also 2Cone probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli with acceptable identity scores. Thus 2C not added. Cj0179-Cj0181 28exbB1 2C exbD1 2CtonB1 29 function as an outer-membrane energy transducer system. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:7642501 2C PMID:8437515 2C PMID:15632442 2CPMID:12069882 NC_002163.1 RefSeq region 176815 177195 . + . ID=id454;gene=exbD1;Name=id454;Dbxref=GeneID:904523;gbkey=misc_feature;Note=HMMPfam hit to PF02472 2C Biopolymer transport protein ExbD 2FTolR 2C score 8.4e-22 NC_002163.1 RefSeq region 176827 176895 . + . ID=id455;gene=exbD1;Name=id455;Dbxref=GeneID:904523;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0180 by TMHMM2.0 at aa 13-35 ### NC_002163.1 RefSeq gene 177203 177949 . + . ID=gene173;gene=tonB1;Name=tonB1;locus_tag=Cj0181;Dbxref=GeneID:904524;gbkey=Gene NC_002163.1 RefSeq CDS 177203 177949 . + 0 ID=cds164;Parent=gene173;gene=tonB1;Name=YP_002343639.1;Dbxref=GOA:Q0PBV8 InterPro:IPR006260 UniProtKB FTrEMBL:Q0PBV8 Genbank:YP_002343639.1 GeneID:904524;gbkey=CDS;product=TonB transport protein;Note=Original 282000 29 note: Cj0181 2C tonB1 2C possible tonB transport protein 2C len 248 aa 3B similar to e.g. TONB_PSEPU tonB protein 28243 aa 29 2C fasta scores 3B opt: 220 z-score: 317.2 E 28 29: 2.1e-10 2C 29.5 25 identity in 149 aa overlap. No Hp match 7EUpdated 282006 29 note: One probable transmembrane helices predicted by TMHMM2.0. Characterised within Pseudomonas putida with marginal identity score. not added. Cj0179-Cj0181 28exbB1 2C exbD1 2C tonB1 29 function as an outer-membrane energy transducer system. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:7642501 2C PMID:8437515 2C PMID:15632442 2CPMID:12069882 NC_002163.1 RefSeq region 177221 177289 . + . ID=id456;gene=tonB1;Name=id456;Dbxref=GeneID:904524;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0181 by TMHMM2.0 at aa 7-29 ### NC_002163.1 UTR_Extractor 5'-UTR 177984 177994 . + . ID=utr65;locus_tag=Cj0182;product=putative transporter NC_002163.1 RefSeq CDS 177995 179200 . + 0 ID=cds165;Parent=gene174;Name=YP_002343640.1;Dbxref=GOA:Q0PBV7 InterPro:IPR009248 InterPro:IPR011527 UniProtKB FTrEMBL:Q0PBV7 Genbank:YP_002343640.1 GeneID:904525;gbkey=CDS;product=transporter;Note=in Escherichia coli SbmA is involved in uptake of microcin J25 3B functions along with FhuA 2C TonB 2C and ExbB 2FD in this capacity 3B in Sinorhizobium meliloti 2C BacA is essential and required for symbiosis 3B defects appear to affect the cell envelope NC_002163.1 RefSeq gene 177995 179200 . + . ID=gene174;Name=Cj0182;locus_tag=Cj0182;Dbxref=GeneID:904525;gbkey=Gene NC_002163.1 RefSeq region 178031 178099 . + . ID=id457;Name=id457;Dbxref=GeneID:904525;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0182 by TMHMM2.0 at aa 13-35 2C 127-149 2C 197-219 2C 244-266 2C316-330 and 334-356 NC_002163.1 RefSeq region 178373 178441 . + . ID=id457;Name=id457;Dbxref=GeneID:904525;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0182 by TMHMM2.0 at aa 13-35 2C 127-149 2C 197-219 2C 244-266 2C316-330 and 334-356 NC_002163.1 RefSeq region 178583 178651 . + . ID=id457;Name=id457;Dbxref=GeneID:904525;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0182 by TMHMM2.0 at aa 13-35 2C 127-149 2C 197-219 2C 244-266 2C316-330 and 334-356 NC_002163.1 RefSeq region 178724 178792 . + . ID=id457;Name=id457;Dbxref=GeneID:904525;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0182 by TMHMM2.0 at aa 13-35 2C 127-149 2C 197-219 2C 244-266 2C316-330 and 334-356 NC_002163.1 RefSeq region 178940 178984 . + . ID=id457;Name=id457;Dbxref=GeneID:904525;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0182 by TMHMM2.0 at aa 13-35 2C 127-149 2C 197-219 2C 244-266 2C316-330 and 334-356 NC_002163.1 RefSeq region 178994 179062 . + . ID=id457;Name=id457;Dbxref=GeneID:904525;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0182 by TMHMM2.0 at aa 13-35 2C 127-149 2C 197-219 2C 244-266 2C316-330 and 334-356 ### NC_002163.1 UTR_Extractor 5'-UTR 179270 179298 . + . ID=utr66;locus_tag=Cj0183;product=putative integral membrane protein NC_002163.1 RefSeq CDS 179299 180657 . + 0 ID=cds166;Parent=gene175;Name=YP_002343641.1;Dbxref=GOA:Q0PBV6 InterPro:IPR000644 InterPro:IPR002550 InterPro:IPR005170 UniProtKB FTrEMBL:Q0PBV6 Genbank:YP_002343641.1 GeneID:904526;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0183 2C probable integral membrane protein with haemolysin domain 2C len: 452 aa 3B similar to many members of the UPF0053 family e.g. YUGS_BACSU 28434 aa 29 2C fasta scores 3B opt: 999 z-score: 1508.9 E 28 29: 0 2C 38.1 25 identity in 430 aa overlap. Also similar in C-terminal half to haemolysins e.g. HLYC_TREHY Treponema hyodysenteriae hemolysin C 28268 aa 29 2C fasta scores 3B opt: 447 z-score: 468.1 E 28 29: 8.1e-19 2C 32.5 25 identity in 237 aa overlap. 54.3 25 identity to HP1490. Contains 2x Pfam match to entry PF00571 CBS 2C CBS domain 2Cscores 26.10 2C E-value 0.00082 and 40.50 2C E-value 3.7e-08 7EUpdated 282006 29 note: Four probable transmembrane helices predicted by TMHMM2.0. No specific characterisation with acceptable identity scores identified yet. Thus 2C kept within product function. Functional classification - Pathogenicity NC_002163.1 RefSeq gene 179299 180657 . + . ID=gene175;Name=Cj0183;locus_tag=Cj0183;Dbxref=GeneID:904526;gbkey=Gene NC_002163.1 RefSeq region 179356 179424 . + . ID=id458;Name=id458;Dbxref=GeneID:904526;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0183 by TMHMM2.0 at aa 20-42 2C 75-97 2C 117-139 and 162-184 NC_002163.1 RefSeq region 179368 179961 . + . ID=id459;Name=id459;Dbxref=GeneID:904526;gbkey=misc_feature;Note=HMMPfam hit to PF01595 2C Domain of unknown function DUF21 2C score 3.2e-83 NC_002163.1 RefSeq region 179521 179589 . + . ID=id458;Name=id458;Dbxref=GeneID:904526;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0183 by TMHMM2.0 at aa 20-42 2C 75-97 2C 117-139 and 162-184 NC_002163.1 RefSeq region 179647 179715 . + . ID=id458;Name=id458;Dbxref=GeneID:904526;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0183 by TMHMM2.0 at aa 20-42 2C 75-97 2C 117-139 and 162-184 NC_002163.1 RefSeq region 179782 179850 . + . ID=id458;Name=id458;Dbxref=GeneID:904526;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0183 by TMHMM2.0 at aa 20-42 2C 75-97 2C 117-139 and 162-184 NC_002163.1 RefSeq region 180016 180180 . + . ID=id460;Name=id460;Dbxref=GeneID:904526;gbkey=misc_feature;Note=HMMPfam hit to PF00571 2C CBS domain 2C score 2.5e-08 NC_002163.1 RefSeq region 180202 180363 . + . ID=id461;Name=id461;Dbxref=GeneID:904526;gbkey=misc_feature;Note=HMMPfam hit to PF00571 2C CBS domain 2C score 6.5e-12 NC_002163.1 RefSeq region 180400 180639 . + . ID=id462;Name=id462;Dbxref=GeneID:904526;gbkey=misc_feature;Note=HMMPfam hit to PF03471 2C Transporter associated domain 2C score 1.3e-22 ### NC_002163.1 RefSeq gene 180702 181856 . - . ID=gene176;Name=Cj0184c;locus_tag=Cj0184c;Dbxref=GeneID:904527;gbkey=Gene NC_002163.1 RefSeq CDS 180702 181856 . - 0 ID=cds167;Parent=gene176;Name=YP_002343642.1;Dbxref=GOA:Q0PBV5 InterPro:IPR004843 InterPro:IPR006186 UniProtKB FTrEMBL:Q0PBV5 Genbank:YP_002343642.1 GeneID:904527;gbkey=CDS;product=serine 2Fthreonine protein phosphatase;Note=Original 282000 29 note: Cj0184c 2C possible serine 2Fthreonine protein phosphatase 2C len: 384 aa 3B similar in part to many eukarotic serine 2Fthreonine protein phosphatases e.g. PP12_SCHPO serine 2Fthreonine protein phosphatase PP1-2 28322 aa 29 2C fasta scores 3B opt: 140 z-score: 290.0 E 28 29: 6.8e-09 2C 31.3 25 identity in 131 aa overlap. No Hp match. Contains Pfam match to entry PF00149 STphosphatase 2C Ser 2FThr protein phosphatases 2C score 6.90 2CE-value 0.39 7EUpdated 282006 29 note: Pfam domain PF00149 STphosphatase was changed in Pfam database to Calcineurin-like phosphoesterase. Characterisation work has been carried out mainly in eukaryotes with marginal identity scores. Possible was changed to . Functional classification - Signal transduction NC_002163.1 RefSeq region 180813 181355 . - . ID=id463;Name=id463;Dbxref=GeneID:904527;gbkey=misc_feature;Note=HMMPfam hit to PF00149 2C Calcineurin-like phosphoesterase 2C score 6.6e-12 ### NC_002163.1 RefSeq region 181911 182075 . - . ID=id464;Name=id464;gbkey=misc_feature;Note=HMMPfam hit to PF03831 2C PhnA protein 2C score 3.1e-30 NC_002163.1 RefSeq gene 182068 182787 . - . ID=gene177;Name=Cj0186c;locus_tag=Cj0186c;Dbxref=GeneID:904529;gbkey=Gene NC_002163.1 RefSeq CDS 182068 182787 . - 0 ID=cds168;Parent=gene177;Name=YP_002343644.1;Dbxref=GOA:Q0PBV3 InterPro:IPR005496 UniProtKB FTrEMBL:Q0PBV3 Genbank:YP_002343644.1 GeneID:904529;gbkey=CDS;product=TerC family integral membrane protein;Note=Original 282000 29 note: Cj0186c 2C probable integral membrane protein 2C len: 239 aa 3B similar to many hypothetical proteins e.g. YGDQ_HAEIN HI0056 28237 aa 29 2Cfasta scores 3B opt: 964 z-score: 1727.7 E 28 29: 0 2C 64.3 25 identity in 230 aa overlap. 50.0 25 identity to HP1343 7EUpdated 282006 29 note: Pfam domain PF03741 Integral membrane protein TerC family was identified within CDS. Seven probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Product modified to more specific family member based on motif match. No specific characterisation with acceptable identity scores has been carried out yet. Thus 2C kept within product function. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 182095 182151 . - . ID=id15;Name=id15;Dbxref=GeneID:904529;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0186c by TMHMM2.0 at aa 15-37 2C 50-69 2C 84-103 2C 124-146 2C151-173 2C 186-203 and 213-231 NC_002163.1 RefSeq region 182110 182751 . - . ID=id465;Name=id465;Dbxref=GeneID:904529;gbkey=misc_feature;Note=HMMPfam hit to PF03741 2C Integral membrane protein TerC family 2C score 2.9e-96 NC_002163.1 RefSeq region 182179 182232 . - . ID=id15;Name=id15;Dbxref=GeneID:904529;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0186c by TMHMM2.0 at aa 15-37 2C 50-69 2C 84-103 2C 124-146 2C151-173 2C 186-203 and 213-231 NC_002163.1 RefSeq region 182269 182337 . - . ID=id15;Name=id15;Dbxref=GeneID:904529;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0186c by TMHMM2.0 at aa 15-37 2C 50-69 2C 84-103 2C 124-146 2C151-173 2C 186-203 and 213-231 NC_002163.1 RefSeq region 182350 182418 . - . ID=id15;Name=id15;Dbxref=GeneID:904529;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0186c by TMHMM2.0 at aa 15-37 2C 50-69 2C 84-103 2C 124-146 2C151-173 2C 186-203 and 213-231 NC_002163.1 RefSeq region 182479 182538 . - . ID=id15;Name=id15;Dbxref=GeneID:904529;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0186c by TMHMM2.0 at aa 15-37 2C 50-69 2C 84-103 2C 124-146 2C151-173 2C 186-203 and 213-231 NC_002163.1 RefSeq region 182581 182640 . - . ID=id15;Name=id15;Dbxref=GeneID:904529;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0186c by TMHMM2.0 at aa 15-37 2C 50-69 2C 84-103 2C 124-146 2C151-173 2C 186-203 and 213-231 NC_002163.1 RefSeq region 182677 182745 . - . ID=id15;Name=id15;Dbxref=GeneID:904529;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0186c by TMHMM2.0 at aa 15-37 2C 50-69 2C 84-103 2C 124-146 2C151-173 2C 186-203 and 213-231 ### NC_002163.1 UTR_Extractor 5'-UTR 182788 182820 . - . ID=utr67;locus_tag=Cj0186c;product=putative TerC family integral membrane protein NC_002163.1 RefSeq CDS 182859 183425 . - 0 ID=cds169;Parent=gene178;gene=purN;Name=YP_002343645.1;Dbxref=GOA:Q0PBV2 InterPro:IPR002376 InterPro:IPR004607 UniProtKB FTrEMBL:Q0PBV2 Genbank:YP_002343645.1 GeneID:904530;gbkey=CDS;product=phosphoribosylglycinamide formyltransferase;Note=Original 282000 29 note: Cj0187c 2C purN 2C probable phosphoribosylglycinamide formyltransferase 2C len: 188 aa 3B similar to e.g. PUR3_ECOLI phosphoribosylglycinamide formyltransferase 28EC 2.1.2.2 29 28212 aa 29 2C fasta scores 3B opt: 406 z-score: 654.6 E 28 29: 3.3e-29 2C 38.6 25 identity in 189 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00551 formyl_transf 2C Formyl transferase 2C score 177.90 2C E-value 4.4e-50 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity scores. not added to product function. Functional classification -Purine ribonucleotide biosynthesis 7EPMID:3301838 NC_002163.1 RefSeq gene 182859 183425 . - . ID=gene178;gene=purN;Name=purN;locus_tag=Cj0187c;Dbxref=GeneID:904530;gbkey=Gene NC_002163.1 RefSeq region 182877 183419 . - . ID=id466;gene=purN;Name=id466;Dbxref=GeneID:904530;gbkey=misc_feature;Note=HMMPfam hit to PF00551 2C Formyl transferase 2C score 2.9e-50 NC_002163.1 RefSeq gene 183416 184786 . - . ID=gene179;gene=Cj0188c;Name=Cj0188c;locus_tag=Cj0188c;Dbxref=GeneID:904531;gbkey=Gene NC_002163.1 RefSeq CDS 183416 184786 . - 0 ID=cds170;Parent=gene179;Name=YP_002343646.1;Dbxref=GOA:Q0PBV1 InterPro:IPR000631 InterPro:IPR004443 UniProtKB FTrEMBL:Q0PBV1 Genbank:YP_002343646.1 GeneID:904531;gbkey=CDS;product=kinase;Note=Original 282000 29 note: Cj0188c 2C unknown 2C len: 456 aa 3B similar to members of the UPF0031 family e.g. YJEF_ECOLI 28515 aa 29 2C fasta scores 3B opt: 267 z-score: 441.8 E 28 29: 2.4e-17 2C 29.9 25 identity in 418 aa overlap. 35.9 25 identity to HP1363. Contains PS01050 Uncharacterized protein family UPF0031 signature 2 and Pfam match to entry PF01256 UPF0031 2C Uncharacterized protein family UPF0031 2Cscore 96.30 2C E-value 6e-25 7EUpdated 282006 29 note: Previous uncharacterised Pfam motifs have now been designated as PF01256 Carbohydrate kinase and PF03853 YjeF-related protein N-terminus. Product modified to more specific family member based on motif match. No specific characterisation has yet been carried out. kept within product function. Functional classification - Misc NC_002163.1 RefSeq region 183422 184087 . - . ID=id467;Name=id467;Dbxref=GeneID:904531;gbkey=misc_feature;Note=HMMPfam hit to PF01256 2C Carbohydrate kinase 2C score 4.5e-26 NC_002163.1 UTR_Extractor 5'-UTR 183426 183609 . - . ID=utr68;locus_tag=Cj0187c;product=phosphoribosylglycinamide formyltransferase NC_002163.1 RefSeq region 183560 183592 . - . ID=id468;Name=id468;Dbxref=GeneID:904531;gbkey=misc_feature;Note=PS01050 Uncharacterized protein family UPF0031 signature 2 NC_002163.1 RefSeq region 184253 184735 . - . ID=id469;Name=id469;Dbxref=GeneID:904531;gbkey=misc_feature;Note=HMMPfam hit to PF03853 2C YjeF-related protein N-terminus 2C score 2.1e-54 NC_002163.1 RefSeq CDS 184770 185468 . - 0 ID=cds171;Parent=gene180;Name=YP_002343647.1;Dbxref=InterPro:IPR002790 UniProtKB FTrEMBL:Q0PBV0 Genbank:YP_002343647.1 GeneID:904532;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0189c 2C unknown 2C len: 232 aa 3B similar to hypothetical proteins e.g. TR:P73622 28EMBL:D90908 29 Synechocystis sp. 28249 aa 29 2C fasta scores 3B opt: 351 z-score: 629.7 E 28 29: 8.1e-28 2C 30.1 25 identity in 246 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam PF01936 Protein of unknown function 28DUF88 29 was present within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 184770 185468 . - . ID=gene180;Name=Cj0189c;locus_tag=Cj0189c;Dbxref=GeneID:904532;gbkey=Gene NC_002163.1 RefSeq region 185037 185462 . - . ID=id470;Name=id470;Dbxref=GeneID:904532;gbkey=misc_feature;Note=HMMPfam hit to PF01936 2C Protein of unknown function DUF88 2C score 1.1e-05 ### NC_002163.1 RefSeq CDS 185470 186975 . - 0 ID=cds172;Parent=gene181;Name=YP_002343648.1;Dbxref=GOA:Q0PBU9 InterPro:IPR000523 InterPro:IPR004482 UniProtKB FTrEMBL:Q0PBU9 Genbank:YP_002343648.1 GeneID:904533;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0190c 2C unknown 2C len: 501 aa 3B similar to prokaryotic hypothetical proteins e.g. YIFB_ECOLI 28516 aa 29 2C fasta scores 3B opt: 670 z-score: 1088.3 E 28 29: 0 2C 34.0 25 identity in 497 aa overlap 2C and more distantly to members of the eukaryotic MCM family of DNA replication regulatory factors e.g. MCM6_RAT DNA replication licensing factor MCM6 28509 aa 29 2C fasta scores 3B opt: 152 z-score: 247.8 E 28 29: 1.5e-06 2C 23.5 25 identity in 345 aa overlap. 47.7 25 identity to HP0792 28anotated as sigma-54 interacting protein 29. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 and Pfam match to entry PF01078 Mg_chelatase 2C Magnesium chelatase 2C subunit ChlI 2C score 127.80 2C E-value 2e-34. Functional classification - Misc NC_002163.1 RefSeq gene 185470 186975 . - . ID=gene181;Name=Cj0190c;locus_tag=Cj0190c;Dbxref=GeneID:904533;gbkey=Gene NC_002163.1 RefSeq region 185923 186927 . - . ID=id471;Name=id471;Dbxref=GeneID:904533;gbkey=misc_feature;Note=HMMPfam hit to PF01078 2C Magnesium chelatase 2Csubunit ChlI 2C score 9.4e-40 NC_002163.1 RefSeq region 186277 186300 . - . ID=id472;Name=id472;Dbxref=GeneID:904533;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 186972 187499 . - 0 ID=cds173;Parent=gene182;gene=def;Name=YP_002343649.1;Dbxref=GOA:Q9PIT8 HSSP:Q9I7A8 InterPro:IPR000181 UniProtKB FSwiss-Prot:Q9PIT8 Genbank:YP_002343649.1 GeneID:904534;gbkey=CDS;product=peptide deformylase;Note=cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins 3B binds iron 282 2B 29 NC_002163.1 RefSeq gene 186972 187499 . - . ID=gene182;gene=def;Name=def;locus_tag=Cj0191c;Dbxref=GeneID:904534;gbkey=Gene NC_002163.1 RefSeq region 187026 187496 . - . ID=id473;gene=def;Name=id473;Dbxref=GeneID:904534;gbkey=misc_feature;Note=HMMPfam hit to PF01327 2C Polypeptide deformylase 2Cscore 4.7e-50 ### NC_002163.1 RefSeq CDS 187535 188119 . - 0 ID=cds174;Parent=gene183;gene=clpP;Name=YP_002343650.1;Dbxref=GOA:P54413 HSSP:P19245 InterPro:IPR001907 UniProtKB FSwiss-Prot:P54413 Genbank:YP_002343650.1 GeneID:906014;gbkey=CDS;product=ATP-dependent Clp protease proteolytic subunit;Note=hydrolyzes proteins to small peptides 3B with the ATPase subunits ClpA or ClpX 2C ClpP degrades specific substrates NC_002163.1 RefSeq gene 187535 188119 . - . ID=gene183;gene=clpP;Name=clpP;locus_tag=Cj0192c;Dbxref=GeneID:906014;gbkey=Gene NC_002163.1 RefSeq region 187544 188089 . - . ID=id474;gene=clpP;Name=id474;Dbxref=GeneID:906014;gbkey=misc_feature;Note=HMMPfam hit to PF00574 2C Clp protease 2C score 4e-136 NC_002163.1 RefSeq region 187748 187789 . - . ID=id475;gene=clpP;Name=id475;Dbxref=GeneID:906014;gbkey=misc_feature;Note=PS00382 Endopeptidase Clp histidine active site NC_002163.1 RefSeq region 187805 187837 . - . ID=id476;gene=clpP;Name=id476;Dbxref=GeneID:906014;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 187820 187855 . - . ID=id477;gene=clpP;Name=id477;Dbxref=GeneID:906014;gbkey=misc_feature;Note=PS00381 Endopeptidase Clp serine active site NC_002163.1 RefSeq CDS 188119 189453 . - 0 ID=cds175;Parent=gene184;gene=tig;Name=YP_002343651.1;Dbxref=GOA:Q46108 HSSP:P47480 InterPro:IPR001179 InterPro:IPR005215 InterPro:IPR008880 InterPro:IPR008881 UniProtKB FSwiss-Prot:Q46108 Genbank:YP_002343651.1 GeneID:904535;gbkey=CDS;product=trigger factor;Note=Tig 3B RopA 3B peptidyl-prolyl cis 2Ftrans isomerase 3B promotes folding of newly synthesized proteins 3B binds ribosomal 50S subunit 3B forms a homodimer NC_002163.1 RefSeq gene 188119 189453 . - . ID=gene184;gene=tig;Name=tig;locus_tag=Cj0193c;Dbxref=GeneID:904535;gbkey=Gene NC_002163.1 RefSeq region 188185 188727 . - . ID=id478;gene=tig;Name=id478;Dbxref=GeneID:904535;gbkey=misc_feature;Note=HMMPfam hit to PF05698 2C Bacterial trigger factor protein 28TF 29 C-ter 2C score 2e-42 NC_002163.1 RefSeq region 188728 188985 . - . ID=id479;gene=tig;Name=id479;Dbxref=GeneID:904535;gbkey=misc_feature;Note=HMMPfam hit to PF00254 2C FKBP-type peptidyl-prolyl cis-trans isomera 2C score 1.2e-27 NC_002163.1 RefSeq region 188995 189453 . - . ID=id480;gene=tig;Name=id480;Dbxref=GeneID:904535;gbkey=misc_feature;Note=HMMPfam hit to PF05697 2C Bacterial trigger factor protein 28TF 29 2C score 1.3e-44 ### NC_002163.1 UTR_Extractor 5'-UTR 189454 189481 . - . ID=utr69;locus_tag=Cj0193c;product=trigger factor NC_002163.1 UTR_Extractor 5'-UTR 189552 189595 . + . ID=utr70;locus_tag=Cj0194;product=GTP cyclohydrolase I NC_002163.1 RefSeq CDS 189596 190168 . + 0 ID=cds176;Parent=gene185;gene=folE;Name=YP_002343652.1;Dbxref=GOA:P51594 HSSP:P22288 InterPro:IPR001474 UniProtKB FSwiss-Prot:P51594 Genbank:YP_002343652.1 GeneID:904536;gbkey=CDS;product=GTP cyclohydrolase I;Note=involved in the first step of tetrahydrofolate biosynthesis 3B catalyzes the formation of formate and 2-amino-4-hydroxy-6- 28erythro-1 2C2 2C3-trihydroxypropyl 29dihydropteridine triphosphate from GTP and water 3B forms a homopolymer NC_002163.1 RefSeq gene 189596 190168 . + . ID=gene185;gene=folE;Name=folE;locus_tag=Cj0194;Dbxref=GeneID:904536;gbkey=Gene NC_002163.1 RefSeq region 189779 189829 . + . ID=id482;gene=folE;Name=id482;Dbxref=GeneID:904536;gbkey=misc_feature;Note=PS00859 GTP cyclohydrolase I signature 1 NC_002163.1 RefSeq region 189779 190093 . + . ID=id481;gene=folE;Name=id481;Dbxref=GeneID:904536;gbkey=misc_feature;Note=HMMPfam hit to PF01227 2C GTP cyclohydrolase I 2C score 9.9e-56 NC_002163.1 RefSeq gene 190168 191553 . + . ID=gene186;gene=fliI;Name=fliI;locus_tag=Cj0195;Dbxref=GeneID:904537;gbkey=Gene NC_002163.1 RefSeq CDS 190168 191553 . + 0 ID=cds177;Parent=gene186;gene=fliI;Name=YP_002343653.1;Dbxref=GOA:Q0PBU4 InterPro:IPR000194 InterPro:IPR003593 InterPro:IPR005714 InterPro:IPR013379 UniProtKB FTrEMBL:Q0PBU4 Genbank:YP_002343653.1 GeneID:904537;gbkey=CDS;product=flagellum-specific ATP synthase;Note=involved in type III protein export during flagellum assembly NC_002163.1 RefSeq region 190597 191229 . + . ID=id483;gene=fliI;Name=id483;Dbxref=GeneID:904537;gbkey=misc_feature;Note=HMMPfam hit to PF00006 2C ATP synthase alpha 2Fbeta family 2C nucleotid 2C score 4.1e-104 NC_002163.1 RefSeq region 190660 190683 . + . ID=id484;gene=fliI;Name=id484;Dbxref=GeneID:904537;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 191200 191229 . + . ID=id485;gene=fliI;Name=id485;Dbxref=GeneID:904537;gbkey=misc_feature;Note=PS00152 ATP synthase alpha and beta subunits signature ### NC_002163.1 RefSeq CDS 191556 192893 . - 0 ID=cds178;Parent=gene187;gene=purF;Name=YP_002343654.1;Dbxref=GOA:Q0PBU3 InterPro:IPR000583 InterPro:IPR000836 InterPro:IPR002375 InterPro:IPR005854 UniProtKB FTrEMBL:Q0PBU3 Genbank:YP_002343654.1 GeneID:904538;gbkey=CDS;product=amidophosphoribosyltransferase;Note=Catalyzes first step of the de novo purine nucleotide biosynthetic pathway NC_002163.1 RefSeq gene 191556 192893 . - . ID=gene187;gene=purF;Name=purF;locus_tag=Cj0196c;Dbxref=GeneID:904538;gbkey=Gene NC_002163.1 RefSeq region 191730 192149 . - . ID=id486;gene=purF;Name=id486;Dbxref=GeneID:904538;gbkey=misc_feature;Note=HMMPfam hit to PF00156 2C Phosphoribosyl transferase domain 2C score 2.2e-12 NC_002163.1 RefSeq region 191829 191867 . - . ID=id487;gene=purF;Name=id487;Dbxref=GeneID:904538;gbkey=misc_feature;Note=PS00103 Purine 2Fpyrimidine phosphoribosyl transferases signature NC_002163.1 RefSeq region 192306 192890 . - . ID=id488;gene=purF;Name=id488;Dbxref=GeneID:904538;gbkey=misc_feature;Note=HMMPfam hit to PF00310 2C Glutamine amidotransferases class-II 2C score 2.8e-27 ### NC_002163.1 RefSeq CDS 192895 193623 . - 0 ID=cds179;Parent=gene188;gene=dapB;Name=YP_002343655.1;Dbxref=GOA:Q9PIT2 HSSP:P04036 InterPro:IPR000846 InterPro:IPR011770 InterPro:IPR016040 UniProtKB FSwiss-Prot:Q9PIT2 Genbank:YP_002343655.1 GeneID:904539;gbkey=CDS;product=dihydrodipicolinate reductase;Note=catalyzes the reduction of 2 2C3-dihydrodipicolinate to 2 2C3 2C4 2C5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis NC_002163.1 RefSeq gene 192895 193623 . - . ID=gene188;gene=dapB;Name=dapB;locus_tag=Cj0197c;Dbxref=GeneID:904539;gbkey=Gene NC_002163.1 RefSeq region 192901 193311 . - . ID=id489;gene=dapB;Name=id489;Dbxref=GeneID:904539;gbkey=misc_feature;Note=HMMPfam hit to PF05173 2C Dihydrodipicolinate reductase 2C C-terminus 2C score 1e-75 NC_002163.1 RefSeq region 193195 193248 . - . ID=id490;gene=dapB;Name=id490;Dbxref=GeneID:904539;gbkey=misc_feature;Note=PS01298 Dihydrodipicolinate reductase signature NC_002163.1 RefSeq region 193318 193620 . - . ID=id491;gene=dapB;Name=id491;Dbxref=GeneID:904539;gbkey=misc_feature;Note=HMMPfam hit to PF01113 2C Dihydrodipicolinate reductase 2C N-terminus 2C score 1.7e-38 ### NC_002163.1 UTR_Extractor 5'-UTR 193624 193645 . - . ID=utr71;locus_tag=Cj0197c;product=dihydrodipicolinate reductase NC_002163.1 RefSeq CDS 193686 194867 . - 0 ID=cds180;Parent=gene189;Name=YP_002343656.1;Dbxref=GOA:Q0PBU1 InterPro:IPR003593 InterPro:IPR003959 UniProtKB FTrEMBL:Q0PBU1 Genbank:YP_002343656.1 GeneID:904540;gbkey=CDS;product=recombination factor protein RarA;Note=Original 282000 29 note: Cj0198c 2C unknown 2C len: 393 aa 3B similar to hypothetical proteins e.g. YCAJ_ECOLI 28447 aa 29 2C fasta scores 3B opt: 339 z-score: 796.4 E 28 29: 0 2C 32.8 25 identity in 381 aa overlap 2C and less strongly to several helicases e.g. RUVB_HELPY holliday junction DNA helicase ruvB 28336 aa 29 2C fasta scores 3B opt: 204 z-score: 280.5 E 28 29: 2.3e-08 2C 28.8 25 identity in 278 aa overlap. 49.9 25 identity to HP1026. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 7EUpdated 282006 29 note: Pfam domain PF00004 ATPase family associated with various cellular activities 28AAA 29 2Cwas identified within CDS. Further support given to product function. No specific characterisation has been carried out yet. Product function unchanged. Functional classification - DNA replication 2Crestriction 2Fmodification 2C recombination and repair NC_002163.1 RefSeq gene 193686 194867 . - . ID=gene189;Name=Cj0198c;locus_tag=Cj0198c;Dbxref=GeneID:904540;gbkey=Gene NC_002163.1 RefSeq region 194262 194762 . - . ID=id492;Name=id492;Dbxref=GeneID:904540;gbkey=misc_feature;Note=HMMPfam hit to PF00004 2C ATPase family associated with various cellul 2C score 6.5e-07 NC_002163.1 RefSeq region 194724 194747 . - . ID=id493;Name=id493;Dbxref=GeneID:904540;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 194867 195988 . - 0 ID=cds181;Parent=gene190;Name=YP_002343657.1;Dbxref=UniProtKB FTrEMBL:Q0PBU0 Genbank:YP_002343657.1 GeneID:904542;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0199c 2C probable periplasmic protein 2C len: 373 aa 3B no Hp match. Contains N-terminal signal sequence. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 194867 195988 . - . ID=gene190;Name=Cj0199c;locus_tag=Cj0199c;Dbxref=GeneID:904542;gbkey=Gene NC_002163.1 RefSeq region 195917 195976 . - . ID=id494;Name=id494;Dbxref=GeneID:904542;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0199c by TMHMM2.0 at aa 5-24 ### NC_002163.1 UTR_Extractor 5'-UTR 195989 196010 . - . ID=utr72;locus_tag=Cj0199c;product=putative periplasmic protein NC_002163.1 RefSeq gene 196123 196470 . - . ID=gene191;Name=Cj0200c;locus_tag=Cj0200c;Dbxref=GeneID:904543;gbkey=Gene NC_002163.1 RefSeq CDS 196123 196470 . - 0 ID=cds182;Parent=gene191;Name=YP_002343658.1;Dbxref=GOA:Q0PBT9 UniProtKB FTrEMBL:Q0PBT9 Genbank:YP_002343658.1 GeneID:904543;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0200c 2C probable periplasmic protein 2C len: 115 aa 3B no Hp match. Contains N-terminal signal sequence 7EUpdated 282006 29 note: Literature search papers giving further clues to product function. Paper 28PMID:12186869 29 links protein to glycoprotein. Functional classification - Miscellaneous periplasmic proteins 7EPMID:15554967 2C PMID:12186869 NC_002163.1 UTR_Extractor 5'-UTR 196471 196494 . - . ID=utr73;locus_tag=Cj0200c;product=putative periplasmic protein NC_002163.1 RefSeq CDS 196534 197139 . - 0 ID=cds183;Parent=gene192;Name=YP_002343659.1;Dbxref=UniProtKB FTrEMBL:Q0PBT8 Genbank:YP_002343659.1 GeneID:904544;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0201c 2C probable integral membrane protein 2C len: 201 aa 3B no Hp match. Contains possible transmembrane domain at N-terminus and PS00216 Sugar transport proteins signature 1. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 196534 197139 . - . ID=gene192;Name=Cj0201c;locus_tag=Cj0201c;Dbxref=GeneID:904544;gbkey=Gene NC_002163.1 RefSeq region 196711 196758 . - . ID=id495;Name=id495;Dbxref=GeneID:904544;gbkey=misc_feature;Note=PS00216 Sugar transport proteins signature 1 NC_002163.1 RefSeq region 197062 197121 . - . ID=id496;Name=id496;Dbxref=GeneID:904544;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0201c by TMHMM2.0 at aa 7-26 ### NC_002163.1 UTR_Extractor 5'-UTR 197465 197542 . - . ID=utr74;locus_tag=Cj0202c;product=hypothetical protein NC_002163.1 UTR_Extractor 5'-UTR 197601 197706 . + . ID=utr75;locus_tag=Cj0203;product=putative citrate transporter NC_002163.1 RefSeq CDS 197707 199053 . + 0 ID=cds184;Parent=gene193;Name=YP_002343661.1;Dbxref=GOA:Q0PBT6 InterPro:IPR004680 InterPro:IPR014738 UniProtKB FTrEMBL:Q0PBT6 Genbank:YP_002343661.1 GeneID:904545;gbkey=CDS;product=citrate transporter;Note=Original 282000 29 note: Cj0203 2C probable transmembrane transport protein 2C len: 448 aa 3B some similarity to e.g. CITM_BACSU Mg2 2B 2Fcitrate complex secondary transporter 28433 aa 29 2C fasta scores 3B opt: 702 z-score: 964.3 E 28 29: 0 2C 28.7 25 identity in 449 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF03600 Citrate transporter was identified within CDS. Twelve probable transmembrane helices predicted by TMHMM2.0. Product modified to more specific family member due to motif match. Some characterisation work has been carried out within Bacillus subtilis 2C however 2C identity scores were marginal. kept within product function. Functional classification - Transport 2Fbinding proteins -Other 7EPMID:8892821 NC_002163.1 RefSeq gene 197707 199053 . + . ID=gene193;Name=Cj0203;locus_tag=Cj0203;Dbxref=GeneID:904545;gbkey=Gene NC_002163.1 RefSeq region 197716 197769 . + . ID=id497;Name=id497;Dbxref=GeneID:904545;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0203 by TMHMM2.0 at aa 4-21 2C 28-45 2C 50-72 2C 84-106 2C126-148 2C 161-180 2C 195-217 2C 249-282 2C 302-321 2C 341-363 2C373-395 and 428-447 NC_002163.1 RefSeq region 197728 198906 . + . ID=id498;Name=id498;Dbxref=GeneID:904545;gbkey=misc_feature;Note=HMMPfam hit to PF03600 2C Citrate transporter 2C score 7.1e-122 NC_002163.1 RefSeq region 197788 197841 . + . ID=id497;Name=id497;Dbxref=GeneID:904545;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0203 by TMHMM2.0 at aa 4-21 2C 28-45 2C 50-72 2C 84-106 2C126-148 2C 161-180 2C 195-217 2C 249-282 2C 302-321 2C 341-363 2C373-395 and 428-447 NC_002163.1 RefSeq region 197794 197826 . + . ID=id499;Name=id499;Dbxref=GeneID:904545;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 197854 197922 . + . ID=id497;Name=id497;Dbxref=GeneID:904545;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0203 by TMHMM2.0 at aa 4-21 2C 28-45 2C 50-72 2C 84-106 2C126-148 2C 161-180 2C 195-217 2C 249-282 2C 302-321 2C 341-363 2C373-395 and 428-447 NC_002163.1 RefSeq region 197956 198024 . + . ID=id497;Name=id497;Dbxref=GeneID:904545;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0203 by TMHMM2.0 at aa 4-21 2C 28-45 2C 50-72 2C 84-106 2C126-148 2C 161-180 2C 195-217 2C 249-282 2C 302-321 2C 341-363 2C373-395 and 428-447 NC_002163.1 RefSeq region 198082 198150 . + . ID=id497;Name=id497;Dbxref=GeneID:904545;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0203 by TMHMM2.0 at aa 4-21 2C 28-45 2C 50-72 2C 84-106 2C126-148 2C 161-180 2C 195-217 2C 249-282 2C 302-321 2C 341-363 2C373-395 and 428-447 NC_002163.1 RefSeq region 198187 198246 . + . ID=id497;Name=id497;Dbxref=GeneID:904545;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0203 by TMHMM2.0 at aa 4-21 2C 28-45 2C 50-72 2C 84-106 2C126-148 2C 161-180 2C 195-217 2C 249-282 2C 302-321 2C 341-363 2C373-395 and 428-447 NC_002163.1 RefSeq region 198289 198357 . + . ID=id497;Name=id497;Dbxref=GeneID:904545;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0203 by TMHMM2.0 at aa 4-21 2C 28-45 2C 50-72 2C 84-106 2C126-148 2C 161-180 2C 195-217 2C 249-282 2C 302-321 2C 341-363 2C373-395 and 428-447 NC_002163.1 RefSeq region 198451 198552 . + . ID=id497;Name=id497;Dbxref=GeneID:904545;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0203 by TMHMM2.0 at aa 4-21 2C 28-45 2C 50-72 2C 84-106 2C126-148 2C 161-180 2C 195-217 2C 249-282 2C 302-321 2C 341-363 2C373-395 and 428-447 NC_002163.1 RefSeq region 198610 198669 . + . ID=id497;Name=id497;Dbxref=GeneID:904545;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0203 by TMHMM2.0 at aa 4-21 2C 28-45 2C 50-72 2C 84-106 2C126-148 2C 161-180 2C 195-217 2C 249-282 2C 302-321 2C 341-363 2C373-395 and 428-447 NC_002163.1 RefSeq region 198727 198795 . + . ID=id497;Name=id497;Dbxref=GeneID:904545;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0203 by TMHMM2.0 at aa 4-21 2C 28-45 2C 50-72 2C 84-106 2C126-148 2C 161-180 2C 195-217 2C 249-282 2C 302-321 2C 341-363 2C373-395 and 428-447 NC_002163.1 RefSeq region 198823 198891 . + . ID=id497;Name=id497;Dbxref=GeneID:904545;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0203 by TMHMM2.0 at aa 4-21 2C 28-45 2C 50-72 2C 84-106 2C126-148 2C 161-180 2C 195-217 2C 249-282 2C 302-321 2C 341-363 2C373-395 and 428-447 NC_002163.1 RefSeq region 198913 198945 . + . ID=id500;Name=id500;Dbxref=GeneID:904545;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 198988 199047 . + . ID=id497;Name=id497;Dbxref=GeneID:904545;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0203 by TMHMM2.0 at aa 4-21 2C 28-45 2C 50-72 2C 84-106 2C126-148 2C 161-180 2C 195-217 2C 249-282 2C 302-321 2C 341-363 2C373-395 and 428-447 ### NC_002163.1 UTR_Extractor 5'-UTR 199158 199235 . + . ID=utr76;locus_tag=Cj0204;product=putative oligopeptide transporter 2C OPT family NC_002163.1 RefSeq CDS 199236 201233 . + 0 ID=cds185;Parent=gene194;Name=YP_002343662.1;Dbxref=InterPro:IPR004813 InterPro:IPR004814 UniProtKB FTrEMBL:Q0PBT5 Genbank:YP_002343662.1 GeneID:904548;gbkey=CDS;product=oligopeptide transporter;Note=Original 282000 29 note: Cj0204 2C probable integral membrane protein 2C len: 665 aa 3B 98.9 25 identity in 369 aa overlap to TR:Q46110 28EMBL:X76062 29 C. jejuni ORF CJO1.1 28381 aa 29. Similar to hypothetical proteins e.g. Y561_HAEIN HI0561 2F560 28633 aa 29 2C fasta scores 3B opt: 2119 z-score: 1501.8 E 28 29: 0 2C 53.6 25 identity in 640 aa overlap 2C and in C-terminus to TR:Q51156 28EMBL:L09189 29 Neisseria meningitidis ORF associated with capsule gene complex 28282 aa 29 2C fasta scores 3B opt: 880 z-score: 1097.6 E 28 29: 0 2C 51.3 25 identity in 273 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF03169 OPT oligopeptide transporter protein was identified within CDS. Sixteen probable transmembrane helices predicted by TMHMM2.0. Product modified to more specific family member due to motif match. kept within product function. Functional classification - Transport 2Fbinding proteins -Other 7EPMID:7489896 NC_002163.1 RefSeq gene 199236 201233 . + . ID=gene194;Name=Cj0204;locus_tag=Cj0204;Dbxref=GeneID:904548;gbkey=Gene NC_002163.1 RefSeq region 199263 201092 . + . ID=id501;Name=id501;Dbxref=GeneID:904548;gbkey=misc_feature;Note=HMMPfam hit to PF03169 2C OPT oligopeptide transporter protein 2C score 1.1e-95 NC_002163.1 RefSeq region 199272 199340 . + . ID=id502;Name=id502;Dbxref=GeneID:904548;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0204 by TMHMM2.0 at aa 13-35 2C 39-61 2C 73-95 2C 99-121 2C162-184 2C 188-210 2C 212-234 2C 314-333 2C 345-367 2C 377-399 2C406-428 2C 450-472 2C 508-530 2C 545-567 2C 598-620 and 635-657 NC_002163.1 RefSeq region 199350 199418 . + . ID=id502;Name=id502;Dbxref=GeneID:904548;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0204 by TMHMM2.0 at aa 13-35 2C 39-61 2C 73-95 2C 99-121 2C162-184 2C 188-210 2C 212-234 2C 314-333 2C 345-367 2C 377-399 2C406-428 2C 450-472 2C 508-530 2C 545-567 2C 598-620 and 635-657 NC_002163.1 RefSeq region 199452 199520 . + . ID=id502;Name=id502;Dbxref=GeneID:904548;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0204 by TMHMM2.0 at aa 13-35 2C 39-61 2C 73-95 2C 99-121 2C162-184 2C 188-210 2C 212-234 2C 314-333 2C 345-367 2C 377-399 2C406-428 2C 450-472 2C 508-530 2C 545-567 2C 598-620 and 635-657 NC_002163.1 RefSeq region 199530 199598 . + . ID=id502;Name=id502;Dbxref=GeneID:904548;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0204 by TMHMM2.0 at aa 13-35 2C 39-61 2C 73-95 2C 99-121 2C162-184 2C 188-210 2C 212-234 2C 314-333 2C 345-367 2C 377-399 2C406-428 2C 450-472 2C 508-530 2C 545-567 2C 598-620 and 635-657 NC_002163.1 RefSeq region 199719 199787 . + . ID=id502;Name=id502;Dbxref=GeneID:904548;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0204 by TMHMM2.0 at aa 13-35 2C 39-61 2C 73-95 2C 99-121 2C162-184 2C 188-210 2C 212-234 2C 314-333 2C 345-367 2C 377-399 2C406-428 2C 450-472 2C 508-530 2C 545-567 2C 598-620 and 635-657 NC_002163.1 RefSeq region 199797 199865 . + . ID=id502;Name=id502;Dbxref=GeneID:904548;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0204 by TMHMM2.0 at aa 13-35 2C 39-61 2C 73-95 2C 99-121 2C162-184 2C 188-210 2C 212-234 2C 314-333 2C 345-367 2C 377-399 2C406-428 2C 450-472 2C 508-530 2C 545-567 2C 598-620 and 635-657 NC_002163.1 RefSeq region 199869 199937 . + . ID=id502;Name=id502;Dbxref=GeneID:904548;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0204 by TMHMM2.0 at aa 13-35 2C 39-61 2C 73-95 2C 99-121 2C162-184 2C 188-210 2C 212-234 2C 314-333 2C 345-367 2C 377-399 2C406-428 2C 450-472 2C 508-530 2C 545-567 2C 598-620 and 635-657 NC_002163.1 RefSeq region 200175 200234 . + . ID=id502;Name=id502;Dbxref=GeneID:904548;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0204 by TMHMM2.0 at aa 13-35 2C 39-61 2C 73-95 2C 99-121 2C162-184 2C 188-210 2C 212-234 2C 314-333 2C 345-367 2C 377-399 2C406-428 2C 450-472 2C 508-530 2C 545-567 2C 598-620 and 635-657 NC_002163.1 RefSeq region 200268 200336 . + . ID=id502;Name=id502;Dbxref=GeneID:904548;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0204 by TMHMM2.0 at aa 13-35 2C 39-61 2C 73-95 2C 99-121 2C162-184 2C 188-210 2C 212-234 2C 314-333 2C 345-367 2C 377-399 2C406-428 2C 450-472 2C 508-530 2C 545-567 2C 598-620 and 635-657 NC_002163.1 RefSeq region 200298 200330 . + . ID=id503;Name=id503;Dbxref=GeneID:904548;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 200364 200432 . + . ID=id502;Name=id502;Dbxref=GeneID:904548;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0204 by TMHMM2.0 at aa 13-35 2C 39-61 2C 73-95 2C 99-121 2C162-184 2C 188-210 2C 212-234 2C 314-333 2C 345-367 2C 377-399 2C406-428 2C 450-472 2C 508-530 2C 545-567 2C 598-620 and 635-657 NC_002163.1 RefSeq region 200451 200519 . + . ID=id502;Name=id502;Dbxref=GeneID:904548;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0204 by TMHMM2.0 at aa 13-35 2C 39-61 2C 73-95 2C 99-121 2C162-184 2C 188-210 2C 212-234 2C 314-333 2C 345-367 2C 377-399 2C406-428 2C 450-472 2C 508-530 2C 545-567 2C 598-620 and 635-657 NC_002163.1 RefSeq region 200583 200651 . + . ID=id502;Name=id502;Dbxref=GeneID:904548;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0204 by TMHMM2.0 at aa 13-35 2C 39-61 2C 73-95 2C 99-121 2C162-184 2C 188-210 2C 212-234 2C 314-333 2C 345-367 2C 377-399 2C406-428 2C 450-472 2C 508-530 2C 545-567 2C 598-620 and 635-657 NC_002163.1 RefSeq region 200757 200825 . + . ID=id502;Name=id502;Dbxref=GeneID:904548;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0204 by TMHMM2.0 at aa 13-35 2C 39-61 2C 73-95 2C 99-121 2C162-184 2C 188-210 2C 212-234 2C 314-333 2C 345-367 2C 377-399 2C406-428 2C 450-472 2C 508-530 2C 545-567 2C 598-620 and 635-657 NC_002163.1 RefSeq region 200868 200936 . + . ID=id502;Name=id502;Dbxref=GeneID:904548;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0204 by TMHMM2.0 at aa 13-35 2C 39-61 2C 73-95 2C 99-121 2C162-184 2C 188-210 2C 212-234 2C 314-333 2C 345-367 2C 377-399 2C406-428 2C 450-472 2C 508-530 2C 545-567 2C 598-620 and 635-657 NC_002163.1 RefSeq region 201027 201095 . + . ID=id502;Name=id502;Dbxref=GeneID:904548;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0204 by TMHMM2.0 at aa 13-35 2C 39-61 2C 73-95 2C 99-121 2C162-184 2C 188-210 2C 212-234 2C 314-333 2C 345-367 2C 377-399 2C406-428 2C 450-472 2C 508-530 2C 545-567 2C 598-620 and 635-657 NC_002163.1 RefSeq region 201138 201206 . + . ID=id502;Name=id502;Dbxref=GeneID:904548;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0204 by TMHMM2.0 at aa 13-35 2C 39-61 2C 73-95 2C 99-121 2C162-184 2C 188-210 2C 212-234 2C 314-333 2C 345-367 2C 377-399 2C406-428 2C 450-472 2C 508-530 2C 545-567 2C 598-620 and 635-657 ### NC_002163.1 RefSeq CDS 201307 202110 . + 0 ID=cds186;Parent=gene195;gene=uppP;Name=YP_002343663.1;Dbxref=GOA:Q9PIS4 InterPro:IPR003824 UniProtKB FSwiss-Prot:Q9PIS4 Genbank:YP_002343663.1 GeneID:904549;gbkey=CDS;product=UDP-diphosphatase;Note=Original 282000 29 note: Cj0205 2C bacA 2C possible undecaprenol kinase 28bacitracin resistance protein 29 2C len: 267 aa 3B 98.6 25 identity in 138 aa overlap to TR:Q46111 C. jejuni ORF CJO1.2 28138 aa 29. Simlar to e.g. BACA_ECOLI bacitracin resistance protein 28 undecaprenol kinase 29 28273 aa 29 2C fasta scores 3B opt: 483 z-score: 947.5 E 28 29: 0 2C 43.7 25 identity in 270 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02673 Bacitracin resistance protein BacA was identified within CDS. Seven probable transmembrane helices predicted by TMHMM2.0. Literature search identified characterisation papers within Escherichia coli that show further specification with product functionality 28PMID:15778224 29. Product function modified to more specific family member. Identity scores were acceptable. Thus 2C not added to product function. Functional classification -Drug 2Fanalogue sensitivity 7EPMID:7489896 2C PMID:8389741 2C PMID:15138271 2CPMID:15778224 NC_002163.1 RefSeq gene 201307 202110 . + . ID=gene195;gene=uppP;Name=uppP;locus_tag=Cj0205;Dbxref=GeneID:904549;gbkey=Gene NC_002163.1 RefSeq region 201319 202056 . + . ID=id504;gene=uppP;Name=id504;Dbxref=GeneID:904549;gbkey=misc_feature;Note=HMMPfam hit to PF02673 2C Bacitracin resistance protein BacA 2C score 3.2e-133 NC_002163.1 RefSeq region 201325 201393 . + . ID=id505;gene=uppP;Name=id505;Dbxref=GeneID:904549;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0205 by TMHMM2.0 at aa 7-29 2C 44-66 2C 71-90 2C 100-119 2C172-194 2C 209-231 and 236-258 NC_002163.1 RefSeq region 201436 201504 . + . ID=id505;gene=uppP;Name=id505;Dbxref=GeneID:904549;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0205 by TMHMM2.0 at aa 7-29 2C 44-66 2C 71-90 2C 100-119 2C172-194 2C 209-231 and 236-258 NC_002163.1 RefSeq region 201517 201576 . + . ID=id505;gene=uppP;Name=id505;Dbxref=GeneID:904549;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0205 by TMHMM2.0 at aa 7-29 2C 44-66 2C 71-90 2C 100-119 2C172-194 2C 209-231 and 236-258 NC_002163.1 RefSeq region 201604 201663 . + . ID=id505;gene=uppP;Name=id505;Dbxref=GeneID:904549;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0205 by TMHMM2.0 at aa 7-29 2C 44-66 2C 71-90 2C 100-119 2C172-194 2C 209-231 and 236-258 NC_002163.1 RefSeq region 201820 201888 . + . ID=id505;gene=uppP;Name=id505;Dbxref=GeneID:904549;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0205 by TMHMM2.0 at aa 7-29 2C 44-66 2C 71-90 2C 100-119 2C172-194 2C 209-231 and 236-258 NC_002163.1 RefSeq region 201931 201999 . + . ID=id505;gene=uppP;Name=id505;Dbxref=GeneID:904549;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0205 by TMHMM2.0 at aa 7-29 2C 44-66 2C 71-90 2C 100-119 2C172-194 2C 209-231 and 236-258 NC_002163.1 RefSeq region 202012 202080 . + . ID=id505;gene=uppP;Name=id505;Dbxref=GeneID:904549;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0205 by TMHMM2.0 at aa 7-29 2C 44-66 2C 71-90 2C 100-119 2C172-194 2C 209-231 and 236-258 ### NC_002163.1 UTR_Extractor 5'-UTR 202196 202240 . + . ID=utr77;locus_tag=Cj0206;product=threonyl-tRNA synthetase NC_002163.1 RefSeq CDS 202241 204049 . + 0 ID=cds187;Parent=gene196;gene=thrS;Name=YP_002343664.1;Dbxref=GOA:Q9PIS3 HSSP:P00955 InterPro:IPR002314 InterPro:IPR002320 InterPro:IPR004154 InterPro:IPR006195 InterPro:IPR012947 UniProtKB FSwiss-Prot:Q9PIS3 Genbank:YP_002343664.1 GeneID:904952;gbkey=CDS;product=threonyl-tRNA synthetase;Note=catalyzes the formation of threonyl-tRNA 28Thr 29 from threonine and tRNA 28Thr 29 3B catalyzes a two-step reaction 2C first charging a threonine molecule by linking its carboxyl group to the alpha-phosphate of ATP 2C followed by transfer of the aminoacyl-adenylate to its tRNA NC_002163.1 RefSeq gene 202241 204049 . + . ID=gene196;gene=thrS;Name=thrS;locus_tag=Cj0206;Dbxref=GeneID:904952;gbkey=Gene NC_002163.1 RefSeq region 202922 203383 . + . ID=id506;gene=thrS;Name=id506;Dbxref=GeneID:904952;gbkey=misc_feature;Note=HMMPfam hit to PF00587 2C tRNA synthetase class II core domain 28 2C score 1e-48 NC_002163.1 RefSeq region 203222 203287 . + . ID=id507;gene=thrS;Name=id507;Dbxref=GeneID:904952;gbkey=misc_feature;Note=PS00179 Aminoacyl-transfer RNA synthetases class-II signature 1 NC_002163.1 RefSeq region 203678 203707 . + . ID=id508;gene=thrS;Name=id508;Dbxref=GeneID:904952;gbkey=misc_feature;Note=PS00339 Aminoacyl-transfer RNA synthetases class-II signature 2 NC_002163.1 RefSeq region 203756 204028 . + . ID=id509;gene=thrS;Name=id509;Dbxref=GeneID:904952;gbkey=misc_feature;Note=HMMPfam hit to PF03129 2C Anticodon binding domain 2Cscore 2.9e-26 NC_002163.1 RefSeq CDS 204046 204564 . + 0 ID=cds188;Parent=gene197;gene=infC;Name=YP_002343665.1;Dbxref=GOA:Q9PIS2 HSSP:P02999 InterPro:IPR001288 UniProtKB FSwiss-Prot:Q9PIS2 Genbank:YP_002343665.1 GeneID:904550;gbkey=CDS;product=translation initiation factor IF-3;Note=IF-3 has several functions that are required and promote translation initiation including 3B preventing association of 70S by binding to 30S 3B monitoring codon-anticodon interactions by promoting disassociation of fMet-tRNA 28fMet 29 from initiation complexes formed on leaderless mRNAs or incorrectly bound noninitiatior tRNAs and complexes with noncanonical start sites 3B stimulates codon-anticodon interactions at P-site 3B involved in moving mRNA to the P-site 3B and in recycling subunits NC_002163.1 RefSeq gene 204046 204564 . + . ID=gene197;gene=infC;Name=infC;locus_tag=Cj0207;Dbxref=GeneID:904550;gbkey=Gene NC_002163.1 RefSeq region 204055 204282 . + . ID=id510;gene=infC;Name=id510;Dbxref=GeneID:904550;gbkey=misc_feature;Note=HMMPfam hit to PF05198 2C Translation initiation factor IF-3 2C N-termin 2C score 2.5e-47 NC_002163.1 RefSeq region 204223 204264 . + . ID=id511;gene=infC;Name=id511;Dbxref=GeneID:904550;gbkey=misc_feature;Note=PS00938 Initiation factor 3 signature NC_002163.1 RefSeq region 204295 204558 . + . ID=id512;gene=infC;Name=id512;Dbxref=GeneID:904550;gbkey=misc_feature;Note=HMMPfam hit to PF00707 2C Translation initiation factor IF-3 2C C-termin 2C score 3.5e-31 ### NC_002163.1 RefSeq CDS 204603 205694 . + 0 ID=cds189;Parent=gene198;Name=YP_002343666.1;Dbxref=GOA:Q0PBT1 InterPro:IPR002052 InterPro:IPR002294 InterPro:IPR012327 UniProtKB FTrEMBL:Q0PBT1 Genbank:YP_002343666.1 GeneID:904551;gbkey=CDS;product=DNA modification methylase;Note=Original 282000 29 note: Cj0208 2C probable DNA modification methylase 28adenine-specific methyltransferase 29 2C len: 363 aa 3B similar to many e.g. MTN3_NEILA modification methylase NlaIII 28EC 2.1.1.72 29 28334 aa 29 2C fasta scores 3B opt: 215 z-score: 401.1 E 28 29: 4.4e-15 2C 31.7 25 identity in 366 aa overlap. 29.6 25 identity to HP1208 ulcer associated adenine specific DNA methyltransferase. Contains PS00092 N-6 Adenine-specific DNA methylases signature 7EUpdated 282006 29 note: Pfam domain PF02086 D12 class N6 adenine-specific DNA methyltransferase was identified within CDS. Further support given to product function. Characterised within Neisseria lactamica with marginal identity scores. kept within product function. Functional classification - DNA replication 2Crestriction 2Fmodification 2C recombination and repair 7EPMID:2277628 NC_002163.1 RefSeq gene 204603 205694 . + . ID=gene198;Name=Cj0208;locus_tag=Cj0208;Dbxref=GeneID:904551;gbkey=Gene NC_002163.1 RefSeq region 204645 205571 . + . ID=id513;Name=id513;Dbxref=GeneID:904551;gbkey=misc_feature;Note=HMMPfam hit to PF02086 2C D12 class N6 adenine-specific DNA met 2C score 2.6e-08 NC_002163.1 RefSeq region 205314 205334 . + . ID=id514;Name=id514;Dbxref=GeneID:904551;gbkey=misc_feature;Note=PS00092 N-6 Adenine-specific DNA methylases signature ### NC_002163.1 RefSeq region 206063 206308 . + . ID=id515;Name=id515;Dbxref=GeneID:904552;gbkey=misc_feature;Note=Original 282000 29 note: Cj0223 2C probable pseudogene 2Clen: 3423 bp similar to several members of the IgA protease 2Fhaemaglutinin 2FsepA family e.g. IGA2_HAEIN immunoglobulin A1 protease precursor 28EC 3.4.21.72 29 2CTR:Q54151 28EMBL:U35656 29 Shigella flexneri she hemagglutinin 2C and TR:Q54165 28EMBL:Z48219 29 Shigella flexneri sepA gene precursor. No apparent Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score 28aligning whole sequence 29 2Chas been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Pathogenicity 7EPMID:10225873 2C PMID:10531204 NC_002163.1 RefSeq pseudogene 206063 209195 . + . ID=gene199;Name=Cj0223;locus_tag=Cj0223;Dbxref=GeneID:904552;gbkey=Gene NC_002163.1 RefSeq region 206308 206691 . + . ID=id515;Name=id515;Dbxref=GeneID:904552;gbkey=misc_feature;Note=Original 282000 29 note: Cj0223 2C probable pseudogene 2Clen: 3423 bp similar to several members of the IgA protease 2Fhaemaglutinin 2FsepA family e.g. IGA2_HAEIN immunoglobulin A1 protease precursor 28EC 3.4.21.72 29 2CTR:Q54151 28EMBL:U35656 29 Shigella flexneri she hemagglutinin 2C and TR:Q54165 28EMBL:Z48219 29 Shigella flexneri sepA gene precursor. No apparent Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score 28aligning whole sequence 29 2Chas been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Pathogenicity 7EPMID:10225873 2C PMID:10531204 NC_002163.1 RefSeq region 206724 206939 . + . ID=id515;Name=id515;Dbxref=GeneID:904552;gbkey=misc_feature;Note=Original 282000 29 note: Cj0223 2C probable pseudogene 2Clen: 3423 bp similar to several members of the IgA protease 2Fhaemaglutinin 2FsepA family e.g. IGA2_HAEIN immunoglobulin A1 protease precursor 28EC 3.4.21.72 29 2CTR:Q54151 28EMBL:U35656 29 Shigella flexneri she hemagglutinin 2C and TR:Q54165 28EMBL:Z48219 29 Shigella flexneri sepA gene precursor. No apparent Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score 28aligning whole sequence 29 2Chas been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Pathogenicity 7EPMID:10225873 2C PMID:10531204 NC_002163.1 RefSeq region 206939 206974 . + . ID=id515;Name=id515;Dbxref=GeneID:904552;gbkey=misc_feature;Note=Original 282000 29 note: Cj0223 2C probable pseudogene 2Clen: 3423 bp similar to several members of the IgA protease 2Fhaemaglutinin 2FsepA family e.g. IGA2_HAEIN immunoglobulin A1 protease precursor 28EC 3.4.21.72 29 2CTR:Q54151 28EMBL:U35656 29 Shigella flexneri she hemagglutinin 2C and TR:Q54165 28EMBL:Z48219 29 Shigella flexneri sepA gene precursor. No apparent Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score 28aligning whole sequence 29 2Chas been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Pathogenicity 7EPMID:10225873 2C PMID:10531204 NC_002163.1 RefSeq region 206974 207063 . + . ID=id515;Name=id515;Dbxref=GeneID:904552;gbkey=misc_feature;Note=Original 282000 29 note: Cj0223 2C probable pseudogene 2Clen: 3423 bp similar to several members of the IgA protease 2Fhaemaglutinin 2FsepA family e.g. IGA2_HAEIN immunoglobulin A1 protease precursor 28EC 3.4.21.72 29 2CTR:Q54151 28EMBL:U35656 29 Shigella flexneri she hemagglutinin 2C and TR:Q54165 28EMBL:Z48219 29 Shigella flexneri sepA gene precursor. No apparent Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score 28aligning whole sequence 29 2Chas been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Pathogenicity 7EPMID:10225873 2C PMID:10531204 NC_002163.1 RefSeq region 207095 207310 . + . ID=id515;Name=id515;Dbxref=GeneID:904552;gbkey=misc_feature;Note=Original 282000 29 note: Cj0223 2C probable pseudogene 2Clen: 3423 bp similar to several members of the IgA protease 2Fhaemaglutinin 2FsepA family e.g. IGA2_HAEIN immunoglobulin A1 protease precursor 28EC 3.4.21.72 29 2CTR:Q54151 28EMBL:U35656 29 Shigella flexneri she hemagglutinin 2C and TR:Q54165 28EMBL:Z48219 29 Shigella flexneri sepA gene precursor. No apparent Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score 28aligning whole sequence 29 2Chas been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Pathogenicity 7EPMID:10225873 2C PMID:10531204 NC_002163.1 RefSeq region 207314 207637 . + . ID=id515;Name=id515;Dbxref=GeneID:904552;gbkey=misc_feature;Note=Original 282000 29 note: Cj0223 2C probable pseudogene 2Clen: 3423 bp similar to several members of the IgA protease 2Fhaemaglutinin 2FsepA family e.g. IGA2_HAEIN immunoglobulin A1 protease precursor 28EC 3.4.21.72 29 2CTR:Q54151 28EMBL:U35656 29 Shigella flexneri she hemagglutinin 2C and TR:Q54165 28EMBL:Z48219 29 Shigella flexneri sepA gene precursor. No apparent Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score 28aligning whole sequence 29 2Chas been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Pathogenicity 7EPMID:10225873 2C PMID:10531204 NC_002163.1 RefSeq region 207636 207770 . + . ID=id515;Name=id515;Dbxref=GeneID:904552;gbkey=misc_feature;Note=Original 282000 29 note: Cj0223 2C probable pseudogene 2Clen: 3423 bp similar to several members of the IgA protease 2Fhaemaglutinin 2FsepA family e.g. IGA2_HAEIN immunoglobulin A1 protease precursor 28EC 3.4.21.72 29 2CTR:Q54151 28EMBL:U35656 29 Shigella flexneri she hemagglutinin 2C and TR:Q54165 28EMBL:Z48219 29 Shigella flexneri sepA gene precursor. No apparent Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score 28aligning whole sequence 29 2Chas been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Pathogenicity 7EPMID:10225873 2C PMID:10531204 NC_002163.1 RefSeq region 207775 207843 . + . ID=id515;Name=id515;Dbxref=GeneID:904552;gbkey=misc_feature;Note=Original 282000 29 note: Cj0223 2C probable pseudogene 2Clen: 3423 bp similar to several members of the IgA protease 2Fhaemaglutinin 2FsepA family e.g. IGA2_HAEIN immunoglobulin A1 protease precursor 28EC 3.4.21.72 29 2CTR:Q54151 28EMBL:U35656 29 Shigella flexneri she hemagglutinin 2C and TR:Q54165 28EMBL:Z48219 29 Shigella flexneri sepA gene precursor. No apparent Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score 28aligning whole sequence 29 2Chas been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Pathogenicity 7EPMID:10225873 2C PMID:10531204 NC_002163.1 RefSeq region 207843 207980 . + . ID=id515;Name=id515;Dbxref=GeneID:904552;gbkey=misc_feature;Note=Original 282000 29 note: Cj0223 2C probable pseudogene 2Clen: 3423 bp similar to several members of the IgA protease 2Fhaemaglutinin 2FsepA family e.g. IGA2_HAEIN immunoglobulin A1 protease precursor 28EC 3.4.21.72 29 2CTR:Q54151 28EMBL:U35656 29 Shigella flexneri she hemagglutinin 2C and TR:Q54165 28EMBL:Z48219 29 Shigella flexneri sepA gene precursor. No apparent Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score 28aligning whole sequence 29 2Chas been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Pathogenicity 7EPMID:10225873 2C PMID:10531204 NC_002163.1 RefSeq region 208012 208203 . + . ID=id515;Name=id515;Dbxref=GeneID:904552;gbkey=misc_feature;Note=Original 282000 29 note: Cj0223 2C probable pseudogene 2Clen: 3423 bp similar to several members of the IgA protease 2Fhaemaglutinin 2FsepA family e.g. IGA2_HAEIN immunoglobulin A1 protease precursor 28EC 3.4.21.72 29 2CTR:Q54151 28EMBL:U35656 29 Shigella flexneri she hemagglutinin 2C and TR:Q54165 28EMBL:Z48219 29 Shigella flexneri sepA gene precursor. No apparent Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score 28aligning whole sequence 29 2Chas been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Pathogenicity 7EPMID:10225873 2C PMID:10531204 NC_002163.1 RefSeq region 208203 208337 . + . ID=id515;Name=id515;Dbxref=GeneID:904552;gbkey=misc_feature;Note=Original 282000 29 note: Cj0223 2C probable pseudogene 2Clen: 3423 bp similar to several members of the IgA protease 2Fhaemaglutinin 2FsepA family e.g. IGA2_HAEIN immunoglobulin A1 protease precursor 28EC 3.4.21.72 29 2CTR:Q54151 28EMBL:U35656 29 Shigella flexneri she hemagglutinin 2C and TR:Q54165 28EMBL:Z48219 29 Shigella flexneri sepA gene precursor. No apparent Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score 28aligning whole sequence 29 2Chas been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Pathogenicity 7EPMID:10225873 2C PMID:10531204 NC_002163.1 RefSeq region 208336 208473 . + . ID=id515;Name=id515;Dbxref=GeneID:904552;gbkey=misc_feature;Note=Original 282000 29 note: Cj0223 2C probable pseudogene 2Clen: 3423 bp similar to several members of the IgA protease 2Fhaemaglutinin 2FsepA family e.g. IGA2_HAEIN immunoglobulin A1 protease precursor 28EC 3.4.21.72 29 2CTR:Q54151 28EMBL:U35656 29 Shigella flexneri she hemagglutinin 2C and TR:Q54165 28EMBL:Z48219 29 Shigella flexneri sepA gene precursor. No apparent Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score 28aligning whole sequence 29 2Chas been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Pathogenicity 7EPMID:10225873 2C PMID:10531204 NC_002163.1 RefSeq region 208475 208666 . + . ID=id515;Name=id515;Dbxref=GeneID:904552;gbkey=misc_feature;Note=Original 282000 29 note: Cj0223 2C probable pseudogene 2Clen: 3423 bp similar to several members of the IgA protease 2Fhaemaglutinin 2FsepA family e.g. IGA2_HAEIN immunoglobulin A1 protease precursor 28EC 3.4.21.72 29 2CTR:Q54151 28EMBL:U35656 29 Shigella flexneri she hemagglutinin 2C and TR:Q54165 28EMBL:Z48219 29 Shigella flexneri sepA gene precursor. No apparent Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score 28aligning whole sequence 29 2Chas been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Pathogenicity 7EPMID:10225873 2C PMID:10531204 NC_002163.1 RefSeq region 208673 208846 . + . ID=id515;Name=id515;Dbxref=GeneID:904552;gbkey=misc_feature;Note=Original 282000 29 note: Cj0223 2C probable pseudogene 2Clen: 3423 bp similar to several members of the IgA protease 2Fhaemaglutinin 2FsepA family e.g. IGA2_HAEIN immunoglobulin A1 protease precursor 28EC 3.4.21.72 29 2CTR:Q54151 28EMBL:U35656 29 Shigella flexneri she hemagglutinin 2C and TR:Q54165 28EMBL:Z48219 29 Shigella flexneri sepA gene precursor. No apparent Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score 28aligning whole sequence 29 2Chas been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Pathogenicity 7EPMID:10225873 2C PMID:10531204 NC_002163.1 RefSeq region 208852 208950 . + . ID=id515;Name=id515;Dbxref=GeneID:904552;gbkey=misc_feature;Note=Original 282000 29 note: Cj0223 2C probable pseudogene 2Clen: 3423 bp similar to several members of the IgA protease 2Fhaemaglutinin 2FsepA family e.g. IGA2_HAEIN immunoglobulin A1 protease precursor 28EC 3.4.21.72 29 2CTR:Q54151 28EMBL:U35656 29 Shigella flexneri she hemagglutinin 2C and TR:Q54165 28EMBL:Z48219 29 Shigella flexneri sepA gene precursor. No apparent Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score 28aligning whole sequence 29 2Chas been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Pathogenicity 7EPMID:10225873 2C PMID:10531204 NC_002163.1 RefSeq region 208954 209055 . + . ID=id515;Name=id515;Dbxref=GeneID:904552;gbkey=misc_feature;Note=Original 282000 29 note: Cj0223 2C probable pseudogene 2Clen: 3423 bp similar to several members of the IgA protease 2Fhaemaglutinin 2FsepA family e.g. IGA2_HAEIN immunoglobulin A1 protease precursor 28EC 3.4.21.72 29 2CTR:Q54151 28EMBL:U35656 29 Shigella flexneri she hemagglutinin 2C and TR:Q54165 28EMBL:Z48219 29 Shigella flexneri sepA gene precursor. No apparent Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score 28aligning whole sequence 29 2Chas been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Pathogenicity 7EPMID:10225873 2C PMID:10531204 NC_002163.1 RefSeq region 209055 209195 . + . ID=id515;Name=id515;Dbxref=GeneID:904552;gbkey=misc_feature;Note=Original 282000 29 note: Cj0223 2C probable pseudogene 2Clen: 3423 bp similar to several members of the IgA protease 2Fhaemaglutinin 2FsepA family e.g. IGA2_HAEIN immunoglobulin A1 protease precursor 28EC 3.4.21.72 29 2CTR:Q54151 28EMBL:U35656 29 Shigella flexneri she hemagglutinin 2C and TR:Q54165 28EMBL:Z48219 29 Shigella flexneri sepA gene precursor. No apparent Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score 28aligning whole sequence 29 2Chas been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Pathogenicity 7EPMID:10225873 2C PMID:10531204 ### NC_002163.1 UTR_Extractor 5'-UTR 209258 209278 . + . ID=utr78;locus_tag=Cj0224;product=N-acetyl-gamma-glutamyl-phosphate reductase NC_002163.1 RefSeq CDS 209279 210307 . + 0 ID=cds190;Parent=gene200;gene=argC;Name=YP_002343667.1;Dbxref=GOA:Q9PIS0 InterPro:IPR000534 InterPro:IPR000706 InterPro:IPR012280 UniProtKB FSwiss-Prot:Q9PIS0 Genbank:YP_002343667.1 GeneID:906012;gbkey=CDS;product=N-acetyl-gamma-glutamyl-phosphate reductase;Note=catalyzes the reduction of N-acetyl-5-glutamyl phosphate to N-acetyl-L-glutamate 5-semialdehyde in arginine biosynthesis and the reduction of N-acetyl-gamma-aminoadipyl-phosphate to N-acetyl-L-aminoadipate-semialdehyde in lysine biosynthesis 3B involved in both the arginine and lysine biosynthetic pathways 3B lysine is produced via the AAA pathway 2C lysine from alpha-aminoadipate NC_002163.1 RefSeq gene 209279 210307 . + . ID=gene200;gene=argC;Name=argC;locus_tag=Cj0224;Dbxref=GeneID:906012;gbkey=Gene NC_002163.1 RefSeq region 209282 209707 . + . ID=id516;gene=argC;Name=id516;Dbxref=GeneID:906012;gbkey=misc_feature;Note=HMMPfam hit to PF01118 2C Semialdehyde dehydrogenase 2CNAD bindi 2C score 1.1e-35 NC_002163.1 RefSeq region 209744 210220 . + . ID=id517;gene=argC;Name=id517;Dbxref=GeneID:906012;gbkey=misc_feature;Note=HMMPfam hit to PF02774 2C Semialdehyde dehydrogenase 2Cdimerisat 2C score 2.1e-41 ### NC_002163.1 RefSeq CDS 210317 210763 . + 0 ID=cds191;Parent=gene201;Name=YP_002343668.1;Dbxref=GOA:Q0PBS9 InterPro:IPR000182 InterPro:IPR016181 UniProtKB FTrEMBL:Q0PBS9 Genbank:YP_002343668.1 GeneID:904553;gbkey=CDS;product=acetyltransferase;Note=Original 282000 29 note: Cj0225 2C probable acetyltransferase 2C len: 148 aa 3B some simlarity to STA_ECOLI streptothricin acetyltransferase 28plasmid borne 29 28EC 2.3.-.- 29 28174 aa 29 2C fasta scores 3B opt: 118 z-score: 186.2 E 28 29: 0.0041 2C 27.3 25 identity in 110 aa overlap. No Hp match. Contains Pfam match to entry PF00583 Acetyltransf 2C Acetyltransferase 28GNAT 29 family 2C score 57.00 2C E-value 4.1e-13 7EUpdated 282006 29 note: Characterisation carried out within Escherichia coil 2C however 2C identity score was marginal. kept within product function. Functional classification - Misc 7EPMID:2157196 NC_002163.1 RefSeq gene 210317 210763 . + . ID=gene201;Name=Cj0225;locus_tag=Cj0225;Dbxref=GeneID:904553;gbkey=Gene NC_002163.1 RefSeq region 210458 210694 . + . ID=id518;Name=id518;Dbxref=GeneID:904553;gbkey=misc_feature;Note=HMMPfam hit to PF00583 2C Acetyltransferase 28GNAT 29 family 2C score 4.1e-15 NC_002163.1 UTR_Extractor 5'-UTR 210749 210766 . + . ID=utr79;locus_tag=Cj0226;product=acetylglutamate kinase ### NC_002163.1 RefSeq CDS 210767 211612 . + 0 ID=cds192;Parent=gene202;gene=argB;Name=YP_002343669.1;Dbxref=GOA:Q9PIR8 HSSP:P11445 InterPro:IPR001048 InterPro:IPR001057 InterPro:IPR004662 InterPro:IPR011148 UniProtKB FSwiss-Prot:Q9PIR8 Genbank:YP_002343669.1 GeneID:904554;gbkey=CDS;product=acetylglutamate kinase;Note=catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate NC_002163.1 RefSeq gene 210767 211612 . + . ID=gene202;gene=argB;Name=argB;locus_tag=Cj0226;Dbxref=GeneID:904554;gbkey=Gene NC_002163.1 RefSeq region 210842 211543 . + . ID=id519;gene=argB;Name=id519;Dbxref=GeneID:904554;gbkey=misc_feature;Note=HMMPfam hit to PF00696 2C Amino acid kinase family 2Cscore 3.1e-51 NC_002163.1 UTR_Extractor 5'-UTR 211456 211615 . + . ID=utr80;locus_tag=Cj0227;product=putative acetylornithine 2Fsuccinyldiaminopimelate aminotransferase ### NC_002163.1 RefSeq gene 211616 212803 . + . ID=gene203;gene=argD;Name=argD;locus_tag=Cj0227;Dbxref=GeneID:904555;gbkey=Gene NC_002163.1 RefSeq CDS 211616 212803 . + 0 ID=cds193;Parent=gene203;gene=argD;Name=YP_002343670.1;Dbxref=GOA:Q9PIR7 HSSP:P12995 InterPro:IPR004636 InterPro:IPR005814 InterPro:IPR015421 UniProtKB FSwiss-Prot:Q9PIR7 Genbank:YP_002343670.1 GeneID:904555;gbkey=CDS;product=acetylornithine 2Fsuccinyldiaminopimelate aminotransferase;Note=Original 282000 29 note: Cj0227 2C argD 2C probable acetylornithine aminotransferase 2C len: 395 aa 3B simlar to many e.g. ARGD_ECOLI acetylornithine aminotransferase 28EC 2.6.1.11 29 28406 aa 29 2C fasta scores 3B opt: 921 z-score: 1042.0 E 28 29: 0 2C 36.6 25 identity in 385 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00202 aminotran_3 2CAminotransferases class-III pyridoxal-phosphate 2C score 378.20 2C E-value 5.1e-131 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. Based on current literature 2C product function has been modified and additional EC number has been added. kept within product function. Functional classification - Amino acid biosynthesis - Glutamate family 7EPMID:10588044 2C PMID:10074354 NC_002163.1 RefSeq region 211643 212800 . + . ID=id520;gene=argD;Name=id520;Dbxref=GeneID:904555;gbkey=misc_feature;Note=HMMPfam hit to PF00202 2C Aminotransferase class-III 2Cscore 4.3e-133 ### NC_002163.1 RefSeq gene 212822 213451 . - . ID=gene204;gene=pcm;Name=pcm;locus_tag=Cj0228c;Dbxref=GeneID:906010;gbkey=Gene NC_002163.1 RefSeq CDS 212822 213451 . - 0 ID=cds194;Parent=gene204;gene=pcm;Name=YP_002343671.1;Dbxref=GOA:Q0PBS6 InterPro:IPR000682 UniProtKB FTrEMBL:Q0PBS6 Genbank:YP_002343671.1 GeneID:906010;gbkey=CDS;product=protein-L-isoaspartate O-methyltransferase;Note=catalyzes the methyl esterification of L-isoaspartyl residues that are formed in damaged proteins NC_002163.1 RefSeq region 212825 213439 . - . ID=id521;gene=pcm;Name=id521;Dbxref=GeneID:906010;gbkey=misc_feature;Note=HMMPfam hit to PF01135 2CProtein-L-isoaspartate 28D-aspartate 29 O-methyl 2C score 1e-51 ### NC_002163.1 UTR_Extractor 5'-UTR 213452 213471 . - . ID=utr81;locus_tag=Cj0228c;product=protein-L-isoaspartate O-methyltransferase NC_002163.1 RefSeq CDS 213540 214088 . + 0 ID=cds195;Parent=gene205;Name=YP_002343672.1;Dbxref=GOA:Q0PBS5 InterPro:IPR001451 UniProtKB FTrEMBL:Q0PBS5 Genbank:YP_002343672.1 GeneID:904556;gbkey=CDS;product=acetyltransferase;Note=Original 282000 29 note: Cj0229 2C possible acetyltransferase 2C len: 182 aa 3B similar to e.g. CAIE_ECOLI carnitine operon protein caiE 28203 aa 29 2C fasta scores 3B opt: 251 z-score: 517.5 E 28 29: 1.4e-21 2C 33.1 25 identity in 169 aa overlap. No Hp ortholog. Contains 3x Pfam match to entry PF00132 hexapep 2C Bacterial transferase hexapeptide 28four repeats 29 2C scores 16.60 2C E-value 0.0071 3B 9.10 2C E-value 0.97 and 24.70 2C E-value 3.7e-05 7EUpdated 282006 29 note: Some characterisation work within Escherichia coli 2C however 2C identity score was marginal. kept within product function. Functional classification - Misc 7EPMID:7815937 NC_002163.1 RefSeq gene 213540 214088 . + . ID=gene205;Name=Cj0229;locus_tag=Cj0229;Dbxref=GeneID:904556;gbkey=Gene NC_002163.1 RefSeq region 213582 213635 . + . ID=id522;Name=id522;Dbxref=GeneID:904556;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 7.6 NC_002163.1 RefSeq region 213681 213734 . + . ID=id523;Name=id523;Dbxref=GeneID:904556;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 1.1e 2B02 NC_002163.1 RefSeq region 213783 213836 . + . ID=id524;Name=id524;Dbxref=GeneID:904556;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 0.0059 NC_002163.1 RefSeq region 213837 213887 . + . ID=id525;Name=id525;Dbxref=GeneID:904556;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 21 NC_002163.1 RefSeq region 213888 213941 . + . ID=id526;Name=id526;Dbxref=GeneID:904556;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 8.1 NC_002163.1 RefSeq CDS 214057 215430 . - 0 ID=cds196;Parent=gene206;Name=YP_002343673.1;Dbxref=GOA:Q0PBS4 InterPro:IPR006405 InterPro:IPR007229 InterPro:IPR015977 UniProtKB FTrEMBL:Q0PBS4 Genbank:YP_002343673.1 GeneID:904557;gbkey=CDS;product=nicotinate phosphoribosyltransferase;Note=catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate NC_002163.1 RefSeq gene 214057 215430 . - . ID=gene206;Name=Cj0230c;locus_tag=Cj0230c;Dbxref=GeneID:904557;gbkey=Gene NC_002163.1 RefSeq region 214336 215409 . - . ID=id527;Name=id527;Dbxref=GeneID:904557;gbkey=misc_feature;Note=HMMPfam hit to PF04095 2C Nicotinate phosphoribosyltransferase 28NAPRTa 2C score 3.6e-11 NC_002163.1 RefSeq region 214873 214905 . - . ID=id528;Name=id528;Dbxref=GeneID:904557;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq CDS 215417 216439 . - 0 ID=cds197;Parent=gene207;gene=nrdF;Name=YP_002343674.1;Dbxref=GOA:Q0PBS3 InterPro:IPR000358 InterPro:IPR012348 UniProtKB FTrEMBL:Q0PBS3 Genbank:YP_002343674.1 GeneID:904558;gbkey=CDS;product=ribonucleotide-diphosphate reductase subunit beta;Note=B2 or R2 protein 3B type 1b enzyme 3B catalyzes the rate-limiting step in dNTP synthesis 3B converts nucleotides to deoxynucleotides 3B forms a homodimer and then a multimeric complex with NrdE NC_002163.1 RefSeq gene 215417 216439 . - . ID=gene207;gene=nrdF;Name=nrdF;locus_tag=Cj0231c;Dbxref=GeneID:904558;gbkey=Gene NC_002163.1 RefSeq region 215504 216388 . - . ID=id529;gene=nrdF;Name=id529;Dbxref=GeneID:904558;gbkey=misc_feature;Note=HMMPfam hit to PF00268 2C Ribonucleotide reductase 2Csmall chain 2C score 1.8e-30 ### NC_002163.1 RefSeq CDS 216453 216863 . - 0 ID=cds198;Parent=gene208;Name=YP_002343675.1;Dbxref=GOA:Q0PBS2 InterPro:IPR010432 UniProtKB FTrEMBL:Q0PBS2 Genbank:YP_002343675.1 GeneID:904559;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0232c 2C probable integral membrane protein 2C len: 136 aa 3B 37.9 25 identity to HP1258 28called conserved hypothetical mitochondrial protein 4 29. Contains three possible transmembrane domains 7EUpdated 282006 29 note: Pfam domain PF06271 RDD family was identified within CDS. This family of proteins contain three highly conserved amino acids: one arginine and two aspartates 2C hence the name of RDD family. This region contains two predicted transmembrane regions. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 216453 216863 . - . ID=gene208;Name=Cj0232c;locus_tag=Cj0232c;Dbxref=GeneID:904559;gbkey=Gene NC_002163.1 RefSeq region 216462 216845 . - . ID=id530;Name=id530;Dbxref=GeneID:904559;gbkey=misc_feature;Note=HMMPfam hit to PF06271 2C RDD family 2C score 1e-13 NC_002163.1 RefSeq region 216516 216584 . - . ID=id16;Name=id16;Dbxref=GeneID:904559;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0232c by TMHMM2.0 at aa 15-37 2C 42-64 and 94-116 NC_002163.1 RefSeq region 216672 216740 . - . ID=id16;Name=id16;Dbxref=GeneID:904559;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0232c by TMHMM2.0 at aa 15-37 2C 42-64 and 94-116 NC_002163.1 RefSeq region 216753 216821 . - . ID=id16;Name=id16;Dbxref=GeneID:904559;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0232c by TMHMM2.0 at aa 15-37 2C 42-64 and 94-116 ### NC_002163.1 RefSeq CDS 216864 217472 . - 0 ID=cds199;Parent=gene209;gene=pyrE;Name=YP_002343676.1;Dbxref=GOA:Q9PIR1 InterPro:IPR000836 InterPro:IPR002375 InterPro:IPR006273 UniProtKB FSwiss-Prot:Q9PIR1 Genbank:YP_002343676.1 GeneID:904560;gbkey=CDS;product=orotate phosphoribosyltransferase;Note=involved in fifth step of pyrimidine biosynthesis 3B converts orotidine 5 27-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate NC_002163.1 RefSeq gene 216864 217472 . - . ID=gene209;gene=pyrE;Name=pyrE;locus_tag=Cj0233c;Dbxref=GeneID:904560;gbkey=Gene NC_002163.1 RefSeq region 217017 217382 . - . ID=id531;gene=pyrE;Name=id531;Dbxref=GeneID:904560;gbkey=misc_feature;Note=HMMPfam hit to PF00156 2C Phosphoribosyl transferase domain 2C score 2.3e-22 NC_002163.1 RefSeq region 217110 217148 . - . ID=id532;gene=pyrE;Name=id532;Dbxref=GeneID:904560;gbkey=misc_feature;Note=PS00103 Purine 2Fpyrimidine phosphoribosyl transferases signature ### NC_002163.1 UTR_Extractor 5'-UTR 217473 217553 . - . ID=utr82;locus_tag=Cj0233c;product=orotate phosphoribosyltransferase NC_002163.1 RefSeq gene 217475 218038 . - . ID=gene210;gene=frr;Name=frr;locus_tag=Cj0234c;Dbxref=GeneID:904561;gbkey=Gene NC_002163.1 RefSeq CDS 217475 218038 . - 0 ID=cds200;Parent=gene210;gene=frr;Name=YP_002343677.1;Dbxref=GOA:Q9PIR0 HSSP:Q9X1B9 InterPro:IPR002661 InterPro:IPR015998 UniProtKB FSwiss-Prot:Q9PIR0 Genbank:YP_002343677.1 GeneID:904561;gbkey=CDS;product=ribosome recycling factor;Note=Rrf 3B Frr 3B ribosome-recycling factor 3B release factor 4 3B RF4 3B recycles ribosomes upon translation termination along with release factor RF-3 and elongation factor EF-G 3B A GTPase-dependent process results in release of 50S from 70S 3B inhibited by release factor RF-1 3B essential for viability 3B structurally similar to tRNAs NC_002163.1 RefSeq region 217484 217978 . - . ID=id533;gene=frr;Name=id533;Dbxref=GeneID:904561;gbkey=misc_feature;Note=HMMPfam hit to PF01765 2C Ribosome recycling factor 2Cscore 4.9e-88 ### NC_002163.1 RefSeq CDS 218048 218419 . - 0 ID=cds201;Parent=gene211;gene=secG;Name=YP_002343678.1;Dbxref=GOA:Q0PBR9 InterPro:IPR004692 UniProtKB FTrEMBL:Q0PBR9 Genbank:YP_002343678.1 GeneID:904562;gbkey=CDS;product=preprotein translocase subunit SecG;Note=Original 282000 29 note: Cj0235c 2C secG 2C possible protein-export membrane protein 2C len: 123 aa 3B similar to e.g. SECG_PSESY protein-export membrane protein secG 28126 aa 29 2C fasta scores 3B opt: 157 z-score: 210.5 E 28 29: 0.00018 2C25.2 25 identity in 119 aa overlap. 48.8 25 identity to HP1255 7EUpdated 282006 29 note: Pfam domain PF03840 Preprotein translocase SecG subunit was identified within CDS. Also 2Ctwo probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity scores have been carried out yet. kept within product function. Functional classification - Protein and peptide secretion NC_002163.1 RefSeq gene 218048 218419 . - . ID=gene211;gene=secG;Name=secG;locus_tag=Cj0235c;Dbxref=GeneID:904562;gbkey=Gene NC_002163.1 RefSeq region 218201 218416 . - . ID=id534;gene=secG;Name=id534;Dbxref=GeneID:904562;gbkey=misc_feature;Note=HMMPfam hit to PF03840 2C Preprotein translocase SecG subunit 2C score 2.8e-24 NC_002163.1 RefSeq region 218207 218275 . - . ID=id17;gene=secG;Name=id17;Dbxref=GeneID:904562;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0235c by TMHMM2.0 at aa 5-22 and 49-71 NC_002163.1 RefSeq region 218354 218407 . - . ID=id17;gene=secG;Name=id17;Dbxref=GeneID:904562;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0235c by TMHMM2.0 at aa 5-22 and 49-71 ### NC_002163.1 UTR_Extractor 5'-UTR 218420 218446 . - . ID=utr83;locus_tag=Cj0235c;product=preprotein translocase subunit SecG NC_002163.1 RefSeq CDS 218523 219218 . - 0 ID=cds202;Parent=gene212;Name=YP_002343679.1;Dbxref=GOA:Q9PIQ8 InterPro:IPR006214 UniProtKB FSwiss-Prot:Q9PIQ8 Genbank:YP_002343679.1 GeneID:904563;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0236c 2C probable integral membrane protein 2C len: 231 aa similar to members of the UPF0005 family e.g. YCCA_PSEAE 28222 aa 29 2C fasta scores 3B opt: 377 z-score: 628.9 E 28 29: 8.9e-28 2C 37.7 25 identity in 207 aa overlap. 49.1 25 identity to HP0920. Contains Pfam match to entry PF01027 UPF0005 2C Uncharacterized protein family 2C score 128.30 2C E-value 1.4e-34 7EUpdated 282006 29 note: Six probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 218523 219218 . - . ID=gene212;Name=Cj0236c;locus_tag=Cj0236c;Dbxref=GeneID:904563;gbkey=Gene NC_002163.1 RefSeq region 218532 219167 . - . ID=id535;Name=id535;Dbxref=GeneID:904563;gbkey=misc_feature;Note=HMMPfam hit to PF01027 2C Uncharacterised protein family UPF0005 2C score 2.5e-36 NC_002163.1 RefSeq region 218649 218708 . - . ID=id18;Name=id18;Dbxref=GeneID:904563;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0236c by TMHMM2.0 at aa 32-54 2C 59-76 2C 89-111 2C 116-138 2C145-167 and 171-190 NC_002163.1 RefSeq region 218718 218786 . - . ID=id18;Name=id18;Dbxref=GeneID:904563;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0236c by TMHMM2.0 at aa 32-54 2C 59-76 2C 89-111 2C 116-138 2C145-167 and 171-190 NC_002163.1 RefSeq region 218805 218873 . - . ID=id18;Name=id18;Dbxref=GeneID:904563;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0236c by TMHMM2.0 at aa 32-54 2C 59-76 2C 89-111 2C 116-138 2C145-167 and 171-190 NC_002163.1 RefSeq region 218886 218954 . - . ID=id18;Name=id18;Dbxref=GeneID:904563;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0236c by TMHMM2.0 at aa 32-54 2C 59-76 2C 89-111 2C 116-138 2C145-167 and 171-190 NC_002163.1 RefSeq region 218991 219044 . - . ID=id18;Name=id18;Dbxref=GeneID:904563;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0236c by TMHMM2.0 at aa 32-54 2C 59-76 2C 89-111 2C 116-138 2C145-167 and 171-190 NC_002163.1 RefSeq region 219057 219125 . - . ID=id18;Name=id18;Dbxref=GeneID:904563;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0236c by TMHMM2.0 at aa 32-54 2C 59-76 2C 89-111 2C 116-138 2C145-167 and 171-190 ### NC_002163.1 UTR_Extractor 5'-UTR 219219 219258 . - . ID=utr84;locus_tag=Cj0236c;product=putative integral membrane protein NC_002163.1 UTR_Extractor 5'-UTR 219355 219377 . + . ID=utr85;locus_tag=Cj0237;product=carbonic anyhydrase NC_002163.1 RefSeq CDS 219378 220013 . + 0 ID=cds203;Parent=gene213;gene=cynT;Name=YP_002343680.1;Dbxref=GOA:Q0PBR7 InterPro:IPR001765 InterPro:IPR015892 UniProtKB FTrEMBL:Q0PBR7 Genbank:YP_002343680.1 GeneID:904564;gbkey=CDS;product=carbonic anyhydrase;Note=Original 282000 29 note: Cj0237 2C cynT 2C probable carbonic anyhydrase 2C len: 211 aa 3B similar to e.g. CYNT_ECOLI carbonic anhydrase 28EC 4.2.1.1 29 28219 aa 29 2C fasta scores 3B opt: 541 z-score: 776.7 E 28 29: 0 2C 41.2 25 identity in 204 aa overlap. 43.5 25 identity to HP0004. Contains PS00704 and PS00705 Prokaryotic-type carbonic anhydrases signatures 1 and 2 2C and Pfam match to entry PF00484 Pro_CA 2C Prokaryotic-type carbonic anhydrases 2C score 208.10 2C E-value 2.7e-59 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Central intermediary metabolism - General 7EPMID:1740425 2C PMID:14563877 NC_002163.1 RefSeq gene 219378 220013 . + . ID=gene213;gene=cynT;Name=cynT;locus_tag=Cj0237;Dbxref=GeneID:904564;gbkey=Gene NC_002163.1 RefSeq region 219456 219965 . + . ID=id536;gene=cynT;Name=id536;Dbxref=GeneID:904564;gbkey=misc_feature;Note=HMMPfam hit to PF00484 2C Carbonic anhydrase 2C score 1.9e-45 NC_002163.1 RefSeq region 219492 219515 . + . ID=id537;gene=cynT;Name=id537;Dbxref=GeneID:904564;gbkey=misc_feature;Note=PS00704 Prokaryotic-type carbonic anhydrases signature 1 NC_002163.1 RefSeq region 219627 219689 . + . ID=id538;gene=cynT;Name=id538;Dbxref=GeneID:904564;gbkey=misc_feature;Note=PS00705 Prokaryotic-type carbonic anhydrases signature 2 NC_002163.1 RefSeq gene 220010 221893 . + . ID=gene214;gene=mscS;Name=mscS;locus_tag=Cj0238;Dbxref=GeneID:904565;gbkey=Gene NC_002163.1 RefSeq CDS 220010 221893 . + 0 ID=cds204;Parent=gene214;Name=YP_002343681.1;Dbxref=GOA:Q0PBR6 InterPro:IPR006685 UniProtKB FTrEMBL:Q0PBR6 Genbank:YP_002343681.1 GeneID:904565;gbkey=CDS;product=mechanosensitive ion channel family protein;Note=Original 282000 29 note: Cj0238 2C probable integral membrane protein 2C len: 627 aa 3B similar in C-terminus to many hypothetical proteins 2C e.g. YB43_METJA MJ1143 28361 aa 29 2C fasta scores 3B opt: 413 z-score: 535.7 E 28 29: 1.4e-22 2C23.9 25 identity in 372 aa overlap. 36.3 25 identity in 608 aa overlap to HP0415. Contains Pfam match to entry PF00924 UPF0003 2C Uncharacterized protein family UPF0003 2C score 145.90 2C E-value 6.9e-40 7EUpdated 282006 29 note: Pfam domain PF00924 Mechanosensitive ion channel was identified within CDS. Product modified to more specific family member due to motif match. Paper identified linking protein to glycoprotein. No specific characterisation has been carried out yet 2C so kept within product function. Functional classification - Transport 2Fbinding proteins -Other NC_002163.1 RefSeq region 220721 220789 . + . ID=id539;Name=id539;Dbxref=GeneID:904565;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0238 by TMHMM2.0 at aa 238-260 2C 265-279 2C 300-322 2C332-354 2C 366-388 and 392-411 NC_002163.1 RefSeq region 220802 220846 . + . ID=id539;Name=id539;Dbxref=GeneID:904565;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0238 by TMHMM2.0 at aa 238-260 2C 265-279 2C 300-322 2C332-354 2C 366-388 and 392-411 NC_002163.1 RefSeq region 220907 220975 . + . ID=id539;Name=id539;Dbxref=GeneID:904565;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0238 by TMHMM2.0 at aa 238-260 2C 265-279 2C 300-322 2C332-354 2C 366-388 and 392-411 NC_002163.1 RefSeq region 221003 221071 . + . ID=id539;Name=id539;Dbxref=GeneID:904565;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0238 by TMHMM2.0 at aa 238-260 2C 265-279 2C 300-322 2C332-354 2C 366-388 and 392-411 NC_002163.1 RefSeq region 221105 221173 . + . ID=id539;Name=id539;Dbxref=GeneID:904565;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0238 by TMHMM2.0 at aa 238-260 2C 265-279 2C 300-322 2C332-354 2C 366-388 and 392-411 NC_002163.1 RefSeq region 221123 221824 . + . ID=id540;Name=id540;Dbxref=GeneID:904565;gbkey=misc_feature;Note=HMMPfam hit to PF00924 2C Mechanosensitive ion channel 2C score 2e-68 NC_002163.1 RefSeq region 221183 221242 . + . ID=id539;Name=id539;Dbxref=GeneID:904565;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0238 by TMHMM2.0 at aa 238-260 2C 265-279 2C 300-322 2C332-354 2C 366-388 and 392-411 ### NC_002163.1 RefSeq CDS 221916 222887 . - 0 ID=cds205;Parent=gene215;Name=YP_002343682.1;Dbxref=GOA:Q0PBR5 InterPro:IPR001075 InterPro:IPR002871 InterPro:IPR007419 InterPro:IPR016217 UniProtKB FTrEMBL:Q0PBR5 Genbank:YP_002343682.1 GeneID:904566;gbkey=CDS;product=NifU protein;Note=Original 282000 29 note: Cj0239c 2C nifU protein homolog 2C len: 323 aa 3B similar to many e.g. NIFU_AZOVI nifU protein 28312 aa 29 2C fasta scores 3B opt: 627 z-score: 910.4 E 28 29: 0 2C 37.0 25 identity in 330 aa overlap. 68.8 25 identity to HP0221. Also similar in C-terminus to Cj1639 2838.2 25 identity in 76 aa overlap 29. Contains Pfam match to entry PF01106 NifU-like 2C NifU-like domain 2C score 100.40 2C E-value 3.5e-26 7EUpdated 282006 29 note: Pfam domains PF01592 NifU-like N terminal domain and PF04324 which is a BFD-like 5B2Fe-2S 5D binding domain identified within CDS. Further support given to product function. Functional classification -Conserved hypothetical proteins 7EPMID:7947754 2C PMID:10819462 NC_002163.1 RefSeq gene 221916 222887 . - . ID=gene215;Name=Cj0239c;locus_tag=Cj0239c;Dbxref=GeneID:904566;gbkey=Gene NC_002163.1 RefSeq region 221919 222140 . - . ID=id541;Name=id541;Dbxref=GeneID:904566;gbkey=misc_feature;Note=HMMPfam hit to PF01106 2C NifU-like domain 2C score 2.1e-27 NC_002163.1 RefSeq region 222255 222416 . - . ID=id542;Name=id542;Dbxref=GeneID:904566;gbkey=misc_feature;Note=HMMPfam hit to PF04324 2C BFD-like 5B2Fe-2S 5D binding domain 2C score 5.7e-15 NC_002163.1 RefSeq region 222429 222848 . - . ID=id543;Name=id543;Dbxref=GeneID:904566;gbkey=misc_feature;Note=HMMPfam hit to PF01592 2C NifU-like N terminal domain 2C score 2.9e-64 ### NC_002163.1 RefSeq CDS 222897 224078 . - 0 ID=cds206;Parent=gene216;gene=iscS;Name=YP_002343683.1;Dbxref=GOA:Q0PBR4 InterPro:IPR000192 InterPro:IPR000834 InterPro:IPR015421 InterPro:IPR016454 InterPro:IPR017773 UniProtKB FTrEMBL:Q0PBR4 Genbank:YP_002343683.1 GeneID:904567;gbkey=CDS;product=cysteine desulfurase;Note=Original 282000 29 note: Cj0240c 2C probable aminotransferase 28nifS protein homolog 29 2C len: 393 aa 3B similar to many e.g. NIFS_KLEPN nifS protein 28397 aa 29 2Cfasta scores 3B opt: 1067 z-score: 1533.6 E 28 29: 0 2C 47.0 25 identity in 383 aa overlap. 62.8 25 identity to HP0220. Contains PS00132 Zinc carboxypeptidases 2C zinc-binding region 1 signature 2C PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site 2C and Pfam match to entry PF00266 aminotran_5 2C Aminotransferases class-V 2Cscore 358.80 2C E-value 5.9e-104 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. Product modified to more specific family member based on characterisation papers. not added to product function. Functional classification - Misc 7EPMID:10908675 2C PMID:10781607 2C PMID:12860127 2CPMID:3040672 2C PMID:8464885 NC_002163.1 RefSeq gene 222897 224078 . - . ID=gene216;gene=iscS;Name=iscS;locus_tag=Cj0240c;Dbxref=GeneID:904567;gbkey=Gene NC_002163.1 RefSeq region 222978 224042 . - . ID=id544;gene=iscS;Name=id544;Dbxref=GeneID:904567;gbkey=misc_feature;Note=HMMPfam hit to PF00266 2C Aminotransferase class-V 2Cscore 3.2e-105 NC_002163.1 RefSeq region 223101 223133 . - . ID=id545;gene=iscS;Name=id545;Dbxref=GeneID:904567;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 223359 223427 . - . ID=id546;gene=iscS;Name=id546;Dbxref=GeneID:904567;gbkey=misc_feature;Note=PS00132 Zinc carboxypeptidases 2C zinc-binding region 1 signature NC_002163.1 RefSeq region 223437 223496 . - . ID=id547;gene=iscS;Name=id547;Dbxref=GeneID:904567;gbkey=misc_feature;Note=PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site ### NC_002163.1 RefSeq CDS 224256 224657 . - 0 ID=cds207;Parent=gene217;Name=YP_002343684.1;Dbxref=GOA:Q9PIQ3 InterPro:IPR012312 InterPro:IPR012827 InterPro:IPR016131 UniProtKB FSwiss-Prot:Q9PIQ3 Genbank:YP_002343684.1 GeneID:904568;gbkey=CDS;product=iron-binding protein;Note=Original 282000 29 note: Cj0241c 2C possible iron-binding protein 2C len: 133 aa 3B Weak similarity to members of the eukaryotic iron-binding hemerythrin family 2Ce.g. HEMT_LINUN hemerythrin alpha chain 28117 aa 29 2C fasta scores 3B opt: 93 z-score: 135.4 E 28 29: 3.1 2C 27.3 25 identity in 77 aa overlap. Note that all of the iron-binding residues are conserved. No Hp match. Also similar to Cj1224 2834.7 25 identity in 118 aa overlap 29 2C Cj0072c 2840.5 25 identity in 79 aa overlap 29 and Cj0045c 2830.9 25 identity in 123 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01814 Hemerythrin HHE cation binding domain identified within CDS. No specific characterisation with acceptable identity score has been carried out yet. Thus 2C kept within product function. Functional classification -Transport 2Fbinding proteins - Cations NC_002163.1 RefSeq gene 224256 224657 . - . ID=gene217;Name=Cj0241c;locus_tag=Cj0241c;Dbxref=GeneID:904568;gbkey=Gene NC_002163.1 RefSeq region 224280 224447 . - . ID=id548;Name=id548;Dbxref=GeneID:904568;gbkey=misc_feature;Note=HMMPfam hit to PF01814 2C Hemerythrin HHE cation binding domain 2C score 0.0029 NC_002163.1 RefSeq region 224457 224627 . - . ID=id549;Name=id549;Dbxref=GeneID:904568;gbkey=misc_feature;Note=HMMPfam hit to PF01814 2C Hemerythrin HHE cation binding domain 2C score 0.0079 ### NC_002163.1 RefSeq gene 224794 225960 . - . ID=gene218;Name=Cj0243c;locus_tag=Cj0243c;Dbxref=GeneID:904569;gbkey=Gene NC_002163.1 RefSeq CDS 224794 225960 . - 0 ID=cds208;Parent=gene218;Name=YP_002343685.1;Dbxref=UniProtKB FTrEMBL:Q0PBR2 Genbank:YP_002343685.1 GeneID:904569;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0243c 2C unknown 2C len: 388 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 UTR_Extractor 5'-UTR 226068 226115 . + . ID=utr86;locus_tag=Cj0244;product=50S ribosomal protein L35 NC_002163.1 RefSeq gene 226116 226307 . + . ID=gene219;gene=rpmI;Name=rpmI;locus_tag=Cj0244;Dbxref=GeneID:904570;gbkey=Gene NC_002163.1 RefSeq CDS 226116 226307 . + 0 ID=cds209;Parent=gene219;gene=rpmI;Name=YP_002343686.1;Dbxref=GOA:Q9PIQ1 InterPro:IPR001706 UniProtKB FSwiss-Prot:Q9PIQ1 Genbank:YP_002343686.1 GeneID:904570;gbkey=CDS;product=50S ribosomal protein L35;Note=Original 282000 29 note: Cj0244 2C rpmI 2C 50s ribosomal protein L35 2C len: 63 aa 3B similar to many e.g. RL35_ECOLI 50s ribosomal protein L35 2864 aa 29 2C fasta scores 3B opt: 133 z-score: 282.3 E 28 29: 1.8e-08. 45.6 25 identity in 57 aa overlap. 60.7 25 identity to HP0125 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Ribosomal protein synthesis and modification 7EPMID:16272117 NC_002163.1 RefSeq region 226125 226298 . + . ID=id550;gene=rpmI;Name=id550;Dbxref=GeneID:904570;gbkey=misc_feature;Note=HMMPfam hit to PF01632 2C Ribosomal protein L35 2Cscore 4.9e-18 ### NC_002163.1 RefSeq CDS 226401 226754 . + 0 ID=cds210;Parent=gene220;gene=rplT;Name=YP_002343687.1;Dbxref=GOA:Q9PIQ0 HSSP:O67086 InterPro:IPR005812 InterPro:IPR005813 UniProtKB FSwiss-Prot:Q9PIQ0 Genbank:YP_002343687.1 GeneID:904571;gbkey=CDS;product=50S ribosomal protein L20;Note=binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit NC_002163.1 RefSeq gene 226401 226754 . + . ID=gene220;gene=rplT;Name=rplT;locus_tag=Cj0245;Dbxref=GeneID:904571;gbkey=Gene NC_002163.1 RefSeq region 226404 226727 . + . ID=id551;gene=rplT;Name=id551;Dbxref=GeneID:904571;gbkey=misc_feature;Note=HMMPfam hit to PF00453 2C Ribosomal protein L20 2Cscore 4.5e-51 NC_002163.1 RefSeq region 226560 226610 . + . ID=id552;gene=rplT;Name=id552;Dbxref=GeneID:904571;gbkey=misc_feature;Note=PS00937 Ribosomal protein L20 signature ### NC_002163.1 UTR_Extractor 5'-UTR 227935 228028 . - . ID=utr87;locus_tag=Cj0246c;product=putative MCP-domain signal transduction protein NC_002163.1 UTR_Extractor 5'-UTR 228913 228945 . + . ID=utr88;locus_tag=Cj0248;product=hypothetical protein NC_002163.1 RefSeq gene 228946 229803 . + . ID=gene221;Name=Cj0248;locus_tag=Cj0248;Dbxref=GeneID:904574;gbkey=Gene NC_002163.1 RefSeq CDS 228946 229803 . + 0 ID=cds211;Parent=gene221;Name=YP_002343690.1;Dbxref=InterPro:IPR013976 UniProtKB FTrEMBL:Q0PBQ7 Genbank:YP_002343690.1 GeneID:904574;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0248 2C unknown 2C len: 285 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to proteins from other bacteria. Literature search identified papers giving structural characterisation and clues to product function. Currently unknown function but may be some kind of hydrolase or signal-transduction protein. Cj0248 has been implicated as a virulence factor and has been shown to play a role in motility. Functional classification -Unknown 7EPMID:16287129 2C PMID:15066034 2C PMID:11298288 NC_002163.1 RefSeq CDS 229831 230310 . + 0 ID=cds212;Parent=gene222;Name=YP_002343691.1;Dbxref=UniProtKB FTrEMBL:Q0PBQ6 Genbank:YP_002343691.1 GeneID:904575;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0249 2C unknown 2C len: 159 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 RefSeq gene 229831 230310 . + . ID=gene222;Name=Cj0249;locus_tag=Cj0249;Dbxref=GeneID:904575;gbkey=Gene NC_002163.1 RefSeq CDS 230279 231589 . - 0 ID=cds213;Parent=gene223;Name=YP_002343692.1;Dbxref=GOA:Q0PBQ5 InterPro:IPR007114 InterPro:IPR011701 UniProtKB FTrEMBL:Q0PBQ5 Genbank:YP_002343692.1 GeneID:904576;gbkey=CDS;product=MFS transport protein;Note=Original 282000 29 note: Cj0250c 2C probable transmembrane transport protein 2C len: 436 aa 3B similar to many members of the sugar transport protein family 2C e.g. PROP_ECOLI proline 2Fbetaine transporter 28500 aa 29 2C fasta scores 3B opt: 602 z-score: 791.3 E 28 29: 0 2C 31.7 25 identity in 394 aa overlapCIT1_SALTY citrate-proton symport 28citrate transporter 29 28434 aa 29 2C fasta scores 3B opt: 580 z-score: 734.9 E 28 29: 0 2C 28.0 25 identity in 396 aa overlap. 50.9 25 identity to HP0936. Contains Pfam match to entry PF00083 sugar_tr 2C Sugar 28and other 29 transporters 2C score 93.10 2CE-value 5.5e-24 7EUpdated 282006 29 note: Pfam domain PF07690 Major Facilitator Superfamily was identified within CDS in addition to previous PF0083. Prosite domain PS50850 MFS 2CMajor facilitator superfamily was also identified. Also 2Ctwelve probable transmembrane helices predicted by TMHMM2.0. Product modified to more specific family member due to motif match. kept within product function. Functional classification - Transport 2Fbinding proteins -Other NC_002163.1 RefSeq gene 230279 231589 . - . ID=gene223;Name=Cj0250c;locus_tag=Cj0250c;Dbxref=GeneID:904576;gbkey=Gene NC_002163.1 RefSeq region 230288 231556 . - . ID=id553;Name=id553;Dbxref=GeneID:904576;gbkey=misc_feature;Note=HMMPfam hit to PF00083 2C Sugar 28and other 29 transporter 2C score 4.5e-24 NC_002163.1 RefSeq region 230309 230377 . - . ID=id19;Name=id19;Dbxref=GeneID:904576;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0250c by TMHMM2.0 at aa 13-35 2C 55-77 2C 84-103 2C 108-130 2C151-173 2C 186-208 2C 238-260 2C 275-297 2C 302-324 2C 334-356 2C368-390 and 405-427 NC_002163.1 RefSeq region 230420 230488 . - . ID=id19;Name=id19;Dbxref=GeneID:904576;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0250c by TMHMM2.0 at aa 13-35 2C 55-77 2C 84-103 2C 108-130 2C151-173 2C 186-208 2C 238-260 2C 275-297 2C 302-324 2C 334-356 2C368-390 and 405-427 NC_002163.1 RefSeq region 230426 231508 . - . ID=id554;Name=id554;Dbxref=GeneID:904576;gbkey=misc_feature;Note=HMMPfam hit to PF07690 2C Major Facilitator Superfamily 2C score 3.4e-20 NC_002163.1 RefSeq region 230522 230590 . - . ID=id19;Name=id19;Dbxref=GeneID:904576;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0250c by TMHMM2.0 at aa 13-35 2C 55-77 2C 84-103 2C 108-130 2C151-173 2C 186-208 2C 238-260 2C 275-297 2C 302-324 2C 334-356 2C368-390 and 405-427 NC_002163.1 RefSeq region 230618 230686 . - . ID=id19;Name=id19;Dbxref=GeneID:904576;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0250c by TMHMM2.0 at aa 13-35 2C 55-77 2C 84-103 2C 108-130 2C151-173 2C 186-208 2C 238-260 2C 275-297 2C 302-324 2C 334-356 2C368-390 and 405-427 NC_002163.1 RefSeq region 230699 230767 . - . ID=id19;Name=id19;Dbxref=GeneID:904576;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0250c by TMHMM2.0 at aa 13-35 2C 55-77 2C 84-103 2C 108-130 2C151-173 2C 186-208 2C 238-260 2C 275-297 2C 302-324 2C 334-356 2C368-390 and 405-427 NC_002163.1 RefSeq region 230810 230878 . - . ID=id19;Name=id19;Dbxref=GeneID:904576;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0250c by TMHMM2.0 at aa 13-35 2C 55-77 2C 84-103 2C 108-130 2C151-173 2C 186-208 2C 238-260 2C 275-297 2C 302-324 2C 334-356 2C368-390 and 405-427 NC_002163.1 RefSeq region 230834 230866 . - . ID=id555;Name=id555;Dbxref=GeneID:904576;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 230966 231034 . - . ID=id19;Name=id19;Dbxref=GeneID:904576;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0250c by TMHMM2.0 at aa 13-35 2C 55-77 2C 84-103 2C 108-130 2C151-173 2C 186-208 2C 238-260 2C 275-297 2C 302-324 2C 334-356 2C368-390 and 405-427 NC_002163.1 RefSeq region 231071 231139 . - . ID=id19;Name=id19;Dbxref=GeneID:904576;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0250c by TMHMM2.0 at aa 13-35 2C 55-77 2C 84-103 2C 108-130 2C151-173 2C 186-208 2C 238-260 2C 275-297 2C 302-324 2C 334-356 2C368-390 and 405-427 NC_002163.1 RefSeq region 231200 231268 . - . ID=id19;Name=id19;Dbxref=GeneID:904576;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0250c by TMHMM2.0 at aa 13-35 2C 55-77 2C 84-103 2C 108-130 2C151-173 2C 186-208 2C 238-260 2C 275-297 2C 302-324 2C 334-356 2C368-390 and 405-427 NC_002163.1 RefSeq region 231281 231340 . - . ID=id19;Name=id19;Dbxref=GeneID:904576;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0250c by TMHMM2.0 at aa 13-35 2C 55-77 2C 84-103 2C 108-130 2C151-173 2C 186-208 2C 238-260 2C 275-297 2C 302-324 2C 334-356 2C368-390 and 405-427 NC_002163.1 RefSeq region 231359 231427 . - . ID=id19;Name=id19;Dbxref=GeneID:904576;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0250c by TMHMM2.0 at aa 13-35 2C 55-77 2C 84-103 2C 108-130 2C151-173 2C 186-208 2C 238-260 2C 275-297 2C 302-324 2C 334-356 2C368-390 and 405-427 NC_002163.1 RefSeq region 231485 231553 . - . ID=id19;Name=id19;Dbxref=GeneID:904576;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0250c by TMHMM2.0 at aa 13-35 2C 55-77 2C 84-103 2C 108-130 2C151-173 2C 186-208 2C 238-260 2C 275-297 2C 302-324 2C 334-356 2C368-390 and 405-427 ### NC_002163.1 RefSeq gene 231592 231747 . - . ID=gene224;Name=Cj0251c;locus_tag=Cj0251c;Dbxref=GeneID:904577;gbkey=Gene NC_002163.1 RefSeq CDS 231592 231747 . - 0 ID=cds214;Parent=gene224;Name=YP_002343693.1;Dbxref=UniProtKB FTrEMBL:Q0PBQ4 Genbank:YP_002343693.1 GeneID:904577;gbkey=CDS;product=highly acidic protein;Note=Original 282000 29 note: Cj0251c 2C highly acidic protein 2C len: 51 aa 3B 47.9 25 identity to HP0756. Functional classification - Conserved hypothetical proteins NC_002163.1 UTR_Extractor 5'-UTR 231748 231771 . - . ID=utr89;locus_tag=Cj0251c;product=highly acidic protein NC_002163.1 UTR_Extractor 5'-UTR 231819 231839 . + . ID=utr90;locus_tag=Cj0252;product=molybdenum cofactor biosynthesis protein MoaC NC_002163.1 RefSeq CDS 231840 232313 . + 0 ID=cds215;Parent=gene225;gene=moaC;Name=YP_002343694.1;Dbxref=GOA:Q9PIP3 HSSP:P30747 InterPro:IPR002820 UniProtKB FSwiss-Prot:Q9PIP3 Genbank:YP_002343694.1 GeneID:904578;gbkey=CDS;product=molybdenum cofactor biosynthesis protein MoaC;Note=MoaC 3B along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z 3B involved in molybdenum cofactor biosynthesis NC_002163.1 RefSeq gene 231840 232313 . + . ID=gene225;gene=moaC;Name=moaC;locus_tag=Cj0252;Dbxref=GeneID:904578;gbkey=Gene NC_002163.1 RefSeq region 231879 232286 . + . ID=id556;gene=moaC;Name=id556;Dbxref=GeneID:904578;gbkey=misc_feature;Note=HMMPfam hit to PF01967 2C MoaC family 2C score 6.3e-78 NC_002163.1 RefSeq CDS 232291 232554 . + 0 ID=cds216;Parent=gene226;Name=YP_002343695.1;Dbxref=UniProtKB FSwiss-Prot:Q9PIP2 Genbank:YP_002343695.1 GeneID:904579;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0253 2C unknown 2C len: 87 aa 3B 33.8 25 identity to HP0495. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 232291 232554 . + . ID=gene226;gene=Cj0253;Name=Cj0253;locus_tag=Cj0253;Dbxref=GeneID:904579;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 232533 232543 . + . ID=utr91;locus_tag=Cj0254;product=hypothetical protein NC_002163.1 RefSeq gene 232544 233704 . + . ID=gene227;Name=Cj0254;locus_tag=Cj0254;Dbxref=GeneID:904580;gbkey=Gene NC_002163.1 RefSeq CDS 232544 233704 . + 0 ID=cds217;Parent=gene227;Name=YP_002343696.1;Dbxref=UniProtKB FTrEMBL:Q0PBQ1 Genbank:YP_002343696.1 GeneID:904580;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0254 2C unknown 2C len: 386 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown ### NC_002163.1 RefSeq gene 233723 234481 . - . ID=gene228;gene=exoA;Name=exoA;locus_tag=Cj0255c;Dbxref=GeneID:904581;gbkey=Gene NC_002163.1 RefSeq CDS 233723 234481 . - 0 ID=cds218;Parent=gene228;gene=exoA;Name=YP_002343697.1;Dbxref=GOA:Q0PBQ0 InterPro:IPR000097 InterPro:IPR004808 InterPro:IPR005135 UniProtKB FTrEMBL:Q0PBQ0 Genbank:YP_002343697.1 GeneID:904581;gbkey=CDS;product=exodeoxyribonuclease;Note=Original 282000 29 note: Cj0255c 2C probable exodeoxyribonuclease 2C len: 252 aa 3B similar to many e.g. EXOA_BACSU exodeoxyribonuclease 28EC 3.1.11.2 29 28252 aa 29 2Cfasta scores 3B opt: 676 z-score: 868.1 E 28 29: 0 2C 40.5 25 identity in 259 aa overlap. 41.1 25 identity to HP1526. Contains Pfam match to entry PF01260 AP_endonulease1 2C AP endonucleases family 1 2C score 282.10 2C E-value 7.3e-81 7EUpdated 282006 29 note: Pfam domain PF03372 2CEndonuclease 2FExonuclease 2Fphosphatase family identified within CDS. Further support given to product function. Characterised within Bacillus subtilis with acceptable identity score. not added to product function. Functional classification - DNA replication 2Crestriction 2Fmodification 2C recombination and repair 7EPMID:10540738 NC_002163.1 RefSeq region 233732 234481 . - . ID=id557;gene=exoA;Name=id557;Dbxref=GeneID:904581;gbkey=misc_feature;Note=HMMPfam hit to PF03372 2CEndonuclease 2FExonuclease 2Fphosphatase fa 2C score 5.2e-47 ### NC_002163.1 UTR_Extractor 5'-UTR 234482 234509 . - . ID=utr92;locus_tag=Cj0255c;product=exodeoxyribonuclease NC_002163.1 UTR_Extractor 5'-UTR 234574 234598 . + . ID=utr93;locus_tag=Cj0256;product=putative sulfatase family protein NC_002163.1 RefSeq CDS 234599 236137 . + 0 ID=cds219;Parent=gene229;Name=YP_002343698.1;Dbxref=GOA:Q0PBP9 InterPro:IPR000917 InterPro:IPR012549 UniProtKB FTrEMBL:Q0PBP9 Genbank:YP_002343698.1 GeneID:904582;gbkey=CDS;product=sulfatase family protein;Note=Original 282000 29 note: Cj0256 2C probable integral membrane protein 2C len: 512 aa 3B similar to hypothetical proteins e.g. YJDB_ECOLI 28547 aa 29 2C fasta scores 3B opt: 646 z-score: 1169.8 E 28 29: 0 2C 38.9 25 identity in 530 aa overlap. 34.1 25 identity to HP0022 7EUpdated 282006 29 note: Pfam domain PF00884 Sulfatase identified within CDS. Also 2C five probable transmembrane helices predicted by TMHMM2.0. Product modified to more specific family member based on motif match. No specific characterisation has been carried out yet 2C so kept within product function. Literature search identified paper giving further clues to product function. Functional classification - Misc 7EPMID:11895937 NC_002163.1 RefSeq gene 234599 236137 . + . ID=gene229;Name=Cj0256;locus_tag=Cj0256;Dbxref=GeneID:904582;gbkey=Gene NC_002163.1 RefSeq region 234611 234679 . + . ID=id558;Name=id558;Dbxref=GeneID:904582;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0256 by TMHMM2.0 at aa 5-27 2C 37-59 2C 66-88 2C 108-127 and 148-170 NC_002163.1 RefSeq region 234707 234775 . + . ID=id558;Name=id558;Dbxref=GeneID:904582;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0256 by TMHMM2.0 at aa 5-27 2C 37-59 2C 66-88 2C 108-127 and 148-170 NC_002163.1 RefSeq region 234794 234862 . + . ID=id558;Name=id558;Dbxref=GeneID:904582;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0256 by TMHMM2.0 at aa 5-27 2C 37-59 2C 66-88 2C 108-127 and 148-170 NC_002163.1 RefSeq region 234920 234979 . + . ID=id558;Name=id558;Dbxref=GeneID:904582;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0256 by TMHMM2.0 at aa 5-27 2C 37-59 2C 66-88 2C 108-127 and 148-170 NC_002163.1 RefSeq region 235040 235108 . + . ID=id558;Name=id558;Dbxref=GeneID:904582;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0256 by TMHMM2.0 at aa 5-27 2C 37-59 2C 66-88 2C 108-127 and 148-170 NC_002163.1 RefSeq region 235247 236128 . + . ID=id559;Name=id559;Dbxref=GeneID:904582;gbkey=misc_feature;Note=HMMPfam hit to PF00884 2C Sulfatase 2C score 1.3e-98 NC_002163.1 RefSeq region 236134 236478 . + . ID=id560;gene=dgkA;Name=id560;Dbxref=GeneID:904583;gbkey=misc_feature;Note=HMMPfam hit to PF01219 2C Prokaryotic diacylglycerol kinase 2C score 3.3e-32 NC_002163.1 RefSeq gene 236134 236490 . + . ID=gene230;gene=dgkA;Name=dgkA;locus_tag=Cj0257;Dbxref=GeneID:904583;gbkey=Gene NC_002163.1 RefSeq CDS 236134 236490 . + 0 ID=cds220;Parent=gene230;gene=dgkA;Name=YP_002343699.1;Dbxref=GOA:Q0PBP8 InterPro:IPR000829 UniProtKB FTrEMBL:Q0PBP8 Genbank:YP_002343699.1 GeneID:904583;gbkey=CDS;product=diacylglycerol kinase;Note=Original 282000 29 note: Cj0257 2C dgkA 2C probale diacylglycerol kinase 2C len: 118 aa 3B similar to many e.g. KDGL_ECOLI diacylglycerol kinase 28EC 2.7.1.107 29 28121 aa 29 2Cfasta scores 3B opt: 263 z-score: 425.4 E 28 29: 1.9e-16 2C 41.7 25 identity in 108 aa overlap. 38.7 25 identity to HP0700. Contains PS01069 Prokaryotic diacylglycerol kinase signature and Pfam match to entry PF01219 DAGK_prokar 2CProkaryotic diacylglycerol kinase 2C score 114.40 2C E-value 2.2e-30 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Synthesis and modification of macromolecules -Phospholipids 7EPMID:2984194 2C PMID:3015952 NC_002163.1 RefSeq region 236209 236268 . + . ID=id561;gene=dgkA;Name=id561;Dbxref=GeneID:904583;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0257 by TMHMM2.0 at aa 26-45 2C 52-74 and 94-116 NC_002163.1 RefSeq region 236287 236355 . + . ID=id561;gene=dgkA;Name=id561;Dbxref=GeneID:904583;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0257 by TMHMM2.0 at aa 26-45 2C 52-74 and 94-116 NC_002163.1 RefSeq region 236329 236364 . + . ID=id562;gene=dgkA;Name=id562;Dbxref=GeneID:904583;gbkey=misc_feature;Note=PS01069 Prokaryotic diacylglycerol kinase signature NC_002163.1 RefSeq region 236413 236481 . + . ID=id561;gene=dgkA;Name=id561;Dbxref=GeneID:904583;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0257 by TMHMM2.0 at aa 26-45 2C 52-74 and 94-116 NC_002163.1 UTR_Extractor 5'-UTR 236485 236486 . + . ID=utr94;locus_tag=Cj0258;product=ArsR family regulatory protein NC_002163.1 RefSeq gene 236487 236732 . + . ID=gene231;gene=arsR;Name=arsR;locus_tag=Cj0258;Dbxref=GeneID:904584;gbkey=Gene NC_002163.1 RefSeq CDS 236487 236732 . + 0 ID=cds221;Parent=gene231;Name=YP_002343700.1;Dbxref=UniProtKB FTrEMBL:Q0PBP7 Genbank:YP_002343700.1 GeneID:904584;gbkey=CDS;product=ArsR family transcriptional regulator;Note=Original 282000 29 note: Cj0258 2C possible DNA binding protein 2C len: 81 aa 3B no Hp match. Contains probable helix-turn-helix motif at aa 35-56 28Score 1128 2C 2B3.03 SD 29 7EUpdated 282006 29 note: Pfam domain PF01022 Bacterial regulatory protein 2C arsR family was identified within CDS. This was found by carrying out own Pfam search. Product modified to more specific family member due to motif match. No specific characterisation has been carried out yet 2C so kept within product function. Literature search identified paper with some additional information. Functional classification - Broad regulatory functions 7EPMID:15231810 NC_002163.1 RefSeq CDS 236722 237729 . + 0 ID=cds222;Parent=gene232;gene=pyrC;Name=YP_002343701.1;Dbxref=GOA:Q0PBP6 InterPro:IPR002195 InterPro:IPR004721 InterPro:IPR006992 UniProtKB FTrEMBL:Q0PBP6 Genbank:YP_002343701.1 GeneID:904585;gbkey=CDS;product=dihydroorotase;Note=catalyzes the formation of N-carbamoyl-L-aspartate from 28S 29-dihydroorotate in pyrimidine biosynthesis NC_002163.1 RefSeq gene 236722 237729 . + . ID=gene232;gene=pyrC;Name=pyrC;locus_tag=Cj0259;Dbxref=GeneID:904585;gbkey=Gene NC_002163.1 RefSeq region 236725 237726 . + . ID=id563;gene=pyrC;Name=id563;Dbxref=GeneID:904585;gbkey=misc_feature;Note=HMMPfam hit to PF01979 2C Amidohydrolase family 2Cscore 1.7e-60 NC_002163.1 RefSeq region 236743 236769 . + . ID=id564;gene=pyrC;Name=id564;Dbxref=GeneID:904585;gbkey=misc_feature;Note=PS00482 Dihydroorotase signature 1 NC_002163.1 RefSeq region 237424 237459 . + . ID=id565;gene=pyrC;Name=id565;Dbxref=GeneID:904585;gbkey=misc_feature;Note=PS00483 Dihydroorotase signature 2 NC_002163.1 RefSeq sRNA 237728 237792 . - . ID=NC_002163.1:CJnc11:unknown_transcript_1;Parent=NC_002163.1:CJnc11;Name=NC_002163.1:CJnc11:unknown_transcript_1;locus_tag=CJnc11;gbkey=misc_RNA;product=CJnc11 NC_002163.1 RefSeq gene 237728 237792 . - . ID=NC_002163.1:CJnc11;Name=NC_002163.1:CJnc11;locus_tag=CJnc11 NC_002163.1 RefSeq CDS 237761 237976 . - 0 ID=cds223;Parent=gene233;Name=YP_002343702.1;Dbxref=UniProtKB FTrEMBL:Q0PBP5 Genbank:YP_002343702.1 GeneID:904586;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0260c 2C unknown 2C len: 71 aa 3B no Hp match 2C very hydrophobic 7EUpdated 282006 29 note: Two probable transmembrane helices identified by TMHMM2.0. Functional classification - Unknown NC_002163.1 RefSeq gene 237761 237976 . - . ID=gene233;Name=Cj0260c;locus_tag=Cj0260c;Dbxref=GeneID:904586;gbkey=Gene NC_002163.1 RefSeq region 237797 237865 . - . ID=id20;Name=id20;Dbxref=GeneID:904586;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0260c by TMHMM2.0 at aa 12-34 and 38-60 NC_002163.1 RefSeq region 237875 237943 . - . ID=id20;Name=id20;Dbxref=GeneID:904586;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0260c by TMHMM2.0 at aa 12-34 and 38-60 ### NC_002163.1 UTR_Extractor 5'-UTR 237977 237997 . - . ID=utr95;locus_tag=Cj0260c;product=hypothetical protein NC_002163.1 RefSeq gene 238032 238751 . - . ID=gene234;Name=Cj0261c;locus_tag=Cj0261c;Dbxref=GeneID:904587;gbkey=Gene NC_002163.1 RefSeq CDS 238032 238751 . - 0 ID=cds224;Parent=gene234;Name=YP_002343703.1;Dbxref=GOA:Q0PBP4 InterPro:IPR013217 UniProtKB FTrEMBL:Q0PBP4 Genbank:YP_002343703.1 GeneID:904587;gbkey=CDS;product=SAM-dependent methyltransferase;Note=Original 282000 29 note: Cj0261c 2C unknown 2C len: 239 aa 3B some similarity in N-terminus to YC73_HAEIN hypothetical protein HI1273 28268 aa 29 2C fasta scores 3B opt: 208 z-score: 260.9 E 28 29: 2.8e-07 2C 29.0 25 identity in 176 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF08241 and PF08242 Methyltransferase domains were identified within CDS. ProfileScan also identified PS50193 SAM_BIND domain. Members from methyltransferase family are SAM dependent methyltransferases. This was found by carrying out own Pfam search. Product modified to more specific family member due to motif match. No specific characterisation has been carried out yet 2C so kept within product function. Functional classification - Misc NC_002163.1 UTR_Extractor 5'-UTR 238752 238772 . - . ID=utr96;locus_tag=Cj0261c;product=putative SAM-dependent methyltransferase NC_002163.1 RefSeq repeat_region 238818 239964 . - . ID=id566;Name=id566;gbkey=repeat_region;Note=repeat 1: identical to 147606..148684 and 1492913..1493990 28approximate numbers 29 NC_002163.1 RefSeq CDS 238832 240829 . - 0 ID=cds225;Parent=gene235;Name=YP_002343704.1;Dbxref=GOA:Q0PBP3 InterPro:IPR003660 InterPro:IPR004010 InterPro:IPR004089 InterPro:IPR008762 UniProtKB FTrEMBL:Q0PBP3 Genbank:YP_002343704.1 GeneID:904377;gbkey=CDS;product=methyl-accepting chemotaxis signal transduction protein;Note=Original 282000 29 note: Cj0262c 2C probable methyl-accepting chemotaxis signal transduction protein 2Clen: 665 aa 3B similar to many e.g. TR:O32443 28EMBL:D86947 29 Pseudomonas aeruginosa chemotactic transducer 28629 aa 29 2Cfasta scores 3B opt: 283 z-score: 635.0 E 28 29: 4.1e-28 2C 25.3 25 identity in 667 aa overlap 2C and MCP1_ECOLI methyl-accepting chemotaxis protein I 28551 aa 29 2C fasta scores 3B opt: 280 z-score: 519.1 E 28 29: 1.2e-21. 29.1 25 identity in 302 aa overlap. No Hp ortholog. C-terminus contains repeat1 2C and is identical to the other repeat 1-containing genes Cj0262c and Cj1564. Contains N-terminal signal sequence and transmembrane anchor around aa 300. Also contains Pfam match to entry PF00015 MCPsignal 2CMethyl-accepting chemotaxis protein 28MCP 29 signaling domain 2C score 110.60 2C E-value 4.1e-30 7EUpdated 282006 29 note: Pfam motifs PF05581 Vibrio chemotaxis protein N terminus 2C PF02743 Cache domain and PF00672 HAMP domain were identified within CDS. Further support given to product function. Literature search identified supporting papers giving further clues to product function. No specific characterisation with acceptable identity score has been carried out yet. kept within product function. Functional classification - Chemotaxis and mobility 7EPMID:14985343 2C PMID:15066034 NC_002163.1 RefSeq gene 238832 240829 . - . ID=gene235;Name=Cj0262c;locus_tag=Cj0262c;Dbxref=GeneID:904377;gbkey=Gene NC_002163.1 RefSeq region 238838 239332 . - . ID=id567;Name=id567;Dbxref=GeneID:904377;gbkey=misc_feature;Note=HMMPfam hit to PF00015 2C Methyl-accepting chemotaxis protein 28MCP 29 s 2C score 6.4e-21 NC_002163.1 RefSeq region 239717 239941 . - . ID=id568;Name=id568;Dbxref=GeneID:904377;gbkey=misc_feature;Note=HMMPfam hit to PF00672 2C HAMP domain 2C score 0.0012 NC_002163.1 RefSeq region 239879 239938 . - . ID=id21;Name=id21;Dbxref=GeneID:904377;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0262c by TMHMM2.0 at aa 15-37 and 298-317 NC_002163.1 RefSeq region 240146 240382 . - . ID=id569;Name=id569;Dbxref=GeneID:904377;gbkey=misc_feature;Note=HMMPfam hit to PF02743 2C Cache domain 2C score 0.00011 NC_002163.1 RefSeq region 240491 240802 . - . ID=id570;Name=id570;Dbxref=GeneID:904377;gbkey=misc_feature;Note=HMMPfam hit to PF05581 2C Vibrio chemotaxis protein N terminus 2C score 4.3e-68 NC_002163.1 RefSeq region 240719 240787 . - . ID=id21;Name=id21;Dbxref=GeneID:904377;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0262c by TMHMM2.0 at aa 15-37 and 298-317 ### NC_002163.1 UTR_Extractor 5'-UTR 240830 240868 . - . ID=utr97;locus_tag=Cj0262c;product=putative methyl-accepting chemotaxis signal transduction protein NC_002163.1 UTR_Extractor 5'-UTR 241004 241021 . + . ID=utr98;locus_tag=Cj0263;product=zinc transporter ZupT NC_002163.1 RefSeq CDS 241022 241897 . + 0 ID=cds226;Parent=gene236;Name=YP_002343705.1;Dbxref=GOA:Q9PIN2 InterPro:IPR003689 UniProtKB FSwiss-Prot:Q9PIN2 Genbank:YP_002343705.1 GeneID:904588;gbkey=CDS;product=zinc transporter ZupT;Note=Original 282000 29 note: Cj0263 2C probable integral membrane protein 2C len: 291 aa 3B similar to hypothetical proteins e.g. YGIE_ECOLI 28257 aa 29 2C fasta scores 3B opt: 498 z-score: 952.9 E 28 29: 0 2C 40.0 25 identity in 280 aa overlap and GUFA_MYXXA 28254 aa 29 2C fasta scores 3B opt: 252 z-score: 298.8 E 28 29: 2.2e-09 2C 26.3 25 identity in 285 aa overlap. No Hp match. Contains PS00107 Protein kinases ATP-binding region signature 7EUpdated 282006 29 note: Pfam domain PF02535 ZIP Zinc transporter was identified within CDS. Eight probable transmembrane helices predicted by TMHMM2.0. Product modified to more specific family member due to motif match. Characterised within Escherichia coli with acceptable identity score. Thus 2C not added. Functional classification - Transport 2Fbinding proteins -Other 7EPMID:11790762 2C PMID:15716430 NC_002163.1 RefSeq gene 241022 241897 . + . ID=gene236;Name=Cj0263;locus_tag=Cj0263;Dbxref=GeneID:904588;gbkey=Gene NC_002163.1 RefSeq region 241046 241879 . + . ID=id571;Name=id571;Dbxref=GeneID:904588;gbkey=misc_feature;Note=HMMPfam hit to PF02535 2C ZIP Zinc transporter 2C score 5.8e-38 NC_002163.1 RefSeq region 241049 241117 . + . ID=id572;Name=id572;Dbxref=GeneID:904588;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0263 by TMHMM2.0 at aa 10-32 2C 39-60 2C 75-94 2C 148-170 2C174-196 2C 209-231 2C 237-259 and 271-290 NC_002163.1 RefSeq region 241136 241201 . + . ID=id572;Name=id572;Dbxref=GeneID:904588;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0263 by TMHMM2.0 at aa 10-32 2C 39-60 2C 75-94 2C 148-170 2C174-196 2C 209-231 2C 237-259 and 271-290 NC_002163.1 RefSeq region 241145 241216 . + . ID=id573;Name=id573;Dbxref=GeneID:904588;gbkey=misc_feature;Note=PS00107 Protein kinases ATP-binding region signature NC_002163.1 RefSeq region 241244 241303 . + . ID=id572;Name=id572;Dbxref=GeneID:904588;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0263 by TMHMM2.0 at aa 10-32 2C 39-60 2C 75-94 2C 148-170 2C174-196 2C 209-231 2C 237-259 and 271-290 NC_002163.1 RefSeq region 241463 241531 . + . ID=id572;Name=id572;Dbxref=GeneID:904588;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0263 by TMHMM2.0 at aa 10-32 2C 39-60 2C 75-94 2C 148-170 2C174-196 2C 209-231 2C 237-259 and 271-290 NC_002163.1 RefSeq region 241541 241609 . + . ID=id572;Name=id572;Dbxref=GeneID:904588;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0263 by TMHMM2.0 at aa 10-32 2C 39-60 2C 75-94 2C 148-170 2C174-196 2C 209-231 2C 237-259 and 271-290 NC_002163.1 RefSeq region 241646 241714 . + . ID=id572;Name=id572;Dbxref=GeneID:904588;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0263 by TMHMM2.0 at aa 10-32 2C 39-60 2C 75-94 2C 148-170 2C174-196 2C 209-231 2C 237-259 and 271-290 NC_002163.1 RefSeq region 241730 241798 . + . ID=id572;Name=id572;Dbxref=GeneID:904588;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0263 by TMHMM2.0 at aa 10-32 2C 39-60 2C 75-94 2C 148-170 2C174-196 2C 209-231 2C 237-259 and 271-290 NC_002163.1 RefSeq region 241832 241891 . + . ID=id572;Name=id572;Dbxref=GeneID:904588;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0263 by TMHMM2.0 at aa 10-32 2C 39-60 2C 75-94 2C 148-170 2C174-196 2C 209-231 2C 237-259 and 271-290 ### NC_002163.1 RefSeq CDS 241921 244437 . - 0 ID=cds227;Parent=gene237;Name=YP_002343706.1;Dbxref=GOA:Q0PBP1 InterPro:IPR006655 InterPro:IPR006656 InterPro:IPR006657 InterPro:IPR009010 UniProtKB FTrEMBL:Q0PBP1 Genbank:YP_002343706.1 GeneID:904589;gbkey=CDS;product=molybdopterin containing oxidoreductase;Note=Original 282000 29 note: Cj0264c 2C probable molybdopterin-containing oxidoreductase 2C len: 838 aa 3B highly similar to many e.g. DMSA_RHOSH dimethyl sulfoxide reductase precursor 28822 aa 29 2C fasta scores 3B opt: 1343 z-score: 2990.1 E 28 29: 0 2C 46.8 25 identity in 842 aa overlap 2Cand BISC_ECOLI biotin sulfoxide reductase 1 28739 aa 29 2Cfasta scores 3B opt: 1263 z-score: 2612.9 E 28 29: 0 2C 46.7 25 identity in 766 aa overlap. 40.9 25 identity to HP0407. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2CPS00932 Prokaryotic molybdopterin oxidoreductases signature 3 2C Pfam match to entry PF00384 molybdopterin 2CProkaryotic molybdopterin oxidoreductases 2C score 110.50 2CE-value 9.4e-35 and N-terminal signal sequence 7EUpdated 282006 29 note: Characterisation work in more than one species with acceptable identity scores. Characterisation work within Campylobacter jejuni shows that Cj0264c is responsible for both trimethylamine-N-oxide 28TMAO 29 and dimethyl sulfoxide 28DMSO 29 reduction. not added to product function. Functional classification - Misc 7EPMID:12107136 2C PMID:11004177 2C PMID:8645727 NC_002163.1 RefSeq gene 241921 244437 . - . ID=gene237;Name=Cj0264c;locus_tag=Cj0264c;Dbxref=GeneID:904589;gbkey=Gene NC_002163.1 RefSeq region 241993 242346 . - . ID=id574;Name=id574;Dbxref=GeneID:904589;gbkey=misc_feature;Note=HMMPfam hit to PF01568 2C Molydopterin dinucleotide binding dom 2C score 5.6e-41 NC_002163.1 RefSeq region 242146 242229 . - . ID=id575;Name=id575;Dbxref=GeneID:904589;gbkey=misc_feature;Note=PS00932 Prokaryotic molybdopterin oxidoreductases signature 3 NC_002163.1 RefSeq region 242719 244170 . - . ID=id576;Name=id576;Dbxref=GeneID:904589;gbkey=misc_feature;Note=HMMPfam hit to PF00384 2C Molybdopterin oxidoreductase 2C score 3.2e-120 NC_002163.1 RefSeq region 243046 243069 . - . ID=id577;Name=id577;Dbxref=GeneID:904589;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 RefSeq gene 244448 245023 . - . ID=gene238;Name=Cj0265c;locus_tag=Cj0265c;Dbxref=GeneID:904590;gbkey=Gene NC_002163.1 RefSeq CDS 244448 245023 . - 0 ID=cds228;Parent=gene238;Name=YP_002343707.1;Dbxref=GOA:Q0PBP0 UniProtKB FTrEMBL:Q0PBP0 Genbank:YP_002343707.1 GeneID:904590;gbkey=CDS;product=cytochrome C-type heme-binding protein;Note=Original 282000 29 note: Cj0265c 2C probable cytochrome C-type haem-binding periplasmic protein 2C len: 191 aa 3B possibly part of electron-transport chain for oxidoreductase Cj0264c. Similar to C-terminus of many e.g. YECK_ECOLI probable cytochrome C-TYPE protein in bisZ-cutC intergenic region 28366 aa 29 2C fasta scores 3B opt: 208 z-score: 216.4 E 28 29: 8.5e-05 2C 27.0 25 identity in 163 aa overlap 2C and TORC_ECOLI cytochrome C-type protein torC 28390 aa 29 2C fasta scores 3B opt: 264 z-score: 216.0 E 28 29: 8.9e-05 2C 26.4 25 identity in 178 aa overlap. No Hp match. Contains N-terminal signal sequence and PS00190 Cytochrome c family heme-binding site signature 7EUpdated 282006 29 note: Characterised within Escherichia coli 2C however 2C identity score was marginal. kept within product function. Functional classification - Energy metabolism - Electron transport 7EPMID:11562502 2C PMID:11056172 NC_002163.1 RefSeq region 244592 244609 . - . ID=id578;Name=id578;Dbxref=GeneID:904590;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature ### NC_002163.1 UTR_Extractor 5'-UTR 245024 245051 . - . ID=utr99;locus_tag=Cj0265c;product=putative cytochrome C-type haem-binding periplasmic protein NC_002163.1 RefSeq gene 245225 245380 . - . ID=NC_002163.1:CJnc20;Name=NC_002163.1:CJnc20;locus_tag=CJnc20 NC_002163.1 RefSeq sRNA 245225 245380 . - . ID=NC_002163.1:CJnc20:unknown_transcript_1;Parent=NC_002163.1:CJnc20;Name=NC_002163.1:CJnc20:unknown_transcript_1;locus_tag=CJnc20;gbkey=misc_RNA;product=CJnc20 NC_002163.1 RefSeq CDS 245504 246013 . - 0 ID=cds229;Parent=gene239;Name=YP_002343708.1;Dbxref=InterPro:IPR010916 UniProtKB FTrEMBL:Q0PBN9 Genbank:YP_002343708.1 GeneID:904591;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0266c 2C probable integral membrane protein 2C len: 169 aa 3B no Hp match 7EUpdated 282006 29 note: Two probable transmembrane helices identified by TMHMM2.0. Prosite PS00430 TONB_DEPENDENT_REC_1 2C TonB box 2C N-terminal also identified. No specific characterisation has been carried out yet. kept within product function. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 245504 246013 . - . ID=gene239;Name=Cj0266c;locus_tag=Cj0266c;Dbxref=GeneID:904591;gbkey=Gene NC_002163.1 RefSeq region 245759 246013 . - . ID=id579;Name=id579;Dbxref=GeneID:904591;gbkey=misc_feature;Note=PS00430 TonB-dependent receptor proteins signature 1 NC_002163.1 RefSeq region 245846 245914 . - . ID=id22;Name=id22;Dbxref=GeneID:904591;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0266c by TMHMM2.0 at aa 5-27 and 34-56 NC_002163.1 RefSeq region 245933 246001 . - . ID=id22;Name=id22;Dbxref=GeneID:904591;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0266c by TMHMM2.0 at aa 5-27 and 34-56 NC_002163.1 RefSeq CDS 246013 246543 . - 0 ID=cds230;Parent=gene240;Name=YP_002343709.1;Dbxref=UniProtKB FTrEMBL:Q0PBN8 Genbank:YP_002343709.1 GeneID:904592;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0267c 2C probable integral membrane protein 2C len: 176 aa 3B no Hp match 7EUpdated 282006 29 note: Two probable transmembrane helices identified by TMHMM2.0. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 246013 246543 . - . ID=gene240;Name=Cj0267c;locus_tag=Cj0267c;Dbxref=GeneID:904592;gbkey=Gene NC_002163.1 RefSeq region 246346 246414 . - . ID=id23;Name=id23;Dbxref=GeneID:904592;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0267c by TMHMM2.0 at aa 15-37 and 44-66 NC_002163.1 RefSeq region 246433 246501 . - . ID=id23;Name=id23;Dbxref=GeneID:904592;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0267c by TMHMM2.0 at aa 15-37 and 44-66 ### NC_002163.1 UTR_Extractor 5'-UTR 246544 246633 . - . ID=utr100;locus_tag=Cj0267c;product=putative integral membrane protein NC_002163.1 RefSeq CDS 246555 247643 . - 0 ID=cds231;Parent=gene241;Name=YP_002343710.1;Dbxref=GOA:Q0PBN7 InterPro:IPR000163 InterPro:IPR001107 UniProtKB FTrEMBL:Q0PBN7 Genbank:YP_002343710.1 GeneID:904593;gbkey=CDS;product=transmembrane protein;Note=Original 282000 29 note: Cj0268c 2C probable transmembrane protein 2C len: 362 aa 3B 55.9 25 identity to HP0248. Contains one transmembrane domain around aa 60 7EUpdated 282006 29 note: Pfam domain PF01145 SPFH domain 2F Band was identified within CDS. FPrintScan PR00679 Prohibitin was also identified. The FPrintScan identified is a child of the Pfam protein. No specific characherisation with acceptable identity scores have been carried out yet. kept within product function. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 246555 247643 . - . ID=gene241;Name=Cj0268c;locus_tag=Cj0268c;Dbxref=GeneID:904593;gbkey=Gene NC_002163.1 RefSeq region 246852 247460 . - . ID=id580;Name=id580;Dbxref=GeneID:904593;gbkey=misc_feature;Note=HMMPfam hit to PF01145 2C SPFH domain 2F Band 2C score 2.3e-37 NC_002163.1 RefSeq region 247446 247514 . - . ID=id581;Name=id581;Dbxref=GeneID:904593;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0268c by TMHMM2.0 at aa 44-66 ### NC_002163.1 RefSeq gene 247656 248570 . - . ID=gene242;gene=ilvE;Name=ilvE;locus_tag=Cj0269c;Dbxref=GeneID:904594;gbkey=Gene NC_002163.1 RefSeq CDS 247656 248570 . - 0 ID=cds232;Parent=gene242;gene=ilvE;Name=YP_002343711.1;Dbxref=GOA:Q0PBN6 InterPro:IPR001544 InterPro:IPR005785 UniProtKB FTrEMBL:Q0PBN6 Genbank:YP_002343711.1 GeneID:904594;gbkey=CDS;product=branched-chain amino acid aminotransferase;Note=catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids NC_002163.1 RefSeq region 247710 248543 . - . ID=id582;gene=ilvE;Name=id582;Dbxref=GeneID:904594;gbkey=misc_feature;Note=HMMPfam hit to PF01063 2C Aminotransferase class IV 2Cscore 6.2e-88 ### NC_002163.1 UTR_Extractor 5'-UTR 248571 248625 . - . ID=utr101;locus_tag=Cj0269c;product=branched-chain amino acid aminotransferase NC_002163.1 RefSeq CDS 248747 248953 . + 0 ID=cds233;Parent=gene243;Name=YP_002343712.1;Dbxref=GOA:Q9PIM5 InterPro:IPR004370 UniProtKB FSwiss-Prot:Q9PIM5 Genbank:YP_002343712.1 GeneID:904595;gbkey=CDS;product=tautomerase family protein;Note=Original 282000 29 note: Cj0270 2C possible isomerase 2Clen: 68 aa 3B some similarity hypothetical proteins and to to e.g. DMPI_PSESP 4-oxalocrotonate tautomerase 28EC 5.3.2.- 29 28 2862 aa 29 2C fasta scores 3B opt: 91 z-score: 182.5 E 28 29: 0.0066 2C 28.0 25 identity in 50 aa overlap 2C and XYLH_PSEPU 4-oxalocrotonate tautomerase 2862 aa 29 2C fasta scores 3B opt: 86 z-score: 164.7 E 28 29: 0.064 2C 25.8 25 identity in 62 aa overlap. No Hp ortholog 2C but 37.3 25 identity to HP0924. Also similar to Cj1255 2837.7 25 identity in 69 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01361 Tautomerase enzyme was identified within CDS. Product modified to more specific family member due to motif match. Some characterisation has been carried out within Pseudomonas species 2C however 2C identity scores were marginal. kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 248747 248953 . + . ID=gene243;Name=Cj0270;locus_tag=Cj0270;Dbxref=GeneID:904595;gbkey=Gene NC_002163.1 RefSeq region 248750 248932 . + . ID=id583;Name=id583;Dbxref=GeneID:904595;gbkey=misc_feature;Note=HMMPfam hit to PF01361 2C Tautomerase enzyme 2C score 1.4e-21 NC_002163.1 RefSeq gene 248950 249405 . + . ID=gene244;Name=Cj0271;locus_tag=Cj0271;Dbxref=GeneID:904596;gbkey=Gene NC_002163.1 RefSeq CDS 248950 249405 . + 0 ID=cds234;Parent=gene244;Name=YP_002343713.1;Dbxref=GOA:Q0PBN4 InterPro:IPR000866 InterPro:IPR012335 UniProtKB FTrEMBL:Q0PBN4 Genbank:YP_002343713.1 GeneID:904596;gbkey=CDS;product=bacterioferritin comigratory protein;Note=Original 282000 29 note: Cj0271 2C bacterioferritin comigratory protein homolog 2C len: 151 aa 3B similar to many e.g. BCP_ECOLI bacterioferritin comigratory protein 28156 aa 29 2C fasta scores 3B opt: 390 z-score: 675.8 E 28 29: 2.2e-30 2C39.6 25 identity in 149 aa overlap. 57.0 25 identity to HP0136. Contains Pfam match to entry PF00578 AhpC-TSA 2CAhpC 2FTSA family 2C score 146.30 2C E-value 5.4e-40 7EUpdated 282006 29 note: Some characterisation work within Escherichia coli shows Cj0271 to be peroxiredoxin 3B bcp. Literature search also identified work within Helicobacter pylori. Product function kept the same. Functional classification - Misc 7EPMID:15618175 2C PMID:12576586 2C PMID:14506251 NC_002163.1 RefSeq region 248962 249387 . + . ID=id584;Name=id584;Dbxref=GeneID:904596;gbkey=misc_feature;Note=HMMPfam hit to PF00578 2C AhpC 2FTSA family 2C score 4e-41 NC_002163.1 RefSeq region 249405 250016 . + . ID=id585;Name=id585;Dbxref=GeneID:904597;gbkey=misc_feature;Note=HMMPfam hit to PF02677 2C Uncharacterized BCR 2CCOG1636 2C score 2.6e-97 NC_002163.1 RefSeq CDS 249405 250496 . + 0 ID=cds235;Parent=gene245;Name=YP_002343714.1;Dbxref=InterPro:IPR003828 UniProtKB FTrEMBL:Q0PBN3 Genbank:YP_002343714.1 GeneID:904597;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0272 2C unknown 2C len: 363 aa 3B similar to hypothetical proteins e.g. TR:O66919 28EMBL: 29 Aquifex aeolicus AQ_701 28413 aa 29 2C fasta scores 3B opt: 830 z-score: 1296.8 E 28 29: 0 2C 48.0 25 identity in 254 aa overlap. 37.4 25 identity to HP0100 7EUpdated 282006 29 note: Pfam PF02677 Uncharacterized BCR was present within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 249405 250496 . + . ID=gene245;Name=Cj0272;locus_tag=Cj0272;Dbxref=GeneID:904597;gbkey=Gene ### NC_002163.1 UTR_Extractor 5'-UTR 250560 250589 . + . ID=utr102;locus_tag=Cj0273;product= 283R 29-hydroxymyristoyl-ACP dehydratase NC_002163.1 RefSeq CDS 250590 251030 . + 0 ID=cds236;Parent=gene246;gene=fabZ;Name=YP_002343715.1;Dbxref=GOA:Q9PIM2 InterPro:IPR010084 InterPro:IPR013114 UniProtKB FSwiss-Prot:Q9PIM2 Genbank:YP_002343715.1 GeneID:904598;gbkey=CDS;product= 283R 29-hydroxymyristoyl-ACP dehydratase;Note=in Pseudomonas aeruginosa this enzyme is a trimer of dimers 3B essential for membrane formation 3B performs third step of type II fatty acid biosynthesis 3B catalyzes dehydration of 283R 29-hydroxyacyl-ACP to trans-2-acyl-ACP NC_002163.1 RefSeq gene 250590 251030 . + . ID=gene246;gene=fabZ;Name=fabZ;locus_tag=Cj0273;Dbxref=GeneID:904598;gbkey=Gene NC_002163.1 RefSeq region 250725 250997 . + . ID=id586;gene=fabZ;Name=id586;Dbxref=GeneID:904598;gbkey=misc_feature;Note=HMMPfam hit to PF03061 2C Thioesterase superfamily 2Cscore 2.4e-21 NC_002163.1 RefSeq gene 251030 251821 . + . ID=gene247;gene=lpxA;Name=lpxA;locus_tag=Cj0274;Dbxref=GeneID:904599;gbkey=Gene NC_002163.1 RefSeq CDS 251030 251821 . + 0 ID=cds237;Parent=gene247;gene=lpxA;Name=YP_002343716.1;Dbxref=GOA:Q9PIM1 HSSP:P10440 InterPro:IPR001451 InterPro:IPR010137 UniProtKB FSwiss-Prot:Q9PIM1 Genbank:YP_002343716.1 GeneID:904599;gbkey=CDS;product=UDP-N-acetylglucosamine acyltransferase;Note=catalyzes the addition of 28R 29-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis NC_002163.1 RefSeq region 251048 251101 . + . ID=id587;gene=lpxA;Name=id587;Dbxref=GeneID:904599;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 0.78 NC_002163.1 RefSeq region 251120 251173 . + . ID=id588;gene=lpxA;Name=id588;Dbxref=GeneID:904599;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 0.072 NC_002163.1 RefSeq region 251174 251227 . + . ID=id589;gene=lpxA;Name=id589;Dbxref=GeneID:904599;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 1.3 NC_002163.1 RefSeq region 251267 251320 . + . ID=id590;gene=lpxA;Name=id590;Dbxref=GeneID:904599;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 0.075 NC_002163.1 RefSeq region 251342 251395 . + . ID=id591;gene=lpxA;Name=id591;Dbxref=GeneID:904599;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 0.011 NC_002163.1 RefSeq region 251414 251467 . + . ID=id592;gene=lpxA;Name=id592;Dbxref=GeneID:904599;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 2.8 NC_002163.1 RefSeq region 251423 251509 . + . ID=id593;gene=lpxA;Name=id593;Dbxref=GeneID:904599;gbkey=misc_feature;Note=PS00101 Hexapeptide-repeat containing-transferases signature NC_002163.1 RefSeq region 251504 251557 . + . ID=id594;gene=lpxA;Name=id594;Dbxref=GeneID:904599;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 50 NC_002163.1 RefSeq CDS 251784 253037 . + 0 ID=cds238;Parent=gene248;gene=clpX;Name=YP_002343717.1;Dbxref=GOA:Q9PIM0 HSSP:P43773 InterPro:IPR002078 InterPro:IPR003593 InterPro:IPR004487 InterPro:IPR010603 InterPro:IPR013093 UniProtKB FSwiss-Prot:Q9PIM0 Genbank:YP_002343717.1 GeneID:904600;gbkey=CDS;product=ATP-dependent protease ATP-binding subunit ClpX;Note=binds and unfolds substrates as part of the ClpXP protease NC_002163.1 RefSeq gene 251784 253037 . + . ID=gene248;gene=clpX;Name=clpX;locus_tag=Cj0275;Dbxref=GeneID:904600;gbkey=Gene NC_002163.1 RefSeq region 251826 251942 . + . ID=id595;gene=clpX;Name=id595;Dbxref=GeneID:904600;gbkey=misc_feature;Note=HMMPfam hit to PF06689 2C ClpX C4-type zinc finger 2Cscore 3.2e-14 NC_002163.1 RefSeq region 252132 252719 . + . ID=id596;gene=clpX;Name=id596;Dbxref=GeneID:904600;gbkey=misc_feature;Note=HMMPfam hit to PF07724 2C ATPase family associated with various cell 2C score 2.7e-77 NC_002163.1 RefSeq region 252144 252767 . + . ID=id597;gene=clpX;Name=id597;Dbxref=GeneID:904600;gbkey=misc_feature;Note=HMMPfam hit to PF00004 2C ATPase family associated with various cell 2C score 1.1e-26 NC_002163.1 RefSeq region 252159 252182 . + . ID=id598;gene=clpX;Name=id598;Dbxref=GeneID:904600;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 252315 252362 . + . ID=id599;gene=clpX;Name=id599;Dbxref=GeneID:904600;gbkey=misc_feature;Note=PS00676 Sigma-54 interaction domain ATP-binding region B signature NC_002163.1 RefSeq repeat_region 252478 252485 . + . ID=id600;gene=clpX;Name=id600;Dbxref=GeneID:904600;gbkey=repeat_region;Note=G 288 29 ### NC_002163.1 RefSeq CDS 253049 254089 . + 0 ID=cds239;Parent=gene249;gene=mreB;Name=YP_002343718.1;Dbxref=GOA:Q0PBM9 InterPro:IPR001023 InterPro:IPR004753 UniProtKB FTrEMBL:Q0PBM9 Genbank:YP_002343718.1 GeneID:904601;gbkey=CDS;product=rod shape-determining protein MreB;Note=functions in MreBCD complex in some organisms NC_002163.1 RefSeq gene 253049 254089 . + . ID=gene249;gene=mreB;Name=mreB;locus_tag=Cj0276;Dbxref=GeneID:904601;gbkey=Gene NC_002163.1 RefSeq region 253079 254071 . + . ID=id601;gene=mreB;Name=id601;Dbxref=GeneID:904601;gbkey=misc_feature;Note=HMMPfam hit to PF06723 2C MreB 2FMbl protein 2C score 6.5e-229 NC_002163.1 RefSeq region 253226 253249 . + . ID=id602;gene=mreB;Name=id602;Dbxref=GeneID:904601;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq gene 254079 254828 . + . ID=gene250;gene=mreC;Name=mreC;locus_tag=Cj0277;Dbxref=GeneID:904602;gbkey=Gene NC_002163.1 RefSeq CDS 254079 254828 . + 0 ID=cds240;Parent=gene250;gene=mreC;Name=YP_002343719.1;Dbxref=GOA:Q0PBM8 InterPro:IPR007221 UniProtKB FTrEMBL:Q0PBM8 Genbank:YP_002343719.1 GeneID:904602;gbkey=CDS;product=rod shape-determining protein MreC;Note=in some organisms this protein is a transmembrane protein while in others it is periplasmic 3B involved in some organisms with other components of the MreBCD complex and with penicillin binding proteins in the periplasm or cell wall NC_002163.1 RefSeq region 254091 254150 . + . ID=id603;gene=mreC;Name=id603;Dbxref=GeneID:904602;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0277 by TMHMM2.0 at aa 5-24 NC_002163.1 RefSeq region 254388 254825 . + . ID=id604;gene=mreC;Name=id604;Dbxref=GeneID:904602;gbkey=misc_feature;Note=HMMPfam hit to PF04085 2C rod shape-determining protein MreC 2C score 2.4e-43 ### NC_002163.1 UTR_Extractor 5'-UTR 255065 255088 . + . ID=utr103;locus_tag=Cj0279;product=carbamoyl phosphate synthase large subunit NC_002163.1 RefSeq CDS 255089 258358 . + 0 ID=cds241;Parent=gene251;gene=carB;Name=YP_002343720.1;Dbxref=GOA:Q9PIL7 HSSP:P00968 InterPro:IPR005479 InterPro:IPR005480 InterPro:IPR005481 InterPro:IPR005483 InterPro:IPR006275 InterPro:IPR011607 InterPro:IPR011761 InterPro:IPR013816 InterPro:IPR013817 UniProtKB FSwiss-Prot:Q9PIL7 Genbank:YP_002343720.1 GeneID:904603;gbkey=CDS;product=carbamoyl phosphate synthase large subunit;Note=four CarB-CarA dimers form the carbamoyl phosphate synthetase holoenzyme that catalyzes the production of carbamoyl phosphate 3B CarB is responsible for the amidotransferase activity NC_002163.1 RefSeq gene 255089 258358 . + . ID=gene251;gene=carB;Name=carB;locus_tag=Cj0279;Dbxref=GeneID:904603;gbkey=Gene NC_002163.1 RefSeq region 255104 255460 . + . ID=id605;gene=carB;Name=id605;Dbxref=GeneID:904603;gbkey=misc_feature;Note=HMMPfam hit to PF00289 2C Carbamoyl-phosphate synthase L chain 2C 2C score 1.8e-45 NC_002163.1 RefSeq region 255128 255160 . + . ID=id606;gene=carB;Name=id606;Dbxref=GeneID:904603;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 255464 256168 . + . ID=id607;gene=carB;Name=id607;Dbxref=GeneID:904603;gbkey=misc_feature;Note=HMMPfam hit to PF02786 2C Carbamoyl-phosphate synthase L chain 2C 2C score 2.3e-112 NC_002163.1 RefSeq region 255572 255616 . + . ID=id608;gene=carB;Name=id608;Dbxref=GeneID:904603;gbkey=misc_feature;Note=PS00866 Carbamoyl-phosphate synthase subdomain signature 1 NC_002163.1 RefSeq region 255971 255994 . + . ID=id609;gene=carB;Name=id609;Dbxref=GeneID:904603;gbkey=misc_feature;Note=PS00867 Carbamoyl-phosphate synthase subdomain signature 2 NC_002163.1 RefSeq region 256334 256717 . + . ID=id610;gene=carB;Name=id610;Dbxref=GeneID:904603;gbkey=misc_feature;Note=HMMPfam hit to PF02787 2C Carbamoyl-phosphate synthetase large c 2C score 2.8e-46 NC_002163.1 RefSeq region 256763 257107 . + . ID=id611;gene=carB;Name=id611;Dbxref=GeneID:904603;gbkey=misc_feature;Note=HMMPfam hit to PF00289 2C Carbamoyl-phosphate synthase L chain 2C 2C score 3.2e-19 NC_002163.1 RefSeq region 257111 257764 . + . ID=id612;gene=carB;Name=id612;Dbxref=GeneID:904603;gbkey=misc_feature;Note=HMMPfam hit to PF02786 2C Carbamoyl-phosphate synthase L chain 2C 2C score 8e-25 NC_002163.1 RefSeq region 257219 257263 . + . ID=id613;gene=carB;Name=id613;Dbxref=GeneID:904603;gbkey=misc_feature;Note=PS00866 Carbamoyl-phosphate synthase subdomain signature 1 NC_002163.1 RefSeq region 257606 257629 . + . ID=id614;gene=carB;Name=id614;Dbxref=GeneID:904603;gbkey=misc_feature;Note=PS00867 Carbamoyl-phosphate synthase subdomain signature 2 NC_002163.1 RefSeq region 257999 258259 . + . ID=id615;gene=carB;Name=id615;Dbxref=GeneID:904603;gbkey=misc_feature;Note=HMMPfam hit to PF02142 2C MGS-like domain 2C score 2.5e-28 NC_002163.1 RefSeq gene 258355 258777 . + . ID=gene252;gene=Cj0280;Name=Cj0280;locus_tag=Cj0280;Dbxref=GeneID:904604;gbkey=Gene NC_002163.1 RefSeq CDS 258355 258777 . + 0 ID=cds242;Parent=gene252;Name=YP_002343721.1;Dbxref=UniProtKB FTrEMBL:Q0PBM6 Genbank:YP_002343721.1 GeneID:904604;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0280 2C unknown 2C len: 140 aa 3B 52.8 25 identity to HP0918. Functional classification -Conserved hypothetical proteins ### NC_002163.1 RefSeq CDS 258778 259755 . - 0 ID=cds243;Parent=gene253;gene=tal;Name=YP_002343722.1;Dbxref=GOA:Q9PIL5 InterPro:IPR001585 InterPro:IPR004732 InterPro:IPR013785 UniProtKB FSwiss-Prot:Q9PIL5 Genbank:YP_002343722.1 GeneID:904605;gbkey=CDS;product=transaldolase;Note=Important for the balance of metabolites in the pentose-phosphate pathway NC_002163.1 RefSeq gene 258778 259755 . - . ID=gene253;gene=tal;Name=tal;locus_tag=Cj0281c;Dbxref=GeneID:904605;gbkey=Gene NC_002163.1 RefSeq region 258781 259719 . - . ID=id616;gene=tal;Name=id616;Dbxref=GeneID:904605;gbkey=misc_feature;Note=HMMPfam hit to PF00923 2C Transaldolase 2C score 7e-34 NC_002163.1 RefSeq region 259642 259668 . - . ID=id617;gene=tal;Name=id617;Dbxref=GeneID:904605;gbkey=misc_feature;Note=PS01054 Transaldolase signature 1 NC_002163.1 RefSeq gene 259755 260378 . - . ID=gene254;gene=serB;Name=serB;locus_tag=Cj0282c;Dbxref=GeneID:904606;gbkey=Gene NC_002163.1 RefSeq CDS 259755 260378 . - 0 ID=cds244;Parent=gene254;gene=serB;Name=YP_002343723.1;Dbxref=GOA:Q0PBM4 InterPro:IPR004469 InterPro:IPR005834 InterPro:IPR006383 UniProtKB FTrEMBL:Q0PBM4 Genbank:YP_002343723.1 GeneID:904606;gbkey=CDS;product=phosphoserine phosphatase;Note=Original 282000 29 note: Cj0282c 2C serB 2C possible phosphoserine phosphatase 2C len: 207 aa 3B similar to C-terminus of SERB_ECOLI phosphoserine phosphatase 28EC 3.1.3.3 29 28322 aa 29 2C fasta scores 3B opt: 361 z-score: 572.4 E 28 29: 1.3e-24 2C 34.3 25 identity in 204 aa overlap. 48.8 25 identity to HP0652 7EUpdated 282006 29 note: Pfam domain PF00702 haloacid dehalogenase-like hydrolase were identified within CDS. TIGRFAM motif TIGR00338 2C serB phosphoserine phosphatase identified along with TIGR01488 HAD-SF-IB: HAD-superfamily hydrolase within CDS. Further support for product function. Characterised within Escherichia coli with acceptable identity scores 2C however 2C alignment was only partial. kept in product function. Functional classification - Amino acid biosynthesis - Serine family 7EPMID:2997734 NC_002163.1 RefSeq region 259824 260375 . - . ID=id618;gene=serB;Name=id618;Dbxref=GeneID:904606;gbkey=misc_feature;Note=HMMPfam hit to PF00702 2C haloacid dehalogenase-like hydrolase 2C score 5.8e-18 NC_002163.1 RefSeq gene 260378 260899 . - . ID=gene255;gene=cheW;Name=cheW;locus_tag=Cj0283c;Dbxref=GeneID:904607;gbkey=Gene NC_002163.1 RefSeq CDS 260378 260899 . - 0 ID=cds245;Parent=gene255;gene=cheW;Name=YP_002343724.1;Dbxref=GOA:Q0PBM3 InterPro:IPR002545 UniProtKB FTrEMBL:Q0PBM3 Genbank:YP_002343724.1 GeneID:904607;gbkey=CDS;product=chemotaxis protein;Note=Original 282000 29 note: Cj0283c 2C cheW 2C probable chemotaxis protein 2C len: 173 aa 3B similar to many e.g. CHEW_ECOLI purine-binding chemotaxis protein 28167 aa 29 2Cfasta scores 3B opt: 236 z-score: 304.4 E 28 29: 1.1e-09 2C 32.4 25 identity in 139 aa overlap. 51.4 25 identity to HP0391 7EUpdated 282006 29 note: Pfam domain PF01584 CheW-like domain identified within CDS. Further support given to product function. Characterised within Escherichia coli with marginal identity score. not added to product function. Functional classification - Chemotaxis and mobility 7EPMID:2068106 2C PMID:3510184 NC_002163.1 RefSeq region 260381 260809 . - . ID=id619;gene=cheW;Name=id619;Dbxref=GeneID:904607;gbkey=misc_feature;Note=HMMPfam hit to PF01584 2C CheW-like domain 2C score 5.9e-30 ### NC_002163.1 RefSeq CDS 260904 263213 . - 0 ID=cds246;Parent=gene256;gene=cheA;Name=YP_002343725.1;Dbxref=GOA:Q0PBM2 InterPro:IPR001789 InterPro:IPR002545 InterPro:IPR003594 InterPro:IPR004105 InterPro:IPR004358 InterPro:IPR005467 InterPro:IPR005829 InterPro:IPR008207 UniProtKB FTrEMBL:Q0PBM2 Genbank:YP_002343725.1 GeneID:904608;gbkey=CDS;product=chemotaxis histidine kinase;Note=Original 282000 29 note: Cj0284c 2C cheA 2C probable chemotaxis histidine kinase 2C len: 769 aa 3B similar to many e.g. CHEA_ECOLI chemotaxis protein cheA 28EC 2.7.3.- 29 28654 aa 29 2C fasta scores 3B opt: 1022 z-score: 1416.0 E 28 29: 0 2C 35.7 25 identity in 658 aa overlap. 64.6 25 identity to HP0392. Contains Pfam matches to entry PF00072 response_reg 2CResponse regulator receiver domain 2C score 103.80 2C E-value 3.4e-27 and to entry PF00512 signal 2C Signal carboxyl-terminal domain 2C score -12.30 2C E-value 0.00013 7EUpdated 282006 29 note: Characterised within Escherichia coli with marginal identity scores. not added to product function. Functional classification -Chemotaxis and mobility 7EPMID:1938941 2C PMID:2068106 NC_002163.1 RefSeq gene 260904 263213 . - . ID=gene256;gene=cheA;Name=cheA;locus_tag=Cj0284c;Dbxref=GeneID:904608;gbkey=Gene NC_002163.1 RefSeq region 260907 261275 . - . ID=id620;gene=cheA;Name=id620;Dbxref=GeneID:904608;gbkey=misc_feature;Note=HMMPfam hit to PF00072 2C Response regulator receiver domain 2C score 4.4e-25 NC_002163.1 RefSeq region 260925 261002 . - . ID=id621;gene=cheA;Name=id621;Dbxref=GeneID:904608;gbkey=misc_feature;Note=PS00217 Sugar transport proteins signature 2 NC_002163.1 RefSeq region 261345 261740 . - . ID=id622;gene=cheA;Name=id622;Dbxref=GeneID:904608;gbkey=misc_feature;Note=HMMPfam hit to PF01584 2C CheW-like domain 2C score 1.8e-28 NC_002163.1 RefSeq region 261753 262181 . - . ID=id623;gene=cheA;Name=id623;Dbxref=GeneID:904608;gbkey=misc_feature;Note=HMMPfam hit to PF02518 2C Histidine kinase- 2C DNA gyrase B- 2C and HS 2C score 3.2e-28 NC_002163.1 RefSeq region 262314 262520 . - . ID=id624;gene=cheA;Name=id624;Dbxref=GeneID:904608;gbkey=misc_feature;Note=HMMPfam hit to PF02895 2C Signal transducing histidine kinase 2C hom 2C score 3.7e-24 NC_002163.1 RefSeq region 262893 263198 . - . ID=id625;gene=cheA;Name=id625;Dbxref=GeneID:904608;gbkey=misc_feature;Note=HMMPfam hit to PF01627 2C Hpt domain 2C score 5.4e-17 ### NC_002163.1 RefSeq CDS 263217 264173 . - 0 ID=cds247;Parent=gene257;gene=cheV;Name=YP_002343726.1;Dbxref=GOA:Q0PBM1 InterPro:IPR001789 InterPro:IPR002545 UniProtKB FTrEMBL:Q0PBM1 Genbank:YP_002343726.1 GeneID:904609;gbkey=CDS;product=chemotaxis protein;Note=Original 282000 29 note: Cj0285c 2C cheV 2C probable chemotaxis protein cheV 2C len: 318 aa 3B similar to e.g. CHEV_BACSU chemotaxis cheV protein 28EC 2.7.3.- 29 28303 aa 29 2Cfasta scores 3B opt: 414 z-score: 344.9 E 28 29: 5.9e-12 2C 28.2 25 identity in 309 aa overlap. 50.8 25 identity to HP0393. Contains Pfam match to entry PF00072 response_reg 2CResponse regulator receiver domain 2C score 50.70 2C E-value 3.1e-11 7EUpdated 282006 29 note: Pfam domain PF01584 CheW-like domain identified within CDS. Further support given to product function. Characterised within Bacillus subtilis with marginal identity score. not added to product function. Functional classification - Chemotaxis and mobility 7EPMID:8169223 2C PMID:8169224 NC_002163.1 RefSeq gene 263217 264173 . - . ID=gene257;gene=cheV;Name=cheV;locus_tag=Cj0285c;Dbxref=GeneID:904609;gbkey=Gene NC_002163.1 RefSeq region 263235 263630 . - . ID=id626;gene=cheV;Name=id626;Dbxref=GeneID:904609;gbkey=misc_feature;Note=HMMPfam hit to PF00072 2C Response regulator receiver domain 2C score 4.1e-15 NC_002163.1 RefSeq region 263682 264083 . - . ID=id627;gene=cheV;Name=id627;Dbxref=GeneID:904609;gbkey=misc_feature;Note=HMMPfam hit to PF01584 2C CheW-like domain 2C score 1.6e-28 NC_002163.1 RefSeq CDS 264166 264783 . - 0 ID=cds248;Parent=gene258;Name=YP_002343727.1;Dbxref=UniProtKB FTrEMBL:Q0PBM0 Genbank:YP_002343727.1 GeneID:904610;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0286c 2C unknown 2C len: 205 aa 3B 28.4 25 identity to HP0394 28252 aa 29. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 264166 264783 . - . ID=gene258;gene=Cj0286c;Name=Cj0286c;locus_tag=Cj0286c;Dbxref=GeneID:904610;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 264174 264212 . - . ID=utr104;locus_tag=Cj0285c;product=chemotaxis protein ### NC_002163.1 RefSeq CDS 264934 265419 . - 0 ID=cds249;Parent=gene259;gene=greA;Name=YP_002343728.1;Dbxref=GOA:Q9PIK9 HSSP:P21346 InterPro:IPR001437 InterPro:IPR006359 UniProtKB FSwiss-Prot:Q9PIK9 Genbank:YP_002343728.1 GeneID:904611;gbkey=CDS;product=transcription elongation factor GreA;Note=necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites 3B arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through 2C resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3 27terminus NC_002163.1 RefSeq gene 264934 265419 . - . ID=gene259;gene=greA;Name=greA;locus_tag=Cj0287c;Dbxref=GeneID:904611;gbkey=Gene NC_002163.1 RefSeq region 264952 265182 . - . ID=id628;gene=greA;Name=id628;Dbxref=GeneID:904611;gbkey=misc_feature;Note=HMMPfam hit to PF01272 2C Prokaryotic transcription elongation fact 2C score 3.2e-27 NC_002163.1 RefSeq region 265012 265062 . - . ID=id629;gene=greA;Name=id629;Dbxref=GeneID:904611;gbkey=misc_feature;Note=PS00830 Prokaryotic transcription elongation factors signature 2 NC_002163.1 RefSeq region 265198 265419 . - . ID=id630;gene=greA;Name=id630;Dbxref=GeneID:904611;gbkey=misc_feature;Note=HMMPfam hit to PF03449 2C Prokaryotic transcription elongation fact 2C score 1.4e-37 NC_002163.1 RefSeq region 265276 265401 . - . ID=id631;gene=greA;Name=id631;Dbxref=GeneID:904611;gbkey=misc_feature;Note=PS00829 Prokaryotic transcription elongation factors signature 1 ### NC_002163.1 UTR_Extractor 5'-UTR 265420 265497 . - . ID=utr105;locus_tag=Cj0287c;product=transcription elongation factor GreA NC_002163.1 RefSeq gene 265431 266525 . - . ID=gene260;gene=lpxB;Name=lpxB;locus_tag=Cj0288c;Dbxref=GeneID:904612;gbkey=Gene NC_002163.1 RefSeq CDS 265431 266525 . - 0 ID=cds250;Parent=gene260;gene=lpxB;Name=YP_002343729.1;Dbxref=GOA:Q9PIK8 InterPro:IPR003835 UniProtKB FSwiss-Prot:Q9PIK8 Genbank:YP_002343729.1 GeneID:904612;gbkey=CDS;product=ipid-A-disaccharide synthase;Note=catalyzes the formation of lipid A disaccharide from UDP-2 2C3-diacylglucosamine and 2 2C3-diacylglucosamine-1-phosphate 2C lipid A disaccharide is a precursor of lipid A that anchors LPS to the OM NC_002163.1 RefSeq region 265452 266516 . - . ID=id632;gene=lpxB;Name=id632;Dbxref=GeneID:904612;gbkey=misc_feature;Note=HMMPfam hit to PF02684 2C Lipid-A-disaccharide synthetase 2C score 4.7e-81 ### NC_002163.1 RefSeq gene 266622 267374 . - . ID=gene261;gene=peb3;Name=peb3;locus_tag=Cj0289c;Dbxref=GeneID:904613;gbkey=Gene NC_002163.1 RefSeq CDS 266622 267374 . - 0 ID=cds251;Parent=gene261;gene=peb3;Name=YP_002343730.1;Dbxref=GOA:Q0PBL7 PDB:2HXW UniProtKB FTrEMBL:Q0PBL7 Genbank:YP_002343730.1 GeneID:904613;gbkey=CDS;product=major antigenic peptide PEB3;Note=Original 282000 29 note: Cj0289c 2C peb3 2C major antigenic peptide PEB3 2C len: 250 aa 3B 94.9 25 identical to TR:G234575 2C sequenced by direct peptide sequencing 3B see: Pei at al. J. Biol. Chem. 266:16363-16369 281991 29. Also similar to TR:Q57410 28EMBL:U39068 29 Vibrio cholerae accessory colonization factor acfC 28253 aa 29 2C fasta scores 3B opt: 855 z-score: 1301.2 E 28 29: 0 2C 53.6 25 identity in 239 aa overlap and TR:P96759 28EMBL:U82533 29 anm 28E. coli 045 attachment and effacement negative mutant 29 28251 aa 29 2C fasta scores 3B opt: 849 z-score: 824.0 E 28 29: 0 2C 51.8 25 identity in 251 aa overlap. No Hp match. Also similar to Cj0778 28peb2 29 2832.4 25 identity in 256 aa overlap 29. Contains N-terminal signal sequence 7EUpdated 282006 29 note: Characterised within Campylobacter jejuni. Paper identified linking protein to glycoprotein 28PMID:12186869 29. Functional classification -Miscellaneous periplasmic proteins 7EPMID:1885571 2C PMID:12186869 NC_002163.1 UTR_Extractor 5'-UTR 267375 267410 . - . ID=utr106;locus_tag=Cj0289c;product=major antigenic peptide PEB3 NC_002163.1 RefSeq region 267516 267629 . - . ID=id633;gene=glpT;Name=id633;Dbxref=GeneID:904616;gbkey=misc_feature;Note=Original 282000 29 note: Cj0290c 2C probable pseudogene representing the C-terminus of Cj0291c 28glpT 27 29 7EOriginal 282000 29 note: Cj0292c 2C probable pseudogene representing the N-terminus of Cj0291c 28glpT 27 29 7EOriginal 282000 29 note: Cj0291c 2C glpT 27 2Cglycerol-3-phosphate transporter 2C possible pseudogene 2Clen: 319 aa 3B similar to the central region of many e.g. GLPT_ECOLI glycerol-3-phosphate transporter 28452 aa 29 2Cfasta scores 3B opt: 473 z-score: 832.3 E 28 29: 0 2C 35.3 25 identity in 323 aa overlap. No Hp match. Contains PS00942 glpT family of transporters signature. Note that the N-terminal 100 aa and the C-terminal 50 aa present in other glpT proteins are out of frame 2C and are represented by the CDSs Cj0292c and Cj0290c respectively. The sequence has been checked 2C and is believed to be correct 7EUpdated 282006 29 note: Pfam domain PF07690 Major Facilitator Superfamily identified within CDS. Also 2Ctwelve probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins -Carbohydrates 2C organic acids and alcohols NC_002163.1 RefSeq pseudogene 267516 268809 . - . ID=gene262;gene=glpT;Name=glpT;locus_tag=Cj0292c;Dbxref=GeneID:904616;gbkey=Gene NC_002163.1 RefSeq region 267540 267608 . - . ID=id25;gene=glpT;Name=id25;Dbxref=GeneID:904616;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0292c by TMHMM2.0 at aa 9-31 2C 41-63 2C 72-94 2C 98-120 2C141-163 2C 178-195 2C 247-269 2C 284-303 2C 310-332 2C 337-359 2C364-386 and 401-423 NC_002163.1 RefSeq region 267627 267629 . - . ID=id24;gene=glpT;Name=id24;Dbxref=GeneID:904616;gbkey=misc_feature;Note=HMMPfam hit to PF07690 2C Major Facilitator Superfamily 2C score 1.8e-34 NC_002163.1 RefSeq region 267638 268597 . - . ID=id633;gene=glpT;Name=id633;Dbxref=GeneID:904616;gbkey=misc_feature;Note=Original 282000 29 note: Cj0290c 2C probable pseudogene representing the C-terminus of Cj0291c 28glpT 27 29 7EOriginal 282000 29 note: Cj0292c 2C probable pseudogene representing the N-terminus of Cj0291c 28glpT 27 29 7EOriginal 282000 29 note: Cj0291c 2C glpT 27 2Cglycerol-3-phosphate transporter 2C possible pseudogene 2Clen: 319 aa 3B similar to the central region of many e.g. GLPT_ECOLI glycerol-3-phosphate transporter 28452 aa 29 2Cfasta scores 3B opt: 473 z-score: 832.3 E 28 29: 0 2C 35.3 25 identity in 323 aa overlap. No Hp match. Contains PS00942 glpT family of transporters signature. Note that the N-terminal 100 aa and the C-terminal 50 aa present in other glpT proteins are out of frame 2C and are represented by the CDSs Cj0292c and Cj0290c respectively. The sequence has been checked 2C and is believed to be correct 7EUpdated 282006 29 note: Pfam domain PF07690 Major Facilitator Superfamily identified within CDS. Also 2Ctwelve probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins -Carbohydrates 2C organic acids and alcohols NC_002163.1 RefSeq region 267638 268597 . - . ID=id24;gene=glpT;Name=id24;Dbxref=GeneID:904616;gbkey=misc_feature;Note=HMMPfam hit to PF07690 2C Major Facilitator Superfamily 2C score 1.8e-34 NC_002163.1 RefSeq region 267659 267727 . - . ID=id25;gene=glpT;Name=id25;Dbxref=GeneID:904616;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0292c by TMHMM2.0 at aa 9-31 2C 41-63 2C 72-94 2C 98-120 2C141-163 2C 178-195 2C 247-269 2C 284-303 2C 310-332 2C 337-359 2C364-386 and 401-423 NC_002163.1 RefSeq region 267740 267808 . - . ID=id25;gene=glpT;Name=id25;Dbxref=GeneID:904616;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0292c by TMHMM2.0 at aa 9-31 2C 41-63 2C 72-94 2C 98-120 2C141-163 2C 178-195 2C 247-269 2C 284-303 2C 310-332 2C 337-359 2C364-386 and 401-423 NC_002163.1 RefSeq region 267821 267889 . - . ID=id25;gene=glpT;Name=id25;Dbxref=GeneID:904616;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0292c by TMHMM2.0 at aa 9-31 2C 41-63 2C 72-94 2C 98-120 2C141-163 2C 178-195 2C 247-269 2C 284-303 2C 310-332 2C 337-359 2C364-386 and 401-423 NC_002163.1 RefSeq region 267908 267967 . - . ID=id25;gene=glpT;Name=id25;Dbxref=GeneID:904616;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0292c by TMHMM2.0 at aa 9-31 2C 41-63 2C 72-94 2C 98-120 2C141-163 2C 178-195 2C 247-269 2C 284-303 2C 310-332 2C 337-359 2C364-386 and 401-423 NC_002163.1 RefSeq region 268010 268078 . - . ID=id25;gene=glpT;Name=id25;Dbxref=GeneID:904616;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0292c by TMHMM2.0 at aa 9-31 2C 41-63 2C 72-94 2C 98-120 2C141-163 2C 178-195 2C 247-269 2C 284-303 2C 310-332 2C 337-359 2C364-386 and 401-423 NC_002163.1 RefSeq region 268232 268285 . - . ID=id25;gene=glpT;Name=id25;Dbxref=GeneID:904616;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0292c by TMHMM2.0 at aa 9-31 2C 41-63 2C 72-94 2C 98-120 2C141-163 2C 178-195 2C 247-269 2C 284-303 2C 310-332 2C 337-359 2C364-386 and 401-423 NC_002163.1 RefSeq region 268328 268396 . - . ID=id25;gene=glpT;Name=id25;Dbxref=GeneID:904616;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0292c by TMHMM2.0 at aa 9-31 2C 41-63 2C 72-94 2C 98-120 2C141-163 2C 178-195 2C 247-269 2C 284-303 2C 310-332 2C 337-359 2C364-386 and 401-423 NC_002163.1 RefSeq region 268457 268525 . - . ID=id25;gene=glpT;Name=id25;Dbxref=GeneID:904616;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0292c by TMHMM2.0 at aa 9-31 2C 41-63 2C 72-94 2C 98-120 2C141-163 2C 178-195 2C 247-269 2C 284-303 2C 310-332 2C 337-359 2C364-386 and 401-423 NC_002163.1 RefSeq region 268535 268597 . - . ID=id25;gene=glpT;Name=id25;Dbxref=GeneID:904616;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0292c by TMHMM2.0 at aa 9-31 2C 41-63 2C 72-94 2C 98-120 2C141-163 2C 178-195 2C 247-269 2C 284-303 2C 310-332 2C 337-359 2C364-386 and 401-423 NC_002163.1 RefSeq region 268591 268597 . - . ID=id25;gene=glpT;Name=id25;Dbxref=GeneID:904616;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0292c by TMHMM2.0 at aa 9-31 2C 41-63 2C 72-94 2C 98-120 2C141-163 2C 178-195 2C 247-269 2C 284-303 2C 310-332 2C 337-359 2C364-386 and 401-423 NC_002163.1 RefSeq region 268591 268785 . - . ID=id24;gene=glpT;Name=id24;Dbxref=GeneID:904616;gbkey=misc_feature;Note=HMMPfam hit to PF07690 2C Major Facilitator Superfamily 2C score 1.8e-34 NC_002163.1 RefSeq region 268591 268809 . - . ID=id633;gene=glpT;Name=id633;Dbxref=GeneID:904616;gbkey=misc_feature;Note=Original 282000 29 note: Cj0290c 2C probable pseudogene representing the C-terminus of Cj0291c 28glpT 27 29 7EOriginal 282000 29 note: Cj0292c 2C probable pseudogene representing the N-terminus of Cj0291c 28glpT 27 29 7EOriginal 282000 29 note: Cj0291c 2C glpT 27 2Cglycerol-3-phosphate transporter 2C possible pseudogene 2Clen: 319 aa 3B similar to the central region of many e.g. GLPT_ECOLI glycerol-3-phosphate transporter 28452 aa 29 2Cfasta scores 3B opt: 473 z-score: 832.3 E 28 29: 0 2C 35.3 25 identity in 323 aa overlap. No Hp match. Contains PS00942 glpT family of transporters signature. Note that the N-terminal 100 aa and the C-terminal 50 aa present in other glpT proteins are out of frame 2C and are represented by the CDSs Cj0292c and Cj0290c respectively. The sequence has been checked 2C and is believed to be correct 7EUpdated 282006 29 note: Pfam domain PF07690 Major Facilitator Superfamily identified within CDS. Also 2Ctwelve probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins -Carbohydrates 2C organic acids and alcohols NC_002163.1 RefSeq region 268621 268689 . - . ID=id25;gene=glpT;Name=id25;Dbxref=GeneID:904616;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0292c by TMHMM2.0 at aa 9-31 2C 41-63 2C 72-94 2C 98-120 2C141-163 2C 178-195 2C 247-269 2C 284-303 2C 310-332 2C 337-359 2C364-386 and 401-423 NC_002163.1 RefSeq region 268717 268785 . - . ID=id25;gene=glpT;Name=id25;Dbxref=GeneID:904616;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0292c by TMHMM2.0 at aa 9-31 2C 41-63 2C 72-94 2C 98-120 2C141-163 2C 178-195 2C 247-269 2C 284-303 2C 310-332 2C 337-359 2C364-386 and 401-423 ### NC_002163.1 UTR_Extractor 5'-UTR 268810 268924 . - . ID=utr107;locus_tag=Cj0292c;product=pseudo NC_002163.1 UTR_Extractor 5'-UTR 269040 269063 . + . ID=utr108;locus_tag=Cj0293;product=stationary phase survival protein SurE NC_002163.1 RefSeq CDS 269064 269840 . + 0 ID=cds252;Parent=gene263;gene=surE;Name=YP_002343731.1;Dbxref=GOA:Q9PIK6 HSSP:Q8ZU79 InterPro:IPR002828 UniProtKB FSwiss-Prot:Q9PIK6 Genbank:YP_002343731.1 GeneID:904617;gbkey=CDS;product=stationary phase survival protein SurE;Note=catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate NC_002163.1 RefSeq gene 269064 269840 . + . ID=gene263;gene=surE;Name=surE;locus_tag=Cj0293;Dbxref=GeneID:904617;gbkey=Gene NC_002163.1 RefSeq region 269067 269645 . + . ID=id634;gene=surE;Name=id634;Dbxref=GeneID:904617;gbkey=misc_feature;Note=HMMPfam hit to PF01975 2C Survival protein SurE 2Cscore 3.9e-78 NC_002163.1 RefSeq gene 269830 270489 . + . ID=gene264;gene=moeB/thiF;Name=moeB/thiF;locus_tag=Cj0294;Dbxref=GeneID:904618;gbkey=Gene NC_002163.1 RefSeq CDS 269830 270489 . + 0 ID=cds253;Parent=gene264;Name=YP_002343732.1;Dbxref=GOA:Q0PBL5 InterPro:IPR000594 InterPro:IPR016040 UniProtKB FTrEMBL:Q0PBL5 Genbank:YP_002343732.1 GeneID:904618;gbkey=CDS;product=MoeB 2FThiF family protein;Note=Original 282000 29 note: Cj0294 2C unknown 2C len: 219 aa 3B similar to members of the hesA 2FmoeB 2FthiF family 2C e.g. YGDL_ECOLI 28268 aa 29 2C fasta scores 3B opt: 219 z-score: 563.3 E 28 29: 4e-24 2C 33.5 25 identity in 254 aa overlap. 48.3 25 identity to HP0755 28described as moeB 29. Contains Pfam match to entry PF00899 ThiF_family 2C ThiF family 2C score 33.10 2C E-value 2e-07. Also similar to Cj1046c 2833.6 25 identity in 146 aa overlap 29 7EUpdated 282006 29 note: No specific characterisation with acceptable identity scores carried out yet. kept within product function. Functional classification -Misc NC_002163.1 RefSeq region 269893 270273 . + . ID=id635;Name=id635;Dbxref=GeneID:904618;gbkey=misc_feature;Note=HMMPfam hit to PF00899 2C ThiF family 2C score 1.3e-09 NC_002163.1 RefSeq region 269905 269958 . + . ID=id636;Name=id636;Dbxref=GeneID:904618;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0294 by TMHMM2.0 at aa 26-43 NC_002163.1 RefSeq gene 270473 270931 . + . ID=gene265;Name=Cj0295;locus_tag=Cj0295;Dbxref=GeneID:904619;gbkey=Gene NC_002163.1 RefSeq CDS 270473 270931 . + 0 ID=cds254;Parent=gene265;Name=YP_002343733.1;Dbxref=GOA:Q0PBL4 InterPro:IPR000182 InterPro:IPR016181 UniProtKB FTrEMBL:Q0PBL4 Genbank:YP_002343733.1 GeneID:904619;gbkey=CDS;product=acetyltransferase;Note=Original 282000 29 note: Cj0295 2C possible acetyltransferase 2C len: 152 aa 3B similar to hypothetical proteins e.g. YAFP_ECOLI 28150 aa 29 2C fasta scores 3B opt: 246 z-score: 340.4 E 28 29: 1.1e-11 2C 27.8 25 identity in 144 aa overlap. No Hp match. Contains Pfam match to entry PF00583 Acetyltransf 2C Acetyltransferase 28GNAT 29 family 2C score 20.20 2C E-value 0.011 7EUpdated 282006 29 note: Some characterisation within Escherichia coli with marginal identity score. kept within product function. Functional classification -Misc NC_002163.1 RefSeq region 270635 270847 . + . ID=id637;Name=id637;Dbxref=GeneID:904619;gbkey=misc_feature;Note=HMMPfam hit to PF00583 2C Acetyltransferase 28GNAT 29 family 2C score 1.2e-07 ### NC_002163.1 RefSeq stem_loop 270978 271021 . + . ID=id638;Name=id638;gbkey=stem_loop NC_002163.1 RefSeq CDS 271041 271421 . - 0 ID=cds255;Parent=gene266;gene=panD;Name=YP_002343734.1;Dbxref=GOA:Q9PIK3 HSSP:P31664 InterPro:IPR003190 InterPro:IPR009010 UniProtKB FSwiss-Prot:Q9PIK3 Genbank:YP_002343734.1 GeneID:904620;gbkey=CDS;product=aspartate alpha-decarboxylase;Note=Converts L-aspartate to beta-alanine and provides the major route of beta-alanine production in bacteria. Beta-alanine is essential for the biosynthesis of pantothenate 28vitamin B5 29 NC_002163.1 RefSeq gene 271041 271421 . - . ID=gene266;gene=panD;Name=panD;locus_tag=Cj0296c;Dbxref=GeneID:904620;gbkey=Gene NC_002163.1 RefSeq region 271077 271421 . - . ID=id639;gene=panD;Name=id639;Dbxref=GeneID:904620;gbkey=misc_feature;Note=HMMPfam hit to PF02261 2C Aspartate decarboxylase 2Cscore 1.5e-61 NC_002163.1 RefSeq gene 271418 272266 . - . ID=gene267;gene=panC;Name=panC;locus_tag=Cj0297c;Dbxref=GeneID:904621;gbkey=Gene NC_002163.1 RefSeq CDS 271418 272266 . - 0 ID=cds256;Parent=gene267;gene=panC;Name=YP_002343735.1;Dbxref=GOA:Q9PIK2 HSSP:O06280 InterPro:IPR003721 InterPro:IPR014729 UniProtKB FSwiss-Prot:Q9PIK2 Genbank:YP_002343735.1 GeneID:904621;gbkey=CDS;product=pantoate--beta-alanine ligase;Note=catalyzes the formation of 28R 29-pantothenate from pantoate and beta-alanine NC_002163.1 RefSeq region 271433 272266 . - . ID=id640;gene=panC;Name=id640;Dbxref=GeneID:904621;gbkey=misc_feature;Note=HMMPfam hit to PF02569 2C Pantoate-beta-alanine ligase 2C score 4.1e-137 ### NC_002163.1 UTR_Extractor 5'-UTR 272267 272383 . - . ID=utr109;locus_tag=Cj0297c;product=pantoate--beta-alanine ligase NC_002163.1 RefSeq gene 272277 273101 . - . ID=gene268;gene=panB;Name=panB;locus_tag=Cj0298c;Dbxref=GeneID:904622;gbkey=Gene NC_002163.1 RefSeq CDS 272277 273101 . - 0 ID=cds257;Parent=gene268;gene=panB;Name=YP_002343736.1;Dbxref=GOA:Q9PIK1 HSSP:Q10505 InterPro:IPR003700 InterPro:IPR015813 UniProtKB FSwiss-Prot:Q9PIK1 Genbank:YP_002343736.1 GeneID:904622;gbkey=CDS;product=3-methyl-2-oxobutanoate hydroxymethyltransferase;Note=catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5 2C10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate NC_002163.1 RefSeq region 272325 273098 . - . ID=id641;gene=panB;Name=id641;Dbxref=GeneID:904622;gbkey=misc_feature;Note=HMMPfam hit to PF02548 2C Ketopantoate hydroxymethyltransferase 2C score 8.3e-137 ### NC_002163.1 UTR_Extractor 5'-UTR 273102 273137 . - . ID=utr110;locus_tag=Cj0298c;product=3-methyl-2-oxobutanoate hydroxymethyltransferase NC_002163.1 UTR_Extractor 5'-UTR 273275 273320 . + . ID=utr111;locus_tag=Cj0299;product=putative periplasmic beta-lactamase NC_002163.1 RefSeq gene 273321 274094 . + . ID=gene269;Name=Cj0299;locus_tag=Cj0299;Dbxref=GeneID:904623;gbkey=Gene NC_002163.1 RefSeq CDS 273321 274094 . + 0 ID=cds258;Parent=gene269;Name=YP_002343737.1;Dbxref=GOA:Q0PBL0 InterPro:IPR001460 UniProtKB FTrEMBL:Q0PBL0 Genbank:YP_002343737.1 GeneID:904623;gbkey=CDS;product=beta-lactamase;Note=Original 282000 29 note: Cj0299 2C possible periplasmic beta-lactamase 2C len: 257 aa 3B similar to members of the class-D beta-lactamase family e.g. BLL1_PSEAE BETA-LACTAMASE LCR-1 PRECURSOR 28EC 3.5.2.6 29 28Pseudomonas aeruginosa plasmid PMG76 29 28260 aa 29 2C fasta scores 3B opt: 423 z-score: 305.2 E 28 29: 9.6e-10 2C 33.7 25 identity in 255 aa overlap. No Hp match. Contains N-terminal signal sequence 7EUpdated 282006 29 note: Some characterisation work within Pseudomonas aeruginosa and Escherichia coli with marginal identity scores. kept within product function. Functional classification - Antibiotic resistance 7EPMID:11188693 2C PMID:7574536 NC_002163.1 RefSeq region 273414 274061 . + . ID=id642;Name=id642;Dbxref=GeneID:904623;gbkey=misc_feature;Note=HMMPfam hit to PF00905 2C Penicillin binding protein transpeptid 2C score 1.3e-33 ### NC_002163.1 RefSeq CDS 274179 275063 . - 0 ID=cds259;Parent=gene270;gene=modC;Name=YP_002343738.1;Dbxref=GOA:Q0PBK9 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FTrEMBL:Q0PBK9 Genbank:YP_002343738.1 GeneID:904624;gbkey=CDS;product=molybdenum transport ATP-binding protein;Note=Original 282000 29 note: Cj0300c 2C modC 2C probable molybdenum transport ATP-binding protein 2C len: 294 aa 3B similar to many ABC-transporter ATP binding proteins 2C and to MODC_ECOLI molybdenum transport ATP-binding protein 28352 aa 29 2C fasta scores 3B opt: 487 z-score: 700.9 E 28 29: 8.7e-32 2C 34.8 25 identity in 270 aa overlap. Identification as modC is based on presence of probable molybdenum-specific permease and periplasmic binding proteins upstream. 46.8 25 identity to HP0475. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00211 ABC transporters family signature and Pfam match to entry PF00005 ABC_tran 2C ABC transporters 2C score 214.40 2C E-value 1.7e-60 7EUpdated 282006 29 note: Characterised more than once within Escherichia coli with marginal identity scores. kept within product function. Functional classification - Transport 2Fbinding proteins - Anions 7EPMID:2188958 2C PMID:7665461 2C PMID:7665460 NC_002163.1 RefSeq gene 274179 275063 . - . ID=gene270;gene=modC;Name=modC;locus_tag=Cj0300c;Dbxref=GeneID:904624;gbkey=Gene NC_002163.1 RefSeq region 274443 274982 . - . ID=id643;gene=modC;Name=id643;Dbxref=GeneID:904624;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 6e-62 NC_002163.1 RefSeq region 274629 274673 . - . ID=id644;gene=modC;Name=id644;Dbxref=GeneID:904624;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq region 274938 274961 . - . ID=id645;gene=modC;Name=id645;Dbxref=GeneID:904624;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 275060 275734 . - 0 ID=cds260;Parent=gene271;gene=modB;Name=YP_002343739.1;Dbxref=GOA:Q0PBK8 InterPro:IPR000515 InterPro:IPR011867 UniProtKB FTrEMBL:Q0PBK8 Genbank:YP_002343739.1 GeneID:904625;gbkey=CDS;product=molybdenum transport system permease;Note=Original 282000 29 note: Cj0301c 2C modB 2C probable molybdenum transport system permease 2C len: 224 aa 3B similar to e.g. MODC_AZOVI molybdenum transport system permease 28226 aa 29 2C fasta scores 3B opt: 562 z-score: 889.7 E 28 29: 0 2C 43.3 25 identity in 210 aa overlap and MODB_ECOLI 28229 aa 29 2C fasta scores 3B opt: 390 z-score: 537.4 E 28 29: 1.1e-22 2C 32.8 25 identity in 183 aa overlap. 55.2 25 identity to HP0474. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 and Pfam match to entry PF00528 BPD_transp 2C Binding-protein-dependent transport systems inner membrane component 2C score 43.10 2C E-value 6.1e-09 7EUpdated 282006 29 note: Characterised in many e.g. Rhodobacter capsulatus and Azotobacter vinelandii with acceptable identity scores. kept within product function. Functional classification - Transport 2Fbinding proteins - Anions 7EPMID:8384683 2C PMID:8491722 NC_002163.1 RefSeq gene 275060 275734 . - . ID=gene271;gene=modB;Name=modB;locus_tag=Cj0301c;Dbxref=GeneID:904625;gbkey=Gene NC_002163.1 RefSeq region 275066 275719 . - . ID=id646;gene=modB;Name=id646;Dbxref=GeneID:904625;gbkey=misc_feature;Note=HMMPfam hit to PF00528 2C Binding-protein-dependent transport syst 2C score 8.6e-19 NC_002163.1 RefSeq region 275084 275152 . - . ID=id26;gene=modB;Name=id26;Dbxref=GeneID:904625;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0301c by TMHMM2.0 at aa 15-37 2C 49-71 2C 86-108 2C 147-169 and 195-217 NC_002163.1 RefSeq region 275228 275296 . - . ID=id26;gene=modB;Name=id26;Dbxref=GeneID:904625;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0301c by TMHMM2.0 at aa 15-37 2C 49-71 2C 86-108 2C 147-169 and 195-217 NC_002163.1 RefSeq region 275342 275365 . - . ID=id647;gene=modB;Name=id647;Dbxref=GeneID:904625;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 275411 275479 . - . ID=id26;gene=modB;Name=id26;Dbxref=GeneID:904625;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0301c by TMHMM2.0 at aa 15-37 2C 49-71 2C 86-108 2C 147-169 and 195-217 NC_002163.1 RefSeq region 275522 275590 . - . ID=id26;gene=modB;Name=id26;Dbxref=GeneID:904625;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0301c by TMHMM2.0 at aa 15-37 2C 49-71 2C 86-108 2C 147-169 and 195-217 NC_002163.1 RefSeq region 275624 275692 . - . ID=id26;gene=modB;Name=id26;Dbxref=GeneID:904625;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0301c by TMHMM2.0 at aa 15-37 2C 49-71 2C 86-108 2C 147-169 and 195-217 NC_002163.1 RefSeq gene 275727 276128 . - . ID=gene272;gene=Cj0302c;Name=Cj0302c;locus_tag=Cj0302c;Dbxref=GeneID:904626;gbkey=Gene NC_002163.1 RefSeq CDS 275727 276128 . - 0 ID=cds261;Parent=gene272;Name=YP_002343740.1;Dbxref=GOA:Q0PBK7 InterPro:IPR005116 UniProtKB FTrEMBL:Q0PBK7 Genbank:YP_002343740.1 GeneID:904626;gbkey=CDS;product=molybdenum-pterin-binding protein;Note=Original 282000 29 note: Cj0302c 2C unknonw 2C len: 133 aa 3B no Hp match 7EUpdated 282006 29 note: Pfam domain PF03459 TOBE domain identified within CDS. TOBE 28Transport-associated OB 29 has had work carried out within Esherichia coli where it has been shown to be involved in the recognition of small ligands such as molybdenum. TOBE has been found in ABC transporters immediately after the ATPase domain. A child process of this family is Molybdenum-pterin binding protein. Product modified to more specific family member based on motif match. Some characterisation work within Clostridium pasteurianum 2C however 2C identity scores were marginal and full length sequence alignment was not achieved. Functional classification - Miscellaneous periplasmic proteins 7EPMID:3540853 2C PMID:2820842 NC_002163.1 RefSeq region 275745 275933 . - . ID=id648;Name=id648;Dbxref=GeneID:904626;gbkey=misc_feature;Note=HMMPfam hit to PF03459 2C TOBE domain 2C score 4.6e-06 NC_002163.1 RefSeq CDS 276125 276874 . - 0 ID=cds262;Parent=gene273;gene=modA;Name=YP_002343741.1;Dbxref=GOA:Q0PBK6 InterPro:IPR005950 InterPro:IPR006059 UniProtKB FTrEMBL:Q0PBK6 Genbank:YP_002343741.1 GeneID:904627;gbkey=CDS;product=molybdate-binding lipoprotein;Note=Original 282000 29 note: Cj0303c 2C modA 2C probable molybdate-binding lipoprotein 2C len: 249 aa 3B similar to e.g. MODA_RHOCA molybdate-binding periplasmic protein precursor 28252 aa 29 2C fasta scores 3B opt: 354 z-score: 449.0 E 28 29: 9.4e-18 2C 30.8 25 identity in 224 aa overlap 2C and MODA_ECOLI 28257 aa 29 2C fasta scores 3B opt: 220 z-score: 245.4 E 28 29: 2.1e-06 2C 25.0 25 identity in 232 aa overlap. 42.3 25 identity to HP0473. Contains probable N-terminal signal sequence with appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site 7EUpdated 282006 29 note: Pfam domain PF01547 Bacterial extracellular solute-binding protein was identified within CDS. Further support given to product function. Characterised in more than one genus e.g. Rhodobacter capsulatus 2C Azotobacter vinelandii and Escherichia coli. Identity scores were marginal and sequence alignment was not full length. kept within product function. Functional classification - Transport 2Fbinding proteins -Anions 7EPMID:8491722 2C PMID:8384683 2C PMID:8564363 NC_002163.1 RefSeq gene 276125 276874 . - . ID=gene273;gene=modA;Name=modA;locus_tag=Cj0303c;Dbxref=GeneID:904627;gbkey=Gene NC_002163.1 RefSeq region 276158 276865 . - . ID=id649;gene=modA;Name=id649;Dbxref=GeneID:904627;gbkey=misc_feature;Note=HMMPfam hit to PF01547 2C Bacterial extracellular solute-binding prot 2C score 4.2e-13 NC_002163.1 RefSeq region 276794 276862 . - . ID=id650;gene=modA;Name=id650;Dbxref=GeneID:904627;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0303c by TMHMM2.0 at aa 5-27 NC_002163.1 RefSeq region 276827 276859 . - . ID=id651;gene=modA;Name=id651;Dbxref=GeneID:904627;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq CDS 276925 277611 . - 0 ID=cds263;Parent=gene274;gene=bioC;Name=YP_002343742.1;Dbxref=GOA:Q0PBK5 InterPro:IPR011814 InterPro:IPR013217 UniProtKB FTrEMBL:Q0PBK5 Genbank:YP_002343742.1 GeneID:904628;gbkey=CDS;product=biotin synthesis protein;Note=Original 282000 29 note: Cj0304c 2C bioC 2C possible biotin synthesis protein 2C len: 228 aa 3B similar to BIOC_HAEIN biotin synthesis protein bioC 28260 aa 29 2C fasta scores 3B opt: 342 z-score: 595.7 E 28 29: 6.4e-26 2C34.0 25 identity in 238 aa overlap. Also some similarity to BIOC_ECOLI 28251 aa 29 2C wublastp scores 3B E 3D 0.00028 2C 24 25 identity in 193 aa overlap. No Hp match 7EUpdated 282006 29 note: Some characterisation within Bacillus subtilis and Escherichia coli 2C however 2C identity scores were unnacceptable. kept within product function. Functional classification - Biosynthesis of cofactors 2C prosthetic groups and carriers - Biotin 7EPMID:3058702 2C PMID:8763940 NC_002163.1 RefSeq gene 276925 277611 . - . ID=gene274;gene=bioC;Name=bioC;locus_tag=Cj0304c;Dbxref=GeneID:904628;gbkey=Gene NC_002163.1 RefSeq CDS 277608 278219 . - 0 ID=cds264;Parent=gene275;Name=YP_002343743.1;Dbxref=InterPro:IPR007398 UniProtKB FTrEMBL:Q0PBK4 Genbank:YP_002343743.1 GeneID:904629;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0305c 2C unknown 2C len: 203 aa 3B similar to a hypothetical protein from H. infuenzae YF52_HAEIN HI1552 28215 aa 29 2C fasta scores 3B opt: 297 z-score: 372.7 E 28 29: 1.7e-13 2C 29.8 25 identity in 215 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam PF04301 2C Protein of unknown function 28DUF452 29 was present within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 277608 278219 . - . ID=gene275;gene=Cj0305c;Name=Cj0305c;locus_tag=Cj0305c;Dbxref=GeneID:904629;gbkey=Gene NC_002163.1 RefSeq region 277611 278219 . - . ID=id652;Name=id652;Dbxref=GeneID:904629;gbkey=misc_feature;Note=HMMPfam hit to PF04301 2C Protein of unknown function 28DUF452 29 2C score 2.5e-153 NC_002163.1 RefSeq CDS 278216 279358 . - 0 ID=cds265;Parent=gene276;gene=bioF;Name=YP_002343744.1;Dbxref=GOA:Q0PBK3 InterPro:IPR001917 InterPro:IPR004839 InterPro:IPR015421 UniProtKB FTrEMBL:Q0PBK3 Genbank:YP_002343744.1 GeneID:904630;gbkey=CDS;product=8-amino-7-oxononanoate synthase;Note=Original 282000 29 note: Cj0306c 2C bioF 2C probable 8-amino-7-oxononanoate synthase 2C len: 380 aa 3B similar to many e.g. BIOF_ECOLI 8-amino-7-oxononanoate synthase 28EC 2.3.1.47 29 28384 aa 29 2C fasta scores 3B opt: 525 z-score: 550.3 E 28 29: 2.1e-23 2C 28.9 25 identity in 387 aa overlap. 29.0 25 identity to HP0598. Contains PS00599 Aminotransferases class-II pyridoxal-phosphate attachment site and Pfam match to entry PF00222 aminotran_2 2C Aminotransferases class-II 2C score 196.30 2C E-value 4.7e-55 7EUpdated 282006 29 note: Characterised within Escherichia coli with marginal identity scores. not added to product function. Functional classification -Biosynthesis of cofactors 2C prosthetic groups and carriers - Biotin 7EPMID:9813126 2C PMID:1575677 2C PMID:1575677 2CPMID:3058702 NC_002163.1 RefSeq gene 278216 279358 . - . ID=gene276;gene=bioF;Name=bioF;locus_tag=Cj0306c;Dbxref=GeneID:904630;gbkey=Gene NC_002163.1 RefSeq region 278219 279097 . - . ID=id653;gene=bioF;Name=id653;Dbxref=GeneID:904630;gbkey=misc_feature;Note=HMMPfam hit to PF00155 2C Aminotransferase class I and II 2C score 2e-07 NC_002163.1 RefSeq region 278624 278653 . - . ID=id654;gene=bioF;Name=id654;Dbxref=GeneID:904630;gbkey=misc_feature;Note=PS00599 Aminotransferases class-II pyridoxal-phosphate attachment site ### NC_002163.1 UTR_Extractor 5'-UTR 279359 279387 . - . ID=utr112;locus_tag=Cj0306c;product=8-amino-7-oxononanoate synthase NC_002163.1 RefSeq CDS 279426 280709 . + 0 ID=cds266;Parent=gene277;gene=bioA;Name=YP_002343745.1;Dbxref=GOA:Q0PBK2 InterPro:IPR005814 InterPro:IPR005815 InterPro:IPR015421 UniProtKB FTrEMBL:Q0PBK2 Genbank:YP_002343745.1 GeneID:904631;gbkey=CDS;product=adenosylmethionine-8-amino-7-oxononanoate aminotransferase;Note=catalyzes the formation of S-adenosyl-4-methylthionine-2-oxobutanoate and 7 2C8-diaminononanoate from S-adenosyl-L-methionine and 8-amino-7-oxononanoate NC_002163.1 RefSeq gene 279426 280709 . + . ID=gene277;gene=bioA;Name=bioA;locus_tag=Cj0307;Dbxref=GeneID:904631;gbkey=Gene NC_002163.1 RefSeq region 279480 280706 . + . ID=id655;gene=bioA;Name=id655;Dbxref=GeneID:904631;gbkey=misc_feature;Note=HMMPfam hit to PF00202 2C Aminotransferase class-III 2Cscore 4.3e-127 NC_002163.1 RefSeq region 280143 280256 . + . ID=id656;gene=bioA;Name=id656;Dbxref=GeneID:904631;gbkey=misc_feature;Note=PS00600 Aminotransferases class-III pyridoxal-phosphate attachment site NC_002163.1 RefSeq gene 280696 281301 . - . ID=gene278;gene=bioD;Name=bioD;locus_tag=Cj0308c;Dbxref=GeneID:904632;gbkey=Gene NC_002163.1 RefSeq CDS 280696 281301 . - 0 ID=cds267;Parent=gene278;gene=bioD;Name=YP_002343746.1;Dbxref=GOA:Q9PIJ1 InterPro:IPR004472 UniProtKB FSwiss-Prot:Q9PIJ1 Genbank:YP_002343746.1 GeneID:904632;gbkey=CDS;product=dethiobiotin synthetase;Note=Original 282000 29 note: Cj0308c 2C bioD 2C possible dethiobiotin synthetase 2C len: 201 aa 3B some similarity to many e.g. BIOD_BACSH dethiobiotin synthetase 28EC 6.3.3.3 29 28234 aa 29 2C fasta scores 3B opt: 206 z-score: 260.4 E 28 29: 3e-07 2C 29.8 25 identity in 215 aa overlap. 31.8 25 identity in 66 aa overlap to HP0029 7EUpdated 282006 29 note: Some characterisation within Bacillus sphaericus 2C however 2C identity score was marginal. kept within product function. Functional classification - Biosynthesis of cofactors 2C prosthetic groups and carriers - Biotin 7EPMID:2110099 2C PMID:3058702 2C PMID:10455485 ### NC_002163.1 UTR_Extractor 5'-UTR 281302 281463 . - . ID=utr113;locus_tag=Cj0308c;product=putative dethiobiotin synthetase NC_002163.1 RefSeq gene 281311 281625 . - . ID=gene279;Name=Cj0309c;locus_tag=Cj0309c;Dbxref=GeneID:904633;gbkey=Gene NC_002163.1 RefSeq CDS 281311 281625 . - 0 ID=cds268;Parent=gene279;Name=YP_002343747.1;Dbxref=GOA:Q0PBK0 InterPro:IPR000390 UniProtKB FTrEMBL:Q0PBK0 Genbank:YP_002343747.1 GeneID:904633;gbkey=CDS;product=efflux protein;Note=Original 282000 29 note: Cj0309c 2C probable efflux protein 2C len: 104 aa 3B similar to many membrane protein of known and unknown function e.g. TR:O34690 28EMBL:AJ002571 29 Bacillus subtilis YKKD 28105 aa 29 2C fasta scores 3B opt: 303 z-score: 547.1 E 28 29: 3.2e-23 2C 44.2 25 identity in 104 aa overlap 2C and EBR_STAAU ethidium bromide resistance protein 28multidrug resistance protein 29 28107 aa 29 2C fasta scores 3B opt: 187 z-score: 272.5 E 28 29: 6.4e-08 2C 27.2 25 identity in 103 aa overlap. No Hp match. Also similar to upstream CDS Cj0310c 2832.4 25 identity in 105 aa overlap 29 2C and to Cj1174 2828.7 25 identity in 94 aa overlap 29 and Cj1173 2824.7 25 identity in 93 aa overlap 29. Contains Pfam match to entry PF00893 DUF7 2C Integral membrane protein 2C score 109.20 2CE-value 7.7e-29 2C and four possible transmembrane domains 7EUpdated 282006 29 note: Pfam domain PF00893 Small Multidrug Resistance 28Smr 29 protein identified within CDS. Previously this was an uncharacterised Pfam domain. Smr proteins are a family of efflux proteins that confer resistance to a wide range of toxic compounds by removing them from the cells. Further support given to product function. kept within product function. Functional classification - Drug 2Fanalogue sensitivity 7EPMID:10735877 2C PMID:11566977 NC_002163.1 RefSeq region 281317 281376 . - . ID=id27;Name=id27;Dbxref=GeneID:904633;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0309c by TMHMM2.0 at aa 3-20 2C 30-49 2C 56-78 and 84-103 NC_002163.1 RefSeq region 281347 281625 . - . ID=id657;Name=id657;Dbxref=GeneID:904633;gbkey=misc_feature;Note=HMMPfam hit to PF00893 2C Small Multidrug Resistance protein 2C score 4.2e-30 NC_002163.1 RefSeq region 281392 281460 . - . ID=id27;Name=id27;Dbxref=GeneID:904633;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0309c by TMHMM2.0 at aa 3-20 2C 30-49 2C 56-78 and 84-103 NC_002163.1 RefSeq region 281479 281538 . - . ID=id27;Name=id27;Dbxref=GeneID:904633;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0309c by TMHMM2.0 at aa 3-20 2C 30-49 2C 56-78 and 84-103 NC_002163.1 RefSeq region 281566 281619 . - . ID=id27;Name=id27;Dbxref=GeneID:904633;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0309c by TMHMM2.0 at aa 3-20 2C 30-49 2C 56-78 and 84-103 ### NC_002163.1 RefSeq CDS 281629 281967 . - 0 ID=cds269;Parent=gene280;Name=YP_002343748.1;Dbxref=GOA:Q0PBJ9 InterPro:IPR000390 UniProtKB FTrEMBL:Q0PBJ9 Genbank:YP_002343748.1 GeneID:904634;gbkey=CDS;product=efflux protein;Note=Original 282000 29 note: Cj0310c 2C possible efflux protein 2C len: 104 aa 3B similar to many membrane proteins of known and unknown function e.g. YKKC_BACSU 28112 aa 29 2C fasta scores 3B opt: 273 z-score: 458.2 E 28 29: 2.9e-18 2C 40.8 25 identity in 103 aa overlap 2C and EBR_STAAU ethidium bromide resistance protein 28107 aa 29 2C fasta scores 3B opt: 135 z-score: 198.9 E 28 29: 0.00088 2C 27.4 25 identity in 84 aa overlap. No Hp match. Also similar to downstream CDS Cj0309c 2832.4 25 identity in 105 aa overlap 29 and to Cj1173 2827.1 25 identity in 107 aa overlap 29. Contains Pfam match to entry PF00893 DUF7 2C Integral membrane protein 2C score 51.40 2C E-value 2e-11 2C and four possible transmembrane domains 7EUpdated 282006 29 note: Pfam domain PF00893 Small Multidrug Resistance 28Smr family 29 protein identified within CDS. Previously this was an uncharacterised Pfam domain. Smr proteins are a family of efflux proteins that confer resistance to a wide range of toxic compounds by removing them from the cells. Further support given to product function. kept within product function. Functional classification - Drug 2Fanalogue sensitivity 7EPMID:10735877 2C PMID:11948170 NC_002163.1 RefSeq gene 281629 281967 . - . ID=gene280;Name=Cj0310c;locus_tag=Cj0310c;Dbxref=GeneID:904634;gbkey=Gene NC_002163.1 RefSeq region 281644 281712 . - . ID=id28;Name=id28;Dbxref=GeneID:904634;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0310c by TMHMM2.0 at aa 7-28 2C 33-55 2C 60-82 and 86-108 NC_002163.1 RefSeq region 281674 281943 . - . ID=id658;Name=id658;Dbxref=GeneID:904634;gbkey=misc_feature;Note=HMMPfam hit to PF00893 2C Small Multidrug Resistance protein 2C score 1.3e-12 NC_002163.1 RefSeq region 281722 281790 . - . ID=id28;Name=id28;Dbxref=GeneID:904634;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0310c by TMHMM2.0 at aa 7-28 2C 33-55 2C 60-82 and 86-108 NC_002163.1 RefSeq region 281803 281871 . - . ID=id28;Name=id28;Dbxref=GeneID:904634;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0310c by TMHMM2.0 at aa 7-28 2C 33-55 2C 60-82 and 86-108 NC_002163.1 RefSeq region 281884 281949 . - . ID=id28;Name=id28;Dbxref=GeneID:904634;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0310c by TMHMM2.0 at aa 7-28 2C 33-55 2C 60-82 and 86-108 ### NC_002163.1 UTR_Extractor 5'-UTR 281968 281996 . - . ID=utr114;locus_tag=Cj0310c;product=putative efflux protein NC_002163.1 UTR_Extractor 5'-UTR 282077 282100 . + . ID=utr115;locus_tag=Cj0311;product=50S ribosomal protein L25 2Fgeneral stress protein Ctc NC_002163.1 RefSeq CDS 282101 282637 . + 0 ID=cds270;Parent=gene281;Name=YP_002343749.1;Dbxref=GOA:Q9PII8 HSSP:P56930 InterPro:IPR001021 UniProtKB FSwiss-Prot:Q9PII8 Genbank:YP_002343749.1 GeneID:904635;gbkey=CDS;product=50S ribosomal protein L25;Note=the Ctc family of proteins consists of two types 2C one that contains the N-terminal ribosomal protein L25 domain only which in Escherichia coli binds the 5S rRNA while a subset of proteins contain a C-terminal extension that is involved in the stress response NC_002163.1 RefSeq gene 282101 282637 . + . ID=gene281;Name=Cj0311;locus_tag=Cj0311;Dbxref=GeneID:904635;gbkey=Gene NC_002163.1 RefSeq region 282104 282361 . + . ID=id659;Name=id659;Dbxref=GeneID:904635;gbkey=misc_feature;Note=HMMPfam hit to PF01386 2C Ribosomal L25p family 2Cscore 1.5e-29 NC_002163.1 RefSeq gene 282634 283179 . + . ID=gene282;gene=pth;Name=pth;locus_tag=Cj0312;Dbxref=GeneID:904636;gbkey=Gene NC_002163.1 RefSeq CDS 282634 283179 . + 0 ID=cds271;Parent=gene282;gene=pth;Name=YP_002343750.1;Dbxref=GOA:Q9PII7 HSSP:P23932 InterPro:IPR001328 UniProtKB FSwiss-Prot:Q9PII7 Genbank:YP_002343750.1 GeneID:904636;gbkey=CDS;product=peptidyl-tRNA hydrolase;Note=Enables the recycling of peptidyl-tRNAs produced at termination of translation NC_002163.1 RefSeq region 282640 283167 . + . ID=id660;gene=pth;Name=id660;Dbxref=GeneID:904636;gbkey=misc_feature;Note=HMMPfam hit to PF01195 2C Peptidyl-tRNA hydrolase 2Cscore 4.2e-68 NC_002163.1 RefSeq region 282673 282714 . + . ID=id661;gene=pth;Name=id661;Dbxref=GeneID:904636;gbkey=misc_feature;Note=PS01195 Peptidyl-tRNA hydrolase signature 1 NC_002163.1 RefSeq region 282940 282972 . + . ID=id662;gene=pth;Name=id662;Dbxref=GeneID:904636;gbkey=misc_feature;Note=PS01196 Peptidyl-tRNA hydrolase signature 2 ### NC_002163.1 RefSeq CDS 283181 284239 . + 0 ID=cds272;Parent=gene283;Name=YP_002343751.1;Dbxref=GOA:Q0PBJ6 InterPro:IPR005495 UniProtKB FTrEMBL:Q0PBJ6 Genbank:YP_002343751.1 GeneID:904637;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0313 2C probable integral membrane protein 2C len: 352 aa 3B 35.9 25 identity to HP1498 7EUpdated 282006 29 note: Pfam domains PF03739 Predicted permease YjgP 2FYjgQ family were identified. Members of this family are predicted integral membrane proteins of unknown function. They are about 350 amino acids long and contain about 6 transmembrane regions. They are predicted to be permeases although there is no verification of this. Six probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 283181 284239 . + . ID=gene283;Name=Cj0313;locus_tag=Cj0313;Dbxref=GeneID:904637;gbkey=Gene NC_002163.1 RefSeq region 283196 284230 . + . ID=id663;Name=id663;Dbxref=GeneID:904637;gbkey=misc_feature;Note=HMMPfam hit to PF03739 2C Predicted permease YjgP 2FYjgQ family 2C score 5.8e-79 NC_002163.1 RefSeq region 283214 283282 . + . ID=id664;Name=id664;Dbxref=GeneID:904637;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0313 by TMHMM2.0 at aa 12-34 2C 49-71 2C 95-117 2C 270-292 2C294-316 and 326-348 NC_002163.1 RefSeq region 283325 283393 . + . ID=id664;Name=id664;Dbxref=GeneID:904637;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0313 by TMHMM2.0 at aa 12-34 2C 49-71 2C 95-117 2C 270-292 2C294-316 and 326-348 NC_002163.1 RefSeq region 283463 283531 . + . ID=id664;Name=id664;Dbxref=GeneID:904637;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0313 by TMHMM2.0 at aa 12-34 2C 49-71 2C 95-117 2C 270-292 2C294-316 and 326-348 NC_002163.1 RefSeq region 283988 284056 . + . ID=id664;Name=id664;Dbxref=GeneID:904637;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0313 by TMHMM2.0 at aa 12-34 2C 49-71 2C 95-117 2C 270-292 2C294-316 and 326-348 NC_002163.1 RefSeq region 284060 284128 . + . ID=id664;Name=id664;Dbxref=GeneID:904637;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0313 by TMHMM2.0 at aa 12-34 2C 49-71 2C 95-117 2C 270-292 2C294-316 and 326-348 NC_002163.1 RefSeq region 284156 284224 . + . ID=id664;Name=id664;Dbxref=GeneID:904637;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0313 by TMHMM2.0 at aa 12-34 2C 49-71 2C 95-117 2C 270-292 2C294-316 and 326-348 NC_002163.1 RefSeq region 284174 284206 . + . ID=id665;Name=id665;Dbxref=GeneID:904637;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 UTR_Extractor 5'-UTR 284265 284282 . + . ID=utr116;locus_tag=Cj0314;product=diaminopimelate decarboxylase NC_002163.1 RefSeq CDS 284283 285491 . + 0 ID=cds273;Parent=gene284;gene=lysA;Name=YP_002343752.1;Dbxref=GOA:Q9PII5 InterPro:IPR000183 InterPro:IPR002986 UniProtKB FSwiss-Prot:Q9PII5 Genbank:YP_002343752.1 GeneID:904638;gbkey=CDS;product=diaminopimelate decarboxylase;Note=Original 282000 29 note: Cj0314 2C lysA 2C probable diaminopimelate decarboxylase 2C len: 402 aa 3B highly similar to mnay e.g. DCDA_PSEAE diaminopimelate decarboxylase 28EC 4.1.1.20 29 28415 aa 29 2C fasta scores 3B opt: 1077 z-score: 968.8 E 28 29: 0 2C 44.7 25 identity in 394 aa overlap. 60.4 25 identity to HP0290. Contains Pfam match to entry PF00278 Orn_DAP_Arg_deC 2C Pyridoxal-dependent decarboxylase 2C score 381.60 2C E-value 2.3e-113 7EUpdated 282006 29 note: Characterised within Pseudomonas aeruginosa with acceptable identity score. not added to product function. Functional classification - Amino acid biosynthesis - Aspartate family 7EPMID:3143046 NC_002163.1 RefSeq gene 284283 285491 . + . ID=gene284;gene=lysA;Name=lysA;locus_tag=Cj0314;Dbxref=GeneID:904638;gbkey=Gene NC_002163.1 RefSeq region 284334 285083 . + . ID=id666;gene=lysA;Name=id666;Dbxref=GeneID:904638;gbkey=misc_feature;Note=HMMPfam hit to PF02784 2C Pyridoxal-dependent decarboxylase 2C py 2C score 2e-76 NC_002163.1 RefSeq region 285096 285410 . + . ID=id667;gene=lysA;Name=id667;Dbxref=GeneID:904638;gbkey=misc_feature;Note=HMMPfam hit to PF00278 2C Pyridoxal-dependent decarboxylase 2C C- 2C score 5.7e-33 ### NC_002163.1 RefSeq CDS 285493 286260 . + 0 ID=cds274;Parent=gene285;Name=YP_002343753.1;Dbxref=GOA:Q0PBJ4 InterPro:IPR006357 UniProtKB FTrEMBL:Q0PBJ4 Genbank:YP_002343753.1 GeneID:904639;gbkey=CDS;product=HAD-superfamily hydrolase;Note=Original 282000 29 note: Cj0315 2C unknown 2C len: 255 aa 3B similar to the hypothetical proteins TR:O59622 28EMBL:AB009530 29 Pyrococcus horikoshii PHBR011 28263 aa 29 2Cfasta scores 3B opt: 185 z-score: 375.5 E 28 29: 1.2e-13 2C 28.1 25 identity in 267 aa overlapNAGD_ECOLI nagD protein 28250 aa 29 2C fasta scores 3B opt: 259 z-score: 266.1 E 28 29: 1.4e-07 2C26.0 25 identity in 250 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domains PF00702 haloacid dehalogenase-like hydrolase 2C PF02142 MGS-like domain and PF03558 TBSV core protein P21 2FP22 were identified with separate Pfam search. This family is a member of the HAD superfamily which includes L-2-haloacid dehalogenase 2Cepoxide hydrolases and phosphatases. Previous matches to nagD protein are also members of this family. Product function modified to more specific family member based on motif match. No specific characterisation has been carried out yet. kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 285493 286260 . + . ID=gene285;Name=Cj0315;locus_tag=Cj0315;Dbxref=GeneID:904639;gbkey=Gene NC_002163.1 RefSeq CDS 286248 287321 . + 0 ID=cds275;Parent=gene286;gene=pheA;Name=YP_002343754.1;Dbxref=GOA:Q0PBJ3 InterPro:IPR001086 InterPro:IPR002701 InterPro:IPR002912 InterPro:IPR008242 InterPro:IPR010957 UniProtKB FTrEMBL:Q0PBJ3 Genbank:YP_002343754.1 GeneID:904640;gbkey=CDS;product=chorismate mutase 2Fprephenate dehydratase;Note=Original 282000 29 note: Cj0316 2C pheA 2C probable chorismate mutase 2Fprephenate dehydratase 2C len: 357 aa 3B similar to many e.g. PHEA_ECOLI chorismate mutase 28EC 5.4.99.5 29 2Fprephenate dehydratase 28EC 4.2.1.51 29 28386 aa 29 2Cfasta scores 3B opt: 482 z-score: 733.8 E 28 29: 0 2C 33.1 25 identity in 366 aa overlap. Similar in N-term to possible truncated pheA in Hp 3B HP0291 hypothetical protein 2896 aa 29 35.8 25 identity in 81 aa overlap. Contains PS00857 and PS00858 Prephenate dehydratase signatures 1 and 2 2C and Pfam match to entry PF00800 PDT 2C Prephenate dehydratase 2Cscore 268.20 2C E-value 1.1e-76 7EUpdated 282006 29 note: Pfam domains PF01817 Chorismate mutase type II and PF01842 ACT domainn were identified. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification - Amino acid biosynthesis -Aromatic amino acid family 7EPMID:9497350 NC_002163.1 RefSeq gene 286248 287321 . + . ID=gene286;gene=pheA;Name=pheA;locus_tag=Cj0316;Dbxref=GeneID:904640;gbkey=Gene NC_002163.1 RefSeq region 286251 286508 . + . ID=id668;gene=pheA;Name=id668;Dbxref=GeneID:904640;gbkey=misc_feature;Note=HMMPfam hit to PF01817 2C Chorismate mutase type II 2Cscore 1.9e-22 NC_002163.1 RefSeq region 286512 287051 . + . ID=id669;gene=pheA;Name=id669;Dbxref=GeneID:904640;gbkey=misc_feature;Note=HMMPfam hit to PF00800 2C Prephenate dehydratase 2Cscore 6.3e-56 NC_002163.1 RefSeq region 286968 287036 . + . ID=id670;gene=pheA;Name=id670;Dbxref=GeneID:904640;gbkey=misc_feature;Note=PS00857 Prephenate dehydratase signature 1 NC_002163.1 RefSeq region 287073 287303 . + . ID=id671;gene=pheA;Name=id671;Dbxref=GeneID:904640;gbkey=misc_feature;Note=HMMPfam hit to PF01842 2C ACT domain 2C score 0.00089 NC_002163.1 RefSeq region 287154 287177 . + . ID=id672;gene=pheA;Name=id672;Dbxref=GeneID:904640;gbkey=misc_feature;Note=PS00858 Prephenate dehydratase signature 2 NC_002163.1 RefSeq CDS 287311 288405 . + 0 ID=cds276;Parent=gene287;gene=hisC;Name=YP_002343755.1;Dbxref=GOA:Q9PII2 InterPro:IPR001917 InterPro:IPR004839 InterPro:IPR005861 InterPro:IPR015421 UniProtKB FSwiss-Prot:Q9PII2 Genbank:YP_002343755.1 GeneID:904641;gbkey=CDS;product=histidinol-phosphate aminotransferase;Note=catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis NC_002163.1 RefSeq gene 287311 288405 . + . ID=gene287;gene=hisC;Name=hisC;locus_tag=Cj0317;Dbxref=GeneID:904641;gbkey=Gene NC_002163.1 RefSeq region 287533 288399 . + . ID=id673;gene=hisC;Name=id673;Dbxref=GeneID:904641;gbkey=misc_feature;Note=HMMPfam hit to PF00155 2C Aminotransferase class I and II 2C score 6.6e-16 ### NC_002163.1 RefSeq CDS 288457 290139 . + 0 ID=cds277;Parent=gene288;gene=fliF;Name=YP_002343756.1;Dbxref=GOA:Q0PBJ1 InterPro:IPR000067 InterPro:IPR006182 InterPro:IPR013556 UniProtKB FTrEMBL:Q0PBJ1 Genbank:YP_002343756.1 GeneID:904642;gbkey=CDS;product=flagellar MS-ring protein;Note=the MS-ring anchors the flagellum to the cytoplasmic membrane 3B part of the flagellar basal body which consists of four rings L 2C P 2C S 2C and M mounted on a central rod NC_002163.1 RefSeq gene 288457 290139 . + . ID=gene288;gene=fliF;Name=fliF;locus_tag=Cj0318;Dbxref=GeneID:904642;gbkey=Gene NC_002163.1 RefSeq region 288505 289146 . + . ID=id674;gene=fliF;Name=id674;Dbxref=GeneID:904642;gbkey=misc_feature;Note=HMMPfam hit to PF01514 2C Secretory protein of YscJ 2FFliF family 2C score 3.9e-54 NC_002163.1 RefSeq region 288523 288582 . + . ID=id675;gene=fliF;Name=id675;Dbxref=GeneID:904642;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0318 by TMHMM2.0 at aa 23-42 NC_002163.1 RefSeq CDS 290139 291167 . + 0 ID=cds278;Parent=gene289;gene=fliG;Name=YP_002343757.1;Dbxref=GOA:Q0PBJ0 InterPro:IPR000090 UniProtKB FTrEMBL:Q0PBJ0 Genbank:YP_002343757.1 GeneID:904643;gbkey=CDS;product=flagellar motor switch protein G;Note=One of three proteins involved in switching the direction of the flagellar rotation NC_002163.1 RefSeq gene 290139 291167 . + . ID=gene289;gene=fliG;Name=fliG;locus_tag=Cj0319;Dbxref=GeneID:904643;gbkey=Gene NC_002163.1 RefSeq region 290814 291143 . + . ID=id676;gene=fliG;Name=id676;Dbxref=GeneID:904643;gbkey=misc_feature;Note=HMMPfam hit to PF01706 2C FliG C-terminal domain 2Cscore 7.5e-48 ### NC_002163.1 RefSeq CDS 291175 292005 . + 0 ID=cds279;Parent=gene290;gene=fliH;Name=YP_002343758.1;Dbxref=GOA:Q0PBI9 UniProtKB FTrEMBL:Q0PBI9 Genbank:YP_002343758.1 GeneID:904644;gbkey=CDS;product=flagellar assembly protein H;Note=binds to and inhibits the function of flagella specific ATPase FliI NC_002163.1 RefSeq gene 291175 292005 . + . ID=gene290;gene=fliH;Name=fliH;locus_tag=Cj0320;Dbxref=GeneID:904644;gbkey=Gene NC_002163.1 RefSeq CDS 291998 293845 . + 0 ID=cds280;Parent=gene291;gene=dxs;Name=YP_002343759.1;Dbxref=GOA:Q9PIH8 InterPro:IPR005474 InterPro:IPR005475 InterPro:IPR005476 InterPro:IPR005477 InterPro:IPR015941 UniProtKB FSwiss-Prot:Q9PIH8 Genbank:YP_002343759.1 GeneID:904645;gbkey=CDS;product=1-deoxy-D-xylulose-5-phosphate synthase;Note=catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate NC_002163.1 RefSeq gene 291998 293845 . + . ID=gene291;gene=dxs;Name=dxs;locus_tag=Cj0321;Dbxref=GeneID:904645;gbkey=Gene NC_002163.1 RefSeq region 292079 292138 . + . ID=id677;gene=dxs;Name=id677;Dbxref=GeneID:904645;gbkey=misc_feature;Note=PS00801 Transketolase signature 1 NC_002163.1 RefSeq region 292337 292369 . + . ID=id678;gene=dxs;Name=id678;Dbxref=GeneID:904645;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 292922 293416 . + . ID=id679;gene=dxs;Name=id679;Dbxref=GeneID:904645;gbkey=misc_feature;Note=HMMPfam hit to PF02779 2C Transketolase 2C pyridine binding domai 2C score 2.1e-48 NC_002163.1 RefSeq region 293240 293290 . + . ID=id680;gene=dxs;Name=id680;Dbxref=GeneID:904645;gbkey=misc_feature;Note=PS00802 Transketolase signature 2 NC_002163.1 RefSeq region 293447 293815 . + . ID=id681;gene=dxs;Name=id681;Dbxref=GeneID:904645;gbkey=misc_feature;Note=HMMPfam hit to PF02780 2C Transketolase 2C C-terminal domain 2C score 6.3e-11 ### NC_002163.1 UTR_Extractor 5'-UTR 293907 293930 . + . ID=utr117;locus_tag=Cj0322;product=peroxide stress regulator NC_002163.1 RefSeq gene 293931 294341 . + . ID=gene292;gene=perR;Name=perR;locus_tag=Cj0322;Dbxref=GeneID:904646;gbkey=Gene NC_002163.1 RefSeq CDS 293931 294341 . + 0 ID=cds281;Parent=gene292;gene=perR;Name=YP_002343760.1;Dbxref=GOA:Q0PBI7 InterPro:IPR002481 UniProtKB FTrEMBL:Q0PBI7 Genbank:YP_002343760.1 GeneID:904646;gbkey=CDS;product=peroxide stress regulator;Note=Original 282000 29 note: Cj0322 2C perR 2C regulator of peroxide stress regulon 2C len: 136 aa 3B similar to many members of the furR family e.g. FUR3_BACSU ferric uptake regulation protein homolog 3 28145 aa 29 2C fasta scores 3B opt: 258 z-score: 379.6 E 28 29: 6.9e-14 2C 32.6 25 identity in 135 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF01475 Ferric uptake regulator family was identified within CDS. Further support given to product function. Marginal identity scores were obtained with many. Appropriate motifs present. not added to product function. Functional classification - Broad regulatory functions 7EPMID:9701813 2C PMID:12100544 NC_002163.1 RefSeq region 293955 294314 . + . ID=id682;gene=perR;Name=id682;Dbxref=GeneID:904646;gbkey=misc_feature;Note=HMMPfam hit to PF01475 2C Ferric uptake regulator family 2C score 4.3e-22 ### NC_002163.1 UTR_Extractor 5'-UTR 294365 294386 . + . ID=utr118;locus_tag=Cj0323;product=hypothetical protein NC_002163.1 RefSeq gene 294387 295583 . + . ID=gene293;Name=Cj0323;locus_tag=Cj0323;Dbxref=GeneID:904647;gbkey=Gene NC_002163.1 RefSeq CDS 294387 295583 . + 0 ID=cds282;Parent=gene293;Name=YP_002343761.1;Dbxref=UniProtKB FTrEMBL:Q0PBI6 Genbank:YP_002343761.1 GeneID:904647;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0323 2C unknown 2C len: 398 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 RefSeq region 295586 296287 . + . ID=id683;gene=ubiE;Name=id683;Dbxref=GeneID:904648;gbkey=misc_feature;Note=HMMPfam hit to PF01209 2C ubiE 2FCOQ5 methyltransferase family 2C score 2.2e-28 NC_002163.1 RefSeq CDS 295586 296293 . + 0 ID=cds283;Parent=gene294;gene=ubiE;Name=YP_002343762.1;Dbxref=GOA:Q9PIH5 InterPro:IPR004033 UniProtKB FSwiss-Prot:Q9PIH5 Genbank:YP_002343762.1 GeneID:904648;gbkey=CDS;product=ubiquinone 2Fmenaquinone biosynthesis methyltransferase;Note=Catalyzes the carbon methylation reaction in the biosynthesis of ubiquinone NC_002163.1 RefSeq gene 295586 296293 . + . ID=gene294;gene=ubiE;Name=ubiE;locus_tag=Cj0324;Dbxref=GeneID:904648;gbkey=Gene NC_002163.1 RefSeq CDS 296290 297453 . + 0 ID=cds284;Parent=gene295;gene=xseA;Name=YP_002343763.1;Dbxref=GOA:Q9PIH4 InterPro:IPR003753 InterPro:IPR004365 UniProtKB FSwiss-Prot:Q9PIH4 Genbank:YP_002343763.1 GeneID:904649;gbkey=CDS;product=exodeoxyribonuclease VII large subunit;Note=bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides NC_002163.1 RefSeq gene 296290 297453 . + . ID=gene295;gene=xseA;Name=xseA;locus_tag=Cj0325;Dbxref=GeneID:904649;gbkey=Gene NC_002163.1 RefSeq region 296350 296577 . + . ID=id684;gene=xseA;Name=id684;Dbxref=GeneID:904649;gbkey=misc_feature;Note=HMMPfam hit to PF01336 2C OB-fold nucleic acid binding domain 2C score 6.9e-11 NC_002163.1 RefSeq region 296854 297333 . + . ID=id685;gene=xseA;Name=id685;Dbxref=GeneID:904649;gbkey=misc_feature;Note=HMMPfam hit to PF02601 2C Exonuclease VII 2C large subunit 2C score 1.1e-27 NC_002163.1 UTR_Extractor 5'-UTR 297380 297462 . + . ID=utr119;locus_tag=Cj0326;product=phosphoserine aminotransferase ### NC_002163.1 RefSeq CDS 297463 298539 . + 0 ID=cds285;Parent=gene296;gene=serC;Name=YP_002343764.1;Dbxref=GOA:Q9PIH3 HSSP:Q59196 InterPro:IPR000192 InterPro:IPR003248 InterPro:IPR015421 InterPro:IPR015422 UniProtKB FSwiss-Prot:Q9PIH3 Genbank:YP_002343764.1 GeneID:904650;gbkey=CDS;product=phosphoserine aminotransferase;Note=catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate 3B required both in major phosphorylated pathway of serine biosynthesis and in the biosynthesis of pyridoxine NC_002163.1 RefSeq gene 297463 298539 . + . ID=gene296;gene=serC;Name=serC;locus_tag=Cj0326;Dbxref=GeneID:904650;gbkey=Gene NC_002163.1 RefSeq region 297499 298500 . + . ID=id686;gene=serC;Name=id686;Dbxref=GeneID:904650;gbkey=misc_feature;Note=HMMPfam hit to PF00266 2C Aminotransferase class-V 2Cscore 3.6e-37 NC_002163.1 RefSeq gene 298536 298886 . + . ID=gene297;gene=Cj0327;Name=Cj0327;locus_tag=Cj0327;Dbxref=GeneID:904651;gbkey=Gene NC_002163.1 RefSeq CDS 298536 298886 . + 0 ID=cds286;Parent=gene297;Name=YP_002343765.1;Dbxref=InterPro:IPR006175 InterPro:IPR013813 UniProtKB FTrEMBL:Q0PBI2 Genbank:YP_002343765.1 GeneID:904651;gbkey=CDS;product=endoribonuclease L-PSP family protein;Note=Original 282000 29 note: Cj0327 2C unknown 2C len: 116 aa 3B similar to hypothetical proteins e.g. YABJ_BACSU 28125 aa 29 2Cfasta scores 3B opt: 211 z-score: 261.9 E 28 29: 2.5e-07 2C 33.0 25 identity in 109 aa overlap 2C and to e.g. UK14_HUMAN 14.5 kd translational inhibitor protein 28137 aa 29 2C fasta scores 3B opt: 173 z-score: 249.5 E 28 29: 1.2e-06 2C 29.2 25 identity in 106 aa overlap. No Hp ortholog. Also similar to Cj1388 2833.3 25 identity in 96 aa overlap 29. Contains Pfam match to entry PF01042 DUF10 2C Domain of unknown function 2C score 69.30 2C E-value 8.4e-17 7EUpdated 282006 29 note: Pfam domain PF01042 Endoribonuclease L-PSP identified within CDS 28previously uncharacterised 29. Product modified to more specific family member due to motif match. No specific characterisation has been carried out yet. kept within product fucntion. Functional classification - Degradation of macromolecules - DNA NC_002163.1 RefSeq region 298554 298874 . + . ID=id687;Name=id687;Dbxref=GeneID:904651;gbkey=misc_feature;Note=HMMPfam hit to PF01042 2C Endoribonuclease L-PSP 2Cscore 3.8e-16 NC_002163.1 RefSeq CDS 298883 299857 . - 0 ID=cds287;Parent=gene298;gene=fabH;Name=YP_002343766.1;Dbxref=GOA:Q9PIH1 HSSP:P24249 InterPro:IPR004655 InterPro:IPR013747 InterPro:IPR013751 UniProtKB FSwiss-Prot:Q9PIH1 Genbank:YP_002343766.1 GeneID:904652;gbkey=CDS;product=3-oxoacyl-ACP synthase;Note=FabH 3B beta-ketoacyl-acyl carrier protein synthase III 3B catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation 3B differs from 3-oxoacyl- 28acyl carrier protein 29 synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs NC_002163.1 RefSeq gene 298883 299857 . - . ID=gene298;gene=fabH;Name=fabH;locus_tag=Cj0328c;Dbxref=GeneID:904652;gbkey=Gene NC_002163.1 RefSeq gene 299850 300836 . - . ID=gene299;gene=plsX;Name=plsX;locus_tag=Cj0329c;Dbxref=GeneID:904653;gbkey=Gene NC_002163.1 RefSeq CDS 299850 300836 . - 0 ID=cds288;Parent=gene299;gene=plsX;Name=YP_002343767.1;Dbxref=GOA:Q9PIH0 InterPro:IPR003664 InterPro:IPR012281 UniProtKB FSwiss-Prot:Q9PIH0 Genbank:YP_002343767.1 GeneID:904653;gbkey=CDS;product=glycerol-3-phosphate acyltransferase PlsX;Note=involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis 3B functions with PlsY NC_002163.1 RefSeq region 299883 300833 . - . ID=id688;gene=plsX;Name=id688;Dbxref=GeneID:904653;gbkey=misc_feature;Note=HMMPfam hit to PF02504 2C Fatty acid synthesis protein 2C score 1.6e-141 ### NC_002163.1 RefSeq gene 300842 300988 . - . ID=gene300;gene=rpmF;Name=rpmF;locus_tag=Cj0330c;Dbxref=GeneID:904654;gbkey=Gene NC_002163.1 RefSeq CDS 300842 300988 . - 0 ID=cds289;Parent=gene300;gene=rpmF;Name=YP_002343768.1;Dbxref=GOA:Q9PIG9 InterPro:IPR002677 UniProtKB FSwiss-Prot:Q9PIG9 Genbank:YP_002343768.1 GeneID:904654;gbkey=CDS;product=50S ribosomal protein L32;Note=some L32 proteins have zinc finger motifs consisting of CXXC while others do not NC_002163.1 RefSeq region 300851 300985 . - . ID=id689;gene=rpmF;Name=id689;Dbxref=GeneID:904654;gbkey=misc_feature;Note=HMMPfam hit to PF01783 2C Ribosomal L32p protein family 2C score 1.8e-05 ### NC_002163.1 UTR_Extractor 5'-UTR 300989 301245 . - . ID=utr120;locus_tag=Cj0330c;product=50S ribosomal protein L32 NC_002163.1 RefSeq gene 301012 301365 . - . ID=gene301;Name=Cj0331c;locus_tag=Cj0331c;Dbxref=GeneID:904655;gbkey=Gene NC_002163.1 RefSeq CDS 301012 301365 . - 0 ID=cds290;Parent=gene301;Name=YP_002343769.1;Dbxref=UniProtKB FTrEMBL:Q0PBH8 Genbank:YP_002343769.1 GeneID:904655;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0331c 2C unknown 2C len: 117 aa 3B 34.7 25 identity to HP0199. Functional classification -Conserved hypothetical proteins ### NC_002163.1 RefSeq CDS 301366 301779 . - 0 ID=cds291;Parent=gene302;gene=ndk;Name=YP_002343770.1;Dbxref=GOA:Q9PIG7 HSSP:P15266 InterPro:IPR001564 UniProtKB FSwiss-Prot:Q9PIG7 Genbank:YP_002343770.1 GeneID:904656;gbkey=CDS;product=nucleoside diphosphate kinase;Note=catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate NC_002163.1 RefSeq gene 301366 301779 . - . ID=gene302;gene=ndk;Name=ndk;locus_tag=Cj0332c;Dbxref=GeneID:904656;gbkey=Gene NC_002163.1 RefSeq region 301369 301776 . - . ID=id690;gene=ndk;Name=id690;Dbxref=GeneID:904656;gbkey=misc_feature;Note=HMMPfam hit to PF00334 2C Nucleoside diphosphate kinase 2C score 6e-80 NC_002163.1 RefSeq region 301420 301446 . - . ID=id691;gene=ndk;Name=id691;Dbxref=GeneID:904656;gbkey=misc_feature;Note=PS00469 Nucleoside diphosphate kinases active site ### NC_002163.1 UTR_Extractor 5'-UTR 301780 301808 . - . ID=utr121;locus_tag=Cj0332c;product=nucleoside diphosphate kinase NC_002163.1 RefSeq CDS 301892 302176 . - 0 ID=cds292;Parent=gene303;gene=fdxA;Name=YP_002343771.1;Dbxref=GOA:Q0PBH6 InterPro:IPR001450 UniProtKB FTrEMBL:Q0PBH6 Genbank:YP_002343771.1 GeneID:904657;gbkey=CDS;product=ferredoxin;Note=Original 282000 29 note: Cj0333c 2C fdxA 2C probable ferredoxin 2C len: 94 aa 3B similar to many e.g. FER_CLOTM ferredoxin 2855 aa 29 2C fasta scores 3B opt: 142 z-score: 311.2 E 28 29: 4.5e-10 2C 45.8 25 identity in 59 aa overlap. No Hp ortholog. Also similar to Cj0354c 2838.8 25 identity in 67 aa overlap 29. Contains PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature and Pfam match to entry PF00037 fer4 2C 4Fe-4S ferredoxins and related iron-sulfur cluster binding domains. 2C score 51.80 2C E-value 8.8e-14 7EUpdated 282006 29 note: Similar to many e.g. Clostridium sp. with acceptable identity scores. not added to product function. Functional classification -Energy metabolism - Electron transport 7EPMID:4433520 NC_002163.1 RefSeq gene 301892 302176 . - . ID=gene303;gene=fdxA;Name=fdxA;locus_tag=Cj0333c;Dbxref=GeneID:904657;gbkey=Gene NC_002163.1 RefSeq region 302102 302173 . - . ID=id692;gene=fdxA;Name=id692;Dbxref=GeneID:904657;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 2.9e-06 NC_002163.1 RefSeq region 302117 302152 . - . ID=id693;gene=fdxA;Name=id693;Dbxref=GeneID:904657;gbkey=misc_feature;Note=PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature ### NC_002163.1 UTR_Extractor 5'-UTR 302353 302382 . + . ID=utr122;locus_tag=Cj0334;product=alkyl hydroperoxide reductase NC_002163.1 RefSeq gene 302383 302979 . + . ID=gene304;gene=ahpC;Name=ahpC;locus_tag=Cj0334;Dbxref=GeneID:904658;gbkey=Gene NC_002163.1 RefSeq CDS 302383 302979 . + 0 ID=cds293;Parent=gene304;gene=ahpC;Name=YP_002343772.1;Dbxref=GOA:Q9ZI13 HSSP:Q63716 InterPro:IPR000866 InterPro:IPR012335 UniProtKB FTrEMBL:Q9ZI13 Genbank:YP_002343772.1 GeneID:904658;gbkey=CDS;product=alkyl hydroperoxide reductase;Note=Original 282000 29 note: Cj0334 2C ahpC 2C probable alkyl hydroperoxide reductase 2C len: 198 aa 3B highly simlar to e.g. TDX1_HUMAN thioredoxin peroxidase 1 28198 aa 29 2C fasta scores 3B opt: 615 z-score: 915.3 E 28 29: 0 2C 46.1 25 identity in 193 aa overlap 2C and to e.g. AHPC_ECOLI P26427 alkyl hydroperoxide reductase C22 protein 28EC 1.6.4.- 29 28186 aa 29 2Cwublastp scores E 3D 8.9e-23 2C 34 25 identity in 149 aa overlap. 67.7 25 identity to HP1563 28Hp 26 kD antigen 29. Contains Pfam match to entry PF00578 AhpC-TSA 2C AhpC 2FTSA family 2C score 208.20 2C E-value 1.2e-58 7EUpdated 282006 29 note: Characterised within Campylobacter jejuni. not added to product function. Literature search identified paper linking protein to glycoprotein 28PMID:12186869 29. Functional classification - Detoxification 7EPMID:10438747 2C PMID:10515927 2C PMID:12186869 NC_002163.1 RefSeq region 302389 302844 . + . ID=id694;gene=ahpC;Name=id694;Dbxref=GeneID:904658;gbkey=misc_feature;Note=HMMPfam hit to PF00578 2C AhpC 2FTSA family 2C score 8.6e-60 ### NC_002163.1 UTR_Extractor 5'-UTR 303066 303097 . + . ID=utr123;locus_tag=Cj0335;product=flagellar biosynthesis protein FlhB NC_002163.1 RefSeq CDS 303098 304186 . + 0 ID=cds294;Parent=gene305;gene=flhB;Name=YP_002343773.1;Dbxref=GOA:Q0PBH4 InterPro:IPR006135 InterPro:IPR006136 UniProtKB FTrEMBL:Q0PBH4 Genbank:YP_002343773.1 GeneID:904659;gbkey=CDS;product=flagellar biosynthesis protein FlhB;Note=membrane protein responsible for substrate specificity switching from rod 2Fhook-type export to filament-type export NC_002163.1 RefSeq gene 303098 304186 . + . ID=gene305;gene=flhB;Name=flhB;locus_tag=Cj0335;Dbxref=GeneID:904659;gbkey=Gene NC_002163.1 RefSeq region 303110 304135 . + . ID=id695;gene=flhB;Name=id695;Dbxref=GeneID:904659;gbkey=misc_feature;Note=HMMPfam hit to PF01312 2C FlhB HrpN YscU SpaS Family 2Cscore 2.4e-119 NC_002163.1 RefSeq region 303191 303259 . + . ID=id696;gene=flhB;Name=id696;Dbxref=GeneID:904659;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0335 by TMHMM2.0 at aa 32-54 2C 83-105 2C 141-163 and 188-210 NC_002163.1 RefSeq region 303344 303412 . + . ID=id696;gene=flhB;Name=id696;Dbxref=GeneID:904659;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0335 by TMHMM2.0 at aa 32-54 2C 83-105 2C 141-163 and 188-210 NC_002163.1 RefSeq region 303518 303586 . + . ID=id696;gene=flhB;Name=id696;Dbxref=GeneID:904659;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0335 by TMHMM2.0 at aa 32-54 2C 83-105 2C 141-163 and 188-210 NC_002163.1 RefSeq region 303659 303727 . + . ID=id696;gene=flhB;Name=id696;Dbxref=GeneID:904659;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0335 by TMHMM2.0 at aa 32-54 2C 83-105 2C 141-163 and 188-210 ### NC_002163.1 RefSeq CDS 304192 304935 . - 0 ID=cds295;Parent=gene306;gene=motB;Name=YP_002343774.1;Dbxref=GOA:Q0PBH3 InterPro:IPR006665 UniProtKB FTrEMBL:Q0PBH3 Genbank:YP_002343774.1 GeneID:904660;gbkey=CDS;product=flagellar motor protein MotB;Note=with MotA forms the ion channels that couple flagellar rotation to proton 2Fsodium motive force across the membrane and forms the stator elements of the rotary flagellar machine NC_002163.1 RefSeq gene 304192 304935 . - . ID=gene306;gene=motB;Name=motB;locus_tag=Cj0336c;Dbxref=GeneID:904660;gbkey=Gene NC_002163.1 RefSeq region 304285 304572 . - . ID=id697;gene=motB;Name=id697;Dbxref=GeneID:904660;gbkey=misc_feature;Note=HMMPfam hit to PF00691 2C OmpA family 2C score 9.1e-07 NC_002163.1 RefSeq region 304822 304890 . - . ID=id698;gene=motB;Name=id698;Dbxref=GeneID:904660;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0336c by TMHMM2.0 at aa 16-38 ### NC_002163.1 RefSeq CDS 304938 305714 . - 0 ID=cds296;Parent=gene307;gene=motA;Name=YP_002343775.1;Dbxref=GOA:Q0PBH2 InterPro:IPR000540 InterPro:IPR002898 UniProtKB FTrEMBL:Q0PBH2 Genbank:YP_002343775.1 GeneID:904661;gbkey=CDS;product=flagellar motor protein MotA;Note=With MotB forms the ion channels that couple flagellar rotation to proton 2Fsodium motive force across the membrane and forms the stator elements of the rotary flagellar machine NC_002163.1 RefSeq gene 304938 305714 . - . ID=gene307;gene=motA;Name=motA;locus_tag=Cj0337c;Dbxref=GeneID:904661;gbkey=Gene NC_002163.1 RefSeq region 305034 305447 . - . ID=id699;gene=motA;Name=id699;Dbxref=GeneID:904661;gbkey=misc_feature;Note=HMMPfam hit to PF01618 2C MotA 2FTolQ 2FExbB proton channel family 2C score 5.5e-09 NC_002163.1 RefSeq region 305109 305162 . - . ID=id700;gene=motA;Name=id700;Dbxref=GeneID:904661;gbkey=misc_feature;Note=PS01307 Flagellar motor protein motA family signature NC_002163.1 RefSeq region 305112 305180 . - . ID=id29;gene=motA;Name=id29;Dbxref=GeneID:904661;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0337c by TMHMM2.0 at aa 28-50 2C 147-169 and 179-201 NC_002163.1 RefSeq region 305208 305276 . - . ID=id29;gene=motA;Name=id29;Dbxref=GeneID:904661;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0337c by TMHMM2.0 at aa 28-50 2C 147-169 and 179-201 NC_002163.1 RefSeq region 305565 305633 . - . ID=id29;gene=motA;Name=id29;Dbxref=GeneID:904661;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0337c by TMHMM2.0 at aa 28-50 2C 147-169 and 179-201 ### NC_002163.1 UTR_Extractor 5'-UTR 305715 305783 . - . ID=utr124;locus_tag=Cj0337c;product=flagellar motor protein MotA NC_002163.1 RefSeq CDS 305730 308369 . - 0 ID=cds297;Parent=gene308;gene=polA;Name=YP_002343776.1;Dbxref=GOA:Q0PBH1 InterPro:IPR001098 InterPro:IPR002298 InterPro:IPR002421 InterPro:IPR002562 InterPro:IPR008918 UniProtKB FTrEMBL:Q0PBH1 Genbank:YP_002343776.1 GeneID:904662;gbkey=CDS;product=DNA polymerase I;Note=has 3 27-5 27 exonuclease 2C 5 27-3 27 exonuclease and 5 27-3 27polymerase activities 2C primarily functions to fill gaps during DNA replication and repair NC_002163.1 RefSeq gene 305730 308369 . - . ID=gene308;gene=polA;Name=polA;locus_tag=Cj0338c;Dbxref=GeneID:904662;gbkey=Gene NC_002163.1 RefSeq region 305736 306854 . - . ID=id701;gene=polA;Name=id701;Dbxref=GeneID:904662;gbkey=misc_feature;Note=HMMPfam hit to PF00476 2C DNA polymerase family A 2Cscore 3.2e-110 NC_002163.1 RefSeq region 306186 306245 . - . ID=id702;gene=polA;Name=id702;Dbxref=GeneID:904662;gbkey=misc_feature;Note=PS00447 DNA polymerase family A signature NC_002163.1 RefSeq region 306936 307481 . - . ID=id703;gene=polA;Name=id703;Dbxref=GeneID:904662;gbkey=misc_feature;Note=HMMPfam hit to PF01612 2C 3 27-5 27 exonuclease 2C score 3e-25 NC_002163.1 RefSeq region 307575 307871 . - . ID=id704;gene=polA;Name=id704;Dbxref=GeneID:904662;gbkey=misc_feature;Note=HMMPfam hit to PF01367 2C 5 27-3 27 exonuclease 2CC-terminal SAM fold 2C score 4.4e-42 NC_002163.1 RefSeq region 307875 308366 . - . ID=id705;gene=polA;Name=id705;Dbxref=GeneID:904662;gbkey=misc_feature;Note=HMMPfam hit to PF02739 2C 5 27-3 27 exonuclease 2CN-terminal resolvase- 2C score 5.4e-48 NC_002163.1 RefSeq region 308181 308204 . - . ID=id706;gene=polA;Name=id706;Dbxref=GeneID:904662;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 UTR_Extractor 5'-UTR 308491 308532 . + . ID=utr125;locus_tag=Cj0339;product=putative MFS transport protein NC_002163.1 RefSeq CDS 308533 309894 . + 0 ID=cds298;Parent=gene309;Name=YP_002343777.1;Dbxref=GOA:Q0PBH0 InterPro:IPR007114 InterPro:IPR011701 UniProtKB FTrEMBL:Q0PBH0 Genbank:YP_002343777.1 GeneID:904663;gbkey=CDS;product=MFS transport protein;Note=Original 282000 29 note: Cj0339 2C probable transmembrane transport protein 2C len: 453 aa 3B similar to e.g. YDFJ_ECOLI hypothetical metabolite transport protein 28427 aa 29 2C fasta scores 3B opt: 1214 z-score: 1428.6 E 28 29: 0 2C42.5 25 identity in 416 aa overlap 2C and SHIA_ECOLI shikimate transporter 28438 aa 29 2C fasta scores 3B opt: 876 z-score: 1104.0 E 28 29: 0 2C 32.3 25 identity in 421 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00083 sugar_tr 2CSugar 28and other 29 transporters 2C score 123.20 2C E-value 4.9e-33 7EUpdated 282006 29 note: Ten probable transmembrace helices identified by TMHMM2.0 within CDS. Pfam domain PF07690 Major Facilitator Superfamily protein identified within CDS. Prosite PS50850 MFS 2C Major facilitator superfamily also identifed within CDS. Product modified to new family member based on motif match. No specific characterisation has been carried out yet. kept within product function. Functional classification -Transport 2Fbinding proteins - Other 7EPMID:15919996 NC_002163.1 RefSeq gene 308533 309894 . + . ID=gene309;Name=Cj0339;locus_tag=Cj0339;Dbxref=GeneID:904663;gbkey=Gene NC_002163.1 RefSeq region 308605 309891 . + . ID=id707;Name=id707;Dbxref=GeneID:904663;gbkey=misc_feature;Note=HMMPfam hit to PF00083 2C Sugar 28and other 29 transporter 2C score 1.3e-35 NC_002163.1 RefSeq region 308620 308688 . + . ID=id708;Name=id708;Dbxref=GeneID:904663;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0339 by TMHMM2.0 at aa 30-52 2C 62-84 2C 105-127 2C 164-186 2C198-220 2C 294-316 2C 323-342 2C 352-374 2C 394-413 and 417-439 NC_002163.1 RefSeq region 308620 309768 . + . ID=id709;Name=id709;Dbxref=GeneID:904663;gbkey=misc_feature;Note=HMMPfam hit to PF07690 2C Major Facilitator Superfamily 2C score 2.5e-24 NC_002163.1 RefSeq region 308716 308784 . + . ID=id708;Name=id708;Dbxref=GeneID:904663;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0339 by TMHMM2.0 at aa 30-52 2C 62-84 2C 105-127 2C 164-186 2C198-220 2C 294-316 2C 323-342 2C 352-374 2C 394-413 and 417-439 NC_002163.1 RefSeq region 308845 308913 . + . ID=id708;Name=id708;Dbxref=GeneID:904663;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0339 by TMHMM2.0 at aa 30-52 2C 62-84 2C 105-127 2C 164-186 2C198-220 2C 294-316 2C 323-342 2C 352-374 2C 394-413 and 417-439 NC_002163.1 RefSeq region 309022 309090 . + . ID=id708;Name=id708;Dbxref=GeneID:904663;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0339 by TMHMM2.0 at aa 30-52 2C 62-84 2C 105-127 2C 164-186 2C198-220 2C 294-316 2C 323-342 2C 352-374 2C 394-413 and 417-439 NC_002163.1 RefSeq region 309124 309192 . + . ID=id708;Name=id708;Dbxref=GeneID:904663;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0339 by TMHMM2.0 at aa 30-52 2C 62-84 2C 105-127 2C 164-186 2C198-220 2C 294-316 2C 323-342 2C 352-374 2C 394-413 and 417-439 NC_002163.1 RefSeq region 309412 309480 . + . ID=id708;Name=id708;Dbxref=GeneID:904663;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0339 by TMHMM2.0 at aa 30-52 2C 62-84 2C 105-127 2C 164-186 2C198-220 2C 294-316 2C 323-342 2C 352-374 2C 394-413 and 417-439 NC_002163.1 RefSeq region 309499 309558 . + . ID=id708;Name=id708;Dbxref=GeneID:904663;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0339 by TMHMM2.0 at aa 30-52 2C 62-84 2C 105-127 2C 164-186 2C198-220 2C 294-316 2C 323-342 2C 352-374 2C 394-413 and 417-439 NC_002163.1 RefSeq region 309586 309654 . + . ID=id708;Name=id708;Dbxref=GeneID:904663;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0339 by TMHMM2.0 at aa 30-52 2C 62-84 2C 105-127 2C 164-186 2C198-220 2C 294-316 2C 323-342 2C 352-374 2C 394-413 and 417-439 NC_002163.1 RefSeq region 309712 309771 . + . ID=id708;Name=id708;Dbxref=GeneID:904663;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0339 by TMHMM2.0 at aa 30-52 2C 62-84 2C 105-127 2C 164-186 2C198-220 2C 294-316 2C 323-342 2C 352-374 2C 394-413 and 417-439 NC_002163.1 RefSeq region 309781 309849 . + . ID=id708;Name=id708;Dbxref=GeneID:904663;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0339 by TMHMM2.0 at aa 30-52 2C 62-84 2C 105-127 2C 164-186 2C198-220 2C 294-316 2C 323-342 2C 352-374 2C 394-413 and 417-439 NC_002163.1 RefSeq region 309891 310808 . + . ID=id710;Name=id710;Dbxref=GeneID:904664;gbkey=misc_feature;Note=HMMPfam hit to PF01156 2C Inosine-uridine preferring nucleoside hy 2C score 5.1e-18 NC_002163.1 RefSeq CDS 309891 310898 . + 0 ID=cds299;Parent=gene310;Name=YP_002343778.1;Dbxref=GOA:Q0PBG9 InterPro:IPR001910 UniProtKB FTrEMBL:Q0PBG9 Genbank:YP_002343778.1 GeneID:904664;gbkey=CDS;product=nucleoside hydrolase;Note=Original 282000 29 note: Cj0340 2C possible nucleoside hydrolase 2C len: 335 aa 3B similar to hypothetical proteins e.g. YAAF_ECOLI 28304 aa 29 2C fasta scores 3B opt: 252 z-score: 377.2 E 28 29: 9.4e-14 2C 25.9 25 identity in 309 aa overlap 2C and to the eukaryotic IUNH_CRIFA inosine-uridine preferring nucleoside hydrolase 28314 aa 29 2C fasta scores 3B opt: 261 z-score: 363.4 E 28 29: 5.5e-13 2C 25.3 25 identity in 296 aa overlap. No Hp match. Contains Pfam match to entry PF01156 IU_nuc_hydro 2C Inosine-uridine preferring nucleoside hydrolase 2C score -11.20 2C E-value 4.8e-12 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score has been carried out yet. kept within product function. Functional classification - Salvage of nucleosides and nucleotides 7EPMID:10409664 NC_002163.1 RefSeq gene 309891 310898 . + . ID=gene310;Name=Cj0340;locus_tag=Cj0340;Dbxref=GeneID:904664;gbkey=Gene NC_002163.1 RefSeq gene 310854 311297 . - . ID=gene311;Name=Cj0341c;locus_tag=Cj0341c;Dbxref=GeneID:904665;gbkey=Gene NC_002163.1 RefSeq CDS 310854 311297 . - 0 ID=cds300;Parent=gene311;Name=YP_002343779.1;Dbxref=GOA:Q0PBG8 InterPro:IPR015414 UniProtKB FTrEMBL:Q0PBG8 Genbank:YP_002343779.1 GeneID:904665;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0341c 2C possible integral membrane protein 2C len: 147 aa 3B similar to hypothetical membrane proteins e.g. Y489_HAEIN HI0489 28157 aa 29 2C fasta scores 3B opt: 252 z-score: 350.5 E 28 29: 2.9e-12 2C 34.0 25 identity in 159 aa overlap. No Hp match 7EUpdated 282006 29 note: Four probable transmembrace helices identified by TMHMM2.0 within CDS. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 310866 310925 . - . ID=id30;Name=id30;Dbxref=GeneID:904665;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0341c by TMHMM2.0 at aa 15-37 2C 44-66 2C 96-118 and 125-144 NC_002163.1 RefSeq region 310944 311012 . - . ID=id30;Name=id30;Dbxref=GeneID:904665;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0341c by TMHMM2.0 at aa 15-37 2C 44-66 2C 96-118 and 125-144 NC_002163.1 RefSeq region 311100 311168 . - . ID=id30;Name=id30;Dbxref=GeneID:904665;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0341c by TMHMM2.0 at aa 15-37 2C 44-66 2C 96-118 and 125-144 NC_002163.1 RefSeq region 311187 311255 . - . ID=id30;Name=id30;Dbxref=GeneID:904665;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0341c by TMHMM2.0 at aa 15-37 2C 44-66 2C 96-118 and 125-144 ### NC_002163.1 RefSeq CDS 311302 314127 . - 0 ID=cds301;Parent=gene312;gene=uvrA;Name=YP_002343780.1;Dbxref=GOA:Q0PBG7 InterPro:IPR003439 InterPro:IPR004602 UniProtKB FTrEMBL:Q0PBG7 Genbank:YP_002343780.1 GeneID:904666;gbkey=CDS;product=excinuclease ABC subunit A;Note=The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 uvrA and 2 uvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by uvrB 2C the uvrA molecules dissociate NC_002163.1 RefSeq gene 311302 314127 . - . ID=gene312;gene=uvrA;Name=uvrA;locus_tag=Cj0342c;Dbxref=GeneID:904666;gbkey=Gene NC_002163.1 RefSeq region 311437 312255 . - . ID=id711;gene=uvrA;Name=id711;Dbxref=GeneID:904666;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 9.1e-19 NC_002163.1 RefSeq region 311620 311664 . - . ID=id712;gene=uvrA;Name=id712;Dbxref=GeneID:904666;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq region 312211 312234 . - . ID=id713;gene=uvrA;Name=id713;Dbxref=GeneID:904666;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 312637 312681 . - . ID=id714;gene=uvrA;Name=id714;Dbxref=GeneID:904666;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq region 314011 314034 . - . ID=id715;gene=uvrA;Name=id715;Dbxref=GeneID:904666;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 UTR_Extractor 5'-UTR 314128 314156 . - . ID=utr126;locus_tag=Cj0342c;product=excinuclease ABC subunit A NC_002163.1 RefSeq CDS 314200 314985 . - 0 ID=cds302;Parent=gene313;Name=YP_002343781.1;Dbxref=GOA:Q0PBG6 InterPro:IPR002781 UniProtKB FTrEMBL:Q0PBG6 Genbank:YP_002343781.1 GeneID:904667;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0343c 2C probable integral membrane protein 2C len: 261 aa 3B similar to many hypothetical membrane proteins e.g. Y441_METJA MJ0441 28267 aa 29 2C fasta scores 3B opt: 152 z-score: 301.8 E 28 29: 1.5e-09 2C30.7 25 identity in 257 aa overlap. 45.1 25 identity to HP0677 and 44.0 25 identity to HP0226 7EUpdated 282006 29 note: Nine probable transmembrace helices identified by TMHMM2.0 within CDS. Pfam PF01925 Domain of unknown function 28DUF81 29 protein identified within CDS. Further support given to product function. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 314200 314985 . - . ID=gene313;Name=Cj0343c;locus_tag=Cj0343c;Dbxref=GeneID:904667;gbkey=Gene NC_002163.1 RefSeq region 314209 314277 . - . ID=id31;Name=id31;Dbxref=GeneID:904667;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0343c by TMHMM2.0 at aa 9-31 2C 41-63 2C 75-92 2C 97-119 2C131-148 2C 152-169 2C 174-193 2C 203-225 and 237-259 NC_002163.1 RefSeq region 314239 314970 . - . ID=id716;Name=id716;Dbxref=GeneID:904667;gbkey=misc_feature;Note=HMMPfam hit to PF01925 2C Domain of unknown function DUF81 2C score 2.6e-34 NC_002163.1 RefSeq region 314311 314379 . - . ID=id31;Name=id31;Dbxref=GeneID:904667;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0343c by TMHMM2.0 at aa 9-31 2C 41-63 2C 75-92 2C 97-119 2C131-148 2C 152-169 2C 174-193 2C 203-225 and 237-259 NC_002163.1 RefSeq region 314407 314466 . - . ID=id31;Name=id31;Dbxref=GeneID:904667;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0343c by TMHMM2.0 at aa 9-31 2C 41-63 2C 75-92 2C 97-119 2C131-148 2C 152-169 2C 174-193 2C 203-225 and 237-259 NC_002163.1 RefSeq region 314479 314532 . - . ID=id31;Name=id31;Dbxref=GeneID:904667;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0343c by TMHMM2.0 at aa 9-31 2C 41-63 2C 75-92 2C 97-119 2C131-148 2C 152-169 2C 174-193 2C 203-225 and 237-259 NC_002163.1 RefSeq region 314542 314595 . - . ID=id31;Name=id31;Dbxref=GeneID:904667;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0343c by TMHMM2.0 at aa 9-31 2C 41-63 2C 75-92 2C 97-119 2C131-148 2C 152-169 2C 174-193 2C 203-225 and 237-259 NC_002163.1 RefSeq region 314629 314697 . - . ID=id31;Name=id31;Dbxref=GeneID:904667;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0343c by TMHMM2.0 at aa 9-31 2C 41-63 2C 75-92 2C 97-119 2C131-148 2C 152-169 2C 174-193 2C 203-225 and 237-259 NC_002163.1 RefSeq region 314659 314691 . - . ID=id717;Name=id717;Dbxref=GeneID:904667;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 314710 314763 . - . ID=id31;Name=id31;Dbxref=GeneID:904667;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0343c by TMHMM2.0 at aa 9-31 2C 41-63 2C 75-92 2C 97-119 2C131-148 2C 152-169 2C 174-193 2C 203-225 and 237-259 NC_002163.1 RefSeq region 314797 314865 . - . ID=id31;Name=id31;Dbxref=GeneID:904667;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0343c by TMHMM2.0 at aa 9-31 2C 41-63 2C 75-92 2C 97-119 2C131-148 2C 152-169 2C 174-193 2C 203-225 and 237-259 NC_002163.1 RefSeq region 314893 314961 . - . ID=id31;Name=id31;Dbxref=GeneID:904667;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0343c by TMHMM2.0 at aa 9-31 2C 41-63 2C 75-92 2C 97-119 2C131-148 2C 152-169 2C 174-193 2C 203-225 and 237-259 ### NC_002163.1 UTR_Extractor 5'-UTR 314986 315020 . - . ID=utr127;locus_tag=Cj0343c;product=putative integral membrane protein NC_002163.1 UTR_Extractor 5'-UTR 315077 315107 . + . ID=utr128;locus_tag=Cj0344;product=hypothetical protein NC_002163.1 RefSeq gene 315108 315233 . + . ID=gene314;Name=Cj0344;locus_tag=Cj0344;Dbxref=GeneID:904668;gbkey=Gene NC_002163.1 RefSeq CDS 315108 315233 . + 0 ID=cds303;Parent=gene314;Name=YP_002343782.1;Dbxref=UniProtKB FTrEMBL:Q0PBG5 Genbank:YP_002343782.1 GeneID:904668;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0344 2C unknown 2C len: 41 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 UTR_Extractor 5'-UTR 315197 315397 . + . ID=utr129;locus_tag=Cj0345;product=putative anthranilate synthase component I ### NC_002163.1 RefSeq CDS 315398 316648 . + 0 ID=cds304;Parent=gene315;gene=trpE;Name=YP_002343783.1;Dbxref=GOA:Q0PBG4 InterPro:IPR005801 InterPro:IPR015890 UniProtKB FTrEMBL:Q0PBG4 Genbank:YP_002343783.1 GeneID:904669;gbkey=CDS;product=anthranilate synthase subunit I;Note=Original 282000 29 note: Cj0345 2C trpE 2C possible anthranilate synthase component I 2C len: 416 aa 3B similar in C-terminal half to many e.g. TRPE_CLOTM anthranilate synthase component I 28EC 4.1.3.27 29 28494 aa 29 2C fasta scores 3B opt: 784 z-score: 1209.9 E 28 29: 0 2C 47.0 25 identity in 281 aa overlap. 35.6 25 identity in 365 aa overlap to HP1282. Contains Pfam match to entry PF00425 chorismate_bind 2Cchorismate binding enzyme 2C score 309.50 2C E-value 3.9e-89 7EUpdated 282006 29 note: Characterised within Clostridium thermocellum with acceptable identity score 2Chowever 2C sequence alignment was only partial. Thus 2C kept within product function. Functional classification - Amino acid biosynthesis - Aromatic amino acid family 7EPMID:2732211 2C PMID:789357 NC_002163.1 RefSeq gene 315398 316648 . + . ID=gene315;gene=trpE;Name=trpE;locus_tag=Cj0345;Dbxref=GeneID:904669;gbkey=Gene NC_002163.1 RefSeq region 315842 316621 . + . ID=id718;gene=trpE;Name=id718;Dbxref=GeneID:904669;gbkey=misc_feature;Note=HMMPfam hit to PF00425 2C chorismate binding enzyme 2Cscore 1.1e-90 NC_002163.1 RefSeq gene 316645 318246 . + . ID=gene316;gene=trpD;Name=trpD;locus_tag=Cj0346;Dbxref=GeneID:904670;gbkey=Gene NC_002163.1 RefSeq CDS 316645 318246 . + 0 ID=cds305;Parent=gene316;gene=trpD;Name=YP_002343784.1;Dbxref=GOA:Q0PBG3 InterPro:IPR000312 InterPro:IPR000991 InterPro:IPR001317 InterPro:IPR005940 InterPro:IPR006220 InterPro:IPR006221 InterPro:IPR011702 InterPro:IPR012998 UniProtKB FTrEMBL:Q0PBG3 Genbank:YP_002343784.1 GeneID:904670;gbkey=CDS;product=anthranilate synthase subunit II;Note=Original 282000 29 note: Cj0346 2C trpD 28trpGD 29 2Cprobable anthranilate synthase component II 2C len: 533 aa 3B 28contains glutamine amidotransferase and anthranilate phosphoribosyltransferase 29 similar to many e.g. TRPG_ECOLI anthranilate synthase component II 28EC 4.1.3.27 29 28530 aa 29 2Cfasta scores 3B opt: 866 z-score: 781.3 E 28 29: 0 2C 32.6 25 identity in 528 aa overlap. N-terminus has 34.6 25 identity to HP1281 2C C-terminus is 33.2 25 identity to HP1280. Contains PS00442 Glutamine amidotransferases class-I active site and Pfam matches to entry PF00117 GATase 2CGlutamine amidotransferases class-I 2C score 252.00 2C E-value 8.4e-72 and to entry PF00591 Glycos_transf_3 2C glycosyl transferase family 2C score 138.60 2C E-value 1.1e-37 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Amino acid biosynthesis - Aromatic amino acid family 7EPMID:6283099 2C PMID:4594441 2C PMID:789357 NC_002163.1 RefSeq region 316651 317205 . + . ID=id719;gene=trpD;Name=id719;Dbxref=GeneID:904670;gbkey=misc_feature;Note=HMMPfam hit to PF00117 2C Glutamine amidotransferase class-I 2C score 5.4e-61 NC_002163.1 RefSeq region 316864 316899 . + . ID=id720;gene=trpD;Name=id720;Dbxref=GeneID:904670;gbkey=misc_feature;Note=PS00442 Glutamine amidotransferases class-I active site NC_002163.1 RefSeq region 317443 318207 . + . ID=id721;gene=trpD;Name=id721;Dbxref=GeneID:904670;gbkey=misc_feature;Note=HMMPfam hit to PF00591 2C Glycosyl transferase family 2C a 2Fb doma 2C score 2.5e-78 NC_002163.1 RefSeq gene 318233 318832 . + . ID=gene317;gene=trpF;Name=trpF;locus_tag=Cj0347;Dbxref=GeneID:904671;gbkey=Gene NC_002163.1 RefSeq CDS 318233 318832 . + 0 ID=cds306;Parent=gene317;gene=trpF;Name=YP_002343785.1;Dbxref=GOA:Q9PIF3 HSSP:Q56320 InterPro:IPR001240 InterPro:IPR013785 UniProtKB FSwiss-Prot:Q9PIF3 Genbank:YP_002343785.1 GeneID:904671;gbkey=CDS;product=N- 285 27-phosphoribosyl 29anthranilate isomerase;Note=Original 282000 29 note: Cj0347 2C trpF 2C probable N- 285 27-phosphoribosyl 29anthranilate isomerase 2C len: 199 aa 3B similar to many trpF e.g. TRPF_LACCA N- 285 27-phosphoribosyl 29anthranilate isomerase 28199 aa 29 28EC 5.3.1.24 29 2C fasta scores 3B opt: 271 z-score: 352.4 E 28 29: 2.3e-12 2C 31.0 25 identity in 200 aa overlap 2C and to the trpF domain of many trpC proteins e.g. TRPC_SALTY indole-3-glycerol phosphate synthase 2C fasta scores 3B opt: 307 z-score: 394.5 E 28 29: 1e-14 2C 30.8 25 identity in 201 aa overlap. 38.2 25 identity to C-terminus of HP1279 28trpC 29 Conatains Pfam match to entry PF00697 PRAI 2CN- 285 27phosphoribosyl 29antranilate 28PRA 29 isomerase 2C score 102.30 2C E-value 9.5e-27 7EUpdated 282006 29 note: Search results match to more than one isomerase with marginal identity scores. not added to product function. Functional classification -Amino acid biosynthesis - Aromatic amino acid family 7EPMID:2299982 2C PMID:2184433 2C PMID:789357 NC_002163.1 RefSeq region 318242 318820 . + . ID=id722;gene=trpF;Name=id722;Dbxref=GeneID:904671;gbkey=misc_feature;Note=HMMPfam hit to PF00697 2CN- 285 27phosphoribosyl 29anthranilate 28PRA 29 isome 2C score 4.5e-31 NC_002163.1 RefSeq gene 318829 320007 . + . ID=gene318;gene=trpB;Name=trpB;locus_tag=Cj0348;Dbxref=GeneID:904672;gbkey=Gene NC_002163.1 RefSeq CDS 318829 320007 . + 0 ID=cds307;Parent=gene318;gene=trpB;Name=YP_002343786.1;Dbxref=GOA:Q9PIF2 HSSP:P00933 InterPro:IPR001926 InterPro:IPR006653 InterPro:IPR006654 UniProtKB FSwiss-Prot:Q9PIF2 Genbank:YP_002343786.1 GeneID:904672;gbkey=CDS;product=tryptophan synthase subunit beta;Note=catalyzes the formation of L-tryptophan from L-serine and 1- 28indol-3-yl 29glycerol 3-phosphate NC_002163.1 RefSeq region 318967 319950 . + . ID=id723;gene=trpB;Name=id723;Dbxref=GeneID:904672;gbkey=misc_feature;Note=HMMPfam hit to PF00291 2C Pyridoxal-phosphate dependent enzyme 2C score 1.8e-108 NC_002163.1 RefSeq region 319057 319086 . + . ID=id724;gene=trpB;Name=id724;Dbxref=GeneID:904672;gbkey=misc_feature;Note=PS00168 Tryptophan synthase beta chain pyridoxal-phosphate attachment site NC_002163.1 RefSeq region 319621 319644 . + . ID=id725;gene=trpB;Name=id725;Dbxref=GeneID:904672;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 320000 320749 . + 0 ID=cds308;Parent=gene319;gene=trpA;Name=YP_002343787.1;Dbxref=GOA:Q9PIF1 HSSP:P00929 InterPro:IPR002028 InterPro:IPR013785 UniProtKB FSwiss-Prot:Q9PIF1 Genbank:YP_002343787.1 GeneID:904673;gbkey=CDS;product=tryptophan synthase subunit alpha;Note=catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis NC_002163.1 RefSeq gene 320000 320749 . + . ID=gene319;gene=trpA;Name=trpA;locus_tag=Cj0349;Dbxref=GeneID:904673;gbkey=Gene NC_002163.1 RefSeq region 320009 320746 . + . ID=id726;gene=trpA;Name=id726;Dbxref=GeneID:904673;gbkey=misc_feature;Note=HMMPfam hit to PF00290 2C Tryptophan synthase alpha chain 2C score 2.2e-73 NC_002163.1 RefSeq region 320123 320164 . + . ID=id727;gene=trpA;Name=id727;Dbxref=GeneID:904673;gbkey=misc_feature;Note=PS00167 Tryptophan synthase alpha chain signature ### NC_002163.1 UTR_Extractor 5'-UTR 320793 320819 . + . ID=utr130;locus_tag=Cj0350;product=hypothetical protein NC_002163.1 RefSeq CDS 320820 321242 . + 0 ID=cds309;Parent=gene320;Name=YP_002343788.1;Dbxref=UniProtKB FTrEMBL:Q0PBF9 Genbank:YP_002343788.1 GeneID:904674;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0350 2C unknown 2C len: 140 aa 3B no Hp match. . Functional classification - Unknown NC_002163.1 RefSeq gene 320820 321242 . + . ID=gene320;Name=Cj0350;locus_tag=Cj0350;Dbxref=GeneID:904674;gbkey=Gene NC_002163.1 RefSeq gene 321242 321550 . + . ID=gene321;gene=fliN;Name=fliN;locus_tag=Cj0351;Dbxref=GeneID:904675;gbkey=Gene NC_002163.1 RefSeq CDS 321242 321550 . + 0 ID=cds310;Parent=gene321;gene=fliN;Name=YP_002343789.1;Dbxref=GOA:O32370 InterPro:IPR001172 InterPro:IPR001543 UniProtKB FTrEMBL:O32370 Genbank:YP_002343789.1 GeneID:904675;gbkey=CDS;product=flagellar motor switch protein;Note=One of three proteins involved in switching the direction of the flagellar rotation NC_002163.1 RefSeq region 321287 321517 . + . ID=id728;gene=fliN;Name=id728;Dbxref=GeneID:904675;gbkey=misc_feature;Note=HMMPfam hit to PF01052 2C Surface presentation of antigens 28SPOA 29 prot 2C score 9e-34 ### NC_002163.1 RefSeq CDS 321551 322348 . + 0 ID=cds311;Parent=gene322;Name=YP_002343790.1;Dbxref=GOA:Q0PBF7 UniProtKB FTrEMBL:Q0PBF7 Genbank:YP_002343790.1 GeneID:904676;gbkey=CDS;product=transmembrane protein;Note=Original 282000 29 note: Cj0352 2C probable transmembrane protein 2C len: 265 aa 3B 99.6 25 identity to TR:O32371 28EMBL:AJ000400 29. No Hp match. Contains probable N-terminal signal sequence and transmembrane domain around aa 160 7EUpdated 282006 29 note: Two probable transmembrane helices identified by TMHMM2.0 within CDS. Literature search identified paper linking CDS with potential new functional assignment as FliO flagellar protein. Functional classification - Membranes 2C lipoproteins and porins 7EPMID:15817382 2C PMID:9894591 NC_002163.1 RefSeq gene 321551 322348 . + . ID=gene322;Name=Cj0352;locus_tag=Cj0352;Dbxref=GeneID:904676;gbkey=Gene NC_002163.1 RefSeq region 321563 321622 . + . ID=id729;Name=id729;Dbxref=GeneID:904676;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0352 by TMHMM2.0 at aa 5-24 and 153-170 NC_002163.1 RefSeq region 322007 322060 . + . ID=id729;Name=id729;Dbxref=GeneID:904676;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0352 by TMHMM2.0 at aa 5-24 and 153-170 NC_002163.1 RefSeq gene 322345 323805 . - . ID=gene323;Name=Cj0353c;locus_tag=Cj0353c;Dbxref=GeneID:904677;gbkey=Gene NC_002163.1 RefSeq CDS 322345 323805 . - 0 ID=cds312;Parent=gene323;Name=YP_002343791.1;Dbxref=GOA:Q0PBF6 InterPro:IPR003695 UniProtKB FTrEMBL:Q0PBF6 Genbank:YP_002343791.1 GeneID:904677;gbkey=CDS;product=phosphatase;Note=Original 282000 29 note: Cj0353c 2C probable phosphatase 2C len: 486 aa 3B similar to e.g. GPPA_ECOLI guanosine-5 27-triphosphate 2C3 27-diphosphate pyrophosphatase 28EC 3.6.1.40 29 28494 aa 29 2C fasta scores 3B opt: 368 z-score: 272.7 E 28 29: 6.2e-08 2C 25.8 25 identity in 480 aa overlap 2C and to PPX_ECOLI EXOPOLYPHOSPHATASE 28EC 3.6.1.11 29 28512 aa 29 2Cfasta scores 3B opt: 340 z-score: 350.9 E 28 29: 2.7e-12 2C 23.8 25 identity in 441 aa overlap. 41.0 25 identity to HP0278 7EUpdated 282006 29 note: Pfam domain PF02541 Ppx 2FGppA phosphatase family identified within CDS. Further support given to product function. Similar to many different annotated phosphatases. not added to product function. Functional classification - Misc 7EPMID:8394006 NC_002163.1 RefSeq region 322906 323754 . - . ID=id730;Name=id730;Dbxref=GeneID:904677;gbkey=misc_feature;Note=HMMPfam hit to PF02541 2C Ppx 2FGppA phosphatase family 2C score 1.5e-46 NC_002163.1 RefSeq gene 323805 324050 . - . ID=gene324;gene=fdxB;Name=fdxB;locus_tag=Cj0354c;Dbxref=GeneID:904678;gbkey=Gene NC_002163.1 RefSeq CDS 323805 324050 . - 0 ID=cds313;Parent=gene324;gene=fdxB;Name=YP_002343792.1;Dbxref=GOA:Q0PBF5 InterPro:IPR001450 UniProtKB FTrEMBL:Q0PBF5 Genbank:YP_002343792.1 GeneID:904678;gbkey=CDS;product=ferredoxin;Note=Original 282000 29 note: Cj0354c 2C fdxB 2C probable ferredoxin 2C len: 81 aa 3B similar to many e.g. FER_CHRVI ferredoxin 2882 aa 29 2C fasta scores 3B opt: 282 z-score: 445.5 E 28 29: 1.5e-17 2C 45.3 25 identity in 75 aa overlap. 58.4 25 identity to HP0277. Also similar to Cj0333c 28fdx 29 3B 38.8 25 identity in 67 aa overlap. Contains PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature and Pfam match to entry PF00037 fer4 2C 4Fe-4S ferredoxins and related iron-sulfur cluster binding domains. 2C score 39.00 2CE-value 4.8e-10 7EUpdated 282006 29 note: Characterised within Chromatium vinosum with acceptable identity scores. Appropriate motifs also present. not added to product function. Functional classification - Energy metabolism - Electron transport 7EPMID:8765743 NC_002163.1 RefSeq region 323976 324047 . - . ID=id731;gene=fdxB;Name=id731;Dbxref=GeneID:904678;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 0.0069 NC_002163.1 RefSeq region 323991 324026 . - . ID=id732;gene=fdxB;Name=id732;Dbxref=GeneID:904678;gbkey=misc_feature;Note=PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature ### NC_002163.1 UTR_Extractor 5'-UTR 324051 324079 . - . ID=utr131;locus_tag=Cj0354c;product=ferredoxin NC_002163.1 RefSeq CDS 324163 324834 . - 0 ID=cds314;Parent=gene325;Name=YP_002343793.1;Dbxref=GOA:Q0PBF4 InterPro:IPR001789 InterPro:IPR001867 InterPro:IPR011991 UniProtKB FTrEMBL:Q0PBF4 Genbank:YP_002343793.1 GeneID:904679;gbkey=CDS;product=two-component regulator;Note=Original 282000 29 note: Cj0355c 2C probable two-component regulator 2C len: 223 aa 3B similar to many e.g. CZCR_ALCEU transcriptional activator protein CZCR 28225 aa 29 2C fasta scores 3B opt: 375 z-score: 570.8 E 28 29: 1.5e-24 2C31.7 25 identity in 218 aa overlap. 59.9 25 identity to HP1043. Contains Pfam match to entry PF00072 response_reg 2CResponse regulator receiver domain 2C score 70.70 2C E-value 3.1e-17 and Pfam match to entry PF00486 trans_reg_C 2CTranscriptional regulatory protein 2C C terminal 2C score 56.60 2C E-value 1.5e-15 7EUpdated 282006 29 note: Characterisation work within many e.g. Ralstonia metallidurans and Escherichia coli with marginal identity scores. Appropriate motifs also present. not added to product function. Literature search identified paper giving further clues to product function 28PMID:15901688 29. Functional classification - Signal transduction 7EPMID:9044283 2C PMID:15901688 NC_002163.1 RefSeq gene 324163 324834 . - . ID=gene325;Name=Cj0355c;locus_tag=Cj0355c;Dbxref=GeneID:904679;gbkey=Gene NC_002163.1 RefSeq region 324184 324411 . - . ID=id733;Name=id733;Dbxref=GeneID:904679;gbkey=misc_feature;Note=HMMPfam hit to PF00486 2C Transcriptional regulatory protein 2C C te 2C score 4.2e-20 NC_002163.1 RefSeq region 324475 324834 . - . ID=id734;Name=id734;Dbxref=GeneID:904679;gbkey=misc_feature;Note=HMMPfam hit to PF00072 2C Response regulator receiver domain 2C score 4e-19 ### NC_002163.1 RefSeq CDS 324913 325230 . - 0 ID=cds315;Parent=gene326;gene=folB;Name=YP_002343794.1;Dbxref=GOA:Q0PBF3 InterPro:IPR006157 UniProtKB FTrEMBL:Q0PBF3 Genbank:YP_002343794.1 GeneID:904680;gbkey=CDS;product=dihydroneopterin aldolase;Note=Original 282000 29 note: Cj0356c 2C unknown 2C len: 105 aa 3B 31.0 25 identity to HP1510 7EUpdated 282006 29 note: Pfam domain PF02152 FolB Dihydroneopterin aldolase was identified within CDS. This enzyme catalyses the conversion of 7 2C8-dihydroneopterin to 6-hydroxymethyl-7 2C8-dihydropterin in the biosynthetic pathway of tetrahydrofolate. This was found by carrying out own Pfam search. Product modified to new family member due to motif match. No specific characterisation has been carried out yet. kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 324913 325230 . - . ID=gene326;gene=folB;Name=folB;locus_tag=Cj0356c;Dbxref=GeneID:904680;gbkey=Gene NC_002163.1 RefSeq CDS 325215 325823 . - 0 ID=cds316;Parent=gene327;Name=YP_002343795.1;Dbxref=GOA:Q9PIE4 InterPro:IPR003811 UniProtKB FSwiss-Prot:Q9PIE4 Genbank:YP_002343795.1 GeneID:904681;gbkey=CDS;product=glycerol-3-phosphate acyltransferase PlsY;Note=involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis 3B functions with PlsX NC_002163.1 RefSeq gene 325215 325823 . - . ID=gene327;Name=Cj0357c;locus_tag=Cj0357c;Dbxref=GeneID:904681;gbkey=Gene NC_002163.1 RefSeq region 325218 325229 . - . ID=id735;gene=folB;Name=id735;Dbxref=GeneID:904680;gbkey=misc_feature;Note=PS00294 Prenyl group binding site 28CAAX box 29 NC_002163.1 RefSeq region 325236 325805 . - . ID=id736;Name=id736;Dbxref=GeneID:904681;gbkey=misc_feature;Note=HMMPfam hit to PF02660 2C Domain of unknown function DUF 2C score 1.3e-44 NC_002163.1 RefSeq region 325239 325307 . - . ID=id32;Name=id32;Dbxref=GeneID:904681;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0357c by TMHMM2.0 at aa 5-27 2C 85-107 2C 117-139 2C 144-163 and 173-195 NC_002163.1 RefSeq region 325335 325394 . - . ID=id32;Name=id32;Dbxref=GeneID:904681;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0357c by TMHMM2.0 at aa 5-27 2C 85-107 2C 117-139 2C 144-163 and 173-195 NC_002163.1 RefSeq region 325407 325475 . - . ID=id32;Name=id32;Dbxref=GeneID:904681;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0357c by TMHMM2.0 at aa 5-27 2C 85-107 2C 117-139 2C 144-163 and 173-195 NC_002163.1 RefSeq region 325503 325571 . - . ID=id32;Name=id32;Dbxref=GeneID:904681;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0357c by TMHMM2.0 at aa 5-27 2C 85-107 2C 117-139 2C 144-163 and 173-195 NC_002163.1 RefSeq region 325743 325811 . - . ID=id32;Name=id32;Dbxref=GeneID:904681;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0357c by TMHMM2.0 at aa 5-27 2C 85-107 2C 117-139 2C 144-163 and 173-195 ### NC_002163.1 UTR_Extractor 5'-UTR 325824 325864 . - . ID=utr132;locus_tag=Cj0357c;product=putative glycerol-3-phosphate acyltransferase PlsY NC_002163.1 UTR_Extractor 5'-UTR 325994 326023 . + . ID=utr133;locus_tag=Cj0358;product=putative cytochrome C551 peroxidase NC_002163.1 RefSeq CDS 326024 327049 . + 0 ID=cds317;Parent=gene328;Name=YP_002343796.1;Dbxref=GOA:Q0PBF1 InterPro:IPR004852 InterPro:IPR009056 UniProtKB FTrEMBL:Q0PBF1 Genbank:YP_002343796.1 GeneID:904682;gbkey=CDS;product=cytochrome C551 peroxidase;Note=Original 282000 29 note: Cj0358 2C probable cytochrome C551 peroxidase 2C len: 341 aa 3B similar to e.g. CCPR_PSEAE cytochrome C551 peroxidase precursor 28EC 1.11.1.5 29 28346 aa 29 2C fasta scores 3B opt: 281 z-score: 1028.0 E 28 29: 0 2C 48.9 25 identity in 313 aa overlap. 58.5 25 identity to HP1461. Also similar to Cj0020c 2845.4 25 identity in 273 aa overlap 29. Contains 2x PS00190 Cytochrome c family heme-binding site signature and probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF03150 Di-haem cytochrome c peroxidase identified within CDS. Further support given to product function. Characterised within Pseudomonas aeruginosa with acceptable identity score 2Chowever 2C only partial sequence alignment was achieved. kept within product function. Functional classification - Detoxification 7EPMID:7781769 2C PMID:8591033 NC_002163.1 RefSeq gene 326024 327049 . + . ID=gene328;Name=Cj0358;locus_tag=Cj0358;Dbxref=GeneID:904682;gbkey=Gene NC_002163.1 RefSeq region 326123 326650 . + . ID=id737;Name=id737;Dbxref=GeneID:904682;gbkey=misc_feature;Note=HMMPfam hit to PF03150 2C Di-haem cytochrome c peroxidase 2C score 1.4e-78 NC_002163.1 RefSeq region 326261 326278 . + . ID=id738;Name=id738;Dbxref=GeneID:904682;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature NC_002163.1 RefSeq region 326696 326713 . + . ID=id739;Name=id739;Dbxref=GeneID:904682;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature ### NC_002163.1 UTR_Extractor 5'-UTR 327120 327142 . + . ID=utr134;locus_tag=Cj0360;product=phosphoglucosamine mutase NC_002163.1 RefSeq region 327143 327553 . + . ID=id740;gene=glmM;Name=id740;Dbxref=GeneID:904683;gbkey=misc_feature;Note=HMMPfam hit to PF02878 2CPhosphoglucomutase 2Fphosphomannomutase 2C al 2C score 2.8e-60 NC_002163.1 RefSeq gene 327143 328480 . + . ID=gene329;gene=glmM;Name=glmM;locus_tag=Cj0360;Dbxref=GeneID:904683;gbkey=Gene NC_002163.1 RefSeq CDS 327143 328480 . + 0 ID=cds318;Parent=gene329;gene=glmM;Name=YP_002343797.1;Dbxref=GOA:Q9PIE2 InterPro:IPR005841 InterPro:IPR005843 InterPro:IPR005844 InterPro:IPR005845 InterPro:IPR005846 InterPro:IPR006352 InterPro:IPR016055 InterPro:IPR016066 UniProtKB FSwiss-Prot:Q9PIE2 Genbank:YP_002343797.1 GeneID:904683;gbkey=CDS;product=phosphoglucosamine mutase;Note=catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate NC_002163.1 RefSeq region 327419 327463 . + . ID=id741;gene=glmM;Name=id741;Dbxref=GeneID:904683;gbkey=misc_feature;Note=PS00710 Phosphoglucomutase and phosphomannomutase phosphoserine signature NC_002163.1 RefSeq region 327611 327913 . + . ID=id742;gene=glmM;Name=id742;Dbxref=GeneID:904683;gbkey=misc_feature;Note=HMMPfam hit to PF02879 2CPhosphoglucomutase 2Fphosphomannomutase 2C al 2C score 2.6e-37 NC_002163.1 RefSeq region 327917 328261 . + . ID=id743;gene=glmM;Name=id743;Dbxref=GeneID:904683;gbkey=misc_feature;Note=HMMPfam hit to PF02880 2CPhosphoglucomutase 2Fphosphomannomutase 2C al 2C score 2.5e-31 NC_002163.1 RefSeq region 328262 328465 . + . ID=id744;gene=glmM;Name=id744;Dbxref=GeneID:904683;gbkey=misc_feature;Note=HMMPfam hit to PF00408 2CPhosphoglucomutase 2Fphosphomannomutase 2C C- 2C score 5.8e-06 NC_002163.1 RefSeq gene 328473 328943 . + . ID=gene330;gene=lspA;Name=lspA;locus_tag=Cj0361;Dbxref=GeneID:904684;gbkey=Gene NC_002163.1 RefSeq CDS 328473 328943 . + 0 ID=cds319;Parent=gene330;gene=lspA;Name=YP_002343798.1;Dbxref=GOA:Q0PBE9 InterPro:IPR001872 UniProtKB FTrEMBL:Q0PBE9 Genbank:YP_002343798.1 GeneID:904684;gbkey=CDS;product=lipoprotein signal peptidase;Note=lipoprotein signal peptidase 3B integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis NC_002163.1 RefSeq region 328491 328544 . + . ID=id745;gene=lspA;Name=id745;Dbxref=GeneID:904684;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0361 by TMHMM2.0 at aa 7-24 2C 39-58 2C 65-84 and 120-142 NC_002163.1 RefSeq region 328497 328931 . + . ID=id746;gene=lspA;Name=id746;Dbxref=GeneID:904684;gbkey=misc_feature;Note=HMMPfam hit to PF01252 2C Signal peptidase 28SPase 29 II 2C score 9.9e-41 NC_002163.1 RefSeq region 328587 328646 . + . ID=id745;gene=lspA;Name=id745;Dbxref=GeneID:904684;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0361 by TMHMM2.0 at aa 7-24 2C 39-58 2C 65-84 and 120-142 NC_002163.1 RefSeq region 328665 328724 . + . ID=id745;gene=lspA;Name=id745;Dbxref=GeneID:904684;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0361 by TMHMM2.0 at aa 7-24 2C 39-58 2C 65-84 and 120-142 NC_002163.1 RefSeq region 328758 328790 . + . ID=id747;gene=lspA;Name=id747;Dbxref=GeneID:904684;gbkey=misc_feature;Note=PS00855 Signal peptidases II signature NC_002163.1 RefSeq region 328830 328898 . + . ID=id745;gene=lspA;Name=id745;Dbxref=GeneID:904684;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0361 by TMHMM2.0 at aa 7-24 2C 39-58 2C 65-84 and 120-142 NC_002163.1 RefSeq CDS 328927 329379 . + 0 ID=cds320;Parent=gene331;Name=YP_002343799.1;Dbxref=InterPro:IPR005265 InterPro:IPR014351 UniProtKB FTrEMBL:Q0PBE8 Genbank:YP_002343799.1 GeneID:904685;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0362 2C probable integral membrane protein 2C len: 150 aa 3B similar to hypothetical proteins e.g. TR:Q53231 28EMBL:L76097 29 from Rhodobacter sphaeroides 28154 aa 29 2C fasta scores 3B opt: 301 z-score: 419.6 E 28 29: 4.1e-16 2C 34.2 25 identity in 149 aa overlap. 47.6 25 identity to HP1484 7EUpdated 282006 29 note: Four probable transmembrace helices identified by TMHMM2.0 within CDS. Pfam domain PF03653 Uncharacterised protein family 28UPF0093 29 identified within CDS. Further support given to product function. Functional classification - Membranes 2Clipoproteins and porins NC_002163.1 RefSeq gene 328927 329379 . + . ID=gene331;gene=Cj0362;Name=Cj0362;locus_tag=Cj0362;Dbxref=GeneID:904685;gbkey=Gene NC_002163.1 RefSeq region 328939 329376 . + . ID=id748;Name=id748;Dbxref=GeneID:904685;gbkey=misc_feature;Note=HMMPfam hit to PF03653 2C Uncharacterised protein family 28UPF0093 29 2C score 9e-53 NC_002163.1 RefSeq region 328969 329034 . + . ID=id749;Name=id749;Dbxref=GeneID:904685;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0362 by TMHMM2.0 at aa 15-36 2C 57-79 2C 83-105 and 126-148 NC_002163.1 RefSeq region 329095 329163 . + . ID=id749;Name=id749;Dbxref=GeneID:904685;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0362 by TMHMM2.0 at aa 15-36 2C 57-79 2C 83-105 and 126-148 NC_002163.1 RefSeq region 329173 329241 . + . ID=id749;Name=id749;Dbxref=GeneID:904685;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0362 by TMHMM2.0 at aa 15-36 2C 57-79 2C 83-105 and 126-148 NC_002163.1 RefSeq region 329302 329370 . + . ID=id749;Name=id749;Dbxref=GeneID:904685;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0362 by TMHMM2.0 at aa 15-36 2C 57-79 2C 83-105 and 126-148 NC_002163.1 RefSeq sRNA 329341 329423 . + . ID=NC_002163.1:CJas_Cj0363c:unknown_transcript_1;Parent=NC_002163.1:CJas_Cj0363c;Name=NC_002163.1:CJas_Cj0363c:unknown_transcript_1;locus_tag=CJas_Cj0363c;gbkey=misc_RNA;product=CJas_Cj0363c NC_002163.1 RefSeq gene 329341 329423 . + . ID=NC_002163.1:CJas_Cj0363c;Name=NC_002163.1:CJas_Cj0363c;locus_tag=CJas_Cj0363c NC_002163.1 RefSeq gene 329376 330722 . - . ID=gene332;Name=Cj0363c;locus_tag=Cj0363c;Dbxref=GeneID:904686;gbkey=Gene NC_002163.1 RefSeq CDS 329376 330722 . - 0 ID=cds321;Parent=gene332;Name=YP_002343800.1;Dbxref=GOA:Q0PBE7 InterPro:IPR006638 InterPro:IPR007197 UniProtKB FTrEMBL:Q0PBE7 Genbank:YP_002343800.1 GeneID:904686;gbkey=CDS;product=coproporphyrinogen III oxidase;Note=catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III NC_002163.1 RefSeq region 329541 329870 . - . ID=id750;Name=id750;Dbxref=GeneID:904686;gbkey=misc_feature;Note=HMMPfam hit to PF06969 2C HemN C-terminal region 2Cscore 0.0012 NC_002163.1 RefSeq region 330084 330587 . - . ID=id751;Name=id751;Dbxref=GeneID:904686;gbkey=misc_feature;Note=HMMPfam hit to PF04055 2C Radical SAM superfamily 2Cscore 3.4e-21 ### NC_002163.1 UTR_Extractor 5'-UTR 330723 330749 . - . ID=utr135;locus_tag=Cj0363c;product=coproporphyrinogen III oxidase NC_002163.1 RefSeq gene 330851 331102 . + . ID=gene333;Name=Cj0364;locus_tag=Cj0364;Dbxref=GeneID:904687;gbkey=Gene NC_002163.1 RefSeq CDS 330851 331102 . + 0 ID=cds322;Parent=gene333;Name=YP_002343801.1;Dbxref=UniProtKB FTrEMBL:Q0PBE6 Genbank:YP_002343801.1 GeneID:904687;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0364 2C unknown 2C len: 83 aa 3B no Hp match 7EUpdated 282006 29 note: Literature search identified paper giving further clues to product function. Functional classification - Unknown NC_002163.1 RefSeq CDS 331125 332603 . - 0 ID=cds323;Parent=gene334;gene=cmeC;Name=YP_002343802.1;Dbxref=GOA:Q0PBE5 InterPro:IPR003423 InterPro:IPR010131 UniProtKB FTrEMBL:Q0PBE5 Genbank:YP_002343802.1 GeneID:904688;gbkey=CDS;product=outer membrane channel protein CmeC;Note=Original 282000 29 note: Cj0365c 2C possible outer membrane channel protein 2C len: 492 aa 3B similar to members of the nodT 2FfusA family e.g. TR:O31101 28EMBL:AF029405 29 Pseudomonas putida outer membrane channel protein SRPC 28470 aa 29 2C fasta scores 3B opt: 645 z-score: 834.4 E 28 29: 0 2C29.2 25 identity in 465 aa overlap. and TR:Q51006 28EMBL:X95635 29 Neisseria gonorrhoeae mtrE gene 28467 aa 2Cfasta scores 3B opt: 663 z-score: 829.8 E 28 29: 0 2C 31.1 25 identity in 476 aa overlap. No Hp match. Also some similarity to Cj0608 2828.6 25 identity in 455 aa overlap 29. Contains N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site 7EUpdated 282006 29 note: Pfam domains x2 PF02321 Outer membrane efflux proteins were identified within CDS. Further support given to product function. Characterised within Campylobacter jejuni. Part of the CmeABC multidrug efflux system. Functional classification - Antibiotic resistance 7EPMID:12069964 2C PMID:15728904 2C PMID:16359189 NC_002163.1 RefSeq gene 331125 332603 . - . ID=gene334;gene=cmeC;Name=cmeC;locus_tag=Cj0365c;Dbxref=GeneID:904688;gbkey=Gene NC_002163.1 RefSeq region 331206 331766 . - . ID=id752;gene=cmeC;Name=id752;Dbxref=GeneID:904688;gbkey=misc_feature;Note=HMMPfam hit to PF02321 2C Outer membrane efflux protein 2C score 1.6e-27 NC_002163.1 RefSeq region 331836 332411 . - . ID=id753;gene=cmeC;Name=id753;Dbxref=GeneID:904688;gbkey=misc_feature;Note=HMMPfam hit to PF02321 2C Outer membrane efflux protein 2C score 3.2e-33 NC_002163.1 RefSeq region 332544 332576 . - . ID=id754;gene=cmeC;Name=id754;Dbxref=GeneID:904688;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq CDS 332596 335718 . - 0 ID=cds324;Parent=gene335;gene=cmeB;Name=YP_002343803.1;Dbxref=GOA:Q0PBE4 InterPro:IPR000731 InterPro:IPR001036 InterPro:IPR004764 UniProtKB FTrEMBL:Q0PBE4 Genbank:YP_002343803.1 GeneID:904689;gbkey=CDS;product=inner membrane efflux transporter CmeB;Note=Original 282000 29 note: Cj0366c 2C probable transmembrane efflux protein 2C len: 1040 aa 3B similar to e.g. TR:P95422 28EMBL:X99514 29 Pseudomonas aeruginosa mexF 28antibiotic efflux system protein 29 281062 aa 29 2C fasta scores 3B opt: 1584 z-score: 3208.4 E 28 29: 0 2C 41.2 25 identity in 1056 aa overlap 2C and ACRB_ECOLI acriflavin resistance protein B 281049 aa 29 2C fasta scores 3B opt: 2739 z-score: 3055.6 E 28 29: 0 2C 41.7 25 identity in 1031 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00873 ACR_tran 2CAcrB 2FAcrD 2FAcrF family 2C score 1415.10 2C E-value 0 7EUpdated 282006 29 note: Thirteen probable transmembrace helices identified by TMHMM2.0 within CDS. Prosite domain PS50156 SSD 2C Sterol-sensing 5TM box also identified within CDS. Further support given to product function. Characterised within Campylobacter jejuni. Part of the CmeABC multidrug efflux system. Functional classification - Antibiotic resistance 7EPMID:12069964 2C PMID:11814661 2C PMID:15728904 2CPMID:16359189 2C PMID:15201231 NC_002163.1 RefSeq gene 332596 335718 . - . ID=gene335;gene=cmeB;Name=cmeB;locus_tag=Cj0366c;Dbxref=GeneID:904689;gbkey=Gene NC_002163.1 RefSeq region 332644 335715 . - . ID=id755;gene=cmeB;Name=id755;Dbxref=GeneID:904689;gbkey=misc_feature;Note=HMMPfam hit to PF00873 2C AcrB 2FAcrD 2FAcrF family 2Cscore 0 NC_002163.1 RefSeq region 332647 332715 . - . ID=id33;gene=cmeB;Name=id33;Dbxref=GeneID:904689;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0366c by TMHMM2.0 at aa 10-32 2C 342-361 2C 366-388 2C393-415 2C 445-467 2C 479-501 2C 516-533 2C 540-562 2C 866-883 2C890-912 2C 922-944 2C 965-987 and 1002-1024 NC_002163.1 RefSeq region 332758 332826 . - . ID=id33;gene=cmeB;Name=id33;Dbxref=GeneID:904689;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0366c by TMHMM2.0 at aa 10-32 2C 342-361 2C 366-388 2C393-415 2C 445-467 2C 479-501 2C 516-533 2C 540-562 2C 866-883 2C890-912 2C 922-944 2C 965-987 and 1002-1024 NC_002163.1 RefSeq region 332887 332955 . - . ID=id33;gene=cmeB;Name=id33;Dbxref=GeneID:904689;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0366c by TMHMM2.0 at aa 10-32 2C 342-361 2C 366-388 2C393-415 2C 445-467 2C 479-501 2C 516-533 2C 540-562 2C 866-883 2C890-912 2C 922-944 2C 965-987 and 1002-1024 NC_002163.1 RefSeq region 332983 333051 . - . ID=id33;gene=cmeB;Name=id33;Dbxref=GeneID:904689;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0366c by TMHMM2.0 at aa 10-32 2C 342-361 2C 366-388 2C393-415 2C 445-467 2C 479-501 2C 516-533 2C 540-562 2C 866-883 2C890-912 2C 922-944 2C 965-987 and 1002-1024 NC_002163.1 RefSeq region 333070 333123 . - . ID=id33;gene=cmeB;Name=id33;Dbxref=GeneID:904689;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0366c by TMHMM2.0 at aa 10-32 2C 342-361 2C 366-388 2C393-415 2C 445-467 2C 479-501 2C 516-533 2C 540-562 2C 866-883 2C890-912 2C 922-944 2C 965-987 and 1002-1024 NC_002163.1 RefSeq region 334033 334101 . - . ID=id33;gene=cmeB;Name=id33;Dbxref=GeneID:904689;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0366c by TMHMM2.0 at aa 10-32 2C 342-361 2C 366-388 2C393-415 2C 445-467 2C 479-501 2C 516-533 2C 540-562 2C 866-883 2C890-912 2C 922-944 2C 965-987 and 1002-1024 NC_002163.1 RefSeq region 334120 334173 . - . ID=id33;gene=cmeB;Name=id33;Dbxref=GeneID:904689;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0366c by TMHMM2.0 at aa 10-32 2C 342-361 2C 366-388 2C393-415 2C 445-467 2C 479-501 2C 516-533 2C 540-562 2C 866-883 2C890-912 2C 922-944 2C 965-987 and 1002-1024 NC_002163.1 RefSeq region 334216 334284 . - . ID=id33;gene=cmeB;Name=id33;Dbxref=GeneID:904689;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0366c by TMHMM2.0 at aa 10-32 2C 342-361 2C 366-388 2C393-415 2C 445-467 2C 479-501 2C 516-533 2C 540-562 2C 866-883 2C890-912 2C 922-944 2C 965-987 and 1002-1024 NC_002163.1 RefSeq region 334318 334386 . - . ID=id33;gene=cmeB;Name=id33;Dbxref=GeneID:904689;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0366c by TMHMM2.0 at aa 10-32 2C 342-361 2C 366-388 2C393-415 2C 445-467 2C 479-501 2C 516-533 2C 540-562 2C 866-883 2C890-912 2C 922-944 2C 965-987 and 1002-1024 NC_002163.1 RefSeq region 334474 334542 . - . ID=id33;gene=cmeB;Name=id33;Dbxref=GeneID:904689;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0366c by TMHMM2.0 at aa 10-32 2C 342-361 2C 366-388 2C393-415 2C 445-467 2C 479-501 2C 516-533 2C 540-562 2C 866-883 2C890-912 2C 922-944 2C 965-987 and 1002-1024 NC_002163.1 RefSeq region 334555 334623 . - . ID=id33;gene=cmeB;Name=id33;Dbxref=GeneID:904689;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0366c by TMHMM2.0 at aa 10-32 2C 342-361 2C 366-388 2C393-415 2C 445-467 2C 479-501 2C 516-533 2C 540-562 2C 866-883 2C890-912 2C 922-944 2C 965-987 and 1002-1024 NC_002163.1 RefSeq region 334636 334695 . - . ID=id33;gene=cmeB;Name=id33;Dbxref=GeneID:904689;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0366c by TMHMM2.0 at aa 10-32 2C 342-361 2C 366-388 2C393-415 2C 445-467 2C 479-501 2C 516-533 2C 540-562 2C 866-883 2C890-912 2C 922-944 2C 965-987 and 1002-1024 NC_002163.1 RefSeq region 335623 335691 . - . ID=id33;gene=cmeB;Name=id33;Dbxref=GeneID:904689;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0366c by TMHMM2.0 at aa 10-32 2C 342-361 2C 366-388 2C393-415 2C 445-467 2C 479-501 2C 516-533 2C 540-562 2C 866-883 2C890-912 2C 922-944 2C 965-987 and 1002-1024 NC_002163.1 RefSeq gene 335718 336821 . - . ID=gene336;gene=cmeA;Name=cmeA;locus_tag=Cj0367c;Dbxref=GeneID:904690;gbkey=Gene NC_002163.1 RefSeq CDS 335718 336821 . - 0 ID=cds325;Parent=gene336;gene=cmeA;Name=YP_002343804.1;Dbxref=GOA:Q0PBE3 InterPro:IPR006143 UniProtKB FTrEMBL:Q0PBE3 Genbank:YP_002343804.1 GeneID:904690;gbkey=CDS;product=fusion protein CmeA;Note=Original 282000 29 note: Cj0367c 2C possible membrane fusion component of efflux system 2C len: 367 aa 3B similar to e.g. MTRC_NEIGO membrane fusion protein MTRC precursor 28412 aa 29 2C fasta scores 3B opt: 592 z-score: 692.4 E 28 29: 2.6e-31 2C 29.9 25 identity in 358 aa overlap 2C and TR:P95421 28EMBL:X99514 29 Pseudomonas aeruginosa mexE 28antibiotic efflux system protein 29 28414 aa 29 2C fasta scores 3B opt: 460 z-score: 570.0 E 28 29: 1.7e-24 2C 26.9 25 identity in 357 aa overlap. No Hp ortholog. Contains N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site 7EUpdated 282006 29 note: Pfam domain PF00529 HlyD family secretion protein identified within CDS. Further support given to product function. Part of the CmeABC multidrug efflux system. Functional classification -Antibiotic resistance 7EPMID:12069964 2C PMID:15728904 2C PMID:16359189 NC_002163.1 RefSeq region 335775 336644 . - . ID=id756;gene=cmeA;Name=id756;Dbxref=GeneID:904690;gbkey=misc_feature;Note=HMMPfam hit to PF00529 2C HlyD family secretion protein 2C score 2.9e-21 NC_002163.1 RefSeq region 336759 336791 . - . ID=id757;gene=cmeA;Name=id757;Dbxref=GeneID:904690;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq CDS 336916 337548 . - 0 ID=cds326;Parent=gene337;gene=cmeR;Name=YP_002343805.1;Dbxref=GOA:Q6PMN0 InterPro:IPR001647 InterPro:IPR012287 UniProtKB FTrEMBL:Q6PMN0 Genbank:YP_002343805.1 GeneID:904691;gbkey=CDS;product=transcriptional regulator CmeR;Note=Original 282000 29 note: Cj0368c 2C probable transcriptional regulatory protein 2C len: 210 aa 3B similar to members of the tetR family e.g. TR:G3327947 28EMBL:AF053772 29 Staphylococcus aureus transcriptional regulator qacR 28regulator of multidrug efflux protein QacB 29 28188 aa 29 2C fasta scores 3B opt: 162 z-score: 285.0 E 28 29: 1.3e-08 2C 29.3 25 identity in 198 aa overlap 2C and MTRR_NEIGO regulatory protein MTRR 28210 aa 29 2C fasta scores 3B opt: 137 z-score: 210.6 E 28 29: 0.00018 2C 31.3 25 identity in 83 aa overlap. No Hp match. Contains Pfam match to entry PF00440 tetR 2C Bacterial regulatory proteins 2C tetR family 2C score 24.00 2C E-value 6.4e-05 7EUpdated 282006 29 note: Characterised within Campylobacter jejuni. Product function modified to more speicific family member. Characterisation paper shows that CmeR is a transcriptional repressor for the downstream CmeABC operon. Functional classification - Broad regulatory functions 7EPMID:15728904 NC_002163.1 RefSeq gene 336916 337548 . - . ID=gene337;gene=cmeR;Name=cmeR;locus_tag=Cj0368c;Dbxref=GeneID:904691;gbkey=Gene NC_002163.1 RefSeq region 337357 337497 . - . ID=id758;gene=cmeR;Name=id758;Dbxref=GeneID:904691;gbkey=misc_feature;Note=HMMPfam hit to PF00440 2C Bacterial regulatory proteins 2C tetR family 2C score 7.1e-10 NC_002163.1 RefSeq gene 337535 338911 . - . ID=gene338;Name=Cj0369c;locus_tag=Cj0369c;Dbxref=GeneID:904692;gbkey=Gene NC_002163.1 RefSeq CDS 337535 338911 . - 0 ID=cds327;Parent=gene338;Name=YP_002343806.1;Dbxref=GOA:Q0PBE1 InterPro:IPR001450 InterPro:IPR014116 UniProtKB FTrEMBL:Q0PBE1 Genbank:YP_002343806.1 GeneID:904692;gbkey=CDS;product=ferredoxin domain-containing integral membrane protein;Note=Original 282000 29 note: Cj0369c 2C ferredoxin domain-containing integral membrane protein 2C len: 458 aa 3B some similarity to e.g. RDXA_RHOSH RDXA protein 28469 aa 29 2Cfasta scores 3B opt: 474 z-score: 657.7 E 28 29: 2.2e-29 2C 24.9 25 identity in 402 aa overlap 2C and FIXG_RHIME nitrogen fixation protein FIXG 28524 aa 29 2C fasta scores 3B opt: 476 z-score: 533.8 E 28 29: 1.8e-22 2C 28.7 25 identity in 296 aa overlap. 45.7 25 identity to HP1508. Contains PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature and Pfam match to entry PF00037 fer4 2C 4Fe-4S ferredoxins and related iron-sulfur cluster binding domains. 2C score 17.10 2CE-value 0.0011 7EUpdated 282006 29 note: Five probable transmembrace helices identified by TMHMM2.0 within CDS. Further support given to product function. No specific characterisation with acceptable identity scores identified yet. kept within product function. Functional classification -Energy metabolism - Electron transport NC_002163.1 RefSeq region 337946 338014 . - . ID=id34;Name=id34;Dbxref=GeneID:904692;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0369c by TMHMM2.0 at aa 13-31 2C 58-80 2C 127-149 2C 164-186 and 300-322 NC_002163.1 RefSeq region 338153 338224 . - . ID=id759;Name=id759;Dbxref=GeneID:904692;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 0.0014 NC_002163.1 RefSeq region 338168 338203 . - . ID=id760;Name=id760;Dbxref=GeneID:904692;gbkey=misc_feature;Note=PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature NC_002163.1 RefSeq region 338354 338422 . - . ID=id34;Name=id34;Dbxref=GeneID:904692;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0369c by TMHMM2.0 at aa 13-31 2C 58-80 2C 127-149 2C 164-186 and 300-322 NC_002163.1 RefSeq region 338465 338533 . - . ID=id34;Name=id34;Dbxref=GeneID:904692;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0369c by TMHMM2.0 at aa 13-31 2C 58-80 2C 127-149 2C 164-186 and 300-322 NC_002163.1 RefSeq region 338672 338740 . - . ID=id34;Name=id34;Dbxref=GeneID:904692;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0369c by TMHMM2.0 at aa 13-31 2C 58-80 2C 127-149 2C 164-186 and 300-322 NC_002163.1 RefSeq region 338819 338875 . - . ID=id34;Name=id34;Dbxref=GeneID:904692;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0369c by TMHMM2.0 at aa 13-31 2C 58-80 2C 127-149 2C 164-186 and 300-322 ### NC_002163.1 UTR_Extractor 5'-UTR 338912 338946 . - . ID=utr136;locus_tag=Cj0369c;product=putative ferredoxin domain-containing integral membrane protein NC_002163.1 UTR_Extractor 5'-UTR 339034 339070 . + . ID=utr137;locus_tag=Cj0370;product=30S ribosomal protein S21 NC_002163.1 RefSeq gene 339071 339283 . + . ID=gene339;gene=rpsU;Name=rpsU;locus_tag=Cj0370;Dbxref=GeneID:904693;gbkey=Gene NC_002163.1 RefSeq CDS 339071 339283 . + 0 ID=cds328;Parent=gene339;gene=rpsU;Name=YP_002343807.1;Dbxref=GOA:Q9PID2 InterPro:IPR001911 UniProtKB FSwiss-Prot:Q9PID2 Genbank:YP_002343807.1 GeneID:904693;gbkey=CDS;product=30S ribosomal protein S21;Note=a small basic protein that is one of the last in the subunit assembly 3B omission does not prevent assembly but the subunit is inactive 3B binds central domain of 16S rRNA NC_002163.1 RefSeq region 339074 339235 . + . ID=id761;gene=rpsU;Name=id761;Dbxref=GeneID:904693;gbkey=misc_feature;Note=HMMPfam hit to PF01165 2C Ribosomal protein S21 2Cscore 1.1e-24 ### NC_002163.1 UTR_Extractor 5'-UTR 339373 339402 . + . ID=utr138;locus_tag=Cj0371;product=hypothetical protein NC_002163.1 RefSeq CDS 339403 340008 . + 0 ID=cds329;Parent=gene340;Name=YP_002343808.1;Dbxref=GOA:Q9PID1 UniProtKB FSwiss-Prot:Q9PID1 Genbank:YP_002343808.1 GeneID:904694;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0371 2C probable lipoprotein 2Clen: 201 aa 3B similar to H. pylori gene fragment reported to be involved in flagellar motility TR:Q48273 28EMBL:Z68311 29 28122 aa 29 2C fasta scores 3B opt: 322 z-score: 449.5 E 28 29: 8.8e-18 2C 46.1 25 identity in 115 aa overlap. 46.4 25 identity to HP0232. Contains N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site 7EUpdated 282006 29 note: One probable transmembrace helices identified by TMHMM2.0 within CDS. Some similarity to Helicobacter pylori gene fragment. kept within product function. Functional classification - Surface structures 7EPMID:8733234 NC_002163.1 RefSeq gene 339403 340008 . + . ID=gene340;Name=Cj0371;locus_tag=Cj0371;Dbxref=GeneID:904694;gbkey=Gene NC_002163.1 RefSeq region 339421 339489 . + . ID=id762;Name=id762;Dbxref=GeneID:904694;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0371 by TMHMM2.0 at aa 7-29 NC_002163.1 RefSeq region 339451 339483 . + . ID=id763;Name=id763;Dbxref=GeneID:904694;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq region 340018 341181 . + . ID=id764;Name=id764;Dbxref=GeneID:904695;gbkey=misc_feature;Note=HMMPfam hit to PF03738 2C Glutathionylspermidine synthase 2C score 3.6e-252 NC_002163.1 RefSeq gene 340018 341187 . + . ID=gene341;Name=Cj0372;locus_tag=Cj0372;Dbxref=GeneID:904695;gbkey=Gene NC_002163.1 RefSeq CDS 340018 341187 . + 0 ID=cds330;Parent=gene341;Name=YP_002343809.1;Dbxref=GOA:Q0PBD8 InterPro:IPR005494 UniProtKB FTrEMBL:Q0PBD8 Genbank:YP_002343809.1 GeneID:904695;gbkey=CDS;product=glutathionylspermidine synthase;Note=Original 282000 29 note: Cj0372 2C unknown 2C len: 389 aa 3B similar to hypothetical proteins e.g. YGIC_ECOLI 28386 aa 29 2Cfasta scores 3B opt: 552 z-score: 508.4 E 28 29: 4.6e-21 2C 31.3 25 identity in 383 aa overlap. Also similar to N-terminus of GSP_ECOLI glutathionylspermidine synthase 28619 aa 29 2C fasta scores 3B opt: 314 z-score: 248.3 E 28 29: 1.4e-06 2C 24.4 25 identity in 381 aa overlap. 60.5 25 identity to HP0233 7EUpdated 282006 29 note: Pfam domain PF03738 Glutathionylspermidine synthase identified within CDS. Characterised within Escherichia coli with marginal identity score. Amidase component is most likely not present due to absence at N-terminal end when aligned to Escherichia coli. Product modified to more specific family member based on motif match and characterisation. kept within product function. Functional classification -Misc 7EPMID:7775463 2C PMID:9398217 NC_002163.1 UTR_Extractor 5'-UTR 340982 341189 . + . ID=utr139;locus_tag=Cj0373;product=2-hydroxyacid dehydrogenase ### NC_002163.1 RefSeq CDS 341190 342125 . + 0 ID=cds331;Parent=gene342;Name=YP_002343810.1;Dbxref=GOA:Q0PBD7 InterPro:IPR006139 InterPro:IPR006140 InterPro:IPR016040 UniProtKB FTrEMBL:Q0PBD7 Genbank:YP_002343810.1 GeneID:904696;gbkey=CDS;product=2-hydroxyacid dehydrogenase;Note=Involved in the metabolism of aromatic amino acids NC_002163.1 RefSeq gene 341190 342125 . + . ID=gene342;Name=Cj0373;locus_tag=Cj0373;Dbxref=GeneID:904696;gbkey=Gene NC_002163.1 RefSeq region 341196 341471 . + . ID=id765;Name=id765;Dbxref=GeneID:904696;gbkey=misc_feature;Note=HMMPfam hit to PF00389 2C D-isomer specific 2-hydroxyacid dehydrog 2C score 3.7e-21 NC_002163.1 RefSeq region 341487 342038 . + . ID=id766;Name=id766;Dbxref=GeneID:904696;gbkey=misc_feature;Note=HMMPfam hit to PF02826 2C D-isomer specific 2-hydroxyacid dehydrog 2C score 1.4e-41 NC_002163.1 RefSeq region 341853 341903 . + . ID=id767;Name=id767;Dbxref=GeneID:904696;gbkey=misc_feature;Note=PS00671 D-isomer specific 2-hydroxyacid dehydrogenases signature 3 NC_002163.1 RefSeq gene 342115 342606 . + . ID=gene343;Name=Cj0374;locus_tag=Cj0374;Dbxref=GeneID:904697;gbkey=Gene NC_002163.1 RefSeq CDS 342115 342606 . + 0 ID=cds332;Parent=gene343;Name=YP_002343811.1;Dbxref=GOA:Q9PIC8 HSSP:P44096 InterPro:IPR007551 UniProtKB FSwiss-Prot:Q9PIC8 Genbank:YP_002343811.1 GeneID:904697;gbkey=CDS;product=nucleotide-binding protein;Note=nucleotide binding property based on structural studies of Haemophilus influenzae crystallized protein in PDB Accession Number 1IN0 and NMR studies of Escherichia coli YajQ 3B the YajQ protein from Pseudomonas synringae appears to play a role in activation of bateriophage phi6 segment L transcription NC_002163.1 RefSeq region 342124 342603 . + . ID=id768;Name=id768;Dbxref=GeneID:904697;gbkey=misc_feature;Note=HMMPfam hit to PF04461 2C Protein of unknown function 28DUF520 29 2C score 3.7e-100 ### NC_002163.1 RefSeq CDS 342615 343091 . + 0 ID=cds333;Parent=gene344;Name=YP_002343812.1;Dbxref=GOA:Q0PBD5 UniProtKB FTrEMBL:Q0PBD5 Genbank:YP_002343812.1 GeneID:904698;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj0375 2C probable lipoprotein 2Clen: 158 aa 3B no Hp match. Contains N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 342615 343091 . + . ID=gene344;Name=Cj0375;locus_tag=Cj0375;Dbxref=GeneID:904698;gbkey=Gene NC_002163.1 RefSeq region 342630 342662 . + . ID=id769;Name=id769;Dbxref=GeneID:904698;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 UTR_Extractor 5'-UTR 343057 343101 . + . ID=utr140;locus_tag=Cj0376;product=putative periplasmic protein ### NC_002163.1 RefSeq CDS 343102 343926 . + 0 ID=cds334;Parent=gene345;Name=YP_002343813.1;Dbxref=UniProtKB FTrEMBL:Q0PBD4 Genbank:YP_002343813.1 GeneID:904699;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0376 2C possible periplasmic protein 2C len: 274 aa 3B no Hp match. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Literature search identified paper linking protein to glycoprotein. Functional classification - Miscellaneous periplasmic proteins 7EPMID:12186869 NC_002163.1 RefSeq gene 343102 343926 . + . ID=gene345;Name=Cj0376;locus_tag=Cj0376;Dbxref=GeneID:904699;gbkey=Gene NC_002163.1 RefSeq CDS 343926 345638 . + 0 ID=cds335;Parent=gene346;Name=YP_002343814.1;Dbxref=GOA:Q0PBD3 InterPro:IPR003593 InterPro:IPR003959 UniProtKB FTrEMBL:Q0PBD3 Genbank:YP_002343814.1 GeneID:904700;gbkey=CDS;product=AAA ATPase;Note=Original 282000 29 note: Cj0377 2C probable ATPase 2C len: 570 aa 3B weak similarity to many members of the AAA family e.g. TR:O28182 28EMBL:O28182 29 cell division control protein 48 28Archaeoglobus fulgidus AF2098 29 28811 aa 29 2C fasta scores 3B opt: 341 z-score: 312.6 E 28 29: 3.7e-10 2C 26.4 25 identity in 435 aa overlap. No Hp match. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 and Pfam match to entry PF00004 AAA 2C ATPases associated with various cellular activities 28AAA 29 2C score 106.20 2C E-value 6.3e-28 7EUpdated 282006 29 note: Probable changed to . No specific characterisation with acceptable identity scores carried out yet. Functional classification - Misc NC_002163.1 RefSeq gene 343926 345638 . + . ID=gene346;Name=Cj0377;locus_tag=Cj0377;Dbxref=GeneID:904700;gbkey=Gene NC_002163.1 RefSeq region 344985 345542 . + . ID=id770;Name=id770;Dbxref=GeneID:904700;gbkey=misc_feature;Note=HMMPfam hit to PF00004 2C ATPase family associated with various cellul 2C score 1.4e-36 NC_002163.1 RefSeq region 345000 345023 . + . ID=id771;Name=id771;Dbxref=GeneID:904700;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq gene 345635 346174 . - . ID=gene347;Name=Cj0378c;locus_tag=Cj0378c;Dbxref=GeneID:904701;gbkey=Gene NC_002163.1 RefSeq CDS 345635 346174 . - 0 ID=cds336;Parent=gene347;Name=YP_002343815.1;Dbxref=GOA:Q0PBD2 InterPro:IPR013130 UniProtKB FTrEMBL:Q0PBD2 Genbank:YP_002343815.1 GeneID:904701;gbkey=CDS;product=ferric reductase-like transmembrane protein;Note=Original 282000 29 note: Cj0378c 2C probable integral membrane protein 2C len: 179 aa 3B no Hp match 7EUpdated 282006 29 note: Pfam domain PF01794 ferric reductase like transmembrane component identified within CDS. This was from a separate Pfam search. Pfam domain PF05252 Uncharacterised protein family 28UPF0191 29 identified within CDS. Six probable transmembrace helices identified by TMHMM2.0 within CDS. Product functionality changed due to motif match. Literature search identified paper giving further support to product function. No specific characterisation has been carried out yet. kept within product function 7EPMID:15632442 NC_002163.1 RefSeq region 345638 346171 . - . ID=id772;Name=id772;Dbxref=GeneID:904701;gbkey=misc_feature;Note=HMMPfam hit to PF05252 2C Uncharacterised protein family 28UPF0191 29 2C score 1.2e-08 NC_002163.1 RefSeq region 345662 345718 . - . ID=id35;Name=id35;Dbxref=GeneID:904701;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0378c by TMHMM2.0 at aa 7-26 2C 36-55 2C 67-86 2C 101-123 2C135-149 and 153-171 NC_002163.1 RefSeq region 345728 345772 . - . ID=id35;Name=id35;Dbxref=GeneID:904701;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0378c by TMHMM2.0 at aa 7-26 2C 36-55 2C 67-86 2C 101-123 2C135-149 and 153-171 NC_002163.1 RefSeq region 345806 345874 . - . ID=id35;Name=id35;Dbxref=GeneID:904701;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0378c by TMHMM2.0 at aa 7-26 2C 36-55 2C 67-86 2C 101-123 2C135-149 and 153-171 NC_002163.1 RefSeq region 345917 345976 . - . ID=id35;Name=id35;Dbxref=GeneID:904701;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0378c by TMHMM2.0 at aa 7-26 2C 36-55 2C 67-86 2C 101-123 2C135-149 and 153-171 NC_002163.1 RefSeq region 346010 346069 . - . ID=id35;Name=id35;Dbxref=GeneID:904701;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0378c by TMHMM2.0 at aa 7-26 2C 36-55 2C 67-86 2C 101-123 2C135-149 and 153-171 NC_002163.1 RefSeq region 346097 346156 . - . ID=id35;Name=id35;Dbxref=GeneID:904701;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0378c by TMHMM2.0 at aa 7-26 2C 36-55 2C 67-86 2C 101-123 2C135-149 and 153-171 NC_002163.1 RefSeq gene 346174 347067 . - . ID=gene348;Name=Cj0379c;locus_tag=Cj0379c;Dbxref=GeneID:904702;gbkey=Gene NC_002163.1 RefSeq CDS 346174 347067 . - 0 ID=cds337;Parent=gene348;Name=YP_002343816.1;Dbxref=GOA:Q9PIC3 InterPro:IPR000572 UniProtKB FSwiss-Prot:Q9PIC3 Genbank:YP_002343816.1 GeneID:904702;gbkey=CDS;product=sulfite oxidase subunit YedY;Note=in Escherichia coli this periplasmic enzyme was found to encode the periplasmic catalytic subunit of an oxidoreductase 3B sulfite oxidase activity not demonstrated 3B requires inner membrane anchor protein YedZ NC_002163.1 RefSeq region 346360 346917 . - . ID=id773;Name=id773;Dbxref=GeneID:904702;gbkey=misc_feature;Note=HMMPfam hit to PF00174 2C Oxidoreductase molybdopterin binding d 2C score 3.2e-05 ### NC_002163.1 RefSeq CDS 347123 347908 . - 0 ID=cds338;Parent=gene349;Name=YP_002343817.1;Dbxref=UniProtKB FTrEMBL:Q0PBD0 Genbank:YP_002343817.1 GeneID:904703;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0380c 2C unknonw 2C len: 261 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 RefSeq gene 347123 347908 . - . ID=gene349;Name=Cj0380c;locus_tag=Cj0380c;Dbxref=GeneID:904703;gbkey=Gene NC_002163.1 RefSeq gene 347905 348744 . - . ID=gene350;gene=pyrF;Name=pyrF;locus_tag=Cj0381c;Dbxref=GeneID:904704;gbkey=Gene NC_002163.1 RefSeq CDS 347905 348744 . - 0 ID=cds339;Parent=gene350;gene=pyrF;Name=YP_002343818.1;Dbxref=GOA:Q9PIC1 HSSP:P25971 InterPro:IPR001754 InterPro:IPR013785 InterPro:IPR014732 UniProtKB FSwiss-Prot:Q9PIC1 Genbank:YP_002343818.1 GeneID:904704;gbkey=CDS;product=orotidine 5 27-phosphate decarboxylase;Note=type 1 subfamily 3B involved in last step of pyrimidine biosynthesis 3B converts orotidine 5 27-phosphate to UMP and carbon dioxide 3B OMP decarboxylase 3B OMPDCase 3B OMPdecase NC_002163.1 RefSeq region 348079 348744 . - . ID=id774;gene=pyrF;Name=id774;Dbxref=GeneID:904704;gbkey=misc_feature;Note=HMMPfam hit to PF00215 2C Orotidine 5 27-phosphate decarboxylase 2F HUMP 2C score 7.3e-82 NC_002163.1 RefSeq region 348541 348582 . - . ID=id775;gene=pyrF;Name=id775;Dbxref=GeneID:904704;gbkey=misc_feature;Note=PS00156 Orotidine 5 27-phosphate decarboxylase active site NC_002163.1 RefSeq CDS 348741 349139 . - 0 ID=cds340;Parent=gene351;gene=nusB;Name=YP_002343819.1;Dbxref=GOA:Q9PIC0 HSSP:P95020 InterPro:IPR006027 InterPro:IPR011605 UniProtKB FSwiss-Prot:Q9PIC0 Genbank:YP_002343819.1 GeneID:904705;gbkey=CDS;product=transcription antitermination protein NusB;Note=Regulates rRNA biosynthesis by transcriptional antitermination NC_002163.1 RefSeq gene 348741 349139 . - . ID=gene351;gene=nusB;Name=nusB;locus_tag=Cj0382c;Dbxref=GeneID:904705;gbkey=Gene NC_002163.1 RefSeq region 348747 349127 . - . ID=id776;gene=nusB;Name=id776;Dbxref=GeneID:904705;gbkey=misc_feature;Note=HMMPfam hit to PF01029 2C NusB family 2C score 1.9e-36 NC_002163.1 RefSeq CDS 349139 349603 . - 0 ID=cds341;Parent=gene352;gene=ribH;Name=YP_002343820.1;Dbxref=GOA:Q9PIB9 HSSP:O66529 InterPro:IPR002180 UniProtKB FSwiss-Prot:Q9PIB9 Genbank:YP_002343820.1 GeneID:904706;gbkey=CDS;product=6 2C7-dimethyl-8-ribityllumazine synthase;Note=RibE 3B 6 2C7-diimethyl-8-ribityllumazine synthase 3B DMRL synthase 3B lumazine synthase 3B beta subunit of riboflavin synthase 3B condenses 5-amino-6- 281 27-D 29-ribityl-amino-2 2C4 281H 2C3H 29-pyrimidinedione with L-3 2C4-dihydrohy-2-butanone-4-phosphate to generate 6 2C6-dimethyl-8-lumazine 28DMRL 29 3B riboflavin synthase then uses 2 molecules of DMRL to produce riboflavin 28vitamin B12 29 3B involved in the last steps of riboflavin biosynthesis 3B forms a 60mer 28icosahedral shell 29 in both Bacillus subtilis and Escherichia coli 3B in Bacillus subtilis this 60mer is associated with the riboflavin synthase subunit 28alpha 29 while in Escherichia coli it is not NC_002163.1 RefSeq gene 349139 349603 . - . ID=gene352;gene=ribH;Name=ribH;locus_tag=Cj0383c;Dbxref=GeneID:904706;gbkey=Gene NC_002163.1 RefSeq region 349142 349573 . - . ID=id777;gene=ribH;Name=id777;Dbxref=GeneID:904706;gbkey=misc_feature;Note=HMMPfam hit to PF00885 2C6 2C7-dimethyl-8-ribityllumazine synthase 2C score 1.8e-77 NC_002163.1 RefSeq gene 349600 350415 . - . ID=gene353;gene=kdsA;Name=kdsA;locus_tag=Cj0384c;Dbxref=GeneID:904707;gbkey=Gene NC_002163.1 RefSeq CDS 349600 350415 . - 0 ID=cds342;Parent=gene353;gene=kdsA;Name=YP_002343821.1;Dbxref=GOA:Q9PIB8 HSSP:O66496 InterPro:IPR006218 InterPro:IPR006269 InterPro:IPR013785 UniProtKB FSwiss-Prot:Q9PIB8 Genbank:YP_002343821.1 GeneID:904707;gbkey=CDS;product=2-dehydro-3-deoxyphosphooctonate aldolase;Note=catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis NC_002163.1 RefSeq region 349609 350415 . - . ID=id778;gene=kdsA;Name=id778;Dbxref=GeneID:904707;gbkey=misc_feature;Note=HMMPfam hit to PF00793 2C DAHP synthetase I family 2Cscore 9.7e-105 NC_002163.1 RefSeq region 349783 349806 . - . ID=id779;gene=kdsA;Name=id779;Dbxref=GeneID:904707;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq gene 350412 351344 . - . ID=gene354;Name=Cj0385c;locus_tag=Cj0385c;Dbxref=GeneID:904708;gbkey=Gene NC_002163.1 RefSeq CDS 350412 351344 . - 0 ID=cds343;Parent=gene354;Name=YP_002343822.1;Dbxref=GOA:Q0PBC5 InterPro:IPR000620 UniProtKB FTrEMBL:Q0PBC5 Genbank:YP_002343822.1 GeneID:904708;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0385c 2C probable integral membrane protein 2C len: 310 aa 3B similar to many hypothetical integral membrane proteins e.g. TR:O29973 28EMBL:AE001087 29 Archaeoglobus fulgidus AF0266 28276 aa 29 2Cfasta scores 3B opt: 155 z-score: 221.8 E 28 29: 4.5e-05 2C 26.9 25 identity in 279 aa overlap. 30.8 25 identity to HP1234. Contains Pfam match to entry PF00892 DUF6 2C Integral membrane protein 2C score 29.90 2C E-value 5.9e-05 7EUpdated 282006 29 note: Pfam domain PF00892 Integral membrane protein DUF6 identified within CDS. Ten probable transmembrace helices identified by TMHMM2.0 within CDS. Further support given to product function. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 UTR_Extractor 5'-UTR 350416 350459 . - . ID=utr141;locus_tag=Cj0384c;product=2-dehydro-3-deoxyphosphooctonate aldolase NC_002163.1 RefSeq region 350433 350492 . - . ID=id36;Name=id36;Dbxref=GeneID:904708;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0385c by TMHMM2.0 at aa 9-28 2C 38-56 2C 65-87 2C 97-116 2C121-143 2C 156-173 2C 185-207 2C 217-239 2C 259-281 and 285-304 NC_002163.1 RefSeq region 350502 350570 . - . ID=id36;Name=id36;Dbxref=GeneID:904708;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0385c by TMHMM2.0 at aa 9-28 2C 38-56 2C 65-87 2C 97-116 2C121-143 2C 156-173 2C 185-207 2C 217-239 2C 259-281 and 285-304 NC_002163.1 RefSeq region 350628 350696 . - . ID=id36;Name=id36;Dbxref=GeneID:904708;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0385c by TMHMM2.0 at aa 9-28 2C 38-56 2C 65-87 2C 97-116 2C121-143 2C 156-173 2C 185-207 2C 217-239 2C 259-281 and 285-304 NC_002163.1 RefSeq region 350724 350792 . - . ID=id36;Name=id36;Dbxref=GeneID:904708;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0385c by TMHMM2.0 at aa 9-28 2C 38-56 2C 65-87 2C 97-116 2C121-143 2C 156-173 2C 185-207 2C 217-239 2C 259-281 and 285-304 NC_002163.1 RefSeq region 350826 350879 . - . ID=id36;Name=id36;Dbxref=GeneID:904708;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0385c by TMHMM2.0 at aa 9-28 2C 38-56 2C 65-87 2C 97-116 2C121-143 2C 156-173 2C 185-207 2C 217-239 2C 259-281 and 285-304 NC_002163.1 RefSeq region 350916 350984 . - . ID=id36;Name=id36;Dbxref=GeneID:904708;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0385c by TMHMM2.0 at aa 9-28 2C 38-56 2C 65-87 2C 97-116 2C121-143 2C 156-173 2C 185-207 2C 217-239 2C 259-281 and 285-304 NC_002163.1 RefSeq region 350925 351290 . - . ID=id780;Name=id780;Dbxref=GeneID:904708;gbkey=misc_feature;Note=HMMPfam hit to PF00892 2C Integral membrane protein DUF6 2C score 6.9e-16 NC_002163.1 RefSeq region 350997 351056 . - . ID=id36;Name=id36;Dbxref=GeneID:904708;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0385c by TMHMM2.0 at aa 9-28 2C 38-56 2C 65-87 2C 97-116 2C121-143 2C 156-173 2C 185-207 2C 217-239 2C 259-281 and 285-304 NC_002163.1 RefSeq region 351084 351152 . - . ID=id36;Name=id36;Dbxref=GeneID:904708;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0385c by TMHMM2.0 at aa 9-28 2C 38-56 2C 65-87 2C 97-116 2C121-143 2C 156-173 2C 185-207 2C 217-239 2C 259-281 and 285-304 NC_002163.1 RefSeq region 351177 351233 . - . ID=id36;Name=id36;Dbxref=GeneID:904708;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0385c by TMHMM2.0 at aa 9-28 2C 38-56 2C 65-87 2C 97-116 2C121-143 2C 156-173 2C 185-207 2C 217-239 2C 259-281 and 285-304 NC_002163.1 RefSeq region 351261 351320 . - . ID=id36;Name=id36;Dbxref=GeneID:904708;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0385c by TMHMM2.0 at aa 9-28 2C 38-56 2C 65-87 2C 97-116 2C121-143 2C 156-173 2C 185-207 2C 217-239 2C 259-281 and 285-304 NC_002163.1 RefSeq region 351291 351323 . - . ID=id781;Name=id781;Dbxref=GeneID:904708;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 UTR_Extractor 5'-UTR 351345 351366 . - . ID=utr142;locus_tag=Cj0385c;product=putative integral membrane protein NC_002163.1 UTR_Extractor 5'-UTR 351421 351445 . + . ID=utr143;locus_tag=Cj0386;product=GTP-binding protein EngA NC_002163.1 RefSeq CDS 351446 352828 . + 0 ID=cds344;Parent=gene355;gene=engA;Name=YP_002343823.1;Dbxref=GOA:Q9PIB6 HSSP:Q9X1F8 InterPro:IPR002917 InterPro:IPR005225 InterPro:IPR005289 InterPro:IPR006073 InterPro:IPR016484 UniProtKB FSwiss-Prot:Q9PIB6 Genbank:YP_002343823.1 GeneID:904709;gbkey=CDS;product=GTP-binding protein EngA;Note=EngA 3B essential Neisserial GTPase 3B synchronizes cellular events by interacting with multiple targets with tandem G-domains 3B overexpression in Escherichia coli suppresses rrmJ mutation 3B structural analysis of the Thermotoga maritima ortholog shows different nucleotide binding affinities in the two binding domains NC_002163.1 RefSeq gene 351446 352828 . + . ID=gene355;gene=engA;Name=engA;locus_tag=Cj0386;Dbxref=GeneID:904709;gbkey=Gene NC_002163.1 RefSeq region 351449 351802 . + . ID=id782;gene=engA;Name=id782;Dbxref=GeneID:904709;gbkey=misc_feature;Note=HMMPfam hit to PF01926 2C GTPase of unknown function 2Cscore 2.7e-36 NC_002163.1 RefSeq region 351467 351490 . + . ID=id783;gene=engA;Name=id783;Dbxref=GeneID:904709;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 352031 352393 . + . ID=id784;gene=engA;Name=id784;Dbxref=GeneID:904709;gbkey=misc_feature;Note=HMMPfam hit to PF01926 2C GTPase of unknown function 2Cscore 1.3e-39 NC_002163.1 RefSeq region 352049 352072 . + . ID=id785;gene=engA;Name=id785;Dbxref=GeneID:904709;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 UTR_Extractor 5'-UTR 352647 352814 . + . ID=utr144;locus_tag=Cj0387;product=shikimate kinase NC_002163.1 RefSeq CDS 352815 353312 . + 0 ID=cds345;Parent=gene356;gene=aroK;Name=YP_002343824.1;Dbxref=GOA:Q0PBC3 InterPro:IPR000623 PDB:1VIA UniProtKB FTrEMBL:Q0PBC3 Genbank:YP_002343824.1 GeneID:904710;gbkey=CDS;product=shikimate kinase;Note=catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis NC_002163.1 RefSeq gene 352815 353312 . + . ID=gene356;gene=aroK;Name=aroK;locus_tag=Cj0387;Dbxref=GeneID:904710;gbkey=Gene NC_002163.1 RefSeq region 352845 352868 . + . ID=id786;gene=aroK;Name=id786;Dbxref=GeneID:904710;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 352851 353309 . + . ID=id787;gene=aroK;Name=id787;Dbxref=GeneID:904710;gbkey=misc_feature;Note=HMMPfam hit to PF01202 2C Shikimate kinase 2C score 3.6e-48 NC_002163.1 UTR_Extractor 5'-UTR 353216 353308 . + . ID=utr145;locus_tag=Cj0388;product=tryptophanyl-tRNA synthetase NC_002163.1 RefSeq region 353309 354133 . + . ID=id788;gene=trpS;Name=id788;Dbxref=GeneID:904711;gbkey=misc_feature;Note=HMMPfam hit to PF00579 2C tRNA synthetases class I 28W and Y 29 2C score 1.1e-66 NC_002163.1 RefSeq CDS 353309 354268 . + 0 ID=cds346;Parent=gene357;gene=trpS;Name=YP_002343825.1;Dbxref=GOA:Q9PIB4 HSSP:P00953 InterPro:IPR001412 InterPro:IPR002305 InterPro:IPR002306 InterPro:IPR014729 UniProtKB FSwiss-Prot:Q9PIB4 Genbank:YP_002343825.1 GeneID:904711;gbkey=CDS;product=tryptophanyl-tRNA synthetase;Note=catalyzes a two-step reaction 2C first charging a tryptophan molecule by linking its carboxyl group to the alpha-phosphate of ATP 2C followed by transfer of the aminoacyl-adenylate to its tRNA NC_002163.1 RefSeq gene 353309 354268 . + . ID=gene357;gene=trpS;Name=trpS;locus_tag=Cj0388;Dbxref=GeneID:904711;gbkey=Gene NC_002163.1 RefSeq region 353333 353362 . + . ID=id789;gene=trpS;Name=id789;Dbxref=GeneID:904711;gbkey=misc_feature;Note=PS00178 Aminoacyl-transfer RNA synthetases class-I signature ### NC_002163.1 RefSeq region 354279 354590 . + . ID=id790;gene=serS;Name=id790;Dbxref=GeneID:904712;gbkey=misc_feature;Note=HMMPfam hit to PF02403 2C Seryl-tRNA synthetase N-terminal domain 2C score 9.1e-26 NC_002163.1 RefSeq CDS 354279 355514 . + 0 ID=cds347;Parent=gene358;gene=serS;Name=YP_002343826.1;Dbxref=GOA:Q9PIB3 HSSP:P34945 InterPro:IPR002314 InterPro:IPR002317 InterPro:IPR006195 InterPro:IPR015866 UniProtKB FSwiss-Prot:Q9PIB3 Genbank:YP_002343826.1 GeneID:904712;gbkey=CDS;product=seryl-tRNA synthetase;Note=catalyzes a two-step reaction 2C first charging a serine molecule by linking its carboxyl group to the alpha-phosphate of ATP 2C followed by transfer of the aminoacyl-adenylate to its tRNA NC_002163.1 RefSeq gene 354279 355514 . + . ID=gene358;gene=serS;Name=serS;locus_tag=Cj0389;Dbxref=GeneID:904712;gbkey=Gene NC_002163.1 RefSeq region 354750 355214 . + . ID=id791;gene=serS;Name=id791;Dbxref=GeneID:904712;gbkey=misc_feature;Note=HMMPfam hit to PF00587 2C tRNA synthetase class II core domain 28G 2C 2C score 1.4e-52 NC_002163.1 RefSeq region 355044 355118 . + . ID=id792;gene=serS;Name=id792;Dbxref=GeneID:904712;gbkey=misc_feature;Note=PS00179 Aminoacyl-transfer RNA synthetases class-II signature 1 ### NC_002163.1 RefSeq CDS 355524 357986 . + 0 ID=cds348;Parent=gene359;Name=YP_002343827.1;Dbxref=GOA:Q0PBC0 InterPro:IPR001440 InterPro:IPR011990 InterPro:IPR013026 UniProtKB FTrEMBL:Q0PBC0 Genbank:YP_002343827.1 GeneID:904713;gbkey=CDS;product=transmembrane protein;Note=Original 282000 29 note: Cj0390 2C possible transmembrane protein 2C len: 820 aa 3B 28.7 25 identity in 703 aa overlap to HP1479. Contains possible transmembrane domain around aa 100 and Pfam match to entry PF00515 TPR 2CTPR Domain 2C score 26.90 2C E-value 0.00047 7EUpdated 282006 29 note: Pfam domains x4 PF07719 Tetratricopeptide repeat were identified within CDS. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 355524 357986 . + . ID=gene359;Name=Cj0390;locus_tag=Cj0390;Dbxref=GeneID:904713;gbkey=Gene NC_002163.1 RefSeq region 355791 355859 . + . ID=id793;Name=id793;Dbxref=GeneID:904713;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0390 by TMHMM2.0 at aa 90-112 NC_002163.1 RefSeq region 355956 356057 . + . ID=id794;Name=id794;Dbxref=GeneID:904713;gbkey=misc_feature;Note=HMMPfam hit to PF00515 2C Tetratricopeptide repeat 2Cscore 0.12 7EHMMPfam hit to PF07719 2C Tetratricopeptide repeat 2Cscore 0.032 NC_002163.1 RefSeq region 356064 356153 . + . ID=id795;Name=id795;Dbxref=GeneID:904713;gbkey=misc_feature;Note=HMMPfam hit to PF00515 2C Tetratricopeptide repeat 2Cscore 0.43 NC_002163.1 RefSeq region 356451 356552 . + . ID=id796;Name=id796;Dbxref=GeneID:904713;gbkey=misc_feature;Note=HMMPfam hit to PF07719 2C Tetratricopeptide repeat 2Cscore 0.15 7EHMMPfam hit to PF00515 2C Tetratricopeptide repeat 2Cscore 0.034 NC_002163.1 RefSeq region 357018 357119 . + . ID=id797;Name=id797;Dbxref=GeneID:904713;gbkey=misc_feature;Note=HMMPfam hit to PF00515 2C Tetratricopeptide repeat 2Cscore 5.3e-06 7EHMMPfam hit to PF07719 2C Tetratricopeptide repeat 2Cscore 0.00052 NC_002163.1 RefSeq stem_loop 357981 358018 . + . ID=id798;Name=id798;gbkey=stem_loop NC_002163.1 RefSeq CDS 358017 358652 . - 0 ID=cds349;Parent=gene360;Name=YP_002343828.1;Dbxref=UniProtKB FTrEMBL:Q0PBB9 Genbank:YP_002343828.1 GeneID:904714;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0391c 2C unknown 2C len: 211 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Literature search identified paper giving further clues to product function. Functional classification - Unknown NC_002163.1 RefSeq gene 358017 358652 . - . ID=gene360;Name=Cj0391c;locus_tag=Cj0391c;Dbxref=GeneID:904714;gbkey=Gene ### NC_002163.1 UTR_Extractor 5'-UTR 358653 358674 . - . ID=utr146;locus_tag=Cj0391c;product=hypothetical protein NC_002163.1 RefSeq CDS 358750 360192 . - 0 ID=cds350;Parent=gene361;gene=pyk;Name=YP_002343829.1;Dbxref=GOA:Q0PBB8 InterPro:IPR001547 InterPro:IPR001697 InterPro:IPR015793 InterPro:IPR015794 InterPro:IPR015813 UniProtKB FTrEMBL:Q0PBB8 Genbank:YP_002343829.1 GeneID:904715;gbkey=CDS;product=pyruvate kinase;Note=Original 282000 29 note: Cj0392c 2C pyk 2C probable pyruvate kinase 2C len: 480 aa 3B similar to e.g. KPYK_BACSU pyruvate kinase 28EC 2.7.1.40 29 28585 aa 29 2C fasta scores 3B opt: 1111 z-score: 1494.8 E 28 29: 0 2C 41.8 25 identity in 476 aa overlap. No Hp match. Contains PS00659 Glycosyl hydrolases family 5 signature and Pfam match to entry PF00224 PK 2CPyruvate kinase 2C score 523.20 2C E-value 1.8e-153 7EUpdated 282006 29 note: Pfam domain PF02887 Pyruvate kinase 2C alpha 2Fbeta domain protein was identified within CDS. Further support given to product function. Characterised within Bacillus subtilis with acceptable identity score. not added to product function. Functional classification - Energy metabolism -Glycolysis 7EPMID:10932722 NC_002163.1 RefSeq gene 358750 360192 . - . ID=gene361;gene=pyk;Name=pyk;locus_tag=Cj0392c;Dbxref=GeneID:904715;gbkey=Gene NC_002163.1 RefSeq region 358780 359130 . - . ID=id799;gene=pyk;Name=id799;Dbxref=GeneID:904715;gbkey=misc_feature;Note=HMMPfam hit to PF02887 2C Pyruvate kinase 2C alpha 2Fbeta domain 2C score 1.4e-11 NC_002163.1 RefSeq region 359152 360189 . - . ID=id800;gene=pyk;Name=id800;Dbxref=GeneID:904715;gbkey=misc_feature;Note=HMMPfam hit to PF00224 2C Pyruvate kinase 2C barrel domain 2C score 2.4e-135 NC_002163.1 RefSeq region 359623 359652 . - . ID=id801;gene=pyk;Name=id801;Dbxref=GeneID:904715;gbkey=misc_feature;Note=PS00659 Glycosyl hydrolases family 5 signature ### NC_002163.1 RefSeq CDS 360241 361587 . - 0 ID=cds351;Parent=gene362;gene=mqo;Name=YP_002343830.1;Dbxref=GOA:P56954 InterPro:IPR006076 UniProtKB FSwiss-Prot:P56954 Genbank:YP_002343830.1 GeneID:904716;gbkey=CDS;product=malate:quinone oxidoreductase;Note=Original 282000 29 note: Cj0393c 2C possible oxidoreductase 2C len: 448 aa 3B some simlarity to MQO_ECOLI probable malate:quinone oxidoreductase 28548 aa 29 2C fasta scores 3B opt: 121 z-score: 223.1 E 28 29: 3.8e-05 2C 24.6 25 identity in 455 aa overlap. 49.3 25 identity to HP0086. Contains PS00110 Pyruvate kinase active site signature 7EUpdated 282006 29 note: Pfam domain PF06039 Malate:quinone oxidoreductase 28Mqo 29 protein was identified within CDS. Characterised within Helicobacter pylori with acceptable identity score. Product modified to more specific family member due to motif match and characterisation work. kept within product function. Functional classification - Misc 7EPMID:10809701 NC_002163.1 RefSeq gene 360241 361587 . - . ID=gene362;gene=mqo;Name=mqo;locus_tag=Cj0393c;Dbxref=GeneID:904716;gbkey=Gene NC_002163.1 RefSeq region 360244 361584 . - . ID=id802;gene=mqo;Name=id802;Dbxref=GeneID:904716;gbkey=misc_feature;Note=HMMPfam hit to PF06039 2C Malate:quinone oxidoreductase 28Mqo 29 2C score 1.3e-08 NC_002163.1 RefSeq region 360331 360363 . - . ID=id803;gene=mqo;Name=id803;Dbxref=GeneID:904716;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 360667 360705 . - . ID=id804;gene=mqo;Name=id804;Dbxref=GeneID:904716;gbkey=misc_feature;Note=PS00110 Pyruvate kinase active site signature ### NC_002163.1 UTR_Extractor 5'-UTR 361588 361757 . - . ID=utr147;locus_tag=Cj0393c;product=putative malate:quinone oxidoreductase NC_002163.1 RefSeq CDS 361706 362335 . - 0 ID=cds352;Parent=gene363;Name=YP_002343831.1;Dbxref=GOA:Q0PBB6 InterPro:IPR004619 PDB:2NRH UniProtKB FSwiss-Prot:Q0PBB6 Genbank:YP_002343831.1 GeneID:904717;gbkey=CDS;product=pantothenate kinase;Note=type III 3B catalyzes the formation of 28R 29-4 27-phosphopantothenate from 28R 29-pantothenate in coenzyme A biosynthesis 3B type III pantothenate kinases are not subject to feedback inhibition from coenzyme A and have a high Km for ATP NC_002163.1 RefSeq gene 361706 362335 . - . ID=gene363;Name=Cj0394c;locus_tag=Cj0394c;Dbxref=GeneID:904717;gbkey=Gene NC_002163.1 RefSeq region 361838 362335 . - . ID=id805;Name=id805;Dbxref=GeneID:904717;gbkey=misc_feature;Note=HMMPfam hit to PF03309 2C Bordetella pertussis Bvg accessory fac 2C score 7.3e-09 NC_002163.1 RefSeq gene 362322 362612 . - . ID=gene364;Name=Cj0395c;locus_tag=Cj0395c;Dbxref=GeneID:904718;gbkey=Gene NC_002163.1 RefSeq CDS 362322 362612 . - 0 ID=cds353;Parent=gene364;Name=YP_002343832.1;Dbxref=UniProtKB FTrEMBL:Q0PBB5 Genbank:YP_002343832.1 GeneID:904718;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0395c 2C unknown 2C len: 96 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 RefSeq CDS 362609 363607 . - 0 ID=cds354;Parent=gene365;Name=YP_002343833.1;Dbxref=GOA:Q0PBB4 UniProtKB FTrEMBL:Q0PBB4 Genbank:YP_002343833.1 GeneID:904719;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj0396c 2C probable lipoprotein 2C len: 332 aa 3B 28.9 25 identity to HP0863. Conatins N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 362609 363607 . - . ID=gene365;Name=Cj0396c;locus_tag=Cj0396c;Dbxref=GeneID:904719;gbkey=Gene NC_002163.1 RefSeq region 363557 363589 . - . ID=id806;Name=id806;Dbxref=GeneID:904719;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq CDS 363604 364182 . - 0 ID=cds355;Parent=gene366;Name=YP_002343834.1;Dbxref=UniProtKB FTrEMBL:Q0PBB3 Genbank:YP_002343834.1 GeneID:904720;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0397c 2C unknown 2C len: 192 aa 3B almost identical to C. jejuni hypothetical protein fragment TR:Q46096 28EMBL:U27272 29 2C 28.5 25 identity to HP0864 7EUpdated 282006 29 note: One probable transmembrace helices identified by TMHMM2.0 within CDS. Literature serach identified paper giving further clues about product function. Functional classification - Conserved hypothetical proteins 7EPMID:10913692 NC_002163.1 RefSeq gene 363604 364182 . - . ID=gene366;Name=Cj0397c;locus_tag=Cj0397c;Dbxref=GeneID:904720;gbkey=Gene NC_002163.1 RefSeq region 364018 364077 . - . ID=id807;Name=id807;Dbxref=GeneID:904720;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0397c by TMHMM2.0 at aa 36-55 ### NC_002163.1 UTR_Extractor 5'-UTR 364183 364226 . - . ID=utr148;locus_tag=Cj0397c;product=hypothetical protein NC_002163.1 UTR_Extractor 5'-UTR 364294 364325 . + . ID=utr149;locus_tag=Cj0398;product=aspartyl 2Fglutamyl-tRNA amidotransferase subunit C NC_002163.1 RefSeq gene 364326 364610 . + . ID=gene367;gene=gatC;Name=gatC;locus_tag=Cj0398;Dbxref=GeneID:904721;gbkey=Gene NC_002163.1 RefSeq CDS 364326 364610 . + 0 ID=cds356;Parent=gene367;gene=gatC;Name=YP_002343835.1;Dbxref=GOA:Q9PIA5 InterPro:IPR003837 UniProtKB FSwiss-Prot:Q9PIA5 Genbank:YP_002343835.1 GeneID:904721;gbkey=CDS;product=aspartyl 2Fglutamyl-tRNA amidotransferase subunit C;Note=allows the formation of correctly charged Asn-tRNA 28Asn 29 or Gln-tRNA 28Gln 29 through the transamidation of misacylated Asp-tRNA 28Asn 29 or Glu-tRNA 28Gln 29 in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases 3B reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA 28Asn 29 or phospho-Glu-tRNA 3B some Mycoplasma proteins contain an N-terminal fusion to an unknown domain NC_002163.1 RefSeq region 364380 364592 . + . ID=id808;gene=gatC;Name=id808;Dbxref=GeneID:904721;gbkey=misc_feature;Note=HMMPfam hit to PF02686 2C Glu-tRNAGln amidotransferase C subunit 2C score 5.1e-09 ### NC_002163.1 RefSeq CDS 364678 365241 . + 0 ID=cds357;Parent=gene368;Name=YP_002343836.1;Dbxref=GOA:Q0PBB1 InterPro:IPR003825 UniProtKB FTrEMBL:Q0PBB1 Genbank:YP_002343836.1 GeneID:904722;gbkey=CDS;product=colicin V production protein;Note=Original 282000 29 note: Cj0399 2C probable integral membrane protein 2C len: 187 aa 3B identical to C. jejuni hypothetical protein fragment TR:O68605 28EMBL:AF052056 29 28123 aa 29. 26.9 25 identity in 171 aa overlap to HP0181 28224 aa 29 7EUpdated 282006 29 note: Four probable transmembrace helices identified by TMHMM2.0 within CDS. Pfam domain PF02674 Colicin V production protein identified within CDS. Product modified to more speicific family member based on motif matches. No specific characterisation with acceptable identity score has been carried out yet. kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 364678 365241 . + . ID=gene368;Name=Cj0399;locus_tag=Cj0399;Dbxref=GeneID:904722;gbkey=Gene NC_002163.1 RefSeq region 364690 364758 . + . ID=id810;Name=id810;Dbxref=GeneID:904722;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0399 by TMHMM2.0 at aa 5-27 2C 31-48 2C 68-90 and 105-127 NC_002163.1 RefSeq region 364690 365163 . + . ID=id809;Name=id809;Dbxref=GeneID:904722;gbkey=misc_feature;Note=HMMPfam hit to PF02674 2C Colicin V production protein 2C score 1.4e-48 NC_002163.1 RefSeq region 364768 364821 . + . ID=id810;Name=id810;Dbxref=GeneID:904722;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0399 by TMHMM2.0 at aa 5-27 2C 31-48 2C 68-90 and 105-127 NC_002163.1 RefSeq region 364879 364947 . + . ID=id810;Name=id810;Dbxref=GeneID:904722;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0399 by TMHMM2.0 at aa 5-27 2C 31-48 2C 68-90 and 105-127 NC_002163.1 RefSeq region 364894 364926 . + . ID=id811;Name=id811;Dbxref=GeneID:904722;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 364990 365058 . + . ID=id810;Name=id810;Dbxref=GeneID:904722;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0399 by TMHMM2.0 at aa 5-27 2C 31-48 2C 68-90 and 105-127 ### NC_002163.1 RefSeq gene 365243 365716 . + . ID=gene369;gene=fur;Name=fur;locus_tag=Cj0400;Dbxref=GeneID:904724;gbkey=Gene NC_002163.1 RefSeq CDS 365243 365716 . + 0 ID=cds358;Parent=gene369;gene=fur;Name=YP_002343837.1;Dbxref=GOA:P0C631 GOA:P48796 InterPro:IPR002481 UniProtKB FSwiss-Prot:P0C631 Genbank:YP_002343837.1 GeneID:904724;gbkey=CDS;product=ferric uptake regulator;Note=Original 282000 29 note: Cj0400 2C fur 2C ferric uptake regulator 2C len: 157 aa 3B identical to FUR_CAMJE ferric uptake regulation protein 2C and highly simliar to many others e.g. FUR_BORPE 28139 aa 29 2C fasta scores 3B opt: 354 z-score: 552.9 E 28 29: 1.7e-23 41.6 25 identity in 137 aa overlap. 40.8 25 identity to HP1027 7EUpdated 282006 29 note: Pfam domain PF01475 Ferric uptake regulator family was identified within CDS. Characterised within Campylobacter jejuni. not added to product function. Functional classification -Broad regulatory functions 7EPMID:8083178 2C PMID:7590316 2C PMID:9765558 NC_002163.1 RefSeq region 365303 365668 . + . ID=id812;gene=fur;Name=id812;Dbxref=GeneID:904724;gbkey=misc_feature;Note=HMMPfam hit to PF01475 2C Ferric uptake regulator family 2C score 1.4e-63 ### NC_002163.1 RefSeq CDS 365717 367222 . + 0 ID=cds359;Parent=gene370;gene=lysS;Name=YP_002343838.1;Dbxref=GOA:P41258 HSSP:P13030 InterPro:IPR002313 InterPro:IPR004364 InterPro:IPR004365 InterPro:IPR006195 UniProtKB FSwiss-Prot:P41258 Genbank:YP_002343838.1 GeneID:904725;gbkey=CDS;product=lysyl-tRNA synthetase;Note=class II 3B LysRS2 3B catalyzes a two-step reaction 2C first charging a lysine molecule by linking its carboxyl group to the alpha-phosphate of ATP 2C followed by transfer of the aminoacyl-adenylate to its tRNA 3B in Methanosarcina barkeri 2C LysRS2 charges both tRNA molecules for lysine that exist in this organism and in addition can charge the tRNAPyl with lysine in the presence of LysRS1 NC_002163.1 RefSeq gene 365717 367222 . + . ID=gene370;gene=lysS;Name=lysS;locus_tag=Cj0401;Dbxref=GeneID:904725;gbkey=Gene NC_002163.1 RefSeq region 365888 366124 . + . ID=id813;gene=lysS;Name=id813;Dbxref=GeneID:904725;gbkey=misc_feature;Note=HMMPfam hit to PF01336 2C OB-fold nucleic acid binding domain 2C score 5e-15 NC_002163.1 RefSeq region 366170 367192 . + . ID=id814;gene=lysS;Name=id814;Dbxref=GeneID:904725;gbkey=misc_feature;Note=HMMPfam hit to PF00152 2C tRNA synthetases class II 28D 2C K and N 29 2C score 4.6e-205 NC_002163.1 RefSeq region 366470 366523 . + . ID=id815;gene=lysS;Name=id815;Dbxref=GeneID:904725;gbkey=misc_feature;Note=PS00179 Aminoacyl-transfer RNA synthetases class-II signature 1 NC_002163.1 RefSeq region 367109 367138 . + . ID=id816;gene=lysS;Name=id816;Dbxref=GeneID:904725;gbkey=misc_feature;Note=PS00339 Aminoacyl-transfer RNA synthetases class-II signature 2 NC_002163.1 RefSeq CDS 367219 368463 . + 0 ID=cds360;Parent=gene371;gene=glyA;Name=YP_002343839.1;Dbxref=GOA:P24531 HSSP:P00477 InterPro:IPR001085 InterPro:IPR015421 UniProtKB FSwiss-Prot:P24531 Genbank:YP_002343839.1 GeneID:904726;gbkey=CDS;product=serine hydroxymethyltransferase;Note=catalyzes the reaction of glycine with 5 2C10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate NC_002163.1 RefSeq gene 367219 368463 . + . ID=gene371;gene=glyA;Name=glyA;locus_tag=Cj0402;Dbxref=GeneID:904726;gbkey=Gene NC_002163.1 RefSeq region 367225 368355 . + . ID=id817;gene=glyA;Name=id817;Dbxref=GeneID:904726;gbkey=misc_feature;Note=HMMPfam hit to PF00464 2C Serine hydroxymethyltransferase 2C score 1.9e-282 NC_002163.1 RefSeq region 367864 367914 . + . ID=id818;gene=glyA;Name=id818;Dbxref=GeneID:904726;gbkey=misc_feature;Note=PS00096 Serine hydroxymethyltransferase pyridoxal-phosphate attachment site NC_002163.1 RefSeq CDS 368460 369005 . + 0 ID=cds361;Parent=gene372;Name=YP_002343840.1;Dbxref=InterPro:IPR015061 UniProtKB FTrEMBL:Q0PBA7 Genbank:YP_002343840.1 GeneID:904727;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0403 2C unknown 2C len: 181 aa 3B 57.8 25 identity to HP0184 7EUpdated 282006 29 note: Literature search identified paper giving further clues to product function. Functional classification - Conserved hypothetical proteins 7EPMID:12595250 NC_002163.1 RefSeq gene 368460 369005 . + . ID=gene372;gene=Cj0403;Name=Cj0403;locus_tag=Cj0403;Dbxref=GeneID:904727;gbkey=Gene ### NC_002163.1 RefSeq CDS 369019 369855 . + 0 ID=cds362;Parent=gene373;Name=YP_002343841.1;Dbxref=GOA:Q0PBA6 InterPro:IPR007730 UniProtKB FTrEMBL:Q0PBA6 Genbank:YP_002343841.1 GeneID:904728;gbkey=CDS;product=transmembrane protein;Note=Original 282000 29 note: Cj0404 2C probable transmembrane protein 2C len: 278 aa 3B no Hp match. Contains probable transmembrane domain around 40 aa 7EUpdated 282006 29 note: Literature search identified paper giving further clues to product function. Functional classification - Membranes 2C lipoproteins and porins 7EPMID:12595250 NC_002163.1 RefSeq gene 369019 369855 . + . ID=gene373;Name=Cj0404;locus_tag=Cj0404;Dbxref=GeneID:904728;gbkey=Gene NC_002163.1 RefSeq region 369091 369144 . + . ID=id819;Name=id819;Dbxref=GeneID:904728;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0404 by TMHMM2.0 at aa 25-42 NC_002163.1 UTR_Extractor 5'-UTR 369717 369851 . + . ID=utr150;locus_tag=Cj0405;product=shikimate 5-dehydrogenase NC_002163.1 RefSeq CDS 369852 370640 . + 0 ID=cds363;Parent=gene374;gene=aroE;Name=YP_002343842.1;Dbxref=GOA:Q0PBA5 InterPro:IPR006151 InterPro:IPR011342 InterPro:IPR013708 UniProtKB FTrEMBL:Q0PBA5 Genbank:YP_002343842.1 GeneID:904729;gbkey=CDS;product=shikimate 5-dehydrogenase;Note=AroE 3B catalyzes the conversion of shikimate to 3-dehydroshikimate NC_002163.1 RefSeq gene 369852 370640 . + . ID=gene374;gene=aroE;Name=aroE;locus_tag=Cj0405;Dbxref=GeneID:904729;gbkey=Gene NC_002163.1 RefSeq region 369906 370583 . + . ID=id820;gene=aroE;Name=id820;Dbxref=GeneID:904729;gbkey=misc_feature;Note=HMMPfam hit to PF01488 2C Shikimate 2F quinate 5-dehydrogenase 2C score 8.1e-54 ### NC_002163.1 RefSeq CDS 370715 371614 . - 0 ID=cds364;Parent=gene375;Name=YP_002343843.1;Dbxref=GOA:Q0PBA4 UniProtKB FTrEMBL:Q0PBA4 Genbank:YP_002343843.1 GeneID:904730;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj0406c 2C probable lipoprotein 2C len: 299 aa 3B no Hp match. Contains N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 370715 371614 . - . ID=gene375;Name=Cj0406c;locus_tag=Cj0406c;Dbxref=GeneID:904730;gbkey=Gene NC_002163.1 RefSeq region 371534 371602 . - . ID=id821;Name=id821;Dbxref=GeneID:904730;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0406c by TMHMM2.0 at aa 5-27 NC_002163.1 RefSeq region 371564 371596 . - . ID=id822;Name=id822;Dbxref=GeneID:904730;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 UTR_Extractor 5'-UTR 371615 371640 . - . ID=utr151;locus_tag=Cj0406c;product=putative lipoprotein NC_002163.1 UTR_Extractor 5'-UTR 371669 371703 . + . ID=utr152;locus_tag=Cj0407;product=prolipoprotein diacylglyceryl transferase NC_002163.1 RefSeq CDS 371704 372519 . + 0 ID=cds365;Parent=gene376;gene=lgt;Name=YP_002343844.1;Dbxref=GOA:Q9PI98 InterPro:IPR001640 UniProtKB FSwiss-Prot:Q9PI98 Genbank:YP_002343844.1 GeneID:904731;gbkey=CDS;product=prolipoprotein diacylglyceryl transferase;Note=transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein NC_002163.1 RefSeq gene 371704 372519 . + . ID=gene376;gene=lgt;Name=lgt;locus_tag=Cj0407;Dbxref=GeneID:904731;gbkey=Gene NC_002163.1 RefSeq region 371734 372504 . + . ID=id823;gene=lgt;Name=id823;Dbxref=GeneID:904731;gbkey=misc_feature;Note=HMMPfam hit to PF01790 2C Prolipoprotein diacylglyceryl transferase 2C score 4e-120 NC_002163.1 RefSeq region 371770 371838 . + . ID=id824;gene=lgt;Name=id824;Dbxref=GeneID:904731;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0407 by TMHMM2.0 at aa 23-45 2C 66-88 2C 103-125 2C 132-154 2C184-201 2C 206-225 and 240-262 NC_002163.1 RefSeq region 371899 371967 . + . ID=id824;gene=lgt;Name=id824;Dbxref=GeneID:904731;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0407 by TMHMM2.0 at aa 23-45 2C 66-88 2C 103-125 2C 132-154 2C184-201 2C 206-225 and 240-262 NC_002163.1 RefSeq region 372010 372078 . + . ID=id824;gene=lgt;Name=id824;Dbxref=GeneID:904731;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0407 by TMHMM2.0 at aa 23-45 2C 66-88 2C 103-125 2C 132-154 2C184-201 2C 206-225 and 240-262 NC_002163.1 RefSeq region 372097 372165 . + . ID=id824;gene=lgt;Name=id824;Dbxref=GeneID:904731;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0407 by TMHMM2.0 at aa 23-45 2C 66-88 2C 103-125 2C 132-154 2C184-201 2C 206-225 and 240-262 NC_002163.1 RefSeq region 372154 372192 . + . ID=id825;gene=lgt;Name=id825;Dbxref=GeneID:904731;gbkey=misc_feature;Note=PS01311 Prolipoprotein diacylglyceryl transferase signature NC_002163.1 RefSeq region 372253 372306 . + . ID=id824;gene=lgt;Name=id824;Dbxref=GeneID:904731;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0407 by TMHMM2.0 at aa 23-45 2C 66-88 2C 103-125 2C 132-154 2C184-201 2C 206-225 and 240-262 NC_002163.1 RefSeq region 372319 372378 . + . ID=id824;gene=lgt;Name=id824;Dbxref=GeneID:904731;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0407 by TMHMM2.0 at aa 23-45 2C 66-88 2C 103-125 2C 132-154 2C184-201 2C 206-225 and 240-262 NC_002163.1 RefSeq region 372421 372489 . + . ID=id824;gene=lgt;Name=id824;Dbxref=GeneID:904731;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0407 by TMHMM2.0 at aa 23-45 2C 66-88 2C 103-125 2C 132-154 2C184-201 2C 206-225 and 240-262 ### NC_002163.1 UTR_Extractor 5'-UTR 372554 372588 . + . ID=utr153;locus_tag=Cj0408;product=fumarate reductase cytochrome b-556 subunit NC_002163.1 RefSeq region 372589 372600 . + . ID=id827;gene=frdC;Name=id827;Dbxref=GeneID:904732;gbkey=misc_feature;Note=PS00228 Tubulin-beta mRNA autoregulation signal NC_002163.1 RefSeq region 372589 373314 . + . ID=id826;gene=frdC;Name=id826;Dbxref=GeneID:904732;gbkey=misc_feature;Note=HMMPfam hit to PF02967 2C Fumarate reductase respiratory complex 2C tr 2C score 8e-102 NC_002163.1 RefSeq gene 372589 373371 . + . ID=gene377;gene=frdC;Name=frdC;locus_tag=Cj0408;Dbxref=GeneID:904732;gbkey=Gene NC_002163.1 RefSeq CDS 372589 373371 . + 0 ID=cds366;Parent=gene377;gene=frdC;Name=YP_002343845.1;Dbxref=GOA:Q0PBA2 InterPro:IPR004224 InterPro:IPR013838 UniProtKB FTrEMBL:Q0PBA2 Genbank:YP_002343845.1 GeneID:904732;gbkey=CDS;product=fumarate reductase cytochrome b-556 subunit;Note=part of three member fumarate reductase enzyme complex FrdABC which catalyzes the reduction of fumarate to succinate during anaerobic respiration 3B FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit 2C respectively 3B FrdC is the cytochrome b-556 subunit NC_002163.1 RefSeq region 372673 372741 . + . ID=id828;gene=frdC;Name=id828;Dbxref=GeneID:904732;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0408 by TMHMM2.0 at aa 29-51 2C 73-95 2C 125-147 2C 167-189 and 213-235 NC_002163.1 RefSeq region 372805 372873 . + . ID=id828;gene=frdC;Name=id828;Dbxref=GeneID:904732;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0408 by TMHMM2.0 at aa 29-51 2C 73-95 2C 125-147 2C 167-189 and 213-235 NC_002163.1 RefSeq region 372808 372840 . + . ID=id829;gene=frdC;Name=id829;Dbxref=GeneID:904732;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 372961 373029 . + . ID=id828;gene=frdC;Name=id828;Dbxref=GeneID:904732;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0408 by TMHMM2.0 at aa 29-51 2C 73-95 2C 125-147 2C 167-189 and 213-235 NC_002163.1 RefSeq region 373087 373155 . + . ID=id828;gene=frdC;Name=id828;Dbxref=GeneID:904732;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0408 by TMHMM2.0 at aa 29-51 2C 73-95 2C 125-147 2C 167-189 and 213-235 NC_002163.1 RefSeq region 373225 373293 . + . ID=id828;gene=frdC;Name=id828;Dbxref=GeneID:904732;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0408 by TMHMM2.0 at aa 29-51 2C 73-95 2C 125-147 2C 167-189 and 213-235 NC_002163.1 RefSeq CDS 373355 375346 . + 0 ID=cds367;Parent=gene378;gene=frdA;Name=YP_002343846.1;Dbxref=GOA:Q0PBA1 InterPro:IPR003953 InterPro:IPR004112 InterPro:IPR014006 UniProtKB FTrEMBL:Q0PBA1 Genbank:YP_002343846.1 GeneID:904733;gbkey=CDS;product=fumarate reductase flavoprotein subunit;Note=part of three member fumarate reductase enzyme complex FrdABC which catalyzes the reduction of fumarate to succinate during anaerobic respiration 3B FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit 2C respectively 3B FrdC is the cytochrome b-556 subunit 3B the catalytic subunits are similar to succinate dehydrogenase SdhAB NC_002163.1 RefSeq gene 373355 375346 . + . ID=gene378;gene=frdA;Name=frdA;locus_tag=Cj0409;Dbxref=GeneID:904733;gbkey=Gene NC_002163.1 RefSeq region 373742 374710 . + . ID=id830;gene=frdA;Name=id830;Dbxref=GeneID:904733;gbkey=misc_feature;Note=HMMPfam hit to PF00890 2C FAD binding domain 2C score 2e-160 NC_002163.1 RefSeq region 374768 375160 . + . ID=id831;gene=frdA;Name=id831;Dbxref=GeneID:904733;gbkey=misc_feature;Note=HMMPfam hit to PF02910 2C Fumarate reductase 2Fsuccinate dehydroge 2C score 6.4e-53 NC_002163.1 RefSeq CDS 375339 376064 . + 0 ID=cds368;Parent=gene379;gene=frdB;Name=YP_002343847.1;Dbxref=GOA:Q0PBA0 InterPro:IPR001041 InterPro:IPR001450 InterPro:IPR004489 InterPro:IPR006058 InterPro:IPR012285 InterPro:IPR012675 UniProtKB FTrEMBL:Q0PBA0 Genbank:YP_002343847.1 GeneID:904734;gbkey=CDS;product=fumarate reductase iron-sulfur subunit;Note=part of three member fumarate reductase enzyme complex FrdABC which catalyzes the reduction of fumarate to succinate during anaerobic respiration 3B FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit 2C respectively 3B FrdC is the cytochrome b-556 subunit 3B the catalytic subunits are similar to succinate dehydrogenase SdhAB NC_002163.1 RefSeq gene 375339 376064 . + . ID=gene379;gene=frdB;Name=frdB;locus_tag=Cj0410;Dbxref=GeneID:904734;gbkey=Gene NC_002163.1 RefSeq region 375420 375587 . + . ID=id832;gene=frdB;Name=id832;Dbxref=GeneID:904734;gbkey=misc_feature;Note=HMMPfam hit to PF00111 2C 2Fe-2S iron-sulfur cluster binding domain 2C score 0.0037 NC_002163.1 RefSeq region 375507 375533 . + . ID=id833;gene=frdB;Name=id833;Dbxref=GeneID:904734;gbkey=misc_feature;Note=PS00197 2Fe-2S ferredoxins 2C iron-sulfur binding region signature NC_002163.1 RefSeq region 375768 375839 . + . ID=id834;gene=frdB;Name=id834;Dbxref=GeneID:904734;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 0.0015 NC_002163.1 RefSeq region 375948 375980 . + . ID=id835;gene=frdB;Name=id835;Dbxref=GeneID:904734;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq CDS 376092 378278 . + 0 ID=cds369;Parent=gene380;Name=YP_002343848.1;Dbxref=GOA:Q0PB99 InterPro:IPR001401 UniProtKB FTrEMBL:Q0PB99 Genbank:YP_002343848.1 GeneID:904735;gbkey=CDS;product=ATP 2FGTP binding protein;Note=Original 282000 29 note: Cj0411 2C probable ATP 2FGTP binding protein 2C len: 728 aa 3B some similarity in C-term to YOR6_CALSR hypothetical protein 28402 aa 29 2C fasta scores 3B opt: 220 z-score: 284.9 E 28 29: 1.4e-08 2C 25.2 25 identity in 425 aa overlap 2C and to C-term of YPBR_BACSU hypothetical protein 281193 aa 29 2C fasta scores 3B opt: 173 z-score: 275.1 E 28 29: 5e-08 2C 20.1 25 identity in 722 aa overlap. No Hp match. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 7EUpdated 282006 29 note: Pfam domain PF00350 Dynamin family protein was identified within CDS. Dynamin is a member of the G-protein superfamily clan. ATP 2FGTP binding proteins fall under this particular clan. Further support given to product function. No specific characterisation has been carried out yet. kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 376092 378278 . + . ID=gene380;Name=Cj0411;locus_tag=Cj0411;Dbxref=GeneID:904735;gbkey=Gene NC_002163.1 RefSeq region 376578 377174 . + . ID=id836;Name=id836;Dbxref=GeneID:904735;gbkey=misc_feature;Note=HMMPfam hit to PF01926 2C GTPase of unknown function 2Cscore 2e-08 NC_002163.1 RefSeq region 376584 377171 . + . ID=id837;Name=id837;Dbxref=GeneID:904735;gbkey=misc_feature;Note=HMMPfam hit to PF00350 2C Dynamin family 2C score 8.1e-52 NC_002163.1 RefSeq region 376596 376619 . + . ID=id838;Name=id838;Dbxref=GeneID:904735;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 378268 380097 . + 0 ID=cds370;Parent=gene381;Name=YP_002343849.1;Dbxref=GOA:Q0PB98 InterPro:IPR001401 UniProtKB FTrEMBL:Q0PB98 Genbank:YP_002343849.1 GeneID:904736;gbkey=CDS;product=ATP 2FGTP binding protein;Note=Original 282000 29 note: Cj0412 2C probable ATP 2FGTP binding protein 2C len: 609 aa 3B some similarity to YPBR_BACSU hypothetical protein 281193 aa 29 2C fasta scores 3B opt: 172 z-score: 237.5 E 28 29: 6.2e-06 2C 23.7 25 identity in 439 aa overlap. No Hp match. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 7EUpdated 282006 29 note: Pfam domain PF00350 Dynamin family protein was identified within CDS. Dynamin is a member of the G-protein superfamily clan. ATP 2FGTP binding proteins fall under this particular clan. Further support given to product function. Literature search identified paper giving further clues to product function. Functional classification - Misc NC_002163.1 RefSeq gene 378268 380097 . + . ID=gene381;Name=Cj0412;locus_tag=Cj0412;Dbxref=GeneID:904736;gbkey=Gene NC_002163.1 RefSeq region 378451 378924 . + . ID=id839;Name=id839;Dbxref=GeneID:904736;gbkey=misc_feature;Note=HMMPfam hit to PF01926 2C GTPase of unknown function 2Cscore 1.5e-07 NC_002163.1 RefSeq region 378457 378921 . + . ID=id840;Name=id840;Dbxref=GeneID:904736;gbkey=misc_feature;Note=HMMPfam hit to PF00350 2C Dynamin family 2C score 6.6e-39 NC_002163.1 RefSeq region 378469 378492 . + . ID=id841;Name=id841;Dbxref=GeneID:904736;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq gene 380097 380801 . + . ID=gene382;Name=Cj0413;locus_tag=Cj0413;Dbxref=GeneID:904737;gbkey=Gene NC_002163.1 RefSeq CDS 380097 380801 . + 0 ID=cds371;Parent=gene382;Name=YP_002343850.1;Dbxref=GOA:Q0PB97 InterPro:IPR006597 InterPro:IPR011990 UniProtKB FTrEMBL:Q0PB97 Genbank:YP_002343850.1 GeneID:904737;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0413 2C probable periplasmic protein 2C len: 234 aa 3B similar to several Hp proteins 3B HP0160 2C 30.3 25 identity 3B HP0211 2C 32.6 25 identity 3B HP1098 31.1 25 identity 3B HP0336 31.3 25 identity 3B HP0235 30.9 25 identity 3B HP0628 26.5 25 identity 3B and HP1117 26.9 25 identity. This is the only copy in C. jejuni 7EUpdated 282006 29 note: Pfam domain PF07719 Tetratricopeptide repeat was identified within CDS. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 380346 380447 . + . ID=id842;Name=id842;Dbxref=GeneID:904737;gbkey=misc_feature;Note=HMMPfam hit to PF07719 2C Tetratricopeptide repeat 2Cscore 0.013 ### NC_002163.1 UTR_Extractor 5'-UTR 380911 380936 . + . ID=utr154;locus_tag=Cj0414;product=putative oxidoreductase subunit NC_002163.1 RefSeq gene 380937 381665 . + . ID=gene383;Name=Cj0414;locus_tag=Cj0414;Dbxref=GeneID:904738;gbkey=Gene NC_002163.1 RefSeq CDS 380937 381665 . + 0 ID=cds372;Parent=gene383;Name=YP_002343851.1;Dbxref=UniProtKB FTrEMBL:Q0PB96 Genbank:YP_002343851.1 GeneID:904738;gbkey=CDS;product=oxidoreductase subunit;Note=Original 282000 29 note: Cj0414 2C possible oxidoreductase subunit 2C len: 242 aa 3B some similarity to TR:O34213 28EMBL:U97665 29 Erwinia cypripedii gluconate dehydrogenase subunit III precursor 28220 aa 29 2C fasta scores 3B opt: 343 z-score: 502.3 E 28 29: 1.1e-20 2C 32.6 25 identity in 193 aa overlap. No Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score has been carried out yet. kept within product function. Literature search identified paper giving further clues to product function. Functional classification - Misc 7EPMID:15231804 NC_002163.1 RefSeq region 380967 381035 . + . ID=id843;Name=id843;Dbxref=GeneID:904738;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0414 by TMHMM2.0 at aa 11-33 ### NC_002163.1 RefSeq gene 381667 383388 . + . ID=gene384;Name=Cj0415;locus_tag=Cj0415;Dbxref=GeneID:904739;gbkey=Gene NC_002163.1 RefSeq CDS 381667 383388 . + 0 ID=cds373;Parent=gene384;Name=YP_002343852.1;Dbxref=GOA:Q0PB95 InterPro:IPR000172 UniProtKB FTrEMBL:Q0PB95 Genbank:YP_002343852.1 GeneID:904739;gbkey=CDS;product=GMC oxidoreductase subunit;Note=Original 282000 29 note: Cj0415 2C possible oxidoreductase subunit 2C len: 573 aa 3B similar to e.g. TR:O34214 28EMBL:U97665 29 Erwinia cypripedii gluconate dehydrogenase subunit precursor 28615 aa 29 2C fasta scores 3B opt: 1025 z-score: 1674.4 E 28 29: 0 2C 40.8 25 identity in 583 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF00732 GMC 28glucose-methanol-choline 29 oxidoreductase was identified within CDS when carrying out own Pfam search. This family is a member of the FAD 2FNAD 28P 29-binding Rossmann fold Superfamily clan. These proteins bind FAD as a cofactor. Product modified to more specific family member due to motif match. Literature search identified paper giving further related functional clues. No specific characterisaion with acceptable identity score has been carried out yet 2C so kept within product function. Literature search identified paper linking protein to glycoprotein 28PMID:12186869 29. Functional classification -Misc 7EPMID:15231804 2C PMID:12186869 NC_002163.1 UTR_Extractor 5'-UTR 383457 383558 . + . ID=utr155;locus_tag=Cj0416;product=hypothetical protein NC_002163.1 RefSeq gene 383559 383657 . + . ID=gene385;Name=Cj0416;locus_tag=Cj0416;Dbxref=GeneID:904740;gbkey=Gene NC_002163.1 RefSeq CDS 383559 383657 . + 0 ID=cds374;Parent=gene385;Name=YP_002343853.1;Dbxref=UniProtKB FTrEMBL:Q0PB94 Genbank:YP_002343853.1 GeneID:904740;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0416 2C unknown 2C len: 32 aa 3B no Hp match 2C highly simlar to N-terminus of Cj0122 2888.2 25 identity in 34 aa overlap 29. Functional classification -Unknown NC_002163.1 RefSeq gene 383677 383823 . + . ID=gene386;Name=Cj0417;locus_tag=Cj0417;Dbxref=GeneID:904741;gbkey=Gene NC_002163.1 RefSeq CDS 383677 383823 . + 0 ID=cds375;Parent=gene386;Name=YP_002343854.1;Dbxref=UniProtKB FTrEMBL:Q0PB93 Genbank:YP_002343854.1 GeneID:904741;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0417 2C unknown 2C len: 48 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 RefSeq gene 383947 384651 . - . ID=gene387;Name=Cj0418c;locus_tag=Cj0418c;Dbxref=GeneID:904742;gbkey=Gene NC_002163.1 RefSeq CDS 383947 384651 . - 0 ID=cds376;Parent=gene387;Name=YP_002343855.1;Dbxref=UniProtKB FTrEMBL:Q0PB92 Genbank:YP_002343855.1 GeneID:904742;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0418c 2C unknown 2C len: 234 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 RefSeq gene 384759 385121 . + . ID=gene388;Name=Cj0419;locus_tag=Cj0419;Dbxref=GeneID:904743;gbkey=Gene NC_002163.1 RefSeq CDS 384759 385121 . + 0 ID=cds377;Parent=gene388;Name=YP_002343856.1;Dbxref=GOA:Q79JB6 InterPro:IPR011151 UniProtKB FTrEMBL:Q79JB6 Genbank:YP_002343856.1 GeneID:904743;gbkey=CDS;product=histidine triad 28HIT 29 family protein;Note=Original 282000 29 note: Cj0419 2C unknown 2C len: 120 aa 3B no Hp match 7EUpdated 282006 29 note: Pfam domain PF01230 HIT 28histidine triad 29 was identified within CDS by carrying out own Pfam search. Product modified to more specific family member due to motif match. No specific characterisation has been carried out yet. Literature search identified paper giving further information on HIT domains. Functional classification - Misc 7EPMID:1472710 2C PMID:9164465 NC_002163.1 UTR_Extractor 5'-UTR 385166 385194 . + . ID=utr156;locus_tag=Cj0420;product=putative periplasmic protein NC_002163.1 RefSeq gene 385195 385767 . + . ID=gene389;Name=Cj0420;locus_tag=Cj0420;Dbxref=GeneID:904744;gbkey=Gene NC_002163.1 RefSeq CDS 385195 385767 . + 0 ID=cds378;Parent=gene389;Name=YP_002343857.1;Dbxref=GOA:Q79JB5 InterPro:IPR007372 UniProtKB FTrEMBL:Q79JB5 Genbank:YP_002343857.1 GeneID:904744;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0420 2C probable periplasmic protein 2C len: 190 aa 3B similar to hypothetical proteins e.g. YCEI_ECOLI 28191 aa 29 2C fasta scores 3B opt: 377 z-score: 504.2 E 28 29: 8.7e-21 2C 37.4 25 identity in 195 aa overlap. 37.8 25 identity to HP1286. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF04264 YceI like family was identified within CDS. Product function was not altered since PF04264 is a base-induced periplasmic protein that has not been characterised. Literature search identified paper linking protein to be a glycoprotein. Functional classification - Miscellaneous periplasmic proteins 7EPMID:15231804 NC_002163.1 RefSeq region 385255 385764 . + . ID=id844;Name=id844;Dbxref=GeneID:904744;gbkey=misc_feature;Note=HMMPfam hit to PF04264 2C YceI like family 2C score 1e-77 ### NC_002163.1 RefSeq CDS 385772 386728 . - 0 ID=cds379;Parent=gene390;Name=YP_002343858.1;Dbxref=InterPro:IPR000160 UniProtKB FTrEMBL:Q0PB89 Genbank:YP_002343858.1 GeneID:904745;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0421c 2C probable integral membrane protein 2C len: 318 aa 3B no Hp match 7EUpdated 282006 29 note: Six probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 385772 386728 . - . ID=gene390;Name=Cj0421c;locus_tag=Cj0421c;Dbxref=GeneID:904745;gbkey=Gene NC_002163.1 RefSeq region 386153 386212 . - . ID=id37;Name=id37;Dbxref=GeneID:904745;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0421c by TMHMM2.0 at aa 2-24 2C 48-70 2C 82-99 2C 122-139 2C146-163 and 173-192 NC_002163.1 RefSeq region 386240 386293 . - . ID=id37;Name=id37;Dbxref=GeneID:904745;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0421c by TMHMM2.0 at aa 2-24 2C 48-70 2C 82-99 2C 122-139 2C146-163 and 173-192 NC_002163.1 RefSeq region 386312 386365 . - . ID=id37;Name=id37;Dbxref=GeneID:904745;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0421c by TMHMM2.0 at aa 2-24 2C 48-70 2C 82-99 2C 122-139 2C146-163 and 173-192 NC_002163.1 RefSeq region 386432 386485 . - . ID=id37;Name=id37;Dbxref=GeneID:904745;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0421c by TMHMM2.0 at aa 2-24 2C 48-70 2C 82-99 2C 122-139 2C146-163 and 173-192 NC_002163.1 RefSeq region 386519 386587 . - . ID=id37;Name=id37;Dbxref=GeneID:904745;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0421c by TMHMM2.0 at aa 2-24 2C 48-70 2C 82-99 2C 122-139 2C146-163 and 173-192 NC_002163.1 RefSeq region 386657 386725 . - . ID=id37;Name=id37;Dbxref=GeneID:904745;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0421c by TMHMM2.0 at aa 2-24 2C 48-70 2C 82-99 2C 122-139 2C146-163 and 173-192 ### NC_002163.1 RefSeq gene 386790 386999 . - . ID=gene391;Name=Cj0422c;locus_tag=Cj0422c;Dbxref=GeneID:904746;gbkey=Gene NC_002163.1 RefSeq CDS 386790 386999 . - 0 ID=cds380;Parent=gene391;Name=YP_002343859.1;Dbxref=GOA:Q0PB88 UniProtKB FTrEMBL:Q0PB88 Genbank:YP_002343859.1 GeneID:904746;gbkey=CDS;product=H-T-H containing protein;Note=Original 282000 29 note: Cj0422c 2C unknown 2C len: 69 aa 3B no Hp match. Contains probable helix-turn-helix motif at aa 5-26 28Score 1410 2C 2B3.99 SD 29. Functional classification - Broad regulatory functions NC_002163.1 UTR_Extractor 5'-UTR 387000 387025 . - . ID=utr157;locus_tag=Cj0422c;product=putative H-T-H containing protein NC_002163.1 RefSeq gene 387168 387395 . + . ID=gene392;Name=Cj0423;locus_tag=Cj0423;Dbxref=GeneID:904747;gbkey=Gene NC_002163.1 RefSeq CDS 387168 387395 . + 0 ID=cds381;Parent=gene392;Name=YP_002343860.1;Dbxref=InterPro:IPR016410 UniProtKB FTrEMBL:Q0PB87 Genbank:YP_002343860.1 GeneID:904747;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0423 2C probable integral membrane protein 2C len: 75 aa 3B similar to immunity proteins of T4 and T2 phage e.g. IMM_BPT4 immunity protein 2883 aa 29 2Cfasta scores 3B opt: 174 z-score: 240.8 E 28 29: 4e-06 2C 40.2 25 identity in 82 aa overlap. No Hp match 7EUpdated 282006 29 note: Two probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 387180 387248 . + . ID=id845;Name=id845;Dbxref=GeneID:904747;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0423 by TMHMM2.0 at aa 5-27 and 37-59 NC_002163.1 RefSeq region 387276 387344 . + . ID=id845;Name=id845;Dbxref=GeneID:904747;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0423 by TMHMM2.0 at aa 5-27 and 37-59 ### NC_002163.1 RefSeq CDS 387404 388036 . + 0 ID=cds382;Parent=gene393;Name=YP_002343861.1;Dbxref=GOA:Q0PB86 InterPro:IPR011652 UniProtKB FTrEMBL:Q0PB86 Genbank:YP_002343861.1 GeneID:904748;gbkey=CDS;product=acidic periplasmic protein;Note=Original 282000 29 note: Cj0424 2C probable acidic periplasmic protein 2C len: 210 aa 3B no Hp match. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF07661 MORN repeat variant was identified within CDS. The MORN 28Membrane Occupation and Recognition Nexus 29 repeat is found in multiple copies in several proteins. The function of this motif is unknown. Literature search identified paper giving functional link to iron stimulation. Functional classification - Miscellaneous periplasmic proteins 7EPMID:15632442 NC_002163.1 RefSeq gene 387404 388036 . + . ID=gene393;Name=Cj0424;locus_tag=Cj0424;Dbxref=GeneID:904748;gbkey=Gene NC_002163.1 RefSeq region 387425 387457 . + . ID=id846;Name=id846;Dbxref=GeneID:904748;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 387488 387553 . + . ID=id847;Name=id847;Dbxref=GeneID:904748;gbkey=misc_feature;Note=HMMPfam hit to PF07661 2C MORN repeat variant 2C score 3.3 NC_002163.1 RefSeq region 387563 387628 . + . ID=id848;Name=id848;Dbxref=GeneID:904748;gbkey=misc_feature;Note=HMMPfam hit to PF07661 2C MORN repeat variant 2C score 0.0044 NC_002163.1 RefSeq region 387635 387700 . + . ID=id849;Name=id849;Dbxref=GeneID:904748;gbkey=misc_feature;Note=HMMPfam hit to PF07661 2C MORN repeat variant 2C score 0.0016 NC_002163.1 RefSeq region 387707 387772 . + . ID=id850;Name=id850;Dbxref=GeneID:904748;gbkey=misc_feature;Note=HMMPfam hit to PF07661 2C MORN repeat variant 2C score 43 NC_002163.1 RefSeq region 387797 387862 . + . ID=id851;Name=id851;Dbxref=GeneID:904748;gbkey=misc_feature;Note=HMMPfam hit to PF07661 2C MORN repeat variant 2C score 0.12 NC_002163.1 RefSeq region 387872 387937 . + . ID=id852;Name=id852;Dbxref=GeneID:904748;gbkey=misc_feature;Note=HMMPfam hit to PF07661 2C MORN repeat variant 2C score 0.0083 NC_002163.1 RefSeq region 387944 388006 . + . ID=id853;Name=id853;Dbxref=GeneID:904748;gbkey=misc_feature;Note=HMMPfam hit to PF07661 2C MORN repeat variant 2C score 4.1 ### NC_002163.1 RefSeq gene 388049 388465 . + . ID=gene394;Name=Cj0425;locus_tag=Cj0425;Dbxref=GeneID:904749;gbkey=Gene NC_002163.1 RefSeq CDS 388049 388465 . + 0 ID=cds383;Parent=gene394;Name=YP_002343862.1;Dbxref=UniProtKB FTrEMBL:Q0PB85 Genbank:YP_002343862.1 GeneID:904749;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0425 2C probable periplasmic protein 2C len: 138 aa 3B no Hp match. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Literature search identified paper giving functional link to iron stimulation. Functional classification - Miscellaneous periplasmic proteins 7EPMID:15632442 NC_002163.1 UTR_Extractor 5'-UTR 388560 388594 . + . ID=utr158;locus_tag=Cj0426;product=putative ABC transporter ATP-binding protein NC_002163.1 RefSeq CDS 388595 390172 . + 0 ID=cds384;Parent=gene395;Name=YP_002343863.1;Dbxref=GOA:Q0PB84 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FTrEMBL:Q0PB84 Genbank:YP_002343863.1 GeneID:904750;gbkey=CDS;product=ABC transporter ATP-binding protein;Note=Original 282000 29 note: Cj0426 2C probable ABC transporter ATP-binding protein 2C len: 525 aa 3B simlar to many e.g. YBIT_ECOLI hypothetical ABC transporter ATP-binding protein 28530 aa 29 2C fasta scores 3B opt: 1461 z-score: 1750.6 E 28 29: 0 2C 42.8 25 identity in 526 aa overlap. 60.5 25 identity to HP0853. Contains 2x PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 and Pfam match to entry PF00005 ABC_tran 2C ABC transporters 2C scores 115.00 2C E-value 1.4e-30 2C and 120.70 2C E-value 2.7e-32 7EUpdated 282006 29 note: Some characterisation within Escherichia coli with acceptable identity score. added to product function as original designation was only hypothetical. Functional classification -Transport 2Fbinding proteins - Other NC_002163.1 RefSeq gene 388595 390172 . + . ID=gene395;Name=Cj0426;locus_tag=Cj0426;Dbxref=GeneID:904750;gbkey=Gene NC_002163.1 RefSeq region 388673 389275 . + . ID=id854;Name=id854;Dbxref=GeneID:904750;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 1.9e-33 NC_002163.1 RefSeq region 388694 388717 . + . ID=id855;Name=id855;Dbxref=GeneID:904750;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 389621 390115 . + . ID=id856;Name=id856;Dbxref=GeneID:904750;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 1.1e-33 NC_002163.1 RefSeq region 389642 389665 . + . ID=id857;Name=id857;Dbxref=GeneID:904750;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 UTR_Extractor 5'-UTR 389864 390161 . + . ID=utr159;locus_tag=Cj0427;product=hypothetical protein NC_002163.1 RefSeq CDS 390162 390497 . + 0 ID=cds385;Parent=gene396;Name=YP_002343864.1;Dbxref=UniProtKB FTrEMBL:Q0PB83 Genbank:YP_002343864.1 GeneID:904751;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0427 2C unknown 2C len: 111 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 RefSeq gene 390162 390497 . + . ID=gene396;Name=Cj0427;locus_tag=Cj0427;Dbxref=GeneID:904751;gbkey=Gene ### NC_002163.1 UTR_Extractor 5'-UTR 390549 390571 . + . ID=utr160;locus_tag=Cj0428;product=hypothetical protein NC_002163.1 RefSeq gene 390572 390955 . + . ID=gene397;Name=Cj0428;locus_tag=Cj0428;Dbxref=GeneID:904752;gbkey=Gene NC_002163.1 RefSeq CDS 390572 390955 . + 0 ID=cds386;Parent=gene397;Name=YP_002343865.1;Dbxref=UniProtKB FTrEMBL:Q0PB82 Genbank:YP_002343865.1 GeneID:904752;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0428 2C unknown 2C len: 127 aa 3B no Hp match 7EUpdated 282006 29 note: Literature search identified papers linking product function to be involved with motility. Functional classification - Unknown 7EPMID:15812042 2C PMID:14985343 NC_002163.1 RefSeq gene 390999 391583 . - . ID=gene398;Name=Cj0429c;locus_tag=Cj0429c;Dbxref=GeneID:904753;gbkey=Gene NC_002163.1 RefSeq CDS 390999 391583 . - 0 ID=cds387;Parent=gene398;Name=YP_002343866.1;Dbxref=InterPro:IPR001498 UniProtKB FTrEMBL:Q0PB81 Genbank:YP_002343866.1 GeneID:904753;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0429c 2C unknown 2C len: 194 aa 3B similar to hypothetical proteins e.g. YIGZ_ECOLI 28205 aa 29 2C fasta scores 3B opt: 241 z-score: 370.8 E 28 29: 2.3e-13 2C40.2 25 identity in 112 aa overlap. 39.1 25 identity to HP1485 28misannotated as proline dipeptidase 29 7EUpdated 282006 29 note: Pfam domain PF01205 Uncharacterized protein family 28UPF0029 29 was identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq region 391224 391544 . - . ID=id858;Name=id858;Dbxref=GeneID:904753;gbkey=misc_feature;Note=HMMPfam hit to PF01205 2C Uncharacterized protein family UPF0029 2C score 3.1e-47 ### NC_002163.1 UTR_Extractor 5'-UTR 391584 391600 . - . ID=utr161;locus_tag=Cj0429c;product=hypothetical protein NC_002163.1 UTR_Extractor 5'-UTR 391708 391710 . + . ID=utr162;locus_tag=Cj0430;product=putative integral membrane protein NC_002163.1 RefSeq CDS 391711 392937 . + 0 ID=cds388;Parent=gene399;Name=YP_002343867.1;Dbxref=UniProtKB FTrEMBL:Q0PB80 Genbank:YP_002343867.1 GeneID:904754;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0430 2C probable integral membrane protein 2C len: 408 aa 3B 33.8 25 identity to HP1235 7EUpdated 282006 29 note: Nine probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Literature search identified paper linking product function to stress response. Functional classification - Membranes 2C lipoproteins and porins 7EPMID:16045618 NC_002163.1 RefSeq gene 391711 392937 . + . ID=gene399;Name=Cj0430;locus_tag=Cj0430;Dbxref=GeneID:904754;gbkey=Gene NC_002163.1 RefSeq region 391735 391803 . + . ID=id859;Name=id859;Dbxref=GeneID:904754;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0430 by TMHMM2.0 at aa 9-31 2C 69-91 2C 104-137 2C 147-169 2C176-195 2C 205-227 2C 239-256 2C 260-277 and 298-320 NC_002163.1 RefSeq region 391915 391983 . + . ID=id859;Name=id859;Dbxref=GeneID:904754;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0430 by TMHMM2.0 at aa 9-31 2C 69-91 2C 104-137 2C 147-169 2C176-195 2C 205-227 2C 239-256 2C 260-277 and 298-320 NC_002163.1 RefSeq region 392020 392121 . + . ID=id859;Name=id859;Dbxref=GeneID:904754;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0430 by TMHMM2.0 at aa 9-31 2C 69-91 2C 104-137 2C 147-169 2C176-195 2C 205-227 2C 239-256 2C 260-277 and 298-320 NC_002163.1 RefSeq region 392149 392217 . + . ID=id859;Name=id859;Dbxref=GeneID:904754;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0430 by TMHMM2.0 at aa 9-31 2C 69-91 2C 104-137 2C 147-169 2C176-195 2C 205-227 2C 239-256 2C 260-277 and 298-320 NC_002163.1 RefSeq region 392236 392295 . + . ID=id859;Name=id859;Dbxref=GeneID:904754;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0430 by TMHMM2.0 at aa 9-31 2C 69-91 2C 104-137 2C 147-169 2C176-195 2C 205-227 2C 239-256 2C 260-277 and 298-320 NC_002163.1 RefSeq region 392323 392391 . + . ID=id859;Name=id859;Dbxref=GeneID:904754;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0430 by TMHMM2.0 at aa 9-31 2C 69-91 2C 104-137 2C 147-169 2C176-195 2C 205-227 2C 239-256 2C 260-277 and 298-320 NC_002163.1 RefSeq region 392425 392478 . + . ID=id859;Name=id859;Dbxref=GeneID:904754;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0430 by TMHMM2.0 at aa 9-31 2C 69-91 2C 104-137 2C 147-169 2C176-195 2C 205-227 2C 239-256 2C 260-277 and 298-320 NC_002163.1 RefSeq region 392488 392541 . + . ID=id859;Name=id859;Dbxref=GeneID:904754;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0430 by TMHMM2.0 at aa 9-31 2C 69-91 2C 104-137 2C 147-169 2C176-195 2C 205-227 2C 239-256 2C 260-277 and 298-320 NC_002163.1 RefSeq region 392602 392670 . + . ID=id859;Name=id859;Dbxref=GeneID:904754;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0430 by TMHMM2.0 at aa 9-31 2C 69-91 2C 104-137 2C 147-169 2C176-195 2C 205-227 2C 239-256 2C 260-277 and 298-320 NC_002163.1 RefSeq gene 392930 393544 . + . ID=gene400;Name=Cj0431;locus_tag=Cj0431;Dbxref=GeneID:904723;gbkey=Gene NC_002163.1 RefSeq CDS 392930 393544 . + 0 ID=cds389;Parent=gene400;Name=YP_002343868.1;Dbxref=UniProtKB FTrEMBL:Q0PB79 Genbank:YP_002343868.1 GeneID:904723;gbkey=CDS;product=ATP 2FGTP-binding protein;Note=Original 282000 29 note: Cj0431 2C possible periplasmic ATP 2FGTP-binding protein 2C len: 204 aa 3B no Hp match 3B contains possible N-terminal signal sequence and PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 7EUpdated 282006 29 note: One probable transmembrane helices predicted by TMHMM2.0. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 392942 393010 . + . ID=id860;Name=id860;Dbxref=GeneID:904723;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0431 by TMHMM2.0 at aa 5-27 NC_002163.1 RefSeq region 393227 393250 . + . ID=id861;Name=id861;Dbxref=GeneID:904723;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 RefSeq gene 394130 395642 . + . ID=gene401;Name=Cjr04;locus_tag=Cjr04;Dbxref=GeneID:3245051;gbkey=Gene NC_002163.1 RefSeq rRNA 394130 395642 . + . ID=rna7;Parent=gene401;Name=rna7;Dbxref=GeneID:3245051;gbkey=rRNA;product=16S ribosomal RNA NC_002163.1 RefSeq exon 394130 395642 . + . ID=id862;Parent=rna7;Name=id862;Dbxref=GeneID:3245051;gbkey=rRNA;product=16S ribosomal RNA NC_002163.1 RefSeq gene 395747 395822 . + . ID=gene402;gene=tRNAAla;Name=tRNAAla;locus_tag=Cjp04;Dbxref=GeneID:904755;gbkey=Gene NC_002163.1 RefSeq tRNA 395747 395822 . + . ID=rna8;Parent=gene402;gene=tRNAAla;Name=rna8;Dbxref=GeneID:904755;gbkey=tRNA;product=tRNA-Ala;Note=tRNA Ala anticodon TGC 2C Cove score 92.14 NC_002163.1 RefSeq exon 395747 395822 . + . ID=id863;Parent=rna8;gene=tRNAAla;Name=id863;Dbxref=GeneID:904755;gbkey=tRNA;product=tRNA-Ala;Note=tRNA Ala anticodon TGC 2C Cove score 92.14 NC_002163.1 RefSeq gene 395831 395907 . + . ID=gene403;gene=tRNAIle;Name=tRNAIle;locus_tag=Cjp05;Dbxref=GeneID:904756;gbkey=Gene NC_002163.1 RefSeq tRNA 395831 395907 . + . ID=rna9;Parent=gene403;gene=tRNAIle;Name=rna9;Dbxref=GeneID:904756;gbkey=tRNA;product=tRNA-Ile;Note=tRNA Ile anticodon GAT 2C Cove score 93.24 NC_002163.1 RefSeq exon 395831 395907 . + . ID=id864;Parent=rna9;gene=tRNAIle;Name=id864;Dbxref=GeneID:904756;gbkey=tRNA;product=tRNA-Ile;Note=tRNA Ile anticodon GAT 2C Cove score 93.24 NC_002163.1 RefSeq gene 396449 399360 . + . ID=gene404;Name=Cjr05;locus_tag=Cjr05;Dbxref=GeneID:3245053;gbkey=Gene NC_002163.1 RefSeq rRNA 396449 399360 . + . ID=rna10;Parent=gene404;Name=rna10;Dbxref=GeneID:3245053;gbkey=rRNA;product=23S ribosomal RNA NC_002163.1 RefSeq exon 396449 399360 . + . ID=id865;Parent=rna10;Name=id865;Dbxref=GeneID:3245053;gbkey=rRNA;product=23S ribosomal RNA NC_002163.1 RefSeq gene 399644 399763 . + . ID=gene405;Name=Cjr06;locus_tag=Cjr06;Dbxref=GeneID:3245056;gbkey=Gene NC_002163.1 RefSeq rRNA 399644 399763 . + . ID=rna11;Parent=gene405;Name=rna11;Dbxref=GeneID:3245056;gbkey=rRNA;product=5S ribosomal RNA NC_002163.1 RefSeq exon 399644 399763 . + . ID=id866;Parent=rna11;Name=id866;Dbxref=GeneID:3245056;gbkey=rRNA;product=5S ribosomal RNA NC_002163.1 RefSeq CDS 399936 401144 . - 0 ID=cds390;Parent=gene406;gene=murD;Name=YP_002343869.1;Dbxref=GOA:Q9PI73 HSSP:P14900 InterPro:IPR004101 InterPro:IPR005762 InterPro:IPR013221 UniProtKB FSwiss-Prot:Q9PI73 Genbank:YP_002343869.1 GeneID:904757;gbkey=CDS;product=UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase;Note=UDP-N-acetylmuramoylalanine--D-glutamate ligase 3B involved in peptidoglycan biosynthesis 3B cytoplasmic 3B catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine during cell wall formation NC_002163.1 RefSeq gene 399936 401144 . - . ID=gene406;gene=murD;Name=murD;locus_tag=Cj0432c;Dbxref=GeneID:904757;gbkey=Gene NC_002163.1 RefSeq region 400119 400352 . - . ID=id867;gene=murD;Name=id867;Dbxref=GeneID:904757;gbkey=misc_feature;Note=HMMPfam hit to PF02875 2C Mur ligase family 2Cglutamate ligase doma 2C score 0.00084 NC_002163.1 RefSeq region 400386 401057 . - . ID=id868;gene=murD;Name=id868;Dbxref=GeneID:904757;gbkey=misc_feature;Note=HMMPfam hit to PF01225 2C Mur ligase family 2Ccatalytic domain 2C score 9.5e-09 NC_002163.1 RefSeq region 400797 400868 . - . ID=id869;gene=murD;Name=id869;Dbxref=GeneID:904757;gbkey=misc_feature;Note=PS01011 Folylpolyglutamate synthase signature 1 NC_002163.1 RefSeq CDS 401144 402205 . - 0 ID=cds391;Parent=gene407;gene=mraY;Name=YP_002343870.1;Dbxref=GOA:Q9PI72 InterPro:IPR000715 InterPro:IPR003524 UniProtKB FSwiss-Prot:Q9PI72 Genbank:YP_002343870.1 GeneID:904758;gbkey=CDS;product=phospho-N-acetylmuramoyl-pentapeptide-transferase;Note=First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan NC_002163.1 RefSeq gene 401144 402205 . - . ID=gene407;gene=mraY;Name=mraY;locus_tag=Cj0433c;Dbxref=GeneID:904758;gbkey=Gene NC_002163.1 RefSeq region 401156 401215 . - . ID=id38;gene=mraY;Name=id38;Dbxref=GeneID:904758;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0433c by TMHMM2.0 at aa 20-42 2C 63-85 2C 90-108 2C 129-147 2C162-184 2C 189-211 2C 226-248 2C 255-277 2C 282-304 and 331-350 NC_002163.1 RefSeq region 401294 401362 . - . ID=id38;gene=mraY;Name=id38;Dbxref=GeneID:904758;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0433c by TMHMM2.0 at aa 20-42 2C 63-85 2C 90-108 2C 129-147 2C162-184 2C 189-211 2C 226-248 2C 255-277 2C 282-304 and 331-350 NC_002163.1 RefSeq region 401357 401932 . - . ID=id870;gene=mraY;Name=id870;Dbxref=GeneID:904758;gbkey=misc_feature;Note=HMMPfam hit to PF00953 2C Glycosyl transferase 2C score 2.9e-62 NC_002163.1 RefSeq region 401375 401443 . - . ID=id38;gene=mraY;Name=id38;Dbxref=GeneID:904758;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0433c by TMHMM2.0 at aa 20-42 2C 63-85 2C 90-108 2C 129-147 2C162-184 2C 189-211 2C 226-248 2C 255-277 2C 282-304 and 331-350 NC_002163.1 RefSeq region 401462 401530 . - . ID=id38;gene=mraY;Name=id38;Dbxref=GeneID:904758;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0433c by TMHMM2.0 at aa 20-42 2C 63-85 2C 90-108 2C 129-147 2C162-184 2C 189-211 2C 226-248 2C 255-277 2C 282-304 and 331-350 NC_002163.1 RefSeq region 401573 401641 . - . ID=id38;gene=mraY;Name=id38;Dbxref=GeneID:904758;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0433c by TMHMM2.0 at aa 20-42 2C 63-85 2C 90-108 2C 129-147 2C162-184 2C 189-211 2C 226-248 2C 255-277 2C 282-304 and 331-350 NC_002163.1 RefSeq region 401654 401722 . - . ID=id38;gene=mraY;Name=id38;Dbxref=GeneID:904758;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0433c by TMHMM2.0 at aa 20-42 2C 63-85 2C 90-108 2C 129-147 2C162-184 2C 189-211 2C 226-248 2C 255-277 2C 282-304 and 331-350 NC_002163.1 RefSeq region 401765 401821 . - . ID=id38;gene=mraY;Name=id38;Dbxref=GeneID:904758;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0433c by TMHMM2.0 at aa 20-42 2C 63-85 2C 90-108 2C 129-147 2C162-184 2C 189-211 2C 226-248 2C 255-277 2C 282-304 and 331-350 NC_002163.1 RefSeq region 401882 401938 . - . ID=id38;gene=mraY;Name=id38;Dbxref=GeneID:904758;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0433c by TMHMM2.0 at aa 20-42 2C 63-85 2C 90-108 2C 129-147 2C162-184 2C 189-211 2C 226-248 2C 255-277 2C 282-304 and 331-350 NC_002163.1 RefSeq region 401951 402019 . - . ID=id38;gene=mraY;Name=id38;Dbxref=GeneID:904758;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0433c by TMHMM2.0 at aa 20-42 2C 63-85 2C 90-108 2C 129-147 2C162-184 2C 189-211 2C 226-248 2C 255-277 2C 282-304 and 331-350 NC_002163.1 RefSeq region 402080 402148 . - . ID=id38;gene=mraY;Name=id38;Dbxref=GeneID:904758;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0433c by TMHMM2.0 at aa 20-42 2C 63-85 2C 90-108 2C 129-147 2C162-184 2C 189-211 2C 226-248 2C 255-277 2C 282-304 and 331-350 ### NC_002163.1 UTR_Extractor 5'-UTR 402206 402234 . - . ID=utr163;locus_tag=Cj0433c;product=phospho-N-acetylmuramoyl-pentapeptide-transferase NC_002163.1 RefSeq region 402285 403325 . + . ID=id871;gene=pgm;Name=id871;Dbxref=GeneID:904759;gbkey=misc_feature;Note=HMMPfam hit to PF06415 2C BPG-independent PGAM N-terminus 28iPGM_N 2C score 1.4e-217 NC_002163.1 RefSeq gene 402285 403763 . + . ID=gene408;gene=pgm;Name=pgm;locus_tag=Cj0434;Dbxref=GeneID:904759;gbkey=Gene NC_002163.1 RefSeq CDS 402285 403763 . + 0 ID=cds392;Parent=gene408;gene=pgm;Name=YP_002343871.1;Dbxref=GOA:Q9PI71 HSSP:Q9X519 InterPro:IPR005995 InterPro:IPR006124 InterPro:IPR011258 InterPro:IPR017849 UniProtKB FSwiss-Prot:Q9PI71 Genbank:YP_002343871.1 GeneID:904759;gbkey=CDS;product=phosphoglyceromutase;Note=catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate NC_002163.1 RefSeq region 403353 403697 . + . ID=id872;gene=pgm;Name=id872;Dbxref=GeneID:904759;gbkey=misc_feature;Note=HMMPfam hit to PF01676 2C Metalloenzyme superfamily 2Cscore 4.8e-35 ### NC_002163.1 UTR_Extractor 5'-UTR 403804 403834 . + . ID=utr164;locus_tag=Cj0435;product=3-ketoacyl- 28acyl-carrier-protein 29 reductase NC_002163.1 RefSeq CDS 403835 404578 . + 0 ID=cds393;Parent=gene409;gene=fabG;Name=YP_002343872.1;Dbxref=GOA:Q0PB75 InterPro:IPR002198 InterPro:IPR002347 InterPro:IPR011284 InterPro:IPR016040 UniProtKB FTrEMBL:Q0PB75 Genbank:YP_002343872.1 GeneID:904760;gbkey=CDS;product=3-ketoacyl-ACP reductase;Note=Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis NC_002163.1 RefSeq gene 403835 404578 . + . ID=gene409;gene=fabG;Name=fabG;locus_tag=Cj0435;Dbxref=GeneID:904760;gbkey=Gene NC_002163.1 RefSeq region 403856 404569 . + . ID=id873;gene=fabG;Name=id873;Dbxref=GeneID:904760;gbkey=misc_feature;Note=HMMPfam hit to PF00106 2C short chain dehydrogenase 2Cscore 3.3e-73 NC_002163.1 RefSeq region 404258 404344 . + . ID=id874;gene=fabG;Name=id874;Dbxref=GeneID:904760;gbkey=misc_feature;Note=PS00061 Short-chain dehydrogenases 2Freductases family signature ### NC_002163.1 RefSeq gene 404585 404995 . + . ID=gene410;Name=Cj0436;locus_tag=Cj0436;Dbxref=GeneID:904761;gbkey=Gene NC_002163.1 RefSeq CDS 404585 404995 . + 0 ID=cds394;Parent=gene410;Name=YP_002343873.1;Dbxref=GOA:Q0PB74 InterPro:IPR011576 UniProtKB FTrEMBL:Q0PB74 Genbank:YP_002343873.1 GeneID:904761;gbkey=CDS;product=pyridoxamine 5 27-phosphate oxidase;Note=Original 282000 29 note: Cj0436 2C unknown 2C len: 136 aa 3B no Hp match 7EUpdated 282006 29 note: Pfam domain PF01243 Pyridoxamine 5 27-phosphate oxidase was identified within CDS. Product function modified to more specific family member based on motif match. Pyridoxamine 5 27-phosphate oxidase 281.4.3.5 29 is a FMN flavoprotein involved in the de novo synthesis of pyridoxine 28vitamin B6 29 and pyridoxal phosphate. It oxidizes pyridoxamine-5-P 28PMP 29 and pyridoxine-5-P 28PNP 29 to pyridoxal-5-P. No specific characterisation with acceptable identity scores has been carried out yet. kept within product function. Functional classification - Biosynthesis of cofactors 2Cprosthetic groups and carriers - Pyridoxine NC_002163.1 RefSeq region 404594 404848 . + . ID=id875;Name=id875;Dbxref=GeneID:904761;gbkey=misc_feature;Note=HMMPfam hit to PF01243 2C Pyridoxamine 5 27-phosphate oxidase 2C score 9.8e-09 ### NC_002163.1 UTR_Extractor 5'-UTR 405091 405332 . + . ID=utr165;locus_tag=Cj0437;product=succinate dehydrogenase flavoprotein subunit NC_002163.1 RefSeq CDS 405333 407168 . + 0 ID=cds395;Parent=gene411;gene=sdhA;Name=YP_002343874.1;Dbxref=GOA:Q0PB73 InterPro:IPR003953 InterPro:IPR004112 InterPro:IPR006311 UniProtKB FTrEMBL:Q0PB73 Genbank:YP_002343874.1 GeneID:904762;gbkey=CDS;product=succinate dehydrogenase flavoprotein subunit;Note=Original 282000 29 note: Cj0437 2C sdhA 2C probable succinate dehydrogenase flavoprotein subunit 2C len: 611 aa 3B similar to many e.g. DHSA_ECOLI succinate dehydrogenase flavoprotein subunit 28EC 1.3.99.1 29 28588 aa 29 2C fasta scores 3B opt: 1036 z-score: 1136.5 E 28 29: 0 2C 37.3 25 identity in 569 aa overlap and to e.g. FRDA_WOLSU fumarate reductase flavoprotein subunit 28656 aa 29 2C fasta scores 3B opt: 862 z-score: 1211.2 E 28 29: 0 2C 33.3 25 identity in 595 aa overlap. No Hp ortholog 2C but 32.3 25 identity to HP0192 fumarate reductase 2C flavoprotein subunit 28frdA 29 2C and 33.8 25 identity to C. jejuni frdA 28Cj0409 29. Contains Pfam match to entry PF00890 FAD_binding_2 2C FAD binding domain 2C score 386.60 2CE-value 2.5e-112 7EUpdated 282006 29 note: Pfam domain PF02910 Fumarate reductase 2Fsuccinate dehydrogenase identified within CDS. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. Recent EC number update has changed fumarate designation to succinate. not added to product function. Functional classification - Energy metabolism -Tricarboxylic acid cycle 7EPMID:1556094 2C PMID:2987185 NC_002163.1 RefSeq gene 405333 407168 . + . ID=gene411;gene=sdhA;Name=sdhA;locus_tag=Cj0437;Dbxref=GeneID:904762;gbkey=Gene NC_002163.1 RefSeq region 405771 406706 . + . ID=id876;gene=sdhA;Name=id876;Dbxref=GeneID:904762;gbkey=misc_feature;Note=HMMPfam hit to PF00890 2C FAD binding domain 2C score 6.2e-115 NC_002163.1 RefSeq region 406785 407165 . + . ID=id877;gene=sdhA;Name=id877;Dbxref=GeneID:904762;gbkey=misc_feature;Note=HMMPfam hit to PF02910 2C Fumarate reductase 2Fsuccinate dehydroge 2C score 1.6e-35 NC_002163.1 RefSeq gene 407165 408130 . + . ID=gene412;gene=sdhB;Name=sdhB;locus_tag=Cj0438;Dbxref=GeneID:904763;gbkey=Gene NC_002163.1 RefSeq CDS 407165 408130 . + 0 ID=cds396;Parent=gene412;gene=sdhB;Name=YP_002343875.1;Dbxref=GOA:Q0PB72 InterPro:IPR001041 InterPro:IPR001450 InterPro:IPR004489 InterPro:IPR006058 InterPro:IPR012285 InterPro:IPR012675 UniProtKB FTrEMBL:Q0PB72 Genbank:YP_002343875.1 GeneID:904763;gbkey=CDS;product=succinate dehydrogenase iron-sulfur protein;Note=Original 282000 29 note: Cj0438 2C sdhB 2C possibleble succinate dehydrogenase iron-sulfur protein 2C len: 321 aa 3B similar to e.g. DHSB_MYCGR succinate dehydrogenase 28ubiquinone 29 iron-sulfur protein 28EC 1.3.5.1 29 28297 aa 29 2Cfasta scores 3B opt: 352 z-score: 442.4 E 28 29: 2.4e-17 2C 29.3 25 identity in 215 aa overlap. No Hp ortholog 2C but 28.1 25 identical to HP0191 fumarate reductase 2C iron-sulfur subunit 28frdB 29. Contains PS00197 2Fe-2S ferredoxins 2Ciron-sulfur binding region signature 2C PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature 2C and Pfam match to entry PF00037 fer4 2C 4Fe-4S ferredoxins and related iron-sulfur cluster binding domains. 2C score 13.70 2CE-value 0.01 7EUpdated 282006 29 note: Pfam domain PF00111 2Fe-2S iron-sulfur cluster binding domain was identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score has been carried out yet. kept within product function. Functional classification - Energy metabolism -Tricarboxylic acid cycle NC_002163.1 RefSeq region 407231 407395 . + . ID=id878;gene=sdhB;Name=id878;Dbxref=GeneID:904763;gbkey=misc_feature;Note=HMMPfam hit to PF00111 2C 2Fe-2S iron-sulfur cluster binding domain 2C score 0.018 NC_002163.1 RefSeq region 407315 407341 . + . ID=id879;gene=sdhB;Name=id879;Dbxref=GeneID:904763;gbkey=misc_feature;Note=PS00197 2Fe-2S ferredoxins 2C iron-sulfur binding region signature NC_002163.1 RefSeq region 407774 407809 . + . ID=id880;gene=sdhB;Name=id880;Dbxref=GeneID:904763;gbkey=misc_feature;Note=PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature ### NC_002163.1 RefSeq CDS 408134 408991 . + 0 ID=cds397;Parent=gene413;gene=sdhC;Name=YP_002343876.1;Dbxref=GOA:Q0PB71 InterPro:IPR004017 UniProtKB FTrEMBL:Q0PB71 Genbank:YP_002343876.1 GeneID:904764;gbkey=CDS;product=succinate dehydrogenase subunit C;Note=Original 282000 29 note: Cj0439 2C sdhC 2C probable succinate dehydrogenase subunit C 2C len: 285 aa 3B similar to e.g. TR:P77945 28EMBL:Y09041 29 Sulfolobus acidocaldarius succinate dehydrogenase subunit C 28EC 1.3.99.1 29 28290 aa 29 2Cfasta scores 3B opt: 612 z-score: 739.6 E 28 29: 0 2C 34.2 25 identity in 275 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domains x2 PF02754 Cysteine-rich domain was identified within CDS. This domain is usually found in two copies per protein. It contains up to four conserved cysteines. No specific characterisation with acceptable identity score has been carried out yet. kept within product function. Functional classification - Energy metabolism -Tricarboxylic acid cycle NC_002163.1 RefSeq gene 408134 408991 . + . ID=gene413;gene=sdhC;Name=sdhC;locus_tag=Cj0439;Dbxref=GeneID:904764;gbkey=Gene NC_002163.1 RefSeq region 408215 408394 . + . ID=id881;gene=sdhC;Name=id881;Dbxref=GeneID:904764;gbkey=misc_feature;Note=HMMPfam hit to PF02754 2C Cysteine-rich domain 2C score 3.7e-06 NC_002163.1 RefSeq region 408659 408841 . + . ID=id882;gene=sdhC;Name=id882;Dbxref=GeneID:904764;gbkey=misc_feature;Note=HMMPfam hit to PF02754 2C Cysteine-rich domain 2C score 6.4e-11 ### NC_002163.1 RefSeq gene 409015 409683 . - . ID=gene414;Name=Cj0440c;locus_tag=Cj0440c;Dbxref=GeneID:904765;gbkey=Gene NC_002163.1 RefSeq CDS 409015 409683 . - 0 ID=cds398;Parent=gene414;Name=YP_002343877.1;Dbxref=InterPro:IPR004305 InterPro:IPR016084 UniProtKB FTrEMBL:Q0PB70 Genbank:YP_002343877.1 GeneID:904765;gbkey=CDS;product=transcriptional regulator;Note=Original 282000 29 note: Cj0440c 2C probable transcriptional regulator 2C len: 222 aa 3B similar to many regulators and to TENA_BACSU transcriptional activator TENA 28236 aa 29 2C fasta scores 3B opt: 250 z-score: 275.4 E 28 29: 4.8e-08 2C 28.8 25 identity in 215 aa overlap. 30.7 25 identity to HP1287 7EUpdated 282006 29 note: Pfam domain PF03070 TENA 2FTHI-4 family was identified within CDS. Further support given to product function. No specific characterisation has been carried out yet. kept within product function. Functional classification - Broad regulatory functions NC_002163.1 RefSeq region 409030 409677 . - . ID=id883;Name=id883;Dbxref=GeneID:904765;gbkey=misc_feature;Note=HMMPfam hit to PF03070 2C TENA 2FTHI-4 family 2C score 1.2e-52 ### NC_002163.1 UTR_Extractor 5'-UTR 409684 409710 . - . ID=utr166;locus_tag=Cj0440c;product=putative transcriptional regulator NC_002163.1 UTR_Extractor 5'-UTR 409765 409792 . + . ID=utr167;locus_tag=Cj0441;product=acyl carrier protein NC_002163.1 RefSeq CDS 409793 410026 . + 0 ID=cds399;Parent=gene415;gene=acpP;Name=YP_002343878.1;Dbxref=GOA:Q9PI64 HSSP:P80643 InterPro:IPR003231 InterPro:IPR006162 InterPro:IPR006163 InterPro:IPR009081 UniProtKB FSwiss-Prot:Q9PI64 Genbank:YP_002343878.1 GeneID:904766;gbkey=CDS;product=acyl carrier protein;Note=carries the fatty acid chain in fatty acid biosynthesis NC_002163.1 RefSeq gene 409793 410026 . + . ID=gene415;gene=acpP;Name=acpP;locus_tag=Cj0441;Dbxref=GeneID:904766;gbkey=Gene NC_002163.1 RefSeq region 409805 410008 . + . ID=id884;gene=acpP;Name=id884;Dbxref=GeneID:904766;gbkey=misc_feature;Note=HMMPfam hit to PF00550 2C Phosphopantetheine attachment site 2C score 3.2e-13 NC_002163.1 RefSeq region 409883 409930 . + . ID=id885;gene=acpP;Name=id885;Dbxref=GeneID:904766;gbkey=misc_feature;Note=PS00012 Phosphopantetheine attachment site ### NC_002163.1 RefSeq CDS 410053 411267 . + 0 ID=cds400;Parent=gene416;gene=fabF;Name=YP_002343879.1;Dbxref=GOA:Q0PB68 InterPro:IPR000794 InterPro:IPR014030 InterPro:IPR014031 InterPro:IPR016038 InterPro:IPR017441 InterPro:IPR017568 UniProtKB FTrEMBL:Q0PB68 Genbank:YP_002343879.1 GeneID:904767;gbkey=CDS;product=3-oxoacyl-ACP synthase;Note=FabF 3B beta-ketoacyl-ACP synthase II 2C KASII 3B catalyzes a condensation reaction in fatty acid biosynthesis: addition of an acyl acceptor of two carbons from malonyl-ACP 3B required for the elongation of short-chain unsaturated acyl-ACP NC_002163.1 RefSeq gene 410053 411267 . + . ID=gene416;gene=fabF;Name=fabF;locus_tag=Cj0442;Dbxref=GeneID:904767;gbkey=Gene NC_002163.1 RefSeq region 410056 410784 . + . ID=id886;gene=fabF;Name=id886;Dbxref=GeneID:904767;gbkey=misc_feature;Note=HMMPfam hit to PF00109 2C Beta-ketoacyl synthase 2CN-terminal do 2C score 1.1e-67 NC_002163.1 RefSeq region 410806 411264 . + . ID=id887;gene=fabF;Name=id887;Dbxref=GeneID:904767;gbkey=misc_feature;Note=HMMPfam hit to PF02801 2C Beta-ketoacyl synthase 2CC-terminal do 2C score 8.4e-54 NC_002163.1 RefSeq region 410818 410892 . + . ID=id888;gene=fabF;Name=id888;Dbxref=GeneID:904767;gbkey=misc_feature;Note=PS00107 Protein kinases ATP-binding region signature ### NC_002163.1 RefSeq gene 411269 412207 . + . ID=gene417;gene=accA;Name=accA;locus_tag=Cj0443;Dbxref=GeneID:904768;gbkey=Gene NC_002163.1 RefSeq CDS 411269 412207 . + 0 ID=cds401;Parent=gene417;gene=accA;Name=YP_002343880.1;Dbxref=GOA:Q9PI62 InterPro:IPR001095 InterPro:IPR011763 UniProtKB FSwiss-Prot:Q9PI62 Genbank:YP_002343880.1 GeneID:904768;gbkey=CDS;product=acetyl-CoA carboxylase carboxyltransferase subunit alpha;Note=catalyzes the carboxylation of acetyl-CoA to malonyl-CoA 3B forms a tetramer composed of two alpha 28AccA 29 and two beta 28AccD 29 subunits 3B one of the two catalytic subunits that can form the acetyl CoA carboxylase enzyme together with a carrier protein NC_002163.1 RefSeq region 411275 411691 . + . ID=id889;gene=accA;Name=id889;Dbxref=GeneID:904768;gbkey=misc_feature;Note=HMMPfam hit to PF03255 2C Acetyl co-enzyme A carboxylase carboxyltrans 2C score 3.3e-66 ### NC_002163.1 RefSeq region 412359 412910 . + . ID=id890;Name=id890;Dbxref=GeneID:904769;gbkey=misc_feature;Note=Original 282000 29 note: Cj0444 2C probable tonB-denpendent outer membrane receptor pseudogene 2C len: 2072 bp 3B similar to parts of various tonB-denpendent outer membrane receptors e.g. IRGA_VIBCH iron-regulated outer membrane virulence protein 28652 aa 29 2C CIRA_ECOLI colicin I receptor precursor 28663 aa 29 2C and FEPA_ECOLI ferrienterobactin receptor precursor 28746 aa 29. No Hp ortholog. Contains N-terminal signal sequence 2C PS01156 TonB-dependent receptor proteins signature 2 and Pfam match to entry PF00593 TonB_boxC 2C TonB dependant receptor C-terminal region 2C score 28.00 2C E-value 4.3e-05. There is at least one frameshift and one stop codon in this CDS 7EUpdated 282006 29 note: Pfam domain PF07715 TonB-dependent Receptor Plug Domain identified within CDS. Further support given to product function. Some characterisation work in various bacteria. However 2Cidentity scores were marginal. Thus 2C was added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:15632442 NC_002163.1 RefSeq pseudogene 412359 414430 . + . ID=gene418;Name=Cj0444;locus_tag=Cj0444;Dbxref=GeneID:904769;gbkey=Gene NC_002163.1 RefSeq region 412473 412811 . + . ID=id891;Name=id891;Dbxref=GeneID:904769;gbkey=misc_feature;Note=HMMPfam hit to PF07715 2C TonB-dependent Receptor Plug Domain 2C score 2e-27 NC_002163.1 RefSeq region 412907 413473 . + . ID=id890;Name=id890;Dbxref=GeneID:904769;gbkey=misc_feature;Note=Original 282000 29 note: Cj0444 2C probable tonB-denpendent outer membrane receptor pseudogene 2C len: 2072 bp 3B similar to parts of various tonB-denpendent outer membrane receptors e.g. IRGA_VIBCH iron-regulated outer membrane virulence protein 28652 aa 29 2C CIRA_ECOLI colicin I receptor precursor 28663 aa 29 2C and FEPA_ECOLI ferrienterobactin receptor precursor 28746 aa 29. No Hp ortholog. Contains N-terminal signal sequence 2C PS01156 TonB-dependent receptor proteins signature 2 and Pfam match to entry PF00593 TonB_boxC 2C TonB dependant receptor C-terminal region 2C score 28.00 2C E-value 4.3e-05. There is at least one frameshift and one stop codon in this CDS 7EUpdated 282006 29 note: Pfam domain PF07715 TonB-dependent Receptor Plug Domain identified within CDS. Further support given to product function. Some characterisation work in various bacteria. However 2Cidentity scores were marginal. Thus 2C was added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:15632442 NC_002163.1 RefSeq region 413477 414430 . + . ID=id890;Name=id890;Dbxref=GeneID:904769;gbkey=misc_feature;Note=Original 282000 29 note: Cj0444 2C probable tonB-denpendent outer membrane receptor pseudogene 2C len: 2072 bp 3B similar to parts of various tonB-denpendent outer membrane receptors e.g. IRGA_VIBCH iron-regulated outer membrane virulence protein 28652 aa 29 2C CIRA_ECOLI colicin I receptor precursor 28663 aa 29 2C and FEPA_ECOLI ferrienterobactin receptor precursor 28746 aa 29. No Hp ortholog. Contains N-terminal signal sequence 2C PS01156 TonB-dependent receptor proteins signature 2 and Pfam match to entry PF00593 TonB_boxC 2C TonB dependant receptor C-terminal region 2C score 28.00 2C E-value 4.3e-05. There is at least one frameshift and one stop codon in this CDS 7EUpdated 282006 29 note: Pfam domain PF07715 TonB-dependent Receptor Plug Domain identified within CDS. Further support given to product function. Some characterisation work in various bacteria. However 2Cidentity scores were marginal. Thus 2C was added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:15632442 NC_002163.1 RefSeq region 413606 414430 . + . ID=id892;Name=id892;Dbxref=GeneID:904769;gbkey=misc_feature;Note=HMMPfam hit to PF00593 2C TonB dependent receptor 2Cscore 3.1e-33 ### NC_002163.1 UTR_Extractor 5'-UTR 414493 414515 . + . ID=utr168;locus_tag=Cj0447;product=putative NUDIX hydrolase family protein NC_002163.1 RefSeq gene 414516 415112 . + . ID=gene419;Name=Cj0447;locus_tag=Cj0447;Dbxref=GeneID:904770;gbkey=Gene NC_002163.1 RefSeq CDS 414516 415112 . + 0 ID=cds402;Parent=gene419;Name=YP_002343881.1;Dbxref=GOA:Q0PB66 InterPro:IPR000086 InterPro:IPR004385 UniProtKB FTrEMBL:Q0PB66 Genbank:YP_002343881.1 GeneID:904770;gbkey=CDS;product=NUDIX hydrolase family protein;Note=Original 282000 29 note: Cj0447 2C unknown 2C len: 198 aa 3B similar to a hypothetical protein from E. coli 3B YFFH_ECOLI 28191 aa 29 2C fasta scores 3B opt: 168 z-score: 344.6 E 28 29: 6.7e-12 2C 31.1 25 identity in 122 aa overlap 3B and to part of a hypothetical protein from C. elegans TR:Q18745 28EMBL:Z70750 29 C50F4.11 281092 aa 29 2C fasta scores 3B opt: 133 z-score: 491.0 E 28 29: 4.7e-20 2C 35.3 25 identity in 215 aa overlap. 45.7 25 identity to HP0507 7EUpdated 282006 29 note: Pfam domain PF00293 NUDIX was identified within CDS. The generic name 27NUDIX hydrolases 27 28NUcleoside DIphosphate linked to some other moiety X 29 has been coined for this domain family . The family can be divided into a number of subgroups 2C of which MutT anti-mutagenic activity represents only one type 3B most of the rest hydrolyse diverse nucleoside diphosphate derivatives 28including ADP-ribose 2C GDP- mannose 2C TDP-glucose 2C NADH 2CUDP-sugars 2C dNTP and NTP 29. Product modified to more specific family member due to motif match. Functional classification - Misc NC_002163.1 RefSeq region 414627 415070 . + . ID=id893;Name=id893;Dbxref=GeneID:904770;gbkey=misc_feature;Note=HMMPfam hit to PF00293 2C NUDIX domain 2C score 7.3e-11 ### NC_002163.1 RefSeq gene 415144 416241 . - . ID=gene420;Name=Cj0448c;locus_tag=Cj0448c;Dbxref=GeneID:904771;gbkey=Gene NC_002163.1 RefSeq CDS 415144 416241 . - 0 ID=cds403;Parent=gene420;Name=YP_002343882.1;Dbxref=GOA:Q0PB65 InterPro:IPR004089 InterPro:IPR004090 UniProtKB FTrEMBL:Q0PB65 Genbank:YP_002343882.1 GeneID:904771;gbkey=CDS;product=MCP-type signal transduction protein;Note=Original 282000 29 note: Cj0448c 2C probable MCP-type signal transduction protein 2C len: 365 aa 3B similar to many proteins with MCP domains e.g. TR:Q56633 28EMBL:L25660 29 Vibrio cholerae acfB accessory colonization factor 28626 aa 29 2C fasta scores 3B opt: 364 z-score: 455.7 E 28 29: 4.4e-18 2C29.9 25 identity in 278 aa overlap 2C and PILJ_PSEAE PILJ protein 28682 aa 29 2C fasta scores 3B opt: 314 z-score: 451.9 E 28 29: 7.1e-18 2C 30.7 25 identity in 189 aa overlap. 31.9 25 identity to HP0599 28called hemolysin secretion protein precursor 28hylB 29 2C but previously sequenced as TR:P94847 H.pylori 48 kDa antigen 28433 aa 29 2C fasta scores 3B opt: 580 z-score: 833.7 E 28 29: 0 2C 32.4 25 identity in 370 aa overlap 29. Contains Pfam match to entry PF00015 MCPsignal 2CMethyl-accepting chemotaxis protein 28MCP 29 signaling domain 2C score 122.40 2C E-value 1.7e-33 7EUpdated 282006 29 note: Prosite domain PS50111 CHEMOTAXIS_TRANSDUC_2 2C Bacterial chemotaxis sensory transducers domain profile identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score has been carried out yet. kept within product function. Functional classification - Signal transduction NC_002163.1 RefSeq region 415426 416010 . - . ID=id894;Name=id894;Dbxref=GeneID:904771;gbkey=misc_feature;Note=HMMPfam hit to PF00015 2C Methyl-accepting chemotaxis protein 28MCP 29 s 2C score 7.4e-12 ### NC_002163.1 RefSeq gene 416251 416466 . - . ID=gene421;Name=Cj0449c;locus_tag=Cj0449c;Dbxref=GeneID:904772;gbkey=Gene NC_002163.1 RefSeq CDS 416251 416466 . - 0 ID=cds404;Parent=gene421;Name=YP_002343883.1;Dbxref=InterPro:IPR007420 UniProtKB FTrEMBL:Q0PB64 Genbank:YP_002343883.1 GeneID:904772;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0449c 2C unknown 2C len: 71 aa 3B similar to E. coli hypothetical protein YDCH_ECOLI 2855 aa 29 2C fasta scores 3B opt: 112 z-score: 209.2 E 28 29: 0.00023 2C42.6 25 identity in 47 aa overlap. 45.1 25 identity to HP1242 7EUpdated 282006 29 note: Pfam domain PF04325 Protein of unknown function 28DUF465 29 was identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq region 416263 416412 . - . ID=id895;Name=id895;Dbxref=GeneID:904772;gbkey=misc_feature;Note=HMMPfam hit to PF04325 2C Protein of unknown function 28DUF465 29 2C score 9.2e-21 ### NC_002163.1 UTR_Extractor 5'-UTR 416467 416506 . - . ID=utr169;locus_tag=Cj0449c;product=hypothetical protein NC_002163.1 RefSeq gene 416651 416845 . - . ID=gene422;gene=rpmB;Name=rpmB;locus_tag=Cj0450c;Dbxref=GeneID:904773;gbkey=Gene NC_002163.1 RefSeq CDS 416651 416845 . - 0 ID=cds405;Parent=gene422;gene=rpmB;Name=YP_002343884.1;Dbxref=GOA:Q9PI58 InterPro:IPR001383 UniProtKB FSwiss-Prot:Q9PI58 Genbank:YP_002343884.1 GeneID:904773;gbkey=CDS;product=50S ribosomal protein L28;Note=required for 70S ribosome assembly NC_002163.1 RefSeq region 416660 416839 . - . ID=id896;gene=rpmB;Name=id896;Dbxref=GeneID:904773;gbkey=misc_feature;Note=HMMPfam hit to PF00830 2C Ribosomal L28 family 2C score 1.3e-23 ### NC_002163.1 UTR_Extractor 5'-UTR 416846 416873 . - . ID=utr170;locus_tag=Cj0450c;product=50S ribosomal protein L28 NC_002163.1 UTR_Extractor 5'-UTR 416953 416984 . + . ID=utr171;locus_tag=Cj0451;product=ribulose-phosphate 3-epimerase NC_002163.1 RefSeq CDS 416985 417632 . + 0 ID=cds406;Parent=gene423;gene=rep;Name=YP_002343885.1;Dbxref=GOA:Q0PB62 InterPro:IPR000056 InterPro:IPR013785 UniProtKB FTrEMBL:Q0PB62 Genbank:YP_002343885.1 GeneID:904774;gbkey=CDS;product=ribulose-phosphate 3-epimerase;Note=catalyzes the interconversion of D-ribulose 5-phosphate to xylulose 5-phosphate NC_002163.1 RefSeq gene 416985 417632 . + . ID=gene423;gene=rep;Name=rep;locus_tag=Cj0451;Dbxref=GeneID:904774;gbkey=Gene NC_002163.1 RefSeq region 416988 417590 . + . ID=id897;gene=rep;Name=id897;Dbxref=GeneID:904774;gbkey=misc_feature;Note=HMMPfam hit to PF00834 2C Ribulose-phosphate 3 epimerase family 2C score 2.7e-102 NC_002163.1 RefSeq region 417072 417116 . + . ID=id898;gene=rep;Name=id898;Dbxref=GeneID:904774;gbkey=misc_feature;Note=PS01085 Ribulose-phosphate 3-epimerase family signature 1 NC_002163.1 RefSeq region 417378 417446 . + . ID=id899;gene=rep;Name=id899;Dbxref=GeneID:904774;gbkey=misc_feature;Note=PS01086 Ribulose-phosphate 3-epimerase family signature 2 NC_002163.1 RefSeq gene 417629 418390 . + . ID=gene424;gene=dnaQ;Name=dnaQ;locus_tag=Cj0452;Dbxref=GeneID:904775;gbkey=Gene NC_002163.1 RefSeq CDS 417629 418390 . + 0 ID=cds407;Parent=gene424;gene=dnaQ;Name=YP_002343886.1;Dbxref=GOA:Q0PB61 InterPro:IPR006054 InterPro:IPR006055 InterPro:IPR013520 UniProtKB FTrEMBL:Q0PB61 Genbank:YP_002343886.1 GeneID:904775;gbkey=CDS;product=DNA polymerase III subunit epsilon;Note=3 27-5 27 exonuclease of DNA polymerase III NC_002163.1 RefSeq region 417842 418300 . + . ID=id900;gene=dnaQ;Name=id900;Dbxref=GeneID:904775;gbkey=misc_feature;Note=HMMPfam hit to PF00929 2C Exonuclease 2C score 1.1e-35 ### NC_002163.1 RefSeq gene 418412 418516 . + . ID=gene425;Name=Cjs02;locus_tag=Cjs02;Dbxref=GeneID:7133894;gbkey=Gene NC_002163.1 RefSeq transcript 418412 418516 . + . ID=rna12;Parent=gene425;Name=TPP riboswitch;Dbxref=GeneID:7133894;gbkey=misc_RNA;Note=TPP riboswitch 28THI element 29 7EUpdated 282006 29 note: Running Rfam search revealed new non-coding RNA families within Campylobacter jejuni. Rfam RF00059 2C TPP riboswitch 28THI element 29 was identified within CDS. Vitamin B 281 29 in its active form thiamin pyrophosphate 28TPP 29 is an essential coenzyme that is synthesised by coupling of pyrimidine and thiazole moieties in bacteria. The previously detected thiamin-regulatory element 2C thi box 28PMID:12376536 29 was extended 2C resulting in a new 2C highly conserved RNA secondary structure 2C the THI element. Analysis of operon structures identified a large number of new candidate thiamin-regulated genes 2C mostly transporters 2C in various prokaryotic organisms 28PMID:1147090 29 NC_002163.1 RefSeq exon 418412 418516 . + . ID=id901;Parent=rna12;Name=id901;Dbxref=GeneID:7133894;gbkey=misc_RNA;Note=TPP riboswitch 28THI element 29 7EUpdated 282006 29 note: Running Rfam search revealed new non-coding RNA families within Campylobacter jejuni. Rfam RF00059 2C TPP riboswitch 28THI element 29 was identified within CDS. Vitamin B 281 29 in its active form thiamin pyrophosphate 28TPP 29 is an essential coenzyme that is synthesised by coupling of pyrimidine and thiazole moieties in bacteria. The previously detected thiamin-regulatory element 2C thi box 28PMID:12376536 29 was extended 2C resulting in a new 2C highly conserved RNA secondary structure 2C the THI element. Analysis of operon structures identified a large number of new candidate thiamin-regulated genes 2C mostly transporters 2C in various prokaryotic organisms 28PMID:1147090 29 NC_002163.1 RefSeq CDS 418573 419865 . + 0 ID=cds408;Parent=gene426;gene=thiC;Name=YP_002343887.1;Dbxref=GOA:Q9PI55 InterPro:IPR002817 UniProtKB FSwiss-Prot:Q9PI55 Genbank:YP_002343887.1 GeneID:904776;gbkey=CDS;product=thiamine biosynthesis protein ThiC;Note=required for the synthesis of the hydromethylpyrimidine moiety of thiamine NC_002163.1 RefSeq gene 418573 419865 . + . ID=gene426;gene=thiC;Name=thiC;locus_tag=Cj0453;Dbxref=GeneID:904776;gbkey=Gene NC_002163.1 RefSeq region 418579 419838 . + . ID=id902;gene=thiC;Name=id902;Dbxref=GeneID:904776;gbkey=misc_feature;Note=HMMPfam hit to PF01964 2C ThiC family 2C score 8.1e-216 NC_002163.1 RefSeq gene 419857 420426 . - . ID=gene427;gene=Cj0454c;Name=Cj0454c;locus_tag=Cj0454c;Dbxref=GeneID:904777;gbkey=Gene NC_002163.1 RefSeq CDS 419857 420426 . - 0 ID=cds409;Parent=gene427;Name=YP_002343888.1;Dbxref=UniProtKB FTrEMBL:Q0PB59 Genbank:YP_002343888.1 GeneID:904777;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0454c 2C possible membrane protein 2C len: 189 aa 3B no Hp match 7EUpdated 282006 29 note: One probable transmembrane helices predicted by TMHMM2.0 within CDS. Literature search identified paper linking product function to motility. Functional classification - Membranes 2Clipoproteins and porins 7EPMID:15066034 NC_002163.1 RefSeq region 420274 420342 . - . ID=id903;Name=id903;Dbxref=GeneID:904777;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0454c by TMHMM2.0 at aa 29-51 NC_002163.1 RefSeq pseudogene 420365 420892 . - . ID=gene428;Name=Cj0455c;locus_tag=Cj0455c;Dbxref=GeneID:904778;gbkey=Gene NC_002163.1 RefSeq region 420776 420835 . - . ID=id904;Name=id904;Dbxref=GeneID:904778;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0455c by TMHMM2.0 at aa 20-39 NC_002163.1 RefSeq CDS 420889 421848 . - 0 ID=cds410;Parent=gene429;Name=YP_002343890.1;Dbxref=UniProtKB FTrEMBL:Q0PB57 Genbank:YP_002343890.1 GeneID:904779;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0456c 2C unknown 2C len: 319 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 RefSeq gene 420889 421848 . - . ID=gene429;Name=Cj0456c;locus_tag=Cj0456c;Dbxref=GeneID:904779;gbkey=Gene ### NC_002163.1 UTR_Extractor 5'-UTR 421849 422128 . - . ID=utr172;locus_tag=Cj0456c;product=hypothetical protein NC_002163.1 RefSeq gene 421850 422479 . - . ID=gene430;Name=Cj0457c;locus_tag=Cj0457c;Dbxref=GeneID:904780;gbkey=Gene NC_002163.1 RefSeq CDS 421850 422479 . - 0 ID=cds411;Parent=gene430;Name=YP_002343891.1;Dbxref=InterPro:IPR007172 UniProtKB FTrEMBL:Q0PB56 Genbank:YP_002343891.1 GeneID:904780;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj0457c 2C probable lipoprotein 2C len: 209 aa 3B similar to hypothetical protein fromRICKETTSIA PROWAZEKII TR:E1342403 28EMBL:AJ235270 29 RP090 28218 aa 29 2C fasta scores 3B opt: 372 z-score: 531.3 E 28 29: 2.7e-22 2C 33.0 25 identity in 212 aa overlap. 35.9 25 identity in 153 aa overlap to HP0270. Contains N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site 7EUpdated 282006 29 note: Pfam domain PF04028 Domain of unknown function 28DUF374 29 identified within CDS. One probable transmembrane helices predicted by TMHMM2.0 within CDS. Further support given to product function. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 422096 422332 . - . ID=id905;Name=id905;Dbxref=GeneID:904780;gbkey=misc_feature;Note=HMMPfam hit to PF04028 2C Domain of unknown function 28DUF374 29 2C score 1.7e-50 NC_002163.1 RefSeq region 422306 422365 . - . ID=id39;Name=id39;Dbxref=GeneID:904780;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0457c by TMHMM2.0 at aa 7-24 and 39-58 NC_002163.1 RefSeq region 422405 422437 . - . ID=id906;Name=id906;Dbxref=GeneID:904780;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 422408 422461 . - . ID=id39;Name=id39;Dbxref=GeneID:904780;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0457c by TMHMM2.0 at aa 7-24 and 39-58 NC_002163.1 RefSeq gene 422463 423764 . - . ID=gene431;gene=miaB;Name=miaB;locus_tag=Cj0458c;Dbxref=GeneID:904781;gbkey=Gene NC_002163.1 RefSeq CDS 422463 423764 . - 0 ID=cds412;Parent=gene431;gene=miaB;Name=YP_002343892.1;Dbxref=GOA:Q0PB55 InterPro:IPR002792 InterPro:IPR005839 InterPro:IPR006463 InterPro:IPR006638 InterPro:IPR007197 InterPro:IPR013848 UniProtKB FTrEMBL:Q0PB55 Genbank:YP_002343892.1 GeneID:904781;gbkey=CDS;product= 28dimethylallyl 29adenosine tRNA methylthiotransferase;Note=catalyzes the formation of 2-methylthio-N6- 28dimethylallyl 29adenosine 28ms 282 29i 286 29A 29 at position 37 in tRNAs that read codons beginning with uridine from N6- 28dimethylallyl 29adenosine 28i 286 29A 29 NC_002163.1 RefSeq region 422466 422648 . - . ID=id907;gene=miaB;Name=id907;Dbxref=GeneID:904781;gbkey=misc_feature;Note=HMMPfam hit to PF01938 2C TRAM domain 2C score 2.9e-10 NC_002163.1 RefSeq region 422805 423332 . - . ID=id908;gene=miaB;Name=id908;Dbxref=GeneID:904781;gbkey=misc_feature;Note=HMMPfam hit to PF04055 2C Radical SAM superfamily 2Cscore 3.8e-32 NC_002163.1 RefSeq region 423249 423281 . - . ID=id909;gene=miaB;Name=id909;Dbxref=GeneID:904781;gbkey=misc_feature;Note=PS00133 Zinc carboxypeptidases 2C zinc-binding region 2 signature NC_002163.1 RefSeq region 423270 423332 . - . ID=id910;gene=miaB;Name=id910;Dbxref=GeneID:904781;gbkey=misc_feature;Note=PS01278 Uncharacterized protein family UPF0004 signature NC_002163.1 RefSeq region 423456 423752 . - . ID=id911;gene=miaB;Name=id911;Dbxref=GeneID:904781;gbkey=misc_feature;Note=HMMPfam hit to PF00919 2C Uncharacterized protein family UPF0004 2C score 1.6e-40 NC_002163.1 RefSeq CDS 423761 424027 . - 0 ID=cds413;Parent=gene432;Name=YP_002343893.1;Dbxref=UniProtKB FTrEMBL:Q0PB54 Genbank:YP_002343893.1 GeneID:904782;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0459c 2C unknown 2C len: 88 aa 3B 32.5 25 identical to HP0268. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 423761 424027 . - . ID=gene432;gene=Cj0459c;Name=Cj0459c;locus_tag=Cj0459c;Dbxref=GeneID:904782;gbkey=Gene ### NC_002163.1 UTR_Extractor 5'-UTR 424028 424033 . - . ID=utr173;locus_tag=Cj0459c;product=hypothetical protein NC_002163.1 UTR_Extractor 5'-UTR 424090 424130 . + . ID=utr174;locus_tag=Cj0460;product=transcription elongation factor NusA NC_002163.1 RefSeq gene 424131 425219 . + . ID=gene433;gene=nusA;Name=nusA;locus_tag=Cj0460;Dbxref=GeneID:904783;gbkey=Gene NC_002163.1 RefSeq CDS 424131 425219 . + 0 ID=cds414;Parent=gene433;gene=nusA;Name=YP_002343894.1;Dbxref=GOA:Q0PB53 InterPro:IPR003029 InterPro:IPR010213 InterPro:IPR012340 InterPro:IPR013735 InterPro:IPR015946 UniProtKB FTrEMBL:Q0PB53 Genbank:YP_002343894.1 GeneID:904783;gbkey=CDS;product=transcription elongation factor NusA;Note=modifies transcription through interactions with RNA polymerase affecting elongation 2C readthrough 2C termination 2C and antitermination NC_002163.1 RefSeq CDS 425235 426422 . - 0 ID=cds415;Parent=gene434;Name=YP_002343895.1;Dbxref=GOA:Q0PB52 InterPro:IPR007427 UniProtKB FTrEMBL:Q0PB52 Genbank:YP_002343895.1 GeneID:904784;gbkey=CDS;product=MFS transport protein;Note=Original 282000 29 note: Cj0461c 2C probable integral membrane protein 2C len: 395 aa 3B some similarity to a hypothetical protein from B. subtilis TR:O31400 28EMBL:AJ222587 29 YKUC 28430 aa 29 2C fasta scores 3B opt: 172 z-score: 369.7 E 28 29: 2.7e-13 2C 23.8 25 identity in 407 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domains PF07690 Major Facilitator Superfamily 28MFS 29 and PF04332 Protein of unknown function 28DUF475 29 were identified within CDS. Twelve probable transmembrane helices predicted by TMHMM2.0. Product modified to more specific family member due to motif match. No specific characterisation has been carried out yet. kept within product function. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 425235 426422 . - . ID=gene434;Name=Cj0461c;locus_tag=Cj0461c;Dbxref=GeneID:904784;gbkey=Gene NC_002163.1 RefSeq region 425238 426257 . - . ID=id912;Name=id912;Dbxref=GeneID:904784;gbkey=misc_feature;Note=HMMPfam hit to PF04332 2C Protein of unknown function 28DUF475 29 2C score 3e-192 NC_002163.1 RefSeq region 425250 425309 . - . ID=id40;Name=id40;Dbxref=GeneID:904784;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0461c by TMHMM2.0 at aa 21-43 2C 48-70 2C 77-99 2C 103-122 2C143-165 2C 169-191 2C 211-233 2C 248-270 2C 282-299 2C 303-325 2C346-368 and 372-391 NC_002163.1 RefSeq region 425319 425387 . - . ID=id40;Name=id40;Dbxref=GeneID:904784;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0461c by TMHMM2.0 at aa 21-43 2C 48-70 2C 77-99 2C 103-122 2C143-165 2C 169-191 2C 211-233 2C 248-270 2C 282-299 2C 303-325 2C346-368 and 372-391 NC_002163.1 RefSeq region 425331 426377 . - . ID=id913;Name=id913;Dbxref=GeneID:904784;gbkey=misc_feature;Note=HMMPfam hit to PF07690 2C Major Facilitator Superfamily 2C score 1.2e-15 NC_002163.1 RefSeq region 425448 425516 . - . ID=id40;Name=id40;Dbxref=GeneID:904784;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0461c by TMHMM2.0 at aa 21-43 2C 48-70 2C 77-99 2C 103-122 2C143-165 2C 169-191 2C 211-233 2C 248-270 2C 282-299 2C 303-325 2C346-368 and 372-391 NC_002163.1 RefSeq region 425526 425579 . - . ID=id40;Name=id40;Dbxref=GeneID:904784;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0461c by TMHMM2.0 at aa 21-43 2C 48-70 2C 77-99 2C 103-122 2C143-165 2C 169-191 2C 211-233 2C 248-270 2C 282-299 2C 303-325 2C346-368 and 372-391 NC_002163.1 RefSeq region 425613 425681 . - . ID=id40;Name=id40;Dbxref=GeneID:904784;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0461c by TMHMM2.0 at aa 21-43 2C 48-70 2C 77-99 2C 103-122 2C143-165 2C 169-191 2C 211-233 2C 248-270 2C 282-299 2C 303-325 2C346-368 and 372-391 NC_002163.1 RefSeq region 425724 425792 . - . ID=id40;Name=id40;Dbxref=GeneID:904784;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0461c by TMHMM2.0 at aa 21-43 2C 48-70 2C 77-99 2C 103-122 2C143-165 2C 169-191 2C 211-233 2C 248-270 2C 282-299 2C 303-325 2C346-368 and 372-391 NC_002163.1 RefSeq region 425850 425918 . - . ID=id40;Name=id40;Dbxref=GeneID:904784;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0461c by TMHMM2.0 at aa 21-43 2C 48-70 2C 77-99 2C 103-122 2C143-165 2C 169-191 2C 211-233 2C 248-270 2C 282-299 2C 303-325 2C346-368 and 372-391 NC_002163.1 RefSeq region 425928 425996 . - . ID=id40;Name=id40;Dbxref=GeneID:904784;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0461c by TMHMM2.0 at aa 21-43 2C 48-70 2C 77-99 2C 103-122 2C143-165 2C 169-191 2C 211-233 2C 248-270 2C 282-299 2C 303-325 2C346-368 and 372-391 NC_002163.1 RefSeq region 426057 426116 . - . ID=id40;Name=id40;Dbxref=GeneID:904784;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0461c by TMHMM2.0 at aa 21-43 2C 48-70 2C 77-99 2C 103-122 2C143-165 2C 169-191 2C 211-233 2C 248-270 2C 282-299 2C 303-325 2C346-368 and 372-391 NC_002163.1 RefSeq region 426126 426194 . - . ID=id40;Name=id40;Dbxref=GeneID:904784;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0461c by TMHMM2.0 at aa 21-43 2C 48-70 2C 77-99 2C 103-122 2C143-165 2C 169-191 2C 211-233 2C 248-270 2C 282-299 2C 303-325 2C346-368 and 372-391 NC_002163.1 RefSeq region 426213 426281 . - . ID=id40;Name=id40;Dbxref=GeneID:904784;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0461c by TMHMM2.0 at aa 21-43 2C 48-70 2C 77-99 2C 103-122 2C143-165 2C 169-191 2C 211-233 2C 248-270 2C 282-299 2C 303-325 2C346-368 and 372-391 NC_002163.1 RefSeq region 426294 426362 . - . ID=id40;Name=id40;Dbxref=GeneID:904784;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0461c by TMHMM2.0 at aa 21-43 2C 48-70 2C 77-99 2C 103-122 2C143-165 2C 169-191 2C 211-233 2C 248-270 2C 282-299 2C 303-325 2C346-368 and 372-391 NC_002163.1 UTR_Extractor 5'-UTR 426422 426422 . - . ID=utr175;locus_tag=Cj0461c;product=putative MFS transport protein ### NC_002163.1 UTR_Extractor 5'-UTR 426470 426495 . + . ID=utr176;locus_tag=Cj0462;product=hypothetical protein NC_002163.1 RefSeq CDS 426496 427542 . + 0 ID=cds416;Parent=gene435;Name=YP_002343896.1;Dbxref=GOA:Q0PB51 InterPro:IPR000160 InterPro:IPR005244 InterPro:IPR006638 InterPro:IPR007197 InterPro:IPR013785 UniProtKB FTrEMBL:Q0PB51 Genbank:YP_002343896.1 GeneID:904785;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0462 2C unknown 2C len: 348 aa 3B similar to many hypothetical proteins e.g. TR:O66979 28EMBL:AE000707 29 Aquifex aeolicus AQ_789 28361 aa 29 2C fasta scores 3B opt: 1202 z-score: 1804.1 E 28 29: 0 2C 51.4 25 identity in 348 aa overlap. 66.2 25 identity to HP0656. Also similar to Cj1368 2835.5 25 identity in 349 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF04055 Radical SAM superfamily identified within CDS. Radical SAM proteins catalyze diverse reactions 2C including unusual methylations 2C isomerization 2C sulphur insertion 2C ring formation 2C anaerobic oxidation and protein radical formation. Prosite PS50887 GGDEF domain identified within CDS. This domain appears to be ubiquitous in bacteria and is often linked to a regulatory domain 2C such as a phosphorylation receiver or oxygen sensing domain. Product modified to more specific family member due to motif match. Functional classification - Misc NC_002163.1 RefSeq gene 426496 427542 . + . ID=gene435;Name=Cj0462;locus_tag=Cj0462;Dbxref=GeneID:904785;gbkey=Gene NC_002163.1 RefSeq region 426631 427155 . + . ID=id914;Name=id914;Dbxref=GeneID:904785;gbkey=misc_feature;Note=HMMPfam hit to PF04055 2C Radical SAM superfamily 2Cscore 9.3e-25 NC_002163.1 RefSeq gene 427542 428762 . + . ID=gene436;Name=Cj0463;locus_tag=Cj0463;Dbxref=GeneID:904786;gbkey=Gene NC_002163.1 RefSeq CDS 427542 428762 . + 0 ID=cds417;Parent=gene436;Name=YP_002343897.1;Dbxref=GOA:Q0PB50 InterPro:IPR007863 InterPro:IPR011237 UniProtKB FTrEMBL:Q0PB50 Genbank:YP_002343897.1 GeneID:904786;gbkey=CDS;product=zinc protease-like protein;Note=Original 282000 29 note: Cj0463 2C zinc protease-like protein 2C len: 406 aa 3B some similarity to members of the peptidase M16 28insulinase 29 family e.g. Y4WB_RHISN hypothetical zinc protease-like protein Y4WB 28447 aa 29 2Cfasta scores 3B opt: 375 z-score: 306.4 E 28 29: 9.1e-10 2C 22.7 25 identity in 396 aa overlap. 39.3 25 identity to HP0657 7EUpdated 282006 29 note: Pfam domain PF05193 Peptidase M16 inactive domain identified within CDS. No specific characterisation has been carried out yet. Product function left unchanged. Functional classification -Degradation of macromolecules - Proteins 2C peptides and glycopeptides NC_002163.1 RefSeq region 428019 428555 . + . ID=id915;Name=id915;Dbxref=GeneID:904786;gbkey=misc_feature;Note=HMMPfam hit to PF05193 2C Peptidase M16 inactive domain 2C score 1.5e-34 NC_002163.1 RefSeq gene 428752 430575 . + . ID=gene437;gene=recG;Name=recG;locus_tag=Cj0464;Dbxref=GeneID:904787;gbkey=Gene NC_002163.1 RefSeq CDS 428752 430575 . + 0 ID=cds418;Parent=gene437;gene=recG;Name=YP_002343898.1;Dbxref=GOA:Q0PB49 InterPro:IPR001650 InterPro:IPR011545 InterPro:IPR014001 InterPro:IPR014021 UniProtKB FTrEMBL:Q0PB49 Genbank:YP_002343898.1 GeneID:904787;gbkey=CDS;product=ATP-dependent DNA helicase RecG;Note=catalyzes branch migration in Holliday junction intermediates NC_002163.1 RefSeq region 429421 429888 . + . ID=id916;gene=recG;Name=id916;Dbxref=GeneID:904787;gbkey=misc_feature;Note=HMMPfam hit to PF04851 2C Type III restriction enzyme 2C res subunit 2C score 4.1e-06 NC_002163.1 RefSeq region 429427 429903 . + . ID=id917;gene=recG;Name=id917;Dbxref=GeneID:904787;gbkey=misc_feature;Note=HMMPfam hit to PF00270 2C DEAD 2FDEAH box helicase 2Cscore 6.9e-25 NC_002163.1 RefSeq region 429508 429531 . + . ID=id918;gene=recG;Name=id918;Dbxref=GeneID:904787;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 430117 430335 . + . ID=id919;gene=recG;Name=id919;Dbxref=GeneID:904787;gbkey=misc_feature;Note=HMMPfam hit to PF00271 2C Helicase conserved C-terminal domain 2C score 2.2e-13 NC_002163.1 RefSeq sRNA 430270 430366 . + . ID=NC_002163.1:CJnc22:unknown_transcript_1;Parent=NC_002163.1:CJnc22;Name=NC_002163.1:CJnc22:unknown_transcript_1;locus_tag=CJnc22;gbkey=misc_RNA;product=CJnc22 NC_002163.1 RefSeq gene 430270 430366 . + . ID=NC_002163.1:CJnc22;Name=NC_002163.1:CJnc22;locus_tag=CJnc22 NC_002163.1 RefSeq CDS 430572 430955 . - 0 ID=cds419;Parent=gene438;gene=ctb;Name=YP_002343899.1;Dbxref=PDB:2IG3 UniProtKB FTrEMBL:Q0PB48 Genbank:YP_002343899.1 GeneID:904788;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0465c 2C unknown 2C len: 127 aa 3B identical to C. jejuni hypothetical protein TR:O52917 28EMBL:CJAJ2417 29 clone 1g9 ORF1 28fragment 29 2874 aa 29. No Hp match 7EUpdated 282006 29 note: Pfam domain PF01152 Bacterial-like globin identified within CDS. This family of heme binding proteins are found mainly in bacteria. Characterised within Campylobacter jejuni. Ctb protein is shown to be involved in moderating oxygen flux within Campylobacter jejuni. NssR 28Nitrosative stress sensing Regulator - Cj0466 29 controls the expression of a nitrosative stress-responsive regulon in Campylobacter jejuni which includes ctb 28Cj0465c 29 and cgb 28Cj1586 29. not added to product function. Functional classification - Energy metabolism - Electron transport 7EPMID:16681372 2C PMID:16339953 2C PMID:16045618 2CPMID:15292134 NC_002163.1 RefSeq gene 430572 430955 . - . ID=gene438;gene=ctb;Name=ctb;locus_tag=Cj0465c;Dbxref=GeneID:904788;gbkey=Gene ### NC_002163.1 UTR_Extractor 5'-UTR 430956 430983 . - . ID=utr177;locus_tag=Cj0465c;product=group III truncated haemoglobin NC_002163.1 UTR_Extractor 5'-UTR 431001 431049 . + . ID=utr178;locus_tag=Cj0466;product=transcriptional regulator NC_002163.1 RefSeq CDS 431050 431646 . + 0 ID=cds420;Parent=gene439;gene=nssR;Name=YP_002343900.1;Dbxref=InterPro:IPR000595 InterPro:IPR014710 UniProtKB FTrEMBL:Q0PB47 Genbank:YP_002343900.1 GeneID:904789;gbkey=CDS;product=transcriptional regulator;Note=Original 282000 29 note: Cj0466 2C probable transcriptional regulator 2C len: 198 aa 3B similar to members of the crp 2Ffnr family e.g. CRP_SALTY catabolite gene activator 28210 aa 29 2C fasta scores 3B opt: 191 z-score: 236.7 E 28 29: 6.9e-06 2C 24.1 25 identity in 195 aa overlap 2C and FNR_BACSU anaerobic regulatory protein 28238 aa 29 2C fasta scores 3B opt: 182 z-score: 215.5 E 28 29: 0.0001 2C 23.0 25 identity in 209 aa overlap. No Hp match. Contains helix-turn-helix motif at aa 150-171 28Score 1452 2C 2B4.13 SD 29 7EUpdated 282006 29 note: Pfam domain PF00027 Cyclic nucleotide-binding domain identified within CDS. Prosite PS50042 CNMP_BINDING_3 2C Cyclic nucleotide-binding identified within CDS. Characterised within Campylobacter jejuni. NssR 28Nitrosative stress sensing Regulator 29 controls the expression of a nitrosative stress-responsive regulon in Campylobacter jejuni which includes ctb 28Cj0465c 29 and cgb 28Cj1586 29. not added to product function. Functional classification - Broad regulatory functions 7EPMID:16045618 2C PMID:15292134 2C PMID:16339953 2CPMID:16681372 NC_002163.1 RefSeq gene 431050 431646 . + . ID=gene439;gene=nssR;Name=nssR;locus_tag=Cj0466;Dbxref=GeneID:904789;gbkey=Gene NC_002163.1 RefSeq region 431080 431361 . + . ID=id920;gene=nssR;Name=id920;Dbxref=GeneID:904789;gbkey=misc_feature;Note=HMMPfam hit to PF00027 2C Cyclic nucleotide-binding domain 2C score 2.2e-15 NC_002163.1 UTR_Extractor 5'-UTR 431609 431661 . + . ID=utr179;locus_tag=Cj0467;product=amino-acid ABC transporter integral membrane protein ### NC_002163.1 RefSeq CDS 431662 432363 . + 0 ID=cds421;Parent=gene440;Name=YP_002343901.1;Dbxref=GOA:Q0PB46 InterPro:IPR000515 InterPro:IPR010065 UniProtKB FTrEMBL:Q0PB46 Genbank:YP_002343901.1 GeneID:904790;gbkey=CDS;product=amino acid ABC transporter integral membrane protein;Note=Original 282000 29 note: Cj0467 2C probable amino-acid ABC transporter integral membrane protein 2C len: 233 aa 3B similar to many e.g. GLNP_ECOLI glutamine transport system permease 28219 aa 29 2C fasta scores 3B opt: 237 z-score: 468.8 E 28 29: 8.1e-19 2C 32.6 25 identity in 233 aa overlap. 45.3 25 identity to HP1169. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp sign. and Pfam match to entry PF00528 BPD_transp 2CBinding-protein-dependent transport systems inner membrane component 2C score 50.10 2C E-value 4.9e-11 7EUpdated 282006 29 note: Literature search identified paper within Campylobacter jejuni linking Cj0467 2C Cj0468 and Cj0469 as cysteine transporters. Three probable transmembrane helices predicted by TMHMM2.0. not added to product function. Functional classification - Transport 2Fbinding proteins - Amino acids and amines 7EPMID:15948956 NC_002163.1 RefSeq gene 431662 432363 . + . ID=gene440;Name=Cj0467;locus_tag=Cj0467;Dbxref=GeneID:904790;gbkey=Gene NC_002163.1 RefSeq region 431704 431772 . + . ID=id921;Name=id921;Dbxref=GeneID:904790;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0467 by TMHMM2.0 at aa 15-37 2C 151-173 and 204-226 NC_002163.1 RefSeq region 431710 432357 . + . ID=id922;Name=id922;Dbxref=GeneID:904790;gbkey=misc_feature;Note=HMMPfam hit to PF00528 2C Binding-protein-dependent transport syst 2C score 1.8e-15 NC_002163.1 RefSeq region 432040 432126 . + . ID=id923;Name=id923;Dbxref=GeneID:904790;gbkey=misc_feature;Note=PS00402 Binding-protein-dependent transport systems inner membrane comp. sign NC_002163.1 RefSeq region 432112 432180 . + . ID=id921;Name=id921;Dbxref=GeneID:904790;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0467 by TMHMM2.0 at aa 15-37 2C 151-173 and 204-226 NC_002163.1 RefSeq region 432271 432339 . + . ID=id921;Name=id921;Dbxref=GeneID:904790;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0467 by TMHMM2.0 at aa 15-37 2C 151-173 and 204-226 NC_002163.1 RefSeq gene 432356 433012 . + . ID=gene441;Name=Cj0468;locus_tag=Cj0468;Dbxref=GeneID:904791;gbkey=Gene NC_002163.1 RefSeq CDS 432356 433012 . + 0 ID=cds422;Parent=gene441;Name=YP_002343902.1;Dbxref=GOA:Q0PB45 InterPro:IPR000515 InterPro:IPR010065 UniProtKB FTrEMBL:Q0PB45 Genbank:YP_002343902.1 GeneID:904791;gbkey=CDS;product=amino acid ABC transporter integral membrane protein;Note=Original 282000 29 note: Cj0468 2C probable amino-acid ABC transporter integral membrane protein 2C len: 218 aa 3B similar to many e.g. GLTJ_ECOLI glutamate 2Faspartate transport system permease 28246 aa 29 2C fasta scores 3B opt: 194 z-score: 425.1 E 28 29: 2.2e-16 2C 25.7 25 identity in 222 aa overlap. 49.3 25 identity to HP1170. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp sign. and Pfam match to entry PF00528 BPD_transp 2CBinding-protein-dependent transport systems inner membrane component 2C score 52.80 2C E-value 7.6e-12 7EUpdated 282006 29 note: Literature search identified paper within Campylobacter jejuni linking Cj0467 2C Cj0468 and Cj0469 as cysteine transporters. Five probable transmembrane helices predicted by TMHMM2.0. not added to product function. Functional classification - Transport 2Fbinding proteins - Amino acids and amines 7EPMID:15948956 NC_002163.1 RefSeq region 432404 433003 . + . ID=id924;Name=id924;Dbxref=GeneID:904791;gbkey=misc_feature;Note=HMMPfam hit to PF00528 2C Binding-protein-dependent transport syst 2C score 8.5e-13 NC_002163.1 RefSeq region 432413 432481 . + . ID=id925;Name=id925;Dbxref=GeneID:904791;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0468 by TMHMM2.0 at aa 20-42 2C 55-77 2C 87-109 2C 151-171 and 186-208 NC_002163.1 RefSeq region 432518 432586 . + . ID=id925;Name=id925;Dbxref=GeneID:904791;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0468 by TMHMM2.0 at aa 20-42 2C 55-77 2C 87-109 2C 151-171 and 186-208 NC_002163.1 RefSeq region 432614 432682 . + . ID=id925;Name=id925;Dbxref=GeneID:904791;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0468 by TMHMM2.0 at aa 20-42 2C 55-77 2C 87-109 2C 151-171 and 186-208 NC_002163.1 RefSeq region 432683 432769 . + . ID=id926;Name=id926;Dbxref=GeneID:904791;gbkey=misc_feature;Note=PS00402 Binding-protein-dependent transport systems inner membrane comp. sign NC_002163.1 UTR_Extractor 5'-UTR 432771 433013 . + . ID=utr180;locus_tag=Cj0469;product=amino-acid ABC transporter ATP-binding protein NC_002163.1 RefSeq region 432806 432868 . + . ID=id925;Name=id925;Dbxref=GeneID:904791;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0468 by TMHMM2.0 at aa 20-42 2C 55-77 2C 87-109 2C 151-171 and 186-208 NC_002163.1 RefSeq region 432911 432979 . + . ID=id925;Name=id925;Dbxref=GeneID:904791;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0468 by TMHMM2.0 at aa 20-42 2C 55-77 2C 87-109 2C 151-171 and 186-208 ### NC_002163.1 RefSeq CDS 433014 433775 . + 0 ID=cds423;Parent=gene442;Name=YP_002343903.1;Dbxref=GOA:Q0PB44 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FTrEMBL:Q0PB44 Genbank:YP_002343903.1 GeneID:904792;gbkey=CDS;product=amino acid ABC transporter ATP-binding protein;Note=Original 282000 29 note: Cj0469 2C probable amino-acid ABC transporter ATP-binding protein 2C len: 2t53 aa 3B highly similar to many e.g. GLNQ_BACST glutamine transport ATP-binding protein 28242 aa 29 2C fasta scores 3B opt: 902 z-score: 1279.6 E 28 29: 0 2C 55.4 25 identity in 242 aa overlap. 61.4 25 identity to HP1171. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00211 ABC transporters family signature 2C and Pfam match to entry PF00005 ABC_tran 2C ABC transporters 2C score 227.80 2C E-value 1.6e-64 7EUpdated 282006 29 note: Literature search identified paper within Campylobacter jejuni linking Cj0467 2C Cj0468 and Cj0469 as cysteine transporters. not added to product function. Functional classification -Transport 2Fbinding proteins - Amino acids and amines 7EPMID:15948956 NC_002163.1 RefSeq gene 433014 433775 . + . ID=gene442;Name=Cj0469;locus_tag=Cj0469;Dbxref=GeneID:904792;gbkey=Gene NC_002163.1 RefSeq region 433098 433655 . + . ID=id927;Name=id927;Dbxref=GeneID:904792;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 1.7e-65 NC_002163.1 RefSeq region 433119 433142 . + . ID=id928;Name=id928;Dbxref=GeneID:904792;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 433428 433472 . + . ID=id929;Name=id929;Dbxref=GeneID:904792;gbkey=misc_feature;Note=PS00211 ABC transporters family signature ### NC_002163.1 RefSeq gene 433867 433942 . + . ID=gene443;gene=tRNAThr;Name=tRNAThr;locus_tag=Cjp06;Dbxref=GeneID:904793;gbkey=Gene NC_002163.1 RefSeq tRNA 433867 433942 . + . ID=rna13;Parent=gene443;gene=tRNAThr;Name=rna13;Dbxref=GeneID:904793;gbkey=tRNA;product=tRNA-Thr;Note=tRNA Thr anticodon TGT 2C Cove score 96.83 NC_002163.1 RefSeq exon 433867 433942 . + . ID=id930;Parent=rna13;gene=tRNAThr;Name=id930;Dbxref=GeneID:904793;gbkey=tRNA;product=tRNA-Thr;Note=tRNA Thr anticodon TGT 2C Cove score 96.83 NC_002163.1 RefSeq gene 433992 434077 . + . ID=gene444;gene=tRNATyr;Name=tRNATyr;locus_tag=Cjp07;Dbxref=GeneID:904794;gbkey=Gene NC_002163.1 RefSeq tRNA 433992 434077 . + . ID=rna14;Parent=gene444;gene=tRNATyr;Name=rna14;Dbxref=GeneID:904794;gbkey=tRNA;product=tRNA-Tyr;Note=tRNA Tyr anticodon GTA 2C Cove score 64.32 NC_002163.1 RefSeq exon 433992 434077 . + . ID=id931;Parent=rna14;gene=tRNATyr;Name=id931;Dbxref=GeneID:904794;gbkey=tRNA;product=tRNA-Tyr;Note=tRNA Tyr anticodon GTA 2C Cove score 64.32 NC_002163.1 RefSeq gene 434084 434160 . + . ID=gene445;gene=tRNAGly;Name=tRNAGly;locus_tag=Cjp08;Dbxref=GeneID:904795;gbkey=Gene NC_002163.1 RefSeq tRNA 434084 434160 . + . ID=rna15;Parent=gene445;gene=tRNAGly;Name=rna15;Dbxref=GeneID:904795;gbkey=tRNA;product=tRNA-Gly;Note=tRNA Gly anticodon TCC 2C Cove score 96.94 NC_002163.1 RefSeq exon 434084 434160 . + . ID=id932;Parent=rna15;gene=tRNAGly;Name=id932;Dbxref=GeneID:904795;gbkey=tRNA;product=tRNA-Gly;Note=tRNA Gly anticodon TCC 2C Cove score 96.94 NC_002163.1 RefSeq gene 434265 434339 . + . ID=gene446;gene=tRNAThr;Name=tRNAThr;locus_tag=Cjt1;Dbxref=GeneID:3245039;gbkey=Gene NC_002163.1 RefSeq tRNA 434265 434339 . + . ID=rna16;Parent=gene446;gene=tRNAThr;Name=rna16;Dbxref=GeneID:3245039;gbkey=tRNA;product=tRNA-Thr;Note=tRNA Thr anticodon GGT 2C Cove score 83.71 NC_002163.1 RefSeq exon 434265 434339 . + . ID=id933;Parent=rna16;gene=tRNAThr;Name=id933;Dbxref=GeneID:3245039;gbkey=tRNA;product=tRNA-Thr;Note=tRNA Thr anticodon GGT 2C Cove score 83.71 NC_002163.1 RefSeq CDS 434408 435607 . + 0 ID=cds424;Parent=gene447;gene=tuf;Name=YP_002343904.1;Dbxref=GOA:O69303 HSSP:P02990 InterPro:IPR000795 InterPro:IPR004160 InterPro:IPR004161 InterPro:IPR004541 InterPro:IPR005225 UniProtKB FSwiss-Prot:O69303 Genbank:YP_002343904.1 GeneID:904796;gbkey=CDS;product=elongation factor Tu;Note=EF-Tu 3B promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis 3B when the tRNA anticodon matches the mRNA codon 2C GTP hydrolysis results 3B the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts 3B many prokaryotes have two copies of the gene encoding EF-Tu NC_002163.1 RefSeq gene 434408 435607 . + . ID=gene447;gene=tuf;Name=tuf;locus_tag=Cj0470;Dbxref=GeneID:904796;gbkey=Gene NC_002163.1 RefSeq region 434435 435034 . + . ID=id934;gene=tuf;Name=id934;Dbxref=GeneID:904796;gbkey=misc_feature;Note=HMMPfam hit to PF00009 2C Elongation factor Tu GTP binding domain 2C score 3.9e-98 NC_002163.1 RefSeq region 434462 434485 . + . ID=id935;gene=tuf;Name=id935;Dbxref=GeneID:904796;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 434558 434605 . + . ID=id936;gene=tuf;Name=id936;Dbxref=GeneID:904796;gbkey=misc_feature;Note=PS00301 GTP-binding elongation factors signature NC_002163.1 RefSeq region 435095 435304 . + . ID=id937;gene=tuf;Name=id937;Dbxref=GeneID:904796;gbkey=misc_feature;Note=HMMPfam hit to PF03144 2C Elongation factor Tu domain 2C score 3.6e-25 NC_002163.1 RefSeq region 435317 435601 . + . ID=id938;gene=tuf;Name=id938;Dbxref=GeneID:904796;gbkey=misc_feature;Note=HMMPfam hit to PF03143 2C Elongation factor Tu C-terminal domain 2C score 1.4e-59 NC_002163.1 RefSeq region 435548 435571 . + . ID=id939;gene=tuf;Name=id939;Dbxref=GeneID:904796;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 RefSeq CDS 435660 435818 . + 0 ID=cds425;Parent=gene448;gene=rpmG;Name=YP_002343905.1;Dbxref=GOA:Q9PI38 InterPro:IPR001705 UniProtKB FSwiss-Prot:Q9PI38 Genbank:YP_002343905.1 GeneID:904797;gbkey=CDS;product=50S ribosomal protein L33;Note=in Escherichia coli BM108 2C a mutation that results in lack of L33 synthesis had no effect on ribosome synthesis or function 3B there are paralogous genes in several bacterial genomes 2C and a CXXC motif for zinc binding and an upstream regulation region of the paralog lacking this motif that are regulated by zinc similar to other ribosomal proteins like L31 3B the proteins in this group lack the CXXC motif NC_002163.1 RefSeq gene 435660 435818 . + . ID=gene448;gene=rpmG;Name=rpmG;locus_tag=Cj0471;Dbxref=GeneID:904797;gbkey=Gene NC_002163.1 RefSeq region 435663 435806 . + . ID=id940;gene=rpmG;Name=id940;Dbxref=GeneID:904797;gbkey=misc_feature;Note=HMMPfam hit to PF00471 2C Ribosomal protein L33 2Cscore 3.3e-21 NC_002163.1 RefSeq region 435708 435767 . + . ID=id941;gene=rpmG;Name=id941;Dbxref=GeneID:904797;gbkey=misc_feature;Note=PS00582 Ribosomal protein L33 signature ### NC_002163.1 RefSeq gene 435831 435906 . + . ID=gene449;gene=tRNATrp;Name=tRNATrp;locus_tag=Cjp09;Dbxref=GeneID:904798;gbkey=Gene NC_002163.1 RefSeq tRNA 435831 435906 . + . ID=rna17;Parent=gene449;gene=tRNATrp;Name=rna17;Dbxref=GeneID:904798;gbkey=tRNA;product=tRNA-Trp;Note=tRNA Trp anticodon CCA 2C Cove score 74.26 NC_002163.1 RefSeq exon 435831 435906 . + . ID=id942;Parent=rna17;gene=tRNATrp;Name=id942;Dbxref=GeneID:904798;gbkey=tRNA;product=tRNA-Trp;Note=tRNA Trp anticodon CCA 2C Cove score 74.26 NC_002163.1 RefSeq CDS 435925 436104 . + 0 ID=cds426;Parent=gene450;gene=secE;Name=YP_002343906.1;Dbxref=GOA:Q0PB41 InterPro:IPR001901 InterPro:IPR005807 UniProtKB FTrEMBL:Q0PB41 Genbank:YP_002343906.1 GeneID:904799;gbkey=CDS;product=preprotein translocase subunit SecE;Note=forms a complex with SecY and SecG 3B SecYEG forms a protein-conducting channel to which secA binds and translocates targeted polypeptides across the cytoplasmic membrane 2C a process driven by ATP and a proton-motive force NC_002163.1 RefSeq gene 435925 436104 . + . ID=gene450;gene=secE;Name=secE;locus_tag=Cj0472;Dbxref=GeneID:904799;gbkey=Gene NC_002163.1 RefSeq region 435931 436101 . + . ID=id943;gene=secE;Name=id943;Dbxref=GeneID:904799;gbkey=misc_feature;Note=HMMPfam hit to PF00584 2C SecE 2FSec61-gamma subunits of protein translo 2C score 4.9e-09 NC_002163.1 RefSeq region 436009 436077 . + . ID=id944;gene=secE;Name=id944;Dbxref=GeneID:904799;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0472 by TMHMM2.0 at aa 29-51 ### NC_002163.1 RefSeq CDS 436114 436647 . + 0 ID=cds427;Parent=gene451;gene=nusG;Name=YP_002343907.1;Dbxref=GOA:Q9PI36 HSSP:O67757 InterPro:IPR001062 InterPro:IPR005824 InterPro:IPR006645 InterPro:IPR015869 UniProtKB FSwiss-Prot:Q9PI36 Genbank:YP_002343907.1 GeneID:904801;gbkey=CDS;product=transcription antitermination protein NusG;Note=Modulates Rho-dependent transcription termination NC_002163.1 RefSeq gene 436114 436647 . + . ID=gene451;gene=nusG;Name=nusG;locus_tag=Cj0473;Dbxref=GeneID:904801;gbkey=Gene NC_002163.1 RefSeq region 436120 436251 . + . ID=id945;gene=nusG;Name=id945;Dbxref=GeneID:904801;gbkey=misc_feature;Note=HMMPfam hit to PF02357 2C Transcription termination factor nusG 2C score 2e-14 NC_002163.1 RefSeq region 436480 436593 . + . ID=id946;gene=nusG;Name=id946;Dbxref=GeneID:904801;gbkey=misc_feature;Note=HMMPfam hit to PF00467 2C KOW motif 2C score 2.4e-07 NC_002163.1 RefSeq region 436588 436617 . + . ID=id947;gene=nusG;Name=id947;Dbxref=GeneID:904801;gbkey=misc_feature;Note=PS01014 Transcription termination factor nusG signature ### NC_002163.1 RefSeq CDS 436673 437098 . + 0 ID=cds428;Parent=gene452;gene=rplK;Name=YP_002343908.1;Dbxref=GOA:Q9PI35 HSSP:P29395 InterPro:IPR000911 InterPro:IPR006519 UniProtKB FSwiss-Prot:Q9PI35 Genbank:YP_002343908.1 GeneID:904802;gbkey=CDS;product=50S ribosomal protein L11;Note=binds directly to 23S ribosomal RNA NC_002163.1 RefSeq gene 436673 437098 . + . ID=gene452;gene=rplK;Name=rplK;locus_tag=Cj0474;Dbxref=GeneID:904802;gbkey=Gene NC_002163.1 RefSeq region 436694 436870 . + . ID=id948;gene=rplK;Name=id948;Dbxref=GeneID:904802;gbkey=misc_feature;Note=HMMPfam hit to PF03946 2C Ribosomal protein L11 2CN-terminal dom 2C score 1.4e-33 NC_002163.1 RefSeq region 436883 437089 . + . ID=id949;gene=rplK;Name=id949;Dbxref=GeneID:904802;gbkey=misc_feature;Note=HMMPfam hit to PF00298 2C Ribosomal protein L11 2C RNA binding do 2C score 9.7e-27 NC_002163.1 RefSeq region 437048 437095 . + . ID=id950;gene=rplK;Name=id950;Dbxref=GeneID:904802;gbkey=misc_feature;Note=PS00359 Ribosomal protein L11 signature ### NC_002163.1 RefSeq CDS 437153 437854 . + 0 ID=cds429;Parent=gene453;gene=rplA;Name=YP_002343909.1;Dbxref=GOA:Q9PI34 HSSP:P27150 InterPro:IPR002143 InterPro:IPR005878 InterPro:IPR016094 UniProtKB FSwiss-Prot:Q9PI34 Genbank:YP_002343909.1 GeneID:904803;gbkey=CDS;product=50S ribosomal protein L1;Note=in Escherichia coli and Methanococcus 2C this protein autoregulates expression 3B the binding site in the mRNA mimics the binding site in the 23S rRNA NC_002163.1 RefSeq gene 437153 437854 . + . ID=gene453;gene=rplA;Name=rplA;locus_tag=Cj0475;Dbxref=GeneID:904803;gbkey=Gene NC_002163.1 RefSeq region 437195 437815 . + . ID=id951;gene=rplA;Name=id951;Dbxref=GeneID:904803;gbkey=misc_feature;Note=HMMPfam hit to PF00687 2C Ribosomal protein L1p 2FL10e family 2C score 3.8e-119 NC_002163.1 RefSeq region 437513 437569 . + . ID=id952;gene=rplA;Name=id952;Dbxref=GeneID:904803;gbkey=misc_feature;Note=PS01199 Ribosomal protein L1 signature ### NC_002163.1 RefSeq stem_loop 437883 437931 . + . ID=id953;Name=id953;gbkey=stem_loop NC_002163.1 UTR_Extractor 5'-UTR 437894 438005 . + . ID=utr181;locus_tag=Cj0476;product=50S ribosomal protein L10 ### NC_002163.1 RefSeq region 438006 438293 . + . ID=id954;gene=rplJ;Name=id954;Dbxref=GeneID:904804;gbkey=misc_feature;Note=HMMPfam hit to PF00466 2C Ribosomal protein L10 2Cscore 9.6e-20 NC_002163.1 RefSeq gene 438006 438485 . + . ID=gene454;gene=rplJ;Name=rplJ;locus_tag=Cj0476;Dbxref=GeneID:904804;gbkey=Gene NC_002163.1 RefSeq CDS 438006 438485 . + 0 ID=cds430;Parent=gene454;gene=rplJ;Name=YP_002343910.1;Dbxref=GOA:Q9PI33 InterPro:IPR001790 InterPro:IPR002363 UniProtKB FSwiss-Prot:Q9PI33 Genbank:YP_002343910.1 GeneID:904804;gbkey=CDS;product=50S ribosomal protein L10;Note=binds the two ribosomal protein L7 2FL12 dimers and anchors them to the large ribosomal subunit NC_002163.1 RefSeq region 438186 438209 . + . ID=id955;gene=rplJ;Name=id955;Dbxref=GeneID:904804;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 RefSeq gene 438506 438883 . + . ID=gene455;gene=rplL;Name=rplL;locus_tag=Cj0477;Dbxref=GeneID:904805;gbkey=Gene NC_002163.1 RefSeq CDS 438506 438883 . + 0 ID=cds431;Parent=gene455;gene=rplL;Name=YP_002343911.1;Dbxref=GOA:Q9PI32 HSSP:P02392 InterPro:IPR000206 InterPro:IPR013823 InterPro:IPR014719 UniProtKB FSwiss-Prot:Q9PI32 Genbank:YP_002343911.1 GeneID:904805;gbkey=CDS;product=50S ribosomal protein L7 2FL12;Note=present in two forms 3B L12 is normal 2C while L7 is aminoacylated at the N-terminal serine 3B the only multicopy ribosomal protein 3B 4:1 ratio of L7 2FL12 per ribosome 3B two L12 dimers bind L10 3B critically important for translation efficiency and fidelity 3B stimulates GTPase activity of translation factors NC_002163.1 RefSeq region 438677 438880 . + . ID=id956;gene=rplL;Name=id956;Dbxref=GeneID:904805;gbkey=misc_feature;Note=HMMPfam hit to PF00542 2C Ribosomal protein L7 2FL12 C-terminal dom 2C score 2.3e-38 ### NC_002163.1 RefSeq CDS 438992 443128 . + 0 ID=cds432;Parent=gene456;gene=rpoB;Name=YP_002343912.1;Dbxref=GOA:Q46124 HSSP:Q9KWU7 InterPro:IPR007120 InterPro:IPR007121 InterPro:IPR007641 InterPro:IPR007642 InterPro:IPR007644 InterPro:IPR007645 InterPro:IPR010243 InterPro:IPR015712 UniProtKB FSwiss-Prot:Q46124 Genbank:YP_002343912.1 GeneID:904806;gbkey=CDS;product=DNA-directed RNA polymerase subunit beta;Note=DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates 3B beta subunit is part of the catalytic core which binds with a sigma factor to produce the holoenzyme NC_002163.1 RefSeq gene 438992 443128 . + . ID=gene456;gene=rpoB;Name=rpoB;locus_tag=Cj0478;Dbxref=GeneID:904806;gbkey=Gene NC_002163.1 RefSeq region 439073 440563 . + . ID=id957;gene=rpoB;Name=id957;Dbxref=GeneID:904806;gbkey=misc_feature;Note=HMMPfam hit to PF04563 2C RNA polymerase beta subunit 2C score 3e-05 NC_002163.1 RefSeq region 439454 440392 . + . ID=id958;gene=rpoB;Name=id958;Dbxref=GeneID:904806;gbkey=misc_feature;Note=HMMPfam hit to PF04561 2C RNA polymerase Rpb2 2Cdomain 2C score 1.8e-11 NC_002163.1 RefSeq region 440564 440782 . + . ID=id959;gene=rpoB;Name=id959;Dbxref=GeneID:904806;gbkey=misc_feature;Note=HMMPfam hit to PF04565 2C RNA polymerase Rpb2 2Cdomain 2C score 3.9e-44 NC_002163.1 RefSeq region 441179 442876 . + . ID=id960;gene=rpoB;Name=id960;Dbxref=GeneID:904806;gbkey=misc_feature;Note=HMMPfam hit to PF00562 2C RNA polymerase Rpb2 2Cdomain 2C score 1.4e-148 NC_002163.1 RefSeq region 442265 442303 . + . ID=id961;gene=rpoB;Name=id961;Dbxref=GeneID:904806;gbkey=misc_feature;Note=PS01166 RNA polymerases beta chain signature NC_002163.1 RefSeq region 442880 443110 . + . ID=id962;gene=rpoB;Name=id962;Dbxref=GeneID:904806;gbkey=misc_feature;Note=HMMPfam hit to PF04560 2C RNA polymerase Rpb2 2Cdomain 2C score 3.7e-46 NC_002163.1 RefSeq CDS 443121 447674 . + 0 ID=cds433;Parent=gene457;gene=rpoC;Name=YP_002343913.1;Dbxref=GOA:Q9PI30 HSSP:Q9KWU6 InterPro:IPR000722 InterPro:IPR006592 InterPro:IPR007066 InterPro:IPR007080 InterPro:IPR007081 InterPro:IPR007083 InterPro:IPR012754 UniProtKB FSwiss-Prot:Q9PI30 Genbank:YP_002343913.1 GeneID:904807;gbkey=CDS;product=DNA-directed RNA polymerase subunit beta 27;Note=Original 282000 29 note: Cj0479 2C rpoC 2C DNA-directed RNA polymerase beta 27 chain 2C len: 1517 aa 3B highly similar to many e.g. RPOC_ECOLI DNA-directed RNA polymerase beta 27 chain 28EC 2.7.7.6 29 281407 aa 29 2C fasta scores 3B opt: 1505 z-score: 5793.8 E 28 29: 0 2C 46.1 25 identity in 1541 aa overlap. 69.7 25 identity to C-terminus of HP1198. Contains Pfam match to entry PF00623 RNA_pol_A 2C RNA polymerase alpha subunit 2C score 779.40 2C E-value 1.4e-230 7EUpdated 282006 29 note: A total of five Pfam domains have now been identified all encoding the same motif 3B RNA polymerase Rpb1 domain. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification - RNA synthesis 2C RNA modification and DNA transcription 7EPMID:6287430 2C PMID:6278450 NC_002163.1 RefSeq gene 443121 447674 . + . ID=gene457;gene=rpoC;Name=rpoC;locus_tag=Cj0479;Dbxref=GeneID:904807;gbkey=Gene NC_002163.1 RefSeq region 443163 444212 . + . ID=id963;gene=rpoC;Name=id963;Dbxref=GeneID:904807;gbkey=misc_feature;Note=HMMPfam hit to PF04997 2C RNA polymerase Rpb1 2Cdomain 2C score 3.7e-127 NC_002163.1 RefSeq region 444216 444644 . + . ID=id964;gene=rpoC;Name=id964;Dbxref=GeneID:904807;gbkey=misc_feature;Note=HMMPfam hit to PF00623 2C RNA polymerase Rpb1 2Cdomain 2C score 6.6e-84 NC_002163.1 RefSeq region 444651 445079 . + . ID=id965;gene=rpoC;Name=id965;Dbxref=GeneID:904807;gbkey=misc_feature;Note=HMMPfam hit to PF04983 2C RNA polymerase Rpb1 2Cdomain 2C score 3.5e-44 NC_002163.1 RefSeq region 445152 445406 . + . ID=id966;gene=rpoC;Name=id966;Dbxref=GeneID:904807;gbkey=misc_feature;Note=HMMPfam hit to PF05000 2C RNA polymerase Rpb1 2Cdomain 2C score 3.6e-33 NC_002163.1 RefSeq region 445410 447512 . + . ID=id967;gene=rpoC;Name=id967;Dbxref=GeneID:904807;gbkey=misc_feature;Note=HMMPfam hit to PF04998 2C RNA polymerase Rpb1 2Cdomain 2C score 6.7e-68 ### NC_002163.1 RefSeq gene 447705 448466 . - . ID=gene458;Name=Cj0480c;locus_tag=Cj0480c;Dbxref=GeneID:904808;gbkey=Gene NC_002163.1 RefSeq CDS 447705 448466 . - 0 ID=cds434;Parent=gene458;Name=YP_002343914.1;Dbxref=GOA:Q0PB33 InterPro:IPR005471 InterPro:IPR014757 UniProtKB FTrEMBL:Q0PB33 Genbank:YP_002343914.1 GeneID:904808;gbkey=CDS;product=transcriptional regulator;Note=Original 282000 29 note: Cj0480c 2C probable transcriptional regulator 2C len: 253 aa 3B similar to many e.g. KDGR_ECOLI transcriptional regulator KDGR 28263 aa 29 2Cfasta scores 3B opt: 305 z-score: 319.1 E 28 29: 1.8e-10 2C 24.1 25 identity in 212 aa overlap. No Hp match. Contains helix-turn-helix motif at aa 21-42 28Score 1424 2C 2B4.04 SD 29 7EUpdated 282006 29 note: Pfam domain PF01614 Bacterial transcriptional regulator identified within CDS. This family of bacterial transcriptional regulators includes the glycerol operon regulatory protein and acetate operon repressor both of which are members of the iclR family. These proteins have a Helix-Turn-Helix motif at the N-terminus. Further support given to product function. No specific characterisation with acceptable identity score has been carried out yet. kept within product function. Functional classification - Broad regulatory functions NC_002163.1 RefSeq region 447744 448295 . - . ID=id968;Name=id968;Dbxref=GeneID:904808;gbkey=misc_feature;Note=HMMPfam hit to PF01614 2C Bacterial transcriptional regulator 2C score 8.6e-16 ### NC_002163.1 UTR_Extractor 5'-UTR 448661 448696 . + . ID=utr182;locus_tag=Cj0481;product=putative dihydrodipicolinate synthase NC_002163.1 RefSeq CDS 448697 449605 . + 0 ID=cds435;Parent=gene459;gene=dapA;Name=YP_002343915.1;Dbxref=GOA:Q0PB32 InterPro:IPR002220 InterPro:IPR013785 UniProtKB FTrEMBL:Q0PB32 Genbank:YP_002343915.1 GeneID:904809;gbkey=CDS;product=dihydrodipicolinate synthase;Note=Original 282000 29 note: Cj0481 2C probable lyase 2C len: 302 aa 3B similar to members of the DHDPS family 3B e.g. DAPA_BACSU dihydrodipicolinate synthase 28290 aa 29 2C fasta scores 3B opt: 444 z-score: 557.2 E 28 29: 9.6e-24 2C 27.6 25 identity in 275 aa overlap 2C and NPL_HAEIN probable N-acetylneuraminate lyase subunit 28293 aa 29 2C fasta scores 3B opt: 358 z-score: 428.6 E 28 29: 1.4e-16 2C 28.5 25 identity in 291 aa overlap. No Hp match. Also similar to C. jejuni dapA 2C Cj0806 3B 26.1 25 identity in 295 aa overlap. ContainsPfam match to entry PF00701 DHDPS 2CDihydrodipicolinate synthetase 2C score 70.30 2C E-value 4e-17 7EUpdated 282006 29 note: Based on similarity search results 2C product modified to more specific family member. Characterised within Bacillus subtilis and Eschereichia coli 2C however identity scores were marginal. kept within product function. Functional classification - Misc 7EPMID:8098035 2C PMID:P9047371 NC_002163.1 RefSeq gene 448697 449605 . + . ID=gene459;gene=dapA;Name=dapA;locus_tag=Cj0481;Dbxref=GeneID:904809;gbkey=Gene NC_002163.1 RefSeq region 448703 449569 . + . ID=id969;gene=dapA;Name=id969;Dbxref=GeneID:904809;gbkey=misc_feature;Note=HMMPfam hit to PF00701 2C Dihydrodipicolinate synthetase family 2C score 3.8e-30 NC_002163.1 RefSeq gene 449602 449865 . + . ID=gene460;gene=uxaA';Name=uxaA';locus_tag=Cj0482;Dbxref=GeneID:5066041;gbkey=Gene NC_002163.1 RefSeq CDS 449602 449865 . + 0 ID=cds436;Parent=gene460;gene=uxaA';Name=YP_002343916.1;Dbxref=GOA:Q0PB31 InterPro:IPR013974 UniProtKB FTrEMBL:Q0PB31 Genbank:YP_002343916.1 GeneID:5066041;gbkey=CDS;product=altronate hydrolase;Note=Original 282000 29 note: Cj0482 2C uxaA 27 possible altronate hydrolase N-terminus 2C len: 87 aa 3B similar to N-terminus of e.g. UXAA_ECOLI altronate hydrolase 28495 aa 29 2C fasta scores 3B opt: 199 z-score: 322.2 E 28 29: 1.2e-10. 46.2 25 identity in 78 aa overlap. Simlarity continues in downstream ORF Cj0485. No Hp match. Note that B. subtilis paralog of uxaA 2C YCBI_BACSU 2C also has a separate N-terminus 28YCBH_BACSU 29 7EUpdated 282006 29 note: Pfam domain PF04292 D-galactarate dehydratase 2F Altronate hydrolase identified within CDS. Further support given to product function. Characterisation work carried out within Escherichia coli with acceptable identity score. C-terminus seems to be downstream Cj0483. Gene names for Cj0482 and Cj0483 are identical with a 27 denoting two separate terminals for the same CDS. May well be a pseudogene. kept within product function. Functional classification - Central intermediary metabolism - General 7EPMID:3038546 2C PMID:10762278 NC_002163.1 RefSeq region 449608 449847 . + . ID=id970;gene=uxaA';Name=id970;Dbxref=GeneID:5066041;gbkey=misc_feature;Note=HMMPfam hit to PF04292 2C D-galactarate dehydratase 2F Altronate hydrol 2C score 1.1e-47 NC_002163.1 RefSeq region 449862 451031 . + . ID=id971;gene=uxaA';Name=id971;Dbxref=GeneID:904810;gbkey=misc_feature;Note=HMMPfam hit to PF04295 2C D-galactarate dehydratase 2F Altronate hydrol 2C score 3.8e-251 NC_002163.1 RefSeq gene 449862 451034 . + . ID=gene461;gene=uxaA';Name=uxaA';locus_tag=Cj0483;Dbxref=GeneID:904810;gbkey=Gene NC_002163.1 RefSeq CDS 449862 451034 . + 0 ID=cds437;Parent=gene461;gene=uxaA';Name=YP_002343917.1;Dbxref=GOA:Q0PB30 InterPro:IPR007392 UniProtKB FTrEMBL:Q0PB30 Genbank:YP_002343917.1 GeneID:904810;gbkey=CDS;product=altronate hydrolase;Note=Original 282000 29 note: Cj0483 2C uxaA 27 possible altronate hydrolase C-terminus 2C len: 390 aa 3B similar to C-terminus of e.g. UXAA_ECOLI altronate hydrolase 28495 aa 29 2C fasta scores 3B opt: 832 z-score: 1121.7 E 28 29: 0 2C 36.1 25 identity in 391 aa overlap. Simlarity continues from upstream ORF Cj0482. No Hp match. Note that B. subtilis paralog of uxaA 2C YCBI_BACSU 2C also has a separate N-terminus 28YCBH_BACSU 29 7EUpdated 282006 29 note: Pfam domain PF04295 D-galactarate dehydratase 2F Altronate hydrolase identified within CDS. Further support given to product function. Characterisation work carried out within Escherichia coli with acceptable identity score. N-terminus seems to be downstream Cj0483. Gene names for Cj0482 and Cj0483 are identical with a 27 denoting two separate terminals for the same CDS. May well be a pseudogene. kept within product function. Functional classification - Central intermediary metabolism - General 7EPMID:3038546 2C PMID:10762278 NC_002163.1 RefSeq region 450090 450122 . + . ID=id972;gene=uxaA';Name=id972;Dbxref=GeneID:904810;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq pseudogene 451046 452278 . + . ID=gene462;Name=Cj0484;locus_tag=Cj0484;Dbxref=GeneID:904811;gbkey=Gene NC_002163.1 RefSeq region 451103 451168 . + . ID=id973;Name=id973;Dbxref=GeneID:904811;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0484 by TMHMM2.0 at aa 20-41 2C 56-78 2C 85-104 2C 114-136 2C145-167 2C 177-199 2C 242-264 2C 279-301 2C 308-330 2C 334-356 and 365-387 NC_002163.1 RefSeq region 451115 452224 . + . ID=id974;Name=id974;Dbxref=GeneID:904811;gbkey=misc_feature;Note=HMMPfam hit to PF07690 2C Major Facilitator Superfamily 2C score 6.8e-47 NC_002163.1 RefSeq region 451211 451279 . + . ID=id973;Name=id973;Dbxref=GeneID:904811;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0484 by TMHMM2.0 at aa 20-41 2C 56-78 2C 85-104 2C 114-136 2C145-167 2C 177-199 2C 242-264 2C 279-301 2C 308-330 2C 334-356 and 365-387 NC_002163.1 RefSeq region 451298 451357 . + . ID=id973;Name=id973;Dbxref=GeneID:904811;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0484 by TMHMM2.0 at aa 20-41 2C 56-78 2C 85-104 2C 114-136 2C145-167 2C 177-199 2C 242-264 2C 279-301 2C 308-330 2C 334-356 and 365-387 NC_002163.1 RefSeq region 451385 451453 . + . ID=id973;Name=id973;Dbxref=GeneID:904811;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0484 by TMHMM2.0 at aa 20-41 2C 56-78 2C 85-104 2C 114-136 2C145-167 2C 177-199 2C 242-264 2C 279-301 2C 308-330 2C 334-356 and 365-387 NC_002163.1 RefSeq region 451478 451546 . + . ID=id973;Name=id973;Dbxref=GeneID:904811;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0484 by TMHMM2.0 at aa 20-41 2C 56-78 2C 85-104 2C 114-136 2C145-167 2C 177-199 2C 242-264 2C 279-301 2C 308-330 2C 334-356 and 365-387 NC_002163.1 RefSeq region 451574 451642 . + . ID=id973;Name=id973;Dbxref=GeneID:904811;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0484 by TMHMM2.0 at aa 20-41 2C 56-78 2C 85-104 2C 114-136 2C145-167 2C 177-199 2C 242-264 2C 279-301 2C 308-330 2C 334-356 and 365-387 NC_002163.1 RefSeq region 451769 451837 . + . ID=id973;Name=id973;Dbxref=GeneID:904811;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0484 by TMHMM2.0 at aa 20-41 2C 56-78 2C 85-104 2C 114-136 2C145-167 2C 177-199 2C 242-264 2C 279-301 2C 308-330 2C 334-356 and 365-387 NC_002163.1 RefSeq region 451880 451948 . + . ID=id973;Name=id973;Dbxref=GeneID:904811;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0484 by TMHMM2.0 at aa 20-41 2C 56-78 2C 85-104 2C 114-136 2C145-167 2C 177-199 2C 242-264 2C 279-301 2C 308-330 2C 334-356 and 365-387 NC_002163.1 RefSeq region 451967 452035 . + . ID=id973;Name=id973;Dbxref=GeneID:904811;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0484 by TMHMM2.0 at aa 20-41 2C 56-78 2C 85-104 2C 114-136 2C145-167 2C 177-199 2C 242-264 2C 279-301 2C 308-330 2C 334-356 and 365-387 NC_002163.1 RefSeq region 452045 452113 . + . ID=id973;Name=id973;Dbxref=GeneID:904811;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0484 by TMHMM2.0 at aa 20-41 2C 56-78 2C 85-104 2C 114-136 2C145-167 2C 177-199 2C 242-264 2C 279-301 2C 308-330 2C 334-356 and 365-387 NC_002163.1 RefSeq region 452138 452206 . + . ID=id973;Name=id973;Dbxref=GeneID:904811;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0484 by TMHMM2.0 at aa 20-41 2C 56-78 2C 85-104 2C 114-136 2C145-167 2C 177-199 2C 242-264 2C 279-301 2C 308-330 2C 334-356 and 365-387 ### NC_002163.1 RefSeq gene 452320 453108 . + . ID=gene463;Name=Cj0485;locus_tag=Cj0485;Dbxref=GeneID:904812;gbkey=Gene NC_002163.1 RefSeq CDS 452320 453108 . + 0 ID=cds438;Parent=gene463;Name=YP_002343919.1;Dbxref=GOA:Q0PB28 InterPro:IPR002198 InterPro:IPR002347 InterPro:IPR016040 UniProtKB FTrEMBL:Q0PB28 Genbank:YP_002343919.1 GeneID:904812;gbkey=CDS;product=short chain dehydrogenase;Note=Original 282000 29 note: Cj0485 2C probable oxidoreductase 2C len: 262 aa 3B similar to many e.g. FABG_AQUAE 3-oxoacyl- 5Bacyl-carrier protein 5D reductase 28248 aa 29 2C fasta scores 3B opt: 384 z-score: 465.5 E 28 29: 1.2e-18 2C34.3 25 identity in 254 aa overlap 2C and BA71_EUBSP 7-alpha-hydroxysteroid dehydrogenase 28249 aa 29 2C fasta scores 3B opt: 349 z-score: 421.2 E 28 29: 3.6e-16 2C 32.3 25 identity in 254 aa overlap. No Hp ortholog. Also similar to C. jejuni fabG 2C Cj0435 2831.7 25 identity in 252 aa overlap 29. Contains Pfam matches to entry PF00106 adh_short 2C Alcohol 2Fother dehydrogenases 2C short chain type 2Cscore 143.40 2C E-value 4e-39 and to entry PF00678 adh_short_C2 2C Short chain dehydrogenase 2Freductase C-terminus 2C score 31.00 2C E-value 2.7e-05 7EUpdated 282006 29 note: Characterisation work in more than one species with marginal identity scores. kept within product function. Functional classification -Misc NC_002163.1 RefSeq region 452347 453069 . + . ID=id975;Name=id975;Dbxref=GeneID:904812;gbkey=misc_feature;Note=HMMPfam hit to PF00106 2C short chain dehydrogenase 2Cscore 2.8e-49 ### NC_002163.1 RefSeq CDS 453119 454375 . + 0 ID=cds439;Parent=gene464;Name=YP_002343920.1;Dbxref=GOA:Q0PB27 InterPro:IPR005275 InterPro:IPR007114 InterPro:IPR011701 UniProtKB FTrEMBL:Q0PB27 Genbank:YP_002343920.1 GeneID:904814;gbkey=CDS;product=sugar transporter;Note=Original 282000 29 note: Cj0486 2C probable sugar transporter 2C len: 418 aa 3B simlar to members of the FHS family e.g. FUCP_ECOLI L-fucose permease 28438 aa 29 2C fasta scores 3B opt: 848 z-score: 1022.1 E 28 29: 0 2C 37.2 25 identity in 390 aa overlap 2C and GLUP_BRUAB glucose 2Fgalactose transporter 28412 aa 29 2C fasta scores 3B opt: 456 z-score: 830.5 E 28 29: 0 2C 33.4 25 identity in 410 aa overlap. 32.6 25 identity to HP1174 7EUpdated 282006 29 note: Pfam domain PF07690 Major Facilitator Superfamily identified within CDS. Prosite PS50850 MFS 2C Major facilitator superfamily also identified along with twelve probable transmembrane helices predicted by TMHMM2.0. TIGRFAM motif TIGR00885 L-fucose permease was also identified. Fasta search gave high score to L-fucose-proton symporter 28L-fucose permease 29. This permease mediates the uptake of L-fucose across the boundary membrane with the concomitant transport of protons into the cell 28symport system 29. It can also transport L-galactose and D-arabinose 2C but at reduced rates compared with L-fucose. Other sugar transporters also identified. Product function kept the same along with . Functional classification - Transport 2Fbinding proteins - Carbohydrates 2C organic acids and alcohols 7EPMID:15919996 2C PMID:7783647 2C PMID:8052131 NC_002163.1 RefSeq gene 453119 454375 . + . ID=gene464;Name=Cj0486;locus_tag=Cj0486;Dbxref=GeneID:904814;gbkey=Gene NC_002163.1 RefSeq region 453143 453211 . + . ID=id976;Name=id976;Dbxref=GeneID:904814;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0486 by TMHMM2.0 at aa 9-31 2C 46-68 2C 75-97 2C 102-124 2C144-163 2C 183-205 2C 236-258 2C 273-290 2C 303-320 2C 325-347 2C359-381 and 385-407 NC_002163.1 RefSeq region 453143 454267 . + . ID=id977;Name=id977;Dbxref=GeneID:904814;gbkey=misc_feature;Note=HMMPfam hit to PF07690 2C Major Facilitator Superfamily 2C score 2.2e-30 NC_002163.1 RefSeq region 453254 453322 . + . ID=id976;Name=id976;Dbxref=GeneID:904814;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0486 by TMHMM2.0 at aa 9-31 2C 46-68 2C 75-97 2C 102-124 2C144-163 2C 183-205 2C 236-258 2C 273-290 2C 303-320 2C 325-347 2C359-381 and 385-407 NC_002163.1 RefSeq region 453341 453409 . + . ID=id976;Name=id976;Dbxref=GeneID:904814;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0486 by TMHMM2.0 at aa 9-31 2C 46-68 2C 75-97 2C 102-124 2C144-163 2C 183-205 2C 236-258 2C 273-290 2C 303-320 2C 325-347 2C359-381 and 385-407 NC_002163.1 RefSeq region 453422 453454 . + . ID=id978;Name=id978;Dbxref=GeneID:904814;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 453422 453490 . + . ID=id976;Name=id976;Dbxref=GeneID:904814;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0486 by TMHMM2.0 at aa 9-31 2C 46-68 2C 75-97 2C 102-124 2C144-163 2C 183-205 2C 236-258 2C 273-290 2C 303-320 2C 325-347 2C359-381 and 385-407 NC_002163.1 RefSeq region 453548 453607 . + . ID=id976;Name=id976;Dbxref=GeneID:904814;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0486 by TMHMM2.0 at aa 9-31 2C 46-68 2C 75-97 2C 102-124 2C144-163 2C 183-205 2C 236-258 2C 273-290 2C 303-320 2C 325-347 2C359-381 and 385-407 NC_002163.1 RefSeq region 453665 453733 . + . ID=id976;Name=id976;Dbxref=GeneID:904814;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0486 by TMHMM2.0 at aa 9-31 2C 46-68 2C 75-97 2C 102-124 2C144-163 2C 183-205 2C 236-258 2C 273-290 2C 303-320 2C 325-347 2C359-381 and 385-407 NC_002163.1 RefSeq region 453824 453892 . + . ID=id976;Name=id976;Dbxref=GeneID:904814;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0486 by TMHMM2.0 at aa 9-31 2C 46-68 2C 75-97 2C 102-124 2C144-163 2C 183-205 2C 236-258 2C 273-290 2C 303-320 2C 325-347 2C359-381 and 385-407 NC_002163.1 RefSeq region 453935 453988 . + . ID=id976;Name=id976;Dbxref=GeneID:904814;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0486 by TMHMM2.0 at aa 9-31 2C 46-68 2C 75-97 2C 102-124 2C144-163 2C 183-205 2C 236-258 2C 273-290 2C 303-320 2C 325-347 2C359-381 and 385-407 NC_002163.1 RefSeq region 454025 454078 . + . ID=id976;Name=id976;Dbxref=GeneID:904814;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0486 by TMHMM2.0 at aa 9-31 2C 46-68 2C 75-97 2C 102-124 2C144-163 2C 183-205 2C 236-258 2C 273-290 2C 303-320 2C 325-347 2C359-381 and 385-407 NC_002163.1 RefSeq region 454091 454159 . + . ID=id976;Name=id976;Dbxref=GeneID:904814;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0486 by TMHMM2.0 at aa 9-31 2C 46-68 2C 75-97 2C 102-124 2C144-163 2C 183-205 2C 236-258 2C 273-290 2C 303-320 2C 325-347 2C359-381 and 385-407 NC_002163.1 RefSeq region 454193 454261 . + . ID=id976;Name=id976;Dbxref=GeneID:904814;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0486 by TMHMM2.0 at aa 9-31 2C 46-68 2C 75-97 2C 102-124 2C144-163 2C 183-205 2C 236-258 2C 273-290 2C 303-320 2C 325-347 2C359-381 and 385-407 NC_002163.1 RefSeq region 454271 454339 . + . ID=id976;Name=id976;Dbxref=GeneID:904814;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0486 by TMHMM2.0 at aa 9-31 2C 46-68 2C 75-97 2C 102-124 2C144-163 2C 183-205 2C 236-258 2C 273-290 2C 303-320 2C 325-347 2C359-381 and 385-407 NC_002163.1 RefSeq gene 454359 455129 . + . ID=gene465;Name=Cj0487;locus_tag=Cj0487;Dbxref=GeneID:904815;gbkey=Gene NC_002163.1 RefSeq CDS 454359 455129 . + 0 ID=cds440;Parent=gene465;Name=YP_002343921.1;Dbxref=GOA:Q0PB26 InterPro:IPR006992 UniProtKB FTrEMBL:Q0PB26 Genbank:YP_002343921.1 GeneID:904815;gbkey=CDS;product=amidohydrolase;Note=Original 282000 29 note: Cj0487 2C unknown 2C len: 256 aa 3B some similarity to Y4MH_RHISN hypothetical protein Y4MH 28297 aa 29 2C fasta scores 3B opt: 98 z-score: 200.8 E 28 29: 0.00069 2C 22.7 25 identity in 295 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF04909 Amidohydrolase identified within CDS. Product modified to more specific family member due to motif match. No specific characterisation has been carried out yet. Thus 2C kept within product function. Functional classification - Misc NC_002163.1 RefSeq region 454371 455123 . + . ID=id979;Name=id979;Dbxref=GeneID:904815;gbkey=misc_feature;Note=HMMPfam hit to PF04909 2C Amidohydrolase 2C score 3.4e-29 ### NC_002163.1 RefSeq gene 455130 455447 . + . ID=gene466;Name=Cj0488;locus_tag=Cj0488;Dbxref=GeneID:904816;gbkey=Gene NC_002163.1 RefSeq CDS 455130 455447 . + 0 ID=cds441;Parent=gene466;Name=YP_002343922.1;Dbxref=InterPro:IPR008000 UniProtKB FTrEMBL:Q0PB25 Genbank:YP_002343922.1 GeneID:904816;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0488 2C unknown 2C len: 3B similar to a hypothetical protein from B. subtilis TR:O05263 28EMBL:Z93938 29 YULD 28104 aa 29 2C fasta scores 3B opt: 183 z-score: 266.1 E 28 29: 1.6e-07 2C 33.6 25 identity in 107 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF05336 Protein of unknown function 28DUF718 29 identified within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq region 455133 455444 . + . ID=id980;Name=id980;Dbxref=GeneID:904816;gbkey=misc_feature;Note=HMMPfam hit to PF05336 2C Protein of unknown function 28DUF718 29 2C score 3e-63 ### NC_002163.1 RefSeq pseudogene 455461 456899 . + . ID=gene467;Name=Cj0489;locus_tag=Cj0489;Dbxref=GeneID:5066042;gbkey=Gene NC_002163.1 RefSeq region 455721 456881 . + . ID=id981;Name=id981;Dbxref=GeneID:5066042;gbkey=misc_feature;Note=HMMPfam hit to PF00171 2C Aldehyde dehydrogenase family 2C score 9.2e-130 NC_002163.1 RefSeq region 455853 455921 . + . ID=id982;Name=id982;Dbxref=GeneID:5066042;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0490 by TMHMM2.0 at aa 46-68 NC_002163.1 RefSeq region 456195 456218 . + . ID=id983;Name=id983;Dbxref=GeneID:5066042;gbkey=misc_feature;Note=PS00687 Aldehyde dehydrogenases glutamic acid active site ### NC_002163.1 UTR_Extractor 5'-UTR 457196 457226 . + . ID=utr183;locus_tag=Cj0491;product=30S ribosomal protein S12 NC_002163.1 RefSeq CDS 457227 457613 . + 0 ID=cds442;Parent=gene468;gene=rpsL;Name=YP_002343925.1;Dbxref=GOA:Q9PI18 HSSP:P17293 InterPro:IPR005679 InterPro:IPR006032 InterPro:IPR012340 UniProtKB FSwiss-Prot:Q9PI18 Genbank:YP_002343925.1 GeneID:904818;gbkey=CDS;product=30S ribosomal protein S12;Note=interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone 3B located at the interface of the 30S and 50S subunits 2C it traverses the body of the 30S subunit contacting proteins on the other side 3B mutations in the S12 gene confer streptomycin resistance NC_002163.1 RefSeq gene 457227 457613 . + . ID=gene468;gene=rpsL;Name=rpsL;locus_tag=Cj0491;Dbxref=GeneID:904818;gbkey=Gene NC_002163.1 RefSeq region 457233 457595 . + . ID=id984;gene=rpsL;Name=id984;Dbxref=GeneID:904818;gbkey=misc_feature;Note=HMMPfam hit to PF00164 2C Ribosomal protein S12 2Cscore 4.3e-73 NC_002163.1 RefSeq region 457353 457376 . + . ID=id985;gene=rpsL;Name=id985;Dbxref=GeneID:904818;gbkey=misc_feature;Note=PS00055 Ribosomal protein S12 signature ### NC_002163.1 RefSeq region 457683 458129 . + . ID=id986;gene=rpsG;Name=id986;Dbxref=GeneID:904819;gbkey=misc_feature;Note=HMMPfam hit to PF00177 2C Ribosomal protein S7p 2FS5e 2Cscore 4.1e-74 NC_002163.1 RefSeq gene 457683 458153 . + . ID=gene469;gene=rpsG;Name=rpsG;locus_tag=Cj0492;Dbxref=GeneID:904819;gbkey=Gene NC_002163.1 RefSeq CDS 457683 458153 . + 0 ID=cds443;Parent=gene469;gene=rpsG;Name=YP_002343926.1;Dbxref=GOA:Q9PI17 HSSP:P17291 InterPro:IPR000235 InterPro:IPR005717 UniProtKB FSwiss-Prot:Q9PI17 Genbank:YP_002343926.1 GeneID:904819;gbkey=CDS;product=30S ribosomal protein S7;Note=binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit NC_002163.1 RefSeq region 457737 457817 . + . ID=id987;gene=rpsG;Name=id987;Dbxref=GeneID:904819;gbkey=misc_feature;Note=PS00052 Ribosomal protein S7 signature ### NC_002163.1 RefSeq CDS 458166 460241 . + 0 ID=cds444;Parent=gene470;gene=fusA;Name=YP_002343927.1;Dbxref=GOA:Q9PI16 HSSP:P13551 InterPro:IPR000640 InterPro:IPR000795 InterPro:IPR004161 InterPro:IPR004540 InterPro:IPR005225 InterPro:IPR005517 InterPro:IPR014721 UniProtKB FSwiss-Prot:Q9PI16 Genbank:YP_002343927.1 GeneID:904822;gbkey=CDS;product=elongation factor G;Note=EF-G 3B promotes GTP-dependent translocation of the ribosome during translation 3B many organisms have multiple copies of this gene NC_002163.1 RefSeq gene 458166 460241 . + . ID=gene470;gene=fusA;Name=fusA;locus_tag=Cj0493;Dbxref=GeneID:904822;gbkey=Gene NC_002163.1 RefSeq region 458187 459014 . + . ID=id988;gene=fusA;Name=id988;Dbxref=GeneID:904822;gbkey=misc_feature;Note=HMMPfam hit to PF00009 2C Elongation factor Tu GTP binding domain 2C score 5.8e-118 NC_002163.1 RefSeq region 458214 458237 . + . ID=id989;gene=fusA;Name=id989;Dbxref=GeneID:904822;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 458316 458363 . + . ID=id990;gene=fusA;Name=id990;Dbxref=GeneID:904822;gbkey=misc_feature;Note=PS00301 GTP-binding elongation factors signature NC_002163.1 RefSeq region 459129 459332 . + . ID=id991;gene=fusA;Name=id991;Dbxref=GeneID:904822;gbkey=misc_feature;Note=HMMPfam hit to PF03144 2C Elongation factor Tu domain 2C score 1.2e-17 NC_002163.1 RefSeq region 459594 459953 . + . ID=id992;gene=fusA;Name=id992;Dbxref=GeneID:904822;gbkey=misc_feature;Note=HMMPfam hit to PF03764 2C Elongation factor G 2C domain IV 2C score 1.6e-75 NC_002163.1 RefSeq region 459957 460220 . + . ID=id993;gene=fusA;Name=id993;Dbxref=GeneID:904822;gbkey=misc_feature;Note=HMMPfam hit to PF00679 2C Elongation factor G C-terminus 2C score 1.1e-53 ### NC_002163.1 RefSeq gene 460270 460346 . + . ID=gene471;gene=tRNAArg;Name=tRNAArg;locus_tag=Cjp10;Dbxref=GeneID:904823;gbkey=Gene NC_002163.1 RefSeq tRNA 460270 460346 . + . ID=rna18;Parent=gene471;gene=tRNAArg;Name=rna18;Dbxref=GeneID:904823;gbkey=tRNA;product=tRNA-Arg;Note=tRNA Arg anticodon CCT 2C Cove score 69.48 NC_002163.1 RefSeq exon 460270 460346 . + . ID=id994;Parent=rna18;gene=tRNAArg;Name=id994;Dbxref=GeneID:904823;gbkey=tRNA;product=tRNA-Arg;Note=tRNA Arg anticodon CCT 2C Cove score 69.48 NC_002163.1 RefSeq gene 460364 460513 . + . ID=gene472;Name=Cj0494;locus_tag=Cj0494;Dbxref=GeneID:904824;gbkey=Gene NC_002163.1 RefSeq CDS 460364 460513 . + 0 ID=cds445;Parent=gene472;Name=YP_002343928.1;Dbxref=UniProtKB FTrEMBL:Q0PB19 Genbank:YP_002343928.1 GeneID:904824;gbkey=CDS;product=exporting protein;Note=Original 282000 29 note: Cj0494 2C small hydrophobic protein 2C len: 49 aa 3B no Hp match 7EUpdated 282006 29 note: Product function modified to more specific family member based on SignalP 2.0 HMM results. kept within product function. Functional classification - Transport 2Fbinding proteins - Other NC_002163.1 UTR_Extractor 5'-UTR 460459 460518 . + . ID=utr184;locus_tag=Cj0495;product=putative methyltransferase domain protein ### NC_002163.1 RefSeq CDS 460519 461220 . + 0 ID=cds446;Parent=gene473;Name=YP_002343929.1;Dbxref=GOA:Q0PB18 InterPro:IPR002052 InterPro:IPR013217 UniProtKB FTrEMBL:Q0PB18 Genbank:YP_002343929.1 GeneID:904825;gbkey=CDS;product=methyltransferase domain-containing protein;Note=Original 282000 29 note: Cj0495 2C unknown 2C len: 233 aa 3B some simillarity to hypothetical proteins e.g. YABB_BACSU 28247 aa 29 2C fasta scores 3B opt: 295 z-score: 352.0 E 28 29: 2.6e-12 2C 23.9 25 identity in 230 aa overlap. 36.9 25 identity to HP1504. Contains PS00092 N-6 Adenine-specific DNA methylases signature 7EUpdated 282006 29 note: Pfam domain PF05175 methyltransferase small domain and PF08242 Methyltransferase domain identified within CDS. Members of this family are SAM dependent methyltransferases. Prosite domain PS50193 SAM_BIND 2C SAM 28and some other nucleotide 29 binding motif also identified within CDS. Product modified to more specific family member due to motif match. No specific characterisation with acceptable identity score has been carried out yet. kept within product function. Functional classification - Misc 7EPMID:9873033 NC_002163.1 RefSeq gene 460519 461220 . + . ID=gene473;Name=Cj0495;locus_tag=Cj0495;Dbxref=GeneID:904825;gbkey=Gene NC_002163.1 RefSeq region 460822 460842 . + . ID=id995;Name=id995;Dbxref=GeneID:904825;gbkey=misc_feature;Note=PS00092 N-6 Adenine-specific DNA methylases signature NC_002163.1 RefSeq gene 461210 461584 . + . ID=gene474;Name=Cj0496;locus_tag=Cj0496;Dbxref=GeneID:904826;gbkey=Gene NC_002163.1 RefSeq CDS 461210 461584 . + 0 ID=cds447;Parent=gene474;Name=YP_002343930.1;Dbxref=GOA:Q0PB17 InterPro:IPR005358 UniProtKB FTrEMBL:Q0PB17 Genbank:YP_002343930.1 GeneID:904826;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0496 2C unknown 2C len: 124 aa 3B similar to hypothetical proteins e.g. TR:O59308 28EMBL:AB009522 29 Pyrococcus horikoshii PHAV002 28141 aa 29 2Cfasta scores 3B opt: 154 z-score: 270.6 E 28 29: 8.8e-08 2C30.1 25 identity in 113 aa overlap. 47.5 25 identity to HP0274 7EUpdated 282006 29 note: Pfam domain PF03692 Uncharacterised protein family 28UPF0153 29 identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq region 461249 461575 . + . ID=id996;Name=id996;Dbxref=GeneID:904826;gbkey=misc_feature;Note=HMMPfam hit to PF03692 2C Uncharacterised protein family 28UPF0153 29 2C score 1.4e-32 NC_002163.1 RefSeq CDS 461557 462834 . + 0 ID=cds448;Parent=gene475;Name=YP_002343931.1;Dbxref=GOA:Q0PB16 InterPro:IPR011990 UniProtKB FTrEMBL:Q0PB16 Genbank:YP_002343931.1 GeneID:904827;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj0497 2C probable lipoprotein 2Clen: 425 aa 3B some similarity to hypothetical prteins e.g. TR:O67021 28EMBL:AE000710 29 Aquifex aeolicus AQ_854 28545 aa 29 2C fasta scores 3B opt: 266 z-score: 326.7 E 28 29: 6.7e-11 2C29.1 25 identity in 412 aa overlap. 26.7 25 identity to HP0275 28misannotated as ATP-dependent nuclease 28addB 29 29. Contains N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 461557 462834 . + . ID=gene475;Name=Cj0497;locus_tag=Cj0497;Dbxref=GeneID:904827;gbkey=Gene NC_002163.1 RefSeq region 461569 461637 . + . ID=id997;Name=id997;Dbxref=GeneID:904827;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0497 by TMHMM2.0 at aa 5-27 NC_002163.1 RefSeq region 461570 461581 . + . ID=id998;Name=id998;Dbxref=GeneID:904826;gbkey=misc_feature;Note=PS00294 Prenyl group binding site 28CAAX box 29 NC_002163.1 RefSeq region 461575 461607 . + . ID=id999;Name=id999;Dbxref=GeneID:904827;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 461965 462066 . + . ID=id1000;Name=id1000;Dbxref=GeneID:904827;gbkey=misc_feature;Note=HMMPfam hit to PF07719 2C Tetratricopeptide repeat 2Cscore 2.3 NC_002163.1 RefSeq CDS 462831 463607 . + 0 ID=cds449;Parent=gene476;gene=trpC;Name=YP_002343932.1;Dbxref=GOA:Q9PI11 HSSP:Q06121 InterPro:IPR001468 InterPro:IPR013785 InterPro:IPR013798 UniProtKB FSwiss-Prot:Q9PI11 Genbank:YP_002343932.1 GeneID:904828;gbkey=CDS;product=Indole-3-glycerol phosphate synthase;Note=involved in tryptophan biosynthesis 3B amino acid biosynthesis 3B converts 1- 282-carboxyphenylamino 29-1-deoxy-D-ribulose 5-phosphate to C 281 29- 283-indolyl 29-glycerol 3-phosphate and carbon dioxide and water NC_002163.1 RefSeq gene 462831 463607 . + . ID=gene476;gene=trpC;Name=trpC;locus_tag=Cj0498;Dbxref=GeneID:904828;gbkey=Gene NC_002163.1 RefSeq region 462834 463601 . + . ID=id1001;gene=trpC;Name=id1001;Dbxref=GeneID:904828;gbkey=misc_feature;Note=HMMPfam hit to PF00218 2C Indole-3-glycerol phosphate synthase 2C score 2.7e-106 NC_002163.1 RefSeq region 462987 463031 . + . ID=id1002;gene=trpC;Name=id1002;Dbxref=GeneID:904828;gbkey=misc_feature;Note=PS00614 Indole-3-glycerol phosphate synthase signature ### NC_002163.1 RefSeq CDS 463617 464102 . + 0 ID=cds450;Parent=gene477;Name=YP_002343933.1;Dbxref=GOA:Q0PB14 InterPro:IPR001310 InterPro:IPR011151 UniProtKB FTrEMBL:Q0PB14 Genbank:YP_002343933.1 GeneID:904829;gbkey=CDS;product=histidine triad 28HIT 29 family protein;Note=Original 282000 29 note: Cj0499 2C unknown 2C len: 161 aa 3B similar to many members of the HIT family e.g. HIT_BACSU HIT protein 28145 aa 29 2C fasta scores 3B opt: 176 z-score: 274.7 E 28 29: 5.2e-08 2C 26.1 25 identity in 111 aa overlap. 42.6 25 identity to HP0741. Contains Pfam match to entry PF01230 HIT 2C HIT family 2C score 19.90 2C E-value 3.6e-06 7EUpdated 282006 29 note: Product modified to more specific family member due to motif match. No specific characterisation has been carried out yet. kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 463617 464102 . + . ID=gene477;Name=Cj0499;locus_tag=Cj0499;Dbxref=GeneID:904829;gbkey=Gene NC_002163.1 RefSeq region 463674 464000 . + . ID=id1003;Name=id1003;Dbxref=GeneID:904829;gbkey=misc_feature;Note=HMMPfam hit to PF01230 2C HIT domain 2C score 7.1e-06 NC_002163.1 RefSeq gene 464092 465090 . + . ID=gene478;Name=Cj0500;locus_tag=Cj0500;Dbxref=GeneID:904830;gbkey=Gene NC_002163.1 RefSeq CDS 464092 465090 . + 0 ID=cds451;Parent=gene478;Name=YP_002343934.1;Dbxref=InterPro:IPR001763 InterPro:IPR017582 UniProtKB FTrEMBL:Q0PB13 Genbank:YP_002343934.1 GeneID:904830;gbkey=CDS;product=tRNA 2-selenouridine synthase;Note=catalyzes the selenophosphate-dependent transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA NC_002163.1 RefSeq region 464524 464547 . + . ID=id1004;Name=id1004;Dbxref=GeneID:904830;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 UTR_Extractor 5'-UTR 465345 465375 . + . ID=utr185;locus_tag=Cj0501;product=pseudo NC_002163.1 RefSeq region 465376 465453 . + . ID=id1005;Name=id1005;Dbxref=PSEUDO:CAL34649.1 GeneID:904831;gbkey=misc_feature;Note=Original 282000 29 note: Cj0501 2C probable ammonium transporter pseudogene 3B len: 1114 bp 3B similar to amny e.g. NRGA_BACSU probable ammonium transporter 28404 aa 29.There is at least one frameshift and one stop codon in this pseudogene. No Hp match. Contains PS01219 Ammonium transporters signature and Pfam match to entry PF00909 Ammonium_transp 2C Ammonium Transporter Family 2C score 29.60 2CE-value 7.1e-12 7EUpdated 282006 29 note: Nine probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli and Bacillus subtilis with acceptable identity scores. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:12023896 2C PMID:10931328 2C PMID:15361618 2CPMID:14600241 NC_002163.1 RefSeq pseudogene 465376 466598 . + . ID=gene479;Name=Cj0501;locus_tag=Cj0501;Dbxref=GeneID:904831;gbkey=Gene NC_002163.1 RefSeq region 465388 465453 . + . ID=id1006;Name=id1006;Dbxref=GeneID:904831;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0501 by TMHMM2.0 at aa 5-27 2C 40-62 2C 94-116 2C 121-143 2C158-180 2C 193-212 2C 222-244 2C 274-296 and 355-377 NC_002163.1 RefSeq region 465394 465453 . + . ID=id1007;Name=id1007;Dbxref=GeneID:904831;gbkey=misc_feature;Note=HMMPfam hit to PF00909 2C Ammonium Transporter Family 2C score 7.1e-121 NC_002163.1 RefSeq region 465453 465455 . + . ID=id1006;Name=id1006;Dbxref=GeneID:904831;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0501 by TMHMM2.0 at aa 5-27 2C 40-62 2C 94-116 2C 121-143 2C158-180 2C 193-212 2C 222-244 2C 274-296 and 355-377 NC_002163.1 RefSeq region 465453 466124 . + . ID=id1005;Name=id1005;Dbxref=PSEUDO:CAL34649.1 GeneID:904831;gbkey=misc_feature;Note=Original 282000 29 note: Cj0501 2C probable ammonium transporter pseudogene 3B len: 1114 bp 3B similar to amny e.g. NRGA_BACSU probable ammonium transporter 28404 aa 29.There is at least one frameshift and one stop codon in this pseudogene. No Hp match. Contains PS01219 Ammonium transporters signature and Pfam match to entry PF00909 Ammonium_transp 2C Ammonium Transporter Family 2C score 29.60 2CE-value 7.1e-12 7EUpdated 282006 29 note: Nine probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli and Bacillus subtilis with acceptable identity scores. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:12023896 2C PMID:10931328 2C PMID:15361618 2CPMID:14600241 NC_002163.1 RefSeq region 465453 466269 . + . ID=id1007;Name=id1007;Dbxref=GeneID:904831;gbkey=misc_feature;Note=HMMPfam hit to PF00909 2C Ammonium Transporter Family 2C score 7.1e-121 NC_002163.1 RefSeq region 465492 465560 . + . ID=id1006;Name=id1006;Dbxref=GeneID:904831;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0501 by TMHMM2.0 at aa 5-27 2C 40-62 2C 94-116 2C 121-143 2C158-180 2C 193-212 2C 222-244 2C 274-296 and 355-377 NC_002163.1 RefSeq region 465654 465722 . + . ID=id1006;Name=id1006;Dbxref=GeneID:904831;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0501 by TMHMM2.0 at aa 5-27 2C 40-62 2C 94-116 2C 121-143 2C158-180 2C 193-212 2C 222-244 2C 274-296 and 355-377 NC_002163.1 RefSeq region 465735 465803 . + . ID=id1006;Name=id1006;Dbxref=GeneID:904831;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0501 by TMHMM2.0 at aa 5-27 2C 40-62 2C 94-116 2C 121-143 2C158-180 2C 193-212 2C 222-244 2C 274-296 and 355-377 NC_002163.1 RefSeq region 465846 465914 . + . ID=id1006;Name=id1006;Dbxref=GeneID:904831;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0501 by TMHMM2.0 at aa 5-27 2C 40-62 2C 94-116 2C 121-143 2C158-180 2C 193-212 2C 222-244 2C 274-296 and 355-377 NC_002163.1 RefSeq region 465951 466010 . + . ID=id1006;Name=id1006;Dbxref=GeneID:904831;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0501 by TMHMM2.0 at aa 5-27 2C 40-62 2C 94-116 2C 121-143 2C158-180 2C 193-212 2C 222-244 2C 274-296 and 355-377 NC_002163.1 RefSeq region 466038 466106 . + . ID=id1006;Name=id1006;Dbxref=GeneID:904831;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0501 by TMHMM2.0 at aa 5-27 2C 40-62 2C 94-116 2C 121-143 2C158-180 2C 193-212 2C 222-244 2C 274-296 and 355-377 NC_002163.1 RefSeq region 466123 466269 . + . ID=id1005;Name=id1005;Dbxref=PSEUDO:CAL34649.1 GeneID:904831;gbkey=misc_feature;Note=Original 282000 29 note: Cj0501 2C probable ammonium transporter pseudogene 3B len: 1114 bp 3B similar to amny e.g. NRGA_BACSU probable ammonium transporter 28404 aa 29.There is at least one frameshift and one stop codon in this pseudogene. No Hp match. Contains PS01219 Ammonium transporters signature and Pfam match to entry PF00909 Ammonium_transp 2C Ammonium Transporter Family 2C score 29.60 2CE-value 7.1e-12 7EUpdated 282006 29 note: Nine probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli and Bacillus subtilis with acceptable identity scores. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:12023896 2C PMID:10931328 2C PMID:15361618 2CPMID:14600241 NC_002163.1 RefSeq region 466192 466260 . + . ID=id1006;Name=id1006;Dbxref=GeneID:904831;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0501 by TMHMM2.0 at aa 5-27 2C 40-62 2C 94-116 2C 121-143 2C158-180 2C 193-212 2C 222-244 2C 274-296 and 355-377 NC_002163.1 RefSeq region 466273 466393 . + . ID=id1007;Name=id1007;Dbxref=GeneID:904831;gbkey=misc_feature;Note=HMMPfam hit to PF00909 2C Ammonium Transporter Family 2C score 7.1e-121 NC_002163.1 RefSeq region 466273 466393 . + . ID=id1005;Name=id1005;Dbxref=PSEUDO:CAL34649.1 GeneID:904831;gbkey=misc_feature;Note=Original 282000 29 note: Cj0501 2C probable ammonium transporter pseudogene 3B len: 1114 bp 3B similar to amny e.g. NRGA_BACSU probable ammonium transporter 28404 aa 29.There is at least one frameshift and one stop codon in this pseudogene. No Hp match. Contains PS01219 Ammonium transporters signature and Pfam match to entry PF00909 Ammonium_transp 2C Ammonium Transporter Family 2C score 29.60 2CE-value 7.1e-12 7EUpdated 282006 29 note: Nine probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli and Bacillus subtilis with acceptable identity scores. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:12023896 2C PMID:10931328 2C PMID:15361618 2CPMID:14600241 NC_002163.1 RefSeq region 466395 466495 . + . ID=id1007;Name=id1007;Dbxref=GeneID:904831;gbkey=misc_feature;Note=HMMPfam hit to PF00909 2C Ammonium Transporter Family 2C score 7.1e-121 NC_002163.1 RefSeq region 466395 466495 . + . ID=id1005;Name=id1005;Dbxref=PSEUDO:CAL34649.1 GeneID:904831;gbkey=misc_feature;Note=Original 282000 29 note: Cj0501 2C probable ammonium transporter pseudogene 3B len: 1114 bp 3B similar to amny e.g. NRGA_BACSU probable ammonium transporter 28404 aa 29.There is at least one frameshift and one stop codon in this pseudogene. No Hp match. Contains PS01219 Ammonium transporters signature and Pfam match to entry PF00909 Ammonium_transp 2C Ammonium Transporter Family 2C score 29.60 2CE-value 7.1e-12 7EUpdated 282006 29 note: Nine probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli and Bacillus subtilis with acceptable identity scores. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:12023896 2C PMID:10931328 2C PMID:15361618 2CPMID:14600241 NC_002163.1 RefSeq region 466439 466495 . + . ID=id1006;Name=id1006;Dbxref=GeneID:904831;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0501 by TMHMM2.0 at aa 5-27 2C 40-62 2C 94-116 2C 121-143 2C158-180 2C 193-212 2C 222-244 2C 274-296 and 355-377 NC_002163.1 RefSeq region 466497 466508 . + . ID=id1006;Name=id1006;Dbxref=GeneID:904831;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0501 by TMHMM2.0 at aa 5-27 2C 40-62 2C 94-116 2C 121-143 2C158-180 2C 193-212 2C 222-244 2C 274-296 and 355-377 NC_002163.1 RefSeq region 466497 466586 . + . ID=id1007;Name=id1007;Dbxref=GeneID:904831;gbkey=misc_feature;Note=HMMPfam hit to PF00909 2C Ammonium Transporter Family 2C score 7.1e-121 NC_002163.1 RefSeq region 466497 466598 . + . ID=id1005;Name=id1005;Dbxref=PSEUDO:CAL34649.1 GeneID:904831;gbkey=misc_feature;Note=Original 282000 29 note: Cj0501 2C probable ammonium transporter pseudogene 3B len: 1114 bp 3B similar to amny e.g. NRGA_BACSU probable ammonium transporter 28404 aa 29.There is at least one frameshift and one stop codon in this pseudogene. No Hp match. Contains PS01219 Ammonium transporters signature and Pfam match to entry PF00909 Ammonium_transp 2C Ammonium Transporter Family 2C score 29.60 2CE-value 7.1e-12 7EUpdated 282006 29 note: Nine probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli and Bacillus subtilis with acceptable identity scores. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:12023896 2C PMID:10931328 2C PMID:15361618 2CPMID:14600241 ### NC_002163.1 RefSeq CDS 466660 467571 . - 0 ID=cds452;Parent=gene480;gene=hemH;Name=YP_002343935.1;Dbxref=GOA:Q9PI08 HSSP:P22830 InterPro:IPR001015 UniProtKB FSwiss-Prot:Q9PI08 Genbank:YP_002343935.1 GeneID:904832;gbkey=CDS;product=ferrochelatase;Note=protoheme ferro-lyase 3B catalyzes the insertion of a ferrous ion into protoporphyrin IX to form protoheme 3B involved in protoheme biosynthesis 3B in some organisms this protein is membrane-associated while in others it is cytosolic NC_002163.1 RefSeq gene 466660 467571 . - . ID=gene480;gene=hemH;Name=hemH;locus_tag=Cj0503c;Dbxref=GeneID:904832;gbkey=Gene NC_002163.1 RefSeq region 466663 467562 . - . ID=id1008;gene=hemH;Name=id1008;Dbxref=GeneID:904832;gbkey=misc_feature;Note=HMMPfam hit to PF00762 2C Ferrochelatase 2C score 3e-72 NC_002163.1 RefSeq region 466978 467034 . - . ID=id1009;gene=hemH;Name=id1009;Dbxref=GeneID:904832;gbkey=misc_feature;Note=PS00534 Ferrochelatase signature NC_002163.1 RefSeq CDS 467568 468434 . - 0 ID=cds453;Parent=gene481;Name=YP_002343936.1;Dbxref=GOA:Q0PB11 InterPro:IPR000683 InterPro:IPR016040 UniProtKB FTrEMBL:Q0PB11 Genbank:YP_002343936.1 GeneID:904833;gbkey=CDS;product=oxidoreductase;Note=Original 282000 29 note: Cj0504c 2C unknown 2C len: 288 aa 3B similar to hypothetical proteins e.g. YISS_BACSU 342 aa 29 2C fasta scores 3B opt: 224 z-score: 359.9 E 28 29: 9.4e-13 2C28.1 25 identity in 192 aa overlap. 26.4 25 identity to HP0679 7EUpdated 282006 29 note: Pfam domain PF01408 Oxidoreductase family 2C NAD-binding Rossmann fold identified within CDS. Product function modified due to motif match. No specific characterisation has been carried out yet. kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 467568 468434 . - . ID=gene481;gene=Cj0504c;Name=Cj0504c;locus_tag=Cj0504c;Dbxref=GeneID:904833;gbkey=Gene NC_002163.1 RefSeq region 468090 468434 . - . ID=id1010;Name=id1010;Dbxref=GeneID:904833;gbkey=misc_feature;Note=HMMPfam hit to PF01408 2C Oxidoreductase family 2CNAD-binding Rossm 2C score 1.2e-20 ### NC_002163.1 RefSeq gene 468439 469512 . - . ID=gene482;Name=Cj0505c;locus_tag=Cj0505c;Dbxref=GeneID:904834;gbkey=Gene NC_002163.1 RefSeq CDS 468439 469512 . - 0 ID=cds454;Parent=gene482;Name=YP_002343937.1;Dbxref=GOA:Q0PB10 InterPro:IPR000653 InterPro:IPR015421 InterPro:IPR015422 UniProtKB FTrEMBL:Q0PB10 Genbank:YP_002343937.1 GeneID:904834;gbkey=CDS;product=DegT family aminotransferase;Note=Updated 282006 29 note: Some characterisation work carried out within Bacillus stearothermophilus with acceptable identity score. kept within product function 7EOriginal 282000 29 note: Cj0505c 2C possible aminotransferase 2C len: 357 aa 3B similar to members of the degT family e.g. DEGT_BACST 28372 aa 29 2C fasta scores 3B opt: 857 z-score: 1253.3 E 28 29: 0 2C 38.8 25 identity in 356 aa overlap. No Hp ortholog. Contains Pfam match to entry PF01041 DegT_DnrJ_EryC1 2C DegT 2FDnrJ 2FEryC1 2FStrS family 2Cscore 441.40 2C E-value 7.9e-129 7EPMID:2104607 NC_002163.1 RefSeq region 468445 469482 . - . ID=id1011;Name=id1011;Dbxref=GeneID:904834;gbkey=misc_feature;Note=HMMPfam hit to PF01041 2C DegT 2FDnrJ 2FEryC1 2FStrS aminotransferase 2C score 4.8e-130 ### NC_002163.1 UTR_Extractor 5'-UTR 469598 469626 . + . ID=utr186;locus_tag=Cj0506;product=alanyl-tRNA synthetase NC_002163.1 RefSeq CDS 469627 472155 . + 0 ID=cds455;Parent=gene483;gene=alaS;Name=YP_002343938.1;Dbxref=GOA:Q9PI05 InterPro:IPR002318 InterPro:IPR003156 InterPro:IPR012947 UniProtKB FSwiss-Prot:Q9PI05 Genbank:YP_002343938.1 GeneID:904835;gbkey=CDS;product=alanyl-tRNA synthetase;Note=Catalyzes a two-step reaction 2C first charging an alanyl molecule by linking its carboxyl group to the alpha-phosphate of ATP 2C followed by transfer of the aminoacyl-adenylate to its tRNA NC_002163.1 RefSeq gene 469627 472155 . + . ID=gene483;gene=alaS;Name=alaS;locus_tag=Cj0506;Dbxref=GeneID:904835;gbkey=Gene NC_002163.1 RefSeq region 469630 471693 . + . ID=id1012;gene=alaS;Name=id1012;Dbxref=GeneID:904835;gbkey=misc_feature;Note=HMMPfam hit to PF01411 2C tRNA synthetases class II 28A 29 2C score 0 NC_002163.1 RefSeq region 470290 470319 . + . ID=id1013;gene=alaS;Name=id1013;Dbxref=GeneID:904835;gbkey=misc_feature;Note=PS00339 Aminoacyl-transfer RNA synthetases class-II signature 2 NC_002163.1 RefSeq region 471928 472134 . + . ID=id1014;gene=alaS;Name=id1014;Dbxref=GeneID:904835;gbkey=misc_feature;Note=HMMPfam hit to PF02272 2C DHHA1 domain 2C score 1.6e-16 NC_002163.1 RefSeq region 472155 472703 . + . ID=id1015;gene=maf;Name=id1015;Dbxref=GeneID:904836;gbkey=misc_feature;Note=HMMPfam hit to PF02545 2C Maf-like protein 2C score 6e-22 NC_002163.1 RefSeq CDS 472155 472706 . + 0 ID=cds456;Parent=gene484;gene=maf;Name=YP_002343939.1;Dbxref=GOA:Q9PI04 InterPro:IPR003697 UniProtKB FSwiss-Prot:Q9PI04 Genbank:YP_002343939.1 GeneID:904836;gbkey=CDS;product=Maf-like protein;Note=Maf 3B overexpression in Bacillus subtilis inhibits septation in the dividing cell NC_002163.1 RefSeq gene 472155 472706 . + . ID=gene484;gene=maf;Name=maf;locus_tag=Cj0507;Dbxref=GeneID:904836;gbkey=Gene NC_002163.1 RefSeq gene 472703 474634 . + . ID=gene485;gene=pbpA;Name=pbpA;locus_tag=Cj0508;Dbxref=GeneID:904837;gbkey=Gene NC_002163.1 RefSeq CDS 472703 474634 . + 0 ID=cds457;Parent=gene485;gene=pbpA;Name=YP_002343940.1;Dbxref=GOA:Q0PB07 InterPro:IPR001264 InterPro:IPR001460 InterPro:IPR011816 UniProtKB FTrEMBL:Q0PB07 Genbank:YP_002343940.1 GeneID:904837;gbkey=CDS;product=penicillin-binding protein;Note=Original 282000 29 note: Cj0508 2C pbpA 2C probable penicillin-binding protein 2C len: 643 aa 3B similar to many e.g. PBPB_ECOLI penicillin-binding protein 1B 28PBP-1B 29 28844 aa 29 2C fasta scores 3B opt: 774 z-score: 915.8 E 28 29: 0 2C32.5 25 identity in 616 aa overlap. 48.0 25 identity to HP0597. Also similar to Cj0525c 2822.9 25 identity in 407 aa overlap 29. Contains Pfam matches to entry PF00912 Transglycosyl 2C Transglycosylase 2C score 299.40 2C E-value 4.5e-86 and Pfam match to entry PF00905 Transpeptidase 2CPenicillin binding protein transpeptidase domain 2C score 103.80 2C E-value 3.3e-27 7EUpdated 282006 29 note: Characterised within Escherichia coli with marginal identity score. not added to product function. Functional classification -Murein sacculus and peptidoglycan 7EPMID:11181392 2C PMID:9841666 2C PMID:8335642 NC_002163.1 RefSeq region 472721 472789 . + . ID=id1016;gene=pbpA;Name=id1016;Dbxref=GeneID:904837;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0508 by TMHMM2.0 at aa 7-29 NC_002163.1 RefSeq region 472835 473341 . + . ID=id1017;gene=pbpA;Name=id1017;Dbxref=GeneID:904837;gbkey=misc_feature;Note=HMMPfam hit to PF00912 2C Transglycosylase 2C score 2.2e-82 NC_002163.1 RefSeq region 473660 474478 . + . ID=id1018;gene=pbpA;Name=id1018;Dbxref=GeneID:904837;gbkey=misc_feature;Note=HMMPfam hit to PF00905 2C Penicillin binding protein transpeptid 2C score 1.1e-33 ### NC_002163.1 RefSeq CDS 474662 477235 . - 0 ID=cds458;Parent=gene486;gene=clpB;Name=YP_002343941.1;Dbxref=GOA:Q9PI02 HSSP:P03815 InterPro:IPR001270 InterPro:IPR003593 InterPro:IPR003959 InterPro:IPR004176 InterPro:IPR013093 UniProtKB FSwiss-Prot:Q9PI02 Genbank:YP_002343941.1 GeneID:904838;gbkey=CDS;product=ATP-dependent Clp protease ATP-binding subunit;Note=Original 282000 29 note: Cj0509c 2C clpB 2C ATP-dependent CLP protease ATP-binding subunit 2C len: 857 aa 3B 98.9 25 identical to C. jejuni TR:O69287 28EMBL:Y13333 29 and similar to many e.g. CLAA_LYCES ATP-dependent CLP protease ATP-binding subunit 28926 aa 29 2C fasta scores 3B opt: 1130 z-score: 2439.8 E 28 29: 0 2C 45.0 25 identity in 845 aa overlap. 61.2 25 identity to HP0264. Also simlar to C. jejuni clpA 28Cj1108 29 3B 36.6 25 identity in 836 aa overlap. Contains 2x PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00870 and PS00871 Chaperonins clpA 2FB signatures 1 and 2 2C and Pfam match to entry PF00495 clpA_B 2C Chaperonins clpA 2FB 2C score 1257.60 2C E-value 0 7EUpdated 282006 29 note: Characterised within Campylobacter jejuni. not added to product function. Functional classification - Chaperones 2Cchaperonins 2C heat shock 7EPMID:10196475 NC_002163.1 RefSeq gene 474662 477235 . - . ID=gene486;gene=clpB;Name=clpB;locus_tag=Cj0509c;Dbxref=GeneID:904838;gbkey=Gene NC_002163.1 RefSeq region 474785 475429 . - . ID=id1019;gene=clpB;Name=id1019;Dbxref=GeneID:904838;gbkey=misc_feature;Note=HMMPfam hit to PF00004 2C ATPase family associated with various cellul 2C score 5.2e-05 NC_002163.1 RefSeq region 474959 475441 . - . ID=id1020;gene=clpB;Name=id1020;Dbxref=GeneID:904838;gbkey=misc_feature;Note=HMMPfam hit to PF07724 2C ATPase family associated with various cellul 2C score 3.2e-102 NC_002163.1 RefSeq region 475280 475336 . - . ID=id1021;gene=clpB;Name=id1021;Dbxref=GeneID:904838;gbkey=misc_feature;Note=PS00871 Chaperonins clpA 2FB signature 2 NC_002163.1 RefSeq region 475391 475414 . - . ID=id1022;gene=clpB;Name=id1022;Dbxref=GeneID:904838;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 476051 476632 . - . ID=id1023;gene=clpB;Name=id1023;Dbxref=GeneID:904838;gbkey=misc_feature;Note=HMMPfam hit to PF00004 2C ATPase family associated with various cellul 2C score 7.4e-21 NC_002163.1 RefSeq region 476318 476356 . - . ID=id1024;gene=clpB;Name=id1024;Dbxref=GeneID:904838;gbkey=misc_feature;Note=PS00870 Chaperonins clpA 2FB signature 1 NC_002163.1 RefSeq region 476594 476617 . - . ID=id1025;gene=clpB;Name=id1025;Dbxref=GeneID:904838;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 476798 476947 . - . ID=id1026;gene=clpB;Name=id1026;Dbxref=GeneID:904838;gbkey=misc_feature;Note=HMMPfam hit to PF02861 2C Clp amino terminal domain 2Cscore 0.0056 NC_002163.1 RefSeq region 477023 477181 . - . ID=id1027;gene=clpB;Name=id1027;Dbxref=GeneID:904838;gbkey=misc_feature;Note=HMMPfam hit to PF02861 2C Clp amino terminal domain 2Cscore 6.5e-11 ### NC_002163.1 UTR_Extractor 5'-UTR 477236 477260 . - . ID=utr187;locus_tag=Cj0509c;product=ATP-dependent Clp protease ATP-binding subunit NC_002163.1 RefSeq gene 477347 477637 . - . ID=gene487;Name=Cj0510c;locus_tag=Cj0510c;Dbxref=GeneID:904839;gbkey=Gene NC_002163.1 RefSeq CDS 477347 477637 . - 0 ID=cds459;Parent=gene487;Name=YP_002343942.1;Dbxref=GOA:Q0PB05 InterPro:IPR003735 UniProtKB FTrEMBL:Q0PB05 Genbank:YP_002343942.1 GeneID:904839;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0510c 2C unknown 2C len: 96 aa 3B similar to hypothetical proteins e.g. TR:O32222 28EMBL:Z99121 29 B. subtilis YVGZ protein 28101 aa 29 2C fasta scores 3B opt: 212 z-score: 338.9 E 28 29: 1.4e-11 2C 40.0 25 identity in 95 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02583 Uncharacterised BCR 2C COG1937 identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq region 477353 477535 . - . ID=id1028;Name=id1028;Dbxref=GeneID:904839;gbkey=misc_feature;Note=HMMPfam hit to PF02583 2C Uncharacterised BCR 2CCOG1937 2C score 2.1e-17 ### NC_002163.1 UTR_Extractor 5'-UTR 477737 477754 . + . ID=utr188;locus_tag=Cj0511;product=putative secreted protease NC_002163.1 RefSeq CDS 477755 479089 . + 0 ID=cds460;Parent=gene488;Name=YP_002343943.1;Dbxref=GOA:Q0PB04 InterPro:IPR001478 InterPro:IPR004447 InterPro:IPR005151 UniProtKB FTrEMBL:Q0PB04 Genbank:YP_002343943.1 GeneID:904840;gbkey=CDS;product=protease;Note=Original 282000 29 note: Cj0511 2C probable secreted protease 2C len: 444 aa 3B similar to many e.g. PRC_ECOLI tail-specific protease precursor 28682 aa 29 2C fasta scores 3B opt: 357 z-score: 500.2 E 28 29: 1.4e-20 2C 29.9 25 identity in 388 aa overlap. 54.3 25 identity to HP1350. Contains possible N-terminal signal sequence and Pfam match to entry PF00595 PDZ 2C PDZ domain 28Also known as DHR or GLGF 29. 2C score 52.00 2C E-value 1.3e-11 7EUpdated 282006 29 note: Pfam domain PF03572 Peptidase family S41 identified within CDS. Further support given to product function. Characterised within Escherichia coli with marginal identity score. kept within product function. Paper identified linking protein to glycoprotein 28PMID:12186869 29. Functional classification - Protein translation and modification 7EPMID:8576225 2C PMID:12186869 NC_002163.1 RefSeq gene 477755 479089 . + . ID=gene488;Name=Cj0511;locus_tag=Cj0511;Dbxref=GeneID:904840;gbkey=Gene NC_002163.1 RefSeq region 477788 477856 . + . ID=id1029;Name=id1029;Dbxref=GeneID:904840;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0511 by TMHMM2.0 at aa 12-34 NC_002163.1 RefSeq region 478049 478285 . + . ID=id1030;Name=id1030;Dbxref=GeneID:904840;gbkey=misc_feature;Note=HMMPfam hit to PF00595 2C PDZ domain 28Also known as DHR or GLGF 29 2C score 1.9e-11 NC_002163.1 RefSeq region 478376 478861 . + . ID=id1031;Name=id1031;Dbxref=GeneID:904840;gbkey=misc_feature;Note=HMMPfam hit to PF03572 2C Peptidase family S41 2C score 7.9e-76 ### NC_002163.1 RefSeq CDS 479091 479801 . + 0 ID=cds461;Parent=gene489;gene=purC;Name=YP_002343944.1;Dbxref=GOA:Q9PHZ9 HSSP:Q9X0X0 InterPro:IPR001636 InterPro:IPR013816 UniProtKB FSwiss-Prot:Q9PHZ9 Genbank:YP_002343944.1 GeneID:904841;gbkey=CDS;product=phosphoribosylaminoimidazolesuccinocarboxamide synthase;Note=catalyzes the formation of 28S 29-2- 285-amino-1- 285-phospho-D-ribosyl 29imidazole-4-carboxamido 29succinate from 5-amino-1- 285-phospho-D-ribosyl 29imidazole-4-carboxylate and L-aspartate in purine biosynthesis 3B SAICAR synthase NC_002163.1 RefSeq gene 479091 479801 . + . ID=gene489;gene=purC;Name=purC;locus_tag=Cj0512;Dbxref=GeneID:904841;gbkey=Gene NC_002163.1 RefSeq region 479097 479795 . + . ID=id1032;gene=purC;Name=id1032;Dbxref=GeneID:904841;gbkey=misc_feature;Note=HMMPfam hit to PF01259 2C SAICAR synthetase 2C score 1.6e-90 NC_002163.1 RefSeq region 479346 479390 . + . ID=id1033;gene=purC;Name=id1033;Dbxref=GeneID:904841;gbkey=misc_feature;Note=PS01057 SAICAR synthetase signature 1 ### NC_002163.1 RefSeq region 479810 480049 . + . ID=id1034;gene=purS;Name=id1034;Dbxref=GeneID:904842;gbkey=misc_feature;Note=HMMPfam hit to PF02700 2CPhosphoribosylformylglycinamidine 28FGAM 29 syn 2C score 1.3e-31 NC_002163.1 RefSeq gene 479810 480055 . + . ID=gene490;gene=purS;Name=purS;locus_tag=Cj0513;Dbxref=GeneID:904842;gbkey=Gene NC_002163.1 RefSeq CDS 479810 480055 . + 0 ID=cds462;Parent=gene490;gene=purS;Name=YP_002343945.1;Dbxref=GOA:Q0PB02 InterPro:IPR003850 UniProtKB FTrEMBL:Q0PB02 Genbank:YP_002343945.1 GeneID:904842;gbkey=CDS;product=phosphoribosylformylglycinamidine synthase;Note=Original 282000 29 note: Cj0513 2C unknown 2C len: 81 aa 3B similar to many e.g. YEXA_BACSU hypothetical 9.7 kd protein in PURC-PURL intergenic region 2884 aa 29 2C fasta scores 3B opt: 248 z-score: 331.6 E 28 29: 3.6e-11 2C 48.1 25 identity in 79 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02700 Phosphoribosylformylglycinamidine 28FGAM 29 synthase identified within CDS. Product function modified to new function based on motif match. Characterisation work carried out within Bacillus subtilis with acceptable identity score. not added to product function. Functional classification - Purine ribonucleotide biosynthesis 7EPMID:15301532 2C PMID:10071207 ### NC_002163.1 RefSeq CDS 480057 480728 . + 0 ID=cds463;Parent=gene491;gene=purQ;Name=YP_002343946.1;Dbxref=GOA:Q9PHZ7 InterPro:IPR010075 InterPro:IPR011698 InterPro:IPR012998 UniProtKB FSwiss-Prot:Q9PHZ7 Genbank:YP_002343946.1 GeneID:904843;gbkey=CDS;product=phosphoribosylformylglycinamidine synthase I;Note=catalyzes the formation of 2- 28formamido 29-N1- 285-phospho-D-ribosyl 29acetamidine from N2-formyl-N1- 285-phospho-D-ribosyl 29glycinamide and L-glutamine in purine biosynthesis NC_002163.1 RefSeq gene 480057 480728 . + . ID=gene491;gene=purQ;Name=purQ;locus_tag=Cj0514;Dbxref=GeneID:904843;gbkey=Gene NC_002163.1 RefSeq region 480156 480647 . + . ID=id1035;gene=purQ;Name=id1035;Dbxref=GeneID:904843;gbkey=misc_feature;Note=HMMPfam hit to PF07685 2C CobB 2FCobQ-like glutamine amidotransferase do 2C score 0.002 NC_002163.1 RefSeq gene 480700 481896 . + . ID=gene492;gene=Cj0515;Name=Cj0515;locus_tag=Cj0515;Dbxref=GeneID:904844;gbkey=Gene NC_002163.1 RefSeq CDS 480700 481896 . + 0 ID=cds464;Parent=gene492;Name=YP_002343947.1;Dbxref=GOA:Q0PB00 InterPro:IPR013247 UniProtKB FTrEMBL:Q0PB00 Genbank:YP_002343947.1 GeneID:904844;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0515 2C possible periplasmic protein 2C len: 398 aa 3B 27.2 25 identity to HP1349 7EUpdated 282006 29 note: One probable transmembrane helices predicted by TMHMM2.0 within CDS. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 481630 481698 . + . ID=id1036;Name=id1036;Dbxref=GeneID:904844;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0515 by TMHMM2.0 at aa 311-333 NC_002163.1 RefSeq region 481877 481909 . + . ID=id1037;gene=plsC;Name=id1037;Dbxref=GeneID:904845;gbkey=misc_feature;Note=PS00989 Clathrin adaptor complexes small chain signature NC_002163.1 RefSeq gene 481877 482569 . + . ID=gene493;gene=plsC;Name=plsC;locus_tag=Cj0516;Dbxref=GeneID:904845;gbkey=Gene NC_002163.1 RefSeq CDS 481877 482569 . + 0 ID=cds465;Parent=gene493;gene=plsC;Name=YP_002343948.1;Dbxref=GOA:Q0PAZ9 InterPro:IPR000804 InterPro:IPR002123 UniProtKB FTrEMBL:Q0PAZ9 Genbank:YP_002343948.1 GeneID:904845;gbkey=CDS;product=1-acyl-SN-glycerol-3-phosphate acyltransferase;Note=Original 282000 29 note: Cj0516 2C plsC 2C possible 1-acyl-SN-glycerol-3-phosphate acyltransferase 2C len: 230 aa 3B similar to e.g. PLCB_HUMAN 1-acyl-SN-glycerol-3-phosphate acyltransferase 28EC 2.3.1.51 29 28278 aa 29 2C fasta scores 3B opt: 227 z-score: 328.0 E 28 29: 5.7e-11 2C 25.7 25 identity in 210 aa overlap. 38.4 25 identity to HP1348 7EUpdated 282006 29 note: Pfam domain PF01553 Acyltransferase along with Prosite domains PS50239 GLYCEROL_ACYLTRANS 2C Phospholipid 2Fglycerol acyltransferase and PS00989 CLAT_ADAPTOR_S 2C Clathrin adaptor complex 2Csmall chain were all identified within CDS. Further support given to product function. No specific characterisation with acceptable identity scores carried out yet. kept within product function. Functional classification - Synthesis and modification of macromolecules - Phospholipids 7EPMID:1557036 NC_002163.1 RefSeq region 481904 481963 . + . ID=id1038;gene=plsC;Name=id1038;Dbxref=GeneID:904845;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0516 by TMHMM2.0 at aa 10-29 NC_002163.1 RefSeq region 482033 482407 . + . ID=id1039;gene=plsC;Name=id1039;Dbxref=GeneID:904845;gbkey=misc_feature;Note=HMMPfam hit to PF01553 2C Acyltransferase 2C score 1.4e-22 NC_002163.1 RefSeq gene 482563 482931 . + . ID=gene494;gene=crcB;Name=crcB;locus_tag=Cj0517;Dbxref=GeneID:904846;gbkey=Gene NC_002163.1 RefSeq CDS 482563 482931 . + 0 ID=cds466;Parent=gene494;gene=crcB;Name=YP_002343949.1;Dbxref=GOA:Q9PHZ4 InterPro:IPR003691 UniProtKB FSwiss-Prot:Q9PHZ4 Genbank:YP_002343949.1 GeneID:904846;gbkey=CDS;product=camphor resistance protein CrcB;Note=Original 282000 29 note: Cj0517 2C crcB 2C probable integral membrane protein 2C len: 122 aa 3B similar to e.g. CRCB_ECOLI CRCB protein 28127 aa 29 2C fasta scores 3B opt: 245 z-score: 278.4 E 28 29: 3.2e-08 2C 37.9 25 identity in 124 aa overlap. 33.9 25 identity to HP1225 7EUpdated 282006 29 note: Pfam domain PF02537 CrcB-like protein identified within CDS. Four probable transmembrane helices predicted by TMHMM2.0 within CDS. Further support given to product function. Functional classification -Membranes 2C lipoproteins and porins 7EPMID:2904550 NC_002163.1 RefSeq region 482575 482631 . + . ID=id1041;gene=crcB;Name=id1041;Dbxref=GeneID:904846;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0517 by TMHMM2.0 at aa 5-23 2C 33-55 2C 62-84 and 99-121 NC_002163.1 RefSeq region 482575 482925 . + . ID=id1040;gene=crcB;Name=id1040;Dbxref=GeneID:904846;gbkey=misc_feature;Note=HMMPfam hit to PF02537 2C CrcB-like protein 2C score 4e-29 NC_002163.1 RefSeq region 482659 482727 . + . ID=id1041;gene=crcB;Name=id1041;Dbxref=GeneID:904846;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0517 by TMHMM2.0 at aa 5-23 2C 33-55 2C 62-84 and 99-121 NC_002163.1 RefSeq region 482746 482814 . + . ID=id1041;gene=crcB;Name=id1041;Dbxref=GeneID:904846;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0517 by TMHMM2.0 at aa 5-23 2C 33-55 2C 62-84 and 99-121 NC_002163.1 RefSeq region 482857 482925 . + . ID=id1041;gene=crcB;Name=id1041;Dbxref=GeneID:904846;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0517 by TMHMM2.0 at aa 5-23 2C 33-55 2C 62-84 and 99-121 ### NC_002163.1 UTR_Extractor 5'-UTR 482978 483002 . + . ID=utr189;locus_tag=Cj0518;product=heat shock protein 90 NC_002163.1 RefSeq CDS 483003 484829 . + 0 ID=cds467;Parent=gene495;gene=htpG;Name=YP_002343950.1;Dbxref=GOA:Q9PHZ3 HSSP:P02829 InterPro:IPR001404 InterPro:IPR003594 UniProtKB FSwiss-Prot:Q9PHZ3 Genbank:YP_002343950.1 GeneID:904847;gbkey=CDS;product=heat shock protein 90;Note=molecular chaperone NC_002163.1 RefSeq gene 483003 484829 . + . ID=gene495;gene=htpG;Name=htpG;locus_tag=Cj0518;Dbxref=GeneID:904847;gbkey=Gene NC_002163.1 RefSeq region 483057 483086 . + . ID=id1042;gene=htpG;Name=id1042;Dbxref=GeneID:904847;gbkey=misc_feature;Note=PS00298 Heat shock hsp90 proteins family signature NC_002163.1 RefSeq region 483063 483524 . + . ID=id1043;gene=htpG;Name=id1043;Dbxref=GeneID:904847;gbkey=misc_feature;Note=HMMPfam hit to PF02518 2C Histidine kinase- 2C DNA gyrase B- 2C and HSP90 2C score 6.5e-13 NC_002163.1 RefSeq region 483525 484826 . + . ID=id1044;gene=htpG;Name=id1044;Dbxref=GeneID:904847;gbkey=misc_feature;Note=HMMPfam hit to PF00183 2C Hsp90 protein 2C score 2.7e-29 NC_002163.1 RefSeq CDS 484826 485143 . + 0 ID=cds468;Parent=gene496;Name=YP_002343951.1;Dbxref=InterPro:IPR001763 UniProtKB FTrEMBL:Q0PAZ6 Genbank:YP_002343951.1 GeneID:904848;gbkey=CDS;product=rhodanese-like domain-containing protein;Note=Original 282000 29 note: Cj0519 2C unknown 2C len: 105 aa 3B similar to hypothetical proteins e.g. TR:E1342888 28EMBL:AJ235272 29 Rickettsia prowazekii RP600 28123 aa 29 2Cfasta scores 3B opt: 151 z-score: 214.9 E 28 29: 0.00011 2C 41.6 25 identity in 89 aa overlap. 34.3 25 identity to HP1223 7EUpdated 282006 29 note: Prosite domain PS50206 RHODANESE_3 2C Rhodanese domain profile also identified within CDS. Rhodanese 2C a sulphurtransferase involved in cyanide detoxification shares evolutionary relationship with a large family of proteins. This domain is found as a single copy in other proteins 2C including phosphatases and ubiquitin C-terminal hydrolases. Product modified to new function based on motif identification. No specific characterisation has been carried out yet 2C so kept within product function. Functional classification -Misc NC_002163.1 RefSeq gene 484826 485143 . + . ID=gene496;gene=Cj0519;Name=Cj0519;locus_tag=Cj0519;Dbxref=GeneID:904848;gbkey=Gene NC_002163.1 RefSeq gene 485143 485577 . + . ID=gene497;Name=Cj0520;locus_tag=Cj0520;Dbxref=GeneID:904849;gbkey=Gene NC_002163.1 RefSeq CDS 485143 485577 . + 0 ID=cds469;Parent=gene497;Name=YP_002343952.1;Dbxref=GOA:Q0PAZ5 UniProtKB FTrEMBL:Q0PAZ5 Genbank:YP_002343952.1 GeneID:904849;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0520 2C possible membrane protein 2C len: 144 aa 3B no Hp match. Contains one possible transmembrane domain at N-terminus. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 485146 485202 . + . ID=id1045;Name=id1045;Dbxref=GeneID:904849;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0520 by TMHMM2.0 at aa 2-20 ### NC_002163.1 RefSeq pseudogene 485698 487343 . + . ID=gene498;Name=Cj0522;locus_tag=Cj0522;Dbxref=GeneID:904850;gbkey=Gene NC_002163.1 RefSeq region 485704 486186 . + . ID=id1046;Name=id1046;Dbxref=GeneID:904850;gbkey=misc_feature;Note=HMMPfam hit to PF02690 2C Na 2B 2FPi-cotransporter 2C score 2.1e-06 NC_002163.1 RefSeq gene 487340 489148 . - . ID=gene499;gene=pbpB;Name=pbpB;locus_tag=Cj0525c;Dbxref=GeneID:904853;gbkey=Gene NC_002163.1 RefSeq CDS 487340 489148 . - 0 ID=cds470;Parent=gene499;gene=pbpB;Name=YP_002343956.1;Dbxref=GOA:Q0PAZ1 InterPro:IPR001460 InterPro:IPR005311 UniProtKB FTrEMBL:Q0PAZ1 Genbank:YP_002343956.1 GeneID:904853;gbkey=CDS;product=penicillin-binding protein;Note=Original 282000 29 note: Cj0525c 2C pbpB 2C probable penicillin-binding protein 2C len: 602 aa 3B similar to many e.g. PBP2_NEIME penicillin-binding protein 2 28581 aa 29 2Cfasta scores 3B opt: 184 z-score: 511.3 E 28 29: 3.5e-21. 28.9 25 identity in 443 aa overlap. 35.8 25 identity to HP1556 28misannotated as cell division protein 28ftsI 29 29. Also similar to Cj0508 2822.6 25 identity in 407 aa overlap 29. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2CPfam match to entry PF00905 Transpeptidase 2C Penicillin binding protein transpeptidase domain 2C score 259.30 2CE-value 5.2e-74 and N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF03717 Penicillin-binding Protein dimerisation domain identified within CDS. Further support given to product function. Characterised in Bacillus subtilis with marginal identity score. kept within product function. Functional classification - Murein sacculus and peptidoglycan 7EPMID:8244929 2C PMID:8289242 NC_002163.1 RefSeq region 487406 488326 . - . ID=id1047;gene=pbpB;Name=id1047;Dbxref=GeneID:904853;gbkey=misc_feature;Note=HMMPfam hit to PF00905 2C Penicillin binding protein transpeptid 2C score 2e-66 NC_002163.1 RefSeq region 487589 487612 . - . ID=id1048;gene=pbpB;Name=id1048;Dbxref=GeneID:904853;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 488444 489010 . - . ID=id1049;gene=pbpB;Name=id1049;Dbxref=GeneID:904853;gbkey=misc_feature;Note=HMMPfam hit to PF03717 2C Penicillin-binding Protein dimerisatio 2C score 6.6e-30 NC_002163.1 RefSeq region 489047 489115 . - . ID=id1050;gene=pbpB;Name=id1050;Dbxref=GeneID:904853;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0525c by TMHMM2.0 at aa 12-34 ### NC_002163.1 RefSeq gene 489155 489451 . - . ID=gene500;gene=fliE;Name=fliE;locus_tag=Cj0526c;Dbxref=GeneID:904854;gbkey=Gene NC_002163.1 RefSeq CDS 489155 489451 . - 0 ID=cds471;Parent=gene500;gene=fliE;Name=YP_002343957.1;Dbxref=GOA:Q9PHY8 InterPro:IPR001624 UniProtKB FSwiss-Prot:Q9PHY8 Genbank:YP_002343957.1 GeneID:904854;gbkey=CDS;product=flagellar hook-basal body protein FliE;Note=forms a junction between the M-ring and FlgB during flagella biosynthesis NC_002163.1 RefSeq region 489158 489439 . - . ID=id1051;gene=fliE;Name=id1051;Dbxref=GeneID:904854;gbkey=misc_feature;Note=HMMPfam hit to PF02049 2C Flagellar hook-basal body complex protein Fl 2C score 4.3e-22 ### NC_002163.1 RefSeq CDS 489458 489952 . - 0 ID=cds472;Parent=gene501;gene=flgC;Name=YP_002343958.1;Dbxref=GOA:Q0PAY9 InterPro:IPR001444 InterPro:IPR006299 InterPro:IPR010930 UniProtKB FTrEMBL:Q0PAY9 Genbank:YP_002343958.1 GeneID:904855;gbkey=CDS;product=flagellar basal body rod protein FlgC;Note=with FlgF and B makes up the proximal portion of the flagellar basal body rod NC_002163.1 RefSeq gene 489458 489952 . - . ID=gene501;gene=flgC;Name=flgC;locus_tag=Cj0527c;Dbxref=GeneID:904855;gbkey=Gene NC_002163.1 RefSeq region 489470 489586 . - . ID=id1052;gene=flgC;Name=id1052;Dbxref=GeneID:904855;gbkey=misc_feature;Note=HMMPfam hit to PF06429 2C Domain of unknown function 28DUF1078 29 2C score 2.2e-06 NC_002163.1 RefSeq region 489842 489934 . - . ID=id1053;gene=flgC;Name=id1053;Dbxref=GeneID:904855;gbkey=misc_feature;Note=HMMPfam hit to PF00460 2C Flagella basal body rod protein 2C score 8.5e-07 NC_002163.1 RefSeq region 489854 489916 . - . ID=id1054;gene=flgC;Name=id1054;Dbxref=GeneID:904855;gbkey=misc_feature;Note=PS00588 Flagella basal body rod proteins signature ### NC_002163.1 RefSeq gene 489962 490393 . - . ID=gene502;gene=flgB;Name=flgB;locus_tag=Cj0528c;Dbxref=GeneID:904856;gbkey=Gene NC_002163.1 RefSeq CDS 489962 490393 . - 0 ID=cds473;Parent=gene502;gene=flgB;Name=YP_002343959.1;Dbxref=GOA:Q0PAY8 InterPro:IPR006300 UniProtKB FTrEMBL:Q0PAY8 Genbank:YP_002343959.1 GeneID:904856;gbkey=CDS;product=flagellar basal body rod protein FlgB;Note=with FlgF and C makes up the proximal portion of the flagellar basal body rod 3B Vibrio parahaemolyticus protein is associated with the polar flagella NC_002163.1 UTR_Extractor 5'-UTR 490394 490416 . - . ID=utr190;locus_tag=Cj0528c;product=flagellar basal body rod protein FlgB NC_002163.1 RefSeq CDS 490474 491475 . - 0 ID=cds474;Parent=gene503;Name=YP_002343960.1;Dbxref=GOA:Q0PAY7 InterPro:IPR003770 UniProtKB FTrEMBL:Q0PAY7 Genbank:YP_002343960.1 GeneID:904857;gbkey=CDS;product=aminodeoxychorismate lyase family protein;Note=Original 282000 29 note: Cj0529c 2C unknown 2C len: 333 aa 3B similar to hypothetical proteins e.g.YCEG_ECOLI hypothetical 38.2 kd protein in PABC-HOLB intergenic region 28340 aa 29 2C fasta scores 3B opt: 326 z-score: 408.1 E 28 29: 1.9e-15 2C 31.3 25 identity in 252 aa overlap. 43.0 25 identity to HP0587 28misannotated as aminodeoxychorismate lyase 28pabC 29 29 7EUpdated 282006 29 note: Pfam domain PF02618 Aminodeoxychorismate lyase identified within CDS. Two probable transmembrane helices predicted by TMHMM2.0 within CDS. This family contains several aminodeoxychorismate lyases. Aminodeoxychorismate lyase is a pyridoxal 5 27-phosphate-dependent enzyme that converts 4-aminodeoxychorismate to pyruvate and p-aminobenzoate 2C a precursor of folic acid in bacteria 28PMID:11011151 29. Product modified to more specific family member based on motif match. No specific characterisation with acceptable identity scores carried out yet. kept within product function. Functional classification -Misc 7EPMID:11011151 NC_002163.1 RefSeq gene 490474 491475 . - . ID=gene503;Name=Cj0529c;locus_tag=Cj0529c;Dbxref=GeneID:904857;gbkey=Gene NC_002163.1 RefSeq region 490477 491322 . - . ID=id1055;Name=id1055;Dbxref=GeneID:904857;gbkey=misc_feature;Note=HMMPfam hit to PF02618 2C Aminodeoxychorismate lyase 2Cscore 4.8e-109 NC_002163.1 UTR_Extractor 5'-UTR 491292 491389 . + . ID=utr191;locus_tag=Cj0530;product=putative periplasmic protein NC_002163.1 RefSeq region 491347 491415 . - . ID=id1056;Name=id1056;Dbxref=GeneID:904857;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0529c by TMHMM2.0 at aa 21-43 NC_002163.1 RefSeq CDS 491390 493960 . + 0 ID=cds475;Parent=gene504;Name=YP_002343961.1;Dbxref=UniProtKB FTrEMBL:Q0PAY6 Genbank:YP_002343961.1 GeneID:904858;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0530 2C probable periplasmic protein 2C len: 856 aa 3B 22.7 25 identity to HP0586. Contains N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 491390 493960 . + . ID=gene504;Name=Cj0530;locus_tag=Cj0530;Dbxref=GeneID:904858;gbkey=Gene NC_002163.1 RefSeq region 491408 491476 . + . ID=id1057;Name=id1057;Dbxref=GeneID:904858;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0530 by TMHMM2.0 at aa 7-29 NC_002163.1 UTR_Extractor 5'-UTR 491476 491505 . - . ID=utr192;locus_tag=Cj0529c;product=putative aminodeoxychorismate lyase family protein ### NC_002163.1 RefSeq CDS 494077 496281 . + 0 ID=cds476;Parent=gene505;gene=icd;Name=YP_002343962.1;Dbxref=GOA:Q0PAY5 InterPro:IPR004436 UniProtKB FTrEMBL:Q0PAY5 Genbank:YP_002343962.1 GeneID:904859;gbkey=CDS;product=isocitrate dehydrogenase;Note=Original 282000 29 note: Cj0531 2C icd 2C probable isocitrate dehydrogenase 2C len: 734 aa 3B highly similar to e.g. IDH2_VIBA1 isocitrate dehydrogenase 28NADP 29 2 28EC 1.1.1.42 29 28741 aa 29 2C fasta scores 3B opt: 2534 z-score: 3250.7 E 28 29: 0 2C 53.3 25 identity in 733 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF03971 Monomeric isocitrate dehydrogenase identified within CDS. Further support given to product function. Characterised within Vibrio sp. strain ABE-1 with acceptable identity score. not added to product function. Functional classification - Energy metabolism - Tricarboxylic acid cycle 7EPMID:8226630 2C PMID:14702320 NC_002163.1 RefSeq gene 494077 496281 . + . ID=gene505;gene=icd;Name=icd;locus_tag=Cj0531;Dbxref=GeneID:904859;gbkey=Gene NC_002163.1 RefSeq region 494080 496266 . + . ID=id1058;gene=icd;Name=id1058;Dbxref=GeneID:904859;gbkey=misc_feature;Note=HMMPfam hit to PF03971 2C Monomeric isocitrate dehydrogenase 2C score 0 NC_002163.1 RefSeq region 496278 496700 . + . ID=id1059;gene=mdh;Name=id1059;Dbxref=GeneID:904860;gbkey=misc_feature;Note=HMMPfam hit to PF00056 2C lactate 2Fmalate dehydrogenase 2C NAD binding do 2C score 2.4e-28 NC_002163.1 RefSeq CDS 496278 497180 . + 0 ID=cds477;Parent=gene506;gene=mdh;Name=YP_002343963.1;Dbxref=GOA:Q9PHY2 HSSP:P80039 InterPro:IPR001236 InterPro:IPR001252 InterPro:IPR001557 InterPro:IPR015955 InterPro:IPR016040 UniProtKB FSwiss-Prot:Q9PHY2 Genbank:YP_002343963.1 GeneID:904860;gbkey=CDS;product=malate dehydrogenase;Note=Original 282000 29 note: Cj0532 2C mdh 2C probable malate dehydrogenase 2C len: 300 aa 3B MDH_CHLTE malate dehydrogenase 28EC 1.1.1.37 29 28310 aa 29 2C fasta scores 3B opt: 652 z-score: 1151.6 E 28 29: 0 2C 35.4 25 identity in 294 aa overlap. No Hp match. Also similar toCj1167 ldh 2825.4 25 identity in 311 aa overlap 29. Contains Pfam match to entry PF00056 ldh 2CL-lactate dehydrogenases 2C score 153.00 2C E-value 1e-42 7EUpdated 282006 29 note: Pfam domain PF02866 lactate 2Fmalate dehydrogenase 2C alpha 2Fbeta C-terminal domain identified within CDS. Further support given to product function. Characterised within Chlorobium tepidum and Bacillus subtilis with acceptable identity scores. not added to product function. Functional classification - Energy metabolism - Tricarboxylic acid cycle 7EPMID:1735722 2C PMID:8550482 2C PMID:14702320 NC_002163.1 RefSeq gene 496278 497180 . + . ID=gene506;gene=mdh;Name=mdh;locus_tag=Cj0532;Dbxref=GeneID:904860;gbkey=Gene NC_002163.1 RefSeq region 496707 497174 . + . ID=id1060;gene=mdh;Name=id1060;Dbxref=GeneID:904860;gbkey=misc_feature;Note=HMMPfam hit to PF02866 2C lactate 2Fmalate dehydrogenase 2C alpha 2Fbeta C-t 2C score 4.6e-09 ### NC_002163.1 RefSeq CDS 497181 498344 . + 0 ID=cds478;Parent=gene507;gene=sucC;Name=YP_002343964.1;Dbxref=GOA:Q9PHY1 HSSP:P07460 InterPro:IPR005809 InterPro:IPR005811 InterPro:IPR011761 InterPro:IPR013650 InterPro:IPR013816 InterPro:IPR016102 UniProtKB FSwiss-Prot:Q9PHY1 Genbank:YP_002343964.1 GeneID:904861;gbkey=CDS;product=succinyl-CoA synthetase subunit beta;Note=catalyzes the interconversion of succinyl-CoA and succinate NC_002163.1 RefSeq gene 497181 498344 . + . ID=gene507;gene=sucC;Name=sucC;locus_tag=Cj0533;Dbxref=GeneID:904861;gbkey=Gene NC_002163.1 RefSeq region 497265 497774 . + . ID=id1061;gene=sucC;Name=id1061;Dbxref=GeneID:904861;gbkey=misc_feature;Note=HMMPfam hit to PF02222 2C ATP-grasp domain 2C score 5e-19 NC_002163.1 RefSeq region 497916 498329 . + . ID=id1062;gene=sucC;Name=id1062;Dbxref=GeneID:904861;gbkey=misc_feature;Note=HMMPfam hit to PF00549 2C CoA-ligase 2C score 1.4e-59 NC_002163.1 RefSeq region 497949 498023 . + . ID=id1063;gene=sucC;Name=id1063;Dbxref=GeneID:904861;gbkey=misc_feature;Note=PS01217 ATP-citrate lyase 2F succinyl-CoA ligases family signature 3 ### NC_002163.1 RefSeq CDS 498354 499223 . + 0 ID=cds479;Parent=gene508;gene=sucD;Name=YP_002343965.1;Dbxref=GOA:Q0PAY2 InterPro:IPR003781 InterPro:IPR005810 InterPro:IPR005811 InterPro:IPR016040 InterPro:IPR016102 InterPro:IPR017440 UniProtKB FTrEMBL:Q0PAY2 Genbank:YP_002343965.1 GeneID:904862;gbkey=CDS;product=succinyl-CoA synthetase subunit alpha;Note=Original 282000 29 note: Cj0534 2C sucD 2C probable succinyl-coA synthetase alpha chain 2C len: 289 aa 3B highly similar to many e.g. SUCD_ECOLI succinyl-coA synthetase alpha chain 28EC 6.2.1.5 29 28288 aa 29 2C fasta scores 3B opt: 1101 z-score: 1532.0 E 28 29: 0 2C 58.5 25 identity in 287 aa overlap. No Hp match. Contains PS01216 ATP-citrate lyase 2F succinyl-CoA ligases family signature 1 2C PS00399 ATP-citrate lyase 2F succinyl-CoA ligases family active site 2C and Pfam match to entry PF00549 ligase-CoA 2CCoA-ligases 2C score 142.30 2C E-value 8.6e-39 7EUpdated 282006 29 note: Pfam domain PF02629 CoA binding domain domain identified within CDS. Further support given to product function. Characterised within Bacillus subtilis and Escherichia coli with acceptable identity scores. not added to product function. Functional classification - Energy metabolism -Tricarboxylic acid cycle 7EPMID:3543212 2C PMID:14702320 NC_002163.1 RefSeq gene 498354 499223 . + . ID=gene508;gene=sucD;Name=sucD;locus_tag=Cj0534;Dbxref=GeneID:904862;gbkey=Gene NC_002163.1 RefSeq region 498363 498698 . + . ID=id1064;gene=sucD;Name=id1064;Dbxref=GeneID:904862;gbkey=misc_feature;Note=HMMPfam hit to PF02629 2C CoA binding domain 2C score 2.2e-59 NC_002163.1 RefSeq region 498750 499175 . + . ID=id1065;gene=sucD;Name=id1065;Dbxref=GeneID:904862;gbkey=misc_feature;Note=HMMPfam hit to PF00549 2C CoA-ligase 2C score 2.3e-39 NC_002163.1 RefSeq region 498807 498896 . + . ID=id1066;gene=sucD;Name=id1066;Dbxref=GeneID:904862;gbkey=misc_feature;Note=PS01216 ATP-citrate lyase 2F succinyl-CoA ligases family signature 1 NC_002163.1 UTR_Extractor 5'-UTR 499058 499237 . + . ID=utr193;locus_tag=Cj0535;product=2-oxoglutarate-acceptor oxidoreductase subunit OorD NC_002163.1 RefSeq region 499059 499100 . + . ID=id1067;gene=sucD;Name=id1067;Dbxref=GeneID:904862;gbkey=misc_feature;Note=PS00399 ATP-citrate lyase 2F succinyl-CoA ligases family active site ### NC_002163.1 RefSeq CDS 499238 499549 . + 0 ID=cds480;Parent=gene509;gene=oorD;Name=YP_002343966.1;Dbxref=GOA:Q0PAY1 InterPro:IPR001450 UniProtKB FTrEMBL:Q0PAY1 Genbank:YP_002343966.1 GeneID:904863;gbkey=CDS;product=2-oxoglutarate-acceptor oxidoreductase subunit OorD;Note=Original 282000 29 note: Cj0535 2C oorD 2C probable OORD subunit of 2-oxoglutarate:acceptor oxidoreductase 2C len: 103 aa 3B similar to TR:O68227 28EMBL:AF021094 29 H. pylori OORD subunit of 2-oxoglutarate:acceptor oxidoreductase 28113 aa 29 2C fasta scores 3B opt: 436 z-score: 768.9 E 28 29: 0 2C59.8 25 identity in 97 aa overlap. 59.8 25 identity to HP0588. Contains 2x PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature and Pfam match to entry PF00037 fer4 2C 4Fe-4S ferredoxins and related iron-sulfur cluster binding domains. 2C score 17.40 2C E-value 0.00091 7EUpdated 282006 29 note: Characterised within Helicobacter pylori with acceptable identity score. not added to product function. Functional classification - Energy metabolism - Electron transport 7EPMID:9495749 2C PMID:7608066 2C PMID:14702320 NC_002163.1 RefSeq gene 499238 499549 . + . ID=gene509;gene=oorD;Name=oorD;locus_tag=Cj0535;Dbxref=GeneID:904863;gbkey=Gene NC_002163.1 RefSeq region 499268 499339 . + . ID=id1068;gene=oorD;Name=id1068;Dbxref=GeneID:904863;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 2.5e-05 NC_002163.1 RefSeq region 499289 499324 . + . ID=id1069;gene=oorD;Name=id1069;Dbxref=GeneID:904863;gbkey=misc_feature;Note=PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature NC_002163.1 RefSeq region 499379 499450 . + . ID=id1070;gene=oorD;Name=id1070;Dbxref=GeneID:904863;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 5.8e-05 NC_002163.1 RefSeq region 499400 499435 . + . ID=id1071;gene=oorD;Name=id1071;Dbxref=GeneID:904863;gbkey=misc_feature;Note=PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature ### NC_002163.1 RefSeq gene 499558 500682 . + . ID=gene510;gene=oorA;Name=oorA;locus_tag=Cj0536;Dbxref=GeneID:904864;gbkey=Gene NC_002163.1 RefSeq CDS 499558 500682 . + 0 ID=cds481;Parent=gene510;gene=oorA;Name=YP_002343967.1;Dbxref=GOA:Q0PAY0 InterPro:IPR002880 InterPro:IPR015941 UniProtKB FTrEMBL:Q0PAY0 Genbank:YP_002343967.1 GeneID:904864;gbkey=CDS;product=2-oxoglutarate-acceptor oxidoreductase subunit OorA;Note=Original 282000 29 note: Cj0536 2C oorA 2C probable OORA subunit of 2-oxoglutarate:acceptor oxidoreductase 2C len: 374 aa 3B similar to TR:O68228 28EMBL:AF021094 29 H. pylori OORA subunit of 2-oxoglutarate:acceptor oxidoreductase 28371 aa 29 2C fasta scores 3B opt: 1447 z-score: 2256.7 E 28 29: 0 2C62.7 25 identity in 351 aa overlap. 63.2 25 identity to HP0589 7EUpdated 282006 29 note: Pfam domain PF01855 Pyruvate flavodoxin 2Fferredoxin oxidoreductase identified within CDS. Further support given to product function. Characterised within Helicobacter pylori with acceptable identity score. not added to product function. Functional classification - Energy metabolism - Electron transport 7EPMID:9495749 2C PMID:7608066 2C PMID:14702320 NC_002163.1 RefSeq region 499597 500304 . + . ID=id1072;gene=oorA;Name=id1072;Dbxref=GeneID:904864;gbkey=misc_feature;Note=HMMPfam hit to PF01855 2C Pyruvate flavodoxin 2Fferredoxin oxidoreductas 2C score 5e-93 ### NC_002163.1 RefSeq CDS 500683 501528 . + 0 ID=cds482;Parent=gene511;gene=oorB;Name=YP_002343968.1;Dbxref=GOA:Q0PAX9 InterPro:IPR011766 UniProtKB FTrEMBL:Q0PAX9 Genbank:YP_002343968.1 GeneID:904963;gbkey=CDS;product=2-oxoglutarate-acceptor oxidoreductase subunit OorB;Note=Original 282000 29 note: Cj0537 2C oorB 2C probable OORB subunit of 2-oxoglutarate:acceptor oxidoreductase 2C len: 281 aa 3B similar to TR:O68229 28EMBL:AF021094 29 H. pylori OORB subunit of 2-oxoglutarate:acceptor oxidoreductase 28274 aa 29 2C fasta scores 3B opt: 1356 z-score: 2118.6 E 28 29: 0 2C69.7 25 identity in 274 aa overlap. 72.9 25 identity to HP0590 7EUpdated 282006 29 note: Pfam domain PF02775 Thiamine pyrophosphate enzyme 2C C-terminal identified within CDS. Further support given to product function. Characterised within Helicobacter pylori with acceptable identity score. not added to product function. Functional classification - Energy metabolism - Electron transport 7EPMID:9495749 2C PMID:7608066 2C PMID:14702320 NC_002163.1 RefSeq gene 500683 501528 . + . ID=gene511;gene=oorB;Name=oorB;locus_tag=Cj0537;Dbxref=GeneID:904963;gbkey=Gene NC_002163.1 RefSeq region 500731 501297 . + . ID=id1073;gene=oorB;Name=id1073;Dbxref=GeneID:904963;gbkey=misc_feature;Note=HMMPfam hit to PF02775 2C Thiamine pyrophosphate enzyme 2C C-termina 2C score 3.8e-87 NC_002163.1 RefSeq gene 501525 502082 . + . ID=gene512;gene=oorC;Name=oorC;locus_tag=Cj0538;Dbxref=GeneID:905096;gbkey=Gene NC_002163.1 RefSeq CDS 501525 502082 . + 0 ID=cds483;Parent=gene512;gene=oorC;Name=YP_002343969.1;Dbxref=GOA:Q0PAX8 InterPro:IPR002869 UniProtKB FTrEMBL:Q0PAX8 Genbank:YP_002343969.1 GeneID:905096;gbkey=CDS;product=2-oxoglutarate-acceptor oxidoreductase subunit OorC;Note=Original 282000 29 note: Cj0538 2C oorC 2C probable OORC subunit of 2-oxoglutarate:acceptor oxidoreductase 2C len: 185 aa 3B similar to TR:O68230 28EMBL:AF021094 29 H. pylori OORC subunit of 2-oxoglutarate:acceptor oxidoreductase 28184 aa 29 2C fasta scores 3B opt: 714 z-score: 1191.4 E 28 29: 0 2C59.7 25 identity in 181 aa overlap. 60.8 25 identity to HP0591 7EUpdated 282006 29 note: Pfam domain PF01558 Pyruvate ferredoxin 2Fflavodoxin oxidoreductase identified within CDS. Further support given to product function. Characterised within Helicobacter pylori with acceptable identity score. not added to product function. Functional classification - Energy metabolism - Electron transport 7EPMID:9495749 2C PMID:7608066 2C PMID:14702320 NC_002163.1 RefSeq region 501555 502052 . + . ID=id1074;gene=oorC;Name=id1074;Dbxref=GeneID:905096;gbkey=misc_feature;Note=HMMPfam hit to PF01558 2C Pyruvate ferredoxin 2Fflavodoxin oxidoreductas 2C score 3.8e-35 ### NC_002163.1 UTR_Extractor 5'-UTR 502198 502220 . + . ID=utr194;locus_tag=Cj0539;product=hypothetical protein NC_002163.1 RefSeq gene 502221 502484 . + . ID=gene513;Name=Cj0539;locus_tag=Cj0539;Dbxref=GeneID:904865;gbkey=Gene NC_002163.1 RefSeq CDS 502221 502484 . + 0 ID=cds484;Parent=gene513;Name=YP_002343970.1;Dbxref=UniProtKB FTrEMBL:Q0PAX7 Genbank:YP_002343970.1 GeneID:904865;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0539 2C unknown 2C len: 87 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 RefSeq gene 502487 503023 . + . ID=gene514;Name=Cj0540;locus_tag=Cj0540;Dbxref=GeneID:904866;gbkey=Gene NC_002163.1 RefSeq CDS 502487 503023 . + 0 ID=cds485;Parent=gene514;Name=YP_002343971.1;Dbxref=UniProtKB FTrEMBL:Q0PAX6 Genbank:YP_002343971.1 GeneID:904866;gbkey=CDS;product=exporting protein;Note=Original 282000 29 note: Cj0540 2C unknown 2C len: 178 aa 3B 30.6 25 identity in 72 aa overlap 28N-terminus 29 to HP0241 7EUpdated 282006 29 note: Product function modified to more specific family member based on SignalP 2.0 HMM results. kept within product function. Functional classification - Protein and peptide secretion NC_002163.1 UTR_Extractor 5'-UTR 502843 503036 . + . ID=utr195;locus_tag=Cj0541;product=polyprenyl synthetase ### NC_002163.1 RefSeq CDS 503037 503930 . + 0 ID=cds486;Parent=gene515;Name=YP_002343972.1;Dbxref=GOA:Q0PAX5 InterPro:IPR000092 InterPro:IPR008949 InterPro:IPR017446 UniProtKB FTrEMBL:Q0PAX5 Genbank:YP_002343972.1 GeneID:904867;gbkey=CDS;product=polyprenyl synthetase;Note=Original 282000 29 note: Cj0541 2C probable polyprenyl synthetase 2C len: 297 aa 3B similar to many e.g. ISPB_ECOLI octaprenyl-diphosphate synthase 28EC 2.5.1.- 29 28323 aa 29 2Cfasta scores 3B opt: 514 z-score: 753.9 E 28 29: 0 2C 35.2 25 identity in 281 aa overlap 2C IDSA_METTM bifunctional short chain isoprenyl diphosphate synthase 28324 aa 29 2C fasta scores 3B opt: 549 z-score: 676.0 E 28 29: 2.3e-30 2C 36.5 25 identity in 277 aa overlap 2C and GGPP_SULAC geranylgeranyl pyrophosphate synthetase 28330 aa 29 2C fasta scores 3B opt: 330 z-score: 653.2 E 28 29: 4.4e-29 2C 32.9 25 identity in 292 aa overlap. 44.6 25 identity to HP0240. Also similar to Cj1644 2827.6 25 identity in 268 aa overlap 29. Contains PS00723 and PS00444 Polyprenyl synthetases signatures 1 and 2 2C and Pfam match to entry PF00348 polyprenyl_synt 2C Polyprenyl synthetases 2C score 153.40 2C E-value 3.8e-42 7EUpdated 282006 29 note: Similarity to more than one characterised genus with acceptable identity scores. not added to product function. Functional classification - Biosynthesis of cofactors 2C prosthetic groups and carriers - Menaquinone and ubiquinine 7EPMID:8037730 NC_002163.1 RefSeq gene 503037 503930 . + . ID=gene515;Name=Cj0541;locus_tag=Cj0541;Dbxref=GeneID:904867;gbkey=Gene NC_002163.1 RefSeq region 503094 503825 . + . ID=id1075;Name=id1075;Dbxref=GeneID:904867;gbkey=misc_feature;Note=HMMPfam hit to PF00348 2C Polyprenyl synthetase 2Cscore 1.4e-43 NC_002163.1 RefSeq region 503223 503267 . + . ID=id1076;Name=id1076;Dbxref=GeneID:904867;gbkey=misc_feature;Note=PS00723 Polyprenyl synthetases signature 1 NC_002163.1 RefSeq region 503577 503615 . + . ID=id1077;Name=id1077;Dbxref=GeneID:904867;gbkey=misc_feature;Note=PS00444 Polyprenyl synthetases signature 2 NC_002163.1 RefSeq CDS 503930 505228 . + 0 ID=cds487;Parent=gene516;gene=hemA;Name=YP_002343973.1;Dbxref=GOA:Q9PHX2 HSSP:Q9UXR8 InterPro:IPR000343 InterPro:IPR006151 InterPro:IPR015895 InterPro:IPR015896 InterPro:IPR016040 UniProtKB FSwiss-Prot:Q9PHX2 Genbank:YP_002343973.1 GeneID:904868;gbkey=CDS;product=glutamyl-tRNA reductase;Note=catalyzes the formation of glutamate-1-semialdehyde from glutamyl-tRNA 28Glu 29 and NADPH 3B the second step of the pathway is catalyzed by glutamate-1-semialdehyde aminomutase which results in the formation of 5-aminolevulinic acid 3B functions in porphyrin 28tetrapyrroles 29 biosynthesis 3B the crystal structure showed a C-terminal dimerization domain that appears to be absent in Chlamydial proteins NC_002163.1 RefSeq gene 503930 505228 . + . ID=gene516;gene=hemA;Name=hemA;locus_tag=Cj0542;Dbxref=GeneID:904868;gbkey=Gene NC_002163.1 RefSeq region 503942 504394 . + . ID=id1078;gene=hemA;Name=id1078;Dbxref=GeneID:904868;gbkey=misc_feature;Note=HMMPfam hit to PF05201 2C Glutamyl-tRNAGlu reductase 2CN-terminal 2C score 4.3e-44 NC_002163.1 RefSeq region 504404 504847 . + . ID=id1079;gene=hemA;Name=id1079;Dbxref=GeneID:904868;gbkey=misc_feature;Note=HMMPfam hit to PF05200 2C Glutamyl-tRNAGlu reductase 2CNAD 28P 29 bin 2C score 2e-66 NC_002163.1 RefSeq region 504857 505159 . + . ID=id1080;gene=hemA;Name=id1080;Dbxref=GeneID:904868;gbkey=misc_feature;Note=HMMPfam hit to PF00745 2C Glutamyl-tRNAGlu reductase 2Cdimerisati 2C score 2.9e-30 NC_002163.1 UTR_Extractor 5'-UTR 505118 505211 . + . ID=utr196;locus_tag=Cj0543;product=prolyl-tRNA synthetase NC_002163.1 RefSeq CDS 505212 506921 . + 0 ID=cds488;Parent=gene517;gene=proS;Name=YP_002343974.1;Dbxref=GOA:Q9PHX1 InterPro:IPR002314 InterPro:IPR002316 InterPro:IPR004154 InterPro:IPR004500 InterPro:IPR006195 InterPro:IPR007214 UniProtKB FSwiss-Prot:Q9PHX1 Genbank:YP_002343974.1 GeneID:904869;gbkey=CDS;product=prolyl-tRNA synthetase;Note=catalyzes the formation of prolyl-tRNA 28Pro 29 from proline and tRNA 28Pro 29 NC_002163.1 RefSeq gene 505212 506921 . + . ID=gene517;gene=proS;Name=proS;locus_tag=Cj0543;Dbxref=GeneID:904869;gbkey=Gene NC_002163.1 RefSeq region 505326 505790 . + . ID=id1081;gene=proS;Name=id1081;Dbxref=GeneID:904869;gbkey=misc_feature;Note=HMMPfam hit to PF00587 2C tRNA synthetase class II core domain 28 2C score 6.1e-53 NC_002163.1 RefSeq region 505629 505691 . + . ID=id1082;gene=proS;Name=id1082;Dbxref=GeneID:904869;gbkey=misc_feature;Note=PS00179 Aminoacyl-transfer RNA synthetases class-II signature 1 NC_002163.1 RefSeq region 505971 506372 . + . ID=id1083;gene=proS;Name=id1083;Dbxref=GeneID:904869;gbkey=misc_feature;Note=HMMPfam hit to PF04073 2C YbaK 2F prolyl-tRNA synthetases associa 2C score 4.8e-06 NC_002163.1 RefSeq region 506640 506912 . + . ID=id1084;gene=proS;Name=id1084;Dbxref=GeneID:904869;gbkey=misc_feature;Note=HMMPfam hit to PF03129 2C Anticodon binding domain 2Cscore 7.4e-20 NC_002163.1 RefSeq CDS 506918 507307 . + 0 ID=cds489;Parent=gene518;Name=YP_002343975.1;Dbxref=UniProtKB FTrEMBL:Q0PAX2 Genbank:YP_002343975.1 GeneID:904870;gbkey=CDS;product=integral memnbrane protein;Note=Original 282000 29 note: Cj0544 2C probable integral membrane protein 2C len: 129 aa 3B no Hp match 7EUpdated 282006 29 note: Three probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 506918 507307 . + . ID=gene518;gene=Cj0544;Name=Cj0544;locus_tag=Cj0544;Dbxref=GeneID:904870;gbkey=Gene NC_002163.1 RefSeq region 506945 507001 . + . ID=id1085;Name=id1085;Dbxref=GeneID:904870;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0544 by TMHMM2.0 at aa 10-28 2C 30-49 and 69-100 NC_002163.1 RefSeq region 507005 507064 . + . ID=id1085;Name=id1085;Dbxref=GeneID:904870;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0544 by TMHMM2.0 at aa 10-28 2C 30-49 and 69-100 NC_002163.1 UTR_Extractor 5'-UTR 507041 507303 . + . ID=utr197;locus_tag=Cj0545;product=porphobilinogen deaminase NC_002163.1 RefSeq region 507122 507217 . + . ID=id1085;Name=id1085;Dbxref=GeneID:904870;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0544 by TMHMM2.0 at aa 10-28 2C 30-49 and 69-100 NC_002163.1 RefSeq gene 507304 508227 . + . ID=gene519;gene=hemC;Name=hemC;locus_tag=Cj0545;Dbxref=GeneID:904871;gbkey=Gene NC_002163.1 RefSeq CDS 507304 508227 . + 0 ID=cds490;Parent=gene519;gene=hemC;Name=YP_002343976.1;Dbxref=GOA:Q9PHW9 HSSP:P06983 InterPro:IPR000860 UniProtKB FSwiss-Prot:Q9PHW9 Genbank:YP_002343976.1 GeneID:904871;gbkey=CDS;product=porphobilinogen deaminase;Note=transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis NC_002163.1 RefSeq region 507307 507945 . + . ID=id1086;gene=hemC;Name=id1086;Dbxref=GeneID:904871;gbkey=misc_feature;Note=HMMPfam hit to PF01379 2C Porphobilinogen deaminase 2Cdipyrometh 2C score 5.7e-107 NC_002163.1 RefSeq region 507967 508188 . + . ID=id1087;gene=hemC;Name=id1087;Dbxref=GeneID:904871;gbkey=misc_feature;Note=HMMPfam hit to PF03900 2C Porphobilinogen deaminase 2CC-terminal 2C score 7.3e-15 NC_002163.1 RefSeq region 507985 508035 . + . ID=id1088;gene=hemC;Name=id1088;Dbxref=GeneID:904871;gbkey=misc_feature;Note=PS00533 Porphobilinogen deaminase cofactor-binding site NC_002163.1 RefSeq CDS 508224 510026 . + 0 ID=cds491;Parent=gene520;gene=ubiD;Name=YP_002343977.1;Dbxref=GOA:Q0PAX0 InterPro:IPR002830 UniProtKB FTrEMBL:Q0PAX0 Genbank:YP_002343977.1 GeneID:904873;gbkey=CDS;product=3-octaprenyl-4-hydroxybenzoate carboxy-lyase;Note=Original 282000 29 note: Cj0546 2C unknown 2C len: 600 aa 3B similar to many hypothetical proteins e.g. YIGC_ECOLI 28497 aa 29 2C fasta scores 3B opt: 837 z-score: 852.4 E 28 29: 0 2C 32.7 25 identity in 459 aa overlap. 51.6 25 identity to HP0396 7EUpdated 282006 29 note: Pfam domain PF01977 3-octaprenyl-4-hydroxybenzoate carboxy-lyase identified within CDS. Product modified to more specific family member due to motif match. Characterised within Escherichia coli with marginal identity scores. Sequence alignment was partial. kept within product function. Functional classification - Misc 7EPMID:782527 2C PMID:11029449 NC_002163.1 RefSeq gene 508224 510026 . + . ID=gene520;gene=ubiD;Name=ubiD;locus_tag=Cj0546;Dbxref=GeneID:904873;gbkey=Gene NC_002163.1 RefSeq region 508236 509504 . + . ID=id1089;gene=ubiD;Name=id1089;Dbxref=GeneID:904873;gbkey=misc_feature;Note=HMMPfam hit to PF01977 2C3-octaprenyl-4-hydroxybenzoate carboxy-lyase 2C score 4.7e-139 ### NC_002163.1 UTR_Extractor 5'-UTR 510149 510183 . + . ID=utr198;locus_tag=Cj0547;product=flagellar protein FlaG NC_002163.1 RefSeq gene 510184 510549 . + . ID=gene521;gene=flaG;Name=flaG;locus_tag=Cj0547;Dbxref=GeneID:904874;gbkey=Gene NC_002163.1 RefSeq CDS 510184 510549 . + 0 ID=cds492;Parent=gene521;gene=flaG;Name=YP_002343978.1;Dbxref=GOA:Q0PAW9 InterPro:IPR005186 UniProtKB FTrEMBL:Q0PAW9 Genbank:YP_002343978.1 GeneID:904874;gbkey=CDS;product=flagellar protein FlaG;Note=possibly involved in flagella export NC_002163.1 RefSeq region 510220 510543 . + . ID=id1090;gene=flaG;Name=id1090;Dbxref=GeneID:904874;gbkey=misc_feature;Note=HMMPfam hit to PF03646 2C FlaG protein 2C score 4.7e-42 ### NC_002163.1 RefSeq CDS 510552 512480 . + 0 ID=cds493;Parent=gene522;gene=fliD;Name=YP_002343979.1;Dbxref=GOA:Q9PHW6 InterPro:IPR003481 InterPro:IPR010809 InterPro:IPR010810 UniProtKB FSwiss-Prot:Q9PHW6 Genbank:YP_002343979.1 GeneID:904875;gbkey=CDS;product=flagellar capping protein;Note=Also called hook-associated protein 2 3B involved in flagellin assembly NC_002163.1 RefSeq gene 510552 512480 . + . ID=gene522;gene=fliD;Name=fliD;locus_tag=Cj0548;Dbxref=GeneID:904875;gbkey=Gene NC_002163.1 RefSeq region 510585 510890 . + . ID=id1091;gene=fliD;Name=id1091;Dbxref=GeneID:904875;gbkey=misc_feature;Note=HMMPfam hit to PF02465 2C Flagellar hook-associated protein 2C score 2.3e-33 NC_002163.1 RefSeq region 510954 511127 . + . ID=id1092;gene=fliD;Name=id1092;Dbxref=GeneID:904875;gbkey=misc_feature;Note=HMMPfam hit to PF07196 2C Flagellin hook IN motif 2Cscore 2.1e-10 NC_002163.1 RefSeq region 511317 512042 . + . ID=id1093;gene=fliD;Name=id1093;Dbxref=GeneID:904875;gbkey=misc_feature;Note=HMMPfam hit to PF07195 2C Flagellar hook-associated protein 2C score 4e-75 ### NC_002163.1 RefSeq CDS 512492 512878 . + 0 ID=cds494;Parent=gene523;gene=fliS;Name=YP_002343980.1;Dbxref=GOA:Q0PAW7 InterPro:IPR003713 UniProtKB FTrEMBL:Q0PAW7 Genbank:YP_002343980.1 GeneID:904876;gbkey=CDS;product=flagellar protein FliS;Note=flagellin specific chaperone NC_002163.1 RefSeq gene 512492 512878 . + . ID=gene523;gene=fliS;Name=fliS;locus_tag=Cj0549;Dbxref=GeneID:904876;gbkey=Gene NC_002163.1 RefSeq region 512495 512863 . + . ID=id1094;gene=fliS;Name=id1094;Dbxref=GeneID:904876;gbkey=misc_feature;Note=HMMPfam hit to PF02561 2C Flagellar protein FliS 2Cscore 7.5e-35 NC_002163.1 RefSeq gene 512859 513134 . + . ID=gene524;gene=Cj0550;Name=Cj0550;locus_tag=Cj0550;Dbxref=GeneID:904877;gbkey=Gene NC_002163.1 RefSeq CDS 512859 513134 . + 0 ID=cds495;Parent=gene524;Name=YP_002343981.1;Dbxref=UniProtKB FTrEMBL:Q0PAW6 Genbank:YP_002343981.1 GeneID:904877;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0550 2C unknown 2C len: 91 aa 3B no Hp match. Functional classification - Unknown ### NC_002163.1 RefSeq gene 513138 513451 . - . ID=gene525;gene=rnpB;Name=rnpB;locus_tag=Cjp11;Dbxref=GeneID:904878;gbkey=Gene NC_002163.1 RefSeq transcript 513138 513451 . - . ID=rna19;Parent=gene525;gene=rnpB;Name=rna19;Dbxref=GeneID:904878;gbkey=misc_RNA;product=RNA component of RNase P;Note=Updated 282006 29 note: Rfam RF00010 2C Bacterial RNase P class A has now been identified within CDS. Further support given to product function 7ErnpB 2C RNA component of RNase P 2C similar to many e.g. EMBL:BBRNASEP Z30953 B.burgdorferi 28B31 29 RNase P RNA gene 2C wublastn score 3B E 3D 9.3e-14 2C 69 25 identity in 204 bp overlap and 74 25 identity in 71 bp overlap NC_002163.1 RefSeq exon 513138 513451 . - . ID=id1095;Parent=rna19;gene=rnpB;Name=id1095;Dbxref=GeneID:904878;gbkey=misc_RNA;product=RNA component of RNase P;Note=Updated 282006 29 note: Rfam RF00010 2C Bacterial RNase P class A has now been identified within CDS. Further support given to product function 7ErnpB 2C RNA component of RNase P 2C similar to many e.g. EMBL:BBRNASEP Z30953 B.burgdorferi 28B31 29 RNase P RNA gene 2C wublastn score 3B E 3D 9.3e-14 2C 69 25 identity in 204 bp overlap and 74 25 identity in 71 bp overlap NC_002163.1 RefSeq gene 513566 514135 . + . ID=gene526;gene=efp;Name=efp;locus_tag=Cj0551;Dbxref=GeneID:904879;gbkey=Gene NC_002163.1 RefSeq CDS 513566 514135 . + 0 ID=cds496;Parent=gene526;gene=efp;Name=YP_002343982.1;Dbxref=GOA:Q9PHW3 HSSP:P56635 InterPro:IPR001059 InterPro:IPR011768 InterPro:IPR012340 InterPro:IPR013185 InterPro:IPR013852 InterPro:IPR014722 InterPro:IPR015365 UniProtKB FSwiss-Prot:Q9PHW3 Genbank:YP_002343982.1 GeneID:904879;gbkey=CDS;product=elongation factor P;Note=Involved in peptide bond synthesis 3B alters the affinity of the ribosome for aminoacyl-tRNA NC_002163.1 RefSeq region 513572 514126 . + . ID=id1096;gene=efp;Name=id1096;Dbxref=GeneID:904879;gbkey=misc_feature;Note=HMMPfam hit to PF01132 2C Elongation factor P 28EF-P 29 2Cscore 1.7e-109 ### NC_002163.1 UTR_Extractor 5'-UTR 514272 514294 . + . ID=utr199;locus_tag=Cj0552;product=hypothetical protein NC_002163.1 RefSeq region 514295 514960 . + . ID=id1097;Name=id1097;Dbxref=GeneID:904880;gbkey=misc_feature;Note=HMMPfam hit to PF06149 2C Protein of unknown function 28DUF969 29 2C score 3.4e-157 NC_002163.1 RefSeq CDS 514295 514987 . + 0 ID=cds497;Parent=gene527;Name=YP_002343983.1;Dbxref=InterPro:IPR010374 UniProtKB FTrEMBL:Q0PAW4 Genbank:YP_002343983.1 GeneID:904880;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0552 2C unknown 2C len: 230 aa 3B no Hp match. Hydrophobic 7EUpdated 282006 29 note: Pfam domain PF06149 Protein of unknown function 28DUF969 29 identified within CDS. This is a family of uncharacterised bacterial membrane proteins. Also identified were four probable transmembrane helices predicted by TMHMM2.0. Product function has been changed due to these results. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 514295 514987 . + . ID=gene527;Name=Cj0552;locus_tag=Cj0552;Dbxref=GeneID:904880;gbkey=Gene NC_002163.1 RefSeq region 514352 514420 . + . ID=id1098;Name=id1098;Dbxref=GeneID:904880;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0552 by TMHMM2.0 at aa 20-42 2C 52-71 2C 99-121 and 192-214 NC_002163.1 RefSeq region 514448 514507 . + . ID=id1098;Name=id1098;Dbxref=GeneID:904880;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0552 by TMHMM2.0 at aa 20-42 2C 52-71 2C 99-121 and 192-214 NC_002163.1 RefSeq region 514589 514657 . + . ID=id1098;Name=id1098;Dbxref=GeneID:904880;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0552 by TMHMM2.0 at aa 20-42 2C 52-71 2C 99-121 and 192-214 NC_002163.1 RefSeq region 514868 514936 . + . ID=id1098;Name=id1098;Dbxref=GeneID:904880;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0552 by TMHMM2.0 at aa 20-42 2C 52-71 2C 99-121 and 192-214 NC_002163.1 RefSeq CDS 514974 515927 . + 0 ID=cds498;Parent=gene528;Name=YP_002343984.1;Dbxref=GOA:Q0PAW3 InterPro:IPR009323 UniProtKB FTrEMBL:Q0PAW3 Genbank:YP_002343984.1 GeneID:904881;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0553 2C probable integral membrane protein 2C len: 317 aa 3B no Hp match 7EUpdated 282006 29 note: Pfam domain PF06166 Protein of unknown function 28DUF979 29 identified within CDS. This family consists of several bacterial membrane proteins. The function of this family is unclear. Also identified were nine probable transmembrane helices predicted by TMHMM2.0. Further support for product function. Functional classification - Membranes 2Clipoproteins and porins NC_002163.1 RefSeq gene 514974 515927 . + . ID=gene528;Name=Cj0553;locus_tag=Cj0553;Dbxref=GeneID:904881;gbkey=Gene NC_002163.1 RefSeq region 514983 515918 . + . ID=id1099;Name=id1099;Dbxref=GeneID:904881;gbkey=misc_feature;Note=HMMPfam hit to PF06166 2C Protein of unknown function 28DUF979 29 2C score 4.2e-214 NC_002163.1 RefSeq region 514989 515048 . + . ID=id1100;Name=id1100;Dbxref=GeneID:904881;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0553 by TMHMM2.0 at aa 6-25 2C 46-68 2C 100-122 2C 129-151 2C166-188 2C 201-223 2C 228-245 2C 252-274 and 294-315 NC_002163.1 RefSeq region 515109 515177 . + . ID=id1100;Name=id1100;Dbxref=GeneID:904881;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0553 by TMHMM2.0 at aa 6-25 2C 46-68 2C 100-122 2C 129-151 2C166-188 2C 201-223 2C 228-245 2C 252-274 and 294-315 NC_002163.1 RefSeq region 515121 515153 . + . ID=id1101;Name=id1101;Dbxref=GeneID:904881;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 515271 515339 . + . ID=id1100;Name=id1100;Dbxref=GeneID:904881;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0553 by TMHMM2.0 at aa 6-25 2C 46-68 2C 100-122 2C 129-151 2C166-188 2C 201-223 2C 228-245 2C 252-274 and 294-315 NC_002163.1 RefSeq region 515358 515426 . + . ID=id1100;Name=id1100;Dbxref=GeneID:904881;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0553 by TMHMM2.0 at aa 6-25 2C 46-68 2C 100-122 2C 129-151 2C166-188 2C 201-223 2C 228-245 2C 252-274 and 294-315 NC_002163.1 RefSeq region 515379 515411 . + . ID=id1102;Name=id1102;Dbxref=GeneID:904881;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 515469 515537 . + . ID=id1100;Name=id1100;Dbxref=GeneID:904881;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0553 by TMHMM2.0 at aa 6-25 2C 46-68 2C 100-122 2C 129-151 2C166-188 2C 201-223 2C 228-245 2C 252-274 and 294-315 NC_002163.1 RefSeq region 515574 515642 . + . ID=id1100;Name=id1100;Dbxref=GeneID:904881;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0553 by TMHMM2.0 at aa 6-25 2C 46-68 2C 100-122 2C 129-151 2C166-188 2C 201-223 2C 228-245 2C 252-274 and 294-315 NC_002163.1 RefSeq region 515655 515708 . + . ID=id1100;Name=id1100;Dbxref=GeneID:904881;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0553 by TMHMM2.0 at aa 6-25 2C 46-68 2C 100-122 2C 129-151 2C166-188 2C 201-223 2C 228-245 2C 252-274 and 294-315 NC_002163.1 RefSeq region 515727 515795 . + . ID=id1100;Name=id1100;Dbxref=GeneID:904881;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0553 by TMHMM2.0 at aa 6-25 2C 46-68 2C 100-122 2C 129-151 2C166-188 2C 201-223 2C 228-245 2C 252-274 and 294-315 NC_002163.1 RefSeq region 515853 515918 . + . ID=id1100;Name=id1100;Dbxref=GeneID:904881;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0553 by TMHMM2.0 at aa 6-25 2C 46-68 2C 100-122 2C 129-151 2C166-188 2C 201-223 2C 228-245 2C 252-274 and 294-315 ### NC_002163.1 RefSeq gene 515937 516941 . + . ID=gene529;Name=Cj0554;locus_tag=Cj0554;Dbxref=GeneID:904341;gbkey=Gene NC_002163.1 RefSeq CDS 515937 516941 . + 0 ID=cds499;Parent=gene529;Name=YP_002343985.1;Dbxref=GOA:Q0PAW2 UniProtKB FTrEMBL:Q0PAW2 Genbank:YP_002343985.1 GeneID:904341;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0554 2C unknown 2C len: 334 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 RefSeq region 517060 517506 . + . ID=id1103;Name=id1103;Dbxref=GeneID:904882;gbkey=misc_feature;Note=HMMPfam hit to PF07158 2C Dicarboxylate carrier protein MatC N-terminu 2C score 5e-36 NC_002163.1 RefSeq CDS 517060 518352 . + 0 ID=cds500;Parent=gene530;Name=YP_002343986.1;Dbxref=InterPro:IPR009827 UniProtKB FTrEMBL:Q0PAW1 Genbank:YP_002343986.1 GeneID:904882;gbkey=CDS;product=dicarboxylate carrier protein MatC;Note=Original 282000 29 note: Cj0555 2C probable integral membrane protein 2C len: 430 aa 3B similar in N-terminus to an ORF within the Streptococcus pneumoniae cps3E and rpt pseudogene region TR:P72556 28EMBL:U66846 29 orf5 28197 aa 29 2Cfasta scores 3B opt: 493 z-score: 726.3 E 28 29: 3.7e-33 2C 47.4 25 identity in 152 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF07158 Dicarboxylate carrier protein MatC N-terminus identified within CDS. This family represents the N-terminal region of the bacterial dicarboxylate carrier protein MatC. MatC protein is an integral membrane protein that can function as a malonate carrier 28PMID:9826185 29. Also identified were eleven probable transmembrane helices predicted by TMHMM2.0. Product modified to more specific family member due to motif match. No specific characterisation has been carried out 2C so kept within product function. Functional classification - Carbohydrates 2C organic acids and alcohols 7EPMID:9826185 NC_002163.1 RefSeq gene 517060 518352 . + . ID=gene530;Name=Cj0555;locus_tag=Cj0555;Dbxref=GeneID:904882;gbkey=Gene NC_002163.1 RefSeq region 517063 517119 . + . ID=id1104;Name=id1104;Dbxref=GeneID:904882;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0555 by TMHMM2.0 at aa 2-20 2C 24-41 2C 48-70 2C 94-116 2C137-159 2C 179-201 2C 222-244 2C 259-276 2C 281-303 2C 323-345 and 407-429 NC_002163.1 RefSeq region 517129 517182 . + . ID=id1104;Name=id1104;Dbxref=GeneID:904882;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0555 by TMHMM2.0 at aa 2-20 2C 24-41 2C 48-70 2C 94-116 2C137-159 2C 179-201 2C 222-244 2C 259-276 2C 281-303 2C 323-345 and 407-429 NC_002163.1 RefSeq region 517201 517269 . + . ID=id1104;Name=id1104;Dbxref=GeneID:904882;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0555 by TMHMM2.0 at aa 2-20 2C 24-41 2C 48-70 2C 94-116 2C137-159 2C 179-201 2C 222-244 2C 259-276 2C 281-303 2C 323-345 and 407-429 NC_002163.1 RefSeq region 517339 517407 . + . ID=id1104;Name=id1104;Dbxref=GeneID:904882;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0555 by TMHMM2.0 at aa 2-20 2C 24-41 2C 48-70 2C 94-116 2C137-159 2C 179-201 2C 222-244 2C 259-276 2C 281-303 2C 323-345 and 407-429 NC_002163.1 RefSeq region 517468 517536 . + . ID=id1104;Name=id1104;Dbxref=GeneID:904882;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0555 by TMHMM2.0 at aa 2-20 2C 24-41 2C 48-70 2C 94-116 2C137-159 2C 179-201 2C 222-244 2C 259-276 2C 281-303 2C 323-345 and 407-429 NC_002163.1 RefSeq region 517594 517662 . + . ID=id1104;Name=id1104;Dbxref=GeneID:904882;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0555 by TMHMM2.0 at aa 2-20 2C 24-41 2C 48-70 2C 94-116 2C137-159 2C 179-201 2C 222-244 2C 259-276 2C 281-303 2C 323-345 and 407-429 NC_002163.1 RefSeq region 517723 517791 . + . ID=id1104;Name=id1104;Dbxref=GeneID:904882;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0555 by TMHMM2.0 at aa 2-20 2C 24-41 2C 48-70 2C 94-116 2C137-159 2C 179-201 2C 222-244 2C 259-276 2C 281-303 2C 323-345 and 407-429 NC_002163.1 RefSeq region 517834 517887 . + . ID=id1104;Name=id1104;Dbxref=GeneID:904882;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0555 by TMHMM2.0 at aa 2-20 2C 24-41 2C 48-70 2C 94-116 2C137-159 2C 179-201 2C 222-244 2C 259-276 2C 281-303 2C 323-345 and 407-429 NC_002163.1 RefSeq region 517900 517968 . + . ID=id1104;Name=id1104;Dbxref=GeneID:904882;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0555 by TMHMM2.0 at aa 2-20 2C 24-41 2C 48-70 2C 94-116 2C137-159 2C 179-201 2C 222-244 2C 259-276 2C 281-303 2C 323-345 and 407-429 NC_002163.1 RefSeq region 518026 518094 . + . ID=id1104;Name=id1104;Dbxref=GeneID:904882;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0555 by TMHMM2.0 at aa 2-20 2C 24-41 2C 48-70 2C 94-116 2C137-159 2C 179-201 2C 222-244 2C 259-276 2C 281-303 2C 323-345 and 407-429 NC_002163.1 RefSeq region 518212 518244 . + . ID=id1105;Name=id1105;Dbxref=GeneID:904882;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 518278 518346 . + . ID=id1104;Name=id1104;Dbxref=GeneID:904882;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0555 by TMHMM2.0 at aa 2-20 2C 24-41 2C 48-70 2C 94-116 2C137-159 2C 179-201 2C 222-244 2C 259-276 2C 281-303 2C 323-345 and 407-429 ### NC_002163.1 RefSeq CDS 518363 519160 . + 0 ID=cds501;Parent=gene531;Name=YP_002343987.1;Dbxref=GOA:Q0PAW0 InterPro:IPR006992 UniProtKB FTrEMBL:Q0PAW0 Genbank:YP_002343987.1 GeneID:904883;gbkey=CDS;product=amidohydrolase family protein;Note=Original 282000 29 note: Cj0556 2C unknown 2C len: 265 aa 3B no Hp match 7EUpdated 282006 29 note: Pfam domain PF04909 Amidohydrolase identified within CDS. Product modified to more specific family member due to motif match. No specific characterisation has been carried out yet. kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 518363 519160 . + . ID=gene531;Name=Cj0556;locus_tag=Cj0556;Dbxref=GeneID:904883;gbkey=Gene NC_002163.1 RefSeq region 518369 519157 . + . ID=id1106;Name=id1106;Dbxref=GeneID:904883;gbkey=misc_feature;Note=HMMPfam hit to PF04909 2C Amidohydrolase 2C score 9.5e-37 NC_002163.1 RefSeq gene 519157 520242 . - . ID=gene532;Name=Cj0557c;locus_tag=Cj0557c;Dbxref=GeneID:904884;gbkey=Gene NC_002163.1 RefSeq CDS 519157 520242 . - 0 ID=cds502;Parent=gene532;Name=YP_002343988.1;Dbxref=GOA:Q0PAV9 UniProtKB FTrEMBL:Q0PAV9 Genbank:YP_002343988.1 GeneID:904884;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0557c 2C probable integral membrane protein 2C len: 361 aa 3B similar in C terminus to hypothetical proteins from B. subtilis and E. coli: TR:O32225 28EMBL:O32225 29 YVAC 28631 aa 29 2C fasta scores 3B opt: 271 z-score: 562.0 E 28 29: 5.2e-24 2C 29.9 25 identity in 187 aa overlap 2C and YHFK_ECOLI 28696 aa 29 2C fasta scores 3B opt: 182 z-score: 212.9 E 28 29: 0.00015 2C 27.8 25 identity in 133 aa overlap. No Hp match 7EUpdated 282006 29 note: Nine probable transmembrane helices predicted by TMHMM2.0. Further support added to product function. Functional classification - Membranes 2Clipoproteins and porins NC_002163.1 RefSeq region 519226 519294 . - . ID=id41;Name=id41;Dbxref=GeneID:904884;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0557c by TMHMM2.0 at aa 23-45 2C 47-66 2C 86-108 2C 115-137 2C152-174 2C 187-209 2C 219-240 2C 283-302 and 317-339 NC_002163.1 RefSeq region 519337 519396 . - . ID=id41;Name=id41;Dbxref=GeneID:904884;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0557c by TMHMM2.0 at aa 23-45 2C 47-66 2C 86-108 2C 115-137 2C152-174 2C 187-209 2C 219-240 2C 283-302 and 317-339 NC_002163.1 RefSeq region 519523 519588 . - . ID=id41;Name=id41;Dbxref=GeneID:904884;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0557c by TMHMM2.0 at aa 23-45 2C 47-66 2C 86-108 2C 115-137 2C152-174 2C 187-209 2C 219-240 2C 283-302 and 317-339 NC_002163.1 RefSeq region 519616 519684 . - . ID=id41;Name=id41;Dbxref=GeneID:904884;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0557c by TMHMM2.0 at aa 23-45 2C 47-66 2C 86-108 2C 115-137 2C152-174 2C 187-209 2C 219-240 2C 283-302 and 317-339 NC_002163.1 RefSeq region 519721 519789 . - . ID=id41;Name=id41;Dbxref=GeneID:904884;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0557c by TMHMM2.0 at aa 23-45 2C 47-66 2C 86-108 2C 115-137 2C152-174 2C 187-209 2C 219-240 2C 283-302 and 317-339 NC_002163.1 RefSeq region 519832 519900 . - . ID=id41;Name=id41;Dbxref=GeneID:904884;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0557c by TMHMM2.0 at aa 23-45 2C 47-66 2C 86-108 2C 115-137 2C152-174 2C 187-209 2C 219-240 2C 283-302 and 317-339 NC_002163.1 RefSeq region 519847 519879 . - . ID=id1107;Name=id1107;Dbxref=GeneID:904884;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 519919 519987 . - . ID=id41;Name=id41;Dbxref=GeneID:904884;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0557c by TMHMM2.0 at aa 23-45 2C 47-66 2C 86-108 2C 115-137 2C152-174 2C 187-209 2C 219-240 2C 283-302 and 317-339 NC_002163.1 RefSeq region 520045 520104 . - . ID=id41;Name=id41;Dbxref=GeneID:904884;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0557c by TMHMM2.0 at aa 23-45 2C 47-66 2C 86-108 2C 115-137 2C152-174 2C 187-209 2C 219-240 2C 283-302 and 317-339 NC_002163.1 RefSeq region 520108 520176 . - . ID=id41;Name=id41;Dbxref=GeneID:904884;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0557c by TMHMM2.0 at aa 23-45 2C 47-66 2C 86-108 2C 115-137 2C152-174 2C 187-209 2C 219-240 2C 283-302 and 317-339 NC_002163.1 RefSeq gene 520239 521471 . - . ID=gene533;gene=proA;Name=proA;locus_tag=Cj0558c;Dbxref=GeneID:904885;gbkey=Gene NC_002163.1 RefSeq CDS 520239 521471 . - 0 ID=cds503;Parent=gene533;gene=proA;Name=YP_002343989.1;Dbxref=GOA:P53000 HSSP:Q9WYC9 InterPro:IPR000965 InterPro:IPR012134 InterPro:IPR016162 InterPro:IPR016163 UniProtKB FSwiss-Prot:P53000 Genbank:YP_002343989.1 GeneID:904885;gbkey=CDS;product=gamma-glutamyl phosphate reductase;Note=Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway NC_002163.1 RefSeq region 520461 520526 . - . ID=id1108;gene=proA;Name=id1108;Dbxref=GeneID:904885;gbkey=misc_feature;Note=PS01223 Gamma-glutamyl phosphate reductase signature ### NC_002163.1 UTR_Extractor 5'-UTR 521472 521498 . - . ID=utr200;locus_tag=Cj0558c;product=gamma-glutamyl phosphate reductase NC_002163.1 RefSeq CDS 521542 522477 . + 0 ID=cds504;Parent=gene534;Name=YP_002343990.1;Dbxref=GOA:Q0PAV7 InterPro:IPR000103 InterPro:IPR001327 InterPro:IPR013027 UniProtKB FTrEMBL:Q0PAV7 Genbank:YP_002343990.1 GeneID:905160;gbkey=CDS;product=pyridine nucleotide-disulfide oxidoreductase;Note=Original 282000 29 note: Cj0559 2C probable oxidoreductase 2C len: 311 aa 3B similar to members of the pyridine nucleotide-disulfide oxidoreductases class-II family e.g. R34K_CLOPA 34.2 KD protein in rubredoxin operon 28308 aa 29 2C fasta scores 3B opt: 217 z-score: 335.8 E 28 29: 2.1e-11 2C 23.2 25 identity in 314 aa overlap 2C and TRXB_BACSU thioredoxin reductase 28315 aa 29 2C fasta scores 3B opt: 192 z-score: 279.9 E 28 29: 2.7e-08 2C 25.9 25 identity in 313 aa overlap. 46.3 25 identity to HP1164. Contains possible N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site 7EUpdated 282006 29 note: Pfam domain PF00070 Pyridine nucleotide-disulfide oxidoreductase identified within CDS. Product modified to more specific family member due to motif match. No specific characterisation with acceptable identity score has been carried out yet. kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 521542 522477 . + . ID=gene534;Name=Cj0559;locus_tag=Cj0559;Dbxref=GeneID:905160;gbkey=Gene NC_002163.1 RefSeq region 521554 522423 . + . ID=id1109;Name=id1109;Dbxref=GeneID:905160;gbkey=misc_feature;Note=HMMPfam hit to PF00070 2C Pyridine nucleotide-disulphide oxidoreducta 2C score 1.7e-25 NC_002163.1 RefSeq region 521563 521595 . + . ID=id1110;Name=id1110;Dbxref=GeneID:905160;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq CDS 522658 523986 . + 0 ID=cds505;Parent=gene535;Name=YP_002343991.1;Dbxref=GOA:Q0PAV6 InterPro:IPR002114 InterPro:IPR002528 InterPro:IPR015522 UniProtKB FTrEMBL:Q0PAV6 Genbank:YP_002343991.1 GeneID:905129;gbkey=CDS;product=MATE family transport protein;Note=Original 282000 29 note: Cj0560 2C probable integral membrane protein 2C len: 442 aa 3B similar to many hypothetical proteins e.g. Y709_METJA MJ0709 28450 aa 29 2Cfasta scores 3B opt: 402 z-score: 324.8 E 28 29: 8.5e-11 2C 21.0 25 identity in 429 aa overlap. 26.3 25 identity to HP1184 7EUpdated 282006 29 note: Pfam domain PF01554 MatE identified within CDS. Prosite domain PS00589 PTS_HPR_SER 2CPhosphotransferase system 2C HPr serine phosphorylation site also identified. Twelve probable transmembrane helices predicted by TMHMM2.0. Characterised members of the Multi Antimicrobial Extrusion 28MATE 29 family function as drug 2Fsodium antiporters. These proteins mediate resistance to a wide range of cationic dyes 2C fluroquinolones 2Caminoglycosides and other structurally diverse antibodies and drugs. MATE proteins are found in bacteria 2C archaea and eukaryotes. These proteins are predicted to have 12 alpha-helical transmembrane regions 28which this one does 29. Product modified to more specific family member due to motif match. No specific characterisation with acceptable identity scores has been carried out yet. kept within product function. Literature search identified paper giving further clues to product function. Functional classification - Central intermediary metabolism -General 7EPMID:16048946 NC_002163.1 RefSeq gene 522658 523986 . + . ID=gene535;Name=Cj0560;locus_tag=Cj0560;Dbxref=GeneID:905129;gbkey=Gene NC_002163.1 RefSeq region 522694 522759 . + . ID=id1111;Name=id1111;Dbxref=GeneID:905129;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0560 by TMHMM2.0 at aa 13-34 2C 49-71 2C 91-113 2C 135-157 2C166-188 2C 192-214 2C 235-257 2C 267-289 2C 310-332 2C 352-374 2C387-409 and 414-433 NC_002163.1 RefSeq region 522715 523200 . + . ID=id1112;Name=id1112;Dbxref=GeneID:905129;gbkey=misc_feature;Note=HMMPfam hit to PF01554 2C MatE 2C score 9.6e-25 NC_002163.1 RefSeq region 522802 522870 . + . ID=id1111;Name=id1111;Dbxref=GeneID:905129;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0560 by TMHMM2.0 at aa 13-34 2C 49-71 2C 91-113 2C 135-157 2C166-188 2C 192-214 2C 235-257 2C 267-289 2C 310-332 2C 352-374 2C387-409 and 414-433 NC_002163.1 RefSeq region 522928 522996 . + . ID=id1111;Name=id1111;Dbxref=GeneID:905129;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0560 by TMHMM2.0 at aa 13-34 2C 49-71 2C 91-113 2C 135-157 2C166-188 2C 192-214 2C 235-257 2C 267-289 2C 310-332 2C 352-374 2C387-409 and 414-433 NC_002163.1 RefSeq region 522937 522969 . + . ID=id1113;Name=id1113;Dbxref=GeneID:905129;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 523060 523128 . + . ID=id1111;Name=id1111;Dbxref=GeneID:905129;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0560 by TMHMM2.0 at aa 13-34 2C 49-71 2C 91-113 2C 135-157 2C166-188 2C 192-214 2C 235-257 2C 267-289 2C 310-332 2C 352-374 2C387-409 and 414-433 NC_002163.1 RefSeq region 523153 523221 . + . ID=id1111;Name=id1111;Dbxref=GeneID:905129;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0560 by TMHMM2.0 at aa 13-34 2C 49-71 2C 91-113 2C 135-157 2C166-188 2C 192-214 2C 235-257 2C 267-289 2C 310-332 2C 352-374 2C387-409 and 414-433 NC_002163.1 RefSeq region 523231 523299 . + . ID=id1111;Name=id1111;Dbxref=GeneID:905129;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0560 by TMHMM2.0 at aa 13-34 2C 49-71 2C 91-113 2C 135-157 2C166-188 2C 192-214 2C 235-257 2C 267-289 2C 310-332 2C 352-374 2C387-409 and 414-433 NC_002163.1 RefSeq region 523339 523386 . + . ID=id1114;Name=id1114;Dbxref=GeneID:905129;gbkey=misc_feature;Note=PS00225 Crystallins beta and gamma 27Greek key 27 motif signature NC_002163.1 RefSeq region 523360 523428 . + . ID=id1111;Name=id1111;Dbxref=GeneID:905129;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0560 by TMHMM2.0 at aa 13-34 2C 49-71 2C 91-113 2C 135-157 2C166-188 2C 192-214 2C 235-257 2C 267-289 2C 310-332 2C 352-374 2C387-409 and 414-433 NC_002163.1 RefSeq region 523456 523524 . + . ID=id1111;Name=id1111;Dbxref=GeneID:905129;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0560 by TMHMM2.0 at aa 13-34 2C 49-71 2C 91-113 2C 135-157 2C166-188 2C 192-214 2C 235-257 2C 267-289 2C 310-332 2C 352-374 2C387-409 and 414-433 NC_002163.1 RefSeq region 523585 523653 . + . ID=id1111;Name=id1111;Dbxref=GeneID:905129;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0560 by TMHMM2.0 at aa 13-34 2C 49-71 2C 91-113 2C 135-157 2C166-188 2C 192-214 2C 235-257 2C 267-289 2C 310-332 2C 352-374 2C387-409 and 414-433 NC_002163.1 RefSeq region 523711 523779 . + . ID=id1111;Name=id1111;Dbxref=GeneID:905129;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0560 by TMHMM2.0 at aa 13-34 2C 49-71 2C 91-113 2C 135-157 2C166-188 2C 192-214 2C 235-257 2C 267-289 2C 310-332 2C 352-374 2C387-409 and 414-433 NC_002163.1 RefSeq region 523816 523884 . + . ID=id1111;Name=id1111;Dbxref=GeneID:905129;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0560 by TMHMM2.0 at aa 13-34 2C 49-71 2C 91-113 2C 135-157 2C166-188 2C 192-214 2C 235-257 2C 267-289 2C 310-332 2C 352-374 2C387-409 and 414-433 NC_002163.1 RefSeq region 523846 523878 . + . ID=id1115;Name=id1115;Dbxref=GeneID:905129;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 523897 523956 . + . ID=id1111;Name=id1111;Dbxref=GeneID:905129;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0560 by TMHMM2.0 at aa 13-34 2C 49-71 2C 91-113 2C 135-157 2C166-188 2C 192-214 2C 235-257 2C 267-289 2C 310-332 2C 352-374 2C387-409 and 414-433 ### NC_002163.1 RefSeq gene 524034 524963 . - . ID=gene536;Name=Cj0561c;locus_tag=Cj0561c;Dbxref=GeneID:905206;gbkey=Gene NC_002163.1 RefSeq CDS 524034 524963 . - 0 ID=cds506;Parent=gene536;Name=YP_002343992.1;Dbxref=InterPro:IPR016896 UniProtKB FTrEMBL:Q0PAV5 Genbank:YP_002343992.1 GeneID:905206;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0561c 2C possible periplasmic protein 2C len: 309 aa 3B no Hp match 7EUpdated 282006 29 note: possible changed to . Functional classification - Miscellaneous periplasmic proteins NC_002163.1 UTR_Extractor 5'-UTR 524964 525005 . - . ID=utr201;locus_tag=Cj0561c;product=putative periplasmic protein NC_002163.1 UTR_Extractor 5'-UTR 525089 525116 . + . ID=utr202;locus_tag=Cj0562;product=replicative DNA helicase NC_002163.1 RefSeq CDS 525117 526493 . + 0 ID=cds507;Parent=gene537;gene=dnaB;Name=YP_002343993.1;Dbxref=GOA:Q0PAV4 InterPro:IPR003593 InterPro:IPR007692 InterPro:IPR007693 InterPro:IPR007694 InterPro:IPR016136 UniProtKB FTrEMBL:Q0PAV4 Genbank:YP_002343993.1 GeneID:904886;gbkey=CDS;product=replicative DNA helicase;Note=unwinds double stranded DNA NC_002163.1 RefSeq gene 525117 526493 . + . ID=gene537;gene=dnaB;Name=dnaB;locus_tag=Cj0562;Dbxref=GeneID:904886;gbkey=Gene NC_002163.1 RefSeq region 525123 525404 . + . ID=id1116;gene=dnaB;Name=id1116;Dbxref=GeneID:904886;gbkey=misc_feature;Note=HMMPfam hit to PF00772 2C DnaB-like helicase N terminal domain 2C score 1.2e-24 NC_002163.1 RefSeq region 525615 526208 . + . ID=id1117;gene=dnaB;Name=id1117;Dbxref=GeneID:904886;gbkey=misc_feature;Note=HMMPfam hit to PF03796 2C DnaB-like helicase C terminal domain 2C score 5.7e-117 NC_002163.1 RefSeq region 525699 525722 . + . ID=id1118;gene=dnaB;Name=id1118;Dbxref=GeneID:904886;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 RefSeq CDS 526556 527158 . + 0 ID=cds508;Parent=gene538;Name=YP_002343994.1;Dbxref=UniProtKB FTrEMBL:Q0PAV3 Genbank:YP_002343994.1 GeneID:905136;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0563 2C unknown 2C len: 200 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 RefSeq gene 526556 527158 . + . ID=gene538;Name=Cj0563;locus_tag=Cj0563;Dbxref=GeneID:905136;gbkey=Gene NC_002163.1 RefSeq gene 527149 527355 . + . ID=gene539;Name=Cj0564;locus_tag=Cj0564;Dbxref=GeneID:904359;gbkey=Gene NC_002163.1 RefSeq CDS 527149 527355 . + 0 ID=cds509;Parent=gene539;Name=YP_002343995.1;Dbxref=UniProtKB FTrEMBL:Q0PAV2 Genbank:YP_002343995.1 GeneID:904359;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0564 2C probable integral membrane protein 2C len: 68 aa 3B no Hp match 7EUpdated 282006 29 note: Two probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 527167 527262 . + . ID=id1119;Name=id1119;Dbxref=GeneID:904359;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0564 by TMHMM2.0 at aa 7-38 and 43-65 NC_002163.1 RefSeq region 527275 527343 . + . ID=id1119;Name=id1119;Dbxref=GeneID:904359;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0564 by TMHMM2.0 at aa 7-38 and 43-65 ### NC_002163.1 RefSeq repeat_region 527378 527389 . + . ID=id1120;Name=id1120;gbkey=repeat_region;Note=G 2812 29 NC_002163.1 UTR_Extractor 5'-UTR 527407 527435 . + . ID=utr203;locus_tag=Cj0565;product=pseudo NC_002163.1 RefSeq region 527436 527714 . + . ID=id1121;Name=id1121;Dbxref=GeneID:904887;gbkey=misc_feature;Note=Original 282000 29 note: Cj0565 2C probable pseudogene 2Clen: 725 bp 3B similar to three consecutive genes in Hp 3B HP1587 2C HP1588 and HP1589 7EUpdated 282006 29 note: Pfam domain PF03667 Uncharacterised protein family 28UPF0174 29 identified within CDS. Conserved introduced to product function as motif identified. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq pseudogene 527436 528163 . + . ID=gene540;Name=Cj0565;locus_tag=Cj0565;Dbxref=GeneID:904887;gbkey=Gene NC_002163.1 RefSeq region 527541 527714 . + . ID=id1122;Name=id1122;Dbxref=GeneID:904887;gbkey=misc_feature;Note=HMMPfam hit to PF03667 2C Uncharacterised protein family 28UPF0174 29 2C score 3.1e-51 NC_002163.1 RefSeq region 527714 528154 . + . ID=id1122;Name=id1122;Dbxref=GeneID:904887;gbkey=misc_feature;Note=HMMPfam hit to PF03667 2C Uncharacterised protein family 28UPF0174 29 2C score 3.1e-51 NC_002163.1 RefSeq region 527714 528163 . + . ID=id1121;Name=id1121;Dbxref=GeneID:904887;gbkey=misc_feature;Note=Original 282000 29 note: Cj0565 2C probable pseudogene 2Clen: 725 bp 3B similar to three consecutive genes in Hp 3B HP1587 2C HP1588 and HP1589 7EUpdated 282006 29 note: Pfam domain PF03667 Uncharacterised protein family 28UPF0174 29 identified within CDS. Conserved introduced to product function as motif identified. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Conserved hypothetical proteins ### NC_002163.1 RefSeq gene 528182 529648 . + . ID=gene541;Name=Cj0566;locus_tag=Cj0566;Dbxref=GeneID:904889;gbkey=Gene NC_002163.1 RefSeq CDS 528182 529648 . + 0 ID=cds510;Parent=gene541;Name=YP_002343996.1;Dbxref=UniProtKB FTrEMBL:Q0PAV1 Genbank:YP_002343996.1 GeneID:904889;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0566 2C unknown 2C len: 488 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 RefSeq gene 528601 528700 . - . ID=NC_002163.1:CJas_Cj0566;Name=NC_002163.1:CJas_Cj0566;locus_tag=CJas_Cj0566 NC_002163.1 RefSeq sRNA 528601 528700 . - . ID=NC_002163.1:CJas_Cj0566:unknown_transcript_1;Parent=NC_002163.1:CJas_Cj0566;Name=NC_002163.1:CJas_Cj0566:unknown_transcript_1;locus_tag=CJas_Cj0566;gbkey=misc_RNA;product=CJas_Cj0566 ### NC_002163.1 RefSeq gene 529659 529772 . + . ID=gene542;Name=Cj0567;locus_tag=Cj0567;Dbxref=GeneID:904890;gbkey=Gene NC_002163.1 RefSeq CDS 529659 529772 . + 0 ID=cds511;Parent=gene542;Name=YP_002343997.1;Dbxref=UniProtKB FTrEMBL:Q0PAV0 Genbank:YP_002343997.1 GeneID:904890;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0567 2C unknown 2C len: 37 aa 3B no Hp match 7EUpdated 282006 29 note: Paper identified linking product function to iron transport or metabolism. Functional classification - Unknown 7EPMID:15632442 NC_002163.1 RefSeq pseudogene 529974 531130 . + . ID=gene543;Name=Cj0568;locus_tag=Cj0568;Dbxref=GeneID:904891;gbkey=Gene NC_002163.1 RefSeq region 530061 530120 . + . ID=id1123;Name=id1123;Dbxref=GeneID:904891;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0568 by TMHMM2.0 at aa 30-49 ### NC_002163.1 RefSeq CDS 531139 532206 . + 0 ID=cds512;Parent=gene544;Name=YP_002344000.1;Dbxref=UniProtKB FTrEMBL:Q0PAU7 Genbank:YP_002344000.1 GeneID:904893;gbkey=CDS;product=ATP 2FGTP binding protein;Note=Original 282000 29 note: Cj0570 2C probable ATP 2FGTP binding protein 2C len: 355 aa 3B 85.1 25 identity to HP0729. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 531139 532206 . + . ID=gene544;Name=Cj0570;locus_tag=Cj0570;Dbxref=GeneID:904893;gbkey=Gene NC_002163.1 RefSeq region 531904 531927 . + . ID=id1124;Name=id1124;Dbxref=GeneID:904893;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq gene 532203 533075 . + . ID=gene545;Name=Cj0571;locus_tag=Cj0571;Dbxref=GeneID:904894;gbkey=Gene NC_002163.1 RefSeq CDS 532203 533075 . + 0 ID=cds513;Parent=gene545;Name=YP_002344001.1;Dbxref=InterPro:IPR013196 UniProtKB FTrEMBL:Q0PAU6 Genbank:YP_002344001.1 GeneID:904894;gbkey=CDS;product=transcriptional regulator;Note=Original 282000 29 note: Cj0571 2C possible transcriptional regulator 3B len: 290 aa 3B similar in C-terminus to two hypothetical deoR family transcriptional regulators from E. coli 3B YFJR_ECOLI 28233 aa 29 2C fasta scores 3B opt: 279 z-score: 374.9 E 28 29: 1.4e-13 2C 27.7 25 identity in 202 aa overlap 2C and YAFY_ECOLI 28285 aa 29 2C fasta scores 3B opt: 167 z-score: 203.3 E 28 29: 0.0005 2C 40.4 25 identity in 57 aa overlap. No Hp match 2C Contains probable helix-turn-helix motif at aa 25-46 28Score 1541 2C 2B4.44 SD 29 7EUpdated 282006 29 note: No specific characterisation with acceptable identity scores carried out yet. kept within product function. Literature search identified paper linking product function to be involved in the stringent and heat shock responses within gut colonization. Functional classification - Broad regulatory functions 7EPMID:15731081 ### NC_002163.1 RefSeq gene 533097 533172 . - . ID=gene546;gene=tRNAMet;Name=tRNAMet;locus_tag=Cjp12;Dbxref=GeneID:904895;gbkey=Gene NC_002163.1 RefSeq tRNA 533097 533172 . - . ID=rna20;Parent=gene546;gene=tRNAMet;Name=rna20;Dbxref=GeneID:904895;gbkey=tRNA;product=tRNA-Met;Note=tRNA Met anticodon CAT 2C Cove score 88.22 NC_002163.1 RefSeq exon 533097 533172 . - . ID=id1125;Parent=rna20;gene=tRNAMet;Name=id1125;Dbxref=GeneID:904895;gbkey=tRNA;product=tRNA-Met;Note=tRNA Met anticodon CAT 2C Cove score 88.22 NC_002163.1 RefSeq gene 533206 533280 . - . ID=gene547;gene=tRNAGln;Name=tRNAGln;locus_tag=Cjp13;Dbxref=GeneID:904896;gbkey=Gene NC_002163.1 RefSeq tRNA 533206 533280 . - . ID=rna21;Parent=gene547;gene=tRNAGln;Name=rna21;Dbxref=GeneID:904896;gbkey=tRNA;product=tRNA-Gln;Note=tRNA Gln anticodon TTG 2C Cove score 71.34 NC_002163.1 RefSeq exon 533206 533280 . - . ID=id1126;Parent=rna21;gene=tRNAGln;Name=id1126;Dbxref=GeneID:904896;gbkey=tRNA;product=tRNA-Gln;Note=tRNA Gln anticodon TTG 2C Cove score 71.34 NC_002163.1 RefSeq region 533373 533648 . + . ID=id1127;gene=ribA;Name=id1127;Dbxref=GeneID:904897;gbkey=misc_feature;Note=PS00430 TonB-dependent receptor proteins signature 1 NC_002163.1 RefSeq gene 533373 534392 . + . ID=gene548;gene=ribA;Name=ribA;locus_tag=Cj0572;Dbxref=GeneID:904897;gbkey=Gene NC_002163.1 RefSeq CDS 533373 534392 . + 0 ID=cds514;Parent=gene548;gene=ribA;Name=YP_002344002.1;Dbxref=GOA:Q9PHU4 HSSP:P24199 InterPro:IPR000422 InterPro:IPR000926 InterPro:IPR016299 UniProtKB FSwiss-Prot:Q9PHU4 Genbank:YP_002344002.1 GeneID:904897;gbkey=CDS;product=bifunctional 3 2C4-dihydroxy-2-butanone 4-phosphate synthase 2FGTP cyclohydrolase II protein;Note=bifunctional enzyme DHBP synthase 2FGTP cyclohydrolase II 3B functions in riboflavin synthesis 3B converts GTP to 2 2C5-diamino-6-hydroxy-4- 285-phosphoribosylamino 29pyrimidine 3B converts ribulose 5-phopshate to 3 2C4-dihydroxy-2-butanone 4-phosphate NC_002163.1 RefSeq region 533388 533972 . + . ID=id1128;gene=ribA;Name=id1128;Dbxref=GeneID:904897;gbkey=misc_feature;Note=HMMPfam hit to PF00926 2C 3 2C4-dihydroxy-2-butanone 4-phosphate sy 2C score 6.2e-114 ### NC_002163.1 RefSeq gene 534404 534847 . + . ID=gene549;Name=Cj0573;locus_tag=Cj0573;Dbxref=GeneID:904898;gbkey=Gene NC_002163.1 RefSeq CDS 534404 534847 . + 0 ID=cds515;Parent=gene549;Name=YP_002344003.1;Dbxref=GOA:Q0PAU4 InterPro:IPR003789 UniProtKB FTrEMBL:Q0PAU4 Genbank:YP_002344003.1 GeneID:904898;gbkey=CDS;product=GatB 2FYqey family protein;Note=Original 282000 29 note: Cj0573 2C unknown 2C len: 147 aa 3B similar to several hypothetical proteins e.g.YQEY_BACSU 28148 aa 29 2C fasta scores 3B opt: 265 z-score: 348.7 E 28 29: 4e-12 2C 32.9 25 identity in 140 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02637 GatB 2FYqey identified within CDS. This domain is found in GatB and proteins related to bacterial Yqey. Typically about 140 aa residues long. This domain is found at the C terminus of GatB which transamidates Glu-tRNA to Gln-tRNA. The function of this domain is uncertain. It does however suggest that Yqey and its relatives have a role in tRNA metabolism. Product modified to more specific family member due to motif match. kept within product function. Functional classification - Misc NC_002163.1 RefSeq region 534419 534841 . + . ID=id1129;Name=id1129;Dbxref=GeneID:904898;gbkey=misc_feature;Note=HMMPfam hit to PF02637 2C GatB 2FYqey domain 2C score 2.7e-29 ### NC_002163.1 RefSeq CDS 534865 536565 . + 0 ID=cds516;Parent=gene550;gene=ilvI;Name=YP_002344004.1;Dbxref=GOA:Q0PAU3 InterPro:IPR011766 InterPro:IPR012000 InterPro:IPR012001 InterPro:IPR012846 UniProtKB FTrEMBL:Q0PAU3 Genbank:YP_002344004.1 GeneID:904899;gbkey=CDS;product=acetolactate synthase 3 catalytic subunit;Note=catalyzes the formation of 2-acetolactate from pyruvate 2C leucine resistant 3B also known as acetolactate synthase 3 large subunit NC_002163.1 RefSeq gene 534865 536565 . + . ID=gene550;gene=ilvI;Name=ilvI;locus_tag=Cj0574;Dbxref=GeneID:904899;gbkey=Gene NC_002163.1 RefSeq region 534874 535386 . + . ID=id1130;gene=ilvI;Name=id1130;Dbxref=GeneID:904899;gbkey=misc_feature;Note=HMMPfam hit to PF02776 2C Thiamine pyrophosphate enzyme 2C N-termina 2C score 2.2e-89 NC_002163.1 RefSeq region 535441 535911 . + . ID=id1131;gene=ilvI;Name=id1131;Dbxref=GeneID:904899;gbkey=misc_feature;Note=HMMPfam hit to PF00205 2C Thiamine pyrophosphate enzyme 2C central d 2C score 2.4e-62 NC_002163.1 RefSeq CDS 536562 537026 . + 0 ID=cds517;Parent=gene551;gene=ilvH;Name=YP_002344005.1;Dbxref=GOA:Q0PAU2 InterPro:IPR002912 InterPro:IPR004789 UniProtKB FTrEMBL:Q0PAU2 Genbank:YP_002344005.1 GeneID:904900;gbkey=CDS;product=acetolactate synthase 3 regulatory subunit;Note=with IlvI catalyzes the formation of 2-acetolactate from pyruvate 2C the small subunit is required for full activity and valine sensitivity 3B E.coli produces 3 isoenzymes of acetolactate synthase which differ in specificity to substrates 2C valine sensitivity and affinity for cofactors 3B also known as acetolactate synthase 3 small subunit NC_002163.1 RefSeq gene 536562 537026 . + . ID=gene551;gene=ilvH;Name=ilvH;locus_tag=Cj0575;Dbxref=GeneID:904900;gbkey=Gene NC_002163.1 RefSeq region 536568 536789 . + . ID=id1132;gene=ilvH;Name=id1132;Dbxref=GeneID:904900;gbkey=misc_feature;Note=HMMPfam hit to PF01842 2C ACT domain 2C score 1.2e-13 NC_002163.1 UTR_Extractor 5'-UTR 536895 537022 . + . ID=utr204;locus_tag=Cj0576;product=UDP-3-O- 5B3-hydroxymyristoyl 5D glucosamine N-acyltransferase NC_002163.1 RefSeq region 537023 537304 . + . ID=id1133;gene=lpxD;Name=id1133;Dbxref=GeneID:904901;gbkey=misc_feature;Note=HMMPfam hit to PF04613 2CUDP-3-O- 5B3-hydroxymyristoyl 5D glucosamine N-a 2C score 1e-36 NC_002163.1 RefSeq CDS 537023 537988 . + 0 ID=cds518;Parent=gene552;gene=lpxD;Name=YP_002344006.1;Dbxref=GOA:Q9PHU0 InterPro:IPR001451 InterPro:IPR007691 UniProtKB FSwiss-Prot:Q9PHU0 Genbank:YP_002344006.1 GeneID:904901;gbkey=CDS;product=UDP-3-O- 5B3-hydroxymyristoyl 5D glucosamine N-acyltransferase;Note=adds the O-linked and N-linked 3 28R 29-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis NC_002163.1 RefSeq gene 537023 537988 . + . ID=gene552;gene=lpxD;Name=lpxD;locus_tag=Cj0576;Dbxref=GeneID:904901;gbkey=Gene NC_002163.1 RefSeq region 537320 537373 . + . ID=id1134;gene=lpxD;Name=id1134;Dbxref=GeneID:904901;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 76 NC_002163.1 RefSeq region 537374 537427 . + . ID=id1135;gene=lpxD;Name=id1135;Dbxref=GeneID:904901;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 0.0021 NC_002163.1 RefSeq region 537383 537469 . + . ID=id1136;gene=lpxD;Name=id1136;Dbxref=GeneID:904901;gbkey=misc_feature;Note=PS00101 Hexapeptide-repeat containing-transferases signature NC_002163.1 RefSeq region 537428 537481 . + . ID=id1137;gene=lpxD;Name=id1137;Dbxref=GeneID:904901;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 0.0029 NC_002163.1 RefSeq region 537482 537535 . + . ID=id1138;gene=lpxD;Name=id1138;Dbxref=GeneID:904901;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 0.12 NC_002163.1 RefSeq region 537596 537649 . + . ID=id1139;gene=lpxD;Name=id1139;Dbxref=GeneID:904901;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 17 NC_002163.1 RefSeq region 537662 537715 . + . ID=id1140;gene=lpxD;Name=id1140;Dbxref=GeneID:904901;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 7.4 NC_002163.1 RefSeq region 537716 537769 . + . ID=id1141;gene=lpxD;Name=id1141;Dbxref=GeneID:904901;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 4 NC_002163.1 RefSeq region 537788 537841 . + . ID=id1142;gene=lpxD;Name=id1142;Dbxref=GeneID:904901;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 93 NC_002163.1 RefSeq gene 537977 539005 . - . ID=gene553;gene=queA;Name=queA;locus_tag=Cj0577c;Dbxref=GeneID:904902;gbkey=Gene NC_002163.1 RefSeq CDS 537977 539005 . - 0 ID=cds519;Parent=gene553;gene=queA;Name=YP_002344007.1;Dbxref=GOA:Q9PHT9 InterPro:IPR003699 UniProtKB FSwiss-Prot:Q9PHT9 Genbank:YP_002344007.1 GeneID:904902;gbkey=CDS;product=S-adenosylmethionine--tRNA ribosyltransferase-isomerase;Note=Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step NC_002163.1 RefSeq region 538331 538993 . - . ID=id1143;gene=queA;Name=id1143;Dbxref=GeneID:904902;gbkey=misc_feature;Note=HMMPfam hit to PF02547 2C Queuosine biosynthesis protein 2C score 1e-85 NC_002163.1 RefSeq gene 538998 539735 . - . ID=gene554;gene=tatC;Name=tatC;locus_tag=Cj0578c;Dbxref=GeneID:904903;gbkey=Gene NC_002163.1 RefSeq CDS 538998 539735 . - 0 ID=cds520;Parent=gene554;gene=tatC;Name=YP_002344008.1;Dbxref=GOA:Q9PHT8 InterPro:IPR002033 UniProtKB FSwiss-Prot:Q9PHT8 Genbank:YP_002344008.1 GeneID:904903;gbkey=CDS;product=Sec-independent protein translocase;Note=Original 282000 29 note: Cj0578c 2C mttB 2C probable sec-independant protein translocase 2C len: 245 aa 3B similar to e.g. TR:G3193219 28EMBL:AF067848 29 E. coli MTTB 28258 aa 29 2Cfasta scores 3B opt: 523 z-score: 804.5 E 28 29: 0 2C36.2 25 identity in 246 aa overlap. 49.6 25 identity to HP1061. Contains Pfam match to entry PF00902 UPF0032 2C Integral membrane protein of unknown function 7EUpdated 282006 29 note: Pfam domain PF00902 Sec-independent protein translocase identified within CDS. This motif was previously annotated as UPF0032 with unknown function. This family of proteins are involved in a sec-independent translocation mechanism. They are involved in export of redox proteins with a twin arginine leader motif 28S 2FT-R-R-X-F-L-K 29. The sec-independent pathway is termed TAT for twin-arginine translocation system. Transport proteins with bound cofactors that require folding prior to export are mainly moved. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. not added to product function. Gene name has also been updated from mttB to tatC. Functional classification - Protein and peptide secretion 7EPMID:9649434 2C PMID:10652088 2C PMID:11781311 NC_002163.1 RefSeq region 539079 539696 . - . ID=id1144;gene=tatC;Name=id1144;Dbxref=GeneID:904903;gbkey=misc_feature;Note=HMMPfam hit to PF00902 2C Sec-independent protein translocase 2C score 1.1e-85 NC_002163.1 RefSeq region 539085 539153 . - . ID=id42;gene=tatC;Name=id42;Dbxref=GeneID:904903;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0578c by TMHMM2.0 at aa 16-38 2C 71-93 2C 105-127 2C 160-182 and 195-217 NC_002163.1 RefSeq region 539190 539258 . - . ID=id42;gene=tatC;Name=id42;Dbxref=GeneID:904903;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0578c by TMHMM2.0 at aa 16-38 2C 71-93 2C 105-127 2C 160-182 and 195-217 NC_002163.1 RefSeq region 539355 539423 . - . ID=id42;gene=tatC;Name=id42;Dbxref=GeneID:904903;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0578c by TMHMM2.0 at aa 16-38 2C 71-93 2C 105-127 2C 160-182 and 195-217 NC_002163.1 RefSeq region 539376 539408 . - . ID=id1145;gene=tatC;Name=id1145;Dbxref=GeneID:904903;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 539457 539525 . - . ID=id42;gene=tatC;Name=id42;Dbxref=GeneID:904903;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0578c by TMHMM2.0 at aa 16-38 2C 71-93 2C 105-127 2C 160-182 and 195-217 NC_002163.1 RefSeq region 539622 539690 . - . ID=id42;gene=tatC;Name=id42;Dbxref=GeneID:904903;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0578c by TMHMM2.0 at aa 16-38 2C 71-93 2C 105-127 2C 160-182 and 195-217 NC_002163.1 RefSeq CDS 539728 540144 . - 0 ID=cds521;Parent=gene555;Name=YP_002344009.1;Dbxref=GOA:Q9PHT7 InterPro:IPR003369 InterPro:IPR003998 UniProtKB FSwiss-Prot:Q9PHT7 Genbank:YP_002344009.1 GeneID:904904;gbkey=CDS;product=Sec-independent translocase;Note=mediates the export of protein precursors bearing twin-arginine signal peptides NC_002163.1 RefSeq gene 539728 540144 . - . ID=gene555;gene=tatC;Name=tatC;locus_tag=Cj0579c;Dbxref=GeneID:904904;gbkey=Gene NC_002163.1 RefSeq region 539959 540144 . - . ID=id1146;Name=id1146;Dbxref=GeneID:904904;gbkey=misc_feature;Note=HMMPfam hit to PF02416 2C mttA 2FHcf106 family 2C score 8.2e-05 ### NC_002163.1 UTR_Extractor 5'-UTR 540145 540173 . - . ID=utr205;locus_tag=Cj0579c;product=sec-independent translocase NC_002163.1 RefSeq CDS 540202 541269 . - 0 ID=cds522;Parent=gene556;Name=YP_002344010.1;Dbxref=GOA:Q0PAT7 InterPro:IPR004559 InterPro:IPR006638 InterPro:IPR007197 InterPro:IPR010723 UniProtKB FTrEMBL:Q0PAT7 Genbank:YP_002344010.1 GeneID:905215;gbkey=CDS;product=coproporphyrinogen III oxidase;Note=catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III NC_002163.1 RefSeq gene 540202 541269 . - . ID=gene556;Name=Cj0580c;locus_tag=Cj0580c;Dbxref=GeneID:905215;gbkey=Gene NC_002163.1 RefSeq region 540253 540540 . - . ID=id1147;Name=id1147;Dbxref=GeneID:905215;gbkey=misc_feature;Note=HMMPfam hit to PF06969 2C HemN C-terminal region 2Cscore 4.5e-09 NC_002163.1 RefSeq region 540757 541260 . - . ID=id1148;Name=id1148;Dbxref=GeneID:905215;gbkey=misc_feature;Note=HMMPfam hit to PF04055 2C Radical SAM superfamily 2Cscore 3.4e-23 ### NC_002163.1 UTR_Extractor 5'-UTR 541348 541370 . + . ID=utr206;locus_tag=Cj0581;product=dinucleoside polyphosphate hydrolase NC_002163.1 RefSeq CDS 541371 541841 . + 0 ID=cds523;Parent=gene557;Name=YP_002344011.1;Dbxref=GOA:Q9PHT5 HSSP:O04841 InterPro:IPR000086 UniProtKB FSwiss-Prot:Q9PHT5 Genbank:YP_002344011.1 GeneID:905255;gbkey=CDS;product=dinucleoside polyphosphate hydrolase;Note=hydrolyzes diadenosine polyphosphate NC_002163.1 RefSeq gene 541371 541841 . + . ID=gene557;Name=Cj0581;locus_tag=Cj0581;Dbxref=GeneID:905255;gbkey=Gene NC_002163.1 RefSeq region 541389 541817 . + . ID=id1149;Name=id1149;Dbxref=GeneID:905255;gbkey=misc_feature;Note=HMMPfam hit to PF00293 2C NUDIX domain 2C score 4.9e-17 NC_002163.1 RefSeq region 541497 541556 . + . ID=id1150;Name=id1150;Dbxref=GeneID:905255;gbkey=misc_feature;Note=PS00893 mutT domain signature ### NC_002163.1 RefSeq region 541843 542529 . + . ID=id1151;gene=lysC;Name=id1151;Dbxref=GeneID:904905;gbkey=misc_feature;Note=HMMPfam hit to PF00696 2C Amino acid kinase family 2Cscore 3.7e-77 NC_002163.1 RefSeq CDS 541843 543045 . + 0 ID=cds524;Parent=gene558;gene=lysC;Name=YP_002344012.1;Dbxref=GOA:Q0PAT5 InterPro:IPR001048 InterPro:IPR001341 InterPro:IPR002912 InterPro:IPR005260 UniProtKB FTrEMBL:Q0PAT5 Genbank:YP_002344012.1 GeneID:904905;gbkey=CDS;product=aspartate kinase;Note=catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP 2C in Bacillus 2C lysine sensitive 3B regulated by response to starvation. NC_002163.1 RefSeq gene 541843 543045 . + . ID=gene558;gene=lysC;Name=lysC;locus_tag=Cj0582;Dbxref=GeneID:904905;gbkey=Gene NC_002163.1 RefSeq region 541852 541878 . + . ID=id1152;gene=lysC;Name=id1152;Dbxref=GeneID:904905;gbkey=misc_feature;Note=PS00324 Aspartokinase signature NC_002163.1 RefSeq region 541876 541905 . + . ID=id1153;gene=lysC;Name=id1153;Dbxref=GeneID:904905;gbkey=misc_feature;Note=PS00339 Aminoacyl-transfer RNA synthetases class-II signature 2 NC_002163.1 RefSeq region 542623 542835 . + . ID=id1154;gene=lysC;Name=id1154;Dbxref=GeneID:904905;gbkey=misc_feature;Note=HMMPfam hit to PF01842 2C ACT domain 2C score 7.1e-09 NC_002163.1 RefSeq region 542857 543042 . + . ID=id1155;gene=lysC;Name=id1155;Dbxref=GeneID:904905;gbkey=misc_feature;Note=HMMPfam hit to PF01842 2C ACT domain 2C score 2.5e-08 ### NC_002163.1 RefSeq gene 543046 543582 . + . ID=gene559;Name=Cj0583;locus_tag=Cj0583;Dbxref=GeneID:904906;gbkey=Gene NC_002163.1 RefSeq CDS 543046 543582 . + 0 ID=cds525;Parent=gene559;Name=YP_002344013.1;Dbxref=UniProtKB FTrEMBL:Q0PAT4 Genbank:YP_002344013.1 GeneID:904906;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0583 2C unknown 2C len: 178 aa 3B 30.8 25 identity to HP1230. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 543101 543269 . + . ID=NC_002163.1:CJnc21;Name=NC_002163.1:CJnc21;locus_tag=CJnc21 NC_002163.1 RefSeq sRNA 543101 543269 . + . ID=NC_002163.1:CJnc21:unknown_transcript_1;Parent=NC_002163.1:CJnc21;Name=NC_002163.1:CJnc21:unknown_transcript_1;locus_tag=CJnc21;gbkey=misc_RNA;product=CJnc21 ### NC_002163.1 RefSeq gene 543588 544187 . + . ID=gene560;Name=Cj0584;locus_tag=Cj0584;Dbxref=GeneID:904907;gbkey=Gene NC_002163.1 RefSeq CDS 543588 544187 . + 0 ID=cds526;Parent=gene560;Name=YP_002344014.1;Dbxref=UniProtKB FTrEMBL:Q0PAT3 Genbank:YP_002344014.1 GeneID:904907;gbkey=CDS;product=DNA polymerase III subunit delta 27;Note=catalyzes the DNA-template-directed extension of the 3 27-end of a DNA strand 3B the delta 27 subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA NC_002163.1 RefSeq gene 544189 545331 . + . ID=gene561;gene=folP;Name=folP;locus_tag=Cj0585;Dbxref=GeneID:904908;gbkey=Gene NC_002163.1 RefSeq CDS 544189 545331 . + 0 ID=cds527;Parent=gene561;gene=folP;Name=YP_002344015.1;Dbxref=GOA:Q0PAT2 InterPro:IPR000489 InterPro:IPR006390 InterPro:IPR016227 UniProtKB FTrEMBL:Q0PAT2 Genbank:YP_002344015.1 GeneID:904908;gbkey=CDS;product=dihydropteroate synthase;Note=Original 282000 29 note: Cj0585 2C folP 2C probable dihydropteroate synthase 2C len: 380 aa 3B simliar in C-terminus to e.g. DHPS_ECOLI dihydropteroate synthase 28EC 2.5.1.15 29 28282 aa 29 2C fasta scores 3B opt: 508 z-score: 504.3 E 28 29: 8.5e-21 2C 35.8 25 identity in 274 aa overlap. 41.6 25 identity to HP1232. Contains Pfam match to entry PF00809 DHPS 2C Dihydropteroate synthase 7EUpdated 282006 29 note: Pfam domain PF00809 DHPS 2CDihydropteroate synthase has now been changed to Pterin binding enzyme. Characterised within Campylobacter jejuni and Escherichia coli with acceptable identity score. removed from product function. Functional classification - Biosynthesis of cofactors 2C prosthetic groups and carriers - Folic acid 7EPMID:10471557 2C PMID:8244950 NC_002163.1 RefSeq region 544555 545181 . + . ID=id1156;gene=folP;Name=id1156;Dbxref=GeneID:904908;gbkey=misc_feature;Note=HMMPfam hit to PF00809 2C Pterin binding enzyme 2Cscore 1.2e-79 ### NC_002163.1 RefSeq gene 545332 547275 . + . ID=gene562;gene=ligA;Name=ligA;locus_tag=Cj0586;Dbxref=GeneID:904909;gbkey=Gene NC_002163.1 RefSeq CDS 545332 547275 . + 0 ID=cds528;Parent=gene562;gene=ligA;Name=YP_002344016.1;Dbxref=GOA:Q0PAT1 InterPro:IPR001357 InterPro:IPR001679 InterPro:IPR003583 InterPro:IPR004150 InterPro:IPR012340 InterPro:IPR013839 InterPro:IPR013840 UniProtKB FSwiss-Prot:Q0PAT1 Genbank:YP_002344016.1 GeneID:904909;gbkey=CDS;product=NAD-dependent DNA ligase LigA;Note=this protein catalyzes the formation of phosphodiester linkages between 5 27-phosphoryl and 3 27-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction 3B essential for DNA replication and repair of damaged DNA 3B similar to ligase LigB NC_002163.1 RefSeq region 545335 546246 . + . ID=id1157;gene=ligA;Name=id1157;Dbxref=GeneID:904909;gbkey=misc_feature;Note=HMMPfam hit to PF01653 2C NAD-dependent DNA ligase adenylation 2C score 3.7e-121 NC_002163.1 RefSeq region 546250 546498 . + . ID=id1158;gene=ligA;Name=id1158;Dbxref=GeneID:904909;gbkey=misc_feature;Note=HMMPfam hit to PF03120 2C NAD-dependent DNA ligase OB-fold doma 2C score 3.9e-41 NC_002163.1 RefSeq region 546283 546330 . + . ID=id1159;gene=ligA;Name=id1159;Dbxref=GeneID:904909;gbkey=misc_feature;Note=PS01056 NAD-dependent DNA ligase signature 2 NC_002163.1 RefSeq region 547039 547266 . + . ID=id1160;gene=ligA;Name=id1160;Dbxref=GeneID:904909;gbkey=misc_feature;Note=HMMPfam hit to PF00533 2C BRCA1 C Terminus 28BRCT 29 domain 2C score 1e-15 NC_002163.1 RefSeq CDS 547256 548260 . + 0 ID=cds529;Parent=gene563;Name=YP_002344017.1;Dbxref=UniProtKB FTrEMBL:Q0PAT0 Genbank:YP_002344017.1 GeneID:904911;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0587 2C probable integral membrane protein 2C len: 334 aa 3B no Hp match 7EUpdated 282006 29 note: Eight probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 547256 548260 . + . ID=gene563;gene=Cj0587;Name=Cj0587;locus_tag=Cj0587;Dbxref=GeneID:904911;gbkey=Gene NC_002163.1 RefSeq region 547274 547327 . + . ID=id1161;Name=id1161;Dbxref=GeneID:904911;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0587 by TMHMM2.0 at aa 7-24 2C 28-50 2C 74-96 2C 101-123 2C135-157 2C 182-204 2C 211-233 and 237-255 NC_002163.1 RefSeq region 547337 547405 . + . ID=id1161;Name=id1161;Dbxref=GeneID:904911;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0587 by TMHMM2.0 at aa 7-24 2C 28-50 2C 74-96 2C 101-123 2C135-157 2C 182-204 2C 211-233 and 237-255 NC_002163.1 RefSeq region 547475 547543 . + . ID=id1161;Name=id1161;Dbxref=GeneID:904911;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0587 by TMHMM2.0 at aa 7-24 2C 28-50 2C 74-96 2C 101-123 2C135-157 2C 182-204 2C 211-233 and 237-255 NC_002163.1 RefSeq region 547556 547624 . + . ID=id1161;Name=id1161;Dbxref=GeneID:904911;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0587 by TMHMM2.0 at aa 7-24 2C 28-50 2C 74-96 2C 101-123 2C135-157 2C 182-204 2C 211-233 and 237-255 NC_002163.1 RefSeq region 547658 547726 . + . ID=id1161;Name=id1161;Dbxref=GeneID:904911;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0587 by TMHMM2.0 at aa 7-24 2C 28-50 2C 74-96 2C 101-123 2C135-157 2C 182-204 2C 211-233 and 237-255 NC_002163.1 RefSeq region 547799 547867 . + . ID=id1161;Name=id1161;Dbxref=GeneID:904911;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0587 by TMHMM2.0 at aa 7-24 2C 28-50 2C 74-96 2C 101-123 2C135-157 2C 182-204 2C 211-233 and 237-255 NC_002163.1 RefSeq region 547886 547954 . + . ID=id1161;Name=id1161;Dbxref=GeneID:904911;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0587 by TMHMM2.0 at aa 7-24 2C 28-50 2C 74-96 2C 101-123 2C135-157 2C 182-204 2C 211-233 and 237-255 NC_002163.1 RefSeq region 547964 548020 . + . ID=id1161;Name=id1161;Dbxref=GeneID:904911;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0587 by TMHMM2.0 at aa 7-24 2C 28-50 2C 74-96 2C 101-123 2C135-157 2C 182-204 2C 211-233 and 237-255 NC_002163.1 RefSeq region 548257 548394 . + . ID=id1162;gene=tlyA;Name=id1162;Dbxref=GeneID:904912;gbkey=misc_feature;Note=HMMPfam hit to PF01479 2C S4 domain 2C score 0.013 NC_002163.1 RefSeq gene 548257 549018 . + . ID=gene564;gene=tlyA;Name=tlyA;locus_tag=Cj0588;Dbxref=GeneID:904912;gbkey=Gene NC_002163.1 RefSeq CDS 548257 549018 . + 0 ID=cds530;Parent=gene564;gene=tlyA;Name=YP_002344018.1;Dbxref=GOA:Q0PAS9 InterPro:IPR002877 InterPro:IPR002942 UniProtKB FTrEMBL:Q0PAS9 Genbank:YP_002344018.1 GeneID:904912;gbkey=CDS;product=hemolysin;Note=Original 282000 29 note: Cj0588 2C tlyA 2C possible haemolysin 2C len: 253 aa 3B similar to e.g. HLYA_TREHY hemolysin A from Treponema hyodysenteriae 28Serpulina hyodysenteriae 29 28240 aa 29 2C fasta scores 3B opt: 342 z-score: 596.3 E 28 29: 6.4e-26 2C 33.7 25 identity in 261 aa overlap. 40.7 25 identity to HP1086 7EUpdated 282006 29 note: Pfam domain PF01479 S4 and PF01728 FtsJ-like methyltransferase domain have been identified within CDS. Further support given to product function. Characterisation work carried out within Treponema hyodysenteriae with marginal identity score. kept within product function. Functional classification - Pathogenicity 7EPMID:1730486 NC_002163.1 RefSeq region 548473 549012 . + . ID=id1163;gene=tlyA;Name=id1163;Dbxref=GeneID:904912;gbkey=misc_feature;Note=HMMPfam hit to PF01728 2C FtsJ-like methyltransferase 2C score 3e-06 NC_002163.1 RefSeq gene 548984 549838 . + . ID=gene565;gene=ribF;Name=ribF;locus_tag=Cj0589;Dbxref=GeneID:904913;gbkey=Gene NC_002163.1 RefSeq CDS 548984 549838 . + 0 ID=cds531;Parent=gene565;gene=ribF;Name=YP_002344019.1;Dbxref=GOA:Q0PAS8 InterPro:IPR002606 InterPro:IPR015864 InterPro:IPR015865 UniProtKB FTrEMBL:Q0PAS8 Genbank:YP_002344019.1 GeneID:904913;gbkey=CDS;product=bifunctional riboflavin kinase 2FFMN adenylyltransferase;Note=catalyzes the formation of FMN from riboflavin and the formation of FAD from FMN 3B in Bacillus the ribC gene has both flavokinase and FAD synthetase activities NC_002163.1 RefSeq region 549017 549403 . + . ID=id1164;gene=ribF;Name=id1164;Dbxref=GeneID:904913;gbkey=misc_feature;Note=HMMPfam hit to PF06574 2C Riboflavin kinase 28Flavokinase 29 2C score 1.5e-10 NC_002163.1 RefSeq region 549449 549820 . + . ID=id1165;gene=ribF;Name=id1165;Dbxref=GeneID:904913;gbkey=misc_feature;Note=HMMPfam hit to PF01687 2C Riboflavin kinase 2F FAD synthetase 2C score 1.2e-24 NC_002163.1 RefSeq gene 549825 550535 . + . ID=gene566;gene=Cj0590;Name=Cj0590;locus_tag=Cj0590;Dbxref=GeneID:904914;gbkey=Gene NC_002163.1 RefSeq CDS 549825 550535 . + 0 ID=cds532;Parent=gene566;Name=YP_002344020.1;Dbxref=GOA:Q0PAS7 InterPro:IPR005271 InterPro:IPR013216 UniProtKB FSwiss-Prot:Q0PAS7 Genbank:YP_002344020.1 GeneID:904914;gbkey=CDS;product=SAM-dependent methyltransferase;Note=Original 282000 29 note: Cj0590 2C unknown 2C len: 236 aa 3B similar to hypothetical proteins e.g. YECO_ECOLI 28247 aa 29 2Cfasta scores 3B opt: 476 z-score: 737.5 E 28 29: 0 2C 35.6 25 identity in 239 aa overlap. 45.3 25 identity to HP0388 7EUpdated 282006 29 note: Prosite domain PS50193 SAM_BIND 2C SAM 28and some other nucleotide 29 binding motif identified within CDS. Product modified to more specific family member due to motif match. No specific characterisation has been carried out yet. kept within product function. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 550525 550746 . - . ID=gene567;Name=Cj0591c;locus_tag=Cj0591c;Dbxref=GeneID:904916;gbkey=Gene NC_002163.1 RefSeq CDS 550525 550746 . - 0 ID=cds533;Parent=gene567;Name=YP_002344021.1;Dbxref=GOA:Q0PAS6 UniProtKB FTrEMBL:Q0PAS6 Genbank:YP_002344021.1 GeneID:904916;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj0591c 2C probable lipoprotein 2C len: 73 aa 3B no Hp match. Contains N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Some similarity to upstream gene Cj0592c 2839.7 25 identity in 63 aa overlap 29. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 550690 550722 . - . ID=id1166;Name=id1166;Dbxref=GeneID:904916;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq gene 550743 551177 . - . ID=gene568;Name=Cj0592c;locus_tag=Cj0592c;Dbxref=GeneID:904917;gbkey=Gene NC_002163.1 RefSeq CDS 550743 551177 . - 0 ID=cds534;Parent=gene568;Name=YP_002344022.1;Dbxref=GOA:Q0PAS5 UniProtKB FTrEMBL:Q0PAS5 Genbank:YP_002344022.1 GeneID:904917;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0592c 2C probable periplasmic protein 2C len: 144 aa 3B no Hp match. Contains N-terminal signal sequence. Some similarity to downstream gene Cj0591c 2839.7 25 identity in 63 aa overlap 29. Functional classification - Miscellaneous periplasmic proteins ### NC_002163.1 RefSeq CDS 551235 551867 . - 0 ID=cds535;Parent=gene569;Name=YP_002344023.1;Dbxref=GOA:Q9PHS3 InterPro:IPR005115 UniProtKB FSwiss-Prot:Q9PHS3 Genbank:YP_002344023.1 GeneID:904918;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0593c 2C probable integral membrane protein 2C len: 210 aa 3B similar to hypothetical proteins e.g. YICG_ECOLI 28205 aa 29 2C fasta scores 3B opt: 783 z-score: 1285.7 E 28 29: 0 2C 57.4 25 identity in 204 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domains x2 PF03458 UPF0126 domain was identified within CDS. This domain is found duplicated in bacterial membrane proteins of unknown function and contains three transmembrane helices. Also seven probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 551235 551867 . - . ID=gene569;Name=Cj0593c;locus_tag=Cj0593c;Dbxref=GeneID:904918;gbkey=Gene NC_002163.1 RefSeq region 551283 551342 . - . ID=id43;Name=id43;Dbxref=GeneID:904918;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0593c by TMHMM2.0 at aa 5-27 2C 34-56 2C 69-87 2C 92-114 2C119-141 2C 153-172 and 176-195 NC_002163.1 RefSeq region 551334 551588 . - . ID=id1167;Name=id1167;Dbxref=GeneID:904918;gbkey=misc_feature;Note=HMMPfam hit to PF03458 2C UPF0126 domain 2C score 2.4e-34 NC_002163.1 RefSeq region 551352 551411 . - . ID=id43;Name=id43;Dbxref=GeneID:904918;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0593c by TMHMM2.0 at aa 5-27 2C 34-56 2C 69-87 2C 92-114 2C119-141 2C 153-172 and 176-195 NC_002163.1 RefSeq region 551445 551513 . - . ID=id43;Name=id43;Dbxref=GeneID:904918;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0593c by TMHMM2.0 at aa 5-27 2C 34-56 2C 69-87 2C 92-114 2C119-141 2C 153-172 and 176-195 NC_002163.1 RefSeq region 551526 551594 . - . ID=id43;Name=id43;Dbxref=GeneID:904918;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0593c by TMHMM2.0 at aa 5-27 2C 34-56 2C 69-87 2C 92-114 2C119-141 2C 153-172 and 176-195 NC_002163.1 RefSeq region 551589 551846 . - . ID=id1168;Name=id1168;Dbxref=GeneID:904918;gbkey=misc_feature;Note=HMMPfam hit to PF03458 2C UPF0126 domain 2C score 6.7e-38 NC_002163.1 RefSeq region 551607 551663 . - . ID=id43;Name=id43;Dbxref=GeneID:904918;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0593c by TMHMM2.0 at aa 5-27 2C 34-56 2C 69-87 2C 92-114 2C119-141 2C 153-172 and 176-195 NC_002163.1 RefSeq region 551700 551768 . - . ID=id43;Name=id43;Dbxref=GeneID:904918;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0593c by TMHMM2.0 at aa 5-27 2C 34-56 2C 69-87 2C 92-114 2C119-141 2C 153-172 and 176-195 NC_002163.1 RefSeq region 551787 551855 . - . ID=id43;Name=id43;Dbxref=GeneID:904918;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0593c by TMHMM2.0 at aa 5-27 2C 34-56 2C 69-87 2C 92-114 2C119-141 2C 153-172 and 176-195 ### NC_002163.1 UTR_Extractor 5'-UTR 551868 551874 . - . ID=utr207;locus_tag=Cj0593c;product=putative integral membrane protein NC_002163.1 RefSeq CDS 551878 552528 . - 0 ID=cds536;Parent=gene570;Name=YP_002344024.1;Dbxref=GOA:Q0PAS3 InterPro:IPR001604 UniProtKB FTrEMBL:Q0PAS3 Genbank:YP_002344024.1 GeneID:904919;gbkey=CDS;product=DNA 2FRNA non-specific endonuclease;Note=Original 282000 29 note: Cj0594c 2C probable periplasmic protein 2C len: 216 aa 3B no Hp match. Contains N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF01223 DNA 2FRNA non-specific endonuclease was identified within CDS. Product modified to more specific family member due to motif match. No specific characterisation with acceptable identity score has been carried out yet. Thus 2C kept within product function. Functional classification -DNA replication 2C restriction 2Fmodification 2C recombination and repair NC_002163.1 RefSeq gene 551878 552528 . - . ID=gene570;Name=Cj0594c;locus_tag=Cj0594c;Dbxref=GeneID:904919;gbkey=Gene NC_002163.1 RefSeq region 551881 552411 . - . ID=id1169;Name=id1169;Dbxref=GeneID:904919;gbkey=misc_feature;Note=HMMPfam hit to PF01223 2C DNA 2FRNA non-specific endonuclease 2C score 5.7e-21 NC_002163.1 RefSeq gene 552525 553151 . - . ID=gene571;gene=nth;Name=nth;locus_tag=Cj0595c;Dbxref=GeneID:904920;gbkey=Gene NC_002163.1 RefSeq CDS 552525 553151 . - 0 ID=cds537;Parent=gene571;gene=nth;Name=YP_002344025.1;Dbxref=GOA:Q0PAS2 InterPro:IPR003265 InterPro:IPR003651 InterPro:IPR004035 InterPro:IPR005759 UniProtKB FTrEMBL:Q0PAS2 Genbank:YP_002344025.1 GeneID:904920;gbkey=CDS;product=endonuclease III;Note=Original 282000 29 note: Cj0595c 2C nth 2C probable endonuclease III 2C len 208 aa 3B similar to many e.g. END3_ECOLI endonuclease III 28EC 4.2.99.18 29 28211 aa 29 2C fasta scores 3B opt: 488 z-score: 749.2 E 28 29: 0 2C 39.7 25 identity in 204 aa overlap. 57.4 25 identity to HP0585. Contains PS00764 Endonuclease III iron-sulfur binding region signature and Pfam match to entry PF00730 Endonuclease_3 2C Endonuclease III 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -DNA replication 2C restriction 2Fmodification 2C recombination and repair 7EPMID:2669955 NC_002163.1 RefSeq region 552552 552602 . - . ID=id1170;gene=nth;Name=id1170;Dbxref=GeneID:904920;gbkey=misc_feature;Note=PS00764 Endonuclease III iron-sulfur binding region signature NC_002163.1 RefSeq region 552651 553058 . - . ID=id1171;gene=nth;Name=id1171;Dbxref=GeneID:904920;gbkey=misc_feature;Note=HMMPfam hit to PF00730 2C HhH-GPD superfamily base excision DNA repair 2C score 9.8e-20 NC_002163.1 UTR_Extractor 5'-UTR 553151 553151 . - . ID=utr208;locus_tag=Cj0595c;product=endonuclease III ### NC_002163.1 UTR_Extractor 5'-UTR 553204 553231 . + . ID=utr209;locus_tag=Cj0596;product=major antigenic peptide PEB-cell binding factor NC_002163.1 RefSeq CDS 553232 554053 . + 0 ID=cds538;Parent=gene572;gene=peb4cbf2;Name=YP_002344026.1;Dbxref=GOA:Q0PAS1 HSSP:Q13526 InterPro:IPR000297 UniProtKB FSwiss-Prot:Q0PAS1 Genbank:YP_002344026.1 GeneID:904921;gbkey=CDS;product=major antigenic peptide PEB-cell binding factor;Note=Original 282000 29 note: Cj0596 2C peb4-cbf2 2C major antigenic peptide PEB4-cell binding factor 2 2C len: 273 aa 3B identical to CBF2_CAMJE cell binding factor 2 precursor 2Cand TR:G451285 peb4 3Dmajor antigenic peptide 2834 aa 29. Also similar to memebers of the PPIC-parvulin family of rotamases e.g. PRTM_LACPA protease maturation protein precursor 28299 aa 29 2C fasta scores 3B opt: 238 z-score: 303.5 E 28 29: 1.3e-09 2C 31.3 25 identity in 240 aa overlap 2C and CYPD_ECOLI peptidyl-prolyl cis-trans isomerase D 28623 aa 29 2Cfasta scores 3B opt: 244 z-score: 293.9 E 28 29: 4.5e-09 2C 27.1 25 identity in 221 aa overlap. 35.7 25 identity to HP0175. Contains PS01096 PpiC-type peptidyl-prolyl cis-trans isomerase signature and Pfam match to entry PF00639 Rotamase 2C PPIC-type PPIASE domain 7EUpdated 282006 29 note: Characterised within Campylobacter jejuni. Functional classification -Miscellaneous periplasmic proteins 7EPMID:8525063 NC_002163.1 RefSeq gene 553232 554053 . + . ID=gene572;gene=peb4cbf2;Name=peb4cbf2;locus_tag=Cj0596;Dbxref=GeneID:904921;gbkey=Gene NC_002163.1 RefSeq region 553244 553312 . + . ID=id1172;gene=peb4cbf2;Name=id1172;Dbxref=GeneID:904921;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0596 by TMHMM2.0 at aa 5-27 NC_002163.1 RefSeq region 553643 553915 . + . ID=id1173;gene=peb4cbf2;Name=id1173;Dbxref=GeneID:904921;gbkey=misc_feature;Note=HMMPfam hit to PF00639 2C PPIC-type PPIASE domain 2Cscore 2.7e-30 NC_002163.1 RefSeq region 553727 553792 . + . ID=id1174;gene=peb4cbf2;Name=id1174;Dbxref=GeneID:904921;gbkey=misc_feature;Note=PS01096 PpiC-type peptidyl-prolyl cis-trans isomerase signature NC_002163.1 RefSeq CDS 554053 555117 . + 0 ID=cds539;Parent=gene573;gene=fba;Name=YP_002344027.1;Dbxref=GOA:Q0PAS0 HSSP:P11604 InterPro:IPR000771 InterPro:IPR006411 InterPro:IPR013785 UniProtKB FSwiss-Prot:Q0PAS0 Genbank:YP_002344027.1 GeneID:904922;gbkey=CDS;product=fructose-bisphosphate aldolase;Note=catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1 2C6 2C bisphosphate NC_002163.1 RefSeq gene 554053 555117 . + . ID=gene573;gene=fba;Name=fba;locus_tag=Cj0597;Dbxref=GeneID:904922;gbkey=Gene NC_002163.1 RefSeq region 554092 555114 . + . ID=id1175;gene=fba;Name=id1175;Dbxref=GeneID:904922;gbkey=misc_feature;Note=HMMPfam hit to PF01116 2C Fructose-bisphosphate aldolase class-II 2C score 9.3e-215 NC_002163.1 RefSeq region 554335 554370 . + . ID=id1176;gene=fba;Name=id1176;Dbxref=GeneID:904922;gbkey=misc_feature;Note=PS00602 Fructose-bisphosphate aldolase class-II signature 1 NC_002163.1 RefSeq region 554548 554583 . + . ID=id1177;gene=fba;Name=id1177;Dbxref=GeneID:904922;gbkey=misc_feature;Note=PS00806 Fructose-bisphosphate aldolase class-II signature 2 ### NC_002163.1 RefSeq CDS 555212 556654 . + 0 ID=cds540;Parent=gene574;Name=YP_002344028.1;Dbxref=UniProtKB FTrEMBL:Q0PAR9 Genbank:YP_002344028.1 GeneID:904923;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0598 2C probable membrane protein 2C len: 480 aa 3B no Hp match 7EUpdated 282006 29 note: Four probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 555212 556654 . + . ID=gene574;Name=Cj0598;locus_tag=Cj0598;Dbxref=GeneID:904923;gbkey=Gene NC_002163.1 RefSeq region 555272 555340 . + . ID=id1178;Name=id1178;Dbxref=GeneID:904923;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0598 by TMHMM2.0 at aa 21-43 2C 53-70 2C 129-151 and 173-195 NC_002163.1 RefSeq region 555368 555421 . + . ID=id1178;Name=id1178;Dbxref=GeneID:904923;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0598 by TMHMM2.0 at aa 21-43 2C 53-70 2C 129-151 and 173-195 NC_002163.1 RefSeq region 555596 555664 . + . ID=id1178;Name=id1178;Dbxref=GeneID:904923;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0598 by TMHMM2.0 at aa 21-43 2C 53-70 2C 129-151 and 173-195 NC_002163.1 RefSeq region 555728 555796 . + . ID=id1178;Name=id1178;Dbxref=GeneID:904923;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0598 by TMHMM2.0 at aa 21-43 2C 53-70 2C 129-151 and 173-195 NC_002163.1 RefSeq gene 556651 557604 . + . ID=gene575;Name=Cj0599;locus_tag=Cj0599;Dbxref=GeneID:904924;gbkey=Gene NC_002163.1 RefSeq CDS 556651 557604 . + 0 ID=cds541;Parent=gene575;Name=YP_002344029.1;Dbxref=GOA:Q0PAR8 InterPro:IPR006665 UniProtKB FTrEMBL:Q0PAR8 Genbank:YP_002344029.1 GeneID:904924;gbkey=CDS;product=OmpA family membrane protein;Note=Original 282000 29 note: Cj0599 2C probable periplasmic protein 2C len: 317 aa 3B no Hp match. Contains N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF00691 OmpA family protein was identified within CDS. Also 2C one probable transmembrane helix predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity scores has been carried out yet. kept within product function. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 556687 556755 . + . ID=id1179;Name=id1179;Dbxref=GeneID:904924;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0599 by TMHMM2.0 at aa 13-35 NC_002163.1 RefSeq region 557209 557532 . + . ID=id1180;Name=id1180;Dbxref=GeneID:904924;gbkey=misc_feature;Note=HMMPfam hit to PF00691 2C OmpA family 2C score 2.1e-05 NC_002163.1 RefSeq gene 557591 558466 . + . ID=gene576;Name=Cj0600;locus_tag=Cj0600;Dbxref=GeneID:904925;gbkey=Gene NC_002163.1 RefSeq CDS 557591 558466 . + 0 ID=cds542;Parent=gene576;Name=YP_002344030.1;Dbxref=GOA:Q0PAR7 UniProtKB FTrEMBL:Q0PAR7 Genbank:YP_002344030.1 GeneID:904925;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0600 2C unknown 2C len: 291 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 RefSeq gene 558458 559801 . - . ID=gene577;Name=Cj0601c;locus_tag=Cj0601c;Dbxref=GeneID:904927;gbkey=Gene NC_002163.1 RefSeq CDS 558458 559801 . - 0 ID=cds543;Parent=gene577;Name=YP_002344031.1;Dbxref=GOA:Q0PAR6 InterPro:IPR000175 UniProtKB FTrEMBL:Q0PAR6 Genbank:YP_002344031.1 GeneID:904927;gbkey=CDS;product=sodium-dependent transmembrane transport protein;Note=Original 282000 29 note: Cj0601c 2C probable sodium-dependent transmembrane transport protein 2C len: 447 aa 3B similar to members of the sodium:neurotransmitter symporter family e.g. YG90_HAEIN hypothetical sodium-dependent transporter HI1690 28457 aa 29 2C fasta scores 3B opt: 1380 z-score: 2645.2 E 28 29: 0 2C 61.0 25 identity in 456 aa overlap 2C and NTSE_RAT sodium-dependent serotonin transporter 28630 aa 29 2C fasta scores 3B opt: 265 z-score: 744.2 E 28 29: 0. 25.8 25 identity in 488 aa overlap. No Hp ortholog. Also similar to Cj0935c 2832.4 25 identity in 451 aa overlap 29 2C and Cj0934c 2828.0 25 identity in 454 aa overlap 29. Contains PS00610 Sodium:neurotransmitter symporter family signature 1 and Pfam match to entry PF00209 SNF 2C Sodium:neurotransmitter symporter family 7EUpdated 282006 29 note: Eleven probable transmembrane helices predicted by TMHMM2.0. No specific characterisation with acceptable identity scores carried out yet. kept within product function. Functional classification - Transport 2Fbinding proteins - Other NC_002163.1 RefSeq region 558464 558532 . - . ID=id44;Name=id44;Dbxref=GeneID:904927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0601c by TMHMM2.0 at aa 5-27 2C 37-59 2C 87-109 2C 135-157 2C168-190 2C 217-239 2C 252-274 2C 296-318 2C 339-361 2C 381-403 and 424-446 NC_002163.1 RefSeq region 558533 559795 . - . ID=id1181;Name=id1181;Dbxref=GeneID:904927;gbkey=misc_feature;Note=HMMPfam hit to PF00209 2C Sodium:neurotransmitter symporter family 2C score 1.2e-14 NC_002163.1 RefSeq region 558593 558661 . - . ID=id44;Name=id44;Dbxref=GeneID:904927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0601c by TMHMM2.0 at aa 5-27 2C 37-59 2C 87-109 2C 135-157 2C168-190 2C 217-239 2C 252-274 2C 296-318 2C 339-361 2C 381-403 and 424-446 NC_002163.1 RefSeq region 558719 558787 . - . ID=id44;Name=id44;Dbxref=GeneID:904927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0601c by TMHMM2.0 at aa 5-27 2C 37-59 2C 87-109 2C 135-157 2C168-190 2C 217-239 2C 252-274 2C 296-318 2C 339-361 2C 381-403 and 424-446 NC_002163.1 RefSeq region 558848 558916 . - . ID=id44;Name=id44;Dbxref=GeneID:904927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0601c by TMHMM2.0 at aa 5-27 2C 37-59 2C 87-109 2C 135-157 2C168-190 2C 217-239 2C 252-274 2C 296-318 2C 339-361 2C 381-403 and 424-446 NC_002163.1 RefSeq region 558980 559048 . - . ID=id44;Name=id44;Dbxref=GeneID:904927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0601c by TMHMM2.0 at aa 5-27 2C 37-59 2C 87-109 2C 135-157 2C168-190 2C 217-239 2C 252-274 2C 296-318 2C 339-361 2C 381-403 and 424-446 NC_002163.1 RefSeq region 559085 559153 . - . ID=id44;Name=id44;Dbxref=GeneID:904927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0601c by TMHMM2.0 at aa 5-27 2C 37-59 2C 87-109 2C 135-157 2C168-190 2C 217-239 2C 252-274 2C 296-318 2C 339-361 2C 381-403 and 424-446 NC_002163.1 RefSeq region 559232 559300 . - . ID=id44;Name=id44;Dbxref=GeneID:904927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0601c by TMHMM2.0 at aa 5-27 2C 37-59 2C 87-109 2C 135-157 2C168-190 2C 217-239 2C 252-274 2C 296-318 2C 339-361 2C 381-403 and 424-446 NC_002163.1 RefSeq region 559331 559399 . - . ID=id44;Name=id44;Dbxref=GeneID:904927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0601c by TMHMM2.0 at aa 5-27 2C 37-59 2C 87-109 2C 135-157 2C168-190 2C 217-239 2C 252-274 2C 296-318 2C 339-361 2C 381-403 and 424-446 NC_002163.1 RefSeq region 559475 559543 . - . ID=id44;Name=id44;Dbxref=GeneID:904927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0601c by TMHMM2.0 at aa 5-27 2C 37-59 2C 87-109 2C 135-157 2C168-190 2C 217-239 2C 252-274 2C 296-318 2C 339-361 2C 381-403 and 424-446 NC_002163.1 RefSeq region 559625 559693 . - . ID=id44;Name=id44;Dbxref=GeneID:904927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0601c by TMHMM2.0 at aa 5-27 2C 37-59 2C 87-109 2C 135-157 2C168-190 2C 217-239 2C 252-274 2C 296-318 2C 339-361 2C 381-403 and 424-446 NC_002163.1 RefSeq region 559679 559723 . - . ID=id1182;Name=id1182;Dbxref=GeneID:904927;gbkey=misc_feature;Note=PS00610 Sodium:neurotransmitter symporter family signature 1 NC_002163.1 RefSeq region 559721 559789 . - . ID=id44;Name=id44;Dbxref=GeneID:904927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0601c by TMHMM2.0 at aa 5-27 2C 37-59 2C 87-109 2C 135-157 2C168-190 2C 217-239 2C 252-274 2C 296-318 2C 339-361 2C 381-403 and 424-446 ### NC_002163.1 UTR_Extractor 5'-UTR 559802 559822 . - . ID=utr210;locus_tag=Cj0601c;product=putative sodium-dependent transmembrane transport protein NC_002163.1 RefSeq CDS 559852 560520 . - 0 ID=cds544;Parent=gene578;Name=YP_002344032.1;Dbxref=GOA:Q0PAR5 InterPro:IPR005163 InterPro:IPR005302 InterPro:IPR015808 UniProtKB FTrEMBL:Q0PAR5 Genbank:YP_002344032.1 GeneID:904928;gbkey=CDS;product=MOSC-domain-containing protein;Note=Original 282000 29 note: Cj0602c 2C unknown 2C len: 222 aa 3B similar to hypothetical proteins e.g. YIIM_ECOLI 28234 aa 29 2C fasta scores 3B opt: 298 z-score: 406.4 E 28 29: 2.4e-15 2C30.4 25 identity in 207 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domains PF03475 3-alpha domain and PF03473 MOSC domain were identified within CDS. Product modified to more specific family member due to motif match. Functional classification - Misc NC_002163.1 RefSeq gene 559852 560520 . - . ID=gene578;Name=Cj0602c;locus_tag=Cj0602c;Dbxref=GeneID:904928;gbkey=Gene NC_002163.1 RefSeq region 559876 560031 . - . ID=id1183;Name=id1183;Dbxref=GeneID:904928;gbkey=misc_feature;Note=HMMPfam hit to PF03475 2C 3-alpha domain 2C score 2.7e-17 NC_002163.1 RefSeq region 560050 560418 . - . ID=id1184;Name=id1184;Dbxref=GeneID:904928;gbkey=misc_feature;Note=HMMPfam hit to PF03473 2C MOSC domain 2C score 2.2e-44 NC_002163.1 RefSeq gene 560517 562220 . - . ID=gene579;gene=dsbD;Name=dsbD;locus_tag=Cj0603c;Dbxref=GeneID:904931;gbkey=Gene NC_002163.1 RefSeq CDS 560517 562220 . - 0 ID=cds545;Parent=gene579;gene=dsbD;Name=YP_002344033.1;Dbxref=GOA:Q9PHR3 InterPro:IPR003834 InterPro:IPR006662 InterPro:IPR012335 InterPro:IPR013766 InterPro:IPR015467 UniProtKB FSwiss-Prot:Q9PHR3 Genbank:YP_002344033.1 GeneID:904931;gbkey=CDS;product=thiol:disulfide interchange protein;Note=Original 282000 29 note: Cj0603c 2C dsbD 2C possible thiol:disulfide interchange protein 2C len: 567 aa 3B similar to e.g. DSBD_ECOLI thiol:disulfide interchange protein DSBD 28488 aa 29 2C fasta scores 3B opt: 795 z-score: 977.8 E 28 29: 0 2C 31.5 25 identity in 496 aa overlap. 27.1 25 identity to HP0265 7EUpdated 282006 29 note: Pfam domain PF02683 Cytochrome C biogenesis protein transmembrane was identified within CDS. Also 2C Prosite domain PS50223 THIOREDOXIN_2 2CThioredoxin domain 2 identified along with eight probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. DsbA and DsbC periplasmic proteins are involved in disulphide bond formation. DsbD generates a reducing source in the periplasm 2C which is required for maintaining proper redox conditions. Characterised within Escherichia coli with marginal identity score. kept within product function. Functional classification - Protein translation and modification 7EPMID:7628442 2C PMID:11085993 NC_002163.1 RefSeq region 560910 560969 . - . ID=id45;gene=dsbD;Name=id45;Dbxref=GeneID:904931;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0603c by TMHMM2.0 at aa 177-199 2C 211-233 2C 248-270 2C290-321 2C 331-353 2C 365-382 2C 386-405 and 418-437 NC_002163.1 RefSeq region 561006 561065 . - . ID=id45;gene=dsbD;Name=id45;Dbxref=GeneID:904931;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0603c by TMHMM2.0 at aa 177-199 2C 211-233 2C 248-270 2C290-321 2C 331-353 2C 365-382 2C 386-405 and 418-437 NC_002163.1 RefSeq region 561075 561128 . - . ID=id45;gene=dsbD;Name=id45;Dbxref=GeneID:904931;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0603c by TMHMM2.0 at aa 177-199 2C 211-233 2C 248-270 2C290-321 2C 331-353 2C 365-382 2C 386-405 and 418-437 NC_002163.1 RefSeq region 561084 561701 . - . ID=id1185;gene=dsbD;Name=id1185;Dbxref=GeneID:904931;gbkey=misc_feature;Note=HMMPfam hit to PF02683 2C Cytochrome C biogenesis protein transmembran 2C score 1.2e-07 NC_002163.1 RefSeq region 561162 561230 . - . ID=id45;gene=dsbD;Name=id45;Dbxref=GeneID:904931;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0603c by TMHMM2.0 at aa 177-199 2C 211-233 2C 248-270 2C290-321 2C 331-353 2C 365-382 2C 386-405 and 418-437 NC_002163.1 RefSeq region 561258 561353 . - . ID=id45;gene=dsbD;Name=id45;Dbxref=GeneID:904931;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0603c by TMHMM2.0 at aa 177-199 2C 211-233 2C 248-270 2C290-321 2C 331-353 2C 365-382 2C 386-405 and 418-437 NC_002163.1 RefSeq region 561411 561479 . - . ID=id45;gene=dsbD;Name=id45;Dbxref=GeneID:904931;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0603c by TMHMM2.0 at aa 177-199 2C 211-233 2C 248-270 2C290-321 2C 331-353 2C 365-382 2C 386-405 and 418-437 NC_002163.1 RefSeq region 561522 561590 . - . ID=id45;gene=dsbD;Name=id45;Dbxref=GeneID:904931;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0603c by TMHMM2.0 at aa 177-199 2C 211-233 2C 248-270 2C290-321 2C 331-353 2C 365-382 2C 386-405 and 418-437 NC_002163.1 RefSeq region 561624 561692 . - . ID=id45;gene=dsbD;Name=id45;Dbxref=GeneID:904931;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj0603c by TMHMM2.0 at aa 177-199 2C 211-233 2C 248-270 2C290-321 2C 331-353 2C 365-382 2C 386-405 and 418-437 ### NC_002163.1 RefSeq CDS 562315 563196 . + 0 ID=cds546;Parent=gene580;Name=YP_002344034.1;Dbxref=GOA:Q0PAR3 InterPro:IPR005660 InterPro:IPR016898 UniProtKB FTrEMBL:Q0PAR3 Genbank:YP_002344034.1 GeneID:904932;gbkey=CDS;product=polyphosphate kinase;Note=Original 282000 29 note: Cj0604 2C unknown 2C len: 293 aa 3B similar to hypothetical proteins e.g. TR:O05877 28EMBL:O05877 29 Mycobacterium tuberculosis Rv3232c 28MTCY20B11.07c 29 28295 aa 29 2C fasta scores 3B opt: 858 z-score: 1317.7 E 28 29: 0 2C 52.0 25 identity in 227 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF03976 Domain of unknown function 28DUF344 29 was identified within CDS This Pfam has now been modified to Polyphosphate kinase 2. Product modified to more specific family member due to motif match. No specific characterisation with acceptable identity score has been carried out yet. kept within product function. Functional classification - Misc 7EPMID:12486232 NC_002163.1 RefSeq gene 562315 563196 . + . ID=gene580;Name=Cj0604;locus_tag=Cj0604;Dbxref=GeneID:904932;gbkey=Gene NC_002163.1 RefSeq region 562387 563073 . + . ID=id1186;Name=id1186;Dbxref=GeneID:904932;gbkey=misc_feature;Note=HMMPfam hit to PF03976 2C Domain of unknown function 28DUF344 29 2C score 3.4e-171 NC_002163.1 UTR_Extractor 5'-UTR 563060 563204 . + . ID=utr211;locus_tag=Cj0605;product=putative amidohydrolase ### NC_002163.1 RefSeq CDS 563205 564395 . + 0 ID=cds547;Parent=gene581;Name=YP_002344035.1;Dbxref=GOA:Q0PAR2 InterPro:IPR002933 InterPro:IPR010168 InterPro:IPR017439 UniProtKB FTrEMBL:Q0PAR2 Genbank:YP_002344035.1 GeneID:904933;gbkey=CDS;product=amidohydrolase;Note=Original 282000 29 note: Cj0605 2C probable amidohydrolase 2C len: 396 aa 3B similar to members of the AMA 2FHIPO 2FHYUC family of hydrolases 28peptidase family M40 29 e.g. AMAA_BACST N-acyl-L-amino acid amidohydrolase 28370 aa 29 2C fasta scores 3B opt: 805 z-score: 1165.8 E 28 29: 0 2C 41.4 25 identity in 307 aa overlap. Also similar to HIPO_CAMJE hippurate hydrolase 28Cj0985c 29 28383 aa 29 2839.1 25 identity in 376 aa overlap 29. No Hp match. Contains PS00070 Aldehyde dehydrogenases cysteine active site 7EUpdated 282006 29 note: Pfam domain PF01546 Peptidase family M20 2FM25 2FM40 was identified within CDS. Further support given to product function. kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 563205 564395 . + . ID=gene581;Name=Cj0605;locus_tag=Cj0605;Dbxref=GeneID:904933;gbkey=Gene NC_002163.1 RefSeq region 563436 564380 . + . ID=id1187;Name=id1187;Dbxref=GeneID:904933;gbkey=misc_feature;Note=HMMPfam hit to PF01546 2C Peptidase family M20 2FM25 2FM40 2C score 1e-43 NC_002163.1 RefSeq region 563919 563954 . + . ID=id1188;Name=id1188;Dbxref=GeneID:904933;gbkey=misc_feature;Note=PS00070 Aldehyde dehydrogenases cysteine active site ### NC_002163.1 UTR_Extractor 5'-UTR 564448 564473 . + . ID=utr212;locus_tag=Cj0606;product=putative secretion protein HlyD NC_002163.1 RefSeq CDS 564474 565646 . + 0 ID=cds548;Parent=gene582;Name=YP_002344036.1;Dbxref=GOA:Q0PAR1 InterPro:IPR000089 InterPro:IPR006143 UniProtKB FTrEMBL:Q0PAR1 Genbank:YP_002344036.1 GeneID:904934;gbkey=CDS;product=secretion protein HlyD;Note=Original 282000 29 note: Cj0606 2C probable periplasmic protein 2C len: 390 aa 3B similar to hypothetical proteins e.g. E. coli TR:P75830 28EMBL:AE000189 29 28380 aa 29 2C fasta scores 3B opt: 522 z-score: 648.1 E 28 29: 8.4e-29 2C 31.3 25 identity in 386 aa overlap. No Hp ortholog. Contains probable N-terminal signal sequence and poly-Serine tract from aa 211 to 225 7EUpdated 282006 29 note: Pfam domain PF00529 HlyD family secretion protein was identified within CDS. Literature search identified paper linking the three-gene operon Cj0606-0608 29 to a type-one secretion system. Each of the three CDSs show characteristics similar to the alpha-haemolysin secretion system of Escherichia coli 28PMID:8137117 29. Product modified to more specific family member due to motif match. Some characterisation work carried out within Escherichia coli 28marginal identity score 29 and designated as macrolide-specific ABC-type efflux transporter. kept within product function. Functional classification - Protein and peptide secretion 7EPMID:15554967 2C PMID:8137117 2C PMID:11544226 NC_002163.1 RefSeq gene 564474 565646 . + . ID=gene582;Name=Cj0606;locus_tag=Cj0606;Dbxref=GeneID:904934;gbkey=Gene NC_002163.1 RefSeq region 564486 564545 . + . ID=id1189;Name=id1189;Dbxref=GeneID:904934;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0606 by TMHMM2.0 at aa 5-24 NC_002163.1 RefSeq region 564639 565418 . + . ID=id1190;Name=id1190;Dbxref=GeneID:904934;gbkey=misc_feature;Note=HMMPfam hit to PF00529 2C HlyD family secretion protein 2C score 0.00033 NC_002163.1 RefSeq gene 565646 567571 . + . ID=gene583;Name=Cj0607;locus_tag=Cj0607;Dbxref=GeneID:904935;gbkey=Gene NC_002163.1 RefSeq CDS 565646 567571 . + 0 ID=cds549;Parent=gene583;Name=YP_002344037.1;Dbxref=GOA:Q0PAR0 InterPro:IPR003439 InterPro:IPR003593 InterPro:IPR003838 UniProtKB FSwiss-Prot:Q0PAR0 Genbank:YP_002344037.1 GeneID:904935;gbkey=CDS;product=ABC transporter;Note=Original 282000 29 note: Cj0607 2C probable ABC-type transmembrane transport protein 2C len: 641 aa 3B similar to many predicted ABC transporters e.g. YBJZ_ECOLI 28648 aa 29 2Cfasta scores 3B opt: 1729 z-score: 1619.1 E 28 29: 0 2C 44.3 25 identity in 632 aa overlap. No Hp ortholog. Contains 2x PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00211 ABC transporters family signature 2C Pfam match to entry PF00005 ABC_tran 2C ABC transporters 2C and two possible membrane-spanning regions 7EUpdated 282006 29 note: Literature search identified paper linking the three-gene operon 28Cj0606-0608 29 to a type-one secretion system. Each of the three CDSs show characteristics similar to the alpha-haemolysin secretion system of E.coli 28PMID:8137117 29. Some characterisation work carried out within Escherichia coli 28marginal identity score 29 and designated as macrolide-specific ABC-type efflux transporter. not added to product function. Functional classification -Transport 2Fbinding proteins - Other 7EPMID:15554967 2C PMID:8137117 2C PMID:11544226 NC_002163.1 RefSeq region 565724 566281 . + . ID=id1191;Name=id1191;Dbxref=GeneID:904935;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 3.9e-54 NC_002163.1 RefSeq region 565745 565768 . + . ID=id1192;Name=id1192;Dbxref=GeneID:904935;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 566057 566101 . + . ID=id1193;Name=id1193;Dbxref=GeneID:904935;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq region 566438 566506 . + . ID=id1194;Name=id1194;Dbxref=GeneID:904935;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0607 by TMHMM2.0 at aa 265-287 2C 516-538 2C 567-589 and 602-624 NC_002163.1 RefSeq region 566582 566605 . + . ID=id1195;Name=id1195;Dbxref=GeneID:904935;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 567029 567547 . + . ID=id1196;Name=id1196;Dbxref=GeneID:904935;gbkey=misc_feature;Note=HMMPfam hit to PF02687 2C Predicted permease 2C score 2.4e-46 NC_002163.1 RefSeq region 567191 567259 . + . ID=id1194;Name=id1194;Dbxref=GeneID:904935;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0607 by TMHMM2.0 at aa 265-287 2C 516-538 2C 567-589 and 602-624 NC_002163.1 RefSeq region 567344 567412 . + . ID=id1194;Name=id1194;Dbxref=GeneID:904935;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0607 by TMHMM2.0 at aa 265-287 2C 516-538 2C 567-589 and 602-624 NC_002163.1 RefSeq region 567449 567517 . + . ID=id1194;Name=id1194;Dbxref=GeneID:904935;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0607 by TMHMM2.0 at aa 265-287 2C 516-538 2C 567-589 and 602-624 ### NC_002163.1 RefSeq CDS 567573 568943 . + 0 ID=cds550;Parent=gene584;Name=YP_002344038.1;Dbxref=GOA:Q0PAQ9 InterPro:IPR003423 InterPro:IPR005829 UniProtKB FTrEMBL:Q0PAQ9 Genbank:YP_002344038.1 GeneID:904936;gbkey=CDS;product=outer membrane efflux protein;Note=Original 282000 29 note: Cj0608 2C possible outer membrane protein 2C len: 456 aa 3B similar to hypothetical proteins e.g. YE62_HAEIN HI1462 28454 aa 29 2C fasta scores 3B opt: 711 z-score: 933.7 E 28 29: 0 2C 29.8 25 identity in 450 aa overlap 2C and weakly to outer membrene proteins e.g. TR:Q51006 28EMBL:X95635 29 Neisseria gonorrhoeae MTRE gene 28fragment 29 28467 aa 29 2C fasta scores 3B opt: 289 z-score: 325.5 E 28 29: 8.3e-11 2C 22.8 25 identity in 465 aa overlap. No Hp match. Also similar to Cj0365c 2828.6 25 identity in 455 aa overlap 29. Contains N-terminal signal sequence 2C PS00013 Prokaryotic membrane lipoprotein lipid attachment site and PS00217 Sugar transport proteins signature 2 7EUpdated 282006 29 note: Pfam domain PF02321 Outer membrane efflux protein was identified within CDS. Product modified to more specific family member due to motif match. Literature search identified paper linking the three-gene operon 28Cj0606-0608 29 to a type-one secretion system. Each of the three CDSs show characteristics similar to the alpha-haemolysin secretion system of E.coli 28PMID:8137117 29. kept within product function. Functional classification -Transport 2Fbinding proteins - Other 7EPMID:15554967 2C PMID:8137117 2C PMID:11544226 NC_002163.1 RefSeq gene 567573 568943 . + . ID=gene584;Name=Cj0608;locus_tag=Cj0608;Dbxref=GeneID:904936;gbkey=Gene NC_002163.1 RefSeq region 567588 567620 . + . ID=id1197;Name=id1197;Dbxref=GeneID:904936;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 567723 568274 . + . ID=id1198;Name=id1198;Dbxref=GeneID:904936;gbkey=misc_feature;Note=HMMPfam hit to PF02321 2C Outer membrane efflux protein 2C score 1.2e-12 NC_002163.1 RefSeq region 568359 568901 . + . ID=id1199;Name=id1199;Dbxref=GeneID:904936;gbkey=misc_feature;Note=HMMPfam hit to PF02321 2C Outer membrane efflux protein 2C score 7.5e-11 NC_002163.1 RefSeq region 568470 568547 . + . ID=id1200;Name=id1200;Dbxref=GeneID:904936;gbkey=misc_feature;Note=PS00217 Sugar transport proteins signature 2 ### NC_002163.1 RefSeq CDS 568946 570124 . - 0 ID=cds551;Parent=gene585;Name=YP_002344039.1;Dbxref=GOA:Q0PAQ8 InterPro:IPR001087 InterPro:IPR013831 UniProtKB FTrEMBL:Q0PAQ8 Genbank:YP_002344039.1 GeneID:904937;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0609c 2C possible periplasmic protein 2C len: 392 aa 3B no Hp match. Contains possible N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 568946 570124 . - . ID=gene585;Name=Cj0609c;locus_tag=Cj0609c;Dbxref=GeneID:904937;gbkey=Gene NC_002163.1 RefSeq CDS 570111 571121 . - 0 ID=cds552;Parent=gene586;Name=YP_002344040.1;Dbxref=GOA:Q0PAQ7 InterPro:IPR007407 InterPro:IPR013831 UniProtKB FTrEMBL:Q0PAQ7 Genbank:YP_002344040.1 GeneID:904522;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0610c 2C probable periplasmic protein 2C len: 336 aa 3B no Hp match. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF04311 Protein of unknown function 28DUF459 29 was identified within CDS. Product function kept the same. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 570111 571121 . - . ID=gene586;Name=Cj0610c;locus_tag=Cj0610c;Dbxref=GeneID:904522;gbkey=Gene NC_002163.1 RefSeq region 570132 571049 . - . ID=id1201;Name=id1201;Dbxref=GeneID:904522;gbkey=misc_feature;Note=HMMPfam hit to PF04311 2C Protein of unknown function 28DUF459 29 2C score 1.7e-184 NC_002163.1 RefSeq region 571035 571103 . - . ID=id1202;Name=id1202;Dbxref=GeneID:904522;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0610c by TMHMM2.0 at aa 7-29 ### NC_002163.1 RefSeq CDS 571122 572498 . - 0 ID=cds553;Parent=gene587;Name=YP_002344041.1;Dbxref=GOA:Q0PAQ6 InterPro:IPR004299 UniProtKB FTrEMBL:Q0PAQ6 Genbank:YP_002344041.1 GeneID:904938;gbkey=CDS;product=acyltransferase family protein;Note=Original 282000 29 note: Cj0611c 2C probable transmembrane transport protein 2C len: 458 aa 3B similar to e.g. TR:Q51392 28EMBL:U50202 29 Pseudomonas aeruginosa ALGI 28520 aa 29 2C fasta scores 3B opt: 729 z-score: 779.3 E 28 29: 0 2C32.5 25 identity in 428 aa overlap 2C and DLTB_BACSU DLTB protein 28395 aa 29 2C fasta scores 3B opt: 431 z-score: 482.4 E 28 29: 1.4e-19 2C 29.6 25 identity in 361 aa overlap. 32.9 25 identity to HP0855 7EUpdated 282006 29 note: Pfam domain PF03062 MBOAT family identified within CDS. Also 2C 11 probable transmembrane helices predicted by TMHMM2.0. Product modified to more specific family member due to motif match. No specific characterisation with acceptable identity scores identified yet. kept within product function. Functional classification - Misc 7EPMID:8636017 2C PMID:11208804 NC_002163.1 RefSeq gene 571122 572498 . - . ID=gene587;Name=Cj0611c;locus_tag=Cj0611c;Dbxref=GeneID:904938;gbkey=Gene NC_002163.1 RefSeq region 571167 571235 . - . ID=id46;Name=id46;Dbxref=GeneID:904938;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0611c by TMHMM2.0 at aa 5-22 2C 32-66 2C 73-95 2C 110-132 2C144-163 2C 183-205 2C 236-258 2C 319-341 2C 348-370 2C 396-415 and 422-444 NC_002163.1 RefSeq region 571254 571313 . - . ID=id46;Name=id46;Dbxref=GeneID:904938;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0611c by TMHMM2.0 at aa 5-22 2C 32-66 2C 73-95 2C 110-132 2C144-163 2C 183-205 2C 236-258 2C 319-341 2C 348-370 2C 396-415 and 422-444 NC_002163.1 RefSeq region 571377 572195 . - . ID=id1203;Name=id1203;Dbxref=GeneID:904938;gbkey=misc_feature;Note=HMMPfam hit to PF03062 2C MBOAT family 2C score 4.1e-80 NC_002163.1 RefSeq region 571389 571457 . - . ID=id46;Name=id46;Dbxref=GeneID:904938;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0611c by TMHMM2.0 at aa 5-22 2C 32-66 2C 73-95 2C 110-132 2C144-163 2C 183-205 2C 236-258 2C 319-341 2C 348-370 2C 396-415 and 422-444 NC_002163.1 RefSeq region 571476 571544 . - . ID=id46;Name=id46;Dbxref=GeneID:904938;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0611c by TMHMM2.0 at aa 5-22 2C 32-66 2C 73-95 2C 110-132 2C144-163 2C 183-205 2C 236-258 2C 319-341 2C 348-370 2C 396-415 and 422-444 NC_002163.1 RefSeq region 571725 571793 . - . ID=id46;Name=id46;Dbxref=GeneID:904938;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0611c by TMHMM2.0 at aa 5-22 2C 32-66 2C 73-95 2C 110-132 2C144-163 2C 183-205 2C 236-258 2C 319-341 2C 348-370 2C 396-415 and 422-444 NC_002163.1 RefSeq region 571884 571952 . - . ID=id46;Name=id46;Dbxref=GeneID:904938;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0611c by TMHMM2.0 at aa 5-22 2C 32-66 2C 73-95 2C 110-132 2C144-163 2C 183-205 2C 236-258 2C 319-341 2C 348-370 2C 396-415 and 422-444 NC_002163.1 RefSeq region 572010 572069 . - . ID=id46;Name=id46;Dbxref=GeneID:904938;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0611c by TMHMM2.0 at aa 5-22 2C 32-66 2C 73-95 2C 110-132 2C144-163 2C 183-205 2C 236-258 2C 319-341 2C 348-370 2C 396-415 and 422-444 NC_002163.1 RefSeq region 572103 572171 . - . ID=id46;Name=id46;Dbxref=GeneID:904938;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0611c by TMHMM2.0 at aa 5-22 2C 32-66 2C 73-95 2C 110-132 2C144-163 2C 183-205 2C 236-258 2C 319-341 2C 348-370 2C 396-415 and 422-444 NC_002163.1 RefSeq region 572214 572282 . - . ID=id46;Name=id46;Dbxref=GeneID:904938;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0611c by TMHMM2.0 at aa 5-22 2C 32-66 2C 73-95 2C 110-132 2C144-163 2C 183-205 2C 236-258 2C 319-341 2C 348-370 2C 396-415 and 422-444 NC_002163.1 RefSeq region 572301 572405 . - . ID=id46;Name=id46;Dbxref=GeneID:904938;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0611c by TMHMM2.0 at aa 5-22 2C 32-66 2C 73-95 2C 110-132 2C144-163 2C 183-205 2C 236-258 2C 319-341 2C 348-370 2C 396-415 and 422-444 NC_002163.1 RefSeq region 572433 572486 . - . ID=id46;Name=id46;Dbxref=GeneID:904938;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0611c by TMHMM2.0 at aa 5-22 2C 32-66 2C 73-95 2C 110-132 2C144-163 2C 183-205 2C 236-258 2C 319-341 2C 348-370 2C 396-415 and 422-444 ### NC_002163.1 RefSeq gene 572541 573044 . - . ID=gene588;gene=cft;Name=cft;locus_tag=Cj0612c;Dbxref=GeneID:904939;gbkey=Gene NC_002163.1 RefSeq CDS 572541 573044 . - 0 ID=cds554;Parent=gene588;gene=cft;Name=YP_002344042.1;Dbxref=GOA:Q46106 InterPro:IPR001519 InterPro:IPR008331 InterPro:IPR009040 InterPro:IPR012347 PDB:1KRQ UniProtKB FSwiss-Prot:Q46106 Genbank:YP_002344042.1 GeneID:904939;gbkey=CDS;product=ferritin;Note=Original 282000 29 note: Cj0612c 2C cft 2C probable ferritin 2C len: 167 aa 3B identical to TR:Q46106 28EMBL:D64082 29 2C and similar to many e.g. FTN_ECOLI ferritin 28165 aa 29 2C fasta scores 3B opt: 535 z-score: 957.6 E 28 29: 0 2C47.2 25 identity in 161 aa overlap. 63.9 25 identity to HP0653. Contains Pfam match to entry PF00210 ferritin 7EUpdated 282006 29 note: Characterised within Campylobacter jejuni. Functional classification -Transport 2Fbinding proteins - Cations 7EPMID:8809765 NC_002163.1 RefSeq region 572613 573026 . - . ID=id1204;gene=cft;Name=id1204;Dbxref=GeneID:904939;gbkey=misc_feature;Note=HMMPfam hit to PF00210 2C Ferritin-like domain 2C score 6.7e-50 ### NC_002163.1 UTR_Extractor 5'-UTR 573045 573073 . - . ID=utr213;locus_tag=Cj0612c;product=ferritin NC_002163.1 UTR_Extractor 5'-UTR 573199 573223 . + . ID=utr214;locus_tag=Cj0613;product=putative periplasmic phosphate binding protein NC_002163.1 RefSeq gene 573224 574219 . + . ID=gene589;gene=pstS;Name=pstS;locus_tag=Cj0613;Dbxref=GeneID:904940;gbkey=Gene NC_002163.1 RefSeq CDS 573224 574219 . + 0 ID=cds555;Parent=gene589;gene=pstS;Name=YP_002344043.1;Dbxref=GOA:Q0PAQ4 UniProtKB FTrEMBL:Q0PAQ4 Genbank:YP_002344043.1 GeneID:904940;gbkey=CDS;product=phosphate-binding protein;Note=Original 282000 29 note: Cj0613 2C pstS 2C possible periplasmic phosphate binding protein 2C len: 167 aa 3B similar to e.g. SPHX_SYNP7 SPHX protein precursor 28337 aa 29 2C fasta scores 3B opt: 346 z-score: 602.6 E 28 29: 2.9e-26 2C33.2 25 identity in 301 aa overlap. No Hp match. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Characterised within Escherichia coli 2C however 2C identity score was unnacceptable. kept within product function. Functional classification - Transport 2Fbinding proteins -Anions 7EPMID:2651888 2C PMID:7741855 NC_002163.1 RefSeq CDS 574229 575143 . + 0 ID=cds556;Parent=gene590;gene=pstC;Name=YP_002344044.1;Dbxref=GOA:Q0PAQ3 InterPro:IPR000515 InterPro:IPR011864 UniProtKB FTrEMBL:Q0PAQ3 Genbank:YP_002344044.1 GeneID:904941;gbkey=CDS;product=phosphate ABC transporter permease;Note=Original 282000 29 note: Cj0614 2C pstC 2C probable phosphate transport system permease 2C len: 304 aa 3B similar to e.g. PSTC_ECOLI phosphate transport system permease 28319 aa 29 2C fasta scores 3B opt: 289 z-score: 590.3 E 28 29: 1.4e-25 2C 28.9 25 identity in 305 aa overlap. No Hp ortholog. Also similar to downstream gene Cj0615 2830.7 25 identity in 254 aa overlap 29. Contains Pfam match to entry PF00528 BPD_transp 2C Binding-protein-dependent transport systems inner membrane component 7EUpdated 282006 29 note: Six probable transmembrane helices predicted by TMHMM2.0. Characterised within Pseudomonas putida and Escherichia coli 2C however 2C identity scores were unnacceptable. kept within product function. Functional classification - Transport 2Fbinding proteins - Anions 7EPMID:16232467 2C PMID:2646285 NC_002163.1 RefSeq gene 574229 575143 . + . ID=gene590;gene=pstC;Name=pstC;locus_tag=Cj0614;Dbxref=GeneID:904941;gbkey=Gene NC_002163.1 RefSeq region 574253 574321 . + . ID=id1205;gene=pstC;Name=id1205;Dbxref=GeneID:904941;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0614 by TMHMM2.0 at aa 9-31 2C 83-105 2C 118-140 2C 155-174 2C199-221 and 273-295 NC_002163.1 RefSeq region 574451 575128 . + . ID=id1206;gene=pstC;Name=id1206;Dbxref=GeneID:904941;gbkey=misc_feature;Note=HMMPfam hit to PF00528 2C Binding-protein-dependent transport syst 2C score 3.6e-16 NC_002163.1 RefSeq region 574475 574543 . + . ID=id1205;gene=pstC;Name=id1205;Dbxref=GeneID:904941;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0614 by TMHMM2.0 at aa 9-31 2C 83-105 2C 118-140 2C 155-174 2C199-221 and 273-295 NC_002163.1 RefSeq region 574580 574648 . + . ID=id1205;gene=pstC;Name=id1205;Dbxref=GeneID:904941;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0614 by TMHMM2.0 at aa 9-31 2C 83-105 2C 118-140 2C 155-174 2C199-221 and 273-295 NC_002163.1 RefSeq region 574691 574750 . + . ID=id1205;gene=pstC;Name=id1205;Dbxref=GeneID:904941;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0614 by TMHMM2.0 at aa 9-31 2C 83-105 2C 118-140 2C 155-174 2C199-221 and 273-295 NC_002163.1 RefSeq region 574823 574891 . + . ID=id1205;gene=pstC;Name=id1205;Dbxref=GeneID:904941;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0614 by TMHMM2.0 at aa 9-31 2C 83-105 2C 118-140 2C 155-174 2C199-221 and 273-295 NC_002163.1 RefSeq region 575045 575113 . + . ID=id1205;gene=pstC;Name=id1205;Dbxref=GeneID:904941;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0614 by TMHMM2.0 at aa 9-31 2C 83-105 2C 118-140 2C 155-174 2C199-221 and 273-295 NC_002163.1 RefSeq gene 575140 576228 . + . ID=gene591;gene=pstA;Name=pstA;locus_tag=Cj0615;Dbxref=GeneID:904942;gbkey=Gene NC_002163.1 RefSeq CDS 575140 576228 . + 0 ID=cds557;Parent=gene591;gene=pstA;Name=YP_002344045.1;Dbxref=GOA:Q0PAQ2 InterPro:IPR000515 InterPro:IPR005672 UniProtKB FTrEMBL:Q0PAQ2 Genbank:YP_002344045.1 GeneID:904942;gbkey=CDS;product=phosphate ABC transporter permease;Note=Original 282000 29 note: Cj0615 2C pstA 2C probable phosphate transport system permease 2C len: 362 aa 3B similar to e.g. PSTA_ECOLI phosphate transport system permease 28296 aa 29 2C fasta scores 3B opt: 346 z-score: 447.5 E 28 29: 1.3e-17 2C 29.2 25 identity in 226 aa overlap. No Hp ortholog. Also similar to upstream gene Cj0614 2830.7 25 identity in 254 aa overlap 29. Contains Pfam match to entry PF00528 BPD_transp 2C Binding-protein-dependent transport systems inner membrane component 7EUpdated 282006 29 note: Six probable transmembrane helices predicted by TMHMM2.0. Characterised within Escherichia coli 2C however 2C identity scores were unnacceptable. kept within product function. Functional classification - Transport 2Fbinding proteins -Anions 7EPMID:2993631 2C PMID:2896188 NC_002163.1 RefSeq region 575200 575268 . + . ID=id1207;gene=pstA;Name=id1207;Dbxref=GeneID:904942;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0615 by TMHMM2.0 at aa 21-43 2C 146-168 2C 188-210 2C 215-237 2C263-285 and 331-353 NC_002163.1 RefSeq region 575566 576213 . + . ID=id1208;gene=pstA;Name=id1208;Dbxref=GeneID:904942;gbkey=misc_feature;Note=HMMPfam hit to PF00528 2C Binding-protein-dependent transport syst 2C score 1.9e-17 NC_002163.1 RefSeq region 575575 575643 . + . ID=id1207;gene=pstA;Name=id1207;Dbxref=GeneID:904942;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0615 by TMHMM2.0 at aa 21-43 2C 146-168 2C 188-210 2C 215-237 2C263-285 and 331-353 NC_002163.1 RefSeq region 575701 575769 . + . ID=id1207;gene=pstA;Name=id1207;Dbxref=GeneID:904942;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0615 by TMHMM2.0 at aa 21-43 2C 146-168 2C 188-210 2C 215-237 2C263-285 and 331-353 NC_002163.1 RefSeq region 575782 575850 . + . ID=id1207;gene=pstA;Name=id1207;Dbxref=GeneID:904942;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0615 by TMHMM2.0 at aa 21-43 2C 146-168 2C 188-210 2C 215-237 2C263-285 and 331-353 NC_002163.1 RefSeq region 575926 575994 . + . ID=id1207;gene=pstA;Name=id1207;Dbxref=GeneID:904942;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0615 by TMHMM2.0 at aa 21-43 2C 146-168 2C 188-210 2C 215-237 2C263-285 and 331-353 NC_002163.1 RefSeq region 576130 576198 . + . ID=id1207;gene=pstA;Name=id1207;Dbxref=GeneID:904942;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0615 by TMHMM2.0 at aa 21-43 2C 146-168 2C 188-210 2C 215-237 2C263-285 and 331-353 NC_002163.1 RefSeq gene 576225 576965 . + . ID=gene592;gene=pstB;Name=pstB;locus_tag=Cj0616;Dbxref=GeneID:904943;gbkey=Gene NC_002163.1 RefSeq CDS 576225 576965 . + 0 ID=cds558;Parent=gene592;gene=pstB;Name=YP_002344046.1;Dbxref=GOA:Q9PHQ1 HSSP:P02915 InterPro:IPR003439 InterPro:IPR003593 InterPro:IPR005670 InterPro:IPR015850 UniProtKB FSwiss-Prot:Q9PHQ1 Genbank:YP_002344046.1 GeneID:904943;gbkey=CDS;product=phosphate ABC transporter ATP-binding protein;Note=ATP-binding protein 3B PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation NC_002163.1 RefSeq region 576306 576875 . + . ID=id1209;gene=pstB;Name=id1209;Dbxref=GeneID:904943;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 3.2e-51 NC_002163.1 RefSeq region 576327 576350 . + . ID=id1210;gene=pstB;Name=id1210;Dbxref=GeneID:904943;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 576651 576695 . + . ID=id1211;gene=pstB;Name=id1211;Dbxref=GeneID:904943;gbkey=misc_feature;Note=PS00211 ABC transporters family signature ### NC_002163.1 UTR_Extractor 5'-UTR 577002 577026 . + . ID=utr215;locus_tag=Cj0617;product=hypothetical protein NC_002163.1 RefSeq pseudogene 577027 578255 . + . ID=gene593;Name=Cj0617;locus_tag=Cj0617;Dbxref=GeneID:904944;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 577528 577607 . + . ID=utr216;locus_tag=Cj0618;product=hypothetical protein NC_002163.1 RefSeq repeat_region 577586 577594 . + . ID=id1212;Name=id1212;Dbxref=GeneID:904944;gbkey=repeat_region;Note=G 289 29 ### NC_002163.1 UTR_Extractor 5'-UTR 578306 578344 . + . ID=utr217;locus_tag=Cj0619;product=putative MATE family transport protein NC_002163.1 RefSeq CDS 578345 579661 . + 0 ID=cds559;Parent=gene594;Name=YP_002344049.1;Dbxref=GOA:Q0PAP8 InterPro:IPR002528 UniProtKB FTrEMBL:Q0PAP8 Genbank:YP_002344049.1 GeneID:904946;gbkey=CDS;product=MATE family transport protein;Note=Original 282000 29 note: Cj0619 2C probable integral membrane protein 2C len: 438 aa 3B similar to hypothetical proteins e.g. TR:O07940 B. subtilis YISQ 28455 aa 29 2C fasta scores 3B opt: 880 z-score: 1364.9 E 28 29: 0 2C 32.1 25 identity in 446 aa overlap 2C and YEEO_ECOLI 28547 aa 29 2C fasta scores 3B opt: 164 z-score: 529.6 E 28 29: 3.3e-22 2C 22.7 25 identity in 437 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF01554 MatE was identified within CDS. This family of protein function as drug 2Fsodium antiporters. These proteins mediate resistance to a wide range of cationic dyes 2C fluroquinolones 2Caminoglycosides and other structurally diverse antibodies and drugs. MatE proteins are found in bacteria 2C archaea and eukaryotes. These proteins are predicted to have 12 alpha-helical transmembrane regions 28which this CDS has 29. Product modified to more specific family member due to motif match. Literature search identified paper giving further support. Functional classification -Membranes 2C lipoproteins and porins 7EPMID:16048946 NC_002163.1 RefSeq gene 578345 579661 . + . ID=gene594;Name=Cj0619;locus_tag=Cj0619;Dbxref=GeneID:904946;gbkey=Gene NC_002163.1 RefSeq region 578381 578449 . + . ID=id1213;Name=id1213;Dbxref=GeneID:904946;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0619 by TMHMM2.0 at aa 13-35 2C 50-69 2C 89-111 2C 126-148 2C155-177 2C 187-209 2C 229-251 2C 266-288 2C 309-328 2C 343-365 2C377-399 and 403-422 NC_002163.1 RefSeq region 578384 578866 . + . ID=id1214;Name=id1214;Dbxref=GeneID:904946;gbkey=misc_feature;Note=HMMPfam hit to PF01554 2C MatE 2C score 3.7e-19 NC_002163.1 RefSeq region 578492 578551 . + . ID=id1213;Name=id1213;Dbxref=GeneID:904946;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0619 by TMHMM2.0 at aa 13-35 2C 50-69 2C 89-111 2C 126-148 2C155-177 2C 187-209 2C 229-251 2C 266-288 2C 309-328 2C 343-365 2C377-399 and 403-422 NC_002163.1 RefSeq region 578507 578539 . + . ID=id1215;Name=id1215;Dbxref=GeneID:904946;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 578609 578677 . + . ID=id1213;Name=id1213;Dbxref=GeneID:904946;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0619 by TMHMM2.0 at aa 13-35 2C 50-69 2C 89-111 2C 126-148 2C155-177 2C 187-209 2C 229-251 2C 266-288 2C 309-328 2C 343-365 2C377-399 and 403-422 NC_002163.1 RefSeq region 578720 578788 . + . ID=id1213;Name=id1213;Dbxref=GeneID:904946;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0619 by TMHMM2.0 at aa 13-35 2C 50-69 2C 89-111 2C 126-148 2C155-177 2C 187-209 2C 229-251 2C 266-288 2C 309-328 2C 343-365 2C377-399 and 403-422 NC_002163.1 RefSeq region 578807 578875 . + . ID=id1213;Name=id1213;Dbxref=GeneID:904946;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0619 by TMHMM2.0 at aa 13-35 2C 50-69 2C 89-111 2C 126-148 2C155-177 2C 187-209 2C 229-251 2C 266-288 2C 309-328 2C 343-365 2C377-399 and 403-422 NC_002163.1 RefSeq region 578903 578971 . + . ID=id1213;Name=id1213;Dbxref=GeneID:904946;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0619 by TMHMM2.0 at aa 13-35 2C 50-69 2C 89-111 2C 126-148 2C155-177 2C 187-209 2C 229-251 2C 266-288 2C 309-328 2C 343-365 2C377-399 and 403-422 NC_002163.1 RefSeq region 579029 579097 . + . ID=id1213;Name=id1213;Dbxref=GeneID:904946;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0619 by TMHMM2.0 at aa 13-35 2C 50-69 2C 89-111 2C 126-148 2C155-177 2C 187-209 2C 229-251 2C 266-288 2C 309-328 2C 343-365 2C377-399 and 403-422 NC_002163.1 RefSeq region 579140 579208 . + . ID=id1213;Name=id1213;Dbxref=GeneID:904946;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0619 by TMHMM2.0 at aa 13-35 2C 50-69 2C 89-111 2C 126-148 2C155-177 2C 187-209 2C 229-251 2C 266-288 2C 309-328 2C 343-365 2C377-399 and 403-422 NC_002163.1 RefSeq region 579269 579328 . + . ID=id1213;Name=id1213;Dbxref=GeneID:904946;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0619 by TMHMM2.0 at aa 13-35 2C 50-69 2C 89-111 2C 126-148 2C155-177 2C 187-209 2C 229-251 2C 266-288 2C 309-328 2C 343-365 2C377-399 and 403-422 NC_002163.1 RefSeq region 579371 579439 . + . ID=id1213;Name=id1213;Dbxref=GeneID:904946;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0619 by TMHMM2.0 at aa 13-35 2C 50-69 2C 89-111 2C 126-148 2C155-177 2C 187-209 2C 229-251 2C 266-288 2C 309-328 2C 343-365 2C377-399 and 403-422 NC_002163.1 RefSeq region 579473 579541 . + . ID=id1213;Name=id1213;Dbxref=GeneID:904946;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0619 by TMHMM2.0 at aa 13-35 2C 50-69 2C 89-111 2C 126-148 2C155-177 2C 187-209 2C 229-251 2C 266-288 2C 309-328 2C 343-365 2C377-399 and 403-422 NC_002163.1 RefSeq region 579551 579610 . + . ID=id1213;Name=id1213;Dbxref=GeneID:904946;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0619 by TMHMM2.0 at aa 13-35 2C 50-69 2C 89-111 2C 126-148 2C155-177 2C 187-209 2C 229-251 2C 266-288 2C 309-328 2C 343-365 2C377-399 and 403-422 NC_002163.1 RefSeq gene 579637 580284 . + . ID=gene595;Name=Cj0620;locus_tag=Cj0620;Dbxref=GeneID:904947;gbkey=Gene NC_002163.1 RefSeq CDS 579637 580284 . + 0 ID=cds560;Parent=gene595;Name=YP_002344050.1;Dbxref=InterPro:IPR002725 UniProtKB FTrEMBL:Q0PAP7 Genbank:YP_002344050.1 GeneID:904947;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0620 2C unknown 2C len: 215 aa 3B some simlarity to TR:O58443 28EMBL:AB009490 29 Pyrococcus horikoshii PHCF016 28230 aa 29 2C fasta scores 3B opt: 229 z-score: 237.3 E 28 29: 6.4e-06 2C 26.9 25 identity in 197 aa overlap. 33.7 25 identity to HP0806 2C 25.0 25 identity to HP1401 7EUpdated 282006 29 note: Pfam domain PF01863 Protein of unknown function DUF45 identified within CDS. This motif has no known function. Members are found in some archaebacteria 2C as well as Helicobacter pylori 28Epsilon Proteobacteria 29. The proteins are 190-240 amino acids long 2C with the C terminus being the most conserved region 2Ccontaining three conserved histidines. This motif is similar to that found in Zinc proteases 2C suggesting a possible role as a protease. Conserved added to product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq region 579682 580281 . + . ID=id1216;Name=id1216;Dbxref=GeneID:904947;gbkey=misc_feature;Note=HMMPfam hit to PF01863 2C Protein of unknown function DUF45 2C score 1.1e-18 ### NC_002163.1 UTR_Extractor 5'-UTR 580302 580325 . + . ID=utr218;locus_tag=Cj0621;product=hypothetical protein NC_002163.1 RefSeq CDS 580326 581846 . + 0 ID=cds561;Parent=gene596;Name=YP_002344051.1;Dbxref=UniProtKB FTrEMBL:Q0PAP6 Genbank:YP_002344051.1 GeneID:904948;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0621 2C unknown 2C len: 506 aa 3B similar to TR:E1186594 28EMBL:AJ003049 29 hypothetical protein HYDE from Wolinella succinogenes 28546 aa 29 2C fasta scores 3B opt: 207 z-score: 285.3 E 28 29: 1.3e-08 2C 25.8 25 identity in 551 aa overlap. 23.2 25 identity to HP0635 7EUpdated 282006 29 note: Literature search identified paper linking product function to hydE-like protein. Functional classification - Conserved hypothetical proteins 7EPMID:10533287 NC_002163.1 RefSeq gene 580326 581846 . + . ID=gene596;Name=Cj0621;locus_tag=Cj0621;Dbxref=GeneID:904948;gbkey=Gene NC_002163.1 RefSeq CDS 581827 584016 . + 0 ID=cds562;Parent=gene597;gene=hypF;Name=YP_002344052.1;Dbxref=GOA:Q0PAP5 InterPro:IPR001792 InterPro:IPR004421 InterPro:IPR006070 InterPro:IPR011125 UniProtKB FTrEMBL:Q0PAP5 Genbank:YP_002344052.1 GeneID:904949;gbkey=CDS;product=carbamoyltransferase;Note=Original 282000 29 note: Cj0622 2C hypF 2C probable transcriptional regulatory protein 2C len: 729 aa 3B similar to many e.g. HYPF_ECOLI transcriptional regulatory protein HYPF 28750 aa 29 2C fasta scores 3B opt: 1166 z-score: 1359.5 E 28 29: 0 2C 34.1 25 identity in 747 aa overlap. 35.0 25 identity to HP0048. Contains PS00150 Acylphosphatase signature 1 and Pfam match to entry PF01300 Sua5_yciO_yrdC 2CSUA5 2FyciO 2FyrdC family 7EUpdated 282006 29 note: Pfam domain PF07503 HypF finger was identified within CDS. Further support given to product function. Characterised within Escherichia coli with marginal identity score. Product function updated with new EC number. not added to product function. Functional classification - Energy metabolism -Respiration 7EPMID:15504408 2C PMID:1849603 NC_002163.1 RefSeq gene 581827 584016 . + . ID=gene597;gene=hypF;Name=hypF;locus_tag=Cj0622;Dbxref=GeneID:904949;gbkey=Gene NC_002163.1 RefSeq region 581845 582093 . + . ID=id1217;gene=hypF;Name=id1217;Dbxref=GeneID:904949;gbkey=misc_feature;Note=HMMPfam hit to PF00708 2C Acylphosphatase 2C score 2.2e-07 NC_002163.1 RefSeq region 581854 581886 . + . ID=id1218;gene=hypF;Name=id1218;Dbxref=GeneID:904949;gbkey=misc_feature;Note=PS00150 Acylphosphatase signature 1 NC_002163.1 RefSeq region 582145 582249 . + . ID=id1219;gene=hypF;Name=id1219;Dbxref=GeneID:904949;gbkey=misc_feature;Note=HMMPfam hit to PF07503 2C HypF finger 2C score 2e-16 NC_002163.1 RefSeq region 582295 582393 . + . ID=id1220;gene=hypF;Name=id1220;Dbxref=GeneID:904949;gbkey=misc_feature;Note=HMMPfam hit to PF07503 2C HypF finger 2C score 3.2e-16 NC_002163.1 RefSeq region 582448 582969 . + . ID=id1221;gene=hypF;Name=id1221;Dbxref=GeneID:904949;gbkey=misc_feature;Note=HMMPfam hit to PF01300 2C yrdC domain 2C score 6.5e-52 NC_002163.1 RefSeq region 583099 583305 . + . ID=id1222;gene=hypF;Name=id1222;Dbxref=GeneID:904949;gbkey=misc_feature;Note=HMMPfam hit to PF00814 2C Glycoprotease family 2C score 2.3e-18 ### NC_002163.1 UTR_Extractor 5'-UTR 584072 584093 . + . ID=utr219;locus_tag=Cj0623;product=hydrogenase isoenzymes formation protein NC_002163.1 RefSeq CDS 584094 584837 . + 0 ID=cds563;Parent=gene598;gene=hypB;Name=YP_002344053.1;Dbxref=GOA:Q0PAP4 InterPro:IPR003495 InterPro:IPR004392 InterPro:IPR007087 InterPro:IPR012202 UniProtKB FTrEMBL:Q0PAP4 Genbank:YP_002344053.1 GeneID:904950;gbkey=CDS;product=hydrogenase isoenzymes formation protein;Note=Original 282000 29 note: Cj0623 2C hypB 2C probable hydrogenase isoenzymes formation protein 2C len: 247 aa 3B similar to many e.g. HYPB_ECOLI hydrogenase isoenzymes formation protein 28290 aa 29 2C fasta scores 3B opt: 691 z-score: 1142.3 E 28 29: 0 2C 46.1 25 identity in 230 aa overlap. 44.2 25 identity to HP0900. Contains PS00028 Zinc finger 2CC2H2 type 2C domain 7EUpdated 282006 29 note: Pfam domain PF02492 CobW 2FHypB 2FUreG 2C nucleotide-binding domain was identified within CDS. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification - Energy metabolism -Respiration 7EPMID:7601092 2C PMID:1849603 NC_002163.1 RefSeq gene 584094 584837 . + . ID=gene598;gene=hypB;Name=hypB;locus_tag=Cj0623;Dbxref=GeneID:904950;gbkey=Gene NC_002163.1 RefSeq region 584097 584162 . + . ID=id1223;gene=hypB;Name=id1223;Dbxref=GeneID:904950;gbkey=misc_feature;Note=PS00028 Zinc finger 2C C2H2 type 2C domain NC_002163.1 RefSeq region 584274 584765 . + . ID=id1224;gene=hypB;Name=id1224;Dbxref=GeneID:904950;gbkey=misc_feature;Note=HMMPfam hit to PF02492 2C CobW 2FHypB 2FUreG 2Cnucleotide-binding domain 2C score 4e-67 NC_002163.1 RefSeq region 584427 584459 . + . ID=id1225;gene=hypB;Name=id1225;Dbxref=GeneID:904950;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 584837 585058 . + . ID=id1226;gene=hypC;Name=id1226;Dbxref=GeneID:904953;gbkey=misc_feature;Note=HMMPfam hit to PF01455 2C HupF 2FHypC family 2C score 2e-26 NC_002163.1 RefSeq CDS 584837 585118 . + 0 ID=cds564;Parent=gene599;gene=hypC;Name=YP_002344054.1;Dbxref=GOA:Q0PAP3 InterPro:IPR001109 UniProtKB FTrEMBL:Q0PAP3 Genbank:YP_002344054.1 GeneID:904953;gbkey=CDS;product=hydrogenase isoenzymes formation protein;Note=Original 282000 29 note: Cj0624 2C hypC 2C probable hydrogenase isoenzymes formation protein 2C len: 93 aa 3B similar to many e.g. HYPC_ECOLI hydrogenase isoenzymes formation protein 2890 aa 29 2C fasta scores 3B opt: 145 z-score: 173.2 E 28 29: 0.024 2C 35.9 25 identity in 78 aa overlap. 53.3 25 identity to HP0899 7EUpdated 282006 29 note: Pfam domain PF01455 HupF 2FHypC family protein was identified within CDS. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Energy metabolism - Respiration 7EPMID:8021226 2C PMID:1849603 NC_002163.1 RefSeq gene 584837 585118 . + . ID=gene599;gene=hypC;Name=hypC;locus_tag=Cj0624;Dbxref=GeneID:904953;gbkey=Gene NC_002163.1 RefSeq CDS 585102 586193 . + 0 ID=cds565;Parent=gene600;gene=hypD;Name=YP_002344055.1;Dbxref=GOA:Q0PAP2 InterPro:IPR002780 UniProtKB FTrEMBL:Q0PAP2 Genbank:YP_002344055.1 GeneID:904954;gbkey=CDS;product=hydrogenase isoenzymes formation protein;Note=Original 282000 29 note: Cj0625 2C hypD 2C probable hydrogenase isoenzymes formation protein 2C len: 363 aa 3B similar to many e.g. HYPD_ECOLI hydrogenase isoenzymes formation protein 28373 aa 29 2C fasta scores 3B opt: 1097 z-score: 1671.2 E 28 29: 0 2C 41.3 25 identity in 368 aa overlap. 58.5 25 identity to HP0898 7EUpdated 282006 29 note: Pfam domain PF01924 Hydrogenase formation hypA family protein was identified within CDS. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification - Energy metabolism -Respiration 7EPMID:1849603 NC_002163.1 RefSeq gene 585102 586193 . + . ID=gene600;gene=hypD;Name=hypD;locus_tag=Cj0625;Dbxref=GeneID:904954;gbkey=Gene NC_002163.1 RefSeq region 585126 586184 . + . ID=id1227;gene=hypD;Name=id1227;Dbxref=GeneID:904954;gbkey=misc_feature;Note=HMMPfam hit to PF01924 2C Hydrogenase formation hypA family 2C score 8.6e-204 NC_002163.1 RefSeq region 586190 586630 . + . ID=id1228;gene=hypE;Name=id1228;Dbxref=GeneID:904955;gbkey=misc_feature;Note=HMMPfam hit to PF00586 2C AIR synthase related protein 2C N-terminal dom 2C score 7.3e-21 NC_002163.1 RefSeq gene 586190 587164 . + . ID=gene601;gene=hypE;Name=hypE;locus_tag=Cj0626;Dbxref=GeneID:904955;gbkey=Gene NC_002163.1 RefSeq CDS 586190 587164 . + 0 ID=cds566;Parent=gene601;gene=hypE;Name=YP_002344056.1;Dbxref=GOA:Q0PAP1 InterPro:IPR000728 InterPro:IPR010918 InterPro:IPR011854 UniProtKB FTrEMBL:Q0PAP1 Genbank:YP_002344056.1 GeneID:904955;gbkey=CDS;product=hydrogenase isoenzymes formation protein;Note=Original 282000 29 note: Cj0626 2C hypE 2C probable hydrogenase isoenzymes formation protein 2C len: 324 aa 3B similar to many e.g. HYPE_ECOLI hydrogenase isoenzymes formation protein 28322 aa 29 2C fasta scores 3B opt: 705 z-score: 923.2 E 28 29: 0 2C 40.4 25 identity in 327 aa overlap. 46.8 25 identity to HP0047. Contains Pfam match to entry PF00586 AIRS 2C AIR synthase related proteins 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Energy metabolism - Respiration 7EPMID:1849603 NC_002163.1 RefSeq region 586649 587098 . + . ID=id1229;gene=hypE;Name=id1229;Dbxref=GeneID:904955;gbkey=misc_feature;Note=HMMPfam hit to PF02769 2C AIR synthase related protein 2C C-terminal dom 2C score 3.7e-36 NC_002163.1 RefSeq region 587164 587505 . + . ID=id1230;gene=hypA;Name=id1230;Dbxref=GeneID:904956;gbkey=misc_feature;Note=HMMPfam hit to PF01155 2C Hydrogenase expression 2Fsynthesis hypA family 2C score 3.3e-50 NC_002163.1 RefSeq gene 587164 587508 . + . ID=gene602;gene=hypA;Name=hypA;locus_tag=Cj0627;Dbxref=GeneID:904956;gbkey=Gene NC_002163.1 RefSeq CDS 587164 587508 . + 0 ID=cds567;Parent=gene602;gene=hypA;Name=YP_002344057.1;Dbxref=GOA:Q9PHP0 InterPro:IPR000688 UniProtKB FSwiss-Prot:Q9PHP0 Genbank:YP_002344057.1 GeneID:904956;gbkey=CDS;product=hydrogenase expression 2Fformation protein;Note=Original 282000 29 note: Cj0627 2C hypA 2C probable hydrogenase isoenzymes formation protein 2C len: 114 aa 3B similar to e.g. HYPA_AZOVI hydrogenase expression 2Fformation protein 28113 aa 29 2C fasta scores 3B opt: 228 z-score: 397.9 E 28 29: 7.2e-15 2C 32.4 25 identity in 111 aa overlap. 39.7 25 identity to HP0869. Contains Pfam match to entry PF01155 HypA 2C Hydrogenase expression 2Fsynthesis hypA family 7EUpdated 282006 29 note: Characterised within Azotobacter vinelandii and Escherichia coli with marginal identity scores. not added to product function. Functional classification - Energy metabolism -Respiration 7EPMID:1849603 2C PMID:1610901 ### NC_002163.1 UTR_Extractor 5'-UTR 587790 587867 . + . ID=utr220;locus_tag=Cj0628;product=putative lipoprotein NC_002163.1 RefSeq CDS 587868 588371 . + 0 ID=cds568a;Parent=gene603;Name=YP_002344058.1;Dbxref=InterPro:IPR005546 UniProtKB FTrEMBL:Q0PAN9 Genbank:YP_002344058.1 GeneID:904958;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj0628 2C probable lipoprotein 2Clen: 171 aa 3B no Hp match. Contains N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. There is a variable poly-T tract at the C-terminus T 284-5 29. T5 causes the ORF to stop here 2C T4 allows translation into the downstream ORF Cj0629. Similar to Cj1677 2842.4 25 identity in 172 aa overlap 29. Cj1677 has a non-variable poly-T tract in an quivalent position 2C which could allow translation into Cj1678 28highly similar to Cj0629 29 7EOriginal 282000 29 note: Cj0629 2C possible lipoprotein 2Clen: 978 aa 3B no Hp match. Contains a variable poly-T tract at the N-terminus T 284-5 29. T5 causes the ORF to start here 2CT4 allows translation from the upstream ORF Cj0628 28which contains a signal sequence and lipid attachment site 29. Highly similar to Cj1678 2890.7 25 identity in 901 aa overlap 29. Cj1678 has a non-variable poly-T tract in an quivalent position 2C which could allow translation from Cj1677 28similar to Cj0628 29 7EUpdated 282006 29 note: Coding sequences have been merged to reflect the complete amino acid sequence for this gene regardless of phase. Previous annotation gave Cj0628 and Cj0629 as seperate CDS. Merging of these CDSs has lead to loss of the downstream CDS. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 587868 591303 . + . ID=gene603;Name=Cj0628;locus_tag=Cj0628;Dbxref=GeneID:904958;gbkey=Gene NC_002163.1 RefSeq region 587946 587978 . + . ID=id1231;Name=id1231;Dbxref=GeneID:904958;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq repeat_region 588369 588378 . + . ID=id1232;Name=id1232;Dbxref=GeneID:904958;gbkey=repeat_region;Note=G 2810 29 NC_002163.1 RefSeq CDS 588373 591303 . + 0 ID=cds568b;Parent=gene603;Name=YP_002344058.1;Dbxref=InterPro:IPR005546 UniProtKB FTrEMBL:Q0PAN9 Genbank:YP_002344058.1 GeneID:904958;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj0628 2C probable lipoprotein 2Clen: 171 aa 3B no Hp match. Contains N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. There is a variable poly-T tract at the C-terminus T 284-5 29. T5 causes the ORF to stop here 2C T4 allows translation into the downstream ORF Cj0629. Similar to Cj1677 2842.4 25 identity in 172 aa overlap 29. Cj1677 has a non-variable poly-T tract in an quivalent position 2C which could allow translation into Cj1678 28highly similar to Cj0629 29 7EOriginal 282000 29 note: Cj0629 2C possible lipoprotein 2Clen: 978 aa 3B no Hp match. Contains a variable poly-T tract at the N-terminus T 284-5 29. T5 causes the ORF to start here 2CT4 allows translation from the upstream ORF Cj0628 28which contains a signal sequence and lipid attachment site 29. Highly similar to Cj1678 2890.7 25 identity in 901 aa overlap 29. Cj1678 has a non-variable poly-T tract in an quivalent position 2C which could allow translation from Cj1677 28similar to Cj0628 29 7EUpdated 282006 29 note: Coding sequences have been merged to reflect the complete amino acid sequence for this gene regardless of phase. Previous annotation gave Cj0628 and Cj0629 as seperate CDS. Merging of these CDSs has lead to loss of the downstream CDS. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq repeat_region 588981 591400 . + . ID=id1233;Name=id1233;gbkey=repeat_region;Note=repeat 2: identical to 1598048..1600468 NC_002163.1 RefSeq region 590479 591276 . + . ID=id1234;Name=id1234;Dbxref=GeneID:904958;gbkey=misc_feature;Note=HMMPfam hit to PF03797 2C Autotransporter beta-domain 2C score 5.9e-38 NC_002163.1 RefSeq gene 591313 591426 . + . ID=NC_002163.1:CJnc30;Name=NC_002163.1:CJnc30;locus_tag=CJnc30 NC_002163.1 RefSeq sRNA 591313 591426 . + . ID=NC_002163.1:CJnc30:unknown_transcript_1;Parent=NC_002163.1:CJnc30;Name=NC_002163.1:CJnc30:unknown_transcript_1;locus_tag=CJnc30;gbkey=misc_RNA;product=CJnc30 NC_002163.1 RefSeq sRNA 591356 591456 . - . ID=NC_002163.1:CJnc40:unknown_transcript_1;Parent=NC_002163.1:CJnc40;Name=NC_002163.1:CJnc40:unknown_transcript_1;locus_tag=CJnc40;gbkey=misc_RNA;product=CJnc40 NC_002163.1 RefSeq gene 591356 591456 . - . ID=NC_002163.1:CJnc40;Name=NC_002163.1:CJnc40;locus_tag=CJnc40 ### NC_002163.1 RefSeq CDS 591537 592502 . - 0 ID=cds569;Parent=gene604;Name=YP_002344059.1;Dbxref=GOA:Q0PAN8 InterPro:IPR010372 UniProtKB FTrEMBL:Q0PAN8 Genbank:YP_002344059.1 GeneID:904888;gbkey=CDS;product=DNA polymerase III subunit delta;Note=required for the assembly and function of the DNAX complex which is required for the assembly of the beta subunit onto primed DNA NC_002163.1 RefSeq gene 591537 592502 . - . ID=gene604;Name=Cj0630c;locus_tag=Cj0630c;Dbxref=GeneID:904888;gbkey=Gene NC_002163.1 RefSeq region 591576 592448 . - . ID=id1235;Name=id1235;Dbxref=GeneID:904888;gbkey=misc_feature;Note=HMMPfam hit to PF06144 2C DNA polymerase III 2C delta subunit 2C score 0.0012 NC_002163.1 RefSeq gene 592495 594429 . - . ID=gene605;Name=Cj0631c;locus_tag=Cj0631c;Dbxref=GeneID:904960;gbkey=Gene NC_002163.1 RefSeq CDS 592495 594429 . - 0 ID=cds570;Parent=gene605;Name=YP_002344060.1;Dbxref=GOA:Q0PAN7 InterPro:IPR001900 InterPro:IPR004476 InterPro:IPR013223 UniProtKB FTrEMBL:Q0PAN7 Genbank:YP_002344060.1 GeneID:904960;gbkey=CDS;product=ribonuclease;Note=Original 282000 29 note: Cj0631c 2C possible ribonuclease 2C len: 644 aa 3B similar to members of the ribonuclease II 28RNB 29 family 2C e.g. VACB_ECOLI VACB protein 28813 aa 29 2C fasta scores 3B opt: 503 z-score: 829.1 E 28 29: 0 2C31.0 25 identity in 580 aa overlap. 35.1 25 identity to HP1248. Contains PS01175 Ribonuclease II family signature 2Cand Pfam match to entry PF00773 RNB 2C RNB-like proteins 7EUpdated 282006 29 note: Some characterisation within Escherichia coli 2C however 2C identity scores were marginal. kept within product function. Functional classification - Degradation of macromolecules 7EPMID:9603904 NC_002163.1 UTR_Extractor 5'-UTR 592503 592524 . - . ID=utr221;locus_tag=Cj0630c;product=DNA polymerase III subunit delta NC_002163.1 RefSeq region 592870 592944 . - . ID=id1236;Name=id1236;Dbxref=GeneID:904960;gbkey=misc_feature;Note=PS01175 Ribonuclease II family signature NC_002163.1 RefSeq region 592957 594024 . - . ID=id1237;Name=id1237;Dbxref=GeneID:904960;gbkey=misc_feature;Note=HMMPfam hit to PF00773 2C RNB-like protein 2C score 1.9e-59 ### NC_002163.1 UTR_Extractor 5'-UTR 594430 594462 . - . ID=utr222;locus_tag=Cj0631c;product=putative ribonuclease NC_002163.1 UTR_Extractor 5'-UTR 594519 594547 . + . ID=utr223;locus_tag=Cj0632;product=ketol-acid reductoisomerase NC_002163.1 RefSeq gene 594548 595570 . + . ID=gene606;gene=ilvC;Name=ilvC;locus_tag=Cj0632;Dbxref=GeneID:904961;gbkey=Gene NC_002163.1 RefSeq CDS 594548 595570 . + 0 ID=cds571;Parent=gene606;gene=ilvC;Name=YP_002344061.1;Dbxref=GOA:Q9PHN5 HSSP:Q9HVA2 InterPro:IPR000506 InterPro:IPR013023 InterPro:IPR013116 InterPro:IPR016040 UniProtKB FSwiss-Prot:Q9PHN5 Genbank:YP_002344061.1 GeneID:904961;gbkey=CDS;product=ketol-acid reductoisomerase;Note=catalyzes the formation of 28R 29-2 2C3-dihydroxy-3-methylbutanoate from 28S 29-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis NC_002163.1 RefSeq region 595100 595537 . + . ID=id1238;gene=ilvC;Name=id1238;Dbxref=GeneID:904961;gbkey=misc_feature;Note=HMMPfam hit to PF01450 2C Acetohydroxy acid isomeroreductase 2C catalyti 2C score 2e-84 ### NC_002163.1 RefSeq CDS 595574 596656 . + 0 ID=cds572;Parent=gene607;Name=YP_002344062.1;Dbxref=GOA:Q0PAN5 InterPro:IPR006837 UniProtKB FTrEMBL:Q0PAN5 Genbank:YP_002344062.1 GeneID:904962;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0633 2C probable periplasmic protein 2C len: 360 aa 3B similar in C-terminus to hypothetical proteins e.g. TR:O51711 28EMBL:AE001176 29 Borrelia burgdorferi BB0770 28293 aa 29 2C fasta scores 3B opt: 425 z-score: 553.2 E 28 29: 1.6e-23 2C 36.3 25 identity in 237 aa overlap. No Hp match. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF04748 Divergent polysaccharide deacetylase identified within CDS. No specific characterisation has been carried out yet. Product function unchanged. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 595574 596656 . + . ID=gene607;Name=Cj0633;locus_tag=Cj0633;Dbxref=GeneID:904962;gbkey=Gene NC_002163.1 RefSeq region 595607 595666 . + . ID=id1239;Name=id1239;Dbxref=GeneID:904962;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0633 by TMHMM2.0 at aa 12-31 NC_002163.1 RefSeq region 596024 596650 . + . ID=id1240;Name=id1240;Dbxref=GeneID:904962;gbkey=misc_feature;Note=HMMPfam hit to PF04748 2C Divergent polysaccharide deacetylase 2C score 1.4e-112 NC_002163.1 RefSeq CDS 596646 597419 . + 0 ID=cds573;Parent=gene608;gene=dprA;Name=YP_002344063.1;Dbxref=GOA:Q0PAN4 InterPro:IPR003488 UniProtKB FTrEMBL:Q0PAN4 Genbank:YP_002344063.1 GeneID:904964;gbkey=CDS;product=DNA processing protein A;Note=Original 282000 29 note: Cj0634 2C unknown 2C len: 257 aa 3B similar 2C in part 2C to members of the SMF family e.g. SMF_HAEIN SMF protein 28DNA processing chain A 29 28373 aa 29 2Cfasta scores 3B opt: 329 z-score: 487.6 E 28 29: 7.2e-20 2C 31.5 25 identity in 213 aa overlap. 48.8 25 identity to HP0333 7EUpdated 282006 29 note: Pfam domain PF02481 SMF family identified within CDS. Further support given to product function. Literature search identified Campylobacter jejuni characterising paper. Product modified to more specific family member. Functional classification - DNA replication 2C restriction 2Fmodification 2C recombination and repair 7EPMID:16194595 NC_002163.1 RefSeq gene 596646 597419 . + . ID=gene608;gene=dprA;Name=dprA;locus_tag=Cj0634;Dbxref=GeneID:904964;gbkey=Gene NC_002163.1 RefSeq region 596649 597236 . + . ID=id1241;gene=dprA;Name=id1241;Dbxref=GeneID:904964;gbkey=misc_feature;Note=HMMPfam hit to PF02481 2C SMF family 2C score 2e-53 NC_002163.1 RefSeq region 597416 597796 . + . ID=id1242;Name=id1242;Dbxref=GeneID:904965;gbkey=misc_feature;Note=HMMPfam hit to PF03652 2C Uncharacterised protein family 28UPF0081 29 2C score 1e-52 NC_002163.1 RefSeq CDS 597416 597799 . + 0 ID=cds574;Parent=gene609;Name=YP_002344064.1;Dbxref=GOA:Q9PHN2 InterPro:IPR005227 InterPro:IPR006641 UniProtKB FSwiss-Prot:Q9PHN2 Genbank:YP_002344064.1 GeneID:904965;gbkey=CDS;product=Holliday junction resolvase-like protein;Note=similar to RuvC resolvase with substantial differences 3B NMR structural information suggests this protein is monomeric 3B unknown cellular function NC_002163.1 RefSeq gene 597416 597799 . + . ID=gene609;gene=Cj0635;Name=Cj0635;locus_tag=Cj0635;Dbxref=GeneID:904965;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 597574 597827 . + . ID=utr224;locus_tag=Cj0636;product=NOL1 2FNOP2 2Fsun family protein ### NC_002163.1 RefSeq gene 597828 598667 . + . ID=gene610;Name=Cj0636;locus_tag=Cj0636;Dbxref=GeneID:904966;gbkey=Gene NC_002163.1 RefSeq CDS 597828 598667 . + 0 ID=cds575;Parent=gene610;Name=YP_002344065.1;Dbxref=InterPro:IPR001678 UniProtKB FTrEMBL:Q0PAN2 Genbank:YP_002344065.1 GeneID:904966;gbkey=CDS;product=NOL1 2FNOP2 2Fsun family protein;Note=Original 282000 29 note: Cj0636 2C unknown 2C len: 279 aa 3B similar to members of the NOL1 2FNOP2 2Fsun family e.g. Y026_METJA MJ0026 28274 aa 29 2C fasta scores 3B opt: 422 z-score: 688.4 E 28 29: 4.8e-31 2C 33.9 25 identity in 280 aa overlap. No Hp match. Contains Pfam match to entry PF01189 Nol1_Nop2_Sun 2C NOL1 2FNOP2 2Fsun family. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq region 597837 598655 . + . ID=id1243;Name=id1243;Dbxref=GeneID:904966;gbkey=misc_feature;Note=HMMPfam hit to PF01189 2C NOL1 2FNOP2 2Fsun family 2C score 2.4e-30 ### NC_002163.1 RefSeq gene 598843 599340 . - . ID=gene611;gene=mrsA;Name=mrsA;locus_tag=Cj0637c;Dbxref=GeneID:904967;gbkey=Gene NC_002163.1 RefSeq CDS 598843 599340 . - 0 ID=cds576;Parent=gene611;gene=mrsA;Name=YP_002344066.1;Dbxref=GOA:Q9PHN0 HSSP:P54149 InterPro:IPR002569 UniProtKB FSwiss-Prot:Q9PHN0 Genbank:YP_002344066.1 GeneID:904967;gbkey=CDS;product=methionine sulfoxide reductase A;Note=this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form 3B provides protection against oxidative stress NC_002163.1 RefSeq region 598873 599337 . - . ID=id1244;gene=mrsA;Name=id1244;Dbxref=GeneID:904967;gbkey=misc_feature;Note=HMMPfam hit to PF01625 2C Peptide methionine sulfoxide reductase 2C score 2.4e-66 ### NC_002163.1 RefSeq CDS 599381 599899 . - 0 ID=cds577;Parent=gene612;gene=ppa;Name=YP_002344067.1;Dbxref=GOA:Q9PHM9 HSSP:P17288 InterPro:IPR008162 UniProtKB FSwiss-Prot:Q9PHM9 Genbank:YP_002344067.1 GeneID:904968;gbkey=CDS;product=inorganic pyrophosphatase;Note=Original 282000 29 note: Cj0638c 2C ppa 2C probable inorganic pyrophosphatase 2C len: 172 aa 3B highly similar to many e.g. IPYR_ECOLI inorganic pyrophosphatase 28EC 3.6.1.1 29 28175 aa 29 2C fasta scores 3B opt: 564 z-score: 990.9 E 28 29: 0 2C 54.0 25 identity in 161 aa overlap. 59.3 25 identity to HP0620. Contains PS00387 Inorganic pyrophosphatase signature and Pfam match to entry PF00719 Pyrophosphatase 2CInorganic pyrophosphatase 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Literature search identified paper linking protein to glycoprotein 28PMID:12186869 29. Functional classification - Central intermediary metabolism - General 7EPMID:12186869 2C PMID:2848015 2C PMID:9201917 NC_002163.1 RefSeq gene 599381 599899 . - . ID=gene612;gene=ppa;Name=ppa;locus_tag=Cj0638c;Dbxref=GeneID:904968;gbkey=Gene NC_002163.1 RefSeq region 599384 599854 . - . ID=id1245;gene=ppa;Name=id1245;Dbxref=GeneID:904968;gbkey=misc_feature;Note=HMMPfam hit to PF00719 2C Inorganic pyrophosphatase 2Cscore 2.4e-53 NC_002163.1 RefSeq region 599690 599710 . - . ID=id1246;gene=ppa;Name=id1246;Dbxref=GeneID:904968;gbkey=misc_feature;Note=PS00387 Inorganic pyrophosphatase signature ### NC_002163.1 RefSeq CDS 599909 600487 . - 0 ID=cds578;Parent=gene613;gene=adk;Name=YP_002344068.1;Dbxref=GOA:Q9PHM8 HSSP:P43188 InterPro:IPR000850 UniProtKB FSwiss-Prot:Q9PHM8 Genbank:YP_002344068.1 GeneID:904969;gbkey=CDS;product=adenylate kinase;Note=essential enzyme that recycles AMP in active cells 3B converts ATP and AMP to two molecules of ADP NC_002163.1 RefSeq gene 599909 600487 . - . ID=gene613;gene=adk;Name=adk;locus_tag=Cj0639c;Dbxref=GeneID:904969;gbkey=Gene NC_002163.1 RefSeq region 599993 600469 . - . ID=id1247;gene=adk;Name=id1247;Dbxref=GeneID:904969;gbkey=misc_feature;Note=HMMPfam hit to PF00406 2C Adenylate kinase 2C score 2.4e-40 NC_002163.1 RefSeq region 600203 600238 . - . ID=id1248;gene=adk;Name=id1248;Dbxref=GeneID:904969;gbkey=misc_feature;Note=PS00113 Adenylate kinase signature NC_002163.1 RefSeq region 600440 600463 . - . ID=id1249;gene=adk;Name=id1249;Dbxref=GeneID:904969;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq gene 600484 602235 . - . ID=gene614;gene=aspS;Name=aspS;locus_tag=Cj0640c;Dbxref=GeneID:904820;gbkey=Gene NC_002163.1 RefSeq CDS 600484 602235 . - 0 ID=cds579;Parent=gene614;gene=aspS;Name=YP_002344069.1;Dbxref=GOA:Q9PHM7 HSSP:P21889 InterPro:IPR002312 InterPro:IPR004115 InterPro:IPR004364 InterPro:IPR004365 InterPro:IPR004524 InterPro:IPR006195 InterPro:IPR012340 UniProtKB FSwiss-Prot:Q9PHM7 Genbank:YP_002344069.1 GeneID:904820;gbkey=CDS;product=aspartyl-tRNA synthetase;Note=catalyzes a two-step reaction 2C first charging an aspartate molecule by linking its carboxyl group to the alpha-phosphate of ATP 2C followed by transfer of the aminoacyl-adenylate to its tRNA 3B contains discriminating and non-discriminating subtypes NC_002163.1 RefSeq region 600574 601881 . - . ID=id1250;gene=aspS;Name=id1250;Dbxref=GeneID:904820;gbkey=misc_feature;Note=HMMPfam hit to PF00152 2C tRNA synthetases class II 28D 2C K and N 29 2C score 1.8e-24 NC_002163.1 RefSeq region 600628 600657 . - . ID=id1251;gene=aspS;Name=id1251;Dbxref=GeneID:904820;gbkey=misc_feature;Note=PS00339 Aminoacyl-transfer RNA synthetases class-II signature 2 NC_002163.1 RefSeq region 601021 601311 . - . ID=id1252;gene=aspS;Name=id1252;Dbxref=GeneID:904820;gbkey=misc_feature;Note=HMMPfam hit to PF02938 2C GAD domain 2C score 1.9e-31 NC_002163.1 RefSeq region 601531 601584 . - . ID=id1253;gene=aspS;Name=id1253;Dbxref=GeneID:904820;gbkey=misc_feature;Note=PS00179 Aminoacyl-transfer RNA synthetases class-II signature 1 NC_002163.1 RefSeq region 601927 602184 . - . ID=id1254;gene=aspS;Name=id1254;Dbxref=GeneID:904820;gbkey=misc_feature;Note=HMMPfam hit to PF01336 2C OB-fold nucleic acid binding domain 2C score 3.7e-26 ### NC_002163.1 UTR_Extractor 5'-UTR 602236 602268 . - . ID=utr225;locus_tag=Cj0640c;product=aspartyl-tRNA synthetase NC_002163.1 UTR_Extractor 5'-UTR 602326 602326 . + . ID=utr226;locus_tag=Cj0641;product=inorganic polyphosphate 2FATP-NAD kinase NC_002163.1 RefSeq CDS 602326 603186 . + 0 ID=cds580;Parent=gene615;gene=pnk;Name=YP_002344070.1;Dbxref=GOA:Q9PHM6 InterPro:IPR002504 InterPro:IPR017437 UniProtKB FSwiss-Prot:Q9PHM6 Genbank:YP_002344070.1 GeneID:905135;gbkey=CDS;product=inorganic polyphosphate 2FATP-NAD kinase;Note=catalyzes the phosphorylation of NAD to NADP NC_002163.1 RefSeq gene 602326 603186 . + . ID=gene615;gene=pnk;Name=pnk;locus_tag=Cj0641;Dbxref=GeneID:905135;gbkey=Gene NC_002163.1 RefSeq region 602359 603135 . + . ID=id1255;gene=pnk;Name=id1255;Dbxref=GeneID:905135;gbkey=misc_feature;Note=HMMPfam hit to PF01513 2C ATP-NAD kinase 2C score 4.4e-54 NC_002163.1 RefSeq gene 603186 604709 . + . ID=gene616;gene=recN;Name=recN;locus_tag=Cj0642;Dbxref=GeneID:905122;gbkey=Gene NC_002163.1 RefSeq CDS 603186 604709 . + 0 ID=cds581;Parent=gene616;gene=recN;Name=YP_002344071.1;Dbxref=GOA:Q9PHM5 InterPro:IPR003395 UniProtKB FSwiss-Prot:Q9PHM5 Genbank:YP_002344071.1 GeneID:905122;gbkey=CDS;product=DNA repair protein;Note=Original 282000 29 note: Cj0642 2C recN 2C possible DNA repair protein 2C len: 507 aa 3B some similarity to e.g. RECN_BACSU DNA repair protein RECN 28576 aa 29 2C fasta scores 3B opt: 272 z-score: 353.1 E 28 29: 2.3e-12 2C 24.5 25 identity in 559 aa overlap. 36.1 25 identity to HP1393. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 7EUpdated 282006 29 note: Characterised within Bacillus subtilis 2C however 2C identity score was unnacceptable. kept within product function. Functional classification - DNA replication 2Crestriction 2Fmodification 2C recombination and repair 7EPMID:9044256 NC_002163.1 RefSeq region 603270 603293 . + . ID=id1256;gene=recN;Name=id1256;Dbxref=GeneID:905122;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 UTR_Extractor 5'-UTR 604744 604814 . + . ID=utr227;locus_tag=Cj0643;product=two-component response regulator NC_002163.1 RefSeq CDS 604815 606059 . + 0 ID=cds582;Parent=gene617;gene=cbrR;Name=YP_002344072.1;Dbxref=GOA:Q0PAM5 InterPro:IPR000160 InterPro:IPR001789 UniProtKB FTrEMBL:Q0PAM5 Genbank:YP_002344072.1 GeneID:904970;gbkey=CDS;product=two-component response regulator;Note=Original 282000 29 note: Cj0643 2C probable two-component response regulator 2C len: 414 aa 3B similar to e.g. TR:P97018 28EMBL:U67070 29 Aeromonas jandaei response regulator protein RRPX 28415 aa 29 2C fasta scores 3B opt: 597 z-score: 530.0 E 28 29: 3.2e-22 2C 25.8 25 identity in 414 aa overlap 2C andTR:Q46020 28EMBL:L42554 29 Caulobacter crescentus response regulator PLED 28454 aa 29 2C fasta scores 3B opt: 286 z-score: 309.9 E 28 29: 5.8e-10 2C 22.0 25 identity in 451 aa overlap. No Hp ortholog. Contains 2x Pfam match to entry PF00072 response_reg 2C Response regulator receiver domain and Pfam match to entry PF00990 DUF9 2C Domain of unknown function 7EUpdated 282006 29 note: Pfam domain PF00990 has now been annotated as GGDEF domain that often happens to be linked to a regulatory domain. Further support given to product function. Literature search identified paper characterising Cj0643 and confirming it as a two-component response regulator and is designated as CbrR 28Campylobacter bile resistance Regulator 29 protein. Functional classification - Signal transduction 7EPMID:15901688 NC_002163.1 RefSeq gene 604815 606059 . + . ID=gene617;gene=cbrR;Name=cbrR;locus_tag=Cj0643;Dbxref=GeneID:904970;gbkey=Gene NC_002163.1 RefSeq region 604821 605171 . + . ID=id1257;gene=cbrR;Name=id1257;Dbxref=GeneID:904970;gbkey=misc_feature;Note=HMMPfam hit to PF00072 2C Response regulator receiver domain 2C score 3.7e-05 NC_002163.1 RefSeq region 605181 605546 . + . ID=id1258;gene=cbrR;Name=id1258;Dbxref=GeneID:904970;gbkey=misc_feature;Note=HMMPfam hit to PF00072 2C Response regulator receiver domain 2C score 4.3e-07 NC_002163.1 RefSeq region 605559 606041 . + . ID=id1259;gene=cbrR;Name=id1259;Dbxref=GeneID:904970;gbkey=misc_feature;Note=HMMPfam hit to PF00990 2C GGDEF domain 2C score 1.3e-23 NC_002163.1 RefSeq CDS 606050 606865 . + 0 ID=cds583;Parent=gene618;Name=YP_002344073.1;Dbxref=GOA:Q0PAM4 InterPro:IPR001130 InterPro:IPR012278 InterPro:IPR015991 InterPro:IPR015992 UniProtKB FTrEMBL:Q0PAM4 Genbank:YP_002344073.1 GeneID:904971;gbkey=CDS;product=TatD-related deoxyribonuclease;Note=Original 282000 29 note: Cj0644 2C unknown 2C len: 271 aa 3B similar to hypothetical proteins e.g. YABD_BACSU 28255 aa 29 2Cfasta scores 3B opt: 614 z-score: 1024.7 E 28 29: 0 2C 38.6 25 identity in 259 aa overlap. 49.2 25 identity to HP1573. Contains PS01137 Uncharacterized protein family UPF0006 signature 1 and Pfam match to entry PF01026 UPF0006 2CUncharacterized protein family 7EUpdated 282006 29 note: Pfam domain PF01026 TatD related DNase and Prosite domain PS01137 TATD_1 2CTatD-related deoxyribonuclease were identified within CDS. Product modified to more specific family member due to motif match. No specific characterisation carried out yet. kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 606050 606865 . + . ID=gene618;gene=tatD;Name=tatD;locus_tag=Cj0644;Dbxref=GeneID:904971;gbkey=Gene NC_002163.1 RefSeq region 606080 606853 . + . ID=id1260;Name=id1260;Dbxref=GeneID:904971;gbkey=misc_feature;Note=HMMPfam hit to PF01026 2C TatD related DNase 2C score 1.2e-106 NC_002163.1 RefSeq region 606086 606112 . + . ID=id1261;Name=id1261;Dbxref=GeneID:904971;gbkey=misc_feature;Note=PS01137 Uncharacterized protein family UPF0006 signature 1 NC_002163.1 RefSeq region 606581 606628 . + . ID=id1262;Name=id1262;Dbxref=GeneID:904971;gbkey=misc_feature;Note=PS00225 Crystallins beta and gamma 27Greek key 27 motif signature NC_002163.1 RefSeq CDS 606865 607983 . + 0 ID=cds584;Parent=gene619;Name=YP_002344074.1;Dbxref=GOA:Q0PAM3 InterPro:IPR002482 InterPro:IPR008258 UniProtKB FTrEMBL:Q0PAM3 Genbank:YP_002344074.1 GeneID:904972;gbkey=CDS;product=transglycosylase;Note=Original 282000 29 note: Cj0645 2C possible secreted transglycosylase 2C len: 372 aa 3B similar to members of the SLT family e.g. MLTD_ECOLI membrane-bound lytic murein transglycosylase D precursor 28EC 3.2.1.- 29 28452 aa 29 2C fasta scores 3B opt: 425 z-score: 431.3 E 28 29: 1e-16 2C 28.4 25 identity in 348 aa overlap. 37.5 25 identity to HP1572. Contains N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domains PF01464 Transglycosylase SLT domain PF01476 LysM domain were identified within CDS. Further support given to product function. Characterised within Escherichia coli with marginal identity score and only partial alignment. kept within product function. Functional classification - Murein sacculus and peptidoglycan 7EPMID:10843862 NC_002163.1 RefSeq gene 606865 607983 . + . ID=gene619;Name=Cj0645;locus_tag=Cj0645;Dbxref=GeneID:904972;gbkey=Gene NC_002163.1 RefSeq region 607081 607428 . + . ID=id1263;Name=id1263;Dbxref=GeneID:904972;gbkey=misc_feature;Note=HMMPfam hit to PF01464 2C Transglycosylase SLT domain 2C score 1.5e-28 NC_002163.1 RefSeq region 607798 607926 . + . ID=id1264;Name=id1264;Dbxref=GeneID:904972;gbkey=misc_feature;Note=HMMPfam hit to PF01476 2C LysM domain 2C score 1.7e-17 NC_002163.1 RefSeq CDS 607943 608770 . + 0 ID=cds585;Parent=gene620;Name=YP_002344075.1;Dbxref=GOA:Q9PHM1 InterPro:IPR005132 InterPro:IPR007730 InterPro:IPR012997 UniProtKB FSwiss-Prot:Q9PHM1 Genbank:YP_002344075.1 GeneID:904973;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj0646 2C probable lipoprotein 2Clen: 275 aa 3B similar to e.g. RLPA_ECOLI rare lipoprotein A precursor 28362 aa 29 2C fasta scores 3B opt: 251 z-score: 431.7 E 28 29: 9.4e-17 2C 33.6 25 identity in 131 aa overlap. 50.2 25 identity to HP1571. Contains N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site 7EUpdated 282006 29 note: Pfam domain PF03330 Rare lipoprotein A 28RlpA 29-like double-psi beta-barrel was identified within CDS. Product modified to more specific family member due to motif match. No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 607943 608770 . + . ID=gene620;Name=Cj0646;locus_tag=Cj0646;Dbxref=GeneID:904973;gbkey=Gene NC_002163.1 RefSeq region 607961 608029 . + . ID=id1265;Name=id1265;Dbxref=GeneID:904973;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0646 by TMHMM2.0 at aa 7-29 NC_002163.1 RefSeq region 607979 608011 . + . ID=id1266;Name=id1266;Dbxref=GeneID:904973;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 608171 608443 . + . ID=id1267;Name=id1267;Dbxref=GeneID:904973;gbkey=misc_feature;Note=HMMPfam hit to PF03330 2C Rare lipoprotein A 28RlpA 29-like double-psi be 2C score 1.9e-44 ### NC_002163.1 RefSeq CDS 608776 609264 . + 0 ID=cds586;Parent=gene621;Name=YP_002344076.1;Dbxref=GOA:Q0PAM1 InterPro:IPR006549 InterPro:IPR008230 InterPro:IPR010023 InterPro:IPR013200 UniProtKB FTrEMBL:Q0PAM1 Genbank:YP_002344076.1 GeneID:904974;gbkey=CDS;product=HAD-superfamily hydrolase;Note=Original 282000 29 note: Cj0647 2C unknown 2C len: 162 aa 3B similar to hypothetical proteins e.g. YRBI_ECOLI 28188 aa 29 2C fasta scores 3B opt: 322 z-score: 399.6 E 28 29: 5.8e-15 2C40.0 25 identity in 155 aa overlap. 40.9 25 identity to HP1570 7EUpdated 282006 29 note: Pfam domain PF08282 haloacid dehalogenase-like hydrolase was identified by running own search within CDS. Product modified to more specific family member due to motif match. No specific characterisation carried out yet. kept within product function. Some similarity to recently characterised Escherichia coli 3-deoxy-d-manno-octulosonate 8-phosphate phosphatase 2C KdsC 2C however 2C alignment was only partial. Functional classification - Misc 7EPMID:12639950 NC_002163.1 RefSeq gene 608776 609264 . + . ID=gene621;Name=Cj0647;locus_tag=Cj0647;Dbxref=GeneID:904974;gbkey=Gene NC_002163.1 RefSeq CDS 609255 609770 . + 0 ID=cds587;Parent=gene622;Name=YP_002344077.1;Dbxref=InterPro:IPR010664 UniProtKB FTrEMBL:Q0PAM0 Genbank:YP_002344077.1 GeneID:904975;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0648 2C unknwn 2C len: 171 aa 3B no Hp match 7EUpdated 282006 29 note: One probable transmembrane helix predicted by TMHMM2.0. Also 2C one N-terminal signal peptide predicted by SignalP 2.0 HMM. Product function modified to more specific family member. kept within product function. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 609255 609770 . + . ID=gene622;Name=Cj0648;locus_tag=Cj0648;Dbxref=GeneID:904975;gbkey=Gene NC_002163.1 RefSeq region 609267 609320 . + . ID=id1268;Name=id1268;Dbxref=GeneID:904975;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0648 by TMHMM2.0 at aa 5-22 NC_002163.1 RefSeq CDS 609752 610213 . + 0 ID=cds588;Parent=gene623;Name=YP_002344078.1;Dbxref=GOA:Q0PAL9 InterPro:IPR005653 UniProtKB FTrEMBL:Q0PAL9 Genbank:YP_002344078.1 GeneID:904976;gbkey=CDS;product=OstA family protein;Note=Original 282000 29 note: Cj0649 2C unknown 2C len: 153 aa 3B 31.6 25 identity to HP1568 7EUpdated 282006 29 note: Pfam domain PF03968 OstA-like protein was identified within CDS. Product modified to more specific family member due to Pfam match. No specific characterisation has been carried out. kept within product function. Functional classification -Conserved hypothetical proteins 7EPMID:7811102 NC_002163.1 RefSeq gene 609752 610213 . + . ID=gene623;Name=Cj0649;locus_tag=Cj0649;Dbxref=GeneID:904976;gbkey=Gene NC_002163.1 RefSeq region 609764 610210 . + . ID=id1269;Name=id1269;Dbxref=GeneID:904976;gbkey=misc_feature;Note=HMMPfam hit to PF03968 2C OstA-like protein 2C score 5.1e-61 NC_002163.1 UTR_Extractor 5'-UTR 610132 610209 . + . ID=utr228;locus_tag=Cj0650;product=ribosome biogenesis GTP-binding protein YsxC NC_002163.1 RefSeq CDS 610210 610806 . + 0 ID=cds589;Parent=gene624;gene=engB;Name=YP_002344079.1;Dbxref=GOA:Q9PHL7 HSSP:P24253 InterPro:IPR002917 InterPro:IPR005225 InterPro:IPR005289 InterPro:IPR006073 UniProtKB FSwiss-Prot:Q9PHL7 Genbank:YP_002344079.1 GeneID:904977;gbkey=CDS;product=ribosome biogenesis GTP-binding protein YsxC;Note=binds guanine nucleotides 3B in Escherichia coli depletion results in defective cell division and filamentation 3B in Bacillus subtilis this gene is essential NC_002163.1 RefSeq gene 610210 610806 . + . ID=gene624;gene=engB;Name=engB;locus_tag=Cj0650;Dbxref=GeneID:904977;gbkey=Gene NC_002163.1 RefSeq region 610276 610671 . + . ID=id1270;gene=engB;Name=id1270;Dbxref=GeneID:904977;gbkey=misc_feature;Note=HMMPfam hit to PF01926 2C GTPase of unknown function 2Cscore 2.6e-26 NC_002163.1 RefSeq region 610294 610317 . + . ID=id1271;gene=engB;Name=id1271;Dbxref=GeneID:904977;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq gene 610803 611297 . + . ID=gene625;gene=Cj0651;Name=Cj0651;locus_tag=Cj0651;Dbxref=GeneID:904978;gbkey=Gene NC_002163.1 RefSeq CDS 610803 611297 . + 0 ID=cds590;Parent=gene625;Name=YP_002344080.1;Dbxref=UniProtKB FTrEMBL:Q0PAL7 Genbank:YP_002344080.1 GeneID:904978;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0651 2C possible integral membrane protein 2C len: 164 aa 3B no Hp match 7EUpdated 282006 29 note: Five probable transmembrane helices predicted by TMHMM2.0 identified within CDS. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 610836 610889 . + . ID=id1272;Name=id1272;Dbxref=GeneID:904978;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0651 by TMHMM2.0 at aa 12-29 2C 33-52 2C 65-96 2C 111-133 and 140-159 NC_002163.1 RefSeq region 610899 610958 . + . ID=id1272;Name=id1272;Dbxref=GeneID:904978;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0651 by TMHMM2.0 at aa 12-29 2C 33-52 2C 65-96 2C 111-133 and 140-159 NC_002163.1 RefSeq region 610995 611090 . + . ID=id1272;Name=id1272;Dbxref=GeneID:904978;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0651 by TMHMM2.0 at aa 12-29 2C 33-52 2C 65-96 2C 111-133 and 140-159 NC_002163.1 RefSeq region 611133 611201 . + . ID=id1272;Name=id1272;Dbxref=GeneID:904978;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0651 by TMHMM2.0 at aa 12-29 2C 33-52 2C 65-96 2C 111-133 and 140-159 NC_002163.1 RefSeq region 611220 611279 . + . ID=id1272;Name=id1272;Dbxref=GeneID:904978;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0651 by TMHMM2.0 at aa 12-29 2C 33-52 2C 65-96 2C 111-133 and 140-159 ### NC_002163.1 RefSeq CDS 611298 613103 . + 0 ID=cds591;Parent=gene626;gene=pbpC;Name=YP_002344081.1;Dbxref=GOA:Q0PAL6 InterPro:IPR001460 InterPro:IPR005311 InterPro:IPR017790 UniProtKB FTrEMBL:Q0PAL6 Genbank:YP_002344081.1 GeneID:904979;gbkey=CDS;product=penicillin-binding protein;Note=Original 282000 29 note: Cj0652 2C pbpC 2C probable penicillin-binding protein 2C len: 601 aa 3B similar to many e.g. PBP2_ECOLI penicillin-binding protein 2 28PBP-2 29 28633 aa 29 2C fasta scores 3B opt: 954 z-score: 1474.4 E 28 29: 0 2C 32.7 25 identity in 609 aa overlap. 43.5 25 identity to HP1565. Contains Pfam match to entry PF00905 Transpeptidase 2CPenicillin binding protein transpeptidase domain 7EUpdated 282006 29 note: Pfam domain PF03717 Penicillin-binding Protein dimerisation domain was identified within CDS. Further support given to product function. Characterised within Escherichia coli with marginal identity score. not added to product function. Functional classification - Murein sacculus and peptidoglycan 7EPMID:9045804 NC_002163.1 RefSeq gene 611298 613103 . + . ID=gene626;gene=pbpC;Name=pbpC;locus_tag=Cj0652;Dbxref=GeneID:904979;gbkey=Gene NC_002163.1 RefSeq region 611310 611369 . + . ID=id1273;gene=pbpC;Name=id1273;Dbxref=GeneID:904979;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0652 by TMHMM2.0 at aa 5-24 NC_002163.1 RefSeq region 611430 611966 . + . ID=id1274;gene=pbpC;Name=id1274;Dbxref=GeneID:904979;gbkey=misc_feature;Note=HMMPfam hit to PF03717 2C Penicillin-binding Protein dimerisatio 2C score 1.9e-53 NC_002163.1 RefSeq region 612054 613085 . + . ID=id1275;gene=pbpC;Name=id1275;Dbxref=GeneID:904979;gbkey=misc_feature;Note=HMMPfam hit to PF00905 2C Penicillin binding protein transpeptid 2C score 1.5e-64 ### NC_002163.1 RefSeq CDS 613224 615014 . - 0 ID=cds592;Parent=gene627;Name=YP_002344082.1;Dbxref=GOA:Q0PAL5 InterPro:IPR000587 InterPro:IPR000994 UniProtKB FTrEMBL:Q0PAL5 Genbank:YP_002344082.1 GeneID:904980;gbkey=CDS;product=aminopeptidase;Note=Original 282000 29 note: Cj0653c 2C probable aminopeptidase 2C len: 596 aa 3B similar to e.g. TR:O54975 28EMBL:AF038591 29 rattus norvegicus cytoplasmic aminopeptidase P 28623 aa 29 2C fasta scores 3B opt: 763 z-score: 1470.5 E 28 29: 0 2C 36.8 25 identity in 612 aa overlap 2C and TR:O51094 28EMBL:AE001119 29 Borrelia burgdorferi peptidase BB0067 28592 aa 29 2C fasta scores 3B opt: 1234 z-score: 1316.7 E 28 29: 0 2C 41.1 25 identity in 609 aa overlap. 25.8 25 identity to HP1037. Contains Pfam match to entry PF00557 pep_M24 2C metallopeptidase family M24 7EUpdated 282006 29 note: No specific characterisation with acceptable identity scores carried out yet. kept within product function. Functional classification -Degradation of macromolecules - Proteins 2C peptides and glycopeptides NC_002163.1 RefSeq gene 613224 615014 . - . ID=gene627;Name=Cj0653c;locus_tag=Cj0653c;Dbxref=GeneID:904980;gbkey=Gene NC_002163.1 RefSeq region 613434 614093 . - . ID=id1276;Name=id1276;Dbxref=GeneID:904980;gbkey=misc_feature;Note=HMMPfam hit to PF00557 2C metallopeptidase family M24 2C score 3.5e-09 NC_002163.1 RefSeq region 615014 615511 . - . ID=id1277;Name=id1277;Dbxref=GeneID:904981;gbkey=misc_feature;Note=Original 282000 29 note: Cj0654c 2C probable transmembrane transport protein pseudogene 2C len: 1433 bp 3B similar to members of the PTR2 family of transporters. No apparent Hp ortholog. Contains PS01023 PTR2 family proton 2Foligopeptide symporters signature 2 7EUpdated 282006 29 note: Pfam domain PF00854 POT family identified within CDS. Also 2C twelve probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity score has been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification -Transport 2Fbinding proteins - Other NC_002163.1 RefSeq pseudogene 615014 616485 . - . ID=gene628;Name=Cj0654c;locus_tag=Cj0654c;Dbxref=GeneID:904981;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 615015 615069 . - . ID=utr229;locus_tag=Cj0653c;product=putative aminopeptidase NC_002163.1 RefSeq region 615062 615130 . - . ID=id47;Name=id47;Dbxref=GeneID:904981;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0654c by TMHMM2.0 at aa 44-66 2C 76-95 2C 100-122 2C 137-159 2C166-188 2C 215-237 2C 249-267 2C 277-296 2C 350-372 2C 392-414 2C427-446 and 456-478 NC_002163.1 RefSeq region 615158 615217 . - . ID=id47;Name=id47;Dbxref=GeneID:904981;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0654c by TMHMM2.0 at aa 44-66 2C 76-95 2C 100-122 2C 137-159 2C166-188 2C 215-237 2C 249-267 2C 277-296 2C 350-372 2C 392-414 2C427-446 and 456-478 NC_002163.1 RefSeq region 615179 615511 . - . ID=id1278;Name=id1278;Dbxref=GeneID:904981;gbkey=misc_feature;Note=HMMPfam hit to PF00854 2C POT family 2C score 8e-11 NC_002163.1 RefSeq region 615254 615322 . - . ID=id47;Name=id47;Dbxref=GeneID:904981;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0654c by TMHMM2.0 at aa 44-66 2C 76-95 2C 100-122 2C 137-159 2C166-188 2C 215-237 2C 249-267 2C 277-296 2C 350-372 2C 392-414 2C427-446 and 456-478 NC_002163.1 RefSeq region 615380 615448 . - . ID=id47;Name=id47;Dbxref=GeneID:904981;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0654c by TMHMM2.0 at aa 44-66 2C 76-95 2C 100-122 2C 137-159 2C166-188 2C 215-237 2C 249-267 2C 277-296 2C 350-372 2C 392-414 2C427-446 and 456-478 NC_002163.1 RefSeq region 615511 615774 . - . ID=id1278;Name=id1278;Dbxref=GeneID:904981;gbkey=misc_feature;Note=HMMPfam hit to PF00854 2C POT family 2C score 8e-11 NC_002163.1 RefSeq region 615511 615774 . - . ID=id1277;Name=id1277;Dbxref=GeneID:904981;gbkey=misc_feature;Note=Original 282000 29 note: Cj0654c 2C probable transmembrane transport protein pseudogene 2C len: 1433 bp 3B similar to members of the PTR2 family of transporters. No apparent Hp ortholog. Contains PS01023 PTR2 family proton 2Foligopeptide symporters signature 2 7EUpdated 282006 29 note: Pfam domain PF00854 POT family identified within CDS. Also 2C twelve probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity score has been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification -Transport 2Fbinding proteins - Other NC_002163.1 RefSeq region 615607 615666 . - . ID=id47;Name=id47;Dbxref=GeneID:904981;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0654c by TMHMM2.0 at aa 44-66 2C 76-95 2C 100-122 2C 137-159 2C166-188 2C 215-237 2C 249-267 2C 277-296 2C 350-372 2C 392-414 2C427-446 and 456-478 NC_002163.1 RefSeq region 615694 615750 . - . ID=id47;Name=id47;Dbxref=GeneID:904981;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0654c by TMHMM2.0 at aa 44-66 2C 76-95 2C 100-122 2C 137-159 2C166-188 2C 215-237 2C 249-267 2C 277-296 2C 350-372 2C 392-414 2C427-446 and 456-478 NC_002163.1 RefSeq region 615768 616022 . - . ID=id1277;Name=id1277;Dbxref=GeneID:904981;gbkey=misc_feature;Note=Original 282000 29 note: Cj0654c 2C probable transmembrane transport protein pseudogene 2C len: 1433 bp 3B similar to members of the PTR2 family of transporters. No apparent Hp ortholog. Contains PS01023 PTR2 family proton 2Foligopeptide symporters signature 2 7EUpdated 282006 29 note: Pfam domain PF00854 POT family identified within CDS. Also 2C twelve probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity score has been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification -Transport 2Fbinding proteins - Other NC_002163.1 RefSeq region 615768 616022 . - . ID=id1278;Name=id1278;Dbxref=GeneID:904981;gbkey=misc_feature;Note=HMMPfam hit to PF00854 2C POT family 2C score 8e-11 NC_002163.1 RefSeq region 615777 615845 . - . ID=id47;Name=id47;Dbxref=GeneID:904981;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0654c by TMHMM2.0 at aa 44-66 2C 76-95 2C 100-122 2C 137-159 2C166-188 2C 215-237 2C 249-267 2C 277-296 2C 350-372 2C 392-414 2C427-446 and 456-478 NC_002163.1 RefSeq region 615924 615992 . - . ID=id47;Name=id47;Dbxref=GeneID:904981;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0654c by TMHMM2.0 at aa 44-66 2C 76-95 2C 100-122 2C 137-159 2C166-188 2C 215-237 2C 249-267 2C 277-296 2C 350-372 2C 392-414 2C427-446 and 456-478 NC_002163.1 RefSeq region 616011 616022 . - . ID=id47;Name=id47;Dbxref=GeneID:904981;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0654c by TMHMM2.0 at aa 44-66 2C 76-95 2C 100-122 2C 137-159 2C166-188 2C 215-237 2C 249-267 2C 277-296 2C 350-372 2C 392-414 2C427-446 and 456-478 NC_002163.1 RefSeq region 616022 616078 . - . ID=id47;Name=id47;Dbxref=GeneID:904981;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0654c by TMHMM2.0 at aa 44-66 2C 76-95 2C 100-122 2C 137-159 2C166-188 2C 215-237 2C 249-267 2C 277-296 2C 350-372 2C 392-414 2C427-446 and 456-478 NC_002163.1 RefSeq region 616022 616267 . - . ID=id1278;Name=id1278;Dbxref=GeneID:904981;gbkey=misc_feature;Note=HMMPfam hit to PF00854 2C POT family 2C score 8e-11 NC_002163.1 RefSeq region 616022 616267 . - . ID=id1277;Name=id1277;Dbxref=GeneID:904981;gbkey=misc_feature;Note=Original 282000 29 note: Cj0654c 2C probable transmembrane transport protein pseudogene 2C len: 1433 bp 3B similar to members of the PTR2 family of transporters. No apparent Hp ortholog. Contains PS01023 PTR2 family proton 2Foligopeptide symporters signature 2 7EUpdated 282006 29 note: Pfam domain PF00854 POT family identified within CDS. Also 2C twelve probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity score has been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification -Transport 2Fbinding proteins - Other NC_002163.1 RefSeq region 616121 616189 . - . ID=id47;Name=id47;Dbxref=GeneID:904981;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0654c by TMHMM2.0 at aa 44-66 2C 76-95 2C 100-122 2C 137-159 2C166-188 2C 215-237 2C 249-267 2C 277-296 2C 350-372 2C 392-414 2C427-446 and 456-478 NC_002163.1 RefSeq region 616202 616261 . - . ID=id47;Name=id47;Dbxref=GeneID:904981;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0654c by TMHMM2.0 at aa 44-66 2C 76-95 2C 100-122 2C 137-159 2C166-188 2C 215-237 2C 249-267 2C 277-296 2C 350-372 2C 392-414 2C427-446 and 456-478 NC_002163.1 RefSeq region 616267 616269 . - . ID=id1278;Name=id1278;Dbxref=GeneID:904981;gbkey=misc_feature;Note=HMMPfam hit to PF00854 2C POT family 2C score 8e-11 NC_002163.1 RefSeq region 616267 616485 . - . ID=id1277;Name=id1277;Dbxref=GeneID:904981;gbkey=misc_feature;Note=Original 282000 29 note: Cj0654c 2C probable transmembrane transport protein pseudogene 2C len: 1433 bp 3B similar to members of the PTR2 family of transporters. No apparent Hp ortholog. Contains PS01023 PTR2 family proton 2Foligopeptide symporters signature 2 7EUpdated 282006 29 note: Pfam domain PF00854 POT family identified within CDS. Also 2C twelve probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity score has been carried out yet. Thus 2C added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification -Transport 2Fbinding proteins - Other NC_002163.1 RefSeq region 616288 616356 . - . ID=id47;Name=id47;Dbxref=GeneID:904981;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0654c by TMHMM2.0 at aa 44-66 2C 76-95 2C 100-122 2C 137-159 2C166-188 2C 215-237 2C 249-267 2C 277-296 2C 350-372 2C 392-414 2C427-446 and 456-478 ### NC_002163.1 UTR_Extractor 5'-UTR 616486 616559 . - . ID=utr230;locus_tag=Cj0654c;product=pseudo NC_002163.1 RefSeq gene 616572 617120 . - . ID=gene629;Name=Cj0659c;locus_tag=Cj0659c;Dbxref=GeneID:904910;gbkey=Gene NC_002163.1 RefSeq CDS 616572 617120 . - 0 ID=cds593;Parent=gene629;Name=YP_002344083.1;Dbxref=UniProtKB FTrEMBL:Q0PAL4 Genbank:YP_002344083.1 GeneID:904910;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0659c 2C possible periplasmic protein 2C len: 182 aa 3B no Hp match. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: One probable transmembrane helices predicted by TMHMM2.0 identified within CDS. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 617004 617072 . - . ID=id1279;Name=id1279;Dbxref=GeneID:904910;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0659c by TMHMM2.0 at aa 17-39 NC_002163.1 RefSeq gene 617113 618219 . - . ID=gene630;Name=Cj0660c;locus_tag=Cj0660c;Dbxref=GeneID:904982;gbkey=Gene NC_002163.1 RefSeq CDS 617113 618219 . - 0 ID=cds594;Parent=gene630;Name=YP_002344084.1;Dbxref=GOA:Q0PAL3 UniProtKB FTrEMBL:Q0PAL3 Genbank:YP_002344084.1 GeneID:904982;gbkey=CDS;product=transmembrane protein;Note=Original 282000 29 note: Cj0660c 2C possible transmembrane protein 2C len: 368 aa 3B no Hp match. Contains a possible transmembrane domain around aa 220 7EUpdated 282006 29 note: One probable transmembrane helices predicted by TMHMM2.0 identified within CDS. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 617533 617601 . - . ID=id1280;Name=id1280;Dbxref=GeneID:904982;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0660c by TMHMM2.0 at aa 207-229 NC_002163.1 RefSeq CDS 618206 619081 . - 0 ID=cds595;Parent=gene631;gene=era;Name=YP_002344085.1;Dbxref=GOA:Q9PHL1 HSSP:Q9X1F8 InterPro:IPR002917 InterPro:IPR004044 InterPro:IPR005225 InterPro:IPR005662 InterPro:IPR006073 InterPro:IPR015946 UniProtKB FSwiss-Prot:Q9PHL1 Genbank:YP_002344085.1 GeneID:904983;gbkey=CDS;product=GTP-binding protein Era;Note=Era 3B Escherichia coli Ras-like protein 3B Bex 3B Bacillus Era-complementing segment 3B essential protein in Escherichia coli that is involved in many cellular processes 3B GTPase 3B binds the cell membrane through apparent C-terminal domain 3B mutants are arrested during the cell cycle 3B Streptococcus pneumoniae Era binds to RNA and Escherichia coli Era binds 16S rRNA and 30S ribosome NC_002163.1 RefSeq gene 618206 619081 . - . ID=gene631;gene=era;Name=era;locus_tag=Cj0661c;Dbxref=GeneID:904983;gbkey=Gene NC_002163.1 RefSeq region 618218 618412 . - . ID=id1281;gene=era;Name=id1281;Dbxref=GeneID:904983;gbkey=misc_feature;Note=HMMPfam hit to PF07650 2C KH domain 2C score 1.1e-22 NC_002163.1 RefSeq region 618725 619072 . - . ID=id1282;gene=era;Name=id1282;Dbxref=GeneID:904983;gbkey=misc_feature;Note=HMMPfam hit to PF01926 2C GTPase of unknown function 2Cscore 1.5e-31 NC_002163.1 RefSeq region 619031 619054 . - . ID=id1283;gene=era;Name=id1283;Dbxref=GeneID:904983;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 619078 620397 . - 0 ID=cds596;Parent=gene632;gene=hslU;Name=YP_002344086.1;Dbxref=GOA:Q9PHL0 HSSP:P43773 InterPro:IPR003593 InterPro:IPR004491 InterPro:IPR013093 UniProtKB FSwiss-Prot:Q9PHL0 Genbank:YP_002344086.1 GeneID:904984;gbkey=CDS;product=ATP-dependent protease ATP-binding subunit HslU;Note=heat shock protein involved in degradation of misfolded proteins NC_002163.1 RefSeq gene 619078 620397 . - . ID=gene632;gene=hslU;Name=hslU;locus_tag=Cj0662c;Dbxref=GeneID:904984;gbkey=Gene NC_002163.1 RefSeq region 619243 620247 . - . ID=id1284;gene=hslU;Name=id1284;Dbxref=GeneID:904984;gbkey=misc_feature;Note=HMMPfam hit to PF00004 2C ATPase family associated with various cellul 2C score 1.5e-12 NC_002163.1 RefSeq region 619423 620256 . - . ID=id1285;gene=hslU;Name=id1285;Dbxref=GeneID:904984;gbkey=misc_feature;Note=HMMPfam hit to PF07724 2C ATPase family associated with various cellul 2C score 4.8e-44 NC_002163.1 RefSeq region 620209 620232 . - . ID=id1286;gene=hslU;Name=id1286;Dbxref=GeneID:904984;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq gene 620394 620936 . - . ID=gene633;gene=hslV;Name=hslV;locus_tag=Cj0663c;Dbxref=GeneID:904986;gbkey=Gene NC_002163.1 RefSeq CDS 620394 620936 . - 0 ID=cds597;Parent=gene633;gene=hslV;Name=YP_002344087.1;Dbxref=GOA:Q9PHK9 HSSP:Q9WYZ1 InterPro:IPR001353 UniProtKB FSwiss-Prot:Q9PHK9 Genbank:YP_002344087.1 GeneID:904986;gbkey=CDS;product=ATP-dependent protease peptidase subunit;Note=heat shock protein involved in degradation of misfolded proteins NC_002163.1 RefSeq region 620409 620936 . - . ID=id1287;gene=hslV;Name=id1287;Dbxref=GeneID:904986;gbkey=misc_feature;Note=HMMPfam hit to PF00227 2C Proteasome A-type and B-type 2C score 1.2e-44 NC_002163.1 RefSeq gene 620936 621379 . - . ID=gene634;gene=rplI;Name=rplI;locus_tag=Cj0664c;Dbxref=GeneID:904987;gbkey=Gene NC_002163.1 RefSeq CDS 620936 621379 . - 0 ID=cds598;Parent=gene634;gene=rplI;Name=YP_002344088.1;Dbxref=GOA:Q9PHK8 HSSP:P02417 InterPro:IPR000244 UniProtKB FSwiss-Prot:Q9PHK8 Genbank:YP_002344088.1 GeneID:904987;gbkey=CDS;product=50S ribosomal protein L9;Note=in Escherichia coli this protein is wrapped around the base of the L1 stalk NC_002163.1 RefSeq region 620939 621196 . - . ID=id1288;gene=rplI;Name=id1288;Dbxref=GeneID:904987;gbkey=misc_feature;Note=HMMPfam hit to PF03948 2C Ribosomal protein L9 2CC-terminal domai 2C score 3.7e-20 NC_002163.1 RefSeq region 621212 621379 . - . ID=id1289;gene=rplI;Name=id1289;Dbxref=GeneID:904987;gbkey=misc_feature;Note=HMMPfam hit to PF01281 2C Ribosomal protein L9 2CN-terminal domai 2C score 2.9e-21 NC_002163.1 RefSeq region 621260 621343 . - . ID=id1290;gene=rplI;Name=id1290;Dbxref=GeneID:904987;gbkey=misc_feature;Note=PS00651 Ribosomal protein L9 signature ### NC_002163.1 RefSeq CDS 621392 622612 . - 0 ID=cds599;Parent=gene635;gene=argG;Name=YP_002344089.1;Dbxref=GOA:Q9PHK7 InterPro:IPR001518 InterPro:IPR014729 UniProtKB FSwiss-Prot:Q9PHK7 Genbank:YP_002344089.1 GeneID:904988;gbkey=CDS;product=argininosuccinate synthase;Note=catalyzes the formation of 2-N 28omega 29- 28L-arginino 29succinate from L-citrulline and L-aspartate in arginine biosynthesis 2C AMP-forming NC_002163.1 RefSeq gene 621392 622612 . - . ID=gene635;gene=argG;Name=argG;locus_tag=Cj0665c;Dbxref=GeneID:904988;gbkey=Gene NC_002163.1 RefSeq region 621407 622588 . - . ID=id1291;gene=argG;Name=id1291;Dbxref=GeneID:904988;gbkey=misc_feature;Note=HMMPfam hit to PF00764 2C Arginosuccinate synthase 2Cscore 1.7e-193 NC_002163.1 RefSeq region 622217 622252 . - . ID=id1292;gene=argG;Name=id1292;Dbxref=GeneID:904988;gbkey=misc_feature;Note=PS00565 Argininosuccinate synthase signature 2 NC_002163.1 RefSeq region 622556 622582 . - . ID=id1293;gene=argG;Name=id1293;Dbxref=GeneID:904988;gbkey=misc_feature;Note=PS00564 Argininosuccinate synthase signature 1 ### NC_002163.1 UTR_Extractor 5'-UTR 622613 622645 . - . ID=utr231;locus_tag=Cj0665c;product=argininosuccinate synthase NC_002163.1 UTR_Extractor 5'-UTR 622768 622768 . + . ID=utr232;locus_tag=Cj0667;product=putative S4 domain protein NC_002163.1 RefSeq region 622768 622908 . + . ID=id1294;Name=id1294;Dbxref=GeneID:904989;gbkey=misc_feature;Note=HMMPfam hit to PF01479 2C S4 domain 2C score 4.5e-06 NC_002163.1 RefSeq gene 622768 623013 . + . ID=gene636;Name=Cj0667;locus_tag=Cj0667;Dbxref=GeneID:904989;gbkey=Gene NC_002163.1 RefSeq CDS 622768 623013 . + 0 ID=cds600;Parent=gene636;Name=YP_002344090.1;Dbxref=GOA:Q0PAK7 InterPro:IPR002942 UniProtKB FTrEMBL:Q0PAK7 Genbank:YP_002344090.1 GeneID:904989;gbkey=CDS;product=S4 domain-containing protein;Note=Original 282000 29 note: Cj0667 2C unknown 2C len: 81 aa 3B similar to many hypothetical proteins e.g. YABO_BACSU 2886 aa 29 2C fasta scores 3B opt: 149 z-score: 259.2 E 28 29: 3.8e-07 2C35.4 25 identity in 79 aa overlap. 43.6 25 identity to HP1423 7EUpdated 282006 29 note: Pfam domain PF01479 S4 domain was identified within CDS. The S4 domain probably mediates binding to RNA. Product modified to more specific family member due to motif match. No specific characterisation has been carried out. kept within product function. Functional classification - Misc NC_002163.1 RefSeq CDS 623010 623417 . + 0 ID=cds601;Parent=gene637;Name=YP_002344091.1;Dbxref=InterPro:IPR003442 UniProtKB FTrEMBL:Q0PAK6 Genbank:YP_002344091.1 GeneID:904990;gbkey=CDS;product=ATP 2FGTP-binding protein;Note=Original 282000 29 note: Cj0668 2C probable ATP 2FGTP-binding protein 2C len: 135 aa 3B similar to hypothetical proteins e.g. YJEE_ECOLI 28153 aa 29 2C fasta scores 3B opt: 164 z-score: 205.3 E 28 29: 0.00039 2C 33.8 25 identity in 80 aa overlap. 44.2 25 identity to HP0716. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 7EUpdated 282006 29 note: Pfam domain PF02367 Uncharacterised P-loop hydrolase UPF0079 was identified within CDS. No specific characterisation has been carried out yet. kept within product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 623010 623417 . + . ID=gene637;Name=Cj0668;locus_tag=Cj0668;Dbxref=GeneID:904990;gbkey=Gene NC_002163.1 RefSeq region 623049 623402 . + . ID=id1295;Name=id1295;Dbxref=GeneID:904990;gbkey=misc_feature;Note=HMMPfam hit to PF02367 2C Uncharacterised P-loop hydrolase UPF0079 2C score 1e-18 NC_002163.1 RefSeq region 623091 623114 . + . ID=id1296;Name=id1296;Dbxref=GeneID:904990;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 623410 624138 . + 0 ID=cds602;Parent=gene638;Name=YP_002344092.1;Dbxref=GOA:Q0PAK5 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FTrEMBL:Q0PAK5 Genbank:YP_002344092.1 GeneID:905196;gbkey=CDS;product=ABC transporter ATP-binding protein;Note=Original 282000 29 note: Cj0669 2C probable ABC-transporter ATP-binding protein 2C len: 242 aa 3B highly similar to many e.g. YHBG_ECOLI probable ABC transporter ATP-binding protein 28240 aa 29 2C fasta scores 3B opt: 840 z-score: 1144.2 E 28 29: 0 2C 54.2 25 identity in 236 aa overlap. 65.8 25 identity to HP0715. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 and Pfam match to entry PF00005 ABC_tran 2C ABC transporters 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. Appropriate motifs also present. not added to product function. Functional classification -Transport 2Fbinding proteins - Other 7EPMID:16079137 NC_002163.1 RefSeq gene 623410 624138 . + . ID=gene638;Name=Cj0669;locus_tag=Cj0669;Dbxref=GeneID:905196;gbkey=Gene NC_002163.1 RefSeq region 623494 624045 . + . ID=id1297;Name=id1297;Dbxref=GeneID:905196;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 8.9e-62 NC_002163.1 RefSeq region 623515 623538 . + . ID=id1298;Name=id1298;Dbxref=GeneID:905196;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 UTR_Extractor 5'-UTR 623984 624137 . + . ID=utr233;locus_tag=Cj0670;product=RNA polymerase factor sigma-54 NC_002163.1 RefSeq CDS 624138 625388 . + 0 ID=cds603;Parent=gene639;gene=rpoN;Name=YP_002344093.1;Dbxref=GOA:Q0PAK4 InterPro:IPR000394 InterPro:IPR007046 InterPro:IPR007634 UniProtKB FTrEMBL:Q0PAK4 Genbank:YP_002344093.1 GeneID:904991;gbkey=CDS;product=RNA polymerase factor sigma-54;Note=sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released 3B sigma 54 factor is responsible for the expression of enzymes involved in nitrogen assimilation and metabolism 3B the rhizobia often have 2 copies of this sigma factor 3B in Rhizobium etli RpoN1 shown to be involved in the assimilation of several nitrogen and carbon sources during free-living aerobic growth and RpoN2 is involved in symbiotic nitrogen fixation 3B in Bradyrhizobium both RpoN1 and N2 are functional in free-living and symbiotic conditions 2C rpoN1 gene was regulated in response to oxygen NC_002163.1 RefSeq gene 624138 625388 . + . ID=gene639;gene=rpoN;Name=rpoN;locus_tag=Cj0670;Dbxref=GeneID:904991;gbkey=Gene NC_002163.1 RefSeq region 624141 624287 . + . ID=id1299;gene=rpoN;Name=id1299;Dbxref=GeneID:904991;gbkey=misc_feature;Note=HMMPfam hit to PF00309 2C Sigma-54 factor 2C Activator interacting do 2C score 1.3e-15 NC_002163.1 RefSeq region 624357 624893 . + . ID=id1300;gene=rpoN;Name=id1300;Dbxref=GeneID:904991;gbkey=misc_feature;Note=HMMPfam hit to PF04963 2C Sigma-54 factor 2C core binding domain 2C score 3.6e-06 NC_002163.1 RefSeq region 624897 625367 . + . ID=id1301;gene=rpoN;Name=id1301;Dbxref=GeneID:904991;gbkey=misc_feature;Note=HMMPfam hit to PF04552 2C Sigma-54 2C DNA binding domain 2C score 3.7e-83 NC_002163.1 RefSeq region 625305 625328 . + . ID=id1302;gene=rpoN;Name=id1302;Dbxref=GeneID:904991;gbkey=misc_feature;Note=PS00718 Sigma-54 factors family signature 2 ### NC_002163.1 UTR_Extractor 5'-UTR 625520 625551 . + . ID=utr234;locus_tag=Cj0671;product=anaerobic C4-dicarboxylate transporter NC_002163.1 RefSeq CDS 625552 626976 . + 0 ID=cds604;Parent=gene640;gene=dcuB;Name=YP_002344094.1;Dbxref=GOA:Q0PAK3 InterPro:IPR004668 UniProtKB FTrEMBL:Q0PAK3 Genbank:YP_002344094.1 GeneID:904992;gbkey=CDS;product=anaerobic C4-dicarboxylate transporter;Note=functions in anaerobic transport of C4-dicarboxylate compounds such as fumarate 3B similar to DcuA 3B DcuA and DcuB function as independent and mutually redundant C4-dicarboxylate 28aspartate 2C malate 2C fumarate and succinate 29 transporters NC_002163.1 RefSeq gene 625552 626976 . + . ID=gene640;gene=dcuB;Name=dcuB;locus_tag=Cj0671;Dbxref=GeneID:904992;gbkey=Gene NC_002163.1 RefSeq region 625579 625635 . + . ID=id1303;gene=dcuB;Name=id1303;Dbxref=GeneID:904992;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0671 by TMHMM2.0 at aa 10-28 2C 33-52 2C 62-84 2C 105-127 2C147-169 2C 182-204 2C 247-269 2C 294-316 2C 331-353 2C 374-396 2C406-428 and 449-471 NC_002163.1 RefSeq region 625597 626763 . + . ID=id1304;gene=dcuB;Name=id1304;Dbxref=GeneID:904992;gbkey=misc_feature;Note=HMMPfam hit to PF03605 2C Anaerobic c4-dicarboxylate membrane transpo 2C score 4.2e-254 NC_002163.1 RefSeq region 625648 625707 . + . ID=id1303;gene=dcuB;Name=id1303;Dbxref=GeneID:904992;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0671 by TMHMM2.0 at aa 10-28 2C 33-52 2C 62-84 2C 105-127 2C147-169 2C 182-204 2C 247-269 2C 294-316 2C 331-353 2C 374-396 2C406-428 and 449-471 NC_002163.1 RefSeq region 625735 625803 . + . ID=id1303;gene=dcuB;Name=id1303;Dbxref=GeneID:904992;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0671 by TMHMM2.0 at aa 10-28 2C 33-52 2C 62-84 2C 105-127 2C147-169 2C 182-204 2C 247-269 2C 294-316 2C 331-353 2C 374-396 2C406-428 and 449-471 NC_002163.1 RefSeq region 625864 625932 . + . ID=id1303;gene=dcuB;Name=id1303;Dbxref=GeneID:904992;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0671 by TMHMM2.0 at aa 10-28 2C 33-52 2C 62-84 2C 105-127 2C147-169 2C 182-204 2C 247-269 2C 294-316 2C 331-353 2C 374-396 2C406-428 and 449-471 NC_002163.1 RefSeq region 625990 626058 . + . ID=id1303;gene=dcuB;Name=id1303;Dbxref=GeneID:904992;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0671 by TMHMM2.0 at aa 10-28 2C 33-52 2C 62-84 2C 105-127 2C147-169 2C 182-204 2C 247-269 2C 294-316 2C 331-353 2C 374-396 2C406-428 and 449-471 NC_002163.1 RefSeq region 626095 626163 . + . ID=id1303;gene=dcuB;Name=id1303;Dbxref=GeneID:904992;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0671 by TMHMM2.0 at aa 10-28 2C 33-52 2C 62-84 2C 105-127 2C147-169 2C 182-204 2C 247-269 2C 294-316 2C 331-353 2C 374-396 2C406-428 and 449-471 NC_002163.1 RefSeq region 626290 626358 . + . ID=id1303;gene=dcuB;Name=id1303;Dbxref=GeneID:904992;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0671 by TMHMM2.0 at aa 10-28 2C 33-52 2C 62-84 2C 105-127 2C147-169 2C 182-204 2C 247-269 2C 294-316 2C 331-353 2C 374-396 2C406-428 and 449-471 NC_002163.1 RefSeq region 626431 626499 . + . ID=id1303;gene=dcuB;Name=id1303;Dbxref=GeneID:904992;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0671 by TMHMM2.0 at aa 10-28 2C 33-52 2C 62-84 2C 105-127 2C147-169 2C 182-204 2C 247-269 2C 294-316 2C 331-353 2C 374-396 2C406-428 and 449-471 NC_002163.1 RefSeq region 626542 626610 . + . ID=id1303;gene=dcuB;Name=id1303;Dbxref=GeneID:904992;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0671 by TMHMM2.0 at aa 10-28 2C 33-52 2C 62-84 2C 105-127 2C147-169 2C 182-204 2C 247-269 2C 294-316 2C 331-353 2C 374-396 2C406-428 and 449-471 NC_002163.1 RefSeq region 626671 626739 . + . ID=id1303;gene=dcuB;Name=id1303;Dbxref=GeneID:904992;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0671 by TMHMM2.0 at aa 10-28 2C 33-52 2C 62-84 2C 105-127 2C147-169 2C 182-204 2C 247-269 2C 294-316 2C 331-353 2C 374-396 2C406-428 and 449-471 NC_002163.1 RefSeq region 626761 626793 . + . ID=id1305;gene=dcuB;Name=id1305;Dbxref=GeneID:904992;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 626767 626835 . + . ID=id1303;gene=dcuB;Name=id1303;Dbxref=GeneID:904992;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0671 by TMHMM2.0 at aa 10-28 2C 33-52 2C 62-84 2C 105-127 2C147-169 2C 182-204 2C 247-269 2C 294-316 2C 331-353 2C 374-396 2C406-428 and 449-471 NC_002163.1 RefSeq region 626896 626964 . + . ID=id1303;gene=dcuB;Name=id1303;Dbxref=GeneID:904992;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0671 by TMHMM2.0 at aa 10-28 2C 33-52 2C 62-84 2C 105-127 2C147-169 2C 182-204 2C 247-269 2C 294-316 2C 331-353 2C 374-396 2C406-428 and 449-471 NC_002163.1 RefSeq region 626902 626934 . + . ID=id1306;gene=dcuB;Name=id1306;Dbxref=GeneID:904992;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 UTR_Extractor 5'-UTR 627105 627117 . + . ID=utr235;locus_tag=Cj0672;product=putative periplasmic protein NC_002163.1 RefSeq gene 627118 627306 . + . ID=gene641;Name=Cj0672;locus_tag=Cj0672;Dbxref=GeneID:904993;gbkey=Gene NC_002163.1 RefSeq CDS 627118 627306 . + 0 ID=cds605;Parent=gene641;Name=YP_002344095.1;Dbxref=InterPro:IPR011726 UniProtKB FTrEMBL:Q0PAK2 Genbank:YP_002344095.1 GeneID:904993;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0672 2C possible periplasmic protein 2C len: 62 aa 3B no Hp match. Contains possible N-terminal signal sequence and second hydrophobic domain 7EUpdated 282006 29 note: Two probable transmembrane helices predicted by TMHMM2.0. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 627145 627213 . + . ID=id1307;Name=id1307;Dbxref=GeneID:904993;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0672 by TMHMM2.0 at aa 10-32 and 39-58 NC_002163.1 RefSeq region 627232 627291 . + . ID=id1307;Name=id1307;Dbxref=GeneID:904993;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0672 by TMHMM2.0 at aa 10-32 and 39-58 ### NC_002163.1 RefSeq region 627316 627776 . + . ID=id1308;gene=kdpA;Name=id1308;Dbxref=GeneID:904994;gbkey=misc_feature;Note=Original 282000 29 note: Cj0676 2C kdpA 2C probable potassium-transporting ATPase A chain pseudogene 2C len: 1744 bp 3B highly similar to e.g. ATKA_ECOLI potassium-transporting ATPase A chain 28EC 3.6.1.36 29 28557 aa 29. No hp match. Note thay kdpB 28Cj0677 29 is intact 2C while kdpC 28Cj0678 29 is a pseudogene 7EUpdated 282006 29 note: Pfam domain PF03814 Potassium-transporting ATPase A subunit identified within CDS. Also 2C ten probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. Thus 2C not used within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins -Cations 7EPMID:6146979 2C PMID:15919996 NC_002163.1 RefSeq pseudogene 627316 628972 . + . ID=gene642;gene=kdpA;Name=kdpA;locus_tag=Cj0676;Dbxref=GeneID:904994;gbkey=Gene NC_002163.1 RefSeq region 627319 627776 . + . ID=id1309;gene=kdpA;Name=id1309;Dbxref=GeneID:904994;gbkey=misc_feature;Note=HMMPfam hit to PF03814 2C Potassium-transporting ATPase A subunit 2C score 4e-243 NC_002163.1 RefSeq region 627325 627384 . + . ID=id1310;gene=kdpA;Name=id1310;Dbxref=GeneID:904994;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0676 by TMHMM2.0 at aa 4-23 2C 60-82 2C 128-150 2C 163-185 2C242-264 2C 281-300 2C 377-399 2C 416-438 2C 484-506 and 523-545 NC_002163.1 RefSeq region 627493 627561 . + . ID=id1310;gene=kdpA;Name=id1310;Dbxref=GeneID:904994;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0676 by TMHMM2.0 at aa 4-23 2C 60-82 2C 128-150 2C 163-185 2C242-264 2C 281-300 2C 377-399 2C 416-438 2C 484-506 and 523-545 NC_002163.1 RefSeq region 627697 627765 . + . ID=id1310;gene=kdpA;Name=id1310;Dbxref=GeneID:904994;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0676 by TMHMM2.0 at aa 4-23 2C 60-82 2C 128-150 2C 163-185 2C242-264 2C 281-300 2C 377-399 2C 416-438 2C 484-506 and 523-545 NC_002163.1 RefSeq region 627776 628126 . + . ID=id1309;gene=kdpA;Name=id1309;Dbxref=GeneID:904994;gbkey=misc_feature;Note=HMMPfam hit to PF03814 2C Potassium-transporting ATPase A subunit 2C score 4e-243 NC_002163.1 RefSeq region 627776 628126 . + . ID=id1308;gene=kdpA;Name=id1308;Dbxref=GeneID:904994;gbkey=misc_feature;Note=Original 282000 29 note: Cj0676 2C kdpA 2C probable potassium-transporting ATPase A chain pseudogene 2C len: 1744 bp 3B highly similar to e.g. ATKA_ECOLI potassium-transporting ATPase A chain 28EC 3.6.1.36 29 28557 aa 29. No hp match. Note thay kdpB 28Cj0677 29 is intact 2C while kdpC 28Cj0678 29 is a pseudogene 7EUpdated 282006 29 note: Pfam domain PF03814 Potassium-transporting ATPase A subunit identified within CDS. Also 2C ten probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. Thus 2C not used within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins -Cations 7EPMID:6146979 2C PMID:15919996 NC_002163.1 RefSeq region 627801 627869 . + . ID=id1310;gene=kdpA;Name=id1310;Dbxref=GeneID:904994;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0676 by TMHMM2.0 at aa 4-23 2C 60-82 2C 128-150 2C 163-185 2C242-264 2C 281-300 2C 377-399 2C 416-438 2C 484-506 and 523-545 NC_002163.1 RefSeq region 628038 628106 . + . ID=id1310;gene=kdpA;Name=id1310;Dbxref=GeneID:904994;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0676 by TMHMM2.0 at aa 4-23 2C 60-82 2C 128-150 2C 163-185 2C242-264 2C 281-300 2C 377-399 2C 416-438 2C 484-506 and 523-545 NC_002163.1 RefSeq region 628129 628954 . + . ID=id1309;gene=kdpA;Name=id1309;Dbxref=GeneID:904994;gbkey=misc_feature;Note=HMMPfam hit to PF03814 2C Potassium-transporting ATPase A subunit 2C score 4e-243 NC_002163.1 RefSeq region 628129 628972 . + . ID=id1308;gene=kdpA;Name=id1308;Dbxref=GeneID:904994;gbkey=misc_feature;Note=Original 282000 29 note: Cj0676 2C kdpA 2C probable potassium-transporting ATPase A chain pseudogene 2C len: 1744 bp 3B highly similar to e.g. ATKA_ECOLI potassium-transporting ATPase A chain 28EC 3.6.1.36 29 28557 aa 29. No hp match. Note thay kdpB 28Cj0677 29 is intact 2C while kdpC 28Cj0678 29 is a pseudogene 7EUpdated 282006 29 note: Pfam domain PF03814 Potassium-transporting ATPase A subunit identified within CDS. Also 2C ten probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. Thus 2C not used within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins -Cations 7EPMID:6146979 2C PMID:15919996 NC_002163.1 RefSeq region 628157 628216 . + . ID=id1310;gene=kdpA;Name=id1310;Dbxref=GeneID:904994;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0676 by TMHMM2.0 at aa 4-23 2C 60-82 2C 128-150 2C 163-185 2C242-264 2C 281-300 2C 377-399 2C 416-438 2C 484-506 and 523-545 NC_002163.1 RefSeq repeat_region 628170 628178 . + . ID=id1311;gene=kdpA;Name=id1311;Dbxref=GeneID:904994;gbkey=repeat_region;Note=G 289 29 NC_002163.1 RefSeq region 628445 628513 . + . ID=id1310;gene=kdpA;Name=id1310;Dbxref=GeneID:904994;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0676 by TMHMM2.0 at aa 4-23 2C 60-82 2C 128-150 2C 163-185 2C242-264 2C 281-300 2C 377-399 2C 416-438 2C 484-506 and 523-545 NC_002163.1 RefSeq region 628562 628630 . + . ID=id1310;gene=kdpA;Name=id1310;Dbxref=GeneID:904994;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0676 by TMHMM2.0 at aa 4-23 2C 60-82 2C 128-150 2C 163-185 2C242-264 2C 281-300 2C 377-399 2C 416-438 2C 484-506 and 523-545 NC_002163.1 RefSeq region 628766 628834 . + . ID=id1310;gene=kdpA;Name=id1310;Dbxref=GeneID:904994;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0676 by TMHMM2.0 at aa 4-23 2C 60-82 2C 128-150 2C 163-185 2C242-264 2C 281-300 2C 377-399 2C 416-438 2C 484-506 and 523-545 NC_002163.1 RefSeq region 628883 628951 . + . ID=id1310;gene=kdpA;Name=id1310;Dbxref=GeneID:904994;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0676 by TMHMM2.0 at aa 4-23 2C 60-82 2C 128-150 2C 163-185 2C242-264 2C 281-300 2C 377-399 2C 416-438 2C 484-506 and 523-545 ### NC_002163.1 RefSeq CDS 629020 631065 . + 0 ID=cds606;Parent=gene643;gene=kdpB;Name=YP_002344096.1;Dbxref=GOA:Q0PAK1 InterPro:IPR001757 InterPro:IPR002048 InterPro:IPR005834 InterPro:IPR006391 InterPro:IPR008250 UniProtKB FTrEMBL:Q0PAK1 Genbank:YP_002344096.1 GeneID:904995;gbkey=CDS;product=potassium-transporting ATPase subunit B;Note=One of the components of the high-affinity ATP-driven potassium transport 28or KDP 29 system 2C which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions NC_002163.1 RefSeq gene 629020 631065 . + . ID=gene643;gene=kdpB;Name=kdpB;locus_tag=Cj0677;Dbxref=GeneID:904995;gbkey=Gene NC_002163.1 RefSeq region 629119 629187 . + . ID=id1312;gene=kdpB;Name=id1312;Dbxref=GeneID:904995;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0677 by TMHMM2.0 at aa 34-56 2C 66-83 2C 218-240 2C 250-272 2C583-601 2C 611-633 and 646-668 NC_002163.1 RefSeq region 629215 629268 . + . ID=id1312;gene=kdpB;Name=id1312;Dbxref=GeneID:904995;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0677 by TMHMM2.0 at aa 34-56 2C 66-83 2C 218-240 2C 250-272 2C583-601 2C 611-633 and 646-668 NC_002163.1 RefSeq region 629233 629904 . + . ID=id1313;gene=kdpB;Name=id1313;Dbxref=GeneID:904995;gbkey=misc_feature;Note=HMMPfam hit to PF00122 2C E1-E2 ATPase 2C score 4.5e-52 NC_002163.1 RefSeq region 629671 629739 . + . ID=id1312;gene=kdpB;Name=id1312;Dbxref=GeneID:904995;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0677 by TMHMM2.0 at aa 34-56 2C 66-83 2C 218-240 2C 250-272 2C583-601 2C 611-633 and 646-668 NC_002163.1 RefSeq region 629767 629835 . + . ID=id1312;gene=kdpB;Name=id1312;Dbxref=GeneID:904995;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0677 by TMHMM2.0 at aa 34-56 2C 66-83 2C 218-240 2C 250-272 2C583-601 2C 611-633 and 646-668 NC_002163.1 RefSeq region 629914 630624 . + . ID=id1314;gene=kdpB;Name=id1314;Dbxref=GeneID:904995;gbkey=misc_feature;Note=HMMPfam hit to PF00702 2C haloacid dehalogenase-like hydrolase 2C score 1.9e-30 NC_002163.1 RefSeq region 629932 629952 . + . ID=id1315;gene=kdpB;Name=id1315;Dbxref=GeneID:904995;gbkey=misc_feature;Note=PS00154 E1-E2 ATPases phosphorylation site NC_002163.1 RefSeq region 630661 630699 . + . ID=id1316;gene=kdpB;Name=id1316;Dbxref=GeneID:904995;gbkey=misc_feature;Note=PS00018 EF-hand calcium-binding domain NC_002163.1 RefSeq region 630766 630822 . + . ID=id1312;gene=kdpB;Name=id1312;Dbxref=GeneID:904995;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0677 by TMHMM2.0 at aa 34-56 2C 66-83 2C 218-240 2C 250-272 2C583-601 2C 611-633 and 646-668 NC_002163.1 RefSeq region 630850 630918 . + . ID=id1312;gene=kdpB;Name=id1312;Dbxref=GeneID:904995;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0677 by TMHMM2.0 at aa 34-56 2C 66-83 2C 218-240 2C 250-272 2C583-601 2C 611-633 and 646-668 NC_002163.1 RefSeq region 630955 631023 . + . ID=id1312;gene=kdpB;Name=id1312;Dbxref=GeneID:904995;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0677 by TMHMM2.0 at aa 34-56 2C 66-83 2C 218-240 2C 250-272 2C583-601 2C 611-633 and 646-668 NC_002163.1 UTR_Extractor 5'-UTR 631002 631066 . + . ID=utr236;locus_tag=Cj0678;product=pseudo ### NC_002163.1 RefSeq region 631067 631075 . + . ID=id1317;gene=kdpC;Name=id1317;Dbxref=GeneID:904996;gbkey=misc_feature;Note=Original 282000 29 note: Cj0678 2C kdpC 2C probable potassium-transporting ATPase C chain pseudogene 2C len: 553 bp 3B similar to e.g. ATKC_ECOLI potassium-transporting ATPase C chain 28EC 3.6.1.36 29 28190 aa 29. No Hp match. Note that kdpA 28Cj0676 29 is a pseudogene 2C but kdpB 28Cj0677 29 is intact 7EUpdated 282006 29 note: Pfam domain PF02669 K 2B-transporting ATPase 2C c chain identified within CDS. Also one probable transmembrane helix predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. Thus 2C not used within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins -Cations 7EPMID:6146979 2C PMID:1532388 NC_002163.1 RefSeq pseudogene 631067 631661 . + . ID=gene644;gene=kdpC;Name=kdpC;locus_tag=Cj0678;Dbxref=GeneID:904996;gbkey=Gene NC_002163.1 RefSeq region 631070 631075 . + . ID=id1318;gene=kdpC;Name=id1318;Dbxref=GeneID:904996;gbkey=misc_feature;Note=HMMPfam hit to PF02669 2C K 2B-transporting ATPase 2C c chain 2C score 8.8e-32 NC_002163.1 RefSeq region 631077 631459 . + . ID=id1318;gene=kdpC;Name=id1318;Dbxref=GeneID:904996;gbkey=misc_feature;Note=HMMPfam hit to PF02669 2C K 2B-transporting ATPase 2C c chain 2C score 8.8e-32 NC_002163.1 RefSeq region 631077 631469 . + . ID=id1317;gene=kdpC;Name=id1317;Dbxref=GeneID:904996;gbkey=misc_feature;Note=Original 282000 29 note: Cj0678 2C kdpC 2C probable potassium-transporting ATPase C chain pseudogene 2C len: 553 bp 3B similar to e.g. ATKC_ECOLI potassium-transporting ATPase C chain 28EC 3.6.1.36 29 28190 aa 29. No Hp match. Note that kdpA 28Cj0676 29 is a pseudogene 2C but kdpB 28Cj0677 29 is intact 7EUpdated 282006 29 note: Pfam domain PF02669 K 2B-transporting ATPase 2C c chain identified within CDS. Also one probable transmembrane helix predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. Thus 2C not used within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins -Cations 7EPMID:6146979 2C PMID:1532388 NC_002163.1 RefSeq region 631080 631139 . + . ID=id1319;gene=kdpC;Name=id1319;Dbxref=GeneID:904996;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0678 by TMHMM2.0 at aa 5-24 NC_002163.1 RefSeq region 631459 631587 . + . ID=id1317;gene=kdpC;Name=id1317;Dbxref=GeneID:904996;gbkey=misc_feature;Note=Original 282000 29 note: Cj0678 2C kdpC 2C probable potassium-transporting ATPase C chain pseudogene 2C len: 553 bp 3B similar to e.g. ATKC_ECOLI potassium-transporting ATPase C chain 28EC 3.6.1.36 29 28190 aa 29. No Hp match. Note that kdpA 28Cj0676 29 is a pseudogene 2C but kdpB 28Cj0677 29 is intact 7EUpdated 282006 29 note: Pfam domain PF02669 K 2B-transporting ATPase 2C c chain identified within CDS. Also one probable transmembrane helix predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. Thus 2C not used within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins -Cations 7EPMID:6146979 2C PMID:1532388 NC_002163.1 RefSeq region 631469 631587 . + . ID=id1318;gene=kdpC;Name=id1318;Dbxref=GeneID:904996;gbkey=misc_feature;Note=HMMPfam hit to PF02669 2C K 2B-transporting ATPase 2C c chain 2C score 8.8e-32 NC_002163.1 RefSeq region 631587 631649 . + . ID=id1318;gene=kdpC;Name=id1318;Dbxref=GeneID:904996;gbkey=misc_feature;Note=HMMPfam hit to PF02669 2C K 2B-transporting ATPase 2C c chain 2C score 8.8e-32 NC_002163.1 RefSeq region 631587 631661 . + . ID=id1317;gene=kdpC;Name=id1317;Dbxref=GeneID:904996;gbkey=misc_feature;Note=Original 282000 29 note: Cj0678 2C kdpC 2C probable potassium-transporting ATPase C chain pseudogene 2C len: 553 bp 3B similar to e.g. ATKC_ECOLI potassium-transporting ATPase C chain 28EC 3.6.1.36 29 28190 aa 29. No Hp match. Note that kdpA 28Cj0676 29 is a pseudogene 2C but kdpB 28Cj0677 29 is intact 7EUpdated 282006 29 note: Pfam domain PF02669 K 2B-transporting ATPase 2C c chain identified within CDS. Also one probable transmembrane helix predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. Thus 2C not used within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins -Cations 7EPMID:6146979 2C PMID:1532388 ### NC_002163.1 RefSeq pseudogene 631667 633487 . + . ID=gene645;gene=kdpD;Name=kdpD;locus_tag=Cj0679;Dbxref=GeneID:904997;gbkey=Gene NC_002163.1 RefSeq region 631739 632365 . + . ID=id1320;gene=kdpD;Name=id1320;Dbxref=GeneID:904997;gbkey=misc_feature;Note=HMMPfam hit to PF02702 2C Osmosensitive K 2B channel His kinase sensor d 2C score 1.3e-150 NC_002163.1 RefSeq region 632738 632797 . + . ID=id1321;gene=kdpD;Name=id1321;Dbxref=GeneID:904997;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0679 by TMHMM2.0 at aa 358-377 2C 384-403 2C 413-427 2C432-454 and 464-486 NC_002163.1 RefSeq region 632816 632875 . + . ID=id1321;gene=kdpD;Name=id1321;Dbxref=GeneID:904997;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0679 by TMHMM2.0 at aa 358-377 2C 384-403 2C 413-427 2C432-454 and 464-486 NC_002163.1 RefSeq region 632903 632947 . + . ID=id1321;gene=kdpD;Name=id1321;Dbxref=GeneID:904997;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0679 by TMHMM2.0 at aa 358-377 2C 384-403 2C 413-427 2C432-454 and 464-486 NC_002163.1 RefSeq region 632960 633028 . + . ID=id1321;gene=kdpD;Name=id1321;Dbxref=GeneID:904997;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0679 by TMHMM2.0 at aa 358-377 2C 384-403 2C 413-427 2C432-454 and 464-486 NC_002163.1 RefSeq region 633056 633124 . + . ID=id1321;gene=kdpD;Name=id1321;Dbxref=GeneID:904997;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0679 by TMHMM2.0 at aa 358-377 2C 384-403 2C 413-427 2C432-454 and 464-486 ### NC_002163.1 RefSeq CDS 633589 635562 . - 0 ID=cds607;Parent=gene646;gene=uvrB;Name=YP_002344098.1;Dbxref=GOA:Q9PPM7 HSSP:P56981 InterPro:IPR001650 InterPro:IPR001943 InterPro:IPR004807 InterPro:IPR006935 InterPro:IPR014001 InterPro:IPR014021 UniProtKB FSwiss-Prot:Q9PPM7 Genbank:YP_002344098.1 GeneID:904998;gbkey=CDS;product=excinuclease ABC subunit B;Note=The UvrABC repair system catalyzes the recognition and processing of DNA lesions. The beta-hairpin of the Uvr-B subunit is inserted between the strands 2C where it probes for the presence of a lesion NC_002163.1 RefSeq gene 633589 635562 . - . ID=gene646;gene=uvrB;Name=uvrB;locus_tag=Cj0680c;Dbxref=GeneID:904998;gbkey=Gene NC_002163.1 RefSeq region 633592 633699 . - . ID=id1322;gene=uvrB;Name=id1322;Dbxref=GeneID:904998;gbkey=misc_feature;Note=HMMPfam hit to PF02151 2C UvrB 2FuvrC motif 2C score 1.2e-11 NC_002163.1 RefSeq region 633925 634170 . - . ID=id1323;gene=uvrB;Name=id1323;Dbxref=GeneID:904998;gbkey=misc_feature;Note=HMMPfam hit to PF00271 2C Helicase conserved C-terminal domain 2C score 7.4e-18 NC_002163.1 RefSeq region 635182 635541 . - . ID=id1324;gene=uvrB;Name=id1324;Dbxref=GeneID:904998;gbkey=misc_feature;Note=HMMPfam hit to PF04851 2C Type III restriction enzyme 2C res subunit 2C score 1.4e-06 NC_002163.1 RefSeq region 635434 635457 . - . ID=id1325;gene=uvrB;Name=id1325;Dbxref=GeneID:904998;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 UTR_Extractor 5'-UTR 635671 635715 . + . ID=utr237;locus_tag=Cj0681;product=hypothetical protein NC_002163.1 RefSeq CDS 635716 635946 . + 0 ID=cds608;Parent=gene647;Name=YP_002344099.1;Dbxref=UniProtKB FTrEMBL:Q0PAJ8 Genbank:YP_002344099.1 GeneID:904999;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0681 2C unknown 2C len: 76 aa 3B 36.2 25 identity to HP0385. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 635716 635946 . + . ID=gene647;Name=Cj0681;locus_tag=Cj0681;Dbxref=GeneID:904999;gbkey=Gene NC_002163.1 RefSeq CDS 635936 636178 . + 0 ID=cds609;Parent=gene648;Name=YP_002344100.1;Dbxref=UniProtKB FTrEMBL:Q0PAJ7 Genbank:YP_002344100.1 GeneID:905000;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0682 2C unknown 2C len: 80 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 RefSeq gene 635936 636178 . + . ID=gene648;Name=Cj0682;locus_tag=Cj0682;Dbxref=GeneID:905000;gbkey=Gene NC_002163.1 RefSeq gene 636175 636612 . + . ID=gene649;Name=Cj0683;locus_tag=Cj0683;Dbxref=GeneID:905001;gbkey=Gene NC_002163.1 RefSeq CDS 636175 636612 . + 0 ID=cds610;Parent=gene649;Name=YP_002344101.1;Dbxref=GOA:Q0PAJ6 InterPro:IPR012902 UniProtKB FTrEMBL:Q0PAJ6 Genbank:YP_002344101.1 GeneID:905001;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0683 2C probable periplasmic protein 2C len: 145 aa 3B no Hp match 7EUpdated 282006 29 note: One probable transmembrane helices predicted by TMHMM2.0. Further support for product function. Pfam domain PF07963 Prokaryotic N-terminal methylation motif was identified within CDS. The motif is involved in methylation and is said to be found at the N-terminus of pilins and other proteins involved in secretion. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 636181 636252 . + . ID=id1326;Name=id1326;Dbxref=GeneID:905001;gbkey=misc_feature;Note=HMMPfam hit to PF07963 2C Prokaryotic N-terminal methylation motif 2C score 0.0002 NC_002163.1 RefSeq region 636187 636255 . + . ID=id1327;Name=id1327;Dbxref=GeneID:905001;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0683 by TMHMM2.0 at aa 5-27 NC_002163.1 RefSeq CDS 636594 638447 . + 0 ID=cds611;Parent=gene650;gene=priA;Name=YP_002344102.1;Dbxref=GOA:Q0PAJ5 InterPro:IPR001650 InterPro:IPR005259 InterPro:IPR011545 InterPro:IPR014001 InterPro:IPR014021 UniProtKB FTrEMBL:Q0PAJ5 Genbank:YP_002344102.1 GeneID:905002;gbkey=CDS;product=primosome assembly protein PriA;Note=binding of PriA to forked DNA starts the assembly of the primosome 2C also possesses 3 27-5 27 helicase activity NC_002163.1 RefSeq gene 636594 638447 . + . ID=gene650;gene=priA;Name=priA;locus_tag=Cj0684;Dbxref=GeneID:905002;gbkey=Gene NC_002163.1 RefSeq region 636933 637415 . + . ID=id1328;gene=priA;Name=id1328;Dbxref=GeneID:905002;gbkey=misc_feature;Note=HMMPfam hit to PF04851 2C Type III restriction enzyme 2C res subunit 2C score 2e-06 NC_002163.1 RefSeq region 636939 637433 . + . ID=id1329;gene=priA;Name=id1329;Dbxref=GeneID:905002;gbkey=misc_feature;Note=HMMPfam hit to PF00270 2C DEAD 2FDEAH box helicase 2Cscore 9.2e-11 NC_002163.1 RefSeq region 637002 637025 . + . ID=id1330;gene=priA;Name=id1330;Dbxref=GeneID:905002;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 637809 638066 . + . ID=id1331;gene=priA;Name=id1331;Dbxref=GeneID:905002;gbkey=misc_feature;Note=HMMPfam hit to PF00271 2C Helicase conserved C-terminal domain 2C score 2.2e-06 ### NC_002163.1 RefSeq gene 638540 639892 . - . ID=gene651;gene=cipA;Name=cipA;locus_tag=Cj0685c;Dbxref=GeneID:905003;gbkey=Gene NC_002163.1 RefSeq CDS 638540 639892 . - 0 ID=cds612;Parent=gene651;gene=cipA;Name=YP_002344103.1;Dbxref=UniProtKB FTrEMBL:Q0PAJ4 Genbank:YP_002344103.1 GeneID:905003;gbkey=CDS;product=invasion protein CipA;Note=Original 282000 29 note: Cj0685c 2C possible sugar transferase 2C len: 450 aa 3B no Hp match. Contains variable poly-G tract near C-terminus 3B G9 28consensus 29 allows complete translation 2C G10 would cause truncation at aa 233. Some similarity to Cj1421c 2828.0 25 identity in 404 aa overlap 29 and Cj1422c 2825.3 25 identity in 442 aa overlap 29 2Cboth of which contain variable polyG tracts 2C though in different positions. functional assignment is based on family clustering 28BLASTP 29 with other C. jejuni predicted sugar transferases e 2Cg 2C Cj1434c 2C and Cj1438c 7EUpdated 282006 29 note: No specific characterisation carried out yet. kept within product function. Original and updated annotation kept designation as sugar transferase. This gene has now been patented as encoding invasion protein of Campylobacter species. Also 2C work has been carried out within a PhD thesis. Functional classification - Surface polysaccharides 2C lipopolysaccharides and antigens 7Ehttp: 2F 2Fwww.freepatentsonline.com 2F6087105.html 7Ehttp: 2F 2Fwww.collectionscanada.ca 2Fobj 2Fs4 2Ff2 2Fdsk1 2Ftape9 2FPQDD_0004 2FMQ46044.pdf 23search 3D 2522cipA 2520AND 2520campylobacter 2522 NC_002163.1 RefSeq region 638948 638995 . - . ID=id1332;gene=cipA;Name=id1332;Dbxref=GeneID:905003;gbkey=misc_feature;Note=PS00225 Crystallins beta and gamma 27Greek key 27 motif signature ### NC_002163.1 UTR_Extractor 5'-UTR 639893 639915 . - . ID=utr238;locus_tag=Cj0685c;product=invasion protein CipA NC_002163.1 UTR_Extractor 5'-UTR 639972 639997 . + . ID=utr239;locus_tag=Cj0686;product=4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase NC_002163.1 RefSeq gene 639998 641071 . + . ID=gene652;gene=ispG;Name=ispG;locus_tag=Cj0686;Dbxref=GeneID:905004;gbkey=Gene NC_002163.1 RefSeq CDS 639998 641071 . + 0 ID=cds613;Parent=gene652;gene=ispG;Name=YP_002344104.1;Dbxref=GOA:Q9PPM1 InterPro:IPR004588 InterPro:IPR016425 UniProtKB FSwiss-Prot:Q9PPM1 Genbank:YP_002344104.1 GeneID:905004;gbkey=CDS;product=4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase;Note=catalyzes the conversion of 2C-methyl-D-erythritol 2 2C4-cyclodiphosphate into 4-hydroxy-3-methyl-2-en-1-yl diphosphate 3B involved in isoprenoid synthesis NC_002163.1 RefSeq region 640010 641059 . + . ID=id1333;gene=ispG;Name=id1333;Dbxref=GeneID:905004;gbkey=misc_feature;Note=HMMPfam hit to PF04551 2C GcpE protein 2C score 7.5e-248 ### NC_002163.1 RefSeq CDS 641102 641800 . - 0 ID=cds614;Parent=gene653;gene=flgH;Name=YP_002344105.1;Dbxref=GOA:Q9PPM0 InterPro:IPR000527 UniProtKB FSwiss-Prot:Q9PPM0 Genbank:YP_002344105.1 GeneID:905006;gbkey=CDS;product=flagellar basal body L-ring protein;Note=part of the flagellar basal body which consists of four rings L 2CP 2C S and M mounted on a central rod NC_002163.1 RefSeq gene 641102 641800 . - . ID=gene653;gene=flgH;Name=flgH;locus_tag=Cj0687c;Dbxref=GeneID:905006;gbkey=Gene NC_002163.1 RefSeq region 641108 641755 . - . ID=id1334;gene=flgH;Name=id1334;Dbxref=GeneID:905006;gbkey=misc_feature;Note=HMMPfam hit to PF02107 2C Flagellar L-ring protein 2Cscore 2.3e-49 NC_002163.1 RefSeq region 641753 641785 . - . ID=id1335;gene=flgH;Name=id1335;Dbxref=GeneID:905006;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 UTR_Extractor 5'-UTR 641801 641959 . - . ID=utr240;locus_tag=Cj0687c;product=flagellar basal body L-ring protein NC_002163.1 UTR_Extractor 5'-UTR 641848 641889 . + . ID=utr241;locus_tag=Cj0688;product=putative phosphate acetyltransferase NC_002163.1 RefSeq gene 641890 643395 . + . ID=gene654;gene=pta;Name=pta;locus_tag=Cj0688;Dbxref=GeneID:905007;gbkey=Gene NC_002163.1 RefSeq CDS 641890 643395 . + 0 ID=cds615;Parent=gene654;gene=pta;Name=YP_002344106.1;Dbxref=GOA:Q0PAJ1 InterPro:IPR002505 InterPro:IPR004614 UniProtKB FTrEMBL:Q0PAJ1 Genbank:YP_002344106.1 GeneID:905007;gbkey=CDS;product=phosphate acetyltransferase;Note=Original 282000 29 note: Cj0688 2C pta 2C probable phosphate acetyltransferase 2C len: 501 aa 3B highly similar in C-terminus to e.g. PTA_ECOLI phosphate acetyltransferase 28EC 2.3.1.8 29 28713 aa 29 2C fasta scores 3B opt: 1012 z-score: 1161.8 E 28 29: 0 2C 48.8 25 identity in 326 aa overlap. 24.8 25 identity in N-terminus to HP0905 7EUpdated 282006 29 note: Pfam domain PF01515 Phosphate acetyl 2Fbutaryl transferase was identified within CDS. Further support given to product function. Characterised within Escherichia coli with acceptable identity score 2Chowever 2C sequence alignment was only partial. kept within product function. Literature search identified paper linking product function to biofilm formation 28PMID:16436427 29. Functional classification - Degradation -Carbon compounds 7EPMID:16436427 2C PMID:7883769 NC_002163.1 RefSeq region 642427 643380 . + . ID=id1336;gene=pta;Name=id1336;Dbxref=GeneID:905007;gbkey=misc_feature;Note=HMMPfam hit to PF01515 2C Phosphate acetyl 2Fbutaryl transferase 2C score 2e-159 ### NC_002163.1 RefSeq CDS 643409 644599 . + 0 ID=cds616;Parent=gene655;gene=ackA;Name=YP_002344107.1;Dbxref=GOA:Q9PPL8 HSSP:P38502 InterPro:IPR000890 InterPro:IPR002035 InterPro:IPR004372 UniProtKB FSwiss-Prot:Q9PPL8 Genbank:YP_002344107.1 GeneID:905008;gbkey=CDS;product=acetate kinase;Note=AckA utilizes acetate and can acetylate CheY which increases signal strength during flagellar rotation 3B utilizes magnesium and ATP 3B also involved in conversion of acetate to aceyl-CoA NC_002163.1 RefSeq gene 643409 644599 . + . ID=gene655;gene=ackA;Name=ackA;locus_tag=Cj0689;Dbxref=GeneID:905008;gbkey=Gene NC_002163.1 RefSeq region 643412 644569 . + . ID=id1337;gene=ackA;Name=id1337;Dbxref=GeneID:905008;gbkey=misc_feature;Note=HMMPfam hit to PF00871 2C Acetokinase family 2C score 1.4e-188 NC_002163.1 RefSeq region 643415 643450 . + . ID=id1338;gene=ackA;Name=id1338;Dbxref=GeneID:905008;gbkey=misc_feature;Note=PS01075 Acetate and butyrate kinases family signature 1 NC_002163.1 RefSeq region 644009 644062 . + . ID=id1339;gene=ackA;Name=id1339;Dbxref=GeneID:905008;gbkey=misc_feature;Note=PS01076 Acetate and butyrate kinases family signature 2 ### NC_002163.1 RefSeq CDS 644627 648379 . - 0 ID=cds617;Parent=gene656;Name=YP_002344108.1;Dbxref=GOA:Q0PAI9 InterPro:IPR002052 InterPro:IPR002296 InterPro:IPR007409 UniProtKB FTrEMBL:Q0PAI9 Genbank:YP_002344108.1 GeneID:905009;gbkey=CDS;product=restriction 2Fmodification enzyme;Note=Original 282000 29 note: Cj0690c 2C possible restriction 2Fmodification enzyme 2C len: 1250 aa 3B similar to Borrelia burgdorferi plasmid TR:O50698 28EMBL:AE000785 29 hypotheticalprotein BBE02 281277 aa 29 2C fasta scores 3B opt: 1517 z-score: 1607.6 E 28 29: 0 2C 35.0 25 identity in 1304 aa overlap. Very weak similarity to T257_ECOLI type IIS restriction enzyme ECO57I 28997 aa 29 2C fasta scores 3B opt: 156 z-score: 163.4 E 28 29: 0.083 2C 19.6 25 identity in 981 aa overlap. No Hp ortholog. Some simlarity to Cj0031 2825.0 25 identity in 859 aa overlap 29. Contains PS00092 N-6 Adenine-specific DNA methylases signature 7EUpdated 282006 29 note: Pfam domain PF04313 Type I restriction enzyme R protein N terminal was identified within CDS. Further support given to product function. Probable replaced with . Product function modified to more specific family member based on motif match. No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification - DNA replication 2Crestriction 2Fmodification 2C recombination and repair NC_002163.1 RefSeq gene 644627 648379 . - . ID=gene656;Name=Cj0690c;locus_tag=Cj0690c;Dbxref=GeneID:905009;gbkey=Gene NC_002163.1 RefSeq region 646106 646126 . - . ID=id1340;Name=id1340;Dbxref=GeneID:905009;gbkey=misc_feature;Note=PS00092 N-6 Adenine-specific DNA methylases signature NC_002163.1 RefSeq region 647846 648214 . - . ID=id1341;Name=id1341;Dbxref=GeneID:905009;gbkey=misc_feature;Note=HMMPfam hit to PF04313 2C Type I restriction enzyme R protein N termin 2C score 3.1e-21 NC_002163.1 UTR_Extractor 5'-UTR 648266 648528 . + . ID=utr242;locus_tag=Cj0691;product=hypothetical protein NC_002163.1 UTR_Extractor 5'-UTR 648380 648415 . - . ID=utr243;locus_tag=Cj0690c;product=putative restriction 2Fmodification enzyme ### NC_002163.1 RefSeq CDS 648529 649020 . + 0 ID=cds618;Parent=gene657;Name=YP_002344109.1;Dbxref=UniProtKB FTrEMBL:Q0PAI8 Genbank:YP_002344109.1 GeneID:905010;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0691 2C possible membrane protein 2C len: 163 aa 3B no Hp match. Contains two possible transmembrane domains. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 648529 649020 . + . ID=gene657;Name=Cj0691;locus_tag=Cj0691;Dbxref=GeneID:905010;gbkey=Gene NC_002163.1 RefSeq region 648685 648753 . + . ID=id1342;Name=id1342;Dbxref=GeneID:905010;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0691 by TMHMM2.0 at aa 53-75 and 80-102 NC_002163.1 RefSeq region 648766 648834 . + . ID=id1342;Name=id1342;Dbxref=GeneID:905010;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0691 by TMHMM2.0 at aa 53-75 and 80-102 NC_002163.1 RefSeq region 648775 648807 . + . ID=id1343;Name=id1343;Dbxref=GeneID:905010;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq gene 649008 649946 . - . ID=gene658;Name=Cj0692c;locus_tag=Cj0692c;Dbxref=GeneID:905011;gbkey=Gene NC_002163.1 RefSeq CDS 649008 649946 . - 0 ID=cds619;Parent=gene658;Name=YP_002344110.1;Dbxref=UniProtKB FTrEMBL:Q0PAI7 Genbank:YP_002344110.1 GeneID:905011;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0692c 2C possible membrane protein 2C len: 312 aa 3B 34.7 25 identity in N-terminus to HP0708 28114 aa 29. Contains one possible transmembrane domain. Functional classification - Membranes 2Clipoproteins and porins NC_002163.1 RefSeq region 649152 649220 . - . ID=id1344;Name=id1344;Dbxref=GeneID:905011;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0692c by TMHMM2.0 at aa 243-265 NC_002163.1 RefSeq gene 649946 650884 . - . ID=gene659;gene=mraW;Name=mraW;locus_tag=Cj0693c;Dbxref=GeneID:905012;gbkey=Gene NC_002163.1 RefSeq CDS 649946 650884 . - 0 ID=cds620;Parent=gene659;gene=mraW;Name=YP_002344111.1;Dbxref=GOA:Q9PPL4 HSSP:Q9WZX6 InterPro:IPR002903 UniProtKB FSwiss-Prot:Q9PPL4 Genbank:YP_002344111.1 GeneID:905012;gbkey=CDS;product=S-adenosyl-methyltransferase MraW;Note=Original 282000 29 note: Cj0693c 2C unknown 2C len: 312 aa 3B similar to members of the YABC 2FYLXA family of hypothetical proteins e.g. YLXA_BACSU 28311 aa 29 2C fasta scores 3B opt: 584 z-score: 670.8 E 28 29: 4.6e-30 2C 39.8 25 identity in 304 aa overlap. 47.4 25 identity to HP0707 7EUpdated 282006 29 note: Pfam domain PF01795 MraW methylase family was identified within CDS. Characterised within Escherichia coli with marginal identity score. Product modified to more specific family member based on motif and characterisation. not added to product function. EC number and gene name added. Functional classification - Aminoacyl tRNA synthetases and their modification 7EPMID:10572301 NC_002163.1 RefSeq region 649964 650875 . - . ID=id1345;gene=mraW;Name=id1345;Dbxref=GeneID:905012;gbkey=misc_feature;Note=HMMPfam hit to PF01795 2C MraW methylase family 2Cscore 7.1e-110 ### NC_002163.1 UTR_Extractor 5'-UTR 651019 651042 . + . ID=utr244;locus_tag=Cj0694;product=putative periplasmic protein NC_002163.1 RefSeq CDS 651043 652533 . + 0 ID=cds621;Parent=gene660;Name=YP_002344112.1;Dbxref=GOA:Q0PAI5 UniProtKB FTrEMBL:Q0PAI5 Genbank:YP_002344112.1 GeneID:905013;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0694 2C probable periplasmic protein 2C len: 496 aa 3B C-terminus is almost identical to C. jejuni ORF TR:Q46115 28EMBL:X95910 29. 31.9 25 identity toHP0977. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Literature search identified paper linking product function to glycoprotein. Functional classification - Miscellaneous periplasmic proteins 7EPMID:12186869 NC_002163.1 RefSeq gene 651043 652533 . + . ID=gene660;Name=Cj0694;locus_tag=Cj0694;Dbxref=GeneID:905013;gbkey=Gene NC_002163.1 RefSeq region 651076 651144 . + . ID=id1346;Name=id1346;Dbxref=GeneID:905013;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0694 by TMHMM2.0 at aa 12-34 NC_002163.1 RefSeq gene 652530 653918 . + . ID=gene661;gene=ftsA;Name=ftsA;locus_tag=Cj0695;Dbxref=GeneID:905014;gbkey=Gene NC_002163.1 RefSeq CDS 652530 653918 . + 0 ID=cds622;Parent=gene661;gene=ftsA;Name=YP_002344113.1;Dbxref=GOA:Q0PAI4 InterPro:IPR003494 UniProtKB FTrEMBL:Q0PAI4 Genbank:YP_002344113.1 GeneID:905014;gbkey=CDS;product=cell division protein FtsA;Note=Original 282000 29 note: Cj0695 2C ftsA 2C probable cell division protein 2C len: 462 3B identical 2C except for a small frameshift 2C to C. jejuni ftsA TR:Q46116 28EMBL:X95910 29. Similar to many e.g. FTSA_ECOLI cell division protein FTSA 28420 aa 29 2C fasta scores 3B opt: 570 z-score: 635.2 E 28 29: 4.4e-28 2C 27.7 25 identity in 382 aa overlap. 37.2 25 identity to HP0978 7EUpdated 282006 29 note: Pfam domains PF02491 28x2 29 Cell division protein FtsA were identified within CDS. Further support given to product function. Characterisation work has been carried out within Campylobacter jejuni. not added to product function. Functional classification -Cell division 7EPMID:8807806 NC_002163.1 RefSeq region 652542 653105 . + . ID=id1347;gene=ftsA;Name=id1347;Dbxref=GeneID:905014;gbkey=misc_feature;Note=HMMPfam hit to PF02491 2C Cell division protein FtsA 2Cscore 4.3e-31 NC_002163.1 RefSeq region 653070 653102 . + . ID=id1348;gene=ftsA;Name=id1348;Dbxref=GeneID:905014;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 653109 653645 . + . ID=id1349;gene=ftsA;Name=id1349;Dbxref=GeneID:905014;gbkey=misc_feature;Note=HMMPfam hit to PF02491 2C Cell division protein FtsA 2Cscore 2.1e-21 NC_002163.1 UTR_Extractor 5'-UTR 653831 653933 . + . ID=utr245;locus_tag=Cj0696;product=cell division protein FtsZ ### NC_002163.1 RefSeq CDS 653934 655046 . + 0 ID=cds623;Parent=gene662;gene=ftsZ;Name=YP_002344114.1;Dbxref=GOA:Q0PAI3 InterPro:IPR000158 InterPro:IPR003008 InterPro:IPR008280 UniProtKB FTrEMBL:Q0PAI3 Genbank:YP_002344114.1 GeneID:905015;gbkey=CDS;product=cell division protein FtsZ;Note=GTPase 3B similar structure to tubulin 3B forms ring-shaped polymers at the site of cell division 3B other proteins such as FtsA 2C ZipA 2C and ZapA 2C interact with and regulate FtsZ function NC_002163.1 RefSeq gene 653934 655046 . + . ID=gene662;gene=ftsZ;Name=ftsZ;locus_tag=Cj0696;Dbxref=GeneID:905015;gbkey=Gene NC_002163.1 RefSeq region 653976 654557 . + . ID=id1350;gene=ftsZ;Name=id1350;Dbxref=GeneID:905015;gbkey=misc_feature;Note=HMMPfam hit to PF00091 2C Tubulin 2FFtsZ family 2C GTPase domain 2C score 1.9e-81 NC_002163.1 RefSeq region 654231 654296 . + . ID=id1351;gene=ftsZ;Name=id1351;Dbxref=GeneID:905015;gbkey=misc_feature;Note=PS01135 FtsZ protein signature 2 NC_002163.1 RefSeq region 654561 654929 . + . ID=id1352;gene=ftsZ;Name=id1352;Dbxref=GeneID:905015;gbkey=misc_feature;Note=HMMPfam hit to PF03953 2C Tubulin 2FFtsZ family 2CC-terminal domain 2C score 4e-25 ### NC_002163.1 RefSeq CDS 655202 656014 . + 0 ID=cds624;Parent=gene663;gene=flgG2;Name=YP_002344115.1;Dbxref=GOA:Q0PAI2 InterPro:IPR001444 InterPro:IPR010930 UniProtKB FTrEMBL:Q0PAI2 Genbank:YP_002344115.1 GeneID:905016;gbkey=CDS;product=flagellar basal-body rod protein;Note=Original 282000 29 note: Cj0697 2C flgG2 2C probable flagellar basal-body rod protein 2C len: 270 aa 3B similar to e.g. FLGG_ECOLI flagellar basal-body rod protein FLGG 28260 aa 29 2C fasta scores 3B opt: 290 z-score: 318.7 E 28 29: 1.9e-10 2C28.7 25 identity in 272 aa overlap. 42.6 25 identity to HP1092. Also similar to downstream gene Cj0698 28flgG 2C29.9 25 identity in 281 aa overlap 29. Contains PS00588 Flagella basal body rod proteins signature and Pfam match to entry PF00460 flg_bb_rod 2C Flagella basal body rod proteins 7EUpdated 282006 29 note: Characterised within Escherichia coli with marginal identity score. Also 2Ccharacterisation work within Campylobacter jejuni. removed from product function. Functional classification - Surface structures 7EPMID:9931471 2C PMID:15228533 NC_002163.1 RefSeq gene 655202 656014 . + . ID=gene663;gene=flgG2;Name=flgG2;locus_tag=Cj0697;Dbxref=GeneID:905016;gbkey=Gene NC_002163.1 RefSeq region 655214 655306 . + . ID=id1353;gene=flgG2;Name=id1353;Dbxref=GeneID:905016;gbkey=misc_feature;Note=HMMPfam hit to PF00460 2C Flagella basal body rod protein 2C score 9.9e-09 NC_002163.1 RefSeq region 655232 655294 . + . ID=id1354;gene=flgG2;Name=id1354;Dbxref=GeneID:905016;gbkey=misc_feature;Note=PS00588 Flagella basal body rod proteins signature NC_002163.1 RefSeq region 655877 655996 . + . ID=id1355;gene=flgG2;Name=id1355;Dbxref=GeneID:905016;gbkey=misc_feature;Note=HMMPfam hit to PF06429 2C Domain of unknown function 28DUF1078 29 2C score 0.0011 ### NC_002163.1 UTR_Extractor 5'-UTR 656033 656042 . + . ID=utr246;locus_tag=Cj0698;product=flagellar basal body rod protein FlgG NC_002163.1 RefSeq CDS 656043 656834 . + 0 ID=cds625;Parent=gene664;gene=flgG;Name=YP_002344116.1;Dbxref=GOA:Q0PAI1 InterPro:IPR001444 InterPro:IPR010930 InterPro:IPR012834 UniProtKB FTrEMBL:Q0PAI1 Genbank:YP_002344116.1 GeneID:905017;gbkey=CDS;product=flagellar basal body rod protein FlgG;Note=makes up the distal portion of the flagellar basal body rod NC_002163.1 RefSeq gene 656043 656834 . + . ID=gene664;gene=flgG;Name=flgG;locus_tag=Cj0698;Dbxref=GeneID:905017;gbkey=Gene NC_002163.1 RefSeq region 656055 656147 . + . ID=id1356;gene=flgG;Name=id1356;Dbxref=GeneID:905017;gbkey=misc_feature;Note=HMMPfam hit to PF00460 2C Flagella basal body rod protein 2C score 5.6e-13 NC_002163.1 RefSeq region 656073 656135 . + . ID=id1357;gene=flgG;Name=id1357;Dbxref=GeneID:905017;gbkey=misc_feature;Note=PS00588 Flagella basal body rod proteins signature NC_002163.1 RefSeq region 656709 656825 . + . ID=id1358;gene=flgG;Name=id1358;Dbxref=GeneID:905017;gbkey=misc_feature;Note=HMMPfam hit to PF06429 2C Domain of unknown function 28DUF1078 29 2C score 1.2e-19 ### NC_002163.1 RefSeq CDS 656901 658331 . - 0 ID=cds626;Parent=gene665;gene=glnA;Name=YP_002344117.1;Dbxref=GOA:Q0PAI0 InterPro:IPR004809 InterPro:IPR008146 InterPro:IPR008147 InterPro:IPR014746 UniProtKB FTrEMBL:Q0PAI0 Genbank:YP_002344117.1 GeneID:905018;gbkey=CDS;product=glutamine synthetase;Note=Original 282000 29 note: Cj0699c 2C glnA 2C probable glutamine synthetase 2C len: 476 aa 3B highly similar to many e.g. GLNA_ECOLI glutamine synthetase 28EC 6.3.1.2 29 28468 aa 29 2C fasta scores 3B opt: 1529 z-score: 1812.8 E 28 29: 0 2C51.5 25 identity in 462 aa overlap. 63.6 25 identity to HP0512. Contains PS00180 Glutamine synthetase signature 1 2CPS00181 Glutamine synthetase ATP-binding region signature 2C and Pfam match to entry PF00120 gln-synt 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Amino acid biosynthesis - Glutamate family 7EPMID:2882477 NC_002163.1 RefSeq gene 656901 658331 . - . ID=gene665;gene=glnA;Name=glnA;locus_tag=Cj0699c;Dbxref=GeneID:905018;gbkey=Gene NC_002163.1 RefSeq region 657165 658013 . - . ID=id1359;gene=glnA;Name=id1359;Dbxref=GeneID:905018;gbkey=misc_feature;Note=HMMPfam hit to PF00120 2C Glutamine synthetase 2Ccatalytic domain 2C score 8.5e-160 NC_002163.1 RefSeq region 657495 657542 . - . ID=id1360;gene=glnA;Name=id1360;Dbxref=GeneID:905018;gbkey=misc_feature;Note=PS00181 Glutamine synthetase ATP-binding region signature NC_002163.1 RefSeq region 658029 658277 . - . ID=id1361;gene=glnA;Name=id1361;Dbxref=GeneID:905018;gbkey=misc_feature;Note=HMMPfam hit to PF03951 2C Glutamine synthetase 2Cbeta-Grasp domain 2C score 6e-42 NC_002163.1 RefSeq region 658113 658169 . - . ID=id1362;gene=glnA;Name=id1362;Dbxref=GeneID:905018;gbkey=misc_feature;Note=PS00180 Glutamine synthetase signature 1 ### NC_002163.1 UTR_Extractor 5'-UTR 658498 658533 . + . ID=utr247;locus_tag=Cj0700;product=hypothetical protein NC_002163.1 RefSeq CDS 658534 659229 . + 0 ID=cds627;Parent=gene666;Name=YP_002344118.1;Dbxref=GOA:Q0PAH9 UniProtKB FTrEMBL:Q0PAH9 Genbank:YP_002344118.1 GeneID:905019;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0700 2C unknown 2C len: 231 aa 3B 49.4 25 identity to HP0170. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 658534 659229 . + . ID=gene666;Name=Cj0700;locus_tag=Cj0700;Dbxref=GeneID:905019;gbkey=Gene NC_002163.1 RefSeq CDS 659226 660479 . + 0 ID=cds628;Parent=gene667;Name=YP_002344119.1;Dbxref=GOA:Q0PAH8 InterPro:IPR001539 UniProtKB FTrEMBL:Q0PAH8 Genbank:YP_002344119.1 GeneID:905020;gbkey=CDS;product=protease;Note=Original 282000 29 note: Cj0701 2C probable protease 2Clen: 417 aa 3B similar to many proteases belonging to the peptidase family U32 2C e.g. YEGQ_ECOLI protease in baer-ogrk intergenic Region 28453 aa 29 2C fasta scores 3B opt: 567 z-score: 648.6 E 28 29: 7.9e-29 2C 34.9 25 identity in 404 aa overlap. 55.5 25 identity to HP0169. Contains PS01276 Peptidase family U32 signature and Pfam match to entry PF01136 Peptidase_U32 7EUpdated 282006 29 note: Similar to many with marginal identity scores. kept within product function. Functional classification - Degradation of macromolecules - Proteins 2C peptides and glycopeptides NC_002163.1 RefSeq gene 659226 660479 . + . ID=gene667;Name=Cj0701;locus_tag=Cj0701;Dbxref=GeneID:905020;gbkey=Gene NC_002163.1 RefSeq region 659451 660149 . + . ID=id1363;Name=id1363;Dbxref=GeneID:905020;gbkey=misc_feature;Note=HMMPfam hit to PF01136 2C Peptidase family U32 2C score 8.5e-117 NC_002163.1 RefSeq region 659709 659765 . + . ID=id1364;Name=id1364;Dbxref=GeneID:905020;gbkey=misc_feature;Note=PS01276 Peptidase family U32 signature ### NC_002163.1 RefSeq gene 660480 660974 . + . ID=gene668;gene=purE;Name=purE;locus_tag=Cj0702;Dbxref=GeneID:905021;gbkey=Gene NC_002163.1 RefSeq CDS 660480 660974 . + 0 ID=cds629;Parent=gene668;gene=purE;Name=YP_002344120.1;Dbxref=GOA:Q0PAH7 InterPro:IPR000031 UniProtKB FTrEMBL:Q0PAH7 Genbank:YP_002344120.1 GeneID:905021;gbkey=CDS;product=phosphoribosylaminoimidazole carboxylase catalytic subunit;Note=Original 282000 29 note: Cj0702 2C purE 2C probable phosphoribosylaminoimidazole carboxylase catalytic subunit 2C len: 164 aa 3B similar to many e.g. PUR6_ECOLI phosphoribosylaminoimidazole carboxylase catalytic subunit 28EC 4.1.1.21 29 28168 aa 29 2C fasta scores 3B opt: 485 z-score: 562.6 E 28 29: 4.9e-24 2C 55.2 25 identity in 143 aa overlap. No Hp match. Contains Pfam match to entry PF00731 AIRC 2C AIR carboxylase 7EUpdated 282006 29 note: Characterised within Escherichia coli and Bacillus subtilus with acceptable identity scores. not added to product function. Functional classification - Purine ribonucleotide biosynthesis 7EPMID:10074353 2C PMID:2464576 NC_002163.1 RefSeq region 660489 660959 . + . ID=id1365;gene=purE;Name=id1365;Dbxref=GeneID:905021;gbkey=misc_feature;Note=HMMPfam hit to PF00731 2C AIR carboxylase 2C score 1.1e-72 ### NC_002163.1 RefSeq gene 660984 661520 . + . ID=gene669;Name=Cj0703;locus_tag=Cj0703;Dbxref=GeneID:905022;gbkey=Gene NC_002163.1 RefSeq CDS 660984 661520 . + 0 ID=cds630;Parent=gene669;Name=YP_002344121.1;Dbxref=UniProtKB FTrEMBL:Q0PAH6 Genbank:YP_002344121.1 GeneID:905022;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0703 2C unknown 2C len: 178 aa 3B 51.0 25 identity to HP0406. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq CDS 661532 662395 . + 0 ID=cds631;Parent=gene670;gene=glyQ;Name=YP_002344122.1;Dbxref=GOA:Q9PPK3 HSSP:Q9WY59 InterPro:IPR002310 InterPro:IPR006194 UniProtKB FSwiss-Prot:Q9PPK3 Genbank:YP_002344122.1 GeneID:905023;gbkey=CDS;product=glycyl-tRNA synthetase subunit alpha;Note=glycine--tRNA ligase alpha chain 3B GlyRS 3B class II aminoacyl tRNA synthetase 3B tetramer of alpha 282 29beta 282 29 3B catalyzes a two-step reaction 3B first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP 3B second by transfer of the aminoacyl-adenylate to its tRNA NC_002163.1 RefSeq gene 661532 662395 . + . ID=gene670;gene=glyQ;Name=glyQ;locus_tag=Cj0704;Dbxref=GeneID:905023;gbkey=Gene NC_002163.1 RefSeq region 661538 662392 . + . ID=id1366;gene=glyQ;Name=id1366;Dbxref=GeneID:905023;gbkey=misc_feature;Note=HMMPfam hit to PF02091 2C Glycyl-tRNA synthetase alpha subunit 2C score 4.8e-203 NC_002163.1 RefSeq gene 661695 661794 . - . ID=NC_002163.1:CJas_Cj0704;Name=NC_002163.1:CJas_Cj0704;locus_tag=CJas_Cj0704 NC_002163.1 RefSeq sRNA 661695 661794 . - . ID=NC_002163.1:CJas_Cj0704:unknown_transcript_1;Parent=NC_002163.1:CJas_Cj0704;Name=NC_002163.1:CJas_Cj0704:unknown_transcript_1;locus_tag=CJas_Cj0704;gbkey=misc_RNA;product=CJas_Cj0704 NC_002163.1 RefSeq region 662003 662032 . + . ID=id1367;gene=glyQ;Name=id1367;Dbxref=GeneID:905023;gbkey=misc_feature;Note=PS00339 Aminoacyl-transfer RNA synthetases class-II signature 2 NC_002163.1 RefSeq gene 662382 663107 . + . ID=gene671;gene=Cj0705;Name=Cj0705;locus_tag=Cj0705;Dbxref=GeneID:905024;gbkey=Gene NC_002163.1 RefSeq CDS 662382 663107 . + 0 ID=cds632;Parent=gene671;Name=YP_002344123.1;Dbxref=InterPro:IPR002678 UniProtKB FSwiss-Prot:Q9PPK2 Genbank:YP_002344123.1 GeneID:905024;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0705 2C unknown 2C len: 241 aa 3B similar to hypothetical proteins e.g. TR:O51424 28EMBL:AE001151 29 Borrelia burgdorferi BB0468 28248 aa 29 2Cfasta scores 3B opt: 240 z-score: 292.4 E 28 29: 5.5e-09 2C 27.0 25 identity in 244 aa overlap. 42.7 25 identity to HP0959 7EUpdated 282006 29 note: Pfam domain PF01784 NIF3 28NGG1p interacting factor 3 29 identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq region 662409 663083 . + . ID=id1368;Name=id1368;Dbxref=GeneID:905024;gbkey=misc_feature;Note=HMMPfam hit to PF01784 2C NIF3 28NGG1p interacting factor 3 29 2C score 3.6e-81 NC_002163.1 UTR_Extractor 5'-UTR 663079 663116 . + . ID=utr248;locus_tag=Cj0706;product=hypothetical protein ### NC_002163.1 RefSeq region 663117 663818 . + . ID=id1369;Name=id1369;Dbxref=GeneID:905025;gbkey=misc_feature;Note=HMMPfam hit to PF02591 2C Uncharacterized ACR 2CCOG1579 2C score 8.4e-50 NC_002163.1 RefSeq gene 663117 663833 . + . ID=gene672;Name=Cj0706;locus_tag=Cj0706;Dbxref=GeneID:905025;gbkey=Gene NC_002163.1 RefSeq CDS 663117 663833 . + 0 ID=cds633;Parent=gene672;Name=YP_002344124.1;Dbxref=InterPro:IPR003743 UniProtKB FTrEMBL:Q0PAH3 Genbank:YP_002344124.1 GeneID:905025;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0706 2C unknown 2C len: 238 aa 3B similar to hypothetical proteins e.g. TR:O67273 28EMBL:AE000729 29 Aquifex aeolicus AQ_1223 28235 aa 29 2C fasta scores 3B opt: 298 z-score: 287.3 E 28 29: 1.1e-08 2C 30.1 25 identity in 236 aa overlap. 37.4 25 identity to HP0958 7EUpdated 282006 29 note: Pfam domain PF02591 Uncharacterized ACR 2C COG1579 identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 663830 664987 . + . ID=gene673;gene=kdtA;Name=kdtA;locus_tag=Cj0707;Dbxref=GeneID:905026;gbkey=Gene NC_002163.1 RefSeq CDS 663830 664987 . + 0 ID=cds634;Parent=gene673;gene=kdtA;Name=YP_002344125.1;Dbxref=GOA:Q0PAH2 InterPro:IPR007507 UniProtKB FTrEMBL:Q0PAH2 Genbank:YP_002344125.1 GeneID:905026;gbkey=CDS;product=3-deoxy-D-manno-octulosonic-acid transferase;Note=catalyzes the transfer of 2-keto-3-deoxy-D-manno-octulosonic acid to lipid A NC_002163.1 RefSeq region 663839 663907 . + . ID=id1370;gene=kdtA;Name=id1370;Dbxref=GeneID:905026;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0707 by TMHMM2.0 at aa 4-26 and 111-130 NC_002163.1 RefSeq region 663917 664444 . + . ID=id1371;gene=kdtA;Name=id1371;Dbxref=GeneID:905026;gbkey=misc_feature;Note=HMMPfam hit to PF04413 2C3-Deoxy-D-manno-octulosonic-acid tran 2C score 7.3e-80 NC_002163.1 RefSeq region 664160 664219 . + . ID=id1370;gene=kdtA;Name=id1370;Dbxref=GeneID:905026;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0707 by TMHMM2.0 at aa 4-26 and 111-130 NC_002163.1 UTR_Extractor 5'-UTR 664890 664967 . + . ID=utr249;locus_tag=Cj0708;product=putative ribosomal pseudouridine synthase NC_002163.1 RefSeq CDS 664968 665720 . + 0 ID=cds635;Parent=gene674;Name=YP_002344126.1;Dbxref=GOA:Q0PAH1 InterPro:IPR006145 InterPro:IPR006224 UniProtKB FTrEMBL:Q0PAH1 Genbank:YP_002344126.1 GeneID:905027;gbkey=CDS;product=ribosomal pseudouridine synthase;Note=Original 282000 29 note: Cj0708 2C possible ribosomal pseudouridine synthase 2C len: 250 aa 3B similar to many hypothetical proteins and to e.g. RLUC_ECOLI ribosomal large subunit pseudouridine synthase D 28EC 4.2.1.70 29 28319 aa 29 2C fasta scores 3B opt: 202 z-score: 252.9 E 28 29: 8.6e-07 2C29.7 25 identity in 175 aa overlap. 47.0 25 identity to HP0956. Contains PS01129 Hypothetical yabO 2FyceC 2FsfhB family signature and Pfam match to entry PF00849 YABO 2CHypothetical yabO 2FyceC 2FsfhB family. Also similar to Cj1280c 2826.9 25 identity in 223 aa overlap 29 and Cj0022c 2827.6 25 identity in 275 aa overlap 29 7EUpdated 282006 29 note: Pfam domain now updated to RNA pseudouridylate synthase. No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification -Ribosome maturation and modification 7EPMID:10089432 NC_002163.1 RefSeq gene 664968 665720 . + . ID=gene674;gene=Cj0708;Name=Cj0708;locus_tag=Cj0708;Dbxref=GeneID:905027;gbkey=Gene NC_002163.1 RefSeq region 665160 665558 . + . ID=id1372;Name=id1372;Dbxref=GeneID:905027;gbkey=misc_feature;Note=HMMPfam hit to PF00849 2C RNA pseudouridylate synthase 2C score 1.7e-20 NC_002163.1 RefSeq region 665232 665276 . + . ID=id1373;Name=id1373;Dbxref=GeneID:905027;gbkey=misc_feature;Note=PS01129 Rlu family of pseudouridine synthase signature ### NC_002163.1 UTR_Extractor 5'-UTR 665755 665787 . + . ID=utr250;locus_tag=Cj0709;product=signal recognition particle protein NC_002163.1 RefSeq CDS 665788 667125 . + 0 ID=cds636;Parent=gene675;gene=ffh;Name=YP_002344127.1;Dbxref=GOA:Q0PAH0 InterPro:IPR000897 InterPro:IPR003593 InterPro:IPR004125 InterPro:IPR004780 InterPro:IPR013822 UniProtKB FTrEMBL:Q0PAH0 Genbank:YP_002344127.1 GeneID:905028;gbkey=CDS;product=signal recognition particle protein;Note=Original 282000 29 note: Cj0709 2C ffh 2C probable signal recognition particle protein 2C len: 445 aa 3B highly similar to many e.g. SR54_ECOLI signal recognition particle protein 28453 aa 29 2C fasta scores 3B opt: 1136 z-score: 1195.2 E 28 29: 0 2C 41.5 25 identity in 441 aa overlap. 61.0 25 identity to HP1152. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00300 SRP54-type proteins GTP-binding domain signature 2C and Pfam match to entry PF00448 SRP54 2CSRP54-type protein 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Protein and peptide secretion 7EPMID:1331806 2C PMID:11976293 NC_002163.1 RefSeq gene 665788 667125 . + . ID=gene675;gene=ffh;Name=ffh;locus_tag=Cj0709;Dbxref=GeneID:905028;gbkey=Gene NC_002163.1 RefSeq region 665791 666027 . + . ID=id1374;gene=ffh;Name=id1374;Dbxref=GeneID:905028;gbkey=misc_feature;Note=HMMPfam hit to PF02881 2C SRP54-type protein 2C helical bundle domain 2C score 2.4e-08 NC_002163.1 RefSeq region 666067 666657 . + . ID=id1375;gene=ffh;Name=id1375;Dbxref=GeneID:905028;gbkey=misc_feature;Note=HMMPfam hit to PF00448 2C SRP54-type protein 2C GTPase domain 2C score 9.5e-103 NC_002163.1 RefSeq region 666091 666114 . + . ID=id1376;gene=ffh;Name=id1376;Dbxref=GeneID:905028;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 666574 666615 . + . ID=id1377;gene=ffh;Name=id1377;Dbxref=GeneID:905028;gbkey=misc_feature;Note=PS00300 SRP54-type proteins GTP-binding domain signature NC_002163.1 RefSeq region 666748 667053 . + . ID=id1378;gene=ffh;Name=id1378;Dbxref=GeneID:905028;gbkey=misc_feature;Note=HMMPfam hit to PF02978 2C Signal peptide binding domain 2C score 4.4e-45 NC_002163.1 RefSeq stem_loop 667124 667169 . + . ID=id1379;gene=ffh;Name=id1379;gbkey=stem_loop ### NC_002163.1 RefSeq CDS 667190 667417 . + 0 ID=cds637;Parent=gene676;gene=rpsP;Name=YP_002344128.1;Dbxref=GOA:Q9PPJ7 HSSP:P80379 InterPro:IPR000307 UniProtKB FSwiss-Prot:Q9PPJ7 Genbank:YP_002344128.1 GeneID:905030;gbkey=CDS;product=30S ribosomal protein S16;Note=binds to lower part of 30S body where it stabilizes two domains 3B required for efficient assembly of 30S 3B in Escherichia coli this protein has nuclease activity NC_002163.1 RefSeq gene 667190 667417 . + . ID=gene676;gene=rpsP;Name=rpsP;locus_tag=Cj0710;Dbxref=GeneID:905030;gbkey=Gene NC_002163.1 RefSeq region 667193 667222 . + . ID=id1380;gene=rpsP;Name=id1380;Dbxref=GeneID:905030;gbkey=misc_feature;Note=PS00732 Ribosomal protein S16 signature NC_002163.1 RefSeq region 667211 667387 . + . ID=id1381;gene=rpsP;Name=id1381;Dbxref=GeneID:905030;gbkey=misc_feature;Note=HMMPfam hit to PF00886 2C Ribosomal protein S16 2Cscore 5.6e-33 ### NC_002163.1 RefSeq CDS 667420 667662 . + 0 ID=cds638;Parent=gene677;Name=YP_002344129.1;Dbxref=UniProtKB FTrEMBL:Q0PAG8 Genbank:YP_002344129.1 GeneID:904497;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0711 2C unknown 2C len: 80 aa 3B simlar to small hypothetical proteins downstream of rpsP in many organisms e.g. TR:O31738 28EMBL:Z99112 29 Bacillus subtilis YLQC 2881 aa 29 2C fasta scores 3B opt: 115 z-score: 178.5 E 28 29: 0.012 2C 32.3 25 identity in 62 aa overlap. 37.7 25 identity to HP1150. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 667420 667662 . + . ID=gene677;Name=Cj0711;locus_tag=Cj0711;Dbxref=GeneID:904497;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 667583 667654 . + . ID=utr251;locus_tag=Cj0712;product=putative 16S rRNA processing protein NC_002163.1 RefSeq gene 667655 668194 . + . ID=gene678;gene=rimM;Name=rimM;locus_tag=Cj0712;Dbxref=GeneID:904519;gbkey=Gene NC_002163.1 RefSeq CDS 667655 668194 . + 0 ID=cds639;Parent=gene678;gene=rimM;Name=YP_002344130.1;Dbxref=GOA:Q9PPJ5 InterPro:IPR002676 InterPro:IPR007903 InterPro:IPR011961 UniProtKB FSwiss-Prot:Q9PPJ5 Genbank:YP_002344130.1 GeneID:904519;gbkey=CDS;product=16S rRNA processing protein;Note=Original 282000 29 note: Cj0712 2C rimM 2C possible 16S rRNA processing protein 2C len: 179 aa 3B similar to e.g. RIMM_ECOLI 16S rRNA processing protein RIMM 28185 aa 29 2Cfasta scores 3B opt: 202 z-score: 255.1 E 28 29: 6.6e-07 2C 24.1 25 identity in 174 aa overlap. 37.8 25 identity to HP1149 7EUpdated 282006 29 note: Pfam domains PF01782 RimM N-terminal domain and PF05239 PRC-barrel domain were identified within CDS. Further support given to product function. Characterised within Escherichia coli with marginal identity score. kept within product function. Functional classification - Ribosome maturation and modification 7EPMID:9422595 NC_002163.1 RefSeq region 667676 667912 . + . ID=id1382;gene=rimM;Name=id1382;Dbxref=GeneID:904519;gbkey=misc_feature;Note=HMMPfam hit to PF01782 2C RimM N-terminal domain 2Cscore 2.2e-20 NC_002163.1 RefSeq region 667937 668179 . + . ID=id1383;gene=rimM;Name=id1383;Dbxref=GeneID:904519;gbkey=misc_feature;Note=HMMPfam hit to PF05239 2C PRC-barrel domain 2C score 1.2e-15 NC_002163.1 RefSeq gene 668191 668895 . + . ID=gene679;gene=trmD;Name=trmD;locus_tag=Cj0713;Dbxref=GeneID:904477;gbkey=Gene NC_002163.1 RefSeq CDS 668191 668895 . + 0 ID=cds640;Parent=gene679;gene=trmD;Name=YP_002344131.1;Dbxref=GOA:Q9PPJ4 HSSP:P43912 InterPro:IPR002649 InterPro:IPR016009 UniProtKB FSwiss-Prot:Q9PPJ4 Genbank:YP_002344131.1 GeneID:904477;gbkey=CDS;product=tRNA 28guanine-N 281 29- 29-methyltransferase;Note=methylates guanosine-37 in various tRNAs 3B uses S-adenosyl-L-methionine to transfer methyl group to tRNA NC_002163.1 RefSeq region 668254 668892 . + . ID=id1384;gene=trmD;Name=id1384;Dbxref=GeneID:904477;gbkey=misc_feature;Note=HMMPfam hit to PF01746 2C tRNA 28Guanine-1 29-methyltransferase 2C score 1.3e-82 NC_002163.1 UTR_Extractor 5'-UTR 668817 668905 . + . ID=utr252;locus_tag=Cj0714;product=50S ribosomal protein L19 ### NC_002163.1 RefSeq gene 668906 669262 . + . ID=gene680;gene=rplS;Name=rplS;locus_tag=Cj0714;Dbxref=GeneID:905031;gbkey=Gene NC_002163.1 RefSeq CDS 668906 669262 . + 0 ID=cds641;Parent=gene680;gene=rplS;Name=YP_002344132.1;Dbxref=GOA:Q9PPJ3 InterPro:IPR001857 UniProtKB FSwiss-Prot:Q9PPJ3 Genbank:YP_002344132.1 GeneID:905031;gbkey=CDS;product=50S ribosomal protein L19;Note=this protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site NC_002163.1 RefSeq region 668912 669256 . + . ID=id1385;gene=rplS;Name=id1385;Dbxref=GeneID:905031;gbkey=misc_feature;Note=HMMPfam hit to PF01245 2C Ribosomal protein L19 2Cscore 5.1e-63 ### NC_002163.1 UTR_Extractor 5'-UTR 669371 669394 . + . ID=utr253;locus_tag=Cj0715;product=transthyretin-like periplasmic protein NC_002163.1 RefSeq CDS 669395 669808 . + 0 ID=cds642;Parent=gene681;Name=YP_002344133.1;Dbxref=GOA:Q0PAG4 InterPro:IPR000895 InterPro:IPR014306 UniProtKB FTrEMBL:Q0PAG4 Genbank:YP_002344133.1 GeneID:905032;gbkey=CDS;product=transthyretin-like periplasmic protein;Note=Original 282000 29 note: Cj0715 2C transthyretin-like periplasmic protein 2C len: 137 aa 3B similar to members of the transthyretin family e.g. YEDX_ECOLI hypothetical transthyretin-like protein precursor 28137 aa 29 2C fasta scores 3B opt: 305 z-score: 409.7 E 28 29: 1.6e-15 2C 38.9 25 identity in 126 aa overlap 2C and TTHY_BOVIN Cow transthyretin precursor 28prealbumin 29 28147 aa 29 2C fasta scores 3B opt: 205 z-score: 279.8 E 28 29: 2.8e-08 2C 33.8 25 identity in 142 aa overlap. No Hp match. Contains Pfam match to entry PF00576 Transthyretin and probable N-terminal signal sequence 7EUpdated 282006 29 note: Prosite domains PS00768 TRANSTHYRETIN_1 2C Transthyretin and PS00769 TRANSTHYRETIN_2 2C Transthyretin were identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score carried out yet. Product function unchanged. Functional classification - Miscellaneous periplasmic proteins 7EPMID:12186869 NC_002163.1 RefSeq gene 669395 669808 . + . ID=gene681;Name=Cj0715;locus_tag=Cj0715;Dbxref=GeneID:905032;gbkey=Gene NC_002163.1 RefSeq region 669461 669802 . + . ID=id1386;Name=id1386;Dbxref=GeneID:905032;gbkey=misc_feature;Note=HMMPfam hit to PF00576 2C Transthyretin precursor 28formerly preal 2C score 7.3e-62 NC_002163.1 RefSeq region 669476 669523 . + . ID=id1387;Name=id1387;Dbxref=GeneID:905032;gbkey=misc_feature;Note=PS00768 Transthyretin signature 1 NC_002163.1 RefSeq region 669752 669790 . + . ID=id1388;Name=id1388;Dbxref=GeneID:905032;gbkey=misc_feature;Note=PS00769 Transthyretin signature 2 ### NC_002163.1 RefSeq region 669832 671145 . + . ID=id1389;Name=id1389;Dbxref=GeneID:905033;gbkey=misc_feature;Note=HMMPfam hit to PF01474 2C Class-II DAHP synthetase family 2C score 8.4e-246 NC_002163.1 RefSeq CDS 669832 671172 . + 0 ID=cds643;Parent=gene682;Name=YP_002344134.1;Dbxref=GOA:Q0PAG3 InterPro:IPR002480 UniProtKB FTrEMBL:Q0PAG3 Genbank:YP_002344134.1 GeneID:905033;gbkey=CDS;product=phospho-2-dehydro-3-deoxyheptonate aldolase;Note=Original 282000 29 note: Cj0716 2C probable phospho-2-dehydro-3-deoxyheptonate aldolase 2C len: 446 aa 3B similar to enzymes from plants e.g. AROF_ARATH phospho-2-dehydro-3-deoxyheptonate aldolase 28EC 4.1.2.15 29 28525 aa 29 2C fasta scores 3B opt: 1680 z-score: 1935.9 E 28 29: 0 2C54.2 25 identity in 445 aa overlap. 59.6 25 identity to HP0134 7EUpdated 282006 29 note: Pfam domain PF01474 Class-II DAHP synthetase family identified within CDS. Product function kept the same 28along with 29 2C as no specific characterisation within related bacteria has been carried out. Functional classification - Amino acid biosynthesis - Aromatic amino acid family NC_002163.1 RefSeq gene 669832 671172 . + . ID=gene682;Name=Cj0716;locus_tag=Cj0716;Dbxref=GeneID:905033;gbkey=Gene NC_002163.1 RefSeq region 670093 670125 . + . ID=id1390;Name=id1390;Dbxref=GeneID:905033;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq gene 671169 671498 . + . ID=gene683;Name=Cj0717;locus_tag=Cj0717;Dbxref=GeneID:905035;gbkey=Gene NC_002163.1 RefSeq CDS 671169 671498 . + 0 ID=cds644;Parent=gene683;Name=YP_002344135.1;Dbxref=GOA:Q0PAG2 InterPro:IPR006660 InterPro:IPR012335 UniProtKB FTrEMBL:Q0PAG2 Genbank:YP_002344135.1 GeneID:905035;gbkey=CDS;product=ArsC family protein;Note=Original 282000 29 note: Cj0717 2C unknown 2C len: aa 3B similar to hypothetical proteins e.g. YFFB_ECOLI 28118 aa 29 2Cfasta scores 3B opt: 164 z-score: 215.8 E 28 29: 0.0001 2C 32.3 25 identity in 93 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF03960 ArsC family identified within CDS. Product modified to more specific family member due to motif match. ArsC is thought to catalyze the reduction of arsenate to arsenite. No specific characterisation has been carried out. kept within product function. Functional classification -Misc 7EPMID:1704144 NC_002163.1 RefSeq region 671178 671489 . + . ID=id1391;Name=id1391;Dbxref=GeneID:905035;gbkey=misc_feature;Note=HMMPfam hit to PF03960 2C ArsC family 2C score 6.9e-34 ### NC_002163.1 RefSeq gene 671518 671798 . - . ID=NC_002163.1:CJnc60;Name=NC_002163.1:CJnc60;locus_tag=CJnc60 NC_002163.1 RefSeq sRNA 671518 671798 . - . ID=NC_002163.1:CJnc60:unknown_transcript_1;Parent=NC_002163.1:CJnc60;Name=NC_002163.1:CJnc60:unknown_transcript_1;locus_tag=CJnc60;gbkey=misc_RNA;product=CJnc60 NC_002163.1 RefSeq CDS 671946 675548 . + 0 ID=cds645;Parent=gene684;gene=dnaE;Name=YP_002344136.1;Dbxref=GOA:Q9PPI9 InterPro:IPR003141 InterPro:IPR004013 InterPro:IPR004805 InterPro:IPR011708 UniProtKB FSwiss-Prot:Q9PPI9 Genbank:YP_002344136.1 GeneID:905036;gbkey=CDS;product=DNA polymerase III subunit alpha;Note=catalyzes DNA-template-directed extension of the 3 27- end of a DNA strand by one nucleotide at a time 3B main replicative polymerase NC_002163.1 RefSeq gene 671946 675548 . + . ID=gene684;gene=dnaE;Name=dnaE;locus_tag=Cj0718;Dbxref=GeneID:905036;gbkey=Gene NC_002163.1 RefSeq region 671958 672155 . + . ID=id1392;gene=dnaE;Name=id1392;Dbxref=GeneID:905036;gbkey=misc_feature;Note=HMMPfam hit to PF02231 2C PHP domain N-terminal region 2C score 4.7e-29 NC_002163.1 RefSeq region 672192 672614 . + . ID=id1393;gene=dnaE;Name=id1393;Dbxref=GeneID:905036;gbkey=misc_feature;Note=HMMPfam hit to PF02811 2C PHP domain C-terminal region 2C score 1.6e-34 NC_002163.1 RefSeq region 672693 674204 . + . ID=id1394;gene=dnaE;Name=id1394;Dbxref=GeneID:905036;gbkey=misc_feature;Note=HMMPfam hit to PF07733 2C Bacterial DNA polymerase III alpha sub 2C score 2.2e-295 ### NC_002163.1 RefSeq CDS 675560 676192 . - 0 ID=cds646;Parent=gene685;Name=YP_002344137.1;Dbxref=InterPro:IPR011078 UniProtKB FTrEMBL:Q0PAG0 Genbank:YP_002344137.1 GeneID:905037;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0719c 2C unknown 2C len: 210 aa 3B similar to hypothetical proteins from many organisms e.g. YGGS_ECOLI 28234 aa 29 2C fasta scores 3B opt: 307 z-score: 380.4 E 28 29: 6.9e-14 2C 34.0 25 identity in 206 aa overlap. 47.5 25 identity to HP0395. Contains PS01211 Uncharacterized protein family UPF0001 signature and Pfam match to entry PF01168 UPF0001 7EUpdated 282006 29 note: Pfam domain PF01168 Alanine racemase 2C N-terminal domain identified within CDS. This is an uncharacterised motif that has some conserved regions. Conserved added due to identification of motif. Literature search identified paper giving further information on product function. Functional classification - Conserved hypothetical proteins 7EPMID:15228533 NC_002163.1 RefSeq gene 675560 676192 . - . ID=gene685;Name=Cj0719c;locus_tag=Cj0719c;Dbxref=GeneID:905037;gbkey=Gene NC_002163.1 RefSeq region 675566 676192 . - . ID=id1395;Name=id1395;Dbxref=GeneID:905037;gbkey=misc_feature;Note=HMMPfam hit to PF01168 2C Alanine racemase 2CN-terminal domain 2C score 2e-05 NC_002163.1 RefSeq region 675965 676009 . - . ID=id1396;Name=id1396;Dbxref=GeneID:905037;gbkey=misc_feature;Note=PS01211 Uncharacterized protein family UPF0001 signature ### NC_002163.1 RefSeq gene 676227 676976 . - . ID=gene686;gene=flaC;Name=flaC;locus_tag=Cj0720c;Dbxref=GeneID:905038;gbkey=Gene NC_002163.1 RefSeq CDS 676227 676976 . - 0 ID=cds647;Parent=gene686;gene=flaC;Name=YP_002344138.1;Dbxref=GOA:P96747 InterPro:IPR001492 UniProtKB FSwiss-Prot:P96747 Genbank:YP_002344138.1 GeneID:905038;gbkey=CDS;product=flagellin;Note=Original 282000 29 note: Cj0720c 2C flaC 2C flagellin 2Clen: 249 aa 3B 99.6 25 identical to TR:P96747 28EMBL:U85622 29 C. jejuni flaC 2C and similar to the N-terminus of e.g. FLAB_CAMJE flagellin B 28CJ1338 29 28575 aa 29 2C fasta scores 3B opt: 236 z-score: 261.7 E 28 29: 2.8e-07 2C 27.2 25 identity in 202 aa overlap. No Hp ortholog 7EUpdated 282006 29 note: Pfam domain PF00669 Bacterial flagellin N-terminus identified within CDS. Further support given to product function. Characterised in Campylobacter and Escherichia coli with acceptable identity score. not added to product function. Literature search identified paper linking product function to adhesion and to play an important role in cell adhesion. Functional classification - Surface structures 7EPMID:15228533 2C PMID:16740937 NC_002163.1 RefSeq region 676479 676871 . - . ID=id1397;gene=flaC;Name=id1397;Dbxref=GeneID:905038;gbkey=misc_feature;Note=HMMPfam hit to PF00669 2C Bacterial flagellin N-terminus 2C score 6.9e-05 ### NC_002163.1 UTR_Extractor 5'-UTR 676977 677004 . - . ID=utr254;locus_tag=Cj0720c;product=flagellin NC_002163.1 RefSeq CDS 677015 677485 . - 0 ID=cds648;Parent=gene687;Name=YP_002344139.1;Dbxref=GOA:Q0PAF8 UniProtKB FTrEMBL:Q0PAF8 Genbank:YP_002344139.1 GeneID:905039;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0721c 2C probable integral membrane protein 2C len: 156 aa 3B 35.9 25 identity to HP0288 7EUpdated 282006 29 note: Four probable transmembrane helices predicted by TMHMM2.0 NC_002163.1 RefSeq gene 677015 677485 . - . ID=gene687;Name=Cj0721c;locus_tag=Cj0721c;Dbxref=GeneID:905039;gbkey=Gene NC_002163.1 RefSeq region 677045 677113 . - . ID=id48;Name=id48;Dbxref=GeneID:905039;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0721c by TMHMM2.0 at aa 7-29 2C 49-68 2C 88-110 and 125-147 NC_002163.1 RefSeq region 677156 677224 . - . ID=id48;Name=id48;Dbxref=GeneID:905039;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0721c by TMHMM2.0 at aa 7-29 2C 49-68 2C 88-110 and 125-147 NC_002163.1 RefSeq region 677282 677341 . - . ID=id48;Name=id48;Dbxref=GeneID:905039;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0721c by TMHMM2.0 at aa 7-29 2C 49-68 2C 88-110 and 125-147 NC_002163.1 RefSeq region 677399 677467 . - . ID=id48;Name=id48;Dbxref=GeneID:905039;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0721c by TMHMM2.0 at aa 7-29 2C 49-68 2C 88-110 and 125-147 ### NC_002163.1 UTR_Extractor 5'-UTR 677486 677502 . - . ID=utr255;locus_tag=Cj0721c;product=putative integral membrane protein NC_002163.1 RefSeq CDS 677498 678313 . - 0 ID=cds649;Parent=gene688;Name=YP_002344140.1;Dbxref=GOA:Q0PAF7 InterPro:IPR002052 InterPro:IPR004556 InterPro:IPR013216 UniProtKB FTrEMBL:Q0PAF7 Genbank:YP_002344140.1 GeneID:905040;gbkey=CDS;product=DNA methylase;Note=Original 282000 29 note: Cj0722c 2C probable DNA methylase 2C len: 271 aa 3B similar to members of the hemK family of methylases 2C e.g. HEMK_ECOLI HEMK protein 28277 aa 29 2C fasta scores 3B opt: 262 z-score: 315.7 E 28 29: 2.7e-10 2C26.1 25 identity in 276 aa overlap. 36.9 25 identity to HP0381. Contains PS00092 N-6 Adenine-specific DNA methylases signature 7EUpdated 282006 29 note: Prosite domain PS50193 SAM_BIND 2C SAM 28and some other nucleotide 29 binding motif identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification - DNA replication 2C restriction 2Fmodification 2C recombination and repair NC_002163.1 RefSeq gene 677498 678313 . - . ID=gene688;Name=Cj0722c;locus_tag=Cj0722c;Dbxref=GeneID:905040;gbkey=Gene NC_002163.1 RefSeq region 677777 677797 . - . ID=id1398;Name=id1398;Dbxref=GeneID:905040;gbkey=misc_feature;Note=PS00092 N-6 Adenine-specific DNA methylases signature NC_002163.1 RefSeq CDS 678310 679497 . - 0 ID=cds650;Parent=gene689;Name=YP_002344141.1;Dbxref=GOA:Q0PAF6 InterPro:IPR001915 InterPro:IPR006025 UniProtKB FTrEMBL:Q0PAF6 Genbank:YP_002344141.1 GeneID:905041;gbkey=CDS;product=integral membrane zinc-metalloprotease;Note=Original 282000 29 note: Cj0723c 2C probable integral membrane zinc-metalloprotease 2C len: 395 aa 3B simimlar to yeast proteases e.g. ST24_YEAST CAAX prenyl protease 1 28453 aa 29 2C fasta scores 3B opt: 494 z-score: 565.5 E 28 29: 3.4e-24 2C 31.6 25 identity in 430 aa overlap 2C and to prokaryotic htpX 2C e.g. HTPX_ECOLI heat shock protein HTPX 28293 aa 29 2C fasta scores 3B opt: 183 z-score: 216.0 E 28 29: 9.9e-05 2C 24.1 25 identity in 295 aa overlap. 38.6 25 identity to HP0382. Contains PS00142 Neutral zinc metallopeptidases 2C zinc-binding region signature 7EUpdated 282006 29 note: Pfam domain PF01435 Peptidase family M48 and Prosite domain PS00142 ZINC_PROTEASE 2CPeptidase M 2C neutral zinc metallopeptidases 2C zinc-binding site were identified within CDS. Also 2C Seven probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation carried out yet. kept within product function. Functional classification - Proteins 2Cpeptides and glycopeptides NC_002163.1 RefSeq gene 678310 679497 . - . ID=gene689;Name=Cj0723c;locus_tag=Cj0723c;Dbxref=GeneID:905041;gbkey=Gene NC_002163.1 RefSeq region 678313 678885 . - . ID=id1399;Name=id1399;Dbxref=GeneID:905041;gbkey=misc_feature;Note=HMMPfam hit to PF01435 2C Peptidase family M48 2C score 1.9e-43 NC_002163.1 RefSeq region 678499 678567 . - . ID=id49;Name=id49;Dbxref=GeneID:905041;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0723c by TMHMM2.0 at aa 4-26 2C 61-83 2C 93-115 2C 138-160 2C164-186 2C 279-301 and 311-333 NC_002163.1 RefSeq region 678595 678663 . - . ID=id49;Name=id49;Dbxref=GeneID:905041;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0723c by TMHMM2.0 at aa 4-26 2C 61-83 2C 93-115 2C 138-160 2C164-186 2C 279-301 and 311-333 NC_002163.1 RefSeq region 678685 678714 . - . ID=id1400;Name=id1400;Dbxref=GeneID:905041;gbkey=misc_feature;Note=PS00142 Neutral zinc metallopeptidases 2Czinc-binding region signature NC_002163.1 RefSeq region 678940 679008 . - . ID=id49;Name=id49;Dbxref=GeneID:905041;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0723c by TMHMM2.0 at aa 4-26 2C 61-83 2C 93-115 2C 138-160 2C164-186 2C 279-301 and 311-333 NC_002163.1 RefSeq region 679018 679086 . - . ID=id49;Name=id49;Dbxref=GeneID:905041;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0723c by TMHMM2.0 at aa 4-26 2C 61-83 2C 93-115 2C 138-160 2C164-186 2C 279-301 and 311-333 NC_002163.1 RefSeq region 679153 679221 . - . ID=id49;Name=id49;Dbxref=GeneID:905041;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0723c by TMHMM2.0 at aa 4-26 2C 61-83 2C 93-115 2C 138-160 2C164-186 2C 279-301 and 311-333 NC_002163.1 RefSeq region 679249 679317 . - . ID=id49;Name=id49;Dbxref=GeneID:905041;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0723c by TMHMM2.0 at aa 4-26 2C 61-83 2C 93-115 2C 138-160 2C164-186 2C 279-301 and 311-333 NC_002163.1 RefSeq region 679420 679488 . - . ID=id49;Name=id49;Dbxref=GeneID:905041;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0723c by TMHMM2.0 at aa 4-26 2C 61-83 2C 93-115 2C 138-160 2C164-186 2C 279-301 and 311-333 ### NC_002163.1 RefSeq CDS 679624 679809 . + 0 ID=cds651;Parent=gene690;Name=YP_002344142.1;Dbxref=GOA:Q0PAF5 UniProtKB FTrEMBL:Q0PAF5 Genbank:YP_002344142.1 GeneID:905042;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0724 2C unknown 2C len: 61 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 RefSeq gene 679624 679809 . + . ID=gene690;Name=Cj0724;locus_tag=Cj0724;Dbxref=GeneID:905042;gbkey=Gene NC_002163.1 RefSeq gene 679806 680348 . - . ID=gene691;gene=mogA;Name=mogA;locus_tag=Cj0725c;Dbxref=GeneID:905043;gbkey=Gene NC_002163.1 RefSeq CDS 679806 680348 . - 0 ID=cds652;Parent=gene691;gene=mogA;Name=YP_002344143.1;Dbxref=GOA:Q0PAF4 InterPro:IPR001453 UniProtKB FTrEMBL:Q0PAF4 Genbank:YP_002344143.1 GeneID:905043;gbkey=CDS;product=molybdenum cofactor biosynthesis protein MogA;Note=forms a trimer 3B related to eukaryotic protein gephyrin 3B functions during molybdenum cofactor biosynthesis NC_002163.1 RefSeq region 679911 680339 . - . ID=id1401;gene=mogA;Name=id1401;Dbxref=GeneID:905043;gbkey=misc_feature;Note=HMMPfam hit to PF00994 2C Probable molybdopterin binding domain 2C score 6.3e-45 ### NC_002163.1 RefSeq CDS 680369 681352 . - 0 ID=cds653;Parent=gene692;gene=corA;Name=YP_002344144.1;Dbxref=GOA:Q9PPI1 InterPro:IPR002523 InterPro:IPR004488 UniProtKB FSwiss-Prot:Q9PPI1 Genbank:YP_002344144.1 GeneID:905044;gbkey=CDS;product=magnesium and cobalt transport protein;Note=Original 282000 29 note: Cj0726c 2C corA 2C probable magnesium and cobalt transport protein 2C len: 327 aa 3B similar to e.g. CORA_ECOLI magnesium and cobalt transport protein CORA 28316 aa 29 2C fasta scores 3B opt: 559 z-score: 616.2 E 28 29: 5.1e-27 2C 31.3 25 identity in 329 aa overlap. 49.4 25 identity to HP1344 7EUpdated 282006 29 note: Pfam domain PF01544 CorA-like Mg2 2B transporter protein identified within CDS. Also 2C two probable transmembrane helices predicted for TMHMM2.0. Further support given to product function. Characterised within Escherichia coli and Salmonella typhimurium with marginal identity scores. not added to product function. Functional classification - Transport 2Fbinding proteins - Cations 7EPMID:1779764 2C PMID:9775386 NC_002163.1 RefSeq gene 680369 681352 . - . ID=gene692;gene=corA;Name=corA;locus_tag=Cj0726c;Dbxref=GeneID:905044;gbkey=Gene NC_002163.1 RefSeq region 680372 681277 . - . ID=id1402;gene=corA;Name=id1402;Dbxref=GeneID:905044;gbkey=misc_feature;Note=HMMPfam hit to PF01544 2C CorA-like Mg2 2B transporter protein 2C score 1.6e-61 NC_002163.1 RefSeq region 680390 680458 . - . ID=id50;gene=corA;Name=id50;Dbxref=GeneID:905044;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0726c by TMHMM2.0 at aa 267-289 and 299-321 NC_002163.1 RefSeq region 680486 680554 . - . ID=id50;gene=corA;Name=id50;Dbxref=GeneID:905044;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0726c by TMHMM2.0 at aa 267-289 and 299-321 ### NC_002163.1 UTR_Extractor 5'-UTR 681353 681372 . - . ID=utr256;locus_tag=Cj0726c;product=magnesium and cobalt transport protein NC_002163.1 RefSeq gene 681469 682515 . + . ID=gene693;Name=Cj0727;locus_tag=Cj0727;Dbxref=GeneID:905045;gbkey=Gene NC_002163.1 RefSeq CDS 681469 682515 . + 0 ID=cds654;Parent=gene693;Name=YP_002344145.1;Dbxref=GOA:Q0PAF2 InterPro:IPR006059 UniProtKB FTrEMBL:Q0PAF2 Genbank:YP_002344145.1 GeneID:905045;gbkey=CDS;product=substrate-binding protein;Note=Original 282000 29 note: Cj0727 2C probable periplasmic solute-binding protein 2C len: 348 aa 3B similar to e.g. SUBI_ECOLI sulfate-binding protein precursor 28329 aa 29 2Cfasta scores 3B opt: 220 z-score: 256.1 E 28 29: 5.8e-07 2C 25.0 25 identity in 220 aa overlap. No Hp match. Contains N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF01547 Bacterial extracellular solute-binding protein identified within CDS. Further support given to product function. Characterised within Escherichia coli 2C however 2C identity scores were unnacceptable. kept within product function. Functional classification - Transport 2Fbinding proteins - Other NC_002163.1 RefSeq region 681487 682323 . + . ID=id1403;Name=id1403;Dbxref=GeneID:905045;gbkey=misc_feature;Note=HMMPfam hit to PF01547 2C Bacterial extracellular solute-binding prot 2C score 0.0028 ### NC_002163.1 RefSeq CDS 682526 683851 . + 0 ID=cds655;Parent=gene694;Name=YP_002344146.1;Dbxref=GOA:Q0PAF1 UniProtKB FTrEMBL:Q0PAF1 Genbank:YP_002344146.1 GeneID:905046;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0728 2C probable periplasmic protein 2C len: 441 aa 3B no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 682526 683851 . + . ID=gene694;Name=Cj0728;locus_tag=Cj0728;Dbxref=GeneID:905046;gbkey=Gene NC_002163.1 RefSeq gene 683848 684657 . + . ID=gene695;Name=Cj0729;locus_tag=Cj0729;Dbxref=GeneID:905047;gbkey=Gene NC_002163.1 RefSeq CDS 683848 684657 . + 0 ID=cds656;Parent=gene695;Name=YP_002344147.1;Dbxref=GOA:Q0PAF0 InterPro:IPR002591 InterPro:IPR017849 UniProtKB FTrEMBL:Q0PAF0 Genbank:YP_002344147.1 GeneID:905047;gbkey=CDS;product=type I phosphodiesterase 2Fnucleotide pyrophosphatase;Note=Original 282000 29 note: Cj0729 2C unknown 2C len: 269 aa 3B no Hp match 7EUpdated 282006 29 note: Pfam domain PF01663 Type I phosphodiesterase 2F nucleotide pyrophosphatase identified within CDS. Product modified to more specific family member due to motif match. No specific characterisation has been carried out yet 2C so kept within product function. Functional classification - Purines 2Cpyrimidines 2C nucleosides and nucleotides - Miscellaneous nucleoside 2Fnucleotide reactions NC_002163.1 RefSeq gene 684654 685493 . + . ID=gene696;Name=Cj0730;locus_tag=Cj0730;Dbxref=GeneID:905048;gbkey=Gene NC_002163.1 RefSeq CDS 684654 685493 . + 0 ID=cds657;Parent=gene696;Name=YP_002344148.1;Dbxref=GOA:Q0PAE9 InterPro:IPR000515 UniProtKB FTrEMBL:Q0PAE9 Genbank:YP_002344148.1 GeneID:905048;gbkey=CDS;product=ABC transporter permease;Note=Original 282000 29 note: Cj0730 2C probable ABC transport system permease 2C len: 279 aa 3B similar to members of the binding protein-dependent permease family e.g. UGPA_ECOLI SN-glycerol-3-phosphate transport system permease 28295 aa 29 2C fasta scores 3B opt: 273 z-score: 324.4 E 28 29: 9.1e-11 2C 25.0 25 identity in 280 aa overlap. No Hp match. Contains Pfam match to entry PF00528 BPD_transp 2CBinding-protein-dependent transport systems inner membrane component 7EUpdated 282006 29 note: Six probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity score has been carried out yet. kept within product function. Functional classification - Transport 2Fbinding proteins - Other NC_002163.1 RefSeq region 684672 684740 . + . ID=id1404;Name=id1404;Dbxref=GeneID:905048;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0730 by TMHMM2.0 at aa 7-29 2C 66-88 2C 108-130 2C 145-167 2C187-209 and 248-270 NC_002163.1 RefSeq region 684819 685490 . + . ID=id1405;Name=id1405;Dbxref=GeneID:905048;gbkey=misc_feature;Note=HMMPfam hit to PF00528 2C Binding-protein-dependent transport syst 2C score 0.0008 NC_002163.1 RefSeq region 684849 684917 . + . ID=id1404;Name=id1404;Dbxref=GeneID:905048;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0730 by TMHMM2.0 at aa 7-29 2C 66-88 2C 108-130 2C 145-167 2C187-209 and 248-270 NC_002163.1 RefSeq region 684975 685043 . + . ID=id1404;Name=id1404;Dbxref=GeneID:905048;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0730 by TMHMM2.0 at aa 7-29 2C 66-88 2C 108-130 2C 145-167 2C187-209 and 248-270 NC_002163.1 RefSeq region 685086 685154 . + . ID=id1404;Name=id1404;Dbxref=GeneID:905048;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0730 by TMHMM2.0 at aa 7-29 2C 66-88 2C 108-130 2C 145-167 2C187-209 and 248-270 NC_002163.1 RefSeq region 685212 685280 . + . ID=id1404;Name=id1404;Dbxref=GeneID:905048;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0730 by TMHMM2.0 at aa 7-29 2C 66-88 2C 108-130 2C 145-167 2C187-209 and 248-270 NC_002163.1 RefSeq region 685395 685463 . + . ID=id1404;Name=id1404;Dbxref=GeneID:905048;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0730 by TMHMM2.0 at aa 7-29 2C 66-88 2C 108-130 2C 145-167 2C187-209 and 248-270 ### NC_002163.1 RefSeq CDS 685494 686273 . + 0 ID=cds658;Parent=gene697;Name=YP_002344149.1;Dbxref=GOA:Q0PAE8 InterPro:IPR000515 UniProtKB FTrEMBL:Q0PAE8 Genbank:YP_002344149.1 GeneID:905049;gbkey=CDS;product=ABC transporter permease;Note=Original 282000 29 note: Cj0731 2C probable ABC transport system permease 2C len: 259 aa 3B similar to members of the binding protein-dependent permease family e.g. POTC_ECOLI spermidine 2Fputrescine transport system permease 28264 aa 29 2C fasta scores 3B opt: 271 z-score: 337.3 E 28 29: 1.7e-11 2C 24.1 25 identity in 241 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00528 BPD_transp 2CBinding-protein-dependent transport systems inner membrane component 7EUpdated 282006 29 note: Seven probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity score has been carried out yet. kept within product function. Functional classification - Transport 2Fbinding proteins - Other NC_002163.1 RefSeq gene 685494 686273 . + . ID=gene697;Name=Cj0731;locus_tag=Cj0731;Dbxref=GeneID:905049;gbkey=Gene NC_002163.1 RefSeq region 685527 685595 . + . ID=id1406;Name=id1406;Dbxref=GeneID:905049;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0731 by TMHMM2.0 at aa 12-34 2C 75-97 2C 104-126 2C 131-153 2C165-187 2C 192-214 and 235-257 NC_002163.1 RefSeq region 685692 686270 . + . ID=id1407;Name=id1407;Dbxref=GeneID:905049;gbkey=misc_feature;Note=HMMPfam hit to PF00528 2C Binding-protein-dependent transport syst 2C score 0.0085 NC_002163.1 RefSeq region 685716 685784 . + . ID=id1406;Name=id1406;Dbxref=GeneID:905049;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0731 by TMHMM2.0 at aa 12-34 2C 75-97 2C 104-126 2C 131-153 2C165-187 2C 192-214 and 235-257 NC_002163.1 RefSeq region 685803 685871 . + . ID=id1406;Name=id1406;Dbxref=GeneID:905049;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0731 by TMHMM2.0 at aa 12-34 2C 75-97 2C 104-126 2C 131-153 2C165-187 2C 192-214 and 235-257 NC_002163.1 RefSeq region 685884 685952 . + . ID=id1406;Name=id1406;Dbxref=GeneID:905049;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0731 by TMHMM2.0 at aa 12-34 2C 75-97 2C 104-126 2C 131-153 2C165-187 2C 192-214 and 235-257 NC_002163.1 RefSeq region 685986 686054 . + . ID=id1406;Name=id1406;Dbxref=GeneID:905049;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0731 by TMHMM2.0 at aa 12-34 2C 75-97 2C 104-126 2C 131-153 2C165-187 2C 192-214 and 235-257 NC_002163.1 RefSeq region 686067 686135 . + . ID=id1406;Name=id1406;Dbxref=GeneID:905049;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0731 by TMHMM2.0 at aa 12-34 2C 75-97 2C 104-126 2C 131-153 2C165-187 2C 192-214 and 235-257 NC_002163.1 RefSeq region 686196 686264 . + . ID=id1406;Name=id1406;Dbxref=GeneID:905049;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0731 by TMHMM2.0 at aa 12-34 2C 75-97 2C 104-126 2C 131-153 2C165-187 2C 192-214 and 235-257 ### NC_002163.1 RefSeq CDS 686277 687266 . + 0 ID=cds659;Parent=gene698;Name=YP_002344150.1;Dbxref=GOA:Q0PAE7 InterPro:IPR003439 InterPro:IPR003593 InterPro:IPR013611 UniProtKB FTrEMBL:Q0PAE7 Genbank:YP_002344150.1 GeneID:905050;gbkey=CDS;product=ABC transporter ATP-binding protein;Note=Original 282000 29 note: Cj0732 2C probable ABC transport system ATP-binding protein 2C len: 329 aa 3B similar to many e.g. POTA_ECOLI spermidine 2Fputrescine transport ATP-binding protein 28378 aa 29 2C fasta scores 3B opt: 802 z-score: 857.8 E 28 29: 0 2C 43.2 25 identity in 292 aa overlap. No Hp otholog. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00211 ABC transporters family signature and Pfam match to entry PF00005 ABC_tran 7EUpdated 282006 29 note: Similar to more than one species with acceptable identity score. not added to product function. Functional classification -Transport 2Fbinding proteins - Other NC_002163.1 RefSeq gene 686277 687266 . + . ID=gene698;Name=Cj0732;locus_tag=Cj0732;Dbxref=GeneID:905050;gbkey=Gene NC_002163.1 RefSeq region 686361 686906 . + . ID=id1408;Name=id1408;Dbxref=GeneID:905050;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 4.1e-70 NC_002163.1 RefSeq region 686382 686405 . + . ID=id1409;Name=id1409;Dbxref=GeneID:905050;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 686676 686720 . + . ID=id1410;Name=id1410;Dbxref=GeneID:905050;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 UTR_Extractor 5'-UTR 687045 687262 . + . ID=utr257;locus_tag=Cj0733;product=putative HAD-superfamily hydrolase NC_002163.1 RefSeq region 687263 687850 . + . ID=id1411;Name=id1411;Dbxref=GeneID:905051;gbkey=misc_feature;Note=HMMPfam hit to PF00702 2C haloacid dehalogenase-like hydrolase 2C score 0.0017 NC_002163.1 RefSeq gene 687263 687901 . + . ID=gene699;Name=Cj0733;locus_tag=Cj0733;Dbxref=GeneID:905051;gbkey=Gene NC_002163.1 RefSeq CDS 687263 687901 . + 0 ID=cds660;Parent=gene699;Name=YP_002344151.1;Dbxref=GOA:Q0PAE6 InterPro:IPR005834 InterPro:IPR006383 InterPro:IPR006385 UniProtKB FTrEMBL:Q0PAE6 Genbank:YP_002344151.1 GeneID:905051;gbkey=CDS;product=HAD-superfamily hydrolase;Note=Original 282000 29 note: Cj0733 2C unknown 2C len: 212 aa 3B some similarity to hypotheical proteins from Actinomycetes e.g. TR:O69629 28EMBL:AL022121 29 Rv3661 28MTV025.009 29 28287 aa 29 2C fasta scores 3B opt: 264 z-score: 321.7 E 28 29: 1.3e-10 2C28.4 25 identity in 215 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF00702 haloacid dehalogenase-like hydrolase identified within CDS. No specific characterisation with acceptable identity score has been carried out yet. kept within product function. Functional classification - Misc NC_002163.1 RefSeq region 687518 687547 . + . ID=id1412;Name=id1412;Dbxref=GeneID:905051;gbkey=misc_feature;Note=PS00215 Mitochondrial energy transfer proteins signature ### NC_002163.1 RefSeq CDS 687925 688680 . - 0 ID=cds661;Parent=gene700;gene=hisJ;Name=YP_002344152.1;Dbxref=GOA:Q46125 HSSP:P39182 InterPro:IPR001638 InterPro:IPR015683 UniProtKB FSwiss-Prot:Q46125 Genbank:YP_002344152.1 GeneID:905052;gbkey=CDS;product=histidine-binding protein;Note=Original 282000 29 note: Cj0734c 2C hisJ 2C probable histidine-binding protein precursor 2C len: 251 aa 3B almost identical to HISJ_CAMJE histidine-binding protein precursor 28256 aa 29 2888.7 25 identity in 256 aa overlap 29 and similar to many priplasmic amino-acid binding proteins e.g. HISJ_ECOLI histidine-binding periplasmic protein precursor 28260 aa 29 2C fasta scores 3B opt: 343 z-score: 390.5 E 28 29: 1.9e-14. 33.5 25 identity in 263 aa overlap. No Hp ortholog. Contains N-terminal signal sequence 2C PS00013 Prokaryotic membrane lipoprotein lipid attachment site 2CPS01039 Bacterial extracellular solute-binding proteins 2Cfamily 3 signature 2C and Pfam match to entry PF00497 SBP_bac_3 2C Bacterial extracellular solute-binding proteins 2C family 3 7EUpdated 282006 29 note: Characterised in Campylobacter jejuni. not added to product function. Functional classification - Transport 2Fbinding proteins - Amino acids and amines 7EPMID:9489038 2C PMID:15063560 2C PMID:9395059 NC_002163.1 RefSeq gene 687925 688680 . - . ID=gene700;gene=hisJ;Name=hisJ;locus_tag=Cj0734c;Dbxref=GeneID:905052;gbkey=Gene NC_002163.1 RefSeq region 687928 688581 . - . ID=id1413;gene=hisJ;Name=id1413;Dbxref=GeneID:905052;gbkey=misc_feature;Note=HMMPfam hit to PF00497 2C Bacterial extracellular solute-binding prot 2C score 4.4e-67 NC_002163.1 RefSeq region 688477 688518 . - . ID=id1414;gene=hisJ;Name=id1414;Dbxref=GeneID:905052;gbkey=misc_feature;Note=PS01039 Bacterial extracellular solute-binding proteins 2C family 3 signature NC_002163.1 RefSeq region 688621 688653 . - . ID=id1415;gene=hisJ;Name=id1415;Dbxref=GeneID:905052;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 UTR_Extractor 5'-UTR 688681 688703 . - . ID=utr258;locus_tag=Cj0734c;product=histidine-binding protein precursor NC_002163.1 UTR_Extractor 5'-UTR 688882 689006 . + . ID=utr259;locus_tag=Cj0735;product=putative periplasmic protein NC_002163.1 RefSeq CDS 689007 689726 . + 0 ID=cds662;Parent=gene701;Name=YP_002344153.1;Dbxref=UniProtKB FTrEMBL:Q0PAE4 Genbank:YP_002344153.1 GeneID:905053;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0735 2C probable periplasmic protein 2C len: 239 aa 3B no Hp match. Similar to N-terminus of Cj0967 28E 28 29: 6.7e-15 2C 34.5 25 identity in 116 aa overlap 29 3B similarity continues in downstream CDS Cj0736. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: One probable transmembrane helix predicted by TMHMM2.0. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 689007 689726 . + . ID=gene701;Name=Cj0735;locus_tag=Cj0735;Dbxref=GeneID:905053;gbkey=Gene NC_002163.1 RefSeq region 689061 689129 . + . ID=id1416;Name=id1416;Dbxref=GeneID:905053;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0735 by TMHMM2.0 at aa 19-41 NC_002163.1 RefSeq gene 689656 691584 . + . ID=gene702;Name=Cj0736;locus_tag=Cj0736;Dbxref=GeneID:905054;gbkey=Gene NC_002163.1 RefSeq CDS 689656 691584 . + 0 ID=cds663;Parent=gene702;Name=YP_002344154.1;Dbxref=UniProtKB FTrEMBL:Q0PAE3 Genbank:YP_002344154.1 GeneID:905054;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0736 2C unknown 2C len: 239 aa 3B no Hp match. Similar to C-terminus of Cj0967 28E 28 29: 0 2C 42.3 25 identity in 562 aa overlap 29 3B similarity continues from upstream CDS Cj0735 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown ### NC_002163.1 RefSeq region 691614 691682 . + . ID=id1417;Name=id1417;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0737 by TMHMM2.0 at aa 7-29 NC_002163.1 UTR_Extractor 5'-UTR 692570 692725 . + . ID=utr260;locus_tag=Cj0738;product=hypothetical protein NC_002163.1 RefSeq pseudogene 693017 694064 . + . ID=gene703;Name=Cj0740;locus_tag=Cj0740;Dbxref=GeneID:905058;gbkey=Gene NC_002163.1 RefSeq region 694230 694694 . + . ID=id1418;Name=id1418;Dbxref=GeneID:905814;gbkey=misc_feature;Note=Original 282000 29 note: Cj0742 2C probable outer membrane protein pseudogene 2C len: 1567 bp 3B similar to parts of Cj0975 28H. inf. hxuB-like 29. No Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity scores. Thus 2C kept within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq pseudogene 694230 695922 . + . ID=gene704;Name=Cj0742;locus_tag=Cj0742;Dbxref=GeneID:905814;gbkey=Gene NC_002163.1 RefSeq region 694694 694936 . + . ID=id1418;Name=id1418;Dbxref=GeneID:905814;gbkey=misc_feature;Note=Original 282000 29 note: Cj0742 2C probable outer membrane protein pseudogene 2C len: 1567 bp 3B similar to parts of Cj0975 28H. inf. hxuB-like 29. No Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity scores. Thus 2C kept within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 694939 695922 . + . ID=id1418;Name=id1418;Dbxref=GeneID:905814;gbkey=misc_feature;Note=Original 282000 29 note: Cj0742 2C probable outer membrane protein pseudogene 2C len: 1567 bp 3B similar to parts of Cj0975 28H. inf. hxuB-like 29. No Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity scores. Thus 2C kept within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification -Membranes 2C lipoproteins and porins ### NC_002163.1 RefSeq gene 696424 697936 . + . ID=gene705;Name=Cjr07;locus_tag=Cjr07;Dbxref=GeneID:3245041;gbkey=Gene NC_002163.1 RefSeq rRNA 696424 697936 . + . ID=rna22;Parent=gene705;Name=rna22;Dbxref=GeneID:3245041;gbkey=rRNA;product=16S ribosomal RNA NC_002163.1 RefSeq exon 696424 697936 . + . ID=id1419;Parent=rna22;Name=id1419;Dbxref=GeneID:3245041;gbkey=rRNA;product=16S ribosomal RNA NC_002163.1 RefSeq gene 698041 698116 . + . ID=gene706;gene=tRNAAla;Name=tRNAAla;locus_tag=Cjp14;Dbxref=GeneID:905060;gbkey=Gene NC_002163.1 RefSeq tRNA 698041 698116 . + . ID=rna23;Parent=gene706;gene=tRNAAla;Name=rna23;Dbxref=GeneID:905060;gbkey=tRNA;product=tRNA-Ala;Note=tRNA Ala anticodon TGC 2C Cove score 92.14 NC_002163.1 RefSeq exon 698041 698116 . + . ID=id1420;Parent=rna23;gene=tRNAAla;Name=id1420;Dbxref=GeneID:905060;gbkey=tRNA;product=tRNA-Ala;Note=tRNA Ala anticodon TGC 2C Cove score 92.14 NC_002163.1 RefSeq gene 698125 698201 . + . ID=gene707;gene=tRNAIle;Name=tRNAIle;locus_tag=Cjp15;Dbxref=GeneID:905061;gbkey=Gene NC_002163.1 RefSeq tRNA 698125 698201 . + . ID=rna24;Parent=gene707;gene=tRNAIle;Name=rna24;Dbxref=GeneID:905061;gbkey=tRNA;product=tRNA-Ile;Note=tRNA Ile anticodon GAT 2C Cove score 93.24 NC_002163.1 RefSeq exon 698125 698201 . + . ID=id1421;Parent=rna24;gene=tRNAIle;Name=id1421;Dbxref=GeneID:905061;gbkey=tRNA;product=tRNA-Ile;Note=tRNA Ile anticodon GAT 2C Cove score 93.24 NC_002163.1 RefSeq gene 698743 701654 . + . ID=gene708;Name=Cjr08;locus_tag=Cjr08;Dbxref=GeneID:3245038;gbkey=Gene NC_002163.1 RefSeq rRNA 698743 701654 . + . ID=rna25;Parent=gene708;Name=rna25;Dbxref=GeneID:3245038;gbkey=rRNA;product=23S ribosomal RNA NC_002163.1 RefSeq exon 698743 701654 . + . ID=id1422;Parent=rna25;Name=id1422;Dbxref=GeneID:3245038;gbkey=rRNA;product=23S ribosomal RNA NC_002163.1 RefSeq gene 701939 702058 . + . ID=gene709;Name=Cjr09;locus_tag=Cjr09;Dbxref=GeneID:3245042;gbkey=Gene NC_002163.1 RefSeq rRNA 701939 702058 . + . ID=rna26;Parent=gene709;Name=rna26;Dbxref=GeneID:3245042;gbkey=rRNA;product=5S ribosomal RNA NC_002163.1 RefSeq exon 701939 702058 . + . ID=id1423;Parent=rna26;Name=id1423;Dbxref=GeneID:3245042;gbkey=rRNA;product=5S ribosomal RNA NC_002163.1 RefSeq gene 702810 702917 . + . ID=gene710;Name=Cj0747;locus_tag=Cj0747;Dbxref=GeneID:905062;gbkey=Gene NC_002163.1 RefSeq CDS 702810 702917 . + 0 ID=cds664;Parent=gene710;Name=YP_002344160.1;Dbxref=UniProtKB FTrEMBL:Q0PAD7 Genbank:YP_002344160.1 GeneID:905062;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0747 2C unknown 2C len: 35 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 UTR_Extractor 5'-UTR 703019 703026 . + . ID=utr261;locus_tag=Cj0748;product=hypothetical protein NC_002163.1 RefSeq gene 703027 703119 . + . ID=gene711;Name=Cj0748;locus_tag=Cj0748;Dbxref=GeneID:905063;gbkey=Gene NC_002163.1 RefSeq CDS 703027 703119 . + 0 ID=cds665;Parent=gene711;Name=YP_002344161.1;Dbxref=UniProtKB FTrEMBL:Q0PAD6 Genbank:YP_002344161.1 GeneID:905063;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0748 2C unknown 2C len: 30 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 RefSeq region 703132 703170 . + . ID=id1424;Name=id1424;Dbxref=GeneID:905064;gbkey=misc_feature;Note=Original 282000 29 note: Cj0752 2C probable IS element transposase pseudogene 2C len: 1113 bp 3B similar to parts of e.g. TR:O06526 28EMBL:U95957 29 H. pylori transposase homolog B 28442 aa 29. Similar to several Hp genes e.g. HP1095 2CHP0997 2C HP0989 2C HP0438 2C HP1534. No other C.j. matches 7EUpdated 282006 29 note: Pfam domains PF01385 Probable transposase and PF07282 transposase DNA-binding domain were both identified within CDS. Further support given to product function. Similarity and characterisation work within Helicobacter pylori has led to not being added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - IS elements 7EPMID:9858724 2C PMID:15019987 NC_002163.1 RefSeq pseudogene 703132 704369 . + . ID=gene712;Name=Cj0752;locus_tag=Cj0752;Dbxref=GeneID:905064;gbkey=Gene NC_002163.1 RefSeq region 703153 703170 . + . ID=id1425;Name=id1425;Dbxref=GeneID:905064;gbkey=misc_feature;Note=HMMPfam hit to PF01385 2C Probable transposase 2C score 7e-08 NC_002163.1 RefSeq region 703172 703219 . + . ID=id1424;Name=id1424;Dbxref=GeneID:905064;gbkey=misc_feature;Note=Original 282000 29 note: Cj0752 2C probable IS element transposase pseudogene 2C len: 1113 bp 3B similar to parts of e.g. TR:O06526 28EMBL:U95957 29 H. pylori transposase homolog B 28442 aa 29. Similar to several Hp genes e.g. HP1095 2CHP0997 2C HP0989 2C HP0438 2C HP1534. No other C.j. matches 7EUpdated 282006 29 note: Pfam domains PF01385 Probable transposase and PF07282 transposase DNA-binding domain were both identified within CDS. Further support given to product function. Similarity and characterisation work within Helicobacter pylori has led to not being added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - IS elements 7EPMID:9858724 2C PMID:15019987 NC_002163.1 RefSeq region 703172 703219 . + . ID=id1425;Name=id1425;Dbxref=GeneID:905064;gbkey=misc_feature;Note=HMMPfam hit to PF01385 2C Probable transposase 2C score 7e-08 NC_002163.1 RefSeq region 703219 703263 . + . ID=id1424;Name=id1424;Dbxref=GeneID:905064;gbkey=misc_feature;Note=Original 282000 29 note: Cj0752 2C probable IS element transposase pseudogene 2C len: 1113 bp 3B similar to parts of e.g. TR:O06526 28EMBL:U95957 29 H. pylori transposase homolog B 28442 aa 29. Similar to several Hp genes e.g. HP1095 2CHP0997 2C HP0989 2C HP0438 2C HP1534. No other C.j. matches 7EUpdated 282006 29 note: Pfam domains PF01385 Probable transposase and PF07282 transposase DNA-binding domain were both identified within CDS. Further support given to product function. Similarity and characterisation work within Helicobacter pylori has led to not being added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - IS elements 7EPMID:9858724 2C PMID:15019987 NC_002163.1 RefSeq region 703219 703263 . + . ID=id1425;Name=id1425;Dbxref=GeneID:905064;gbkey=misc_feature;Note=HMMPfam hit to PF01385 2C Probable transposase 2C score 7e-08 NC_002163.1 RefSeq region 703266 704006 . + . ID=id1425;Name=id1425;Dbxref=GeneID:905064;gbkey=misc_feature;Note=HMMPfam hit to PF01385 2C Probable transposase 2C score 7e-08 NC_002163.1 RefSeq region 703266 704369 . + . ID=id1424;Name=id1424;Dbxref=GeneID:905064;gbkey=misc_feature;Note=Original 282000 29 note: Cj0752 2C probable IS element transposase pseudogene 2C len: 1113 bp 3B similar to parts of e.g. TR:O06526 28EMBL:U95957 29 H. pylori transposase homolog B 28442 aa 29. Similar to several Hp genes e.g. HP1095 2CHP0997 2C HP0989 2C HP0438 2C HP1534. No other C.j. matches 7EUpdated 282006 29 note: Pfam domains PF01385 Probable transposase and PF07282 transposase DNA-binding domain were both identified within CDS. Further support given to product function. Similarity and characterisation work within Helicobacter pylori has led to not being added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - IS elements 7EPMID:9858724 2C PMID:15019987 NC_002163.1 RefSeq region 704067 704276 . + . ID=id1426;Name=id1426;Dbxref=GeneID:905064;gbkey=misc_feature;Note=HMMPfam hit to PF07282 2C transposase DNA-binding domai 2C score 1.1e-33 ### NC_002163.1 RefSeq CDS 704442 705125 . - 0 ID=cds666;Parent=gene713;gene=tonB3;Name=YP_002344162.1;Dbxref=GOA:Q0PAD5 InterPro:IPR003538 InterPro:IPR006260 UniProtKB FTrEMBL:Q0PAD5 Genbank:YP_002344162.1 GeneID:905065;gbkey=CDS;product=TonB transport protein;Note=Original 282000 29 note: Cj0753c 2C tonB3 2C probable tonB transport protein 2C len: 227 aa 3B almost identical to TONB_CAMCO C. coli tonB protein 28232 aa 29 3B 96.6 25 identity in 232 aa overlap 2C and similar to e.g. TONB_ECOLI 28239 aa 2Cfasta scores 3B opt: 154 z-score: 170.4 E 28 29: 0.034 2C 29.6 25 identity in 162 aa overlap. 34.6 25 identity to HP1341. Also similar to tonB2 2C Cj1630 2841.7 25 identity in 230 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF03544 Gram-negative bacterial tonB protein identified within CDS. One probable transmembrane helix predicted by TMHMM2.0. Further support given to product function. Characterised within Campylobacter strains. not added to product function. Functional classification -Transport 2Fbinding proteins - Other 7EPMID:9190817 2C PMID:11395459 NC_002163.1 RefSeq gene 704442 705125 . - . ID=gene713;gene=tonB3;Name=tonB3;locus_tag=Cj0753c;Dbxref=GeneID:905065;gbkey=Gene NC_002163.1 RefSeq region 704568 704672 . - . ID=id1427;gene=tonB3;Name=id1427;Dbxref=GeneID:905065;gbkey=misc_feature;Note=HMMPfam hit to PF03544 2C Gram-negative bacterial tonB protein 2C score 4.1e-13 NC_002163.1 RefSeq region 705039 705092 . - . ID=id1428;gene=tonB3;Name=id1428;Dbxref=GeneID:905065;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0753c by TMHMM2.0 at aa 12-29 ### NC_002163.1 RefSeq CDS 705450 707540 . + 0 ID=cds667;Parent=gene714;gene=cfrA;Name=YP_002344163.1;Dbxref=GOA:Q0PAD4 InterPro:IPR000531 InterPro:IPR012910 UniProtKB FTrEMBL:Q0PAD4 Genbank:YP_002344163.1 GeneID:905066;gbkey=CDS;product=ferric enterobactin uptake receptor;Note=Original 282000 29 note: Cj0755 2C cfrA 2C probable iron uptake protein 28ferric receptor 29 2C len: 696 aa 3B almost identical to TR:O07651 28EMBL:U80812 29 C. coli ferric receptor CFRA 28696 aa 29 3B 98.7 25 identity in 696 aa overlap. Also simimlar to e.g. TR:O87518 28EMBL:AF081285 29 E. coli exogenous ferric siderophore receptor R4 28669 aa 29 2C fasta scores 3B opt: 1127 z-score: 1247.0 E 28 29: 0 2C 34.5 25 identity in 693 aa overlap. 23.4 25 identity to HP0686 7EUpdated 282006 29 note: Pfam domains PF07715 TonB-dependent Receptor Plug Domain and PF00593 TonB dependent receptor identified within CDS. Further support given to product function. Characterisation work within Campylobacter jejuni 28following on from Campylobacter coli 29 2C has led to product function being modified to more specfic family member. not added to product function. Functional classification - Transport 2Fbinding proteins - Cations 7EPMID:9190817 2C PMID:9765558 2C PMID:15231804 2CPMID:15632442 NC_002163.1 RefSeq gene 705450 707540 . + . ID=gene714;gene=cfrA;Name=cfrA;locus_tag=Cj0755;Dbxref=GeneID:905066;gbkey=Gene NC_002163.1 RefSeq region 705561 705902 . + . ID=id1429;gene=cfrA;Name=id1429;Dbxref=GeneID:905066;gbkey=misc_feature;Note=HMMPfam hit to PF07715 2C TonB-dependent Receptor Plug Domain 2C score 4.3e-21 NC_002163.1 RefSeq region 706719 707537 . + . ID=id1430;gene=cfrA;Name=id1430;Dbxref=GeneID:905066;gbkey=misc_feature;Note=HMMPfam hit to PF00593 2C TonB dependent receptor 2Cscore 2.4e-27 ### NC_002163.1 UTR_Extractor 5'-UTR 707802 707839 . + . ID=utr262;locus_tag=Cj0757;product=heat-inducible transcription repressor NC_002163.1 RefSeq CDS 707840 708634 . + 0 ID=cds668;Parent=gene715;gene=hrcA;Name=YP_002344164.1;Dbxref=GOA:Q9PPG2 InterPro:IPR011991 UniProtKB FSwiss-Prot:Q9PPG2 Genbank:YP_002344164.1 GeneID:905067;gbkey=CDS;product=heat-inducible transcription repressor;Note=Acts as a negative regulator of the grpE-dnaK-dnaJ and groELS class I heat shock operons by preventing heat-shock induction NC_002163.1 RefSeq gene 707840 708634 . + . ID=gene715;gene=hrcA;Name=hrcA;locus_tag=Cj0757;Dbxref=GeneID:905067;gbkey=Gene NC_002163.1 RefSeq gene 708631 709161 . + . ID=gene716;gene=grpE;Name=grpE;locus_tag=Cj0758;Dbxref=GeneID:905068;gbkey=Gene NC_002163.1 RefSeq CDS 708631 709161 . + 0 ID=cds669;Parent=gene716;gene=grpE;Name=YP_002344165.1;Dbxref=GOA:O69297 HSSP:P09372 InterPro:IPR000740 InterPro:IPR009012 InterPro:IPR013805 UniProtKB FSwiss-Prot:O69297 Genbank:YP_002344165.1 GeneID:905068;gbkey=CDS;product=heat shock protein GrpE;Note=with DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins 3B may act as a thermosensor NC_002163.1 RefSeq region 708664 709158 . + . ID=id1431;gene=grpE;Name=id1431;Dbxref=GeneID:905068;gbkey=misc_feature;Note=HMMPfam hit to PF01025 2C GrpE 2C score 4.9e-55 ### NC_002163.1 RefSeq CDS 709183 711054 . + 0 ID=cds670;Parent=gene717;gene=dnaK;Name=YP_002344166.1;Dbxref=GOA:O69298 HSSP:P04475 InterPro:IPR001023 InterPro:IPR012725 InterPro:IPR013126 UniProtKB FSwiss-Prot:O69298 Genbank:YP_002344166.1 GeneID:905069;gbkey=CDS;product=molecular chaperone DnaK;Note=heat shock protein 70 3B assists in folding of nascent polypeptide chains 3B refolding of misfolded proteins 3B utilizes ATPase activity to help fold 3B co-chaperones are DnaJ and GrpE 3B multiple copies in some bacteria NC_002163.1 RefSeq gene 709183 711054 . + . ID=gene717;gene=dnaK;Name=dnaK;locus_tag=Cj0759;Dbxref=GeneID:905069;gbkey=Gene NC_002163.1 RefSeq region 709192 710982 . + . ID=id1432;gene=dnaK;Name=id1432;Dbxref=GeneID:905069;gbkey=misc_feature;Note=HMMPfam hit to PF00012 2C Hsp70 protein 2C score 0 NC_002163.1 RefSeq region 709201 709224 . + . ID=id1433;gene=dnaK;Name=id1433;Dbxref=GeneID:905069;gbkey=misc_feature;Note=PS00297 Heat shock hsp70 proteins family signature 1 NC_002163.1 RefSeq region 709750 709791 . + . ID=id1434;gene=dnaK;Name=id1434;Dbxref=GeneID:905069;gbkey=misc_feature;Note=PS00329 Heat shock hsp70 proteins family signature 2 NC_002163.1 RefSeq region 710173 710217 . + . ID=id1435;gene=dnaK;Name=id1435;Dbxref=GeneID:905069;gbkey=misc_feature;Note=PS01036 Heat shock hsp70 proteins family signature 3 ### NC_002163.1 UTR_Extractor 5'-UTR 711296 711313 . + . ID=utr263;locus_tag=Cj0760;product=hypothetical protein NC_002163.1 RefSeq gene 711314 712336 . + . ID=gene718;Name=Cj0760;locus_tag=Cj0760;Dbxref=GeneID:905070;gbkey=Gene NC_002163.1 RefSeq CDS 711314 712336 . + 0 ID=cds671;Parent=gene718;Name=YP_002344167.1;Dbxref=UniProtKB FTrEMBL:Q0PAD0 Genbank:YP_002344167.1 GeneID:905070;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0760 2C unknown 2C len: 340 aa 3B similar to hypothetical proteins e.g. YZ34_MYCTU Rv0906 2C 28MTCY31.34 29 28372 aa 29 2C fasta scores 3B opt: 598 z-score: 724.2 E 28 29: 4.8e-33 2C 29.9 25 identity in 335 aa overlap. Some similarity in C-terminus to ROMA_KLEPN outer membrane protein roma 28fragment 29 28132 aa 29 2C fasta scores 3B opt: 335 z-score: 415.0 E 28 29: 8.1e-16 2C 43.0 25 identity in 114 aa overlap. No Hp match 7EUpdated 282006 29 note: Literature search identified paper giving clues to product function. Product function modified based on literature search. kept within product function. Functional classification - Conserved hypothetical proteins 7EPMID:15758238 NC_002163.1 RefSeq gene 712406 712747 . + . ID=gene719;Name=Cj0761;locus_tag=Cj0761;Dbxref=GeneID:905071;gbkey=Gene NC_002163.1 RefSeq CDS 712406 712747 . + 0 ID=cds672;Parent=gene719;Name=YP_002344168.1;Dbxref=GOA:Q0PAC9 UniProtKB FTrEMBL:Q0PAC9 Genbank:YP_002344168.1 GeneID:905071;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0761 2C unknown 2C len: aa 3B similar to hypothetical proteins e.g. TR:O67079 28EMBL:AE000715 29 Aquifex aeolicus AQ_943 28107 aa 29 2C fasta scores 3B opt: 130 z-score: 186.5 E 28 29: 0.0043 2C 28.6 25 identity in 84 aa overlap. 55.8 25 identity to HP0902 7EUpdated 282006 29 note: Literature search identified paper giving clues to product function. Functional classification - Conserved hypothetical proteins 7EPMID:15758235 NC_002163.1 RefSeq gene 712797 713966 . - . ID=gene720;gene=aspB;Name=aspB;locus_tag=Cj0762c;Dbxref=GeneID:905072;gbkey=Gene NC_002163.1 RefSeq CDS 712797 713966 . - 0 ID=cds673;Parent=gene720;gene=aspB;Name=YP_002344169.1;Dbxref=GOA:Q0PAC8 InterPro:IPR001176 InterPro:IPR004839 InterPro:IPR015421 InterPro:IPR015422 UniProtKB FTrEMBL:Q0PAC8 Genbank:YP_002344169.1 GeneID:905072;gbkey=CDS;product=aspartate aminotransferase;Note=catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate NC_002163.1 RefSeq region 712812 713738 . - . ID=id1436;gene=aspB;Name=id1436;Dbxref=GeneID:905072;gbkey=misc_feature;Note=HMMPfam hit to PF00155 2C Aminotransferase class I and II 2C score 5.3e-50 ### NC_002163.1 RefSeq CDS 714138 714776 . - 0 ID=cds674;Parent=gene721;gene=cysE;Name=YP_002344170.1;Dbxref=GOA:Q0PAC7 InterPro:IPR001451 InterPro:IPR005881 UniProtKB FTrEMBL:Q0PAC7 Genbank:YP_002344170.1 GeneID:905073;gbkey=CDS;product=serine acetyltransferase;Note=Original 282000 29 note: Cj0763c 2C cysE 2C probable serine acetyltransferase 2C len: 212 aa 3B highly similar to many e.g. CYSE_BACSU serine acetyltransferase 28EC 2.3.1.30 29 28217 aa 29 2C fasta scores 3B opt: 598 z-score: 700.2 E 28 29: 1e-31 2C 46.6 25 identity in 204 aa overlap. 50.9 25 identity to HP1210. Contains PS00101 Hexapeptide-repeat containing-transferases signature and 2x Pfam match to entry PF00132 hexapep 2C Bacterial transferase hexapeptide 28four repeats 29 7EUpdated 282006 29 note: Characterised in Bacillus subtilis with acceptable identity score. not added to product function. Functional classification -Amino acid biosynthesis - Serine family 7EPMID:7510287 NC_002163.1 RefSeq gene 714138 714776 . - . ID=gene721;gene=cysE;Name=cysE;locus_tag=Cj0763c;Dbxref=GeneID:905073;gbkey=Gene NC_002163.1 RefSeq region 714306 714392 . - . ID=id1437;gene=cysE;Name=id1437;Dbxref=GeneID:905073;gbkey=misc_feature;Note=PS00101 Hexapeptide-repeat containing-transferases signature NC_002163.1 RefSeq region 714312 714365 . - . ID=id1438;gene=cysE;Name=id1438;Dbxref=GeneID:905073;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 0.31 NC_002163.1 RefSeq region 714366 714419 . - . ID=id1439;gene=cysE;Name=id1439;Dbxref=GeneID:905073;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 17 NC_002163.1 RefSeq region 714447 714500 . - . ID=id1440;gene=cysE;Name=id1440;Dbxref=GeneID:905073;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28three rep 2C score 0.077 ### NC_002163.1 RefSeq CDS 714777 716612 . - 0 ID=cds675;Parent=gene722;gene=speA;Name=YP_002344171.1;Dbxref=GOA:Q0PAC6 InterPro:IPR000183 InterPro:IPR002985 UniProtKB FTrEMBL:Q0PAC6 Genbank:YP_002344171.1 GeneID:905074;gbkey=CDS;product=arginine decarboxylase;Note=catalyzes the formation of agmatine from arginine in putrescine and spermidine biosynthesis NC_002163.1 RefSeq gene 714777 716612 . - . ID=gene722;gene=speA;Name=speA;locus_tag=Cj0764c;Dbxref=GeneID:905074;gbkey=Gene NC_002163.1 RefSeq region 714996 715397 . - . ID=id1441;gene=speA;Name=id1441;Dbxref=GeneID:905074;gbkey=misc_feature;Note=HMMPfam hit to PF00278 2C Pyridoxal-dependent decarboxylase 2C C- 2C score 2.2e-08 NC_002163.1 RefSeq region 715629 716441 . - . ID=id1442;gene=speA;Name=id1442;Dbxref=GeneID:905074;gbkey=misc_feature;Note=HMMPfam hit to PF02784 2C Pyridoxal-dependent decarboxylase 2C py 2C score 1.7e-39 NC_002163.1 RefSeq region 716310 716366 . - . ID=id1443;gene=speA;Name=id1443;Dbxref=GeneID:905074;gbkey=misc_feature;Note=PS00878 Orn 2FDAP 2FArg decarboxylases family 2 pyridoxal-P attachment site NC_002163.1 RefSeq gene 716609 717835 . - . ID=gene723;gene=hisS;Name=hisS;locus_tag=Cj0765c;Dbxref=GeneID:905075;gbkey=Gene NC_002163.1 RefSeq CDS 716609 717835 . - 0 ID=cds676;Parent=gene723;gene=hisS;Name=YP_002344172.1;Dbxref=GOA:Q9PPF4 HSSP:O32422 InterPro:IPR002314 InterPro:IPR004154 InterPro:IPR004516 InterPro:IPR006195 InterPro:IPR015805 InterPro:IPR015807 UniProtKB FSwiss-Prot:Q9PPF4 Genbank:YP_002344172.1 GeneID:905075;gbkey=CDS;product=histidyl-tRNA synthetase;Note=catalyzes a two-step reaction 2C first charging a histidine molecule by linking its carboxyl group to the alpha-phosphate of ATP 2C followed by transfer of the aminoacyl-adenylate to its tRNA 3B class II aminoacyl-tRNA synthetase 3B forms homodimers 3B some organisms have a paralogous gene 2C hisZ 2C that is similar to hisS and produces a protein that performs the first step in histidine biosynthesis along with HisG NC_002163.1 RefSeq region 716612 716872 . - . ID=id1444;gene=hisS;Name=id1444;Dbxref=GeneID:905075;gbkey=misc_feature;Note=HMMPfam hit to PF03129 2C Anticodon binding domain 2Cscore 0.018 NC_002163.1 UTR_Extractor 5'-UTR 716613 716628 . - . ID=utr264;locus_tag=Cj0764c;product=arginine decarboxylase NC_002163.1 RefSeq region 716906 716935 . - . ID=id1445;gene=hisS;Name=id1445;Dbxref=GeneID:905075;gbkey=misc_feature;Note=PS00339 Aminoacyl-transfer RNA synthetases class-II signature 2 NC_002163.1 RefSeq region 717365 717817 . - . ID=id1446;gene=hisS;Name=id1446;Dbxref=GeneID:905075;gbkey=misc_feature;Note=HMMPfam hit to PF00587 2C tRNA synthetase class II core domain 28 2C score 1.5e-36 NC_002163.1 RefSeq gene 717832 718410 . - . ID=gene724;gene=tmk;Name=tmk;locus_tag=Cj0766c;Dbxref=GeneID:905076;gbkey=Gene NC_002163.1 RefSeq CDS 717832 718410 . - 0 ID=cds677;Parent=gene724;gene=tmk;Name=YP_002344173.1;Dbxref=GOA:Q9PPF3 HSSP:P37345 InterPro:IPR000062 UniProtKB FSwiss-Prot:Q9PPF3 Genbank:YP_002344173.1 GeneID:905076;gbkey=CDS;product=thymidylate kinase;Note=catalyzes the reversible phosphoryl transfer from adenosine triphosphate 28ATP 29 to thymidine monophosphate 28dTMP 29 to form thymidine diphosphate 28dTDP 29 NC_002163.1 RefSeq region 717850 718398 . - . ID=id1447;gene=tmk;Name=id1447;Dbxref=GeneID:905076;gbkey=misc_feature;Note=HMMPfam hit to PF02223 2C Thymidylate kinase 2C score 5.9e-33 NC_002163.1 RefSeq region 718126 718164 . - . ID=id1448;gene=tmk;Name=id1448;Dbxref=GeneID:905076;gbkey=misc_feature;Note=PS01331 Thymidylate kinase signature NC_002163.1 RefSeq region 718369 718392 . - . ID=id1449;gene=tmk;Name=id1449;Dbxref=GeneID:905076;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq gene 718401 718877 . - . ID=gene725;gene=coaD;Name=coaD;locus_tag=Cj0767c;Dbxref=GeneID:905077;gbkey=Gene NC_002163.1 RefSeq CDS 718401 718877 . - 0 ID=cds678;Parent=gene725;gene=coaD;Name=YP_002344174.1;Dbxref=GOA:Q9PPF2 HSSP:P23875 InterPro:IPR001980 InterPro:IPR004820 InterPro:IPR004821 InterPro:IPR014729 UniProtKB FSwiss-Prot:Q9PPF2 Genbank:YP_002344174.1 GeneID:905077;gbkey=CDS;product=phosphopantetheine adenylyltransferase;Note=Catalyzes the conversion of ATP and pantetheine 4 27-phosphate to diphosphate and 3 27-dephospho-coA NC_002163.1 RefSeq region 718479 718868 . - . ID=id1450;gene=coaD;Name=id1450;Dbxref=GeneID:905077;gbkey=misc_feature;Note=HMMPfam hit to PF01467 2C Cytidylyltransferase 2C score 1.9e-29 ### NC_002163.1 RefSeq CDS 718917 719480 . - 0 ID=cds679;Parent=gene726;Name=YP_002344175.1;Dbxref=GOA:Q9PPF1 InterPro:IPR003382 InterPro:IPR004507 UniProtKB FSwiss-Prot:Q9PPF1 Genbank:YP_002344175.1 GeneID:905078;gbkey=CDS;product=3-octaprenyl-4-hydroxybenzoate carboxy-lyase;Note=catalyzes the formation of 2-octaprenylphenol from 3-octaprenyl-4-hydroxybenzoate NC_002163.1 RefSeq gene 718917 719480 . - . ID=gene726;Name=Cj0768c;locus_tag=Cj0768c;Dbxref=GeneID:905078;gbkey=Gene NC_002163.1 RefSeq region 719112 719480 . - . ID=id1451;Name=id1451;Dbxref=GeneID:905078;gbkey=misc_feature;Note=HMMPfam hit to PF02441 2C Flavoprotein 2C score 2.5e-29 NC_002163.1 RefSeq gene 719477 720139 . - . ID=gene727;gene=flgA;Name=flgA;locus_tag=Cj0769c;Dbxref=GeneID:905079;gbkey=Gene NC_002163.1 RefSeq CDS 719477 720139 . - 0 ID=cds680;Parent=gene727;gene=flgA;Name=YP_002344176.1;Dbxref=GOA:Q0PAC1 InterPro:IPR013974 InterPro:IPR017585 UniProtKB FTrEMBL:Q0PAC1 Genbank:YP_002344176.1 GeneID:905079;gbkey=CDS;product=flagellar basal body P-ring biosynthesis protein FlgA;Note=required for the assembly of the flagellar basal body P-ring NC_002163.1 RefSeq region 719480 719962 . - . ID=id1452;gene=flgA;Name=id1452;Dbxref=GeneID:905079;gbkey=misc_feature;Note=HMMPfam hit to PF03240 2C FlgA family 2C score 8e-05 ### NC_002163.1 UTR_Extractor 5'-UTR 720140 720169 . - . ID=utr265;locus_tag=Cj0769c;product=flagellar basal body P-ring biosynthesis protein FlgA NC_002163.1 RefSeq CDS 720223 720999 . - 0 ID=cds681;Parent=gene728;Name=YP_002344177.1;Dbxref=InterPro:IPR004872 UniProtKB FTrEMBL:Q0PAC0 Genbank:YP_002344177.1 GeneID:905080;gbkey=CDS;product=NLPA family lipoprotein;Note=Original 282000 29 note: Cj0770c 2C probable periplasmic protein 2C len: 258 aa 3B similar to lipoproteins from other organisms e.g. PLPC_PASHA outer membrane lipoprotein 3 precursor 28263 aa 29 2C fasta scores 3B opt: 569 z-score: 657.0 E 28 29: 2.7e-29 2C 38.9 25 identity in 265 aa overlap 2C and TR:O69441 28EMBL:AJ005668 29 Legionella pneumophila 29 kda immunogenic protein 28259 aa 29 2C fasta scores 3B opt: 584 z-score: 674.2 E 28 29: 3e-30 2C 41.0 25 identity in 261 aa overlap. Also similar to Cj0772c 2855.0 25 identity 29 2C Cj0771c 2854.8 25 identity 29 and Cj1200 2844.9 25 identity 29. Single copy in Hp 28HP1564 29 7EUpdated 282006 29 note: Pfam domain PF03180 NLPA lipoprotein identified within CDS. NLPA lipoproteins are a family of bacterial lipoproteins that contain many antigenic members 2C which may be involved in bacterial virulence. The function is currently unknown. Product modified to more specific family member due to motif match. Some characterisation work in more than one species. Highly similar to Cj0771c and Cj0772c. kept within product function. Functional classification -Miscellaneous periplasmic proteins 7EPMID:12169620 NC_002163.1 RefSeq gene 720223 720999 . - . ID=gene728;Name=Cj0770c;locus_tag=Cj0770c;Dbxref=GeneID:905080;gbkey=Gene NC_002163.1 RefSeq region 720226 720930 . - . ID=id1453;Name=id1453;Dbxref=GeneID:905080;gbkey=misc_feature;Note=HMMPfam hit to PF03180 2C NLPA lipoprotein 2C score 5.2e-129 NC_002163.1 RefSeq region 720913 720981 . - . ID=id1454;Name=id1454;Dbxref=GeneID:905080;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0770c by TMHMM2.0 at aa 7-29 ### NC_002163.1 RefSeq gene 721009 721779 . - . ID=gene729;Name=Cj0771c;locus_tag=Cj0771c;Dbxref=GeneID:905081;gbkey=Gene NC_002163.1 RefSeq CDS 721009 721779 . - 0 ID=cds682;Parent=gene729;Name=YP_002344178.1;Dbxref=InterPro:IPR004872 UniProtKB FTrEMBL:Q0PAB9 Genbank:YP_002344178.1 GeneID:905081;gbkey=CDS;product=NLPA family lipoprotein;Note=Original 282000 29 note: Cj0771c 2C probable periplasmic protein 2C len: 258 aa 3B similar to lipoproteins from other organisms e.g. NLPA_ECOLI lipoprotein-28 precursor 28272 aa 29 2C fasta scores 3B opt: 623 z-score: 705.2 E 28 29: 5.6e-32 2C46.4 25 identity in 237 aa overlap 2C and TR:O69441 28EMBL:AJ005668 29 Legionella pneumophila 29 kda immunogenic protein 28259 aa 29 2C fasta scores 3B opt: 661 z-score: 747.9 E 28 29: 0 2C 44.2 25 identity in 258 aa overlap. Also similar to Cj0772c 2852.5 25 identity 29 2C Cj0770c 2854.8 25 identity 29 and Cj1200 2845.6 25 identity 29. Single copy in Hp 28HP1564 29 7EUpdated 282006 29 note: Pfam domain PF03180 NLPA lipoprotein identified within CDS. NLPA lipoproteins are a family of bacterial lipoproteins that contain many antigenic members 2C which may be involved in bacterial virulence. The function is currently unknown. Product modified to more specific family member due to motif match. Some characterisation in more than one species. Also similar to Cj0770c and Cj0772c. kept within product function. Functional classification -Miscellaneous periplasmic proteins 7EPMID:12169620 NC_002163.1 RefSeq region 721012 721713 . - . ID=id1455;Name=id1455;Dbxref=GeneID:905081;gbkey=misc_feature;Note=HMMPfam hit to PF03180 2C NLPA lipoprotein 2C score 2.2e-132 ### NC_002163.1 RefSeq CDS 721828 722601 . - 0 ID=cds683;Parent=gene730;Name=YP_002344179.1;Dbxref=InterPro:IPR004872 UniProtKB FTrEMBL:Q0PAB8 Genbank:YP_002344179.1 GeneID:905082;gbkey=CDS;product=NLPA family lipoprotein;Note=Original 282000 29 note: Cj0772c 2C probable periplasmic protein 2C len: 258 aa 3B similar to lipoproteins from other organisms e.g. PLPC_PASHA outer membrane lipoprotein 3 precursor 28263 aa 29 2C fasta scores 3B opt: 642 z-score: 721.7 E 28 29: 6.7e-33. 40.8 25 identity in 260 aa overlap 2C and TR:O69441 28EMBL:AJ005668 29 Legionella pneumophila 29 kda immunogenic protein 28259 aa 29 2C fasta scores 3B opt: 638 z-score: 717.3 E 28 29: 1.2e-32. 39.8 25 identity in 259 aa overlap. Also similar to Cj0770c 2855.0 25 identity 29 2C Cj0771c 2852.5 25 identity 29 and Cj1200 2857.5 25 identity 29. Single copy in Hp 28HP1564 3B 47.7 25 identity in 243 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF03180 NLPA lipoprotein identified within CDS. NLPA lipoproteins are a family of bacterial lipoproteins that contain many antigenic members 2C which may be involved in bacterial virulence. The function is currently unknown. Product modified to more specific family member due to motif match. Some characterisation in more than one species. Also similar to Cj0770c and Cj0771c. kept within product function. Functional classification -Miscellaneous periplasmic proteins 7EPMID:12169620 NC_002163.1 RefSeq gene 721828 722601 . - . ID=gene730;Name=Cj0772c;locus_tag=Cj0772c;Dbxref=GeneID:905082;gbkey=Gene NC_002163.1 RefSeq region 721831 722532 . - . ID=id1456;Name=id1456;Dbxref=GeneID:905082;gbkey=misc_feature;Note=HMMPfam hit to PF03180 2C NLPA lipoprotein 2C score 1.1e-145 NC_002163.1 RefSeq region 722515 722601 . - . ID=id1457;Name=id1457;Dbxref=GeneID:905082;gbkey=misc_feature;Note=PS00430 TonB-dependent receptor proteins signature 1 ### NC_002163.1 RefSeq CDS 722791 723702 . - 0 ID=cds684;Parent=gene731;Name=YP_002344180.1;Dbxref=GOA:Q0PAB7 InterPro:IPR000515 UniProtKB FTrEMBL:Q0PAB7 Genbank:YP_002344180.1 GeneID:905083;gbkey=CDS;product=binding-protein dependent transport system permease;Note=Original 282000 29 note: Cj0773c 2C probable binding-protein dependent transport system permease 2C len: 303 aa 3B similar to many e.g. PROW_BACSU glycine betaine 2FL-proline transport system permease 28217 aa 29 2C fasta scores 3B opt: 212 z-score: 249.9 E 28 29: 1.3e-06 2C 30.0 25 identity in 190 aa overlap. 43.9 25 identity in 205 aa overlap to HP1577. Contains Pfam match to entry PF00528 BPD_transp 2C Binding-protein-dependent transport systems inner membrane component 7EUpdated 282006 29 note: Seven probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity score carried out yet. added to product function. Functional classification -Transport 2Fbinding proteins - Other 7EPMID:12169620 NC_002163.1 RefSeq gene 722791 723702 . - . ID=gene731;Name=Cj0773c;locus_tag=Cj0773c;Dbxref=GeneID:905083;gbkey=Gene NC_002163.1 RefSeq region 722800 722859 . - . ID=id51;Name=id51;Dbxref=GeneID:905083;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0773c by TMHMM2.0 at aa 57-79 2C 92-114 2C 119-141 2C 184-206 2C226-248 2C 260-277 and 282-301 NC_002163.1 RefSeq region 722872 722925 . - . ID=id51;Name=id51;Dbxref=GeneID:905083;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0773c by TMHMM2.0 at aa 57-79 2C 92-114 2C 119-141 2C 184-206 2C226-248 2C 260-277 and 282-301 NC_002163.1 RefSeq region 722941 723552 . - . ID=id1458;Name=id1458;Dbxref=GeneID:905083;gbkey=misc_feature;Note=HMMPfam hit to PF00528 2C Binding-protein-dependent transport syst 2C score 1.9e-15 NC_002163.1 RefSeq region 722959 723027 . - . ID=id51;Name=id51;Dbxref=GeneID:905083;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0773c by TMHMM2.0 at aa 57-79 2C 92-114 2C 119-141 2C 184-206 2C226-248 2C 260-277 and 282-301 NC_002163.1 RefSeq region 723085 723153 . - . ID=id51;Name=id51;Dbxref=GeneID:905083;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0773c by TMHMM2.0 at aa 57-79 2C 92-114 2C 119-141 2C 184-206 2C226-248 2C 260-277 and 282-301 NC_002163.1 RefSeq region 723280 723348 . - . ID=id51;Name=id51;Dbxref=GeneID:905083;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0773c by TMHMM2.0 at aa 57-79 2C 92-114 2C 119-141 2C 184-206 2C226-248 2C 260-277 and 282-301 NC_002163.1 RefSeq region 723361 723429 . - . ID=id51;Name=id51;Dbxref=GeneID:905083;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0773c by TMHMM2.0 at aa 57-79 2C 92-114 2C 119-141 2C 184-206 2C226-248 2C 260-277 and 282-301 NC_002163.1 RefSeq region 723466 723534 . - . ID=id51;Name=id51;Dbxref=GeneID:905083;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0773c by TMHMM2.0 at aa 57-79 2C 92-114 2C 119-141 2C 184-206 2C226-248 2C 260-277 and 282-301 NC_002163.1 RefSeq gene 723699 724709 . - . ID=gene732;Name=Cj0774c;locus_tag=Cj0774c;Dbxref=GeneID:905084;gbkey=Gene NC_002163.1 RefSeq CDS 723699 724709 . - 0 ID=cds685;Parent=gene732;Name=YP_002344181.1;Dbxref=GOA:Q0PAB6 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FSwiss-Prot:Q0PAB6 Genbank:YP_002344181.1 GeneID:905084;gbkey=CDS;product=ABC transporter ATP-binding protein;Note=Original 282000 29 note: Cj0774c 2C probable ABC transport system ATP-binding protein 2C len: 336 aa 3B similar to many e.g. HISP_ECOLI histidine transport ATP-binding protein 28257 aa 29 2C fasta scores 3B opt: 497 z-score: 566.5 E 28 29: 2.9e-24 2C 38.5 25 identity in 262 aa overlap 2C and OCCP_AGRT6 octopine permease ATP-binding protein P 28262 aa 29 2C fasta scores 3B opt: 511 z-score: 582.1 E 28 29: 4e-25 2C36.9 25 identity in 260 aa overlap. 38.9 25 identity to HP1576. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00211 ABC transporters family signature 2C and Pfam match to entry PF00005 ABC_tran 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Transport 2Fbinding proteins - Other 7EPMID:3313284 NC_002163.1 RefSeq region 724020 724631 . - . ID=id1459;Name=id1459;Dbxref=GeneID:905084;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 1.8e-69 NC_002163.1 RefSeq region 724206 724250 . - . ID=id1460;Name=id1460;Dbxref=GeneID:905084;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq region 724587 724610 . - . ID=id1461;Name=id1461;Dbxref=GeneID:905084;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 UTR_Extractor 5'-UTR 724710 724920 . - . ID=utr266;locus_tag=Cj0774c;product=ABC transporter ATP-binding protein NC_002163.1 RefSeq CDS 724714 727326 . - 0 ID=cds686;Parent=gene733;gene=valS;Name=YP_002344182.1;Dbxref=GOA:Q9PPE4 HSSP:P96142 InterPro:IPR001412 InterPro:IPR002300 InterPro:IPR002303 InterPro:IPR013155 InterPro:IPR014729 UniProtKB FSwiss-Prot:Q9PPE4 Genbank:YP_002344182.1 GeneID:904417;gbkey=CDS;product=valyl-tRNA synthetase;Note=valine--tRNA ligase 3B ValRS 3B converts valine ATP and tRNA 28Val 29 to AMP PPi and valyl-tRNA 28Val 29 3B class-I aminoacyl-tRNA synthetase type 1 subfamily 3B has a posttransfer editing process to hydrolyze mischarged Thr-tRNA 28Val 29 which is done by the editing domain NC_002163.1 RefSeq gene 724714 727326 . - . ID=gene733;gene=valS;Name=valS;locus_tag=Cj0775c;Dbxref=GeneID:904417;gbkey=Gene NC_002163.1 RefSeq region 725626 727302 . - . ID=id1462;gene=valS;Name=id1462;Dbxref=GeneID:904417;gbkey=misc_feature;Note=HMMPfam hit to PF00133 2C tRNA synthetases class I 28I 2C L 2C M and V 29 2C score 1.7e-207 NC_002163.1 RefSeq region 727168 727203 . - . ID=id1463;gene=valS;Name=id1463;Dbxref=GeneID:904417;gbkey=misc_feature;Note=PS00178 Aminoacyl-transfer RNA synthetases class-I signature ### NC_002163.1 RefSeq gene 727349 728371 . - . ID=gene734;Name=Cj0776c;locus_tag=Cj0776c;Dbxref=GeneID:905085;gbkey=Gene NC_002163.1 RefSeq CDS 727349 728371 . - 0 ID=cds687;Parent=gene734;Name=YP_002344183.1;Dbxref=UniProtKB FTrEMBL:Q0PAB4 Genbank:YP_002344183.1 GeneID:905085;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0776c 2C probable periplasmic protein 2C len: 340 aa 3B no Hp match. Contains N-terminal signal sequence. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 728291 728359 . - . ID=id1464;Name=id1464;Dbxref=GeneID:905085;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0776c by TMHMM2.0 at aa 5-27 ### NC_002163.1 UTR_Extractor 5'-UTR 728372 728404 . - . ID=utr267;locus_tag=Cj0776c;product=putative periplasmic protein NC_002163.1 UTR_Extractor 5'-UTR 728484 728499 . + . ID=utr268;locus_tag=Cj0777;product=putative ATP-dependent DNA helicase NC_002163.1 RefSeq CDS 728500 730530 . + 0 ID=cds688;Parent=gene735;Name=YP_002344184.1;Dbxref=GOA:Q0PAB3 InterPro:IPR000212 InterPro:IPR014016 InterPro:IPR014017 UniProtKB FTrEMBL:Q0PAB3 Genbank:YP_002344184.1 GeneID:905086;gbkey=CDS;product=ATP-dependent DNA helicase;Note=Original 282000 29 note: Cj0777 2C probable ATP-dependent DNA helicase 2C len: 676 aa 3B similar to many members of the uvrD family of helicases 2C e.g. PCRA_STAAU ATP-dependent helicase PCRA 28675 aa 29 2C fasta scores 3B opt: 561 z-score: 634.4 E 28 29: 4.9e-28 2C 29.0 25 identity in 694 aa overlap 2C and REP_ECOLI ATP-dependent DNA helicase REP 28673 aa 29 2C fasta scores 3B opt: 423 z-score: 478.5 E 28 29: 2.4e-19 2C27.3 25 identity in 682 aa overlap. 47.5 25 identity to HP0911. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 and Pfam match to entry PF00580 UvrD-helicase 2CUvrD 2FREP helicase 7EUpdated 282006 29 note: Characterisation work carried out within more than one species with marginal identity score. kept within product function. Functional classification - DNA replication 2Crestriction 2Fmodification 2C recombination and repair NC_002163.1 RefSeq gene 728500 730530 . + . ID=gene735;Name=Cj0777;locus_tag=Cj0777;Dbxref=GeneID:905086;gbkey=Gene NC_002163.1 RefSeq region 728515 729927 . + . ID=id1465;Name=id1465;Dbxref=GeneID:905086;gbkey=misc_feature;Note=HMMPfam hit to PF00580 2C UvrD 2FREP helicase 2C score 1.6e-90 NC_002163.1 RefSeq region 728572 728595 . + . ID=id1466;Name=id1466;Dbxref=GeneID:905086;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 UTR_Extractor 5'-UTR 730544 730568 . + . ID=utr269;locus_tag=Cj0778;product=major antigenic peptide PEB2 NC_002163.1 RefSeq gene 730569 731306 . + . ID=gene736;gene=peb2;Name=peb2;locus_tag=Cj0778;Dbxref=GeneID:905087;gbkey=Gene NC_002163.1 RefSeq CDS 730569 731306 . + 0 ID=cds689;Parent=gene736;gene=peb2;Name=YP_002344185.1;Dbxref=GOA:Q0PAB2 UniProtKB FTrEMBL:Q0PAB2 Genbank:YP_002344185.1 GeneID:905087;gbkey=CDS;product=major antigenic peptide PEB2;Note=Original 282000 29 note: Cj0778 2C peb2 2C major antigenic peptide PEB2 2C len: 245 aa 3B 94.9 25 identical to TR:G234576 2Csequenced by direct peptide sequencing 3B see: J. Biol. Chem. 266:16363-16369 281991 29. Also similar to TR:Q57410 28EMBL:U39068 2C U15606 29 Vibrio cholerae accessory colonization factor ACFC 28253 aa 29 2C fasta scores 3B opt: 430 z-score: 499.2 E 28 29: 1.7e-20 2C 33.9 25 identity in 248 aa overlap 2C and TR:P96759 28EMBL:U82533 29E. coli O45 ANM protein 28251 aa 29 2C fasta scores 3B opt: 417 z-score: 484.4 E 28 29: 1.1e-19 2C 33.2 25 identity in 247 aa overlap. Contains N-terminal signal sequence 7EUpdated 282006 29 note: Characterised in Campylobacter jejuni in 1991. not added to product function. Functional classification - Miscellaneous periplasmic proteins 7EPMID:1885571 NC_002163.1 UTR_Extractor 5'-UTR 731358 731404 . + . ID=utr270;locus_tag=Cj0779;product=thiol peroxidase NC_002163.1 RefSeq CDS 731405 731932 . + 0 ID=cds690;Parent=gene737;gene=tpx;Name=YP_002344186.1;Dbxref=GOA:Q9PPE0 HSSP:P72500 InterPro:IPR002065 InterPro:IPR012335 InterPro:IPR013740 UniProtKB FSwiss-Prot:Q9PPE0 Genbank:YP_002344186.1 GeneID:905088;gbkey=CDS;product=thiol peroxidase;Note=Original 282000 29 note: Cj0779 2C tpx 2C probable thiol peroxidase 2C len: 175 aa 3B similar to e.g. TPX_ECOLI thiol peroxidase 28EC 1.11.1.- 29 28167 aa 29 2C fasta scores 3B opt: 407 z-score: 489.0 E 28 29: 6.1e-20 2C 44.2 25 identity in 154 aa overlap 2C and TAGD_VIBCH TAGD protein 28164 aa 29 2C fasta scores 3B opt: 381 z-score: 458.8 E 28 29: 3e-18 2C 39.9 25 identity in 158 aa overlap. 42.2 25 identity to HP0390. Contains PS01265 Tpx family signature 2C and Pfam match to entry PF00578 AhpC-TSA 2C AhpC 2FTSA family 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Literature search also revealed additional papers with experiments in Campylobacter. Paper identified linking protein to glycoprotein 28PMID:12186869 29. Functional classification -Detoxification 7EPMID:15632442 2C PMID:12069882 2C PMID:12186869 NC_002163.1 RefSeq gene 731405 731932 . + . ID=gene737;gene=tpx;Name=tpx;locus_tag=Cj0779;Dbxref=GeneID:905088;gbkey=Gene NC_002163.1 RefSeq region 731462 731884 . + . ID=id1467;gene=tpx;Name=id1467;Dbxref=GeneID:905088;gbkey=misc_feature;Note=HMMPfam hit to PF00578 2C AhpC 2FTSA family 2C score 3.8e-21 NC_002163.1 RefSeq region 731648 731683 . + . ID=id1468;gene=tpx;Name=id1468;Dbxref=GeneID:905088;gbkey=misc_feature;Note=PS01265 Tpx family signature NC_002163.1 RefSeq region 731894 731926 . + . ID=id1469;gene=tpx;Name=id1469;Dbxref=GeneID:905088;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 UTR_Extractor 5'-UTR 732153 732178 . + . ID=utr271;locus_tag=Cj0780;product=nitrate reductase catalytic subunit NC_002163.1 RefSeq CDS 732179 734953 . + 0 ID=cds691;Parent=gene738;gene=napA;Name=YP_002344187.1;Dbxref=GOA:Q9PPD9 HSSP:Q53176 InterPro:IPR006311 InterPro:IPR006655 InterPro:IPR006656 InterPro:IPR006657 InterPro:IPR006963 InterPro:IPR009010 InterPro:IPR010051 UniProtKB FSwiss-Prot:Q9PPD9 Genbank:YP_002344187.1 GeneID:905089;gbkey=CDS;product=nitrate reductase catalytic subunit;Note=periplasmic 3B catalytic subunit 3B with NapBC catalyzes the reduction of nitrate to nitrite 3B NapAB receives electrons from NapC NC_002163.1 RefSeq gene 732179 734953 . + . ID=gene738;gene=napA;Name=napA;locus_tag=Cj0780;Dbxref=GeneID:905089;gbkey=Gene NC_002163.1 RefSeq region 732281 732445 . + . ID=id1470;gene=napA;Name=id1470;Dbxref=GeneID:905089;gbkey=misc_feature;Note=HMMPfam hit to PF04879 2C Molybdopterin oxidoreductase Fe4S4 do 2C score 2.3e-23 NC_002163.1 RefSeq region 732296 732349 . + . ID=id1471;gene=napA;Name=id1471;Dbxref=GeneID:905089;gbkey=misc_feature;Note=PS00551 Prokaryotic molybdopterin oxidoreductases signature 1 NC_002163.1 RefSeq region 732452 734014 . + . ID=id1472;gene=napA;Name=id1472;Dbxref=GeneID:905089;gbkey=misc_feature;Note=HMMPfam hit to PF00384 2C Molybdopterin oxidoreductase 2C score 6.2e-85 NC_002163.1 RefSeq region 734606 734932 . + . ID=id1473;gene=napA;Name=id1473;Dbxref=GeneID:905089;gbkey=misc_feature;Note=HMMPfam hit to PF01568 2C Molydopterin dinucleotide binding dom 2C score 3e-32 ### NC_002163.1 RefSeq gene 734971 735711 . + . ID=gene739;gene=napG;Name=napG;locus_tag=Cj0781;Dbxref=GeneID:904514;gbkey=Gene NC_002163.1 RefSeq CDS 734971 735711 . + 0 ID=cds692;Parent=gene739;gene=napG;Name=YP_002344188.1;Dbxref=GOA:Q0PAA9 InterPro:IPR001450 InterPro:IPR004494 UniProtKB FTrEMBL:Q0PAA9 Genbank:YP_002344188.1 GeneID:904514;gbkey=CDS;product=quinol dehydrogenase periplasmic subunit;Note=part of NapHG quinol dehydrogenase 3B couples electron transfer from ubiquinone-ubiquinol couple via NapC 2FB to NapA 3B secreted by twin arginine translocation pathway NC_002163.1 RefSeq region 734989 735057 . + . ID=id1474;gene=napG;Name=id1474;Dbxref=GeneID:904514;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0781 by TMHMM2.0 at aa 7-29 NC_002163.1 RefSeq region 735103 735174 . + . ID=id1475;gene=napG;Name=id1475;Dbxref=GeneID:904514;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 6.2e-06 NC_002163.1 RefSeq region 735124 735159 . + . ID=id1476;gene=napG;Name=id1476;Dbxref=GeneID:904514;gbkey=misc_feature;Note=PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature NC_002163.1 RefSeq region 735481 735558 . + . ID=id1477;gene=napG;Name=id1477;Dbxref=GeneID:904514;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 0.0011 NC_002163.1 RefSeq CDS 735708 736490 . + 0 ID=cds693;Parent=gene740;gene=napH;Name=YP_002344189.1;Dbxref=GOA:Q0PAA8 InterPro:IPR001450 InterPro:IPR011886 UniProtKB FTrEMBL:Q0PAA8 Genbank:YP_002344189.1 GeneID:904348;gbkey=CDS;product=quinol dehydrogenase membrane subunit;Note=part of NapHG quinol dehydrogenase 3B couples electron transfer from ubiquinone-ubiquinol couple via NapC 2FB to NapA NC_002163.1 RefSeq gene 735708 736490 . + . ID=gene740;gene=napH;Name=napH;locus_tag=Cj0782;Dbxref=GeneID:904348;gbkey=Gene NC_002163.1 RefSeq region 735744 735803 . + . ID=id1478;gene=napH;Name=id1478;Dbxref=GeneID:904348;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0782 by TMHMM2.0 at aa 13-32 2C 52-74 2C 81-99 2C 119-141 2C148-170 and 174-195 NC_002163.1 RefSeq region 735861 735929 . + . ID=id1478;gene=napH;Name=id1478;Dbxref=GeneID:904348;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0782 by TMHMM2.0 at aa 13-32 2C 52-74 2C 81-99 2C 119-141 2C148-170 and 174-195 NC_002163.1 RefSeq region 735948 736004 . + . ID=id1478;gene=napH;Name=id1478;Dbxref=GeneID:904348;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0782 by TMHMM2.0 at aa 13-32 2C 52-74 2C 81-99 2C 119-141 2C148-170 and 174-195 NC_002163.1 RefSeq region 736062 736130 . + . ID=id1478;gene=napH;Name=id1478;Dbxref=GeneID:904348;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0782 by TMHMM2.0 at aa 13-32 2C 52-74 2C 81-99 2C 119-141 2C148-170 and 174-195 NC_002163.1 RefSeq region 736149 736217 . + . ID=id1478;gene=napH;Name=id1478;Dbxref=GeneID:904348;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0782 by TMHMM2.0 at aa 13-32 2C 52-74 2C 81-99 2C 119-141 2C148-170 and 174-195 NC_002163.1 RefSeq region 736227 736292 . + . ID=id1478;gene=napH;Name=id1478;Dbxref=GeneID:904348;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0782 by TMHMM2.0 at aa 13-32 2C 52-74 2C 81-99 2C 119-141 2C148-170 and 174-195 NC_002163.1 RefSeq region 736296 736367 . + . ID=id1479;gene=napH;Name=id1479;Dbxref=GeneID:904348;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 0.00013 NC_002163.1 RefSeq region 736317 736352 . + . ID=id1480;gene=napH;Name=id1480;Dbxref=GeneID:904348;gbkey=misc_feature;Note=PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature NC_002163.1 RefSeq region 736389 736460 . + . ID=id1481;gene=napH;Name=id1481;Dbxref=GeneID:904348;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 0.0015 NC_002163.1 RefSeq CDS 736487 737011 . + 0 ID=cds694;Parent=gene741;gene=napB;Name=YP_002344190.1;Dbxref=InterPro:IPR005591 InterPro:IPR011031 UniProtKB FTrEMBL:Q0PAA7 Genbank:YP_002344190.1 GeneID:904951;gbkey=CDS;product=nitrate reductase small subunit;Note=Original 282000 29 note: Cj0783 2C napB 2C probable cytochrome C-type protein 28periplasmic nitrate reductase small subunit 29 2C len: 174 aa 3B similar to e.g. NAPB_ECOLI cytochrome C-type protein NAPB precursor 28149 aa 29 2C fasta scores 3B opt: 269 z-score: 327.2 E 28 29: 6.3e-11 2C38.1 25 identity in 97 aa overlap. No Hp match. Contains 2x PS00190 Cytochrome c family heme-binding site signature 2CN-terminla signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site 7EUpdated 282006 29 note: Pfam domain PF03892 Nitrate reductase cytochrome c-type subunit identified within CDS. Further support given to product function. Characterised in Escherichia coli and Wolinella succinogenes with acceptable identity score 2C thus not needed. Literature search identified paper given further information on product function. Functional classification - Respiration - Electron transport 7EPMID:12107136 2C PMID:16436444 2C PMID:12823811 NC_002163.1 RefSeq gene 736487 737011 . + . ID=gene741;gene=napB;Name=napB;locus_tag=Cj0783;Dbxref=GeneID:904951;gbkey=Gene NC_002163.1 RefSeq region 736499 736957 . + . ID=id1482;gene=napB;Name=id1482;Dbxref=GeneID:904951;gbkey=misc_feature;Note=HMMPfam hit to PF03892 2C Nitrate reductase cytochrome c-type subunit 2C score 2.5e-103 NC_002163.1 RefSeq region 736505 736564 . + . ID=id1483;gene=napB;Name=id1483;Dbxref=GeneID:904951;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0783 by TMHMM2.0 at aa 7-26 NC_002163.1 RefSeq region 736514 736546 . + . ID=id1484;gene=napB;Name=id1484;Dbxref=GeneID:904951;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 736754 736771 . + . ID=id1485;gene=napB;Name=id1485;Dbxref=GeneID:904951;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature NC_002163.1 RefSeq region 736880 736897 . + . ID=id1486;gene=napB;Name=id1486;Dbxref=GeneID:904951;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature ### NC_002163.1 RefSeq CDS 737016 737930 . + 0 ID=cds695;Parent=gene742;gene=napL;Name=YP_002344191.1;Dbxref=InterPro:IPR001680 InterPro:IPR015943 UniProtKB FTrEMBL:Q0PAA6 Genbank:YP_002344191.1 GeneID:905090;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0784 2C probable periplasmic protein 2C len: 304 aa 3B no Hp match. Contains N-terminal signal sequence 7EUpdated 282006 29 note: Some characterisation work within Wolinella succinogenes with acceptable identity score. Functional classification - Miscellaneous periplasmic proteins 7EPMID:12823811 NC_002163.1 RefSeq gene 737016 737930 . + . ID=gene742;gene=napL;Name=napL;locus_tag=Cj0784;Dbxref=GeneID:905090;gbkey=Gene NC_002163.1 RefSeq region 737923 738153 . + . ID=id1487;gene=napD;Name=id1487;Dbxref=GeneID:905091;gbkey=misc_feature;Note=HMMPfam hit to PF03927 2C NapD protein 2C score 4.9e-34 NC_002163.1 RefSeq gene 737923 738261 . + . ID=gene743;gene=napD;Name=napD;locus_tag=Cj0785;Dbxref=GeneID:905091;gbkey=Gene NC_002163.1 RefSeq CDS 737923 738261 . + 0 ID=cds696;Parent=gene743;gene=napD;Name=YP_002344192.1;Dbxref=InterPro:IPR016774 UniProtKB FTrEMBL:Q0PAA5 Genbank:YP_002344192.1 GeneID:905091;gbkey=CDS;product=nitrate reductase subunit NapD;Note=Original 282000 29 note: Cj0785 2C napD 2C possible napD protein 2C len: 112 aa 3B very weak similarity to e.g. NAPD_PARDT NAPD protein 28112 aa 29 2C fasta scores 3B opt: 102 z-score: 146.1 E 28 29: 0.77 2C 22.9 25 identity in 83 aa overlap 2Cand NAPD_ECOLI NAPD protein 2887 aa 29 2C blastp scores 3B E 3D 4.7e-05 2C 23 25 identity in 72 bp overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF03927 NapD protein identified within CDS. Further support given to product function. Some work carried out within Wolinella succinogenes. kept within product function. Literature search identified papers giving further information on protein product. Functional classification - Energy metabolism - Electron transport 7EPMID:12107136 2C PMID:12823811 ### NC_002163.1 RefSeq gene 738274 738447 . + . ID=gene744;Name=Cj0786;locus_tag=Cj0786;Dbxref=GeneID:905092;gbkey=Gene NC_002163.1 RefSeq CDS 738274 738447 . + 0 ID=cds697;Parent=gene744;Name=YP_002344193.1;Dbxref=UniProtKB FTrEMBL:Q0PAA4 Genbank:YP_002344193.1 GeneID:905092;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0786 2C small hydrophobic protein 2C len: 57 aa 3B no Hp match 7EUpdated 282006 29 note: One probable transmembrane helix predicted by TMHMM2.0. Functional classification -Unknown NC_002163.1 RefSeq region 738283 738339 . + . ID=id1488;Name=id1488;Dbxref=GeneID:905092;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0786 by TMHMM2.0 at aa 4-22 ### NC_002163.1 RefSeq CDS 738526 738774 . + 0 ID=cds698;Parent=gene745;Name=YP_002344194.1;Dbxref=InterPro:IPR013026 UniProtKB FTrEMBL:Q0PAA3 Genbank:YP_002344194.1 GeneID:905224;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0787 2C unknown 2C len: 82 aa 3B 38.1 25 identity to HP0168 7EUpdated 282006 29 note: Prosite domain PS50293 TPR_REGION 2C Tetratricopeptide region identified within CDS. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 738526 738774 . + . ID=gene745;Name=Cj0787;locus_tag=Cj0787;Dbxref=GeneID:905224;gbkey=Gene NC_002163.1 RefSeq gene 738771 739262 . + . ID=gene746;Name=Cj0788;locus_tag=Cj0788;Dbxref=GeneID:905093;gbkey=Gene NC_002163.1 RefSeq CDS 738771 739262 . + 0 ID=cds699;Parent=gene746;Name=YP_002344195.1;Dbxref=GOA:Q0PAA2 UniProtKB FTrEMBL:Q0PAA2 Genbank:YP_002344195.1 GeneID:905093;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0788 2C unknown 2C len: 163 aa 3B 30.8 25 identity to HP0167. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 739231 740349 . + . ID=gene747;gene=cca;Name=cca;locus_tag=Cj0789;Dbxref=GeneID:905094;gbkey=Gene NC_002163.1 RefSeq CDS 739231 740349 . + 0 ID=cds700;Parent=gene747;gene=cca;Name=YP_002344196.1;Dbxref=GOA:Q0PAA1 InterPro:IPR002646 UniProtKB FTrEMBL:Q0PAA1 Genbank:YP_002344196.1 GeneID:905094;gbkey=CDS;product=poly 28A 29 polymerase family protein;Note=Original 282000 29 note: Cj0789 2C probable RNA nucleotidyltransferase 2C len: 372 aa 3Bp similar in C-terminus to C-terminus of e.g. CCA_ECOLI tRNA nucleotidyltransferase 28412 aa 29 2C fasta scores 3B opt: 343 z-score: 412.9 E 28 29: 1.1e-15 2C 35.4 25 identity in 212 aa overlap 2C and PAPS_BACSU poly 28A 29 polymerase 28397 aa 29 2C fasta scores 3B opt: 338 z-score: 407.2 E 28 29: 2.2e-15 2C 29.3 25 identity in 294 aa overlap. 24.9 25 identity to HP0640. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 7EUpdated 282006 29 note: Pfam domain PF01743 Poly A polymerase family protein identified within CDS. Further support to product function. Product function modified based on updated characterisation naming within Escherichia coli. Functional classification - RNA synthesis 2C RNA modification and DNA transcription 7EPMID:3009457 2C PMID:3516995 2C PMID:15210699 NC_002163.1 RefSeq region 739429 739452 . + . ID=id1489;gene=cca;Name=id1489;Dbxref=GeneID:905094;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 739483 739938 . + . ID=id1490;gene=cca;Name=id1490;Dbxref=GeneID:905094;gbkey=misc_feature;Note=HMMPfam hit to PF01743 2C Poly A polymerase family 2Cscore 5.6e-32 NC_002163.1 UTR_Extractor 5'-UTR 740286 740345 . + . ID=utr272;locus_tag=Cj0790;product=formyltetrahydrofolate deformylase NC_002163.1 RefSeq gene 740346 741170 . + . ID=gene748;gene=purU;Name=purU;locus_tag=Cj0790;Dbxref=GeneID:905095;gbkey=Gene NC_002163.1 RefSeq CDS 740346 741170 . + 0 ID=cds701;Parent=gene748;gene=purU;Name=YP_002344197.1;Dbxref=GOA:Q0PAA0 InterPro:IPR002376 InterPro:IPR004810 UniProtKB FTrEMBL:Q0PAA0 Genbank:YP_002344197.1 GeneID:905095;gbkey=CDS;product=formyltetrahydrofolate deformylase;Note=produces formate from formyl-tetrahydrofolate which is the major source of formate for PurT in de novo purine nucleotide biosynthesis 3B has a role in one-carbon metabolism 3B forms a homohexamer 3B activated by methionine and inhibited by glycine NC_002163.1 RefSeq region 740580 741113 . + . ID=id1491;gene=purU;Name=id1491;Dbxref=GeneID:905095;gbkey=misc_feature;Note=HMMPfam hit to PF00551 2C Formyl transferase 2C score 4e-55 NC_002163.1 RefSeq CDS 741167 742441 . - 0 ID=cds702;Parent=gene749;Name=YP_002344198.1;Dbxref=GOA:Q0PA99 InterPro:IPR000192 InterPro:IPR000873 InterPro:IPR015421 UniProtKB FTrEMBL:Q0PA99 Genbank:YP_002344198.1 GeneID:905097;gbkey=CDS;product=aminotransferase;Note=Original 282000 29 note: Cj0791c 2C probable aminotransferase 2C len: 424 aa 3B similar to many members of the nifS family e.g. TR:O32164 28EMBL:Z99120 29 B. subtilis YURW protein 28406 aa 29 2C fasta scores 3B opt: 289 z-score: 340.6 E 28 29: 1.1e-11 2C 23.9 25 identity in 431 aa overlap. 45.4 25 identity to HP0405. Contains PS00455 AMP-binding domain signature and PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification -Misc NC_002163.1 RefSeq gene 741167 742441 . - . ID=gene749;gene=Cj0791c;Name=Cj0791c;locus_tag=Cj0791c;Dbxref=GeneID:905097;gbkey=Gene NC_002163.1 RefSeq region 741719 741781 . - . ID=id1492;Name=id1492;Dbxref=GeneID:905097;gbkey=misc_feature;Note=PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site NC_002163.1 RefSeq region 742163 742198 . - . ID=id1493;Name=id1493;Dbxref=GeneID:905097;gbkey=misc_feature;Note=PS00455 AMP-binding domain signature ### NC_002163.1 UTR_Extractor 5'-UTR 742442 742457 . - . ID=utr273;locus_tag=Cj0791c;product=putative aminotransferase NC_002163.1 UTR_Extractor 5'-UTR 742471 742476 . + . ID=utr274;locus_tag=Cj0792;product=hypothetical protein NC_002163.1 RefSeq gene 742477 743355 . + . ID=gene750;Name=Cj0792;locus_tag=Cj0792;Dbxref=GeneID:905098;gbkey=Gene NC_002163.1 RefSeq CDS 742477 743355 . + 0 ID=cds703;Parent=gene750;Name=YP_002344199.1;Dbxref=InterPro:IPR004256 UniProtKB FTrEMBL:Q0PA98 Genbank:YP_002344199.1 GeneID:905098;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0792 2C unknown 2C len: 292 aa 3B some similarity to hypothetical proteins e.g. YZ04_METJA hypothetical protein MJECL04 28439 aa 29 2C fasta scores 3B opt: 175 z-score: 208.0 E 28 29: 0.00027 2C 26.5 25 identity in 309 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF03008 Archaea bacterial proteins of unknown function identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq region 742930 743196 . + . ID=id1494;Name=id1494;Dbxref=GeneID:905098;gbkey=misc_feature;Note=HMMPfam hit to PF03008 2C Archaea bacterial proteins of unknown functi 2C score 1.6e-05 ### NC_002163.1 RefSeq CDS 743359 744378 . + 0 ID=cds704;Parent=gene751;gene=flgS;Name=YP_002344200.1;Dbxref=GOA:Q0PA97 InterPro:IPR003594 InterPro:IPR003661 InterPro:IPR004358 InterPro:IPR005467 UniProtKB FTrEMBL:Q0PA97 Genbank:YP_002344200.1 GeneID:905099;gbkey=CDS;product=signal transduction histidine kinase;Note=Original 282000 29 note: Cj0793 2C probable signal transduction histidine kinase 2C len: 339 aa 3B similar to e.g. the C-terminus of ATOS_ECOLI sensor protein ATOS 28608 aa 29 2C fasta scores 3B opt: 357 z-score: 408.3 E 28 29: 1.9e-15 2C33.3 25 identity in 222 aa overlap. 42.4 25 identity to HP0244. Contains Pfam match to entry PF00512 signal 2CSignal carboxyl-terminal domain 7EUpdated 282006 29 note: Characterised within Campylobacter jejuni and Helicobacter pylori. not added to product function. Literature search identified papers linking Cj0793 and Cj1024 to a two-component signal transduction system 28FlgS 2FFlgR 29 that regulates the fla regulon in Campylobacter jejuni 28similar to that found in Helicobacter pylori 29. Functional classification - Signal transduction 7EPMID:14960570 2C PMID:15231786 2C PMID:14617189 NC_002163.1 RefSeq gene 743359 744378 . + . ID=gene751;gene=flgS;Name=flgS;locus_tag=Cj0793;Dbxref=GeneID:905099;gbkey=Gene NC_002163.1 RefSeq region 743749 743943 . + . ID=id1495;gene=flgS;Name=id1495;Dbxref=GeneID:905099;gbkey=misc_feature;Note=HMMPfam hit to PF00512 2C His Kinase A 28phosphoacceptor 29 domain 2C score 5.3e-09 NC_002163.1 RefSeq region 744061 744375 . + . ID=id1496;gene=flgS;Name=id1496;Dbxref=GeneID:905099;gbkey=misc_feature;Note=HMMPfam hit to PF02518 2C Histidine kinase- 2C DNA gyrase B- 2C and HSP90 2C score 1.1e-21 ### NC_002163.1 UTR_Extractor 5'-UTR 744431 744494 . + . ID=utr275;locus_tag=Cj0794;product=hypothetical protein NC_002163.1 RefSeq gene 744495 745775 . + . ID=gene752;Name=Cj0794;locus_tag=Cj0794;Dbxref=GeneID:905100;gbkey=Gene NC_002163.1 RefSeq CDS 744495 745775 . + 0 ID=cds705;Parent=gene752;Name=YP_002344201.1;Dbxref=UniProtKB FTrEMBL:Q0PA96 Genbank:YP_002344201.1 GeneID:905100;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0794 2C unknown 2C len: 426 aa 3B no Hp match. Has consecutive regions of near-identity to Cj0814 2873.9 25 identity in 253 aa overlap 29 2C Cj0815 2861.6 25 identity in 86 aa overlap 29 and Cj0816 2863.6 25 identity in 44 aa overlap 29 2C which may represent a pseudogene copy of this CDS 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 RefSeq CDS 745833 747260 . - 0 ID=cds706;Parent=gene753;gene=murF;Name=YP_002344202.1;Dbxref=GOA:Q0PA95 InterPro:IPR005863 InterPro:IPR013221 UniProtKB FTrEMBL:Q0PA95 Genbank:YP_002344202.1 GeneID:905101;gbkey=CDS;product=UDP-N-acetylmuramoyl-tripeptide D-alanyl-D-alanine ligase;Note=Original 282000 29 note: Cj0795c 2C murF 2C possible UDP-N-acetylmuramoylalanyl-D-glutamyl-2 2C6-diaminopimelate -- ligase 2C len: 475 aa 3B some similarity to e.g. MURF_BACSU UDP-N-acetylmuramoylalanyl-D-glutamyl-2 2C6-diaminopimelate -- ligase 28EC 6.3.2.15 29 28457 aa 29 2C fasta scores 3B opt: 235 z-score: 258.7 E 28 29: 4.1e-07 2C 26.7 25 identity in 348 aa overlap. 41.5 25 identity to HP0740 7EUpdated 282006 29 note: Pfam domains PF01225 Mur ligase family 2C catalytic domain and PF02875 Mur ligase family 2C glutamate ligase domain were identified within CDS. Also 2C three probable transmembrane helices predicted by TMHMM2.0 within CDS. Further support given to product function. Characterisation work carried out within Escherichia coli and Bacillus subtilis with mariginal identity scores. not added to product function. Product function and EC number updated. Functional classification - Murein sacculus and peptidoglycan 7EPMID:11090285 2C PMID:2668880 2C PMID:9305945 NC_002163.1 RefSeq gene 745833 747260 . - . ID=gene753;gene=murF;Name=murF;locus_tag=Cj0795c;Dbxref=GeneID:905101;gbkey=Gene NC_002163.1 RefSeq region 745965 746201 . - . ID=id1497;gene=murF;Name=id1497;Dbxref=GeneID:905101;gbkey=misc_feature;Note=HMMPfam hit to PF02875 2C Mur ligase family 2Cglutamate ligase doma 2C score 0.0036 NC_002163.1 RefSeq region 746226 746972 . - . ID=id1498;gene=murF;Name=id1498;Dbxref=GeneID:905101;gbkey=misc_feature;Note=HMMPfam hit to PF01225 2C Mur ligase family 2Ccatalytic domain 2C score 3.5e-15 NC_002163.1 RefSeq region 746910 746978 . - . ID=id52;gene=murF;Name=id52;Dbxref=GeneID:905101;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0795c by TMHMM2.0 at aa 7-29 2C 49-71 and 95-117 NC_002163.1 RefSeq region 747048 747116 . - . ID=id52;gene=murF;Name=id52;Dbxref=GeneID:905101;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0795c by TMHMM2.0 at aa 7-29 2C 49-71 and 95-117 NC_002163.1 RefSeq region 747174 747242 . - . ID=id52;gene=murF;Name=id52;Dbxref=GeneID:905101;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0795c by TMHMM2.0 at aa 7-29 2C 49-71 and 95-117 ### NC_002163.1 RefSeq gene 747261 747980 . - . ID=gene754;Name=Cj0796c;locus_tag=Cj0796c;Dbxref=GeneID:905199;gbkey=Gene NC_002163.1 RefSeq CDS 747261 747980 . - 0 ID=cds707;Parent=gene754;Name=YP_002344203.1;Dbxref=GOA:Q0PA94 InterPro:IPR000073 UniProtKB FTrEMBL:Q0PA94 Genbank:YP_002344203.1 GeneID:905199;gbkey=CDS;product=hydrolase;Note=Original 282000 29 note: Cj0796c 2C unknown 2C len: 239 aa 3B 46.3 25 identity to HP0739 28annotated as 2-hydroxy-6-oxohepta-2 2C4-dienoate hydrolase 29 7EUpdated 282006 29 note: Pfam domain PF00561 alpha 2Fbeta hydrolase fold and Prosite domain PS50187 Esterase 2Flipase 2Fthioesterase active site serine identified within CDS. The latter are found in alpha 2Fbeta fold hydrolase. Product function modified due to motif match. No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification - Misc NC_002163.1 RefSeq region 747267 747827 . - . ID=id1499;Name=id1499;Dbxref=GeneID:905199;gbkey=misc_feature;Note=HMMPfam hit to PF00561 2C alpha 2Fbeta hydrolase fold 2Cscore 0.0025 ### NC_002163.1 RefSeq gene 747982 748197 . - . ID=gene755;Name=Cj0797c;locus_tag=Cj0797c;Dbxref=GeneID:905230;gbkey=Gene NC_002163.1 RefSeq CDS 747982 748197 . - 0 ID=cds708;Parent=gene755;Name=YP_002344204.1;Dbxref=GOA:Q0PA93 UniProtKB FTrEMBL:Q0PA93 Genbank:YP_002344204.1 GeneID:905230;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0797c 2C unknown 2C len: 71 aa 3B weak similarity to TR:O68849 28EMBL:AF055586 29 ORF10 in Vibrio cholerae integron InVch 2880 aa 29 2C fasta scores 3B opt: 95 z-score: 151.4 E 28 29: 0.39 2C 39.2 25 identity in 51 aa overlap. No Hp match. Functional classification -Conserved hypothetical proteins NC_002163.1 UTR_Extractor 5'-UTR 748198 748226 . - . ID=utr276;locus_tag=Cj0797c;product=hypothetical protein NC_002163.1 RefSeq CDS 748257 749297 . - 0 ID=cds709;Parent=gene756;gene=ddl;Name=YP_002344205.1;Dbxref=GOA:Q9PPC2 HSSP:P25051 InterPro:IPR000291 InterPro:IPR005905 InterPro:IPR011095 InterPro:IPR011127 InterPro:IPR011761 InterPro:IPR013816 InterPro:IPR013817 UniProtKB FSwiss-Prot:Q9PPC2 Genbank:YP_002344205.1 GeneID:905128;gbkey=CDS;product=D-alanyl-alanine synthetase A;Note=D-alanine--D-alanine ligase 3B DdlA 3B DdlB 3B cytoplasmic 3B catalyzes the formation of D-alanyl-D-alanine from two D-alanines in peptidoglycan synthesis 3B there are two forms of this enzyme in Escherichia coli NC_002163.1 RefSeq gene 748257 749297 . - . ID=gene756;gene=ddl;Name=ddl;locus_tag=Cj0798c;Dbxref=GeneID:905128;gbkey=Gene NC_002163.1 RefSeq region 748320 748916 . - . ID=id1500;gene=ddl;Name=id1500;Dbxref=GeneID:905128;gbkey=misc_feature;Note=HMMPfam hit to PF07478 2C D-ala D-ala ligase C-terminus 2C score 3.3e-23 NC_002163.1 RefSeq region 748392 748475 . - . ID=id1501;gene=ddl;Name=id1501;Dbxref=GeneID:905128;gbkey=misc_feature;Note=PS00844 D-alanine--D-alanine ligase signature 2 NC_002163.1 RefSeq region 748980 749015 . - . ID=id1502;gene=ddl;Name=id1502;Dbxref=GeneID:905128;gbkey=misc_feature;Note=PS00843 D-alanine--D-alanine ligase signature 1 ### NC_002163.1 RefSeq CDS 749307 749858 . - 0 ID=cds710;Parent=gene757;gene=ruvA;Name=YP_002344206.1;Dbxref=GOA:Q9PPC1 HSSP:P08576 InterPro:IPR000085 InterPro:IPR003583 InterPro:IPR011114 InterPro:IPR012340 InterPro:IPR013849 UniProtKB FSwiss-Prot:Q9PPC1 Genbank:YP_002344206.1 GeneID:905102;gbkey=CDS;product=Holliday junction DNA helicase RuvA;Note=plays an essential role in ATP-dependent branch migration of the Holliday junction NC_002163.1 RefSeq gene 749307 749858 . - . ID=gene757;gene=ruvA;Name=ruvA;locus_tag=Cj0799c;Dbxref=GeneID:905102;gbkey=Gene NC_002163.1 RefSeq region 749310 749441 . - . ID=id1503;gene=ruvA;Name=id1503;Dbxref=GeneID:905102;gbkey=misc_feature;Note=HMMPfam hit to PF07499 2C RuvA 2C C-terminal domain 2Cscore 7.9e-06 NC_002163.1 RefSeq region 749478 749567 . - . ID=id1504;gene=ruvA;Name=id1504;Dbxref=GeneID:905102;gbkey=misc_feature;Note=HMMPfam hit to PF00633 2C Helix-hairpin-helix motif 2Cscore 0.13 NC_002163.1 RefSeq region 749583 749672 . - . ID=id1505;gene=ruvA;Name=id1505;Dbxref=GeneID:905102;gbkey=misc_feature;Note=HMMPfam hit to PF00633 2C Helix-hairpin-helix motif 2Cscore 0.66 NC_002163.1 RefSeq region 749673 749858 . - . ID=id1506;gene=ruvA;Name=id1506;Dbxref=GeneID:905102;gbkey=misc_feature;Note=HMMPfam hit to PF01330 2C RuvA N terminal domain 2Cscore 1.7e-20 NC_002163.1 RefSeq region 749748 749816 . - . ID=id1507;gene=ruvA;Name=id1507;Dbxref=GeneID:905102;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0799c by TMHMM2.0 at aa 15-37 NC_002163.1 RefSeq gene 749834 751693 . - . ID=gene758;gene=Cj0800c;Name=Cj0800c;locus_tag=Cj0800c;Dbxref=GeneID:905103;gbkey=Gene NC_002163.1 RefSeq CDS 749834 751693 . - 0 ID=cds711;Parent=gene758;Name=YP_002344207.1;Dbxref=InterPro:IPR000711 UniProtKB FTrEMBL:Q0PA90 Genbank:YP_002344207.1 GeneID:905103;gbkey=CDS;product=ATPase;Note=Original 282000 29 note: Cj0800c 2C unknown 2C len: 619 aa 3B 24.7 25 identity to HP0884. Also similar to Cj0044c 2828.6 25 identity in 622 aa overlap 29 7EUpdated 282006 29 note: Prosite domain PS00389 ATPase 2CF1 complex 2C OSCP 2Fdelta subunit signature identified within CDS. Product modified to more specific family member due to motif match. Not fully characterised so kept within product function. Functional classification - Misc NC_002163.1 RefSeq region 750710 750769 . - . ID=id1508;Name=id1508;Dbxref=GeneID:905103;gbkey=misc_feature;Note=PS00389 ATP synthase delta 28OSCP 29 subunit signature ### NC_002163.1 UTR_Extractor 5'-UTR 751694 751718 . - . ID=utr277;locus_tag=Cj0800c;product=putative ATPase NC_002163.1 UTR_Extractor 5'-UTR 751766 751796 . + . ID=utr278;locus_tag=Cj0801;product=putative integral membrane protein NC_002163.1 RefSeq CDS 751797 753248 . + 0 ID=cds712;Parent=gene759;Name=YP_002344208.1;Dbxref=GOA:Q0PA89 InterPro:IPR004268 UniProtKB FTrEMBL:Q0PA89 Genbank:YP_002344208.1 GeneID:905104;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0801 2C probable integral membrane protein 2C len: 483 aa 3B similar to MVIN_SALTY virulence factor MVIN 28524 aa 29 2C fasta scores 3B opt: 725 z-score: 828.0 E 28 29: 0 2C 32.4 25 identity in 463 aa overlap 2Cand to homologs from other organisms. 45.8 25 identity to HP0885 7EUpdated 282006 29 note: Eleven probable transmembrane helices predicted by TMHMM2.0. Also 2C Pfam domain PF03023 MviN-like protein identified within CDS. Still not functionally characterised. Homolog designation kept within product function. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 751797 753248 . + . ID=gene759;Name=Cj0801;locus_tag=Cj0801;Dbxref=GeneID:905104;gbkey=Gene NC_002163.1 RefSeq region 751809 751868 . + . ID=id1509;Name=id1509;Dbxref=GeneID:905104;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0801 by TMHMM2.0 at aa 5-24 2C 28-47 2C 79-101 2C 123-145 2C152-171 2C 181-203 2C 310-332 2C 347-369 2C 382-404 2C 408-430 and 442-464 NC_002163.1 RefSeq region 751878 751937 . + . ID=id1509;Name=id1509;Dbxref=GeneID:905104;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0801 by TMHMM2.0 at aa 5-24 2C 28-47 2C 79-101 2C 123-145 2C152-171 2C 181-203 2C 310-332 2C 347-369 2C 382-404 2C 408-430 and 442-464 NC_002163.1 RefSeq region 751884 753233 . + . ID=id1510;Name=id1510;Dbxref=GeneID:905104;gbkey=misc_feature;Note=HMMPfam hit to PF03023 2C MviN-like protein 2C score 1.6e-84 NC_002163.1 RefSeq region 752031 752099 . + . ID=id1509;Name=id1509;Dbxref=GeneID:905104;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0801 by TMHMM2.0 at aa 5-24 2C 28-47 2C 79-101 2C 123-145 2C152-171 2C 181-203 2C 310-332 2C 347-369 2C 382-404 2C 408-430 and 442-464 NC_002163.1 RefSeq region 752163 752231 . + . ID=id1509;Name=id1509;Dbxref=GeneID:905104;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0801 by TMHMM2.0 at aa 5-24 2C 28-47 2C 79-101 2C 123-145 2C152-171 2C 181-203 2C 310-332 2C 347-369 2C 382-404 2C 408-430 and 442-464 NC_002163.1 RefSeq region 752250 752309 . + . ID=id1509;Name=id1509;Dbxref=GeneID:905104;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0801 by TMHMM2.0 at aa 5-24 2C 28-47 2C 79-101 2C 123-145 2C152-171 2C 181-203 2C 310-332 2C 347-369 2C 382-404 2C 408-430 and 442-464 NC_002163.1 RefSeq region 752337 752405 . + . ID=id1509;Name=id1509;Dbxref=GeneID:905104;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0801 by TMHMM2.0 at aa 5-24 2C 28-47 2C 79-101 2C 123-145 2C152-171 2C 181-203 2C 310-332 2C 347-369 2C 382-404 2C 408-430 and 442-464 NC_002163.1 RefSeq region 752469 752516 . + . ID=id1511;Name=id1511;Dbxref=GeneID:905104;gbkey=misc_feature;Note=PS00225 Crystallins beta and gamma 27Greek key 27 motif signature NC_002163.1 RefSeq region 752724 752792 . + . ID=id1509;Name=id1509;Dbxref=GeneID:905104;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0801 by TMHMM2.0 at aa 5-24 2C 28-47 2C 79-101 2C 123-145 2C152-171 2C 181-203 2C 310-332 2C 347-369 2C 382-404 2C 408-430 and 442-464 NC_002163.1 RefSeq region 752835 752903 . + . ID=id1509;Name=id1509;Dbxref=GeneID:905104;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0801 by TMHMM2.0 at aa 5-24 2C 28-47 2C 79-101 2C 123-145 2C152-171 2C 181-203 2C 310-332 2C 347-369 2C 382-404 2C 408-430 and 442-464 NC_002163.1 RefSeq region 752940 753008 . + . ID=id1509;Name=id1509;Dbxref=GeneID:905104;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0801 by TMHMM2.0 at aa 5-24 2C 28-47 2C 79-101 2C 123-145 2C152-171 2C 181-203 2C 310-332 2C 347-369 2C 382-404 2C 408-430 and 442-464 NC_002163.1 RefSeq region 753018 753086 . + . ID=id1509;Name=id1509;Dbxref=GeneID:905104;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0801 by TMHMM2.0 at aa 5-24 2C 28-47 2C 79-101 2C 123-145 2C152-171 2C 181-203 2C 310-332 2C 347-369 2C 382-404 2C 408-430 and 442-464 NC_002163.1 RefSeq region 753120 753188 . + . ID=id1509;Name=id1509;Dbxref=GeneID:905104;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0801 by TMHMM2.0 at aa 5-24 2C 28-47 2C 79-101 2C 123-145 2C152-171 2C 181-203 2C 310-332 2C 347-369 2C 382-404 2C 408-430 and 442-464 NC_002163.1 UTR_Extractor 5'-UTR 753126 753247 . + . ID=utr279;locus_tag=Cj0802;product=cysteinyl-tRNA synthetase NC_002163.1 RefSeq CDS 753248 754636 . + 0 ID=cds713;Parent=gene760;gene=cysS;Name=YP_002344209.1;Dbxref=GOA:Q9PPB8 HSSP:P21888 InterPro:IPR001412 InterPro:IPR002308 InterPro:IPR014729 InterPro:IPR015803 InterPro:IPR015804 UniProtKB FSwiss-Prot:Q9PPB8 Genbank:YP_002344209.1 GeneID:905105;gbkey=CDS;product=cysteinyl-tRNA synthetase;Note=catalyzes a two-step reaction 3B charges a cysteine by linking its carboxyl group to the alpha-phosphate of ATP then transfers the aminoacyl-adenylate to its tRNA NC_002163.1 RefSeq gene 753248 754636 . + . ID=gene760;gene=cysS;Name=cysS;locus_tag=Cj0802;Dbxref=GeneID:905105;gbkey=Gene NC_002163.1 RefSeq region 753275 754159 . + . ID=id1512;gene=cysS;Name=id1512;Dbxref=GeneID:905105;gbkey=misc_feature;Note=HMMPfam hit to PF01406 2C tRNA synthetases class I 28C 29 catalytic d 2C score 5.6e-134 NC_002163.1 RefSeq gene 754629 756371 . + . ID=gene761;gene=msbA;Name=msbA;locus_tag=Cj0803;Dbxref=GeneID:905106;gbkey=Gene NC_002163.1 RefSeq CDS 754629 756371 . + 0 ID=cds714;Parent=gene761;gene=msbA;Name=YP_002344210.1;Dbxref=GOA:Q0PA87 InterPro:IPR001140 InterPro:IPR003439 InterPro:IPR003593 InterPro:IPR011527 UniProtKB FTrEMBL:Q0PA87 Genbank:YP_002344210.1 GeneID:905106;gbkey=CDS;product=lipid export ABC transport protein;Note=Original 282000 29 note: Cj0803 2C msbA 2C probable lipid export ABC transport protein 2C len: 580 aa 3B similar to lipid export protein MSBA_ECOLI probable transport ATP-binding protein MSBA 28582 aa 29 2C fasta scores 3B opt: 1032 z-score: 1135.9 E 28 29: 0 2C 29.6 25 identity in 575 aa overlap 2Cand to other members of the mutidrug-resistance family of ABC transporters. 42.7 25 identity to HP1082. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00211 ABC transporters family signature 2C Pfam match to entry PF00664 ABC_membrane 2C ABC transporter transmembrane region 2C and Pfam match to entry PF00005 ABC_tran 2C ABC transporters 7EUpdated 282006 29 note: Characterised in Escherichia coli with marginal identity score. Appropriate motifs present. not needed to product function. Functional classification - Transport 2Fbinding proteins -Other 7EPMID:16159769 2C PMID:12119303 NC_002163.1 RefSeq region 754701 754769 . + . ID=id1514;gene=msbA;Name=id1514;Dbxref=GeneID:905106;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0803 by TMHMM2.0 at aa 25-47 2C 60-82 2C 165-184 and 272-294 NC_002163.1 RefSeq region 754701 755516 . + . ID=id1513;gene=msbA;Name=id1513;Dbxref=GeneID:905106;gbkey=misc_feature;Note=HMMPfam hit to PF00664 2C ABC transporter transmembrane region 2C score 8.8e-42 NC_002163.1 RefSeq region 754806 754874 . + . ID=id1514;gene=msbA;Name=id1514;Dbxref=GeneID:905106;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0803 by TMHMM2.0 at aa 25-47 2C 60-82 2C 165-184 and 272-294 NC_002163.1 RefSeq region 755121 755180 . + . ID=id1514;gene=msbA;Name=id1514;Dbxref=GeneID:905106;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0803 by TMHMM2.0 at aa 25-47 2C 60-82 2C 165-184 and 272-294 NC_002163.1 RefSeq region 755442 755510 . + . ID=id1514;gene=msbA;Name=id1514;Dbxref=GeneID:905106;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0803 by TMHMM2.0 at aa 25-47 2C 60-82 2C 165-184 and 272-294 NC_002163.1 RefSeq region 755724 756272 . + . ID=id1515;gene=msbA;Name=id1515;Dbxref=GeneID:905106;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 4.9e-51 NC_002163.1 RefSeq region 755745 755768 . + . ID=id1516;gene=msbA;Name=id1516;Dbxref=GeneID:905106;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 756051 756095 . + . ID=id1517;gene=msbA;Name=id1517;Dbxref=GeneID:905106;gbkey=misc_feature;Note=PS00211 ABC transporters family signature ### NC_002163.1 UTR_Extractor 5'-UTR 756388 756402 . + . ID=utr280;locus_tag=Cj0804;product=dihydroorotate dehydrogenase 2 NC_002163.1 RefSeq CDS 756403 757461 . + 0 ID=cds715;Parent=gene762;gene=pyrD;Name=YP_002344211.1;Dbxref=GOA:Q0PA86 InterPro:IPR001295 InterPro:IPR005719 InterPro:IPR012135 InterPro:IPR013785 UniProtKB FTrEMBL:Q0PA86 Genbank:YP_002344211.1 GeneID:905107;gbkey=CDS;product=dihydroorotate dehydrogenase 2;Note=catalyzes the conversion of dihydroorotate to orotate in the pyrimidine biosynthesis pathway 3B uses a flavin nucleotide as an essential cofactor 3B class 2 enzymes are monomeric and compared to the class 1 class 2 possess an extended N terminus 2C which plays a role in the membrane association of the enzyme and provides the binding site for the respiratory quinones that serve as physiological electron acceptors NC_002163.1 RefSeq gene 756403 757461 . + . ID=gene762;gene=pyrD;Name=pyrD;locus_tag=Cj0804;Dbxref=GeneID:905107;gbkey=Gene NC_002163.1 RefSeq region 756550 757407 . + . ID=id1518;gene=pyrD;Name=id1518;Dbxref=GeneID:905107;gbkey=misc_feature;Note=HMMPfam hit to PF01180 2C Dihydroorotate dehydrogenase 2C score 6.1e-84 NC_002163.1 RefSeq region 756658 756717 . + . ID=id1519;gene=pyrD;Name=id1519;Dbxref=GeneID:905107;gbkey=misc_feature;Note=PS00911 Dihydroorotate dehydrogenase signature 1 NC_002163.1 RefSeq region 757261 757323 . + . ID=id1520;gene=pyrD;Name=id1520;Dbxref=GeneID:905107;gbkey=misc_feature;Note=PS00912 Dihydroorotate dehydrogenase signature 2 NC_002163.1 RefSeq CDS 757458 758708 . + 0 ID=cds716;Parent=gene763;Name=YP_002344212.1;Dbxref=GOA:Q0PA85 InterPro:IPR001431 InterPro:IPR007863 InterPro:IPR011237 InterPro:IPR011765 UniProtKB FTrEMBL:Q0PA85 Genbank:YP_002344212.1 GeneID:905108;gbkey=CDS;product=zinc protease;Note=Original 282000 29 note: Cj0805 2C probable zinc protease 2C len: 416 aa 3B similar to many members of the insulinase family e.g. Y4WA_RHISN hypothetical zinc protease Y4WA 28512 aa 29 2C fasta scores 3B opt: 664 z-score: 739.8 E 28 29: 0 2C 31.8 25 identity in 415 aa overlap. 57.2 25 identity to HP1012. Contains PS00143 Insulinase family 2Czinc-binding region signature 2C and Pfam match to entry PF00675 Insulinase 2C Insulinase 28proteinase M16 29 7EUpdated 282006 29 note: Pfam domain PF05193 Peptidase M16 inactive domain identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification -Proteins 2C peptides and glycopeptides NC_002163.1 RefSeq gene 757458 758708 . + . ID=gene763;gene=Cj0805;Name=Cj0805;locus_tag=Cj0805;Dbxref=GeneID:905108;gbkey=Gene NC_002163.1 RefSeq region 757503 757919 . + . ID=id1521;Name=id1521;Dbxref=GeneID:905108;gbkey=misc_feature;Note=HMMPfam hit to PF00675 2C Insulinase 28Peptidase family M16 29 2C score 1.2e-15 NC_002163.1 RefSeq region 757563 757634 . + . ID=id1522;Name=id1522;Dbxref=GeneID:905108;gbkey=misc_feature;Note=PS00143 Insulinase family 2C zinc-binding region signature NC_002163.1 RefSeq region 757962 758498 . + . ID=id1523;Name=id1523;Dbxref=GeneID:905108;gbkey=misc_feature;Note=HMMPfam hit to PF05193 2C Peptidase M16 inactive domain 2C score 4.8e-42 NC_002163.1 RefSeq gene 758701 759597 . + . ID=gene764;gene=dapA;Name=dapA;locus_tag=Cj0806;Dbxref=GeneID:905109;gbkey=Gene NC_002163.1 RefSeq CDS 758701 759597 . + 0 ID=cds717;Parent=gene764;gene=dapA;Name=YP_002344213.1;Dbxref=GOA:Q9PPB4 HSSP:P05640 InterPro:IPR002220 InterPro:IPR005263 InterPro:IPR013785 UniProtKB FSwiss-Prot:Q9PPB4 Genbank:YP_002344213.1 GeneID:905109;gbkey=CDS;product=dihydrodipicolinate synthase;Note=catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis NC_002163.1 RefSeq region 758713 759582 . + . ID=id1524;gene=dapA;Name=id1524;Dbxref=GeneID:905109;gbkey=misc_feature;Note=HMMPfam hit to PF00701 2C Dihydrodipicolinate synthetase family 2C score 2e-106 NC_002163.1 RefSeq region 758821 758874 . + . ID=id1525;gene=dapA;Name=id1525;Dbxref=GeneID:905109;gbkey=misc_feature;Note=PS00665 Dihydrodipicolinate synthetase signature 1 NC_002163.1 RefSeq region 759109 759204 . + . ID=id1526;gene=dapA;Name=id1526;Dbxref=GeneID:905109;gbkey=misc_feature;Note=PS00666 Dihydrodipicolinate synthetase signature 2 NC_002163.1 RefSeq CDS 759597 760376 . + 0 ID=cds718;Parent=gene765;Name=YP_002344214.1;Dbxref=GOA:Q0PA83 InterPro:IPR002198 InterPro:IPR002347 InterPro:IPR016040 UniProtKB FTrEMBL:Q0PA83 Genbank:YP_002344214.1 GeneID:905110;gbkey=CDS;product=7-alpha-hydroxysteroid dehydrogenase;Note=Acts on the hydroxyl group at position 7 of the steroid frame NC_002163.1 RefSeq gene 759597 760376 . + . ID=gene765;gene=Cj0807;Name=Cj0807;locus_tag=Cj0807;Dbxref=GeneID:905110;gbkey=Gene NC_002163.1 RefSeq region 759624 760364 . + . ID=id1527;Name=id1527;Dbxref=GeneID:905110;gbkey=misc_feature;Note=HMMPfam hit to PF00106 2C short chain dehydrogenase 2Cscore 1e-43 ### NC_002163.1 RefSeq CDS 760417 760722 . - 0 ID=cds719;Parent=gene766;Name=YP_002344215.1;Dbxref=UniProtKB FTrEMBL:Q0PA82 Genbank:YP_002344215.1 GeneID:905112;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0808c 2C small hydrophobic protein 2C len: 101 aa 3B no Hp match 7EUpdated 282006 29 note: Three probable transmembrane helices predicted by TMHMM2.0. Functional classification -Unknown NC_002163.1 RefSeq gene 760417 760722 . - . ID=gene766;Name=Cj0808c;locus_tag=Cj0808c;Dbxref=GeneID:905112;gbkey=Gene NC_002163.1 RefSeq region 760435 760503 . - . ID=id53;Name=id53;Dbxref=GeneID:905112;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0808c by TMHMM2.0 at aa 5-26 2C 47-69 and 74-96 NC_002163.1 RefSeq region 760516 760584 . - . ID=id53;Name=id53;Dbxref=GeneID:905112;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0808c by TMHMM2.0 at aa 5-26 2C 47-69 and 74-96 NC_002163.1 RefSeq region 760645 760710 . - . ID=id53;Name=id53;Dbxref=GeneID:905112;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0808c by TMHMM2.0 at aa 5-26 2C 47-69 and 74-96 ### NC_002163.1 RefSeq gene 760734 761330 . - . ID=gene767;Name=Cj0809c;locus_tag=Cj0809c;Dbxref=GeneID:905113;gbkey=Gene NC_002163.1 RefSeq CDS 760734 761330 . - 0 ID=cds720;Parent=gene767;Name=YP_002344216.1;Dbxref=GOA:Q6B8H9 InterPro:IPR001279 UniProtKB FTrEMBL:Q6B8H9 Genbank:YP_002344216.1 GeneID:905113;gbkey=CDS;product=hydrolase;Note=Original 282000 29 note: Cj0809c 2C possible hydrolase 2Clen: 198 aa 3B similar to many hypothetical proteins belonging to the glyoxalase II family e.g. YQGX_BACSU 28211 aa 29 2C fasta scores 3B opt: 289 z-score: 365.7 E 28 29: 4.5e-13 2C32.8 25 identity in 204 aa overlap. 44.3 25 identity to HP0813. Contains Pfam match to entry PF00753 lactamase_B 2CMetallo-beta-lactamase superfamily 7EUpdated 282006 29 note: No specific characterisation with acceptable identity scores carried out yet. kept within product function. Functional classification -Misc NC_002163.1 RefSeq region 760797 761297 . - . ID=id1528;Name=id1528;Dbxref=GeneID:905113;gbkey=misc_feature;Note=HMMPfam hit to PF00753 2C Metallo-beta-lactamase superfamily 2C score 3.6e-34 ### NC_002163.1 UTR_Extractor 5'-UTR 761331 761370 . - . ID=utr281;locus_tag=Cj0809c;product=putative hydrolase NC_002163.1 UTR_Extractor 5'-UTR 761379 761403 . + . ID=utr282;locus_tag=Cj0810;product=NAD synthetase NC_002163.1 RefSeq gene 761404 762144 . + . ID=gene768;gene=nadE;Name=nadE;locus_tag=Cj0810;Dbxref=GeneID:906011;gbkey=Gene NC_002163.1 RefSeq CDS 761404 762144 . + 0 ID=cds721;Parent=gene768;gene=nadE;Name=YP_002344217.1;Dbxref=GOA:Q9PPB0 HSSP:P08164 InterPro:IPR003694 InterPro:IPR014729 UniProtKB FSwiss-Prot:Q9PPB0 Genbank:YP_002344217.1 GeneID:906011;gbkey=CDS;product=NAD synthetase;Note=catalyzes the formation of nicotinamide adenine dinucleotide 28NAD 29 from nicotinic acid adenine dinucleotide 28NAAD 29 using either ammonia or glutamine as the amide donor and ATP 3B ammonia-utilizing enzymes include the ones from Bacillus and Escherichia coli while glutamine-utilizing enzymes include the Mycobacterial one 3B forms homodimers NC_002163.1 RefSeq region 761569 762138 . + . ID=id1529;gene=nadE;Name=id1529;Dbxref=GeneID:906011;gbkey=misc_feature;Note=HMMPfam hit to PF02540 2C NAD synthase 2C score 7.9e-62 ### NC_002163.1 RefSeq CDS 762148 763074 . + 0 ID=cds722;Parent=gene769;gene=lpxK;Name=YP_002344218.1;Dbxref=GOA:Q9PPA9 InterPro:IPR003758 UniProtKB FSwiss-Prot:Q9PPA9 Genbank:YP_002344218.1 GeneID:905114;gbkey=CDS;product=tetraacyldisaccharide 4 27-kinase;Note=transfers the gamma-phosphate of ATP to the 4 27 position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1 2C4 27-bis-phosphate NC_002163.1 RefSeq gene 762148 763074 . + . ID=gene769;gene=lpxK;Name=lpxK;locus_tag=Cj0811;Dbxref=GeneID:905114;gbkey=Gene NC_002163.1 RefSeq region 762187 763071 . + . ID=id1530;gene=lpxK;Name=id1530;Dbxref=GeneID:905114;gbkey=misc_feature;Note=HMMPfam hit to PF02606 2C Tetraacyldisaccharide-1-P 4 27-kinase 2C score 1e-24 NC_002163.1 RefSeq region 762217 762285 . + . ID=id1531;gene=lpxK;Name=id1531;Dbxref=GeneID:905114;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0811 by TMHMM2.0 at aa 24-46 NC_002163.1 UTR_Extractor 5'-UTR 762949 763070 . + . ID=utr283;locus_tag=Cj0812;product=threonine synthase NC_002163.1 RefSeq gene 763071 764483 . + . ID=gene770;gene=thrC;Name=thrC;locus_tag=Cj0812;Dbxref=GeneID:905115;gbkey=Gene NC_002163.1 RefSeq CDS 763071 764483 . + 0 ID=cds723;Parent=gene770;gene=thrC;Name=YP_002344219.1;Dbxref=GOA:Q0PA78 InterPro:IPR000634 InterPro:IPR001926 InterPro:IPR004450 UniProtKB FTrEMBL:Q0PA78 Genbank:YP_002344219.1 GeneID:905115;gbkey=CDS;product=threonine synthase;Note=catalyzes the formation of L-threonine from O-phospho-L-homoserine NC_002163.1 RefSeq region 763293 764165 . + . ID=id1532;gene=thrC;Name=id1532;Dbxref=GeneID:905115;gbkey=misc_feature;Note=HMMPfam hit to PF00291 2C Pyridoxal-phosphate dependent enzyme 2C score 4e-08 NC_002163.1 RefSeq region 763359 763403 . + . ID=id1533;gene=thrC;Name=id1533;Dbxref=GeneID:905115;gbkey=misc_feature;Note=PS00165 Serine 2Fthreonine dehydratases pyridoxal-phosphate attachment site NC_002163.1 RefSeq region 764480 765112 . + . ID=id1534;gene=kdsB;Name=id1534;Dbxref=GeneID:905116;gbkey=misc_feature;Note=HMMPfam hit to PF02348 2C Cytidylyltransferase 2C score 1.9e-54 NC_002163.1 RefSeq CDS 764480 765199 . + 0 ID=cds724;Parent=gene771;gene=kdsB;Name=YP_002344220.1;Dbxref=GOA:Q0PA77 InterPro:IPR003329 InterPro:IPR004528 UniProtKB FTrEMBL:Q0PA77 Genbank:YP_002344220.1 GeneID:905116;gbkey=CDS;product=3-deoxy-manno-octulosonate cytidylyltransferase;Note=CMP-2-keto-3-deoxyoctulosonic acid synthetase 3B catalyzes the formation of CMP-3-deoxy-D-manno-octulosonate from CTP and 3-deoxy-D-manno-octulosonate which is incorporated into LPS NC_002163.1 RefSeq gene 764480 765199 . + . ID=gene771;gene=kdsB;Name=kdsB;locus_tag=Cj0813;Dbxref=GeneID:905116;gbkey=Gene ### NC_002163.1 UTR_Extractor 5'-UTR 765240 765303 . + . ID=utr284;locus_tag=Cj0814;product=hypothetical protein NC_002163.1 RefSeq pseudogene 765285 766597 . + . ID=gene772;Name=Cj0814;locus_tag=Cj0814;Dbxref=GeneID:905117;gbkey=Gene ### NC_002163.1 UTR_Extractor 5'-UTR 766669 766691 . + . ID=utr285;locus_tag=Cj0817;product=putative glutamine binding periplasmic protein NC_002163.1 RefSeq gene 766692 767462 . + . ID=gene773;gene=glnH;Name=glnH;locus_tag=Cj0817;Dbxref=GeneID:905120;gbkey=Gene NC_002163.1 RefSeq CDS 766692 767462 . + 0 ID=cds725;Parent=gene773;gene=glnH;Name=YP_002344224.1;Dbxref=GOA:Q0PA73 InterPro:IPR001638 InterPro:IPR015683 UniProtKB FTrEMBL:Q0PA73 Genbank:YP_002344224.1 GeneID:905120;gbkey=CDS;product=glutamine-binding protein;Note=Original 282000 29 note: Cj0817 2C glnH 2C probable glutamine-binding periplasmic protein 2C len: 256 aa 3B similar to e.g. GLNH_ECOLI glutamine-binding periplasmic protein precursor 28248 aa 29 2C fasta scores 3B opt: 382 z-score: 441.9 E 28 29: 2.6e-17 2C 32.5 25 identity in 243 aa overlap. 29.0 25 identity to HP0940. Contains Pfam match to entry PF00497 SBP_bac_3 2C Bacterial extracellular solute-binding proteins 2C family 3 7EUpdated 282006 29 note: Characterised with marginal identity scores in more than one bacteria. Prosite domain PS50121 2C Solute binding protein 2Fglutamate receptor domain identified within CDS. Further support given to product function. added to product function. Functional classification - Transport 2Fbinding proteins - Amino acids and amines 7EPMID:3027504 2C PMID:9571045 2C PMID:9142743 NC_002163.1 RefSeq region 766752 767417 . + . ID=id1535;gene=glnH;Name=id1535;Dbxref=GeneID:905120;gbkey=misc_feature;Note=HMMPfam hit to PF00497 2C Bacterial extracellular solute-binding prot 2C score 1.3e-79 ### NC_002163.1 UTR_Extractor 5'-UTR 767524 767554 . + . ID=utr286;locus_tag=Cj0818;product=putative lipoprotein NC_002163.1 RefSeq CDS 767555 767782 . + 0 ID=cds726;Parent=gene774;Name=YP_002344225.1;Dbxref=UniProtKB FTrEMBL:Q0PA72 Genbank:YP_002344225.1 GeneID:905121;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj0818 2C probable lipoprotein 2Clen: 75 aa 3B no Hp match. Contains N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 767555 767782 . + . ID=gene774;Name=Cj0818;locus_tag=Cj0818;Dbxref=GeneID:905121;gbkey=Gene NC_002163.1 RefSeq region 767564 767617 . + . ID=id1536;Name=id1536;Dbxref=GeneID:905121;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0818 by TMHMM2.0 at aa 4-21 NC_002163.1 RefSeq region 767567 767599 . + . ID=id1537;Name=id1537;Dbxref=GeneID:905121;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq CDS 767808 768032 . + 0 ID=cds727;Parent=gene775;Name=YP_002344226.1;Dbxref=UniProtKB FTrEMBL:Q0PA71 Genbank:YP_002344226.1 GeneID:905123;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0819 2C small hydrophobic protein 2C len 74 aa 3B no Hp match 7EUpdated 282006 29 note: Two probable transmembrane helices predicted by TMHMM2.0. Functional classification -Unknown NC_002163.1 RefSeq gene 767808 768032 . + . ID=gene775;Name=Cj0819;locus_tag=Cj0819;Dbxref=GeneID:905123;gbkey=Gene NC_002163.1 RefSeq region 767874 767933 . + . ID=id1538;Name=id1538;Dbxref=GeneID:905123;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0819 by TMHMM2.0 at aa 23-42 and 47-69 NC_002163.1 RefSeq region 767946 768014 . + . ID=id1538;Name=id1538;Dbxref=GeneID:905123;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0819 by TMHMM2.0 at aa 23-42 and 47-69 NC_002163.1 RefSeq gene 768029 768763 . - . ID=gene776;gene=fliP;Name=fliP;locus_tag=Cj0820c;Dbxref=GeneID:905124;gbkey=Gene NC_002163.1 RefSeq CDS 768029 768763 . - 0 ID=cds728;Parent=gene776;gene=fliP;Name=YP_002344227.1;Dbxref=GOA:Q0PA70 InterPro:IPR005837 InterPro:IPR005838 UniProtKB FTrEMBL:Q0PA70 Genbank:YP_002344227.1 GeneID:905124;gbkey=CDS;product=flagellar biosynthesis protein FliP;Note=FliP 2C with proteins FliQ and FliR 2C forms the core of the central channel in the flagella export apparatus NC_002163.1 RefSeq region 768047 768628 . - . ID=id1539;gene=fliP;Name=id1539;Dbxref=GeneID:905124;gbkey=misc_feature;Note=HMMPfam hit to PF00813 2C FliP family 2C score 1.4e-113 NC_002163.1 RefSeq region 768059 768118 . - . ID=id54;gene=fliP;Name=id54;Dbxref=GeneID:905124;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0820c by TMHMM2.0 at aa 4-26 2C 39-61 2C 76-98 2C 184-206 and 216-235 NC_002163.1 RefSeq region 768071 768109 . - . ID=id1540;gene=fliP;Name=id1540;Dbxref=GeneID:905124;gbkey=misc_feature;Note=PS01061 Flagella transport protein fliP family signature 2 NC_002163.1 RefSeq region 768146 768214 . - . ID=id54;gene=fliP;Name=id54;Dbxref=GeneID:905124;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0820c by TMHMM2.0 at aa 4-26 2C 39-61 2C 76-98 2C 184-206 and 216-235 NC_002163.1 RefSeq region 768206 768253 . - . ID=id1541;gene=fliP;Name=id1541;Dbxref=GeneID:905124;gbkey=misc_feature;Note=PS01060 Flagella transport protein fliP family signature 1 NC_002163.1 RefSeq region 768470 768538 . - . ID=id54;gene=fliP;Name=id54;Dbxref=GeneID:905124;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0820c by TMHMM2.0 at aa 4-26 2C 39-61 2C 76-98 2C 184-206 and 216-235 NC_002163.1 RefSeq region 768581 768649 . - . ID=id54;gene=fliP;Name=id54;Dbxref=GeneID:905124;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0820c by TMHMM2.0 at aa 4-26 2C 39-61 2C 76-98 2C 184-206 and 216-235 NC_002163.1 RefSeq region 768686 768754 . - . ID=id54;gene=fliP;Name=id54;Dbxref=GeneID:905124;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0820c by TMHMM2.0 at aa 4-26 2C 39-61 2C 76-98 2C 184-206 and 216-235 ### NC_002163.1 UTR_Extractor 5'-UTR 768876 768905 . + . ID=utr287;locus_tag=Cj0821;product=bifunctional N-acetylglucosamine-1-phosphate uridyltransferase 2Fglucosamine-1-phosphate acetyltransferase NC_002163.1 RefSeq CDS 768906 770195 . + 0 ID=cds729;Parent=gene777;gene=glmU;Name=YP_002344228.1;Dbxref=GOA:Q9PPA2 HSSP:Q97R46 InterPro:IPR001451 InterPro:IPR005835 InterPro:IPR005882 UniProtKB FSwiss-Prot:Q9PPA2 Genbank:YP_002344228.1 GeneID:905125;gbkey=CDS;product=bifunctional N-acetylglucosamine-1-phosphate uridyltransferase 2Fglucosamine-1-phosphate acetyltransferase;Note=forms a homotrimer 3B catalyzes the acetylation of glucosamine-1-phosphate and uridylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc 3B function in cell wall synthesis NC_002163.1 RefSeq gene 768906 770195 . + . ID=gene777;gene=glmU;Name=glmU;locus_tag=Cj0821;Dbxref=GeneID:905125;gbkey=Gene NC_002163.1 RefSeq region 768921 769586 . + . ID=id1542;gene=glmU;Name=id1542;Dbxref=GeneID:905125;gbkey=misc_feature;Note=HMMPfam hit to PF00483 2C Nucleotidyl transferase 2Cscore 1.9e-06 NC_002163.1 RefSeq region 769662 769715 . + . ID=id1543;gene=glmU;Name=id1543;Dbxref=GeneID:905125;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28th 2C score 15 NC_002163.1 RefSeq region 769929 769982 . + . ID=id1544;gene=glmU;Name=id1544;Dbxref=GeneID:905125;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28th 2C score 45 NC_002163.1 RefSeq region 770004 770057 . + . ID=id1545;gene=glmU;Name=id1545;Dbxref=GeneID:905125;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28th 2C score 15 NC_002163.1 RefSeq region 770058 770111 . + . ID=id1546;gene=glmU;Name=id1546;Dbxref=GeneID:905125;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C Bacterial transferase hexapeptide 28th 2C score 58 NC_002163.1 RefSeq CDS 770192 771346 . + 0 ID=cds730;Parent=gene778;gene=dfp;Name=YP_002344229.1;Dbxref=GOA:Q0PA68 InterPro:IPR003382 InterPro:IPR005252 InterPro:IPR007085 UniProtKB FTrEMBL:Q0PA68 Genbank:YP_002344229.1 GeneID:905213;gbkey=CDS;product=bifunctional phosphopantothenoylcysteine decarboxylase 2Fphosphopantothenate synthase;Note=catalyzes the conjugation of cysteine to 4 27-phosphopantothenate to form 4-phosphopantothenoylcysteine 2C which is then decarboxylated to form 4 27-phosphopantotheine NC_002163.1 RefSeq gene 770192 771346 . + . ID=gene778;gene=dfp;Name=dfp;locus_tag=Cj0822;Dbxref=GeneID:905213;gbkey=Gene NC_002163.1 RefSeq region 770195 770542 . + . ID=id1547;gene=dfp;Name=id1547;Dbxref=GeneID:905213;gbkey=misc_feature;Note=HMMPfam hit to PF02441 2C Flavoprotein 2C score 1.3e-25 NC_002163.1 RefSeq region 770735 771307 . + . ID=id1548;gene=dfp;Name=id1548;Dbxref=GeneID:905213;gbkey=misc_feature;Note=HMMPfam hit to PF04127 2C DNA 2F pantothenate metabolism flavoprote 2C score 1.2e-16 NC_002163.1 RefSeq CDS 771343 771960 . + 0 ID=cds731;Parent=gene779;Name=YP_002344230.1;Dbxref=UniProtKB FTrEMBL:Q0PA67 Genbank:YP_002344230.1 GeneID:905126;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0823 2C unknown 2C len: 205 aa 3B 24.3 25 identity to HP0842 7EUpdated 282006 29 note: One probable transmembrane helix predicted by TMHMM2.0. Functional classification -Unknown NC_002163.1 RefSeq gene 771343 771960 . + . ID=gene779;gene=Cj0823;Name=Cj0823;locus_tag=Cj0823;Dbxref=GeneID:905126;gbkey=Gene NC_002163.1 RefSeq region 771775 771843 . + . ID=id1549;Name=id1549;Dbxref=GeneID:905126;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0823 by TMHMM2.0 at aa 145-167 ### NC_002163.1 RefSeq gene 771964 772632 . + . ID=gene780;gene=uppS;Name=uppS;locus_tag=Cj0824;Dbxref=GeneID:905127;gbkey=Gene NC_002163.1 RefSeq CDS 771964 772632 . + 0 ID=cds732;Parent=gene780;gene=uppS;Name=YP_002344231.1;Dbxref=GOA:Q9PP99 HSSP:Q47675 InterPro:IPR001441 UniProtKB FSwiss-Prot:Q9PP99 Genbank:YP_002344231.1 GeneID:905127;gbkey=CDS;product=UDP diphosphate synthase;Note=Original 282000 29 note: Cj0824 2C uppS 2C probable UDP diphosphate synthase 2C len: 222 aa 3B similar to TR:O82827 28EMBL:AB004319 29 Micrococcus luteus UDP diphosphate synthase 28249 aa 29 2C fasta scores 3B opt: 365 z-score: 445.7 E 28 29: 1.6e-17 2C 35.2 25 identity in 227 aa overlap 2C and to other members of the UPF0015 family e.g. YAES_ECOLI 28252 aa 29 2C fasta scores 3B opt: 371 z-score: 452.7 E 28 29: 6.4e-18 2C 37.2 25 identity in 226 aa overlap. 42.6 25 identity to HP1221. Contains Pfam match to entry PF01255 UPF0015 7EUpdated 282006 29 note: Previous Pfam domain has now been given a classification as PF01255 UDP diphosphate synthase. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. UPPS 28UDP pyrophosphate synthase 29 catalyses consecutive condensation reactions of FPP 28farnesyl pyrophosphate 29 with eight isopentenyl pyrophosphates to generate C55 UPP 2C which serves as a lipid carrier for bacterial peptidoglycan biosynthesis. removed from product function. Functional classification - Synthesis and modification of macromolecules - Phospholipids 7EPMID:9882662 2C PMID:12756244 2C PMID:15447632 NC_002163.1 RefSeq region 771991 772629 . + . ID=id1550;gene=uppS;Name=id1550;Dbxref=GeneID:905127;gbkey=misc_feature;Note=HMMPfam hit to PF01255 2C UDP diphosphate syntha 2C score 2.6e-72 NC_002163.1 RefSeq region 772629 772661 . + . ID=id1551;Name=id1551;Dbxref=GeneID:905130;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq gene 772629 773405 . + . ID=gene781;gene=Cj0825;Name=Cj0825;locus_tag=Cj0825;Dbxref=GeneID:905130;gbkey=Gene NC_002163.1 RefSeq CDS 772629 773405 . + 0 ID=cds733;Parent=gene781;Name=YP_002344232.1;Dbxref=GOA:Q0PA65 InterPro:IPR000045 InterPro:IPR010627 UniProtKB FTrEMBL:Q0PA65 Genbank:YP_002344232.1 GeneID:905130;gbkey=CDS;product=processing peptidase;Note=Original 282000 29 note: Cj0825 2C possible processing peptidase 2C len: 258 aa 3B similar to e.g. LEP3_VIBCH type 4 prepilin-like protein specific leader peptidase 28253 aa 29 2Cfasta scores 3B opt: 261 z-score: 323.9 E 28 29: 9.7e-11 2C 28.5 25 identity in 260 aa overlap. No Hp match. Contains several probable membrane spanning domains 7EUpdated 282006 29 note: Pfam domains PF06750 Bacterial Peptidase A24 N-terminal domain and PF01478 Type IV leader peptidase family were identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score carried out yet. kept within product function. Literature search identified literature giving further clues to product function. Functional classification - Protein translation and modification 7EPMID:12949093 2C PMID:2553669 NC_002163.1 RefSeq region 772641 772700 . + . ID=id1552;Name=id1552;Dbxref=GeneID:905130;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0825 by TMHMM2.0 at aa 5-24 2C 67-89 2C 93-112 2C 119-136 2C151-173 2C 203-225 and 235-257 NC_002163.1 RefSeq region 772647 772904 . + . ID=id1553;Name=id1553;Dbxref=GeneID:905130;gbkey=misc_feature;Note=HMMPfam hit to PF06750 2C Bacterial Peptidase A24 N-terminal doma 2C score 1.1e-39 NC_002163.1 RefSeq region 772827 772895 . + . ID=id1552;Name=id1552;Dbxref=GeneID:905130;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0825 by TMHMM2.0 at aa 5-24 2C 67-89 2C 93-112 2C 119-136 2C151-173 2C 203-225 and 235-257 NC_002163.1 RefSeq region 772905 772964 . + . ID=id1552;Name=id1552;Dbxref=GeneID:905130;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0825 by TMHMM2.0 at aa 5-24 2C 67-89 2C 93-112 2C 119-136 2C151-173 2C 203-225 and 235-257 NC_002163.1 RefSeq region 772926 773300 . + . ID=id1554;Name=id1554;Dbxref=GeneID:905130;gbkey=misc_feature;Note=HMMPfam hit to PF01478 2C Type IV leader peptidase family 2C score 2.3e-17 NC_002163.1 RefSeq region 772983 773036 . + . ID=id1552;Name=id1552;Dbxref=GeneID:905130;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0825 by TMHMM2.0 at aa 5-24 2C 67-89 2C 93-112 2C 119-136 2C151-173 2C 203-225 and 235-257 NC_002163.1 RefSeq region 773079 773147 . + . ID=id1552;Name=id1552;Dbxref=GeneID:905130;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0825 by TMHMM2.0 at aa 5-24 2C 67-89 2C 93-112 2C 119-136 2C151-173 2C 203-225 and 235-257 NC_002163.1 RefSeq region 773235 773303 . + . ID=id1552;Name=id1552;Dbxref=GeneID:905130;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0825 by TMHMM2.0 at aa 5-24 2C 67-89 2C 93-112 2C 119-136 2C151-173 2C 203-225 and 235-257 NC_002163.1 RefSeq region 773331 773399 . + . ID=id1552;Name=id1552;Dbxref=GeneID:905130;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0825 by TMHMM2.0 at aa 5-24 2C 67-89 2C 93-112 2C 119-136 2C151-173 2C 203-225 and 235-257 NC_002163.1 UTR_Extractor 5'-UTR 773349 773404 . + . ID=utr288;locus_tag=Cj0826;product=putative integral membrane protein NC_002163.1 RefSeq gene 773405 774430 . + . ID=gene782;Name=Cj0826;locus_tag=Cj0826;Dbxref=GeneID:905219;gbkey=Gene NC_002163.1 RefSeq CDS 773405 774430 . + 0 ID=cds734;Parent=gene782;Name=YP_002344233.1;Dbxref=GOA:Q0PA64 InterPro:IPR005495 UniProtKB FTrEMBL:Q0PA64 Genbank:YP_002344233.1 GeneID:905219;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0826 2C probable integral membrane protein 2C len: 341 aa 3B similar to hypothetical membrane proteins e.g. YJGP_HAEIN 28372 aa 29 2C fasta scores 3B opt: 203 z-score: 236.9 E 28 29: 6.8e-06 2C 21.7 25 identity in 314 aa overlap. 32.3 25 identity to HP0362 7EUpdated 282006 29 note: Pfam domain PF03739 Predicted permease YjgP 2FYjgQ family identified within CDS. Members of this family are predicted integral membrane proteins of unknown function. Also 2C six probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 773420 774421 . + . ID=id1555;Name=id1555;Dbxref=GeneID:905219;gbkey=misc_feature;Note=HMMPfam hit to PF03739 2C Predicted permease YjgP 2FYjgQ family 2C score 1.5e-77 NC_002163.1 RefSeq region 773441 773509 . + . ID=id1556;Name=id1556;Dbxref=GeneID:905219;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0826 by TMHMM2.0 at aa 13-35 2C 55-77 2C 106-128 2C 261-283 2C290-307 and 311-333 NC_002163.1 RefSeq region 773567 773635 . + . ID=id1556;Name=id1556;Dbxref=GeneID:905219;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0826 by TMHMM2.0 at aa 13-35 2C 55-77 2C 106-128 2C 261-283 2C290-307 and 311-333 NC_002163.1 RefSeq region 773720 773788 . + . ID=id1556;Name=id1556;Dbxref=GeneID:905219;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0826 by TMHMM2.0 at aa 13-35 2C 55-77 2C 106-128 2C 261-283 2C290-307 and 311-333 NC_002163.1 RefSeq region 774185 774253 . + . ID=id1556;Name=id1556;Dbxref=GeneID:905219;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0826 by TMHMM2.0 at aa 13-35 2C 55-77 2C 106-128 2C 261-283 2C290-307 and 311-333 NC_002163.1 RefSeq region 774272 774325 . + . ID=id1556;Name=id1556;Dbxref=GeneID:905219;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0826 by TMHMM2.0 at aa 13-35 2C 55-77 2C 106-128 2C 261-283 2C290-307 and 311-333 NC_002163.1 RefSeq region 774335 774403 . + . ID=id1556;Name=id1556;Dbxref=GeneID:905219;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0826 by TMHMM2.0 at aa 13-35 2C 55-77 2C 106-128 2C 261-283 2C290-307 and 311-333 NC_002163.1 RefSeq gene 774427 775152 . + . ID=gene783;gene=truA;Name=truA;locus_tag=Cj0827;Dbxref=GeneID:904389;gbkey=Gene NC_002163.1 RefSeq CDS 774427 775152 . + 0 ID=cds735;Parent=gene783;gene=truA;Name=YP_002344234.1;Dbxref=GOA:Q9PP96 InterPro:IPR001406 UniProtKB FSwiss-Prot:Q9PP96 Genbank:YP_002344234.1 GeneID:904389;gbkey=CDS;product=tRNA pseudouridine synthase A;Note=mediates pseudouridylation 28positions 38 2C 39 2C 40 29 at the tRNA anticodon region which contributes to the structural stability NC_002163.1 RefSeq region 774442 774738 . + . ID=id1557;gene=truA;Name=id1557;Dbxref=GeneID:904389;gbkey=misc_feature;Note=HMMPfam hit to PF01416 2C tRNA pseudouridine synthase 2C score 1.1e-21 NC_002163.1 RefSeq region 774847 775149 . + . ID=id1558;gene=truA;Name=id1558;Dbxref=GeneID:904389;gbkey=misc_feature;Note=HMMPfam hit to PF01416 2C tRNA pseudouridine synthase 2C score 2.4e-12 NC_002163.1 RefSeq CDS 775149 776360 . - 0 ID=cds736;Parent=gene784;gene=ilvA;Name=YP_002344235.1;Dbxref=GOA:Q0PA62 InterPro:IPR000634 InterPro:IPR001926 InterPro:IPR005789 UniProtKB FTrEMBL:Q0PA62 Genbank:YP_002344235.1 GeneID:904335;gbkey=CDS;product=threonine dehydratase;Note=catalyzes the formation of 2-oxobutanoate from L-threonine NC_002163.1 RefSeq gene 775149 776360 . - . ID=gene784;gene=ilvA;Name=ilvA;locus_tag=Cj0828c;Dbxref=GeneID:904335;gbkey=Gene NC_002163.1 RefSeq region 775446 776321 . - . ID=id1559;gene=ilvA;Name=id1559;Dbxref=GeneID:904335;gbkey=misc_feature;Note=HMMPfam hit to PF00291 2C Pyridoxal-phosphate dependent enzyme 2C score 1e-81 NC_002163.1 RefSeq region 776196 776237 . - . ID=id1560;gene=ilvA;Name=id1560;Dbxref=GeneID:904335;gbkey=misc_feature;Note=PS00165 Serine 2Fthreonine dehydratases pyridoxal-phosphate attachment site NC_002163.1 RefSeq gene 776360 776773 . - . ID=gene785;gene=Cj0829c;Name=Cj0829c;locus_tag=Cj0829c;Dbxref=GeneID:905131;gbkey=Gene NC_002163.1 RefSeq CDS 776360 776773 . - 0 ID=cds737;Parent=gene785;Name=YP_002344236.1;Dbxref=GOA:Q0PA61 InterPro:IPR003781 InterPro:IPR016040 UniProtKB FTrEMBL:Q0PA61 Genbank:YP_002344236.1 GeneID:905131;gbkey=CDS;product=CoA-binding domain-containing protein;Note=Original 282000 29 note: Cj0829c 2C unknown 2C len: 137 aa 3B similar to hypothetical proteins e.g. TR:P75874 28EMBL:AE000198 29 E. coli b0965 28164 aa 29 2C fasta scores 3B opt: 240 z-score: 312.1 E 28 29: 4.4e-10 2C 30.3 25 identity in 132 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02629 CoA binding domain identified within CDS. Product modified to new family member based on motif match. No specific characterisation has been carried out yet. kept within product function. Functional classification - Misc NC_002163.1 UTR_Extractor 5'-UTR 776361 776382 . - . ID=utr289;locus_tag=Cj0828c;product=threonine dehydratase NC_002163.1 RefSeq region 776429 776743 . - . ID=id1561;Name=id1561;Dbxref=GeneID:905131;gbkey=misc_feature;Note=HMMPfam hit to PF02629 2C CoA binding domain 2C score 0.00014 ### NC_002163.1 UTR_Extractor 5'-UTR 776774 776786 . - . ID=utr290;locus_tag=Cj0829c;product=putative CoA binding domain containing protein NC_002163.1 UTR_Extractor 5'-UTR 776863 776891 . + . ID=utr291;locus_tag=Cj0830;product=putative integral membrane protein NC_002163.1 RefSeq gene 776892 777308 . + . ID=gene786;Name=Cj0830;locus_tag=Cj0830;Dbxref=GeneID:904930;gbkey=Gene NC_002163.1 RefSeq CDS 776892 777308 . + 0 ID=cds738;Parent=gene786;Name=YP_002344237.1;Dbxref=InterPro:IPR007418 UniProtKB FTrEMBL:Q0PA60 Genbank:YP_002344237.1 GeneID:904930;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0830 2C probable integral membrane protein 2C len: 138 aa 3B 42.7 25 identity to HP1502 7EUpdated 282006 29 note: Pfam domain PF04323 Protein of unknown function 28DUF474 29 identified within CDS. Also 2Cfour probable transmembrane helices predicted by TMHMM2.0. Literature search identified paper giving potential clues to product function. Functional classification -Membranes 2C lipoproteins and porins 7EPMID:16045618 NC_002163.1 RefSeq region 776919 776987 . + . ID=id1562;Name=id1562;Dbxref=GeneID:904930;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0830 by TMHMM2.0 at aa 10-32 2C 45-67 2C 77-99 and 112-134 NC_002163.1 RefSeq region 777006 777290 . + . ID=id1563;Name=id1563;Dbxref=GeneID:904930;gbkey=misc_feature;Note=HMMPfam hit to PF04323 2C Protein of unknown function 28DUF474 29 2C score 2.5e-45 NC_002163.1 RefSeq region 777024 777092 . + . ID=id1562;Name=id1562;Dbxref=GeneID:904930;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0830 by TMHMM2.0 at aa 10-32 2C 45-67 2C 77-99 and 112-134 NC_002163.1 RefSeq region 777120 777188 . + . ID=id1562;Name=id1562;Dbxref=GeneID:904930;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0830 by TMHMM2.0 at aa 10-32 2C 45-67 2C 77-99 and 112-134 NC_002163.1 RefSeq region 777225 777293 . + . ID=id1562;Name=id1562;Dbxref=GeneID:904930;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0830 by TMHMM2.0 at aa 10-32 2C 45-67 2C 77-99 and 112-134 NC_002163.1 RefSeq gene 777295 778368 . - . ID=gene787;gene=trmA;Name=trmA;locus_tag=Cj0831c;Dbxref=GeneID:905134;gbkey=Gene NC_002163.1 RefSeq CDS 777295 778368 . - 0 ID=cds739;Parent=gene787;gene=trmA;Name=YP_002344238.1;Dbxref=GOA:Q9PP92 InterPro:IPR010280 InterPro:IPR011869 UniProtKB FSwiss-Prot:Q9PP92 Genbank:YP_002344238.1 GeneID:905134;gbkey=CDS;product=tRNA 28uracil-5- 29-methyltransferase;Note=catalyzes the formation of 5-methyl-uridine at position 54 in all tRNAs NC_002163.1 RefSeq region 777298 778350 . - . ID=id1564;gene=trmA;Name=id1564;Dbxref=GeneID:905134;gbkey=misc_feature;Note=HMMPfam hit to PF05958 2C tRNA 28Uracil-5- 29-methyltransferase 2C score 2.6e-240 NC_002163.1 RefSeq region 777412 777501 . - . ID=id1565;gene=trmA;Name=id1565;Dbxref=GeneID:905134;gbkey=misc_feature;Note=PS01230 RNA methyltransferase trmA family signature 1 NC_002163.1 RefSeq gene 778365 780098 . - . ID=gene788;Name=Cj0832c;locus_tag=Cj0832c;Dbxref=GeneID:904915;gbkey=Gene NC_002163.1 RefSeq CDS 778365 780098 . - 0 ID=cds740;Parent=gene788;Name=YP_002344239.1;Dbxref=GOA:Q0PA58 InterPro:IPR004770 UniProtKB FTrEMBL:Q0PA58 Genbank:YP_002344239.1 GeneID:904915;gbkey=CDS;product=Na 2B 2FH 2B antiporter family protein;Note=Original 282000 29 note: Cj0832c 2C probable integral membrane protein 2C len: 577 aa 3B similar to hypothetical proteins e.g. TR:O59530 28EMBL:AP000007 29 Pyrococcus horikoshii PH1889 28533 aa 29 2C fasta scores 3B opt: 628 z-score: 744.4 E 28 29: 0 2C 39.2 25 identity in 558 aa overlap. 26.9 25 identity to HP0946 7EUpdated 282006 29 note: Pfam domain PF03553 Na 2B 2FH 2B antiporter family identified within CDS. Also 2C thirteen probable transmembrane helices predicted by TMHMM2. Product modified to more specific family member based on motif match. No specific characterisation carried out yet 2Cso kept within product function. Functional classification - Transport 2Fbinding proteins - Cations NC_002163.1 RefSeq region 778380 778448 . - . ID=id55;Name=id55;Dbxref=GeneID:904915;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0832c by TMHMM2.0 at aa 22-44 2C 49-71 2C 106-128 2C 149-171 2C186-208 2C 220-237 2C 242-259 2C 306-328 2C 358-377 2C 390-412 2C434-456 2C 530-547 and 551-573 NC_002163.1 RefSeq region 778449 779513 . - . ID=id1566;Name=id1566;Dbxref=GeneID:904915;gbkey=misc_feature;Note=HMMPfam hit to PF03553 2C Na 2B 2FH 2B antiporter family 2Cscore 5.2e-102 NC_002163.1 RefSeq region 778458 778511 . - . ID=id55;Name=id55;Dbxref=GeneID:904915;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0832c by TMHMM2.0 at aa 22-44 2C 49-71 2C 106-128 2C 149-171 2C186-208 2C 220-237 2C 242-259 2C 306-328 2C 358-377 2C 390-412 2C434-456 2C 530-547 and 551-573 NC_002163.1 RefSeq region 778731 778799 . - . ID=id55;Name=id55;Dbxref=GeneID:904915;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0832c by TMHMM2.0 at aa 22-44 2C 49-71 2C 106-128 2C 149-171 2C186-208 2C 220-237 2C 242-259 2C 306-328 2C 358-377 2C 390-412 2C434-456 2C 530-547 and 551-573 NC_002163.1 RefSeq region 778863 778931 . - . ID=id55;Name=id55;Dbxref=GeneID:904915;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0832c by TMHMM2.0 at aa 22-44 2C 49-71 2C 106-128 2C 149-171 2C186-208 2C 220-237 2C 242-259 2C 306-328 2C 358-377 2C 390-412 2C434-456 2C 530-547 and 551-573 NC_002163.1 RefSeq region 778968 779027 . - . ID=id55;Name=id55;Dbxref=GeneID:904915;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0832c by TMHMM2.0 at aa 22-44 2C 49-71 2C 106-128 2C 149-171 2C186-208 2C 220-237 2C 242-259 2C 306-328 2C 358-377 2C 390-412 2C434-456 2C 530-547 and 551-573 NC_002163.1 RefSeq region 779115 779183 . - . ID=id55;Name=id55;Dbxref=GeneID:904915;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0832c by TMHMM2.0 at aa 22-44 2C 49-71 2C 106-128 2C 149-171 2C186-208 2C 220-237 2C 242-259 2C 306-328 2C 358-377 2C 390-412 2C434-456 2C 530-547 and 551-573 NC_002163.1 RefSeq region 779322 779375 . - . ID=id55;Name=id55;Dbxref=GeneID:904915;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0832c by TMHMM2.0 at aa 22-44 2C 49-71 2C 106-128 2C 149-171 2C186-208 2C 220-237 2C 242-259 2C 306-328 2C 358-377 2C 390-412 2C434-456 2C 530-547 and 551-573 NC_002163.1 RefSeq region 779388 779441 . - . ID=id55;Name=id55;Dbxref=GeneID:904915;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0832c by TMHMM2.0 at aa 22-44 2C 49-71 2C 106-128 2C 149-171 2C186-208 2C 220-237 2C 242-259 2C 306-328 2C 358-377 2C 390-412 2C434-456 2C 530-547 and 551-573 NC_002163.1 RefSeq region 779475 779543 . - . ID=id55;Name=id55;Dbxref=GeneID:904915;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0832c by TMHMM2.0 at aa 22-44 2C 49-71 2C 106-128 2C 149-171 2C186-208 2C 220-237 2C 242-259 2C 306-328 2C 358-377 2C 390-412 2C434-456 2C 530-547 and 551-573 NC_002163.1 RefSeq region 779586 779654 . - . ID=id55;Name=id55;Dbxref=GeneID:904915;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0832c by TMHMM2.0 at aa 22-44 2C 49-71 2C 106-128 2C 149-171 2C186-208 2C 220-237 2C 242-259 2C 306-328 2C 358-377 2C 390-412 2C434-456 2C 530-547 and 551-573 NC_002163.1 RefSeq region 779715 779783 . - . ID=id55;Name=id55;Dbxref=GeneID:904915;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0832c by TMHMM2.0 at aa 22-44 2C 49-71 2C 106-128 2C 149-171 2C186-208 2C 220-237 2C 242-259 2C 306-328 2C 358-377 2C 390-412 2C434-456 2C 530-547 and 551-573 NC_002163.1 RefSeq region 779886 779954 . - . ID=id55;Name=id55;Dbxref=GeneID:904915;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0832c by TMHMM2.0 at aa 22-44 2C 49-71 2C 106-128 2C 149-171 2C186-208 2C 220-237 2C 242-259 2C 306-328 2C 358-377 2C 390-412 2C434-456 2C 530-547 and 551-573 NC_002163.1 RefSeq region 779967 780035 . - . ID=id55;Name=id55;Dbxref=GeneID:904915;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0832c by TMHMM2.0 at aa 22-44 2C 49-71 2C 106-128 2C 149-171 2C186-208 2C 220-237 2C 242-259 2C 306-328 2C 358-377 2C 390-412 2C434-456 2C 530-547 and 551-573 NC_002163.1 RefSeq gene 780095 780844 . - . ID=gene789;Name=Cj0833c;locus_tag=Cj0833c;Dbxref=GeneID:905132;gbkey=Gene NC_002163.1 RefSeq CDS 780095 780844 . - 0 ID=cds741;Parent=gene789;Name=YP_002344240.1;Dbxref=GOA:Q0PA57 InterPro:IPR002198 InterPro:IPR002347 InterPro:IPR016040 UniProtKB FTrEMBL:Q0PA57 Genbank:YP_002344240.1 GeneID:905132;gbkey=CDS;product=oxidoreductase;Note=Original 282000 29 note: Cj0833c 2C probable oxidoreductase 2C len: 249 aa 3B simlar to e.g. YDFG_ECOLI probable oxidoreductase 28248 aa 29 2C fasta scores 3B opt: 796 z-score: 943.5 E 28 29: 0 2C 48.8 25 identity in 244 aa overlap. 47.3 25 identity to HP0357. Contains PS00061 Short-chain dehydrogenases 2Freductases family signature 2C and Pfam match to entry PF00106 adh_short 2C Alcohol 2Fother dehydrogenases 2Cshort chain type 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. kept within product function. Functional classification -Misc 7EPMID:12535615 NC_002163.1 RefSeq region 780113 780835 . - . ID=id1567;Name=id1567;Dbxref=GeneID:905132;gbkey=misc_feature;Note=HMMPfam hit to PF00106 2C short chain dehydrogenase 2Cscore 7.9e-49 NC_002163.1 RefSeq region 780356 780442 . - . ID=id1568;Name=id1568;Dbxref=GeneID:905132;gbkey=misc_feature;Note=PS00061 Short-chain dehydrogenases 2Freductases family signature NC_002163.1 RefSeq gene 780841 782079 . - . ID=gene790;Name=Cj0834c;locus_tag=Cj0834c;Dbxref=GeneID:905133;gbkey=Gene NC_002163.1 RefSeq CDS 780841 782079 . - 0 ID=cds742;Parent=gene790;Name=YP_002344241.1;Dbxref=InterPro:IPR002110 UniProtKB FTrEMBL:Q0PA56 Genbank:YP_002344241.1 GeneID:905133;gbkey=CDS;product=ankyrin repeat-containing protein;Note=Original 282000 29 note: Cj0834c 2C possible periplasmic protein 2C len: 412 aa 3B similar in C-terminus to ankyrin repeat-containing proteins e.g. ANKH_CHRVI ankyrin homolog precursor 28323 aa 29 2C fasta scores 3B opt: 194 z-score: 229.9 E 28 29: 1.7e-05 2C 28.9 25 identity in 194 aa overlap. No Hp match. Some similarity to ankyrin repeats in Cj1386 2829.3 25 identity in 99 aa overlap 29. Contains 2x Pfam match to entry PF00023 ank 2C Ank repeat 2C and possible N-terminal signal sequence 7EUpdated 282006 29 note: No specific characterisation with acceptable identity scores carried out yet. kept within product function. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 780961 781059 . - . ID=id1569;Name=id1569;Dbxref=GeneID:905133;gbkey=misc_feature;Note=HMMPfam hit to PF00023 2C Ankyrin repeat 2C score 1.8e-06 NC_002163.1 RefSeq region 781141 781239 . - . ID=id1570;Name=id1570;Dbxref=GeneID:905133;gbkey=misc_feature;Note=HMMPfam hit to PF00023 2C Ankyrin repeat 2C score 1.9e-07 NC_002163.1 RefSeq region 781240 781428 . - . ID=id1571;Name=id1571;Dbxref=GeneID:905133;gbkey=misc_feature;Note=HMMPfam hit to PF00023 2C Ankyrin repeat 2C score 7.2 ### NC_002163.1 RefSeq CDS 782129 784675 . - 0 ID=cds743;Parent=gene791;gene=acnB;Name=YP_002344242.1;Dbxref=GOA:Q0PA55 InterPro:IPR001030 InterPro:IPR004406 InterPro:IPR015928 InterPro:IPR015929 InterPro:IPR015930 InterPro:IPR015931 InterPro:IPR015932 InterPro:IPR015933 InterPro:IPR015937 UniProtKB FTrEMBL:Q0PA55 Genbank:YP_002344242.1 GeneID:905137;gbkey=CDS;product=bifunctional aconitate hydratase 2 2F2-methylisocitrate dehydratase;Note=catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate NC_002163.1 RefSeq gene 782129 784675 . - . ID=gene791;gene=acnB;Name=acnB;locus_tag=Cj0835c;Dbxref=GeneID:905137;gbkey=Gene NC_002163.1 RefSeq region 782252 783571 . - . ID=id1572;gene=acnB;Name=id1572;Dbxref=GeneID:905137;gbkey=misc_feature;Note=HMMPfam hit to PF00330 2C Aconitase family 28aconitate hydratase 29 2C score 2.3e-09 NC_002163.1 RefSeq region 782384 782425 . - . ID=id1573;gene=acnB;Name=id1573;Dbxref=GeneID:905137;gbkey=misc_feature;Note=PS01244 Aconitase family signature 2 NC_002163.1 RefSeq region 782546 782599 . - . ID=id1574;gene=acnB;Name=id1574;Dbxref=GeneID:905137;gbkey=misc_feature;Note=PS00450 Aconitase family signature 1 NC_002163.1 RefSeq region 783572 784666 . - . ID=id1575;gene=acnB;Name=id1575;Dbxref=GeneID:905137;gbkey=misc_feature;Note=HMMPfam hit to PF06434 2C Aconitate hydratase 2C score 3.2e-259 ### NC_002163.1 UTR_Extractor 5'-UTR 784676 784731 . - . ID=utr292;locus_tag=Cj0835c;product=bifunctional aconitate hydratase 2 2F2-methylisocitrate dehydratase NC_002163.1 UTR_Extractor 5'-UTR 784713 784729 . + . ID=utr293;locus_tag=Cj0836;product=methylated-DNA--protein-cysteine methyltransferase NC_002163.1 RefSeq gene 784730 785182 . + . ID=gene792;gene=ogt;Name=ogt;locus_tag=Cj0836;Dbxref=GeneID:904456;gbkey=Gene NC_002163.1 RefSeq CDS 784730 785182 . + 0 ID=cds744;Parent=gene792;gene=ogt;Name=YP_002344243.1;Dbxref=GOA:Q0PA54 InterPro:IPR001497 InterPro:IPR011991 InterPro:IPR014048 UniProtKB FTrEMBL:Q0PA54 Genbank:YP_002344243.1 GeneID:904456;gbkey=CDS;product=methylated-DNA--protein-cysteine methyltransferase;Note=Original 282000 29 note: Cj0836 2C ogt 2C probable methylated-DNA--protein-cysteine methyltransferase 2C len: 150 aa 3B similar to many e.g. OGT_ECOLI methylated-DNA--protein-cysteine methyltransferase 28EC 2.1.1.63 29 28171 aa 29 2C fasta scores 3B opt: 274 z-score: 355.6 E 28 29: 1.6e-12 2C 43.7 25 identity in 103 aa overlap 2C and DAT1_BACSU methylated-DNA--protein-cysteine methyltransferase 28165 aa 29 2C fasta scores 3B opt: 358 z-score: 460.7 E 28 29: 2.3e-18 2C 44.5 25 identity in 137 aa overlap. 45.3 25 identity to HP0676. Contains PS00374 Methylated-DNA--protein-cysteine methyltransferase active site and Pfam match to entry PF01035 Methyltrans 2C6-O-methylguanine DNA methyltransferase 7EUpdated 282006 29 note: Characterised in Escherichia coli and Bacillus subtilis with acceptable identity score. not added to product function. Functional classification - DNA replication 2Crestriction 2Fmodification 2C recombination and repair 7EPMID:2506524 NC_002163.1 RefSeq region 784925 785179 . + . ID=id1576;gene=ogt;Name=id1576;Dbxref=GeneID:904456;gbkey=misc_feature;Note=HMMPfam hit to PF01035 2C 6-O-methylguanine DNA methyltransferas 2C score 1.1e-41 NC_002163.1 RefSeq region 785078 785098 . + . ID=id1577;gene=ogt;Name=id1577;Dbxref=GeneID:904456;gbkey=misc_feature;Note=PS00374 Methylated-DNA--protein-cysteine methyltransferase active site NC_002163.1 RefSeq gene 785174 786115 . - . ID=gene793;gene=Cj0837c;Name=Cj0837c;locus_tag=Cj0837c;Dbxref=GeneID:905005;gbkey=Gene NC_002163.1 RefSeq CDS 785174 786115 . - 0 ID=cds745;Parent=gene793;Name=YP_002344244.1;Dbxref=UniProtKB FTrEMBL:Q0PA53 Genbank:YP_002344244.1 GeneID:905005;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0837c 2C unknown 2C len: 313 aa 3B no Hp match. Contains PS00179 Aminoacyl-transfer RNA synthetases class-II signature 1 2C and PS00030 Eukaryotic RNA-binding region RNP-1 signature. Functional classification - Unknown NC_002163.1 RefSeq region 785741 785764 . - . ID=id1578;Name=id1578;Dbxref=GeneID:905005;gbkey=misc_feature;Note=PS00030 Eukaryotic RNA-binding region RNP-1 signature NC_002163.1 RefSeq region 785837 785896 . - . ID=id1579;Name=id1579;Dbxref=GeneID:905005;gbkey=misc_feature;Note=PS00179 Aminoacyl-transfer RNA synthetases class-II signature 1 ### NC_002163.1 RefSeq CDS 786119 788005 . - 0 ID=cds746;Parent=gene794;gene=metG;Name=YP_002344245.1;Dbxref=GOA:Q9PP85 HSSP:P23395 InterPro:IPR001412 InterPro:IPR002304 InterPro:IPR002547 InterPro:IPR004495 InterPro:IPR012340 InterPro:IPR014729 InterPro:IPR014758 InterPro:IPR015413 UniProtKB FSwiss-Prot:Q9PP85 Genbank:YP_002344245.1 GeneID:905186;gbkey=CDS;product=methionyl-tRNA synthetase;Note=methionine--tRNA ligase 3B MetRS 3B adds methionine to tRNA 28Met 29 with cleavage of ATP to AMP and diphosphate 3B some MetRS enzymes form dimers depending on a C-terminal domain that is also found in other proteins such as Trbp111 in Aquifex aeolicus and the cold-shock protein CsaA from Bacillus subtilis while others do not 3B four subfamilies exist based on sequence motifs and zinc content NC_002163.1 RefSeq gene 786119 788005 . - . ID=gene794;gene=metG;Name=metG;locus_tag=Cj0838c;Dbxref=GeneID:905186;gbkey=Gene NC_002163.1 RefSeq region 786128 786409 . - . ID=id1580;gene=metG;Name=id1580;Dbxref=GeneID:905186;gbkey=misc_feature;Note=HMMPfam hit to PF01588 2C tRNA binding domain 2C score 3.8e-30 NC_002163.1 RefSeq region 787004 788002 . - . ID=id1581;gene=metG;Name=id1581;Dbxref=GeneID:905186;gbkey=misc_feature;Note=HMMPfam hit to PF00133 2C tRNA synthetases class I 28I 2C L 2C M and V 29 2C score 8.9e-08 ### NC_002163.1 RefSeq CDS 788015 788212 . - 0 ID=cds747;Parent=gene795;Name=YP_002344246.1;Dbxref=UniProtKB FTrEMBL:Q0PA51 Genbank:YP_002344246.1 GeneID:905138;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0839c 2C unknown 2C len: 65 aa 3B 43.1 25 identity to HP1384. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 788015 788212 . - . ID=gene795;Name=Cj0839c;locus_tag=Cj0839c;Dbxref=GeneID:905138;gbkey=Gene NC_002163.1 RefSeq gene 788205 789047 . - . ID=gene796;gene=fbp;Name=fbp;locus_tag=Cj0840c;Dbxref=GeneID:905148;gbkey=Gene NC_002163.1 RefSeq CDS 788205 789047 . - 0 ID=cds748;Parent=gene796;gene=fbp;Name=YP_002344247.1;Dbxref=GOA:Q0PA50 InterPro:IPR000146 UniProtKB FTrEMBL:Q0PA50 Genbank:YP_002344247.1 GeneID:905148;gbkey=CDS;product=fructose-1 2C6-bisphosphatase;Note=catalyzes the formation of D-fructose 6-phosphate from fructose-1 2C6-bisphosphate NC_002163.1 RefSeq region 788208 789047 . - . ID=id1582;gene=fbp;Name=id1582;Dbxref=GeneID:905148;gbkey=misc_feature;Note=HMMPfam hit to PF00316 2CFructose-1-6-bisphosphatase 2C score 1.1e-52 ### NC_002163.1 RefSeq CDS 789049 789540 . - 0 ID=cds749;Parent=gene797;gene=mobB;Name=YP_002344248.1;Dbxref=GOA:Q0PA49 InterPro:IPR004435 UniProtKB FTrEMBL:Q0PA49 Genbank:YP_002344248.1 GeneID:904424;gbkey=CDS;product=molybdopterin-guanine dinucleotide biosynthesis protein;Note=Original 282000 29 note: Cj0841c 2C probable ATP 2FGTP binding protein 2C len: 163 aa 3B some similarity to e.g. MOBB_ECOLI molybdopterin-guanine dinucleotide biosynthesis protein B 28174 aa 29 2C fasta scores 3B opt: 148 z-score: 194.1 E 28 29: 0.0016 2C 25.6 25 identity in 168 aa overlap. No Hp match. Contains S00017 ATP 2FGTP-binding site motif A 28P-loop 29 7EUpdated 282006 29 note: Pfam domain PF03205 Molybdopterin guanine dinucleotide synthesis protein B identified within CDS. Further support for product function. Characterisation papers form Escherichia coli have been attached. This information and identification of appropriate motifs has led to product function being modified to a more specific family member. kept within product function. Functional classification -Biosynthesis of cofactors 2C prosthetic groups and carriers - Molybdopterin 7EPMID:12372836 2C PMID:9219527 NC_002163.1 RefSeq gene 789049 789540 . - . ID=gene797;gene=mobB;Name=mobB;locus_tag=Cj0841c;Dbxref=GeneID:904424;gbkey=Gene NC_002163.1 RefSeq region 789148 789531 . - . ID=id1583;gene=mobB;Name=id1583;Dbxref=GeneID:904424;gbkey=misc_feature;Note=HMMPfam hit to PF03205 2C Molybdopterin guanine dinucleotide synthesis 2C score 1.2e-21 NC_002163.1 RefSeq region 789490 789513 . - . ID=id1584;gene=mobB;Name=id1584;Dbxref=GeneID:904424;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 RefSeq CDS 789636 790121 . + 0 ID=cds750;Parent=gene798;Name=YP_002344249.1;Dbxref=UniProtKB FTrEMBL:Q0PA48 Genbank:YP_002344249.1 GeneID:905139;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj0842 2C probable lipoprotein 2Clen: 161 aa 3B no Hp match. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 789636 790121 . + . ID=gene798;Name=Cj0842;locus_tag=Cj0842;Dbxref=GeneID:905139;gbkey=Gene NC_002163.1 RefSeq region 789651 789683 . + . ID=id1585;Name=id1585;Dbxref=GeneID:905139;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq gene 790018 791643 . - . ID=gene799;Name=Cj0843c;locus_tag=Cj0843c;Dbxref=GeneID:905140;gbkey=Gene NC_002163.1 RefSeq CDS 790018 791643 . - 0 ID=cds751;Parent=gene799;Name=YP_002344250.1;Dbxref=InterPro:IPR000189 InterPro:IPR008258 UniProtKB FTrEMBL:Q0PA47 Genbank:YP_002344250.1 GeneID:905140;gbkey=CDS;product=transglycosylase;Note=Original 282000 29 note: Cj0843c 2C probable secreted transglycosylase 2C len: 541 aa 3B some simialarity in C-terminus to SLT_ECOLI soluble lytic murein transglycosylase precursor 28645 aa 29 2C fasta scores 3B opt: 257 z-score: 285.7 E 28 29: 1.3e-08 2C 29.3 25 identity in 208 aa overlap. 31.4 25 identity to HP0645. Contains PS00922 Prokaryotic transglycosylases signature and N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF01464 Transglycosylase SLT domain identified within CDS. Further support given to product function. kept within product function as identity scores were marginal and alignment was only partial. Paper identified linking product function to glycosylation. Functional classification - Degradation of macromolecules - Proteins 2Cpeptides and glycopeptides 7EPMID:12186869 NC_002163.1 RefSeq region 790186 790545 . - . ID=id1586;Name=id1586;Dbxref=GeneID:905140;gbkey=misc_feature;Note=HMMPfam hit to PF01464 2C Transglycosylase SLT domain 2C score 1.1e-20 NC_002163.1 RefSeq region 790402 790488 . - . ID=id1587;Name=id1587;Dbxref=GeneID:905140;gbkey=misc_feature;Note=PS00922 Prokaryotic transglycosylases signature NC_002163.1 RefSeq gene 791640 791921 . - . ID=gene800;Name=Cj0844c;locus_tag=Cj0844c;Dbxref=GeneID:905141;gbkey=Gene NC_002163.1 RefSeq CDS 791640 791921 . - 0 ID=cds752;Parent=gene800;Name=YP_002344251.1;Dbxref=GOA:Q0PA46 InterPro:IPR003425 UniProtKB FTrEMBL:Q0PA46 Genbank:YP_002344251.1 GeneID:905141;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0844c 2C possible integral membrane protein 2C len: 93 aa 3B 38.4 25 identity to HP0644 7EUpdated 282006 29 note: Pfam domain PF02325 YGGT family identified within CDS. This family consists of a repeat found in conserved hypothetical integral membrane proteins. The function of this region and the proteins which possess it is unknown. Also 2C two probable transmembrane helices predicted by TMHMM2.0. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 791655 791723 . - . ID=id56;Name=id56;Dbxref=GeneID:905141;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0844c by TMHMM2.0 at aa 7-29 and 67-89 NC_002163.1 RefSeq region 791658 791903 . - . ID=id1588;Name=id1588;Dbxref=GeneID:905141;gbkey=misc_feature;Note=HMMPfam hit to PF02325 2C YGGT family 2C score 6.1e-20 NC_002163.1 RefSeq region 791835 791903 . - . ID=id56;Name=id56;Dbxref=GeneID:905141;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0844c by TMHMM2.0 at aa 7-29 and 67-89 ### NC_002163.1 RefSeq CDS 791924 793219 . - 0 ID=cds753;Parent=gene801;gene=gltX;Name=YP_002344252.1;Dbxref=GOA:Q9PP78 HSSP:P27000 InterPro:IPR000924 InterPro:IPR001412 InterPro:IPR004527 InterPro:IPR014729 UniProtKB FSwiss-Prot:Q9PP78 Genbank:YP_002344252.1 GeneID:905144;gbkey=CDS;product=glutamylglutaminyl-tRNA synthetase;Note=charges one glutamine molecule and pairs it with tRNA 28Gln 29 NC_002163.1 RefSeq gene 791924 793219 . - . ID=gene801;gene=gltX;Name=gltX;locus_tag=Cj0845c;Dbxref=GeneID:905144;gbkey=Gene NC_002163.1 RefSeq region 792314 793213 . - . ID=id1589;gene=gltX;Name=id1589;Dbxref=GeneID:905144;gbkey=misc_feature;Note=HMMPfam hit to PF00749 2C tRNA synthetases class I 28E and Q 29 2C cata 2C score 1.1e-85 NC_002163.1 RefSeq region 793169 793204 . - . ID=id1590;gene=gltX;Name=id1590;Dbxref=GeneID:905144;gbkey=misc_feature;Note=PS00178 Aminoacyl-transfer RNA synthetases class-I signature ### NC_002163.1 UTR_Extractor 5'-UTR 793220 793246 . - . ID=utr294;locus_tag=Cj0845c;product=glutamylglutaminyl-tRNA synthetase NC_002163.1 UTR_Extractor 5'-UTR 793305 793305 . + . ID=utr295;locus_tag=Cj0846;product=putative metallophosphoesterase NC_002163.1 RefSeq gene 793305 794429 . + . ID=gene802;Name=Cj0846;locus_tag=Cj0846;Dbxref=GeneID:905145;gbkey=Gene NC_002163.1 RefSeq CDS 793305 794429 . + 0 ID=cds754;Parent=gene802;Name=YP_002344253.1;Dbxref=GOA:Q9PP77 InterPro:IPR004843 UniProtKB FSwiss-Prot:Q9PP77 Genbank:YP_002344253.1 GeneID:905145;gbkey=CDS;product=metallophosphoesterase;Note=Original 282000 29 note: Cj0846 2C probable integral membrane protein 2C len: 374 aa 3B contains several probable membrane spanning regions in N-terminal half 2C C-terminal half is simalar to several hypothetical proteins e.g. YPBG_BACSU 28259 aa 29 2C fasta scores 3B opt: 197 z-score: 233.7 E 28 29: 1e-05 2C 28.6 25 identity in 238 aa overlap. 38.8 25 identity to HP1044 7EUpdated 282006 29 note: Pfam domain PF00149 Calcineurin-like phosphoesterase and Prosite domain PS00142 Peptidase M 2C neutral zinc metallopeptidases 2Czinc-binding site identified within CDS. Also 2C four probable transmembrane helices predicted by TMHMM2.0. Product function modified to more specific family member based on motif matches. No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification - Misc NC_002163.1 RefSeq region 793314 793370 . + . ID=id1591;Name=id1591;Dbxref=GeneID:905145;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0846 by TMHMM2.0 at aa 4-22 2C 34-56 2C 71-93 and 106-128 NC_002163.1 RefSeq region 793404 793472 . + . ID=id1591;Name=id1591;Dbxref=GeneID:905145;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0846 by TMHMM2.0 at aa 4-22 2C 34-56 2C 71-93 and 106-128 NC_002163.1 RefSeq region 793515 793583 . + . ID=id1591;Name=id1591;Dbxref=GeneID:905145;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0846 by TMHMM2.0 at aa 4-22 2C 34-56 2C 71-93 and 106-128 NC_002163.1 RefSeq region 793620 793688 . + . ID=id1591;Name=id1591;Dbxref=GeneID:905145;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0846 by TMHMM2.0 at aa 4-22 2C 34-56 2C 71-93 and 106-128 NC_002163.1 RefSeq region 793755 794252 . + . ID=id1592;Name=id1592;Dbxref=GeneID:905145;gbkey=misc_feature;Note=HMMPfam hit to PF00149 2C Calcineurin-like phosphoesterase 2C score 1.2e-12 NC_002163.1 RefSeq region 793959 793988 . + . ID=id1593;Name=id1593;Dbxref=GeneID:905145;gbkey=misc_feature;Note=PS00142 Neutral zinc metallopeptidases 2Czinc-binding region signature NC_002163.1 RefSeq CDS 794426 795226 . + 0 ID=cds755;Parent=gene803;gene=psd;Name=YP_002344254.1;Dbxref=GOA:Q9PP76 InterPro:IPR003817 InterPro:IPR005221 UniProtKB FSwiss-Prot:Q9PP76 Genbank:YP_002344254.1 GeneID:904800;gbkey=CDS;product=phosphatidylserine decarboxylase;Note=catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine NC_002163.1 RefSeq gene 794426 795226 . + . ID=gene803;gene=psd;Name=psd;locus_tag=Cj0847;Dbxref=GeneID:904800;gbkey=Gene NC_002163.1 RefSeq region 794576 795223 . + . ID=id1594;gene=psd;Name=id1594;Dbxref=GeneID:904800;gbkey=misc_feature;Note=HMMPfam hit to PF02666 2C Phosphatidylserine decarboxylase 2C score 1.8e-45 NC_002163.1 RefSeq gene 795223 795504 . - . ID=gene804;gene=Cj0848c;Name=Cj0848c;locus_tag=Cj0848c;Dbxref=GeneID:905149;gbkey=Gene NC_002163.1 RefSeq CDS 795223 795504 . - 0 ID=cds756;Parent=gene804;Name=YP_002344255.1;Dbxref=GOA:Q0PA42 InterPro:IPR004683 InterPro:IPR006135 UniProtKB FTrEMBL:Q0PA42 Genbank:YP_002344255.1 GeneID:905149;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0848c 2C unknown 2C len: 93 aa 3B similar to hypothetical proteins e.g. TR:O34867 28EMBL:AJ000975 29 B. subtilis YLQH protein 2893 aa 29 2C fasta scores 3B opt: 284 z-score: 365.6 E 28 29: 4.5e-13 2C 47.3 25 identity in 91 aa overlap. Also similar to C-terminus of flhB possible flagellar transport proteins e.g. FLHB_ECOLI flagellar biosynthetic protein FLHB 28382 aa 29 2C fasta scores 3B opt: 182 z-score: 232.8 E 28 29: 1.1e-05 2C 41.6 25 identity in 77 aa overlap. 39.2 25 identity to HP1575 28annotated as flhB 29. Also similar to C-terminus of Cj0335 2CflhB 2840.7 25 identity in 81 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01312 Bac_export_2 2C FlhB HrpN YscU SpaS Family identified within CDS. All of these proteins export peptides using the type III secretion system. The peptides exported are quite diverse. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq CDS 795501 797660 . - 0 ID=cds757;Parent=gene805;Name=YP_002344256.1;Dbxref=UniProtKB FTrEMBL:Q0PA41 Genbank:YP_002344256.1 GeneID:905146;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0849c 2C unknown 2C len: 719 aa 3B no Hp ortholog 2C some similarity to Cj0041 2823.1 25 identity in 566 aa overlap 29. Contain Asn-rich region near centre 7EUpdated 282006 29 note: Prosite domain PS00063 Aldo 2Fketo reductase family active site signature found within CDS. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 795501 797660 . - . ID=gene805;Name=Cj0849c;locus_tag=Cj0849c;Dbxref=GeneID:905146;gbkey=Gene NC_002163.1 RefSeq region 795528 795575 . - . ID=id1595;Name=id1595;Dbxref=GeneID:905146;gbkey=misc_feature;Note=PS00063 Aldo 2Fketo reductase family active site signature NC_002163.1 RefSeq gene 797653 798840 . - . ID=gene806;Name=Cj0850c;locus_tag=Cj0850c;Dbxref=GeneID:905150;gbkey=Gene NC_002163.1 RefSeq CDS 797653 798840 . - 0 ID=cds758;Parent=gene806;Name=YP_002344257.1;Dbxref=GOA:Q0PA40 InterPro:IPR005829 InterPro:IPR007114 InterPro:IPR011701 UniProtKB FTrEMBL:Q0PA40 Genbank:YP_002344257.1 GeneID:905150;gbkey=CDS;product=MFS transport protein;Note=Original 282000 29 note: Cj0850c 2C transmembrane transport protein 2C len: 395 aa 3B similar to hypothetical transport proteins e.g. YCAD_ECOLI 28382 aa 29 2C fasta scores 3B opt: 431 z-score: 481.6 E 28 29: 1.6e-19 2C 27.6 25 identity in 366 aa overlap. No Hp ortholog. Contains S00216 Sugar transport proteins signature 1 2C and Pfam match to entry PF00083 sugar_tr 2C Sugar 28and other 29 transporters 7EUpdated 282006 29 note: Pfam domain PF07690 Major Facilitator Superfamily identified within CDS. Also 2Ctwelve probable transmembrane helices predicted by TMHMM2.0. The MFS family contains functions such as uniporters 2C symporters or antiporters. MFS proteins typically contain 12 transmembrane regions. Product modified to more specific family based on motif match. Functional classification - Transport 2Fbinding proteins -Other NC_002163.1 RefSeq region 797671 798819 . - . ID=id1596;Name=id1596;Dbxref=GeneID:905150;gbkey=misc_feature;Note=HMMPfam hit to PF00083 2C Sugar 28and other 29 transporter 2C score 4.6e-05 NC_002163.1 RefSeq region 797704 797772 . - . ID=id57;Name=id57;Dbxref=GeneID:905150;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0850c by TMHMM2.0 at aa 12-34 2C 44-63 2C 70-89 2C 99-121 2C134-156 2C 160-179 2C 204-226 2C 236-258 2C 265-284 2C 288-310 2C330-352 and 357-379 NC_002163.1 RefSeq region 797785 797853 . - . ID=id57;Name=id57;Dbxref=GeneID:905150;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0850c by TMHMM2.0 at aa 12-34 2C 44-63 2C 70-89 2C 99-121 2C134-156 2C 160-179 2C 204-226 2C 236-258 2C 265-284 2C 288-310 2C330-352 and 357-379 NC_002163.1 RefSeq region 797791 798804 . - . ID=id1597;Name=id1597;Dbxref=GeneID:905150;gbkey=misc_feature;Note=HMMPfam hit to PF07690 2C Major Facilitator Superfamily 2C score 3.5e-24 NC_002163.1 RefSeq region 797911 797979 . - . ID=id57;Name=id57;Dbxref=GeneID:905150;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0850c by TMHMM2.0 at aa 12-34 2C 44-63 2C 70-89 2C 99-121 2C134-156 2C 160-179 2C 204-226 2C 236-258 2C 265-284 2C 288-310 2C330-352 and 357-379 NC_002163.1 RefSeq region 797989 798048 . - . ID=id57;Name=id57;Dbxref=GeneID:905150;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0850c by TMHMM2.0 at aa 12-34 2C 44-63 2C 70-89 2C 99-121 2C134-156 2C 160-179 2C 204-226 2C 236-258 2C 265-284 2C 288-310 2C330-352 and 357-379 NC_002163.1 RefSeq region 798028 798081 . - . ID=id1598;Name=id1598;Dbxref=GeneID:905150;gbkey=misc_feature;Note=PS00216 Sugar transport proteins signature 1 NC_002163.1 RefSeq region 798067 798135 . - . ID=id57;Name=id57;Dbxref=GeneID:905150;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0850c by TMHMM2.0 at aa 12-34 2C 44-63 2C 70-89 2C 99-121 2C134-156 2C 160-179 2C 204-226 2C 236-258 2C 265-284 2C 288-310 2C330-352 and 357-379 NC_002163.1 RefSeq region 798163 798231 . - . ID=id57;Name=id57;Dbxref=GeneID:905150;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0850c by TMHMM2.0 at aa 12-34 2C 44-63 2C 70-89 2C 99-121 2C134-156 2C 160-179 2C 204-226 2C 236-258 2C 265-284 2C 288-310 2C330-352 and 357-379 NC_002163.1 RefSeq region 798304 798363 . - . ID=id57;Name=id57;Dbxref=GeneID:905150;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0850c by TMHMM2.0 at aa 12-34 2C 44-63 2C 70-89 2C 99-121 2C134-156 2C 160-179 2C 204-226 2C 236-258 2C 265-284 2C 288-310 2C330-352 and 357-379 NC_002163.1 RefSeq region 798373 798441 . - . ID=id57;Name=id57;Dbxref=GeneID:905150;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0850c by TMHMM2.0 at aa 12-34 2C 44-63 2C 70-89 2C 99-121 2C134-156 2C 160-179 2C 204-226 2C 236-258 2C 265-284 2C 288-310 2C330-352 and 357-379 NC_002163.1 RefSeq region 798478 798546 . - . ID=id57;Name=id57;Dbxref=GeneID:905150;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0850c by TMHMM2.0 at aa 12-34 2C 44-63 2C 70-89 2C 99-121 2C134-156 2C 160-179 2C 204-226 2C 236-258 2C 265-284 2C 288-310 2C330-352 and 357-379 NC_002163.1 RefSeq region 798574 798633 . - . ID=id57;Name=id57;Dbxref=GeneID:905150;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0850c by TMHMM2.0 at aa 12-34 2C 44-63 2C 70-89 2C 99-121 2C134-156 2C 160-179 2C 204-226 2C 236-258 2C 265-284 2C 288-310 2C330-352 and 357-379 NC_002163.1 RefSeq region 798652 798711 . - . ID=id57;Name=id57;Dbxref=GeneID:905150;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0850c by TMHMM2.0 at aa 12-34 2C 44-63 2C 70-89 2C 99-121 2C134-156 2C 160-179 2C 204-226 2C 236-258 2C 265-284 2C 288-310 2C330-352 and 357-379 NC_002163.1 RefSeq region 798688 798720 . - . ID=id1599;Name=id1599;Dbxref=GeneID:905150;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 798739 798807 . - . ID=id57;Name=id57;Dbxref=GeneID:905150;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0850c by TMHMM2.0 at aa 12-34 2C 44-63 2C 70-89 2C 99-121 2C134-156 2C 160-179 2C 204-226 2C 236-258 2C 265-284 2C 288-310 2C330-352 and 357-379 NC_002163.1 RefSeq CDS 798818 799321 . - 0 ID=cds759;Parent=gene807;Name=YP_002344258.1;Dbxref=UniProtKB FTrEMBL:Q0PA39 Genbank:YP_002344258.1 GeneID:905151;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0851c 2C probable integral membrane protein 2C len: 167 aa 3B some similarity to YCIB_BUCAP integral membrane protein from Buchnera aphidicola 28177 aa 29 2C fasta scores 3B opt: 139 z-score: 180.5 E 28 29: 0.0093 2C 30.0 25 identity in 160 aa overlap. No Hp match 7EUpdated 282006 29 note: Four probable transmembrane helices predicted by TMHMM2.0. Paper identified giving further clues to product function. Functional classification - Membranes 2C lipoproteins and porins 7EPMID:16045618 NC_002163.1 RefSeq gene 798818 799321 . - . ID=gene807;Name=Cj0851c;locus_tag=Cj0851c;Dbxref=GeneID:905151;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 798841 799029 . - . ID=utr296;locus_tag=Cj0850c;product=putative MFS transport protein NC_002163.1 RefSeq region 798848 798916 . - . ID=id58;Name=id58;Dbxref=GeneID:905151;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0851c by TMHMM2.0 at aa 7-22 2C 32-54 2C 104-126 and 136-158 NC_002163.1 RefSeq region 798944 799012 . - . ID=id58;Name=id58;Dbxref=GeneID:905151;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0851c by TMHMM2.0 at aa 7-22 2C 32-54 2C 104-126 and 136-158 NC_002163.1 RefSeq region 799160 799228 . - . ID=id58;Name=id58;Dbxref=GeneID:905151;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0851c by TMHMM2.0 at aa 7-22 2C 32-54 2C 104-126 and 136-158 NC_002163.1 RefSeq region 799256 799303 . - . ID=id58;Name=id58;Dbxref=GeneID:905151;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0851c by TMHMM2.0 at aa 7-22 2C 32-54 2C 104-126 and 136-158 NC_002163.1 RefSeq gene 799321 799650 . - . ID=gene808;Name=Cj0852c;locus_tag=Cj0852c;Dbxref=GeneID:905153;gbkey=Gene NC_002163.1 RefSeq CDS 799321 799650 . - 0 ID=cds760;Parent=gene808;Name=YP_002344259.1;Dbxref=UniProtKB FTrEMBL:Q0PA38 Genbank:YP_002344259.1 GeneID:905153;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0852c 2C possible integral membrane protein 2C len: 109 aa 3B some similarity to hypothetical proteins e.g. TR:O27758 28EMBL:AE000929 29 Methanobacterium thermoautotrophicum MTH1725 2892 aa 29 2Cfasta scores 3B opt: 123 z-score: 165.5 E 28 29: 0.064 2C 32.7 25 identity in 98 aa overlap. 55.0 25 identity to HP0307 7EUpdated 282006 29 note: Two probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 799414 799470 . - . ID=id59;Name=id59;Dbxref=GeneID:905153;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0852c by TMHMM2.0 at aa 29-51 and 61-79 NC_002163.1 RefSeq region 799498 799566 . - . ID=id59;Name=id59;Dbxref=GeneID:905153;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0852c by TMHMM2.0 at aa 29-51 and 61-79 NC_002163.1 RefSeq CDS 799647 800921 . - 0 ID=cds761;Parent=gene809;gene=hemL;Name=YP_002344260.1;Dbxref=GOA:Q9PP70 HSSP:P24630 InterPro:IPR004639 InterPro:IPR005814 InterPro:IPR015421 UniProtKB FSwiss-Prot:Q9PP70 Genbank:YP_002344260.1 GeneID:905185;gbkey=CDS;product=glutamate-1-semialdehyde aminotransferase;Note=Converts 28S 29-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway NC_002163.1 RefSeq gene 799647 800921 . - . ID=gene809;gene=hemL;Name=hemL;locus_tag=Cj0853c;Dbxref=GeneID:905185;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 799651 799688 . - . ID=utr297;locus_tag=Cj0852c;product=putative integral membrane protein NC_002163.1 RefSeq region 799659 800858 . - . ID=id1600;gene=hemL;Name=id1600;Dbxref=GeneID:905185;gbkey=misc_feature;Note=HMMPfam hit to PF00202 2C Aminotransferase class-III 2Cscore 3.5e-96 NC_002163.1 RefSeq gene 800918 801265 . - . ID=gene810;gene=Cj0854c;Name=Cj0854c;locus_tag=Cj0854c;Dbxref=GeneID:905154;gbkey=Gene NC_002163.1 RefSeq CDS 800918 801265 . - 0 ID=cds762;Parent=gene810;Name=YP_002344261.1;Dbxref=GOA:Q0PA36 UniProtKB FTrEMBL:Q0PA36 Genbank:YP_002344261.1 GeneID:905154;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0854c 2C probable periplasmic protein 2C len: 115 aa 3B 37.9 25 identity to HP0236. Contains N-terminal signal sequence and PS00190 Cytochrome c family heme-binding site signature. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 801137 801154 . - . ID=id1601;Name=id1601;Dbxref=GeneID:905154;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature ### NC_002163.1 UTR_Extractor 5'-UTR 801266 801287 . - . ID=utr298;locus_tag=Cj0854c;product=putative periplasmic protein NC_002163.1 UTR_Extractor 5'-UTR 801310 801344 . + . ID=utr299;locus_tag=Cj0855;product=bifunctional 5 2C10-methylene-tetrahydrofolate dehydrogenase 2F 5 2C10-methylene-tetrahydrofolate cyclohydrolase NC_002163.1 RefSeq CDS 801345 802193 . + 0 ID=cds763;Parent=gene811;gene=folD;Name=YP_002344262.1;Dbxref=GOA:Q0PA35 InterPro:IPR000672 InterPro:IPR016040 UniProtKB FSwiss-Prot:Q0PA35 Genbank:YP_002344262.1 GeneID:905155;gbkey=CDS;product=bifunctional 5 2C10-methylene-tetrahydrofolate dehydrogenase 2F 5 2C10-methylene-tetrahydrofolate cyclohydrolase;Note=catalyzes the formation of 5 2C10-methenyltetrahydrofolate from 5 2C10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5 2C10-methenyltetrahydrofolate NC_002163.1 RefSeq gene 801345 802193 . + . ID=gene811;gene=folD;Name=folD;locus_tag=Cj0855;Dbxref=GeneID:905155;gbkey=Gene NC_002163.1 RefSeq region 801348 801698 . + . ID=id1602;gene=folD;Name=id1602;Dbxref=GeneID:905155;gbkey=misc_feature;Note=HMMPfam hit to PF00763 2C Tetrahydrofolate dehydrogenase 2Fcyclohyd 2C score 3.6e-53 NC_002163.1 RefSeq region 801561 801638 . + . ID=id1603;gene=folD;Name=id1603;Dbxref=GeneID:905155;gbkey=misc_feature;Note=PS00766 Tetrahydrofolate dehydrogenase 2Fcyclohydrolase signature 1 NC_002163.1 RefSeq region 801702 802187 . + . ID=id1604;gene=folD;Name=id1604;Dbxref=GeneID:905155;gbkey=misc_feature;Note=HMMPfam hit to PF02882 2C Tetrahydrofolate dehydrogenase 2Fcyclohyd 2C score 8.6e-103 NC_002163.1 RefSeq region 802116 802142 . + . ID=id1605;gene=folD;Name=id1605;Dbxref=GeneID:905155;gbkey=misc_feature;Note=PS00767 Tetrahydrofolate dehydrogenase 2Fcyclohydrolase signature 2 ### NC_002163.1 RefSeq CDS 802203 803051 . + 0 ID=cds764;Parent=gene812;gene=lepP;Name=YP_002344263.1;Dbxref=GOA:Q0PA34 InterPro:IPR000223 InterPro:IPR011056 InterPro:IPR014037 UniProtKB FTrEMBL:Q0PA34 Genbank:YP_002344263.1 GeneID:905156;gbkey=CDS;product=signal peptidase I;Note=Original 282000 29 note: Cj0856 2C lepP 2C probable signal peptidase I 2C len: 282 aa 3B similar to many e.g. LEP_ECOLI signal peptidase I 28EC 3.4.21.89 29 28324 aa 29 2C fasta scores 3B opt: 339 z-score: 395.2 E 28 29: 1e-14 2C 33.7 25 identity in 270 aa overlap. 46.2 25 identity to HP0576. Contains PS00761 Signal peptidases I signature 3 and Pfam match to entry PF00461 signal_pept_I 2C Signal peptidases I 7EUpdated 282006 29 note: Pfam domain PF00717 Peptidase S24-like identified within CDS. Also 2C one probable transmembrane helix predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli with marginal identity score. not added to product function. Functional classification -Protein and peptide secretion 7EPMID:9823901 NC_002163.1 RefSeq gene 802203 803051 . + . ID=gene812;gene=lepP;Name=lepP;locus_tag=Cj0856;Dbxref=GeneID:905156;gbkey=Gene NC_002163.1 RefSeq region 802239 802307 . + . ID=id1606;gene=lepP;Name=id1606;Dbxref=GeneID:905156;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0856 by TMHMM2.0 at aa 13-35 NC_002163.1 RefSeq region 802299 802586 . + . ID=id1607;gene=lepP;Name=id1607;Dbxref=GeneID:905156;gbkey=misc_feature;Note=HMMPfam hit to PF00717 2C Peptidase S24-like 2C score 6e-18 NC_002163.1 RefSeq region 802836 802877 . + . ID=id1608;gene=lepP;Name=id1608;Dbxref=GeneID:905156;gbkey=misc_feature;Note=PS00761 Signal peptidases I signature 3 ### NC_002163.1 RefSeq CDS 803073 804233 . - 0 ID=cds765;Parent=gene813;gene=moeA;Name=YP_002344264.1;Dbxref=GOA:Q0PA33 InterPro:IPR001453 InterPro:IPR005110 InterPro:IPR005111 UniProtKB FTrEMBL:Q0PA33 Genbank:YP_002344264.1 GeneID:905221;gbkey=CDS;product=molybdopterin biosynthesis protein;Note=Original 282000 29 note: Cj0857c 2C moeA 2C possible molybdopterin biosynthesis protein 2C len: 386 aa 3B similar to many e.g. MOEA_ECOLI molybdopterin biosynthesis MOEA protein 28411 aa 29 2C fasta scores 3B opt: 602 z-score: 691.1 E 28 29: 3.4e-31 2C 29.2 25 identity in 387 aa overlap. 37.0 25 identity to HP0172. Also similar to Cj1519 2833.3 25 identity in 378 aa overlap 29. Contains Pfam match to entry PF00994 MoCF_biosynth 2C Molybdenum cofactor biosynthesis protein 7EUpdated 282006 29 note: Pfam domains PF03454 MoeA C-terminal region 28domain IV 29 and PF03453 MoeA N-terminal region 28domain I and II 29 were identified within CDS. Further support given to product function. Characterised in Escherichia coli with marginal similaritly score. kept within product function. Functional classification - Biosynthesis of cofactors 2C prosthetic groups and carriers - Molybdopterin 7EPMID:9515915 2C PMID:12719427 NC_002163.1 RefSeq gene 803073 804233 . - . ID=gene813;gene=moeA;Name=moeA;locus_tag=Cj0857c;Dbxref=GeneID:905221;gbkey=Gene NC_002163.1 RefSeq region 803079 803285 . - . ID=id1609;gene=moeA;Name=id1609;Dbxref=GeneID:905221;gbkey=misc_feature;Note=HMMPfam hit to PF03454 2C MoeA C-terminal region 28domain IV 29 2C score 0.01 NC_002163.1 RefSeq region 803340 803726 . - . ID=id1610;gene=moeA;Name=id1610;Dbxref=GeneID:905221;gbkey=misc_feature;Note=HMMPfam hit to PF00994 2C Probable molybdopterin binding domain 2C score 4.8e-24 NC_002163.1 RefSeq region 803754 804233 . - . ID=id1611;gene=moeA;Name=id1611;Dbxref=GeneID:905221;gbkey=misc_feature;Note=HMMPfam hit to PF03453 2C MoeA N-terminal region 28domain I and II 2C score 6.8e-67 NC_002163.1 RefSeq CDS 804230 805486 . - 0 ID=cds766;Parent=gene814;gene=murA;Name=YP_002344265.1;Dbxref=GOA:Q9PP65 HSSP:P33038 InterPro:IPR001986 InterPro:IPR005750 UniProtKB FSwiss-Prot:Q9PP65 Genbank:YP_002344265.1 GeneID:905157;gbkey=CDS;product=UDP-N-acetylglucosamine 1-carboxyvinyltransferase;Note=adds enolpyruvyl to UDP-N-acetylglucosamine as a component of cell wall formation 3B gram-positive bacteria have 2 copies of MurA which are active NC_002163.1 RefSeq gene 804230 805486 . - . ID=gene814;gene=murA;Name=murA;locus_tag=Cj0858c;Dbxref=GeneID:905157;gbkey=Gene NC_002163.1 RefSeq region 804269 805465 . - . ID=id1612;gene=murA;Name=id1612;Dbxref=GeneID:905157;gbkey=misc_feature;Note=HMMPfam hit to PF00275 2C EPSP synthase 283-phosphoshikimate 1-car 2C score 6.4e-129 NC_002163.1 RefSeq region 804950 804973 . - . ID=id1613;gene=murA;Name=id1613;Dbxref=GeneID:905157;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 UTR_Extractor 5'-UTR 805487 805512 . - . ID=utr300;locus_tag=Cj0858c;product=UDP-N-acetylglucosamine 1-carboxyvinyltransferase NC_002163.1 RefSeq gene 805552 805980 . - . ID=gene815;Name=Cj0859c;locus_tag=Cj0859c;Dbxref=GeneID:905158;gbkey=Gene NC_002163.1 RefSeq CDS 805552 805980 . - 0 ID=cds767;Parent=gene815;Name=YP_002344266.1;Dbxref=UniProtKB FTrEMBL:Q0PA31 Genbank:YP_002344266.1 GeneID:905158;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0859c 2C unknown 2C len: 142 aa 3B no Hp match. Gln-rich in C-term 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 UTR_Extractor 5'-UTR 805981 806007 . - . ID=utr301;locus_tag=Cj0859c;product=hypothetical protein NC_002163.1 UTR_Extractor 5'-UTR 806052 806074 . + . ID=utr302;locus_tag=Cj0860;product=putative integral membrane protein NC_002163.1 RefSeq CDS 806075 806947 . + 0 ID=cds768;Parent=gene816;Name=YP_002344267.1;Dbxref=GOA:Q0PA30 InterPro:IPR000620 UniProtKB FTrEMBL:Q0PA30 Genbank:YP_002344267.1 GeneID:905161;gbkey=CDS;product=integral membrane protein;Note=Updated 282006 29 note: Ten probable transmembrane helices predicted by TMHMM2.0 7EOriginal 282000 29 note: Cj0860 2C probable integral membrane protein 2C len: 290 aa 3B similar to hypothetical proteins e.g. YICL_ECOLI 28307 aa 29 2C fasta scores 3B opt: 516 z-score: 611.4 E 28 29: 9.3e-27 2C 32.0 25 identity in 284 aa overlap. No Hp match. Contains 2x Pfam match to entry PF00892 DUF6 2C Integral membrane protein. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 806075 806947 . + . ID=gene816;Name=Cj0860;locus_tag=Cj0860;Dbxref=GeneID:905161;gbkey=Gene NC_002163.1 RefSeq region 806078 806146 . + . ID=id1614;Name=id1614;Dbxref=GeneID:905161;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0860 by TMHMM2.0 at aa 2-24 2C 28-50 2C 63-82 2C 92-111 2C118-136 2C 146-168 2C 175-197 2C 212-231 2C 238-260 and 265-284 NC_002163.1 RefSeq region 806105 806485 . + . ID=id1615;Name=id1615;Dbxref=GeneID:905161;gbkey=misc_feature;Note=HMMPfam hit to PF00892 2C Integral membrane protein DUF6 2C score 4.2e-14 NC_002163.1 RefSeq region 806156 806224 . + . ID=id1614;Name=id1614;Dbxref=GeneID:905161;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0860 by TMHMM2.0 at aa 2-24 2C 28-50 2C 63-82 2C 92-111 2C118-136 2C 146-168 2C 175-197 2C 212-231 2C 238-260 and 265-284 NC_002163.1 RefSeq region 806261 806320 . + . ID=id1614;Name=id1614;Dbxref=GeneID:905161;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0860 by TMHMM2.0 at aa 2-24 2C 28-50 2C 63-82 2C 92-111 2C118-136 2C 146-168 2C 175-197 2C 212-231 2C 238-260 and 265-284 NC_002163.1 RefSeq region 806348 806407 . + . ID=id1614;Name=id1614;Dbxref=GeneID:905161;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0860 by TMHMM2.0 at aa 2-24 2C 28-50 2C 63-82 2C 92-111 2C118-136 2C 146-168 2C 175-197 2C 212-231 2C 238-260 and 265-284 NC_002163.1 RefSeq region 806426 806482 . + . ID=id1614;Name=id1614;Dbxref=GeneID:905161;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0860 by TMHMM2.0 at aa 2-24 2C 28-50 2C 63-82 2C 92-111 2C118-136 2C 146-168 2C 175-197 2C 212-231 2C 238-260 and 265-284 NC_002163.1 RefSeq region 806510 806578 . + . ID=id1614;Name=id1614;Dbxref=GeneID:905161;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0860 by TMHMM2.0 at aa 2-24 2C 28-50 2C 63-82 2C 92-111 2C118-136 2C 146-168 2C 175-197 2C 212-231 2C 238-260 and 265-284 NC_002163.1 RefSeq region 806549 806929 . + . ID=id1616;Name=id1616;Dbxref=GeneID:905161;gbkey=misc_feature;Note=HMMPfam hit to PF00892 2C Integral membrane protein DUF6 2C score 5.2e-17 NC_002163.1 RefSeq region 806597 806665 . + . ID=id1614;Name=id1614;Dbxref=GeneID:905161;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0860 by TMHMM2.0 at aa 2-24 2C 28-50 2C 63-82 2C 92-111 2C118-136 2C 146-168 2C 175-197 2C 212-231 2C 238-260 and 265-284 NC_002163.1 RefSeq region 806708 806767 . + . ID=id1614;Name=id1614;Dbxref=GeneID:905161;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0860 by TMHMM2.0 at aa 2-24 2C 28-50 2C 63-82 2C 92-111 2C118-136 2C 146-168 2C 175-197 2C 212-231 2C 238-260 and 265-284 NC_002163.1 RefSeq region 806786 806854 . + . ID=id1614;Name=id1614;Dbxref=GeneID:905161;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0860 by TMHMM2.0 at aa 2-24 2C 28-50 2C 63-82 2C 92-111 2C118-136 2C 146-168 2C 175-197 2C 212-231 2C 238-260 and 265-284 NC_002163.1 RefSeq region 806867 806926 . + . ID=id1614;Name=id1614;Dbxref=GeneID:905161;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0860 by TMHMM2.0 at aa 2-24 2C 28-50 2C 63-82 2C 92-111 2C118-136 2C 146-168 2C 175-197 2C 212-231 2C 238-260 and 265-284 NC_002163.1 RefSeq gene 806934 807500 . - . ID=gene817;gene=pabA;Name=pabA;locus_tag=Cj0861c;Dbxref=GeneID:905163;gbkey=Gene NC_002163.1 RefSeq CDS 806934 807500 . - 0 ID=cds769;Parent=gene817;gene=pabA;Name=YP_002344268.1;Dbxref=GOA:Q0PA29 InterPro:IPR000991 InterPro:IPR006220 InterPro:IPR006221 InterPro:IPR011702 UniProtKB FTrEMBL:Q0PA29 Genbank:YP_002344268.1 GeneID:905163;gbkey=CDS;product=para-aminobenzoate synthase glutamine amidotransferase subunit II;Note=Original 282000 29 note: Cj0861c 2C pabA 2C probable para-aminobenzoate synthase glutamine amidotransferase component II 2C len: 188 aa 3B simlar to e.g. PABA_BACSU para-aminobenzoate synthase glutamine amidotransferase component II 28EC 4.1.3.- 29 28194 aa 29 2C fasta scores 3B opt: 534 z-score: 632.3 E 28 29: 6.4e-28 2C 44.6 25 identity in 186 aa overlap 2C and PABA_ECOLI 28187 aa 29 2C fasta scores 3B opt: 475 z-score: 564.2 E 28 29: 4e-24 2C 36.8 25 identity in 185 aa overlap. 38.6 25 identity to HP1281 annotated as anthranilate synthase component II 28trpD 29. Contains Pfam match to entry PF00117 GATase 2C Glutamine amidotransferases class-I 7EUpdated 282006 29 note: Characterised in Escherichia coli with acceptable identity score. not added to product function. Functional classification - Biosynthesis of cofactors 2C prosthetic groups and carriers - Folic acid 7EPMID:8096767 2C PMID:2123867 NC_002163.1 RefSeq region 806937 807488 . - . ID=id1617;gene=pabA;Name=id1617;Dbxref=GeneID:905163;gbkey=misc_feature;Note=HMMPfam hit to PF00117 2C Glutamine amidotransferase class-I 2C score 1.2e-59 NC_002163.1 RefSeq gene 807497 809281 . - . ID=gene818;gene=pabB;Name=pabB;locus_tag=Cj0862c;Dbxref=GeneID:905164;gbkey=Gene NC_002163.1 RefSeq CDS 807497 809281 . - 0 ID=cds770;Parent=gene818;gene=pabB;Name=YP_002344269.1;Dbxref=GOA:Q0PA28 InterPro:IPR005801 InterPro:IPR015890 UniProtKB FTrEMBL:Q0PA28 Genbank:YP_002344269.1 GeneID:905164;gbkey=CDS;product=para-aminobenzoate synthase subunit I;Note=Original 282000 29 note: Cj0862c 2C pabB 2C probable para-aminobenzoate synthase component I 2C len: 594 aa 3B simlar to e.g. PABB_ECOLI para-aminobenzoate synthase component I 28EC 4.1.3.- 29 28453 aa 29 2C fasta scores 3B opt: 541 z-score: 604.3 E 28 29: 2.3e-26 2C 35.7 25 identity in 252 aa overlap. 39.3 25 identity to HP0293. Contains Pfam match to entry PF00425 chorismate_bind 2C chorismate binding enzyme 7EUpdated 282006 29 note: Characterised in Escherichia coli with acceptable identity score. not added to product function. Functional classification - Biosynthesis of cofactors 2C prosthetic groups and carriers - Folic acid 7EPMID:11841211 2C PMID:2251281 NC_002163.1 RefSeq region 808220 808987 . - . ID=id1618;gene=pabB;Name=id1618;Dbxref=GeneID:905164;gbkey=misc_feature;Note=HMMPfam hit to PF00425 2C chorismate binding enzyme 2Cscore 7.6e-45 NC_002163.1 RefSeq gene 809271 810335 . - . ID=gene819;gene=xerD;Name=xerD;locus_tag=Cj0863c;Dbxref=GeneID:905165;gbkey=Gene NC_002163.1 RefSeq CDS 809271 810335 . - 0 ID=cds771;Parent=gene819;gene=xerD;Name=YP_002344270.1;Dbxref=GOA:Q0PA27 InterPro:IPR002104 InterPro:IPR013762 UniProtKB FTrEMBL:Q0PA27 Genbank:YP_002344270.1 GeneID:905165;gbkey=CDS;product=DNA recombinase;Note=Original 282000 29 note: Cj0863c 2C xerD 2C probable DNA recombinase 2C len: 354 aa 3B similar to e.g. XERD_ECOLI integrase 2Frecombinase XERD 28298 aa 29 2C fasta scores 3B opt: 336 z-score: 389.2 E 28 29: 2.2e-14 2C 29.5 25 identity in 298 aa overlap. 47.5 25 identity to HP0675 28xerC 29 and 30.5 25 identity to HP0995 28xerD 29. Contains Pfam match to entry PF00589 Phage_integrase 2C 27Phage 27 integrase family 7EUpdated 282006 29 note: Characterised in Escherichia coli with acceptable identity score. not added to product function. Functional classification - DNA replication 2C restriction 2Fmodification 2C recombination and repair 7EPMID:9311978 2C PMID10635320 2C PMID11832210 NC_002163.1 RefSeq region 809307 809834 . - . ID=id1619;gene=xerD;Name=id1619;Dbxref=GeneID:905165;gbkey=misc_feature;Note=HMMPfam hit to PF00589 2C Phage integrase family 2Cscore 9.8e-27 ### NC_002163.1 UTR_Extractor 5'-UTR 810336 810377 . - . ID=utr303;locus_tag=Cj0863c;product=DNA recombinase NC_002163.1 UTR_Extractor 5'-UTR 810910 810962 . + . ID=utr304;locus_tag=Cj0864;product=putative periplasmic protein NC_002163.1 RefSeq CDS 810963 811322 . + 0 ID=cds772;Parent=gene820;Name=YP_002344271.1;Dbxref=GOA:Q0PA26 InterPro:IPR012335 UniProtKB FTrEMBL:Q0PA26 Genbank:YP_002344271.1 GeneID:904441;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0864 2C probable periplasmic protein 2C len: 119 aa 3B some similarity in C-terminus to C-terminus of thiol:disulfide interchange proteins 28not including active site 29 e.g. TR:P97037 28EMBL:U32616 29 Klebsiella pneumoniae disulfide isomerase 28222 aa 29 2C fasta scores 3B opt: 184 z-score: 240.3 E 28 29: 4.4e-06 2C 36.9 25 identity in 84 aa overlap. No Hp match. Also similar to C-term of Cj0872 dsbA 2857.3 25 identity in 82 aa overlap 29 7EUpdated 282006 29 note: Interpro result 28ipr012335 29 shows a thioredoxin fold within the CDS. Further support given to product function. No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 810963 811322 . + . ID=gene820;Name=Cj0864;locus_tag=Cj0864;Dbxref=GeneID:904441;gbkey=Gene NC_002163.1 RefSeq CDS 811319 812119 . + 0 ID=cds773;Parent=gene821;gene=dsbB;Name=YP_002344272.1;Dbxref=GOA:Q0PA25 UniProtKB FSwiss-Prot:Q0PA25 Genbank:YP_002344272.1 GeneID:905166;gbkey=CDS;product=disulfide oxidoreductase;Note=Original 282000 29 note: Cj0865 2C dsbB 2C possible disulfide oxidoreductase 2C len: 266 aa 3B similar to e.g. DSBB_ECOLI disulfide bond formation protein B 28disulfide oxidoreductase 29 28176 aa 29 2C fasta scores 3B opt: 200 z-score: 250.0 E 28 29: 1.3e-06 2C 29.9 25 identity in 137 aa overlap 28the essential Cysteine residues are conserved 29. No Hp match 7EUpdated 282006 29 note: Four probable transmembrane helices predicted by TMHMM2.0. This CDS has been characterised as DsbB protein 28PMID:15632440 29. It has been demonstrated that Cj0865 is indeed a disulfide oxidoreductase. This has been shown via in silico and in vivo work in E. coli and also complementation and enzymatic tests in C. jejuni. There is an alignment of different DsbB proteins 28including Cj0865 29 with prediction of 5 transmembranehelises 28not 4 as stated in annotation 29 3B 28P24-A39 3B F60-I74 3B S87-L101 3B F194-A214 3B F231-G246 29. There are some differences in amino acid sequences between Cj0865 and its ortholog from 81-176 28CJJ81176_0881 29. It is stated that its translation starts from the second Met 28although the predicted N-terminal amino acid sequences of both proteins are identical 29 2C there is also an insertion of 3 amino acids at the COOH end of protein. Thus 2C not added to protein function. Functional classification -Protein translation and modification 7EPMID:15632440 2C PMID:7957076 NC_002163.1 RefSeq gene 811319 812119 . + . ID=gene821;gene=dsbB;Name=dsbB;locus_tag=Cj0865;Dbxref=GeneID:905166;gbkey=Gene NC_002163.1 RefSeq region 811391 811459 . + . ID=id1620;gene=dsbB;Name=id1620;Dbxref=GeneID:905166;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0865 by TMHMM2.0 at aa 25-47 2C 62-81 2C 198-220 and 230-247 NC_002163.1 RefSeq region 811502 811561 . + . ID=id1620;gene=dsbB;Name=id1620;Dbxref=GeneID:905166;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0865 by TMHMM2.0 at aa 25-47 2C 62-81 2C 198-220 and 230-247 NC_002163.1 RefSeq region 811910 811978 . + . ID=id1620;gene=dsbB;Name=id1620;Dbxref=GeneID:905166;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0865 by TMHMM2.0 at aa 25-47 2C 62-81 2C 198-220 and 230-247 NC_002163.1 RefSeq region 812006 812059 . + . ID=id1620;gene=dsbB;Name=id1620;Dbxref=GeneID:905166;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0865 by TMHMM2.0 at aa 25-47 2C 62-81 2C 198-220 and 230-247 ### NC_002163.1 RefSeq region 812155 812364 . + . ID=id1621;Name=id1621;Dbxref=GeneID:905188;gbkey=misc_feature;Note=Original 282000 29 note: Cj0866 2C ast 2C arylsulfatase pseudogene 2C len: 1434 bp 3B almost identical to parts of TR:Q46098 28EMBL:U38280 Campylobacter jejuni strain 81-176 arylsulfatase 28620 aa 29 2C and similar to parts of TR:P97036 28EMBL:U32616 29 Klebsiella pneumoniae arylsulfate sulfotransferase 28EC 2.8.2.22 29 28598 aa 29. No Hp match 7EUpdated 282006 29 note: Pfam domain PF05935 Arylsulfotransferase 28ASST 29 identified within CDS. Part of stem loop also identified within C-terminal. Further support given to product function. Characterisation paper with Campylobacter jejuni included. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Central intermediary metabolism - Sulphur metabolism 7EPMID:8655516 NC_002163.1 RefSeq pseudogene 812155 813591 . + . ID=gene822;Name=Cj0866;locus_tag=Cj0866;Dbxref=GeneID:905188;gbkey=Gene NC_002163.1 RefSeq region 812218 812466 . + . ID=id1622;Name=id1622;Dbxref=GeneID:905188;gbkey=misc_feature;Note=HMMPfam hit to PF05935 2C Arylsulfotransferase 28ASST 29 2C score 8.2e-179 NC_002163.1 RefSeq region 812363 812470 . + . ID=id1621;Name=id1621;Dbxref=GeneID:905188;gbkey=misc_feature;Note=Original 282000 29 note: Cj0866 2C ast 2C arylsulfatase pseudogene 2C len: 1434 bp 3B almost identical to parts of TR:Q46098 28EMBL:U38280 Campylobacter jejuni strain 81-176 arylsulfatase 28620 aa 29 2C and similar to parts of TR:P97036 28EMBL:U32616 29 Klebsiella pneumoniae arylsulfate sulfotransferase 28EC 2.8.2.22 29 28598 aa 29. No Hp match 7EUpdated 282006 29 note: Pfam domain PF05935 Arylsulfotransferase 28ASST 29 identified within CDS. Part of stem loop also identified within C-terminal. Further support given to product function. Characterisation paper with Campylobacter jejuni included. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Central intermediary metabolism - Sulphur metabolism 7EPMID:8655516 NC_002163.1 RefSeq region 812466 812564 . + . ID=id1621;Name=id1621;Dbxref=GeneID:905188;gbkey=misc_feature;Note=Original 282000 29 note: Cj0866 2C ast 2C arylsulfatase pseudogene 2C len: 1434 bp 3B almost identical to parts of TR:Q46098 28EMBL:U38280 Campylobacter jejuni strain 81-176 arylsulfatase 28620 aa 29 2C and similar to parts of TR:P97036 28EMBL:U32616 29 Klebsiella pneumoniae arylsulfate sulfotransferase 28EC 2.8.2.22 29 28598 aa 29. No Hp match 7EUpdated 282006 29 note: Pfam domain PF05935 Arylsulfotransferase 28ASST 29 identified within CDS. Part of stem loop also identified within C-terminal. Further support given to product function. Characterisation paper with Campylobacter jejuni included. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Central intermediary metabolism - Sulphur metabolism 7EPMID:8655516 NC_002163.1 RefSeq region 812470 812564 . + . ID=id1622;Name=id1622;Dbxref=GeneID:905188;gbkey=misc_feature;Note=HMMPfam hit to PF05935 2C Arylsulfotransferase 28ASST 29 2C score 8.2e-179 NC_002163.1 RefSeq region 812566 812751 . + . ID=id1621;Name=id1621;Dbxref=GeneID:905188;gbkey=misc_feature;Note=Original 282000 29 note: Cj0866 2C ast 2C arylsulfatase pseudogene 2C len: 1434 bp 3B almost identical to parts of TR:Q46098 28EMBL:U38280 Campylobacter jejuni strain 81-176 arylsulfatase 28620 aa 29 2C and similar to parts of TR:P97036 28EMBL:U32616 29 Klebsiella pneumoniae arylsulfate sulfotransferase 28EC 2.8.2.22 29 28598 aa 29. No Hp match 7EUpdated 282006 29 note: Pfam domain PF05935 Arylsulfotransferase 28ASST 29 identified within CDS. Part of stem loop also identified within C-terminal. Further support given to product function. Characterisation paper with Campylobacter jejuni included. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Central intermediary metabolism - Sulphur metabolism 7EPMID:8655516 NC_002163.1 RefSeq region 812566 812751 . + . ID=id1622;Name=id1622;Dbxref=GeneID:905188;gbkey=misc_feature;Note=HMMPfam hit to PF05935 2C Arylsulfotransferase 28ASST 29 2C score 8.2e-179 NC_002163.1 RefSeq region 812753 812902 . + . ID=id1622;Name=id1622;Dbxref=GeneID:905188;gbkey=misc_feature;Note=HMMPfam hit to PF05935 2C Arylsulfotransferase 28ASST 29 2C score 8.2e-179 NC_002163.1 RefSeq region 812753 812902 . + . ID=id1621;Name=id1621;Dbxref=GeneID:905188;gbkey=misc_feature;Note=Original 282000 29 note: Cj0866 2C ast 2C arylsulfatase pseudogene 2C len: 1434 bp 3B almost identical to parts of TR:Q46098 28EMBL:U38280 Campylobacter jejuni strain 81-176 arylsulfatase 28620 aa 29 2C and similar to parts of TR:P97036 28EMBL:U32616 29 Klebsiella pneumoniae arylsulfate sulfotransferase 28EC 2.8.2.22 29 28598 aa 29. No Hp match 7EUpdated 282006 29 note: Pfam domain PF05935 Arylsulfotransferase 28ASST 29 identified within CDS. Part of stem loop also identified within C-terminal. Further support given to product function. Characterisation paper with Campylobacter jejuni included. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Central intermediary metabolism - Sulphur metabolism 7EPMID:8655516 NC_002163.1 RefSeq region 812902 812952 . + . ID=id1621;Name=id1621;Dbxref=GeneID:905188;gbkey=misc_feature;Note=Original 282000 29 note: Cj0866 2C ast 2C arylsulfatase pseudogene 2C len: 1434 bp 3B almost identical to parts of TR:Q46098 28EMBL:U38280 Campylobacter jejuni strain 81-176 arylsulfatase 28620 aa 29 2C and similar to parts of TR:P97036 28EMBL:U32616 29 Klebsiella pneumoniae arylsulfate sulfotransferase 28EC 2.8.2.22 29 28598 aa 29. No Hp match 7EUpdated 282006 29 note: Pfam domain PF05935 Arylsulfotransferase 28ASST 29 identified within CDS. Part of stem loop also identified within C-terminal. Further support given to product function. Characterisation paper with Campylobacter jejuni included. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Central intermediary metabolism - Sulphur metabolism 7EPMID:8655516 NC_002163.1 RefSeq region 812902 812952 . + . ID=id1622;Name=id1622;Dbxref=GeneID:905188;gbkey=misc_feature;Note=HMMPfam hit to PF05935 2C Arylsulfotransferase 28ASST 29 2C score 8.2e-179 NC_002163.1 RefSeq region 812954 812980 . + . ID=id1621;Name=id1621;Dbxref=GeneID:905188;gbkey=misc_feature;Note=Original 282000 29 note: Cj0866 2C ast 2C arylsulfatase pseudogene 2C len: 1434 bp 3B almost identical to parts of TR:Q46098 28EMBL:U38280 Campylobacter jejuni strain 81-176 arylsulfatase 28620 aa 29 2C and similar to parts of TR:P97036 28EMBL:U32616 29 Klebsiella pneumoniae arylsulfate sulfotransferase 28EC 2.8.2.22 29 28598 aa 29. No Hp match 7EUpdated 282006 29 note: Pfam domain PF05935 Arylsulfotransferase 28ASST 29 identified within CDS. Part of stem loop also identified within C-terminal. Further support given to product function. Characterisation paper with Campylobacter jejuni included. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Central intermediary metabolism - Sulphur metabolism 7EPMID:8655516 NC_002163.1 RefSeq region 812954 812980 . + . ID=id1622;Name=id1622;Dbxref=GeneID:905188;gbkey=misc_feature;Note=HMMPfam hit to PF05935 2C Arylsulfotransferase 28ASST 29 2C score 8.2e-179 NC_002163.1 RefSeq region 812983 813011 . + . ID=id1622;Name=id1622;Dbxref=GeneID:905188;gbkey=misc_feature;Note=HMMPfam hit to PF05935 2C Arylsulfotransferase 28ASST 29 2C score 8.2e-179 NC_002163.1 RefSeq region 812983 813018 . + . ID=id1621;Name=id1621;Dbxref=GeneID:905188;gbkey=misc_feature;Note=Original 282000 29 note: Cj0866 2C ast 2C arylsulfatase pseudogene 2C len: 1434 bp 3B almost identical to parts of TR:Q46098 28EMBL:U38280 Campylobacter jejuni strain 81-176 arylsulfatase 28620 aa 29 2C and similar to parts of TR:P97036 28EMBL:U32616 29 Klebsiella pneumoniae arylsulfate sulfotransferase 28EC 2.8.2.22 29 28598 aa 29. No Hp match 7EUpdated 282006 29 note: Pfam domain PF05935 Arylsulfotransferase 28ASST 29 identified within CDS. Part of stem loop also identified within C-terminal. Further support given to product function. Characterisation paper with Campylobacter jejuni included. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Central intermediary metabolism - Sulphur metabolism 7EPMID:8655516 NC_002163.1 RefSeq region 813011 813019 . + . ID=id1621;Name=id1621;Dbxref=GeneID:905188;gbkey=misc_feature;Note=Original 282000 29 note: Cj0866 2C ast 2C arylsulfatase pseudogene 2C len: 1434 bp 3B almost identical to parts of TR:Q46098 28EMBL:U38280 Campylobacter jejuni strain 81-176 arylsulfatase 28620 aa 29 2C and similar to parts of TR:P97036 28EMBL:U32616 29 Klebsiella pneumoniae arylsulfate sulfotransferase 28EC 2.8.2.22 29 28598 aa 29. No Hp match 7EUpdated 282006 29 note: Pfam domain PF05935 Arylsulfotransferase 28ASST 29 identified within CDS. Part of stem loop also identified within C-terminal. Further support given to product function. Characterisation paper with Campylobacter jejuni included. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Central intermediary metabolism - Sulphur metabolism 7EPMID:8655516 NC_002163.1 RefSeq region 813018 813019 . + . ID=id1622;Name=id1622;Dbxref=GeneID:905188;gbkey=misc_feature;Note=HMMPfam hit to PF05935 2C Arylsulfotransferase 28ASST 29 2C score 8.2e-179 NC_002163.1 RefSeq region 813021 813275 . + . ID=id1622;Name=id1622;Dbxref=GeneID:905188;gbkey=misc_feature;Note=HMMPfam hit to PF05935 2C Arylsulfotransferase 28ASST 29 2C score 8.2e-179 NC_002163.1 RefSeq region 813021 813278 . + . ID=id1621;Name=id1621;Dbxref=GeneID:905188;gbkey=misc_feature;Note=Original 282000 29 note: Cj0866 2C ast 2C arylsulfatase pseudogene 2C len: 1434 bp 3B almost identical to parts of TR:Q46098 28EMBL:U38280 Campylobacter jejuni strain 81-176 arylsulfatase 28620 aa 29 2C and similar to parts of TR:P97036 28EMBL:U32616 29 Klebsiella pneumoniae arylsulfate sulfotransferase 28EC 2.8.2.22 29 28598 aa 29. No Hp match 7EUpdated 282006 29 note: Pfam domain PF05935 Arylsulfotransferase 28ASST 29 identified within CDS. Part of stem loop also identified within C-terminal. Further support given to product function. Characterisation paper with Campylobacter jejuni included. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Central intermediary metabolism - Sulphur metabolism 7EPMID:8655516 NC_002163.1 RefSeq region 813275 813445 . + . ID=id1621;Name=id1621;Dbxref=GeneID:905188;gbkey=misc_feature;Note=Original 282000 29 note: Cj0866 2C ast 2C arylsulfatase pseudogene 2C len: 1434 bp 3B almost identical to parts of TR:Q46098 28EMBL:U38280 Campylobacter jejuni strain 81-176 arylsulfatase 28620 aa 29 2C and similar to parts of TR:P97036 28EMBL:U32616 29 Klebsiella pneumoniae arylsulfate sulfotransferase 28EC 2.8.2.22 29 28598 aa 29. No Hp match 7EUpdated 282006 29 note: Pfam domain PF05935 Arylsulfotransferase 28ASST 29 identified within CDS. Part of stem loop also identified within C-terminal. Further support given to product function. Characterisation paper with Campylobacter jejuni included. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Central intermediary metabolism - Sulphur metabolism 7EPMID:8655516 NC_002163.1 RefSeq region 813278 813445 . + . ID=id1622;Name=id1622;Dbxref=GeneID:905188;gbkey=misc_feature;Note=HMMPfam hit to PF05935 2C Arylsulfotransferase 28ASST 29 2C score 8.2e-179 NC_002163.1 RefSeq region 813448 813573 . + . ID=id1622;Name=id1622;Dbxref=GeneID:905188;gbkey=misc_feature;Note=HMMPfam hit to PF05935 2C Arylsulfotransferase 28ASST 29 2C score 8.2e-179 NC_002163.1 RefSeq region 813448 813591 . + . ID=id1621;Name=id1621;Dbxref=GeneID:905188;gbkey=misc_feature;Note=Original 282000 29 note: Cj0866 2C ast 2C arylsulfatase pseudogene 2C len: 1434 bp 3B almost identical to parts of TR:Q46098 28EMBL:U38280 Campylobacter jejuni strain 81-176 arylsulfatase 28620 aa 29 2C and similar to parts of TR:P97036 28EMBL:U32616 29 Klebsiella pneumoniae arylsulfate sulfotransferase 28EC 2.8.2.22 29 28598 aa 29. No Hp match 7EUpdated 282006 29 note: Pfam domain PF05935 Arylsulfotransferase 28ASST 29 identified within CDS. Part of stem loop also identified within C-terminal. Further support given to product function. Characterisation paper with Campylobacter jejuni included. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Central intermediary metabolism - Sulphur metabolism 7EPMID:8655516 NC_002163.1 RefSeq stem_loop 813583 813628 . + . ID=id1623;Name=id1623;gbkey=stem_loop ### NC_002163.1 UTR_Extractor 5'-UTR 813646 813674 . + . ID=utr305;locus_tag=Cj0872;product=putative protein disulphide isomerase NC_002163.1 RefSeq gene 813675 814316 . + . ID=gene823;gene=dsbA;Name=dsbA;locus_tag=Cj0872;Dbxref=GeneID:905167;gbkey=Gene NC_002163.1 RefSeq CDS 813675 814316 . + 0 ID=cds774;Parent=gene823;gene=dsbA;Name=YP_002344273.1;Dbxref=GOA:Q0PA24 InterPro:IPR001853 InterPro:IPR012335 UniProtKB FTrEMBL:Q0PA24 Genbank:YP_002344273.1 GeneID:905167;gbkey=CDS;product=protein disulfide isomerase;Note=Original 282000 29 note: Cj0872 2C dsbA 2C possible protein disulphide isomerase 2C len: 213 aa 3B some similarity to e.g. DSBA_ECOLI thiol:disulfide interchange protein DSBA precursor 28208 aa 29 2C fasta scores 3B opt: 128 z-score: 159.8 E 28 29: 0.13 2C 23.1 25 identity in 216 aa overlap 28active site is conserved 29. No Hp match 7EUpdated 282006 29 note: Pfam domain PF01323 DSBA-like thioredoxin domain identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score identified yet. kept within product function. Functional classification -Protein translation and modification 7EPMID:8494885 NC_002163.1 RefSeq region 813786 814295 . + . ID=id1624;gene=dsbA;Name=id1624;Dbxref=GeneID:905167;gbkey=misc_feature;Note=HMMPfam hit to PF01323 2C DSBA-like thioredoxin domain 2C score 1.1e-05 ### NC_002163.1 RefSeq terminator 814319 814352 . + . ID=id1625;Name=id1625;gbkey=terminator;Note=15 bp stem-loop 3B possible termination of replication 3F NC_002163.1 RefSeq pseudogene 814351 815337 . - . ID=gene824;Name=Cj0873c;locus_tag=Cj0873c;Dbxref=GeneID:905147;gbkey=Gene NC_002163.1 RefSeq region 814701 814718 . - . ID=id1626;Name=id1626;Dbxref=GeneID:905147;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature NC_002163.1 RefSeq region 815025 815042 . - . ID=id1627;Name=id1627;Dbxref=GeneID:905147;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature ### NC_002163.1 UTR_Extractor 5'-UTR 815338 815366 . - . ID=utr306;locus_tag=Cj0876c;product=putative periplasmic protein NC_002163.1 RefSeq gene 815432 815524 . - . ID=gene825;Name=Cj0877c;locus_tag=Cj0877c;Dbxref=GeneID:905171;gbkey=Gene NC_002163.1 RefSeq CDS 815432 815524 . - 0 ID=cds775;Parent=gene825;Name=YP_002344277.1;Dbxref=UniProtKB FTrEMBL:Q0PA20 Genbank:YP_002344277.1 GeneID:905171;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0877c 2C questionable ORF 2Clen: 30 aa 3B no Hp match. Functional classification -Unknown NC_002163.1 UTR_Extractor 5'-UTR 815519 815544 . + . ID=utr307;locus_tag=Cj0878;product=hypothetical protein ### NC_002163.1 RefSeq CDS 815545 815691 . + 0 ID=cds776;Parent=gene826;Name=YP_002344278.1;Dbxref=UniProtKB FTrEMBL:Q0PA19 Genbank:YP_002344278.1 GeneID:905143;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0878 2C unknown 2C len: 48 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 RefSeq gene 815545 815691 . + . ID=gene826;Name=Cj0878;locus_tag=Cj0878;Dbxref=GeneID:905143;gbkey=Gene NC_002163.1 RefSeq CDS 815669 816301 . - 0 ID=cds777;Parent=gene827;Name=YP_002344279.1;Dbxref=UniProtKB FTrEMBL:Q0PA18 Genbank:YP_002344279.1 GeneID:904821;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0879c 2C probable periplasmic protein 2C len: 210 aa 3B no Hp match. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 815669 816301 . - . ID=gene827;Name=Cj0879c;locus_tag=Cj0879c;Dbxref=GeneID:904821;gbkey=Gene NC_002163.1 RefSeq gene 816298 816540 . - . ID=gene828;Name=Cj0880c;locus_tag=Cj0880c;Dbxref=GeneID:905170;gbkey=Gene NC_002163.1 RefSeq CDS 816298 816540 . - 0 ID=cds778;Parent=gene828;Name=YP_002344280.1;Dbxref=GOA:Q0PA17 UniProtKB FTrEMBL:Q0PA17 Genbank:YP_002344280.1 GeneID:905170;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0880c 2C unknown 2C len: 240 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 RefSeq gene 816524 817570 . - . ID=gene829;Name=Cj0881c;locus_tag=Cj0881c;Dbxref=GeneID:905173;gbkey=Gene NC_002163.1 RefSeq CDS 816524 817570 . - 0 ID=cds779;Parent=gene829;Name=YP_002344281.1;Dbxref=GOA:Q0PA16 UniProtKB FTrEMBL:Q0PA16 Genbank:YP_002344281.1 GeneID:905173;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0881c 2C unknown 2C len: 348 aa 3B 40.6 25 identity to HP1042. Functional classification -Conserved hypothetical proteins ### NC_002163.1 UTR_Extractor 5'-UTR 817571 817662 . - . ID=utr308;locus_tag=Cj0881c;product=hypothetical protein NC_002163.1 RefSeq CDS 817579 819753 . - 0 ID=cds780;Parent=gene830;gene=flhA;Name=YP_002344282.1;Dbxref=GOA:Q0PA15 InterPro:IPR001712 InterPro:IPR006301 UniProtKB FTrEMBL:Q0PA15 Genbank:YP_002344282.1 GeneID:905174;gbkey=CDS;product=flagellar biosynthesis protein FlhA;Note=membrane protein involved in the flagellar export apparatus NC_002163.1 RefSeq gene 817579 819753 . - . ID=gene830;gene=flhA;Name=flhA;locus_tag=Cj0882c;Dbxref=GeneID:905174;gbkey=Gene NC_002163.1 RefSeq region 817612 819651 . - . ID=id1628;gene=flhA;Name=id1628;Dbxref=GeneID:905174;gbkey=misc_feature;Note=HMMPfam hit to PF00771 2C FHIPEP family 2C score 4.4e-295 NC_002163.1 RefSeq region 818794 818862 . - . ID=id60;gene=flhA;Name=id60;Dbxref=GeneID:905174;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0882c by TMHMM2.0 at aa 21-43 2C 48-70 2C 82-102 2C 122-144 2C214-236 2C 251-273 and 298-320 NC_002163.1 RefSeq region 818935 819003 . - . ID=id60;gene=flhA;Name=id60;Dbxref=GeneID:905174;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0882c by TMHMM2.0 at aa 21-43 2C 48-70 2C 82-102 2C 122-144 2C214-236 2C 251-273 and 298-320 NC_002163.1 RefSeq region 819046 819114 . - . ID=id60;gene=flhA;Name=id60;Dbxref=GeneID:905174;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0882c by TMHMM2.0 at aa 21-43 2C 48-70 2C 82-102 2C 122-144 2C214-236 2C 251-273 and 298-320 NC_002163.1 RefSeq region 819322 819390 . - . ID=id60;gene=flhA;Name=id60;Dbxref=GeneID:905174;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0882c by TMHMM2.0 at aa 21-43 2C 48-70 2C 82-102 2C 122-144 2C214-236 2C 251-273 and 298-320 NC_002163.1 RefSeq region 819448 819510 . - . ID=id60;gene=flhA;Name=id60;Dbxref=GeneID:905174;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0882c by TMHMM2.0 at aa 21-43 2C 48-70 2C 82-102 2C 122-144 2C214-236 2C 251-273 and 298-320 NC_002163.1 RefSeq region 819544 819612 . - . ID=id60;gene=flhA;Name=id60;Dbxref=GeneID:905174;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0882c by TMHMM2.0 at aa 21-43 2C 48-70 2C 82-102 2C 122-144 2C214-236 2C 251-273 and 298-320 NC_002163.1 RefSeq region 819625 819693 . - . ID=id60;gene=flhA;Name=id60;Dbxref=GeneID:905174;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj0882c by TMHMM2.0 at aa 21-43 2C 48-70 2C 82-102 2C 122-144 2C214-236 2C 251-273 and 298-320 NC_002163.1 RefSeq CDS 819740 820150 . - 0 ID=cds781;Parent=gene831;Name=YP_002344283.1;Dbxref=GOA:Q0PA14 InterPro:IPR000944 UniProtKB FTrEMBL:Q0PA14 Genbank:YP_002344283.1 GeneID:905175;gbkey=CDS;product=transcriptional regulator;Note=Original 282000 29 note: Cj0883c 2C unknown 2C len: 136 aa 3B identical to TR:Q46090 28EMBL:U06951 29 Campylobacter jejuni 81-176 ORF3 in region upstream of the flhA gene. 28136 aa 29 2C and similar to hypothetical proteins e.g. Y379_HAEIN 28150 aa 29 2C fasta scores 3B opt: 174 z-score: 226.5 E 28 29: 2.6e-05 2C 28.3 25 identity in 138 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02082 Transcriptional regulator identified within CDS. Product modified to more specific family member based on motif match. No specific characterisation carried out yet 2C so kept in product function. Literature search identified papers giving further clues to product function. Functional classification - Broad regulatory functions 7EPMID:8063102 2C PMID:15066034 2C PMID:14985343 NC_002163.1 RefSeq gene 819740 820150 . - . ID=gene831;gene=Cj0883c;Name=Cj0883c;locus_tag=Cj0883c;Dbxref=GeneID:905175;gbkey=Gene NC_002163.1 RefSeq region 819788 820150 . - . ID=id1629;Name=id1629;Dbxref=GeneID:905175;gbkey=misc_feature;Note=HMMPfam hit to PF02082 2C Transcriptional regulator 2Cscore 3e-31 NC_002163.1 RefSeq region 819956 820012 . - . ID=id1630;Name=id1630;Dbxref=GeneID:905175;gbkey=misc_feature;Note=PS01332 Uncharacterized protein family UPF0074 signature ### NC_002163.1 UTR_Extractor 5'-UTR 820151 820179 . - . ID=utr309;locus_tag=Cj0883c;product=putative transcriptional regulator NC_002163.1 UTR_Extractor 5'-UTR 820287 820324 . + . ID=utr310;locus_tag=Cj0884;product=30S ribosomal protein S15 NC_002163.1 RefSeq CDS 820325 820597 . + 0 ID=cds782;Parent=gene832;gene=rpsO;Name=YP_002344284.1;Dbxref=GOA:Q0PA13 HSSP:P80378 InterPro:IPR000589 InterPro:IPR005290 InterPro:IPR009068 UniProtKB FSwiss-Prot:Q0PA13 Genbank:YP_002344284.1 GeneID:905176;gbkey=CDS;product=30S ribosomal protein S15;Note=primary rRNA binding protein 3B helps nucleate assembly of 30S 3B binds directly to the 16S rRNA and an intersubunit bridge to the 23S rRNA 3B autoregulates translation through interactions with the mRNA leader sequence NC_002163.1 RefSeq gene 820325 820597 . + . ID=gene832;gene=rpsO;Name=rpsO;locus_tag=Cj0884;Dbxref=GeneID:905176;gbkey=Gene NC_002163.1 RefSeq region 820340 820588 . + . ID=id1631;gene=rpsO;Name=id1631;Dbxref=GeneID:905176;gbkey=misc_feature;Note=HMMPfam hit to PF00312 2C Ribosomal protein S15 2Cscore 2.4e-33 NC_002163.1 RefSeq region 820439 820531 . + . ID=id1632;gene=rpsO;Name=id1632;Dbxref=GeneID:905176;gbkey=misc_feature;Note=PS00362 Ribosomal protein S15 signature ### NC_002163.1 RefSeq CDS 820683 823523 . - 0 ID=cds783;Parent=gene833;gene=ftsK;Name=YP_002344285.1;Dbxref=GOA:Q0PA12 InterPro:IPR002543 UniProtKB FSwiss-Prot:Q0PA12 Genbank:YP_002344285.1 GeneID:905152;gbkey=CDS;product=cell division protein;Note=Original 282000 29 note: Cj0886c 2C ftsK 2C probable cell division protein 2C len: 946 aa 3B 96.7 25 identity to YRO1_CAMJE 28941 aa 29 2C and similar to e.g. FTSK_ECOLI cell division protein FTSK 281329 aa 29 2C fasta scores 3B opt: 803 z-score: 772.9 E 28 29: 0 2C 45.2 25 identity in 522 aa overlap 2Cand SP3E_BACSU stage III sporulation protein E 28787 aa 29 2Cfasta scores 3B opt: 1488 z-score: 1436.1 E 28 29: 0 2C 48.3 25 identity in 476 aa overlap. 52.0 25 identity to HP1090. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 7EUpdated 282006 29 note: Pfam domain PF01580 FtsK 2FSpoIIIE family identified within CDS. Further support given to product function. Three probable transmembrane helices predicted by TMHMM2.0. Similar to more than one annotated function in different genus. kept within product function. Functional classification - Cell division 7EPMID:8063102 2C PMID:11778051 2C PMID:7592387 NC_002163.1 RefSeq gene 820683 823523 . - . ID=gene833;gene=ftsK;Name=ftsK;locus_tag=Cj0886c;Dbxref=GeneID:905152;gbkey=Gene NC_002163.1 RefSeq region 821172 821747 . - . ID=id1633;gene=ftsK;Name=id1633;Dbxref=GeneID:905152;gbkey=misc_feature;Note=HMMPfam hit to PF01580 2C FtsK 2FSpoIIIE family 2C score 8.5e-94 NC_002163.1 RefSeq region 821592 821615 . - . ID=id1634;gene=ftsK;Name=id1634;Dbxref=GeneID:905152;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 823203 823271 . - . ID=id61;gene=ftsK;Name=id61;Dbxref=GeneID:905152;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0886c by TMHMM2.0 at aa 13-35 2C 50-72 and 85-107 NC_002163.1 RefSeq region 823308 823376 . - . ID=id61;gene=ftsK;Name=id61;Dbxref=GeneID:905152;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0886c by TMHMM2.0 at aa 13-35 2C 50-72 and 85-107 NC_002163.1 RefSeq region 823419 823487 . - . ID=id61;gene=ftsK;Name=id61;Dbxref=GeneID:905152;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0886c by TMHMM2.0 at aa 13-35 2C 50-72 and 85-107 ### NC_002163.1 UTR_Extractor 5'-UTR 823524 823610 . - . ID=utr311;locus_tag=Cj0886c;product=putative cell division protein NC_002163.1 RefSeq gene 823633 825885 . - . ID=gene834;gene=flgL;Name=flgL;locus_tag=Cj0887c;Dbxref=GeneID:905178;gbkey=Gene NC_002163.1 RefSeq CDS 823633 825885 . - 0 ID=cds784;Parent=gene834;gene=flgL;Name=YP_002344286.1;Dbxref=GOA:Q0PA11 InterPro:IPR001492 UniProtKB FTrEMBL:Q0PA11 Genbank:YP_002344286.1 GeneID:905178;gbkey=CDS;product=flagellar hook-associated protein FlgL;Note=with FlgK acts as a hook filament junction protein to join the flagellar filament to the hook NC_002163.1 RefSeq region 825397 825807 . - . ID=id1635;gene=flgL;Name=id1635;Dbxref=GeneID:905178;gbkey=misc_feature;Note=HMMPfam hit to PF00669 2C Bacterial flagellin N-terminus 2C score 1.8e-05 ### NC_002163.1 RefSeq gene 826066 826152 . + . ID=gene835;gene=tRNALeu;Name=tRNALeu;locus_tag=Cjp16;Dbxref=GeneID:905179;gbkey=Gene NC_002163.1 RefSeq tRNA 826066 826152 . + . ID=rna27;Parent=gene835;gene=tRNALeu;Name=rna27;Dbxref=GeneID:905179;gbkey=tRNA;product=tRNA-Leu;Note=tRNA Leu anticodon CAA 2C Cove score 75.00 NC_002163.1 RefSeq exon 826066 826152 . + . ID=id1636;Parent=rna27;gene=tRNALeu;Name=id1636;Dbxref=GeneID:905179;gbkey=tRNA;product=tRNA-Leu;Note=tRNA Leu anticodon CAA 2C Cove score 75.00 NC_002163.1 RefSeq gene 826163 826237 . + . ID=gene836;gene=tRNAGly;Name=tRNAGly;locus_tag=Cjp17;Dbxref=GeneID:904415;gbkey=Gene NC_002163.1 RefSeq tRNA 826163 826237 . + . ID=rna28;Parent=gene836;gene=tRNAGly;Name=rna28;Dbxref=GeneID:904415;gbkey=tRNA;product=tRNA-Gly;Note=tRNA Gly anticodon GCC 2C Cove score 88.10 NC_002163.1 RefSeq exon 826163 826237 . + . ID=id1637;Parent=rna28;gene=tRNAGly;Name=id1637;Dbxref=GeneID:904415;gbkey=tRNA;product=tRNA-Gly;Note=tRNA Gly anticodon GCC 2C Cove score 88.10 NC_002163.1 RefSeq CDS 826268 828199 . - 0 ID=cds785;Parent=gene837;Name=YP_002344287.1;Dbxref=GOA:Q0PA10 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FTrEMBL:Q0PA10 Genbank:YP_002344287.1 GeneID:904350;gbkey=CDS;product=ABC transporter ATP-binding protein;Note=Original 282000 29 note: Cj0888c 2C ABC transport system ATP-binding protein 2C len: 643 aa 3B similar to UUP_ECOLI ABC transporter atp-binding protein UUP 28635 aa 29 2C fasta scores 3B opt: 744 z-score: 763.9 E 28 29: 0 2C 37.1 25 identity in 634 aa overlap. No Hp ortholog. Contains 2x PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C 2x PS00211 ABC transporters family signature 2C and 2x Pfam match to entry PF00005 ABC_tran 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Transport 2Fbinding proteins - Other 7EPMID:9139905 NC_002163.1 RefSeq gene 826268 828199 . - . ID=gene837;Name=Cj0888c;locus_tag=Cj0888c;Dbxref=GeneID:904350;gbkey=Gene NC_002163.1 RefSeq region 826625 827131 . - . ID=id1638;Name=id1638;Dbxref=GeneID:904350;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 2.1e-45 NC_002163.1 RefSeq region 826799 826843 . - . ID=id1639;Name=id1639;Dbxref=GeneID:904350;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq region 827087 827110 . - . ID=id1640;Name=id1640;Dbxref=GeneID:904350;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 827504 828115 . - . ID=id1641;Name=id1641;Dbxref=GeneID:904350;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 7.2e-43 NC_002163.1 RefSeq region 827678 827722 . - . ID=id1642;Name=id1642;Dbxref=GeneID:904350;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq region 828071 828094 . - . ID=id1643;Name=id1643;Dbxref=GeneID:904350;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 RefSeq gene 828203 829492 . - . ID=gene838;Name=Cj0889c;locus_tag=Cj0889c;Dbxref=GeneID:905181;gbkey=Gene NC_002163.1 RefSeq CDS 828203 829492 . - 0 ID=cds786;Parent=gene838;Name=YP_002344288.1;Dbxref=GOA:Q0PA09 InterPro:IPR003594 InterPro:IPR003661 InterPro:IPR004358 InterPro:IPR005467 UniProtKB FTrEMBL:Q0PA09 Genbank:YP_002344288.1 GeneID:905181;gbkey=CDS;product=sensory trasnduction histidine kinase;Note=Original 282000 29 note: Cj0889c 2C probable sensory transduction histidine kinase 2C len: 429 aa 3B similar in C-terminus to many e.g. ENVZ_ECOLI osmolarity sensor protein ENVZ 28450 aa 29 2C fasta scores 3B opt: 210 z-score: 229.3 E 28 29: 1.8e-05. 26.5 25 identity in 204 aa overlap No Hp ortholog. Contains two probable transmembrane domains in N-terminus and Pfam match to entry PF00512 signal 2C Signal carboxyl-terminal domain 7EUpdated 282006 29 note: Pfam domain PF02518 Histidine kinase- 2C DNA gyrase B- 2C and HSP90-like ATPase identified within CDS. Further support given to product function. Some characterisation in Bacillus subtilitis 2C however 2Cidentity score not acceptable. kept in product function. Functional classification - Signal transduction 7EPMID:8002614 2C PMID:14612242 2C PMID:12890034 NC_002163.1 RefSeq region 828206 828514 . - . ID=id1644;Name=id1644;Dbxref=GeneID:905181;gbkey=misc_feature;Note=HMMPfam hit to PF02518 2C Histidine kinase- 2C DNA gyrase B- 2C and HSP90 2C score 1.5e-20 NC_002163.1 RefSeq region 828620 828823 . - . ID=id1645;Name=id1645;Dbxref=GeneID:905181;gbkey=misc_feature;Note=HMMPfam hit to PF00512 2C His Kinase A 28phosphoacceptor 29 domain 2C score 1.3e-11 NC_002163.1 RefSeq region 829025 829093 . - . ID=id62;Name=id62;Dbxref=GeneID:905181;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0889c by TMHMM2.0 at aa 7-26 and 134-156 NC_002163.1 RefSeq region 829415 829474 . - . ID=id62;Name=id62;Dbxref=GeneID:905181;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0889c by TMHMM2.0 at aa 7-26 and 134-156 NC_002163.1 RefSeq CDS 829486 830148 . - 0 ID=cds787;Parent=gene839;Name=YP_002344289.1;Dbxref=GOA:Q0PA08 InterPro:IPR001789 InterPro:IPR001867 UniProtKB FTrEMBL:Q0PA08 Genbank:YP_002344289.1 GeneID:905187;gbkey=CDS;product=sensory transduction transcriptional regulator;Note=Original 282000 29 note: Cj0890c 2C probable sensory transduction transcriptional regulator 2C len: 220 aa 3B similar to many e.g. PHOB_SHIFL phosphate regulon transcriptional regulator 28229 aa 29 2C fasta scores 3B opt: 396 z-score: 471.5 E 28 29: 5.8e-19 2C 29.3 25 identity in 222 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00072 response_reg 2C Response regulator receiver domain and Pfam match to entry PF00486 trans_reg_C 2CTranscriptional regulatory protein 2C C terminal 7EUpdated 282006 29 note: Characterisation within more than one genus 2C however 2C identity scores were marginal. kept within product function. Functional classification - Signal transduction 7EPMID:9141682 NC_002163.1 RefSeq gene 829486 830148 . - . ID=gene839;Name=Cj0890c;locus_tag=Cj0890c;Dbxref=GeneID:905187;gbkey=Gene NC_002163.1 RefSeq region 829492 829710 . - . ID=id1646;Name=id1646;Dbxref=GeneID:905187;gbkey=misc_feature;Note=HMMPfam hit to PF00486 2C Transcriptional regulatory protein 2C C te 2C score 3.4e-18 NC_002163.1 RefSeq region 829780 830139 . - . ID=id1647;Name=id1647;Dbxref=GeneID:905187;gbkey=misc_feature;Note=HMMPfam hit to PF00072 2C Response regulator receiver domain 2C score 5.5e-25 NC_002163.1 RefSeq gene 830135 831718 . - . ID=gene840;gene=serA;Name=serA;locus_tag=Cj0891c;Dbxref=GeneID:905182;gbkey=Gene NC_002163.1 RefSeq CDS 830135 831718 . - 0 ID=cds788;Parent=gene840;gene=serA;Name=YP_002344290.1;Dbxref=GOA:Q0PA07 InterPro:IPR002912 InterPro:IPR006139 InterPro:IPR006140 InterPro:IPR006236 InterPro:IPR015508 InterPro:IPR016040 UniProtKB FTrEMBL:Q0PA07 Genbank:YP_002344290.1 GeneID:905182;gbkey=CDS;product=D-3-phosphoglycerate dehydrogenase;Note=catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis 3B can also reduce alpha ketoglutarate to form 2-hydroxyglutarate NC_002163.1 RefSeq region 830144 830356 . - . ID=id1648;gene=serA;Name=id1648;Dbxref=GeneID:905182;gbkey=misc_feature;Note=HMMPfam hit to PF01842 2C ACT domain 2C score 1.1e-11 NC_002163.1 RefSeq region 830873 831412 . - . ID=id1649;gene=serA;Name=id1649;Dbxref=GeneID:905182;gbkey=misc_feature;Note=HMMPfam hit to PF02826 2C D-isomer specific 2-hydroxyacid dehydrog 2C score 5.9e-52 NC_002163.1 RefSeq region 831068 831136 . - . ID=id1650;gene=serA;Name=id1650;Dbxref=GeneID:905182;gbkey=misc_feature;Note=PS00670 D-isomer specific 2-hydroxyacid dehydrogenases signature 2 NC_002163.1 RefSeq region 831200 831283 . - . ID=id1651;gene=serA;Name=id1651;Dbxref=GeneID:905182;gbkey=misc_feature;Note=PS00065 D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature NC_002163.1 RefSeq region 831428 831712 . - . ID=id1652;gene=serA;Name=id1652;Dbxref=GeneID:905182;gbkey=misc_feature;Note=HMMPfam hit to PF00389 2C D-isomer specific 2-hydroxyacid dehydrog 2C score 2.1e-20 NC_002163.1 RefSeq CDS 831715 832203 . - 0 ID=cds789;Parent=gene841;Name=YP_002344291.1;Dbxref=GOA:Q0PA06 UniProtKB FTrEMBL:Q0PA06 Genbank:YP_002344291.1 GeneID:905183;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0892c 2C probable periplasmic protein 2C len: 162 aa 3B no Hp match. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 831715 832203 . - . ID=gene841;gene=Cj0892c;Name=Cj0892c;locus_tag=Cj0892c;Dbxref=GeneID:905183;gbkey=Gene NC_002163.1 RefSeq region 832126 832185 . - . ID=id1653;Name=id1653;Dbxref=GeneID:905183;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0892c by TMHMM2.0 at aa 7-26 NC_002163.1 RefSeq CDS 832203 833873 . - 0 ID=cds790;Parent=gene842;gene=rpsA;Name=YP_002344292.1;Dbxref=GOA:Q0PA05 InterPro:IPR000110 InterPro:IPR003029 InterPro:IPR012340 UniProtKB FTrEMBL:Q0PA05 Genbank:YP_002344292.1 GeneID:905184;gbkey=CDS;product=30S ribosomal protein S1;Note=in Escherichia coli this protein is involved in binding to the leader sequence of mRNAs and is itself bound to the 30S subunit 3B autoregulates expression via a C-terminal domain 3B in most gram negative organisms this protein is composed of 6 repeats of the S1 domain while in gram positive there are 4 repeats 3B the S1 nucleic acid-binding domain is found associated with other proteins NC_002163.1 RefSeq gene 832203 833873 . - . ID=gene842;gene=rpsA;Name=rpsA;locus_tag=Cj0893c;Dbxref=GeneID:905184;gbkey=Gene NC_002163.1 RefSeq region 832299 832508 . - . ID=id1654;gene=rpsA;Name=id1654;Dbxref=GeneID:905184;gbkey=misc_feature;Note=HMMPfam hit to PF00575 2C S1 RNA binding domain 2Cscore 4.8e-15 NC_002163.1 RefSeq region 832545 832763 . - . ID=id1655;gene=rpsA;Name=id1655;Dbxref=GeneID:905184;gbkey=misc_feature;Note=HMMPfam hit to PF00575 2C S1 RNA binding domain 2Cscore 3.1e-25 NC_002163.1 RefSeq region 832800 833024 . - . ID=id1656;gene=rpsA;Name=id1656;Dbxref=GeneID:905184;gbkey=misc_feature;Note=HMMPfam hit to PF00575 2C S1 RNA binding domain 2Cscore 1.9e-27 NC_002163.1 RefSeq region 833061 833279 . - . ID=id1657;gene=rpsA;Name=id1657;Dbxref=GeneID:905184;gbkey=misc_feature;Note=HMMPfam hit to PF00575 2C S1 RNA binding domain 2Cscore 5.7e-22 NC_002163.1 RefSeq region 833328 833534 . - . ID=id1658;gene=rpsA;Name=id1658;Dbxref=GeneID:905184;gbkey=misc_feature;Note=HMMPfam hit to PF00575 2C S1 RNA binding domain 2Cscore 1.8e-06 ### NC_002163.1 UTR_Extractor 5'-UTR 833874 833903 . - . ID=utr312;locus_tag=Cj0893c;product=30S ribosomal protein S1 NC_002163.1 RefSeq CDS 834005 834838 . - 0 ID=cds791;Parent=gene843;gene=ispH;Name=YP_002344293.1;Dbxref=GOA:P0C632 InterPro:IPR003451 UniProtKB FSwiss-Prot:P0C632 Genbank:YP_002344293.1 GeneID:905189;gbkey=CDS;product=4-hydroxy-3-methylbut-2-enyl diphosphate reductase;Note=catalyzes the conversion of 1-hydroxy-2-methyl-2- 28E 29-butenyl 4-diphosphate into isopentenyl diphosphate 28IPP 29 and dimethylallyl diphosphate 28DMAPP 29 3B functions in the nonmevalonate isoprenoid biosynthesis pathway NC_002163.1 RefSeq gene 834005 834838 . - . ID=gene843;gene=ispH;Name=ispH;locus_tag=Cj0894c;Dbxref=GeneID:905189;gbkey=Gene NC_002163.1 RefSeq region 834017 834832 . - . ID=id1659;gene=ispH;Name=id1659;Dbxref=GeneID:905189;gbkey=misc_feature;Note=HMMPfam hit to PF02401 2C LytB protein 2C score 2.5e-160 NC_002163.1 RefSeq gene 834828 836114 . - . ID=gene844;gene=aroA;Name=aroA;locus_tag=Cj0895c;Dbxref=GeneID:904338;gbkey=Gene NC_002163.1 RefSeq CDS 834828 836114 . - 0 ID=cds792;Parent=gene844;gene=aroA;Name=YP_002344294.1;Dbxref=GOA:P0C630 GOA:P52312 InterPro:IPR001986 InterPro:IPR006264 InterPro:IPR016228 UniProtKB FSwiss-Prot:P0C630 Genbank:YP_002344294.1 GeneID:904338;gbkey=CDS;product=3-phosphoshikimate 1-carboxyvinyltransferase;Note=catalyzes the formation of 5-O- 281-carboxyvinyl 29-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis NC_002163.1 RefSeq region 834858 836099 . - . ID=id1660;gene=aroA;Name=id1660;Dbxref=GeneID:904338;gbkey=misc_feature;Note=HMMPfam hit to PF00275 2C EPSP synthase 283-phosphoshikimate 1-car 2C score 2.1e-163 NC_002163.1 RefSeq region 835818 835862 . - . ID=id1661;gene=aroA;Name=id1661;Dbxref=GeneID:904338;gbkey=misc_feature;Note=PS00104 EPSP synthase signature 1 NC_002163.1 RefSeq gene 836111 838432 . - . ID=gene845;gene=pheT;Name=pheT;locus_tag=Cj0896c;Dbxref=GeneID:905191;gbkey=Gene NC_002163.1 RefSeq CDS 836111 838432 . - 0 ID=cds793;Parent=gene845;gene=pheT;Name=YP_002344295.1;Dbxref=GOA:Q9PP35 HSSP:P42589 InterPro:IPR002547 InterPro:IPR003583 InterPro:IPR004532 InterPro:IPR005121 InterPro:IPR005146 InterPro:IPR005147 InterPro:IPR012340 UniProtKB FSwiss-Prot:Q9PP35 Genbank:YP_002344295.1 GeneID:905191;gbkey=CDS;product=phenylalanyl-tRNA synthetase subunit beta;Note=catalyzes a two-step reaction 2C first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP 2C followed by transfer of the aminoacyl-adenylate to its tRNA 3B forms a tetramer of alpha 282 29beta 282 29 3B binds two magnesium ions per tetramer 3B type 2 subfamily NC_002163.1 RefSeq region 836114 836389 . - . ID=id1662;gene=pheT;Name=id1662;Dbxref=GeneID:905191;gbkey=misc_feature;Note=HMMPfam hit to PF03147 2C Ferredoxin-fold anticodon binding domain 2C score 4.8e-19 NC_002163.1 RefSeq region 837047 837256 . - . ID=id1663;gene=pheT;Name=id1663;Dbxref=GeneID:905191;gbkey=misc_feature;Note=HMMPfam hit to PF03484 2C tRNA synthetase B5 domain 2Cscore 2.7e-21 NC_002163.1 RefSeq region 837302 837787 . - . ID=id1664;gene=pheT;Name=id1664;Dbxref=GeneID:905191;gbkey=misc_feature;Note=HMMPfam hit to PF03483 2C B3 2F4 domain 2C score 5.4e-21 NC_002163.1 RefSeq region 837989 838300 . - . ID=id1665;gene=pheT;Name=id1665;Dbxref=GeneID:905191;gbkey=misc_feature;Note=HMMPfam hit to PF01588 2C tRNA binding domain 2C score 2.9e-27 NC_002163.1 RefSeq gene 838429 839421 . - . ID=gene846;gene=pheS;Name=pheS;locus_tag=Cj0897c;Dbxref=GeneID:905193;gbkey=Gene NC_002163.1 RefSeq CDS 838429 839421 . - 0 ID=cds794;Parent=gene846;gene=pheS;Name=YP_002344296.1;Dbxref=GOA:Q9PP34 HSSP:P27001 InterPro:IPR002319 InterPro:IPR004188 InterPro:IPR004529 InterPro:IPR006195 UniProtKB FSwiss-Prot:Q9PP34 Genbank:YP_002344296.1 GeneID:905193;gbkey=CDS;product=phenylalanyl-tRNA synthetase subunit alpha;Note=catalyzes a two-step reaction 2C first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP 2C followed by transfer of the aminoacyl-adenylate to its tRNA 3B forms a heterotetramer of alpha 282 29beta 282 29 3B binds two magnesium ions per tetramer 3B type 1 subfamily NC_002163.1 RefSeq region 838474 839121 . - . ID=id1666;gene=pheS;Name=id1666;Dbxref=GeneID:905193;gbkey=misc_feature;Note=HMMPfam hit to PF01409 2C tRNA synthetases class II core domain 2C score 7.2e-143 NC_002163.1 RefSeq region 838498 838527 . - . ID=id1667;gene=pheS;Name=id1667;Dbxref=GeneID:905193;gbkey=misc_feature;Note=PS00339 Aminoacyl-transfer RNA synthetases class-II signature 2 NC_002163.1 RefSeq region 838813 838863 . - . ID=id1668;gene=pheS;Name=id1668;Dbxref=GeneID:905193;gbkey=misc_feature;Note=PS00179 Aminoacyl-transfer RNA synthetases class-II signature 1 NC_002163.1 RefSeq region 839179 839397 . - . ID=id1669;gene=pheS;Name=id1669;Dbxref=GeneID:905193;gbkey=misc_feature;Note=HMMPfam hit to PF02912 2C Aminoacyl tRNA synthetase class II 2C N 2C score 2.5e-23 ### NC_002163.1 UTR_Extractor 5'-UTR 839422 839449 . - . ID=utr313;locus_tag=Cj0897c;product=phenylalanyl-tRNA synthetase subunit alpha NC_002163.1 UTR_Extractor 5'-UTR 839518 839543 . + . ID=utr314;locus_tag=Cj0898;product=putative histidine triad 28HIT 29 family protein NC_002163.1 RefSeq gene 839544 839909 . + . ID=gene847;Name=Cj0898;locus_tag=Cj0898;Dbxref=GeneID:905194;gbkey=Gene NC_002163.1 RefSeq CDS 839544 839909 . + 0 ID=cds795;Parent=gene847;Name=YP_002344297.1;Dbxref=GOA:Q0PA00 InterPro:IPR001310 InterPro:IPR011151 UniProtKB FTrEMBL:Q0PA00 Genbank:YP_002344297.1 GeneID:905194;gbkey=CDS;product=histidine triad 28HIT 29 family protein;Note=Original 282000 29 note: Cj0898 2C HIT-family protein 2Clen: 121 aa 3B similar to many members of the HIT family e.g. IPK1_HUMAN HINT protein 28protein kinase C inhibitor 1 29 28125 aa 29 2C fasta scores 3B opt: 286 z-score: 385.9 E 28 29: 3.4e-14 2C 40.6 25 identity in 106 aa overlap 2C and YCFF_ECOLI HYPOTHETICAL 13.2 KD PROTEIN HIT-LIKE PROTE 28119 aa 29 2Cfasta scores 3B opt: 276 z-score: 373.2 E 28 29: 1.7e-13 2C 38.2 25 identity in 110 aa overlap. 56.6 25 identity to HP0404. Contains Pfam match to entry PF01230 HIT 2C HIT family 7EUpdated 282006 29 note: Specific characterisation has not been carried out 2C so kept in product function. Functional classification - Misc NC_002163.1 RefSeq region 839556 839864 . + . ID=id1670;Name=id1670;Dbxref=GeneID:905194;gbkey=misc_feature;Note=HMMPfam hit to PF01230 2C HIT domain 2C score 3.2e-40 ### NC_002163.1 RefSeq CDS 839939 840508 . - 0 ID=cds796;Parent=gene848;gene=thiJ;Name=YP_002344298.1;Dbxref=InterPro:IPR002818 InterPro:IPR006287 UniProtKB FTrEMBL:Q0P9Z9 Genbank:YP_002344298.1 GeneID:905197;gbkey=CDS;product=4-methyl-5 28beta-hydroxyethyl 29-thiazole monophosphate synthesis protein;Note=Original 282000 29 note: Cj0899c 2C thiJ 2C probable 4-methyl-5 28beta-hydroxyethyl 29-thiazole monophosphate synthesis protein 2C len: 189 aa 3B simlar to e.g. THIJ_ECOLI 4-methyl-5 28b-hydroxyethyl 29-thiazole monophosphate biosynthesis enzyme 28198 aa 29 2C fasta scores 3B opt: 265 z-score: 330.3 E 28 29: 4.2e-11 2C 32.6 25 identity in 181 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF01965 DJ-1 2FPfpI family identified within CDS. Further support given to product function. Characterised in Escherichia coli with marginal identity score. not added to protein function. Functional classification - Biosynthesis of cofactors 2C prosthetic groups and carriers - Thiamine 7EPMID:10075431 NC_002163.1 RefSeq gene 839939 840508 . - . ID=gene848;gene=thiJ;Name=thiJ;locus_tag=Cj0899c;Dbxref=GeneID:905197;gbkey=Gene NC_002163.1 RefSeq region 839996 840403 . - . ID=id1671;gene=thiJ;Name=id1671;Dbxref=GeneID:905197;gbkey=misc_feature;Note=HMMPfam hit to PF01965 2C DJ-1 2FPfpI family 2C score 6.9e-32 NC_002163.1 RefSeq region 840434 840481 . - . ID=id1672;gene=thiJ;Name=id1672;Dbxref=GeneID:905197;gbkey=misc_feature;Note=PS00225 Crystallins beta and gamma 27Greek key 27 motif signature NC_002163.1 RefSeq gene 840501 840680 . - . ID=gene849;gene=Cj0900c;Name=Cj0900c;locus_tag=Cj0900c;Dbxref=GeneID:905195;gbkey=Gene NC_002163.1 RefSeq CDS 840501 840680 . - 0 ID=cds797;Parent=gene849;Name=YP_002344299.1;Dbxref=GOA:Q0P9Z8 UniProtKB FTrEMBL:Q0P9Z8 Genbank:YP_002344299.1 GeneID:905195;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0900c 2C small hydrophobic protein 2C len: 59 aa 3B 29.8 25 identity to HP0085. Functional classification - Conserved hypothetical proteins NC_002163.1 UTR_Extractor 5'-UTR 840509 840667 . - . ID=utr315;locus_tag=Cj0899c;product=4-methyl-5 28beta-hydroxyethyl 29-thiazole monophosphate synthesis protein NC_002163.1 RefSeq region 840585 840653 . - . ID=id1673;Name=id1673;Dbxref=GeneID:905195;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0900c by TMHMM2.0 at aa 10-32 ### NC_002163.1 UTR_Extractor 5'-UTR 840730 840762 . + . ID=utr316;locus_tag=Cj0901;product=putative amino acid ABC tansporter permease NC_002163.1 RefSeq CDS 840763 841506 . + 0 ID=cds798;Parent=gene850;Name=YP_002344300.1;Dbxref=GOA:Q0P9Z7 InterPro:IPR000515 InterPro:IPR001991 InterPro:IPR010065 UniProtKB FTrEMBL:Q0P9Z7 Genbank:YP_002344300.1 GeneID:905200;gbkey=CDS;product=amino acid ABC transporter permease;Note=Original 282000 29 note: Cj0901 2C probable amino acid ABC tansporter permease 2C len: 247 aa 3B similar to many e.g. YQIY_BACSU probable amino-acid ABC transporter permease 28219 aa 29 2C fasta scores 3B opt: 552 z-score: 683.2 E 28 29: 9.3e-31 2C 43.6 25 identity in 204 aa overlap. 28.6 25 identity to HP0939. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp signature 2C and Pfam match to entry PF00528 BPD_transp 2C Binding-protein-dependent transport systems inner membrane component 7EUpdated 282006 29 note: Four probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification -Transport 2Fbinding proteins - Amino acids and amines NC_002163.1 RefSeq gene 840763 841506 . + . ID=gene850;Name=Cj0901;locus_tag=Cj0901;Dbxref=GeneID:905200;gbkey=Gene NC_002163.1 RefSeq region 840775 840843 . + . ID=id1674;Name=id1674;Dbxref=GeneID:905200;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0901 by TMHMM2.0 at aa 5-27 2C 54-76 2C 100-122 and 217-236 NC_002163.1 RefSeq region 840904 841497 . + . ID=id1675;Name=id1675;Dbxref=GeneID:905200;gbkey=misc_feature;Note=HMMPfam hit to PF00528 2C Binding-protein-dependent transport syst 2C score 2.6e-34 NC_002163.1 RefSeq region 840913 840945 . + . ID=id1676;Name=id1676;Dbxref=GeneID:905200;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 840922 840990 . + . ID=id1674;Name=id1674;Dbxref=GeneID:905200;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0901 by TMHMM2.0 at aa 5-27 2C 54-76 2C 100-122 and 217-236 NC_002163.1 RefSeq region 841060 841128 . + . ID=id1674;Name=id1674;Dbxref=GeneID:905200;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0901 by TMHMM2.0 at aa 5-27 2C 54-76 2C 100-122 and 217-236 NC_002163.1 RefSeq region 841183 841269 . + . ID=id1677;Name=id1677;Dbxref=GeneID:905200;gbkey=misc_feature;Note=PS00402 Binding-protein-dependent transport systems inner membrane comp. sign NC_002163.1 RefSeq region 841411 841470 . + . ID=id1674;Name=id1674;Dbxref=GeneID:905200;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0901 by TMHMM2.0 at aa 5-27 2C 54-76 2C 100-122 and 217-236 NC_002163.1 RefSeq CDS 841499 842227 . + 0 ID=cds799;Parent=gene851;gene=glnQ;Name=YP_002344301.1;Dbxref=GOA:Q0P9Z6 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FTrEMBL:Q0P9Z6 Genbank:YP_002344301.1 GeneID:905198;gbkey=CDS;product=glutamine transporter ATP-binding protein;Note=Original 282000 29 note: Cj0902 2C glnQ 2C probable glutamine transport ATP-binding protein 2C len: 247 aa 3B highly similar to e.g. GLNQ_BACST glutamine transport ATP-binding protein 28242 aa 29 2C fasta scores 3B opt: 940 z-score: 1074.4 E 28 29: 0 2C 56.2 25 identity in 242 aa overlap. No Hp ortholog. Also similar to Cj0469 2852.9 25 identity in 238 aa overlap 29. Contains S00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C S00211 ABC transporters family signature 2C and Pfam match to entry PF00005 ABC_tran 2C ABC transporters 7EUpdated 282006 29 note: Characterised in Bacillus stearothermophilus with acceptable identity score. kept within product function as not sure whether exact substrate is used in Campylobacter jejuni. Functional classification - Transport 2Fbinding proteins -Amino acids and amines 7EPMID:1856180 NC_002163.1 RefSeq gene 841499 842227 . + . ID=gene851;gene=glnQ;Name=glnQ;locus_tag=Cj0902;Dbxref=GeneID:905198;gbkey=Gene NC_002163.1 RefSeq region 841577 842134 . + . ID=id1678;gene=glnQ;Name=id1678;Dbxref=GeneID:905198;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 2.6e-56 NC_002163.1 RefSeq region 841598 841621 . + . ID=id1679;gene=glnQ;Name=id1679;Dbxref=GeneID:905198;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 841907 841951 . + . ID=id1680;gene=glnQ;Name=id1680;Dbxref=GeneID:905198;gbkey=misc_feature;Note=PS00211 ABC transporters family signature ### NC_002163.1 RefSeq CDS 842255 843721 . - 0 ID=cds800;Parent=gene852;Name=YP_002344302.1;Dbxref=GOA:Q0P9Z5 InterPro:IPR001463 UniProtKB FTrEMBL:Q0P9Z5 Genbank:YP_002344302.1 GeneID:905201;gbkey=CDS;product=amino acid transport protein;Note=Original 282000 29 note: Cj0903c 2C probable amino-acid transport protein 2C len: 488 aa 3B simlar to many hypothetical membaer of the sodium:alanine symporter family e.g. ALST_BACSU amino acid carrier protein ALST 28465 aa 29 2C fasta scores 3B opt: 821 z-score: 946.6 E 28 29: 0 2C41.9 25 identity in 473 aa overlap. 33.6 25 identity to HP0942. Contains PS00873 Sodium:alanine symporter family signature 2C and Pfam match to entry PF01235 Na_Ala_symp 2CSodium:alanine symporter family 7EUpdated 282006 29 note: Nine probable transmembrane helices predicted for TMHMM2.0. Further support given to product function. No specfic characterisation with acceptable identity score carried out yet. kept within product function along with amino-acid designation as not sure whether exact substrate is used in Campylobacter jejuni. Literature search identified paper giving further clues about product function. Functional classification - Transport 2Fbinding proteins - Amino acids and amines 7EPMID:15066034 NC_002163.1 RefSeq gene 842255 843721 . - . ID=gene852;Name=Cj0903c;locus_tag=Cj0903c;Dbxref=GeneID:905201;gbkey=Gene NC_002163.1 RefSeq region 842285 843556 . - . ID=id1681;Name=id1681;Dbxref=GeneID:905201;gbkey=misc_feature;Note=HMMPfam hit to PF01235 2C Sodium:alanine symporter family 2C score 4.2e-138 NC_002163.1 RefSeq region 842345 842413 . - . ID=id63;Name=id63;Dbxref=GeneID:905201;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0903c by TMHMM2.0 at aa 27-49 2C 85-107 2C 149-171 2C 199-221 2C231-253 2C 323-345 2C 371-393 2C 405-422 and 437-459 NC_002163.1 RefSeq region 842456 842509 . - . ID=id63;Name=id63;Dbxref=GeneID:905201;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0903c by TMHMM2.0 at aa 27-49 2C 85-107 2C 149-171 2C 199-221 2C231-253 2C 323-345 2C 371-393 2C 405-422 and 437-459 NC_002163.1 RefSeq region 842543 842611 . - . ID=id63;Name=id63;Dbxref=GeneID:905201;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0903c by TMHMM2.0 at aa 27-49 2C 85-107 2C 149-171 2C 199-221 2C231-253 2C 323-345 2C 371-393 2C 405-422 and 437-459 NC_002163.1 RefSeq region 842687 842755 . - . ID=id63;Name=id63;Dbxref=GeneID:905201;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0903c by TMHMM2.0 at aa 27-49 2C 85-107 2C 149-171 2C 199-221 2C231-253 2C 323-345 2C 371-393 2C 405-422 and 437-459 NC_002163.1 RefSeq region 842963 843031 . - . ID=id63;Name=id63;Dbxref=GeneID:905201;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0903c by TMHMM2.0 at aa 27-49 2C 85-107 2C 149-171 2C 199-221 2C231-253 2C 323-345 2C 371-393 2C 405-422 and 437-459 NC_002163.1 RefSeq region 843059 843127 . - . ID=id63;Name=id63;Dbxref=GeneID:905201;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0903c by TMHMM2.0 at aa 27-49 2C 85-107 2C 149-171 2C 199-221 2C231-253 2C 323-345 2C 371-393 2C 405-422 and 437-459 NC_002163.1 RefSeq region 843209 843277 . - . ID=id63;Name=id63;Dbxref=GeneID:905201;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0903c by TMHMM2.0 at aa 27-49 2C 85-107 2C 149-171 2C 199-221 2C231-253 2C 323-345 2C 371-393 2C 405-422 and 437-459 NC_002163.1 RefSeq region 843377 843424 . - . ID=id1682;Name=id1682;Dbxref=GeneID:905201;gbkey=misc_feature;Note=PS00873 Sodium:alanine symporter family signature NC_002163.1 RefSeq region 843401 843469 . - . ID=id63;Name=id63;Dbxref=GeneID:905201;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0903c by TMHMM2.0 at aa 27-49 2C 85-107 2C 149-171 2C 199-221 2C231-253 2C 323-345 2C 371-393 2C 405-422 and 437-459 NC_002163.1 RefSeq region 843575 843643 . - . ID=id63;Name=id63;Dbxref=GeneID:905201;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0903c by TMHMM2.0 at aa 27-49 2C 85-107 2C 149-171 2C 199-221 2C231-253 2C 323-345 2C 371-393 2C 405-422 and 437-459 ### NC_002163.1 UTR_Extractor 5'-UTR 843722 843745 . - . ID=utr317;locus_tag=Cj0903c;product=putative amino-acid transport protein NC_002163.1 RefSeq gene 843825 844292 . - . ID=gene853;Name=Cj0904c;locus_tag=Cj0904c;Dbxref=GeneID:905203;gbkey=Gene NC_002163.1 RefSeq CDS 843825 844292 . - 0 ID=cds801;Parent=gene853;Name=YP_002344303.1;Dbxref=GOA:Q0P9Z4 InterPro:IPR001537 InterPro:IPR016914 UniProtKB FTrEMBL:Q0P9Z4 Genbank:YP_002344303.1 GeneID:905203;gbkey=CDS;product=RNA methylase;Note=Original 282000 29 note: Cj0904c 2C probable RNA methylase 2C len: 155 aa 3B similar to members of the spoU family e.g. YIBK_ECOLI 28157 aa 29 2C fasta scores 3B opt: 373 z-score: 490.5 E 28 29: 5e-20 2C 43.3 25 identity in 150 aa overlap. No Hp match. Contains Pfam match to entry PF00588 SpoU_methylase 2C SpoU rRNA Methylase family 7EUpdated 282006 29 note: kept within product function 2C as full characterisation has not been carried out. Functional classification - RNA synthesis 2C RNA modification and DNA transcription NC_002163.1 RefSeq region 843864 844292 . - . ID=id1683;Name=id1683;Dbxref=GeneID:905203;gbkey=misc_feature;Note=HMMPfam hit to PF00588 2C SpoU rRNA Methylase family 2Cscore 9.5e-32 ### NC_002163.1 UTR_Extractor 5'-UTR 844293 844320 . - . ID=utr318;locus_tag=Cj0904c;product=putative RNA methylase NC_002163.1 RefSeq CDS 844295 845281 . - 0 ID=cds802;Parent=gene854;gene=alr;Name=YP_002344304.1;Dbxref=GOA:Q9PP26 InterPro:IPR000821 InterPro:IPR001608 InterPro:IPR011079 UniProtKB FSwiss-Prot:Q9PP26 Genbank:YP_002344304.1 GeneID:905209;gbkey=CDS;product=alanine racemase;Note=converts L-alanine to D-alanine which is used in cell wall biosynthesis 3B binds one pyridoxal phosphate per monomer 3B forms a homodimer NC_002163.1 RefSeq gene 844295 845281 . - . ID=gene854;gene=alr;Name=alr;locus_tag=Cj0905c;Dbxref=GeneID:905209;gbkey=Gene NC_002163.1 RefSeq region 844298 844636 . - . ID=id1684;gene=alr;Name=id1684;Dbxref=GeneID:905209;gbkey=misc_feature;Note=HMMPfam hit to PF00842 2C Alanine racemase 2CC-terminal domain 2C score 6.9e-39 NC_002163.1 RefSeq region 844649 845281 . - . ID=id1685;gene=alr;Name=id1685;Dbxref=GeneID:905209;gbkey=misc_feature;Note=HMMPfam hit to PF01168 2C Alanine racemase 2CN-terminal domain 2C score 6.2e-57 ### NC_002163.1 RefSeq gene 845282 846259 . - . ID=gene855;Name=Cj0906c;locus_tag=Cj0906c;Dbxref=GeneID:905204;gbkey=Gene NC_002163.1 RefSeq CDS 845282 846259 . - 0 ID=cds803;Parent=gene855;Name=YP_002344305.1;Dbxref=GOA:Q0P9Z2 UniProtKB FTrEMBL:Q0P9Z2 Genbank:YP_002344305.1 GeneID:905204;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0906c 2C probable periplasmic protein 2C len: 325 aa 3B similar to hypothetical proteins e.g. TR:O66569 28EMBL:AE000677 29 Aquifex aeolicus AQ_183 28397 aa 29 2C fasta scores 3B opt: 380 z-score: 432.9 E 28 29: 8.2e-17 2C 31.1 25 identity in 270 aa overlap. 36.6 25 identity to HP0518. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Paper identified linking protein to glycoprotein. Functional classification -Miscellaneous periplasmic proteins 7EPMID:12186869 NC_002163.1 UTR_Extractor 5'-UTR 846260 846301 . - . ID=utr319;locus_tag=Cj0906c;product=putative periplasmic protein NC_002163.1 UTR_Extractor 5'-UTR 846378 846414 . + . ID=utr320;locus_tag=Cj0908;product=putative periplasmic protein NC_002163.1 RefSeq gene 846415 846885 . + . ID=gene856;Name=Cj0908;locus_tag=Cj0908;Dbxref=GeneID:905208;gbkey=Gene NC_002163.1 RefSeq CDS 846415 846885 . + 0 ID=cds804;Parent=gene856;Name=YP_002344306.1;Dbxref=UniProtKB FTrEMBL:Q0P9Z1 Genbank:YP_002344306.1 GeneID:905208;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0908 2C probable periplasmic protein 2C len: 156 aa 3B no Hp match. Contains probable N-terminal signal sequence. Similar to downstream gene Cj0910 2841.3 25 identity in 143 aa overlap 29. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 846427 846483 . + . ID=id1686;Name=id1686;Dbxref=GeneID:905208;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0908 by TMHMM2.0 at aa 5-23 ### NC_002163.1 UTR_Extractor 5'-UTR 846940 846970 . + . ID=utr321;locus_tag=Cj0909;product=putative periplasmic protein NC_002163.1 RefSeq gene 846971 847390 . + . ID=gene857;Name=Cj0909;locus_tag=Cj0909;Dbxref=GeneID:905210;gbkey=Gene NC_002163.1 RefSeq CDS 846971 847390 . + 0 ID=cds805;Parent=gene857;Name=YP_002344307.1;Dbxref=GOA:Q0P9Z0 InterPro:IPR007410 UniProtKB FTrEMBL:Q0P9Z0 Genbank:YP_002344307.1 GeneID:905210;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0909 2C probable periplasmic protein 2C len: 139 aa 3B similar to TR:O67294 28EMBL:AE000731 29 Aquifex aeolicus AQ_1253 28151 aa 29 2C fasta scores 3B opt: 208 z-score: 273.4 E 28 29: 6.3e-08 2C 34.3 25 identity in 134 aa overlap. No Hp match. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF04314 Protein of unknown function 28DUF461 29 identified within CDS. This Pfam is linked to being a membrane or periplasmic protein. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 847037 847384 . + . ID=id1687;Name=id1687;Dbxref=GeneID:905210;gbkey=misc_feature;Note=HMMPfam hit to PF04314 2C Protein of unknown function 28DUF461 29 2C score 1.3e-62 ### NC_002163.1 RefSeq CDS 847394 847846 . + 0 ID=cds806;Parent=gene858;Name=YP_002344308.1;Dbxref=UniProtKB FTrEMBL:Q0P9Y9 Genbank:YP_002344308.1 GeneID:905190;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0910 2C probable periplasmic protein 2C len: 150 aa 3B no Hp match. Contains probable N-terminal signal sequence. Similar to downstream gene Cj0908 2841.3 25 identity in 145 aa overlap 29. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 847394 847846 . + . ID=gene858;Name=Cj0910;locus_tag=Cj0910;Dbxref=GeneID:905190;gbkey=Gene NC_002163.1 RefSeq region 847403 847471 . + . ID=id1688;Name=id1688;Dbxref=GeneID:905190;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0910 by TMHMM2.0 at aa 4-26 NC_002163.1 RefSeq CDS 847843 848403 . + 0 ID=cds807;Parent=gene859;Name=YP_002344309.1;Dbxref=InterPro:IPR003782 InterPro:IPR012335 UniProtKB FTrEMBL:Q0P9Y8 Genbank:YP_002344309.1 GeneID:905211;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0911 2C probable periplasmic protein 2C len: 186 aa 3B similar to bacterial hypotheticals e.g. TR:O67113 28EMBL:AE000717 29 Aquifex aeolicus AQ_988 28197 aa 29 2C fasta scores 3B opt: 260 z-score: 314.1 E 28 29: 3.4e-10 2C 28.1 25 identity in 167 aa overlap 2C and to N-terminus of eukaryotic proteins e.g. SCO1_YEAST SCO1 protein precursor 28295 aa 29 2C opt: 213 z-score: 257.2 E 28 29: 5e-07 2C 32.1 25 identity in 137 aa overlap. No Hp match. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF02630 SCO1 2FSenC identified within CDS. Characterization has been carried out in Rhodobacter capsulatus 2C however 2C identity scores was unnacceptable. kept in product function. Functional classification - Miscellaneous periplasmic proteins 7EPMID:7592491 NC_002163.1 RefSeq gene 847843 848403 . + . ID=gene859;Name=Cj0911;locus_tag=Cj0911;Dbxref=GeneID:905211;gbkey=Gene NC_002163.1 RefSeq region 847855 847908 . + . ID=id1689;Name=id1689;Dbxref=GeneID:905211;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0911 by TMHMM2.0 at aa 5-22 NC_002163.1 RefSeq region 847858 848352 . + . ID=id1690;Name=id1690;Dbxref=GeneID:905211;gbkey=misc_feature;Note=HMMPfam hit to PF02630 2C SCO1 2FSenC 2C score 2.3e-09 ### NC_002163.1 RefSeq CDS 848410 849309 . - 0 ID=cds808;Parent=gene860;gene=cysM;Name=YP_002344310.1;Dbxref=GOA:P71128 HSSP:Q9WZD3 InterPro:IPR001216 InterPro:IPR001926 InterPro:IPR005856 InterPro:IPR005859 UniProtKB FSwiss-Prot:P71128 Genbank:YP_002344310.1 GeneID:906009;gbkey=CDS;product=cysteine synthase;Note=Original 282000 29 note: Cj0912c 2C cysM 2C cysteine synthase 2C len: 299 aa 3B 98.7 25 identical to CYSM_CAMJE cysteine synthase B 28EC 4.2.99.8 29 28299 aa 29 2C and similar to many e.g. CYSK_BACSU CYSTEINE SYNTHASE 28EC 4.2.99.8 29 28307 aa 29 2C fasta scores 3B opt: 907 z-score: 1020.2 E 28 29: 0 2C 48.5 25 identity in 305 aa overlap. 38.9 25 identity to HP0107. Contains PS00165 Serine 2Fthreonine dehydratases pyridoxal-phosphate attachment site 2C PS00901 Cysteine synthase 2Fcystathionine beta-synthase P-phosphate attachment site 2C and Pfam match to entry PF00291 S_T_dehydratase 2C Pyridoxal-phosphate dependant enzymes 7EUpdated 282006 29 note: Characterised in Campylobacter jejuni 2C so not added to product function. Functional classification - Amino acid biosynthesis -Serine family 7EPMID:9034314 NC_002163.1 RefSeq gene 848410 849309 . - . ID=gene860;gene=cysM;Name=cysM;locus_tag=Cj0912c;Dbxref=GeneID:906009;gbkey=Gene NC_002163.1 RefSeq region 848446 849291 . - . ID=id1691;gene=cysM;Name=id1691;Dbxref=GeneID:906009;gbkey=misc_feature;Note=HMMPfam hit to PF00291 2C Pyridoxal-phosphate dependent enzyme 2C score 2.3e-116 NC_002163.1 RefSeq region 849169 849225 . - . ID=id1692;gene=cysM;Name=id1692;Dbxref=GeneID:906009;gbkey=misc_feature;Note=PS00901 Cysteine synthase 2Fcystathionine beta-synthase P-phosphate attachment site NC_002163.1 RefSeq region 849178 849219 . - . ID=id1693;gene=cysM;Name=id1693;Dbxref=GeneID:906009;gbkey=misc_feature;Note=PS00165 Serine 2Fthreonine dehydratases pyridoxal-phosphate attachment site ### NC_002163.1 RefSeq gene 849436 849732 . - . ID=gene861;gene=hupB;Name=hupB;locus_tag=Cj0913c;Dbxref=GeneID:905212;gbkey=Gene NC_002163.1 RefSeq CDS 849436 849732 . - 0 ID=cds809;Parent=gene861;gene=hupB;Name=YP_002344311.1;Dbxref=GOA:Q46121 HSSP:P36206 InterPro:IPR000119 UniProtKB FSwiss-Prot:Q46121 Genbank:YP_002344311.1 GeneID:905212;gbkey=CDS;product=DNA-binding protein HU;Note=Original 282000 29 note: Cj0913c 2C hupB 2C DNA-binding protein HU homolog 2C len: 98 aa 3B identical to TR:Q46121 28EMBL:L25627 29 DNA-binding protein HU homolog 2898 aa 29 2C and highly similar to many e.g. DBHB_ECOLI DNA-binding protein HU-beta 2890 aa 29 2C fasta scores 3B opt: 272 z-score: 356.7 E 28 29: 1.4e-12 2C 44.9 25 identity in 89 aa overlap. 42.2 25 identity to HP0835. Contains Pfam match to entry PF00216 Bac_DNA_binding 2C Bacterial DNA-binding protein 7EUpdated 282006 29 note: Characterised in Campylobacter jejuni and many others. not added to product function. Functional classification - Synthesis and modification of macromolecules - Nucleoproteins 7EPMID:8063109 NC_002163.1 RefSeq region 849463 849732 . - . ID=id1694;gene=hupB;Name=id1694;Dbxref=GeneID:905212;gbkey=misc_feature;Note=HMMPfam hit to PF00216 2C Bacterial DNA-binding protein 2C score 1.9e-42 ### NC_002163.1 UTR_Extractor 5'-UTR 849733 849758 . - . ID=utr322;locus_tag=Cj0913c;product=DNA-binding protein HU NC_002163.1 RefSeq gene 849834 851666 . - . ID=gene862;gene=ciaB;Name=ciaB;locus_tag=Cj0914c;Dbxref=GeneID:905214;gbkey=Gene NC_002163.1 RefSeq CDS 849834 851666 . - 0 ID=cds810;Parent=gene862;gene=ciaB;Name=YP_002344312.1;Dbxref=InterPro:IPR006025 UniProtKB FTrEMBL:Q0P9Y5 Genbank:YP_002344312.1 GeneID:905214;gbkey=CDS;product=invasion antigen CiaB;Note=Original 282000 29 note: Cj0914c 2C ciaB 2C unknown function 2C len: 610 aa 3B no Hp match. Product is translocated into host cells. Mutants fail to translocate 2Cand fail to translocate other proteins. Contains PS00142 Neutral zinc metallopeptidases 2C zinc-binding region signature 7EUpdated 282006 29 note: Papers attached giving further information regarding this CDS. Functional classification - Pathogenicity 7EPMID:10361274 2C PMID:10540297 2C PMID:10659361 2CPMID:15722140 NC_002163.1 RefSeq region 850365 850394 . - . ID=id1695;gene=ciaB;Name=id1695;Dbxref=GeneID:905214;gbkey=misc_feature;Note=PS00142 Neutral zinc metallopeptidases 2Czinc-binding region signature ### NC_002163.1 UTR_Extractor 5'-UTR 851667 851688 . - . ID=utr323;locus_tag=Cj0914c;product=CiaB protein NC_002163.1 UTR_Extractor 5'-UTR 851706 851727 . + . ID=utr324;locus_tag=Cj0915;product=putative hydrolase NC_002163.1 RefSeq gene 851728 852141 . + . ID=gene863;Name=Cj0915;locus_tag=Cj0915;Dbxref=GeneID:905254;gbkey=Gene NC_002163.1 RefSeq CDS 851728 852141 . + 0 ID=cds811;Parent=gene863;Name=YP_002344313.1;Dbxref=GOA:Q0P9Y4 InterPro:IPR006683 UniProtKB FTrEMBL:Q0P9Y4 Genbank:YP_002344313.1 GeneID:905254;gbkey=CDS;product=hydrolase;Note=Original 282000 29 note: Cj0915 2C possible hydrolase 2Clen: 137 aa 3B similar to prokaryotic hypotheticals e.g. YCIA_ECOLI 28132 aa 29 2C fasta scores 3B opt: 351 z-score: 440.7 E 28 29: 3e-17 2C 41.5 25 identity in 123 aa overlap 2C and to eukaryotic acyl-CoA hydrolases e.g. THCC_HUMAN cytosolic acyl coenzyme A thioester hydrolase 28372 aa 29 2C fasta scores 3B opt: 174 z-score: 220.2 E 28 29: 5.7e-05 2C 31.6 25 identity in 114 aa overlap. 25.4 25 identity to HP0891 28VDLD_HELPY 29 7EUpdated 282006 29 note: Pfam domain PF03061 Thioesterase superfamily identified within CDS. No specific characterisation with acceptable identity score has been carried out yet. kept within product function. Functional classification - Misc 7EPMID:12426338 NC_002163.1 RefSeq region 851788 852021 . + . ID=id1696;Name=id1696;Dbxref=GeneID:905254;gbkey=misc_feature;Note=HMMPfam hit to PF03061 2C Thioesterase superfamily 2Cscore 7.8e-17 ### NC_002163.1 RefSeq CDS 852181 852378 . - 0 ID=cds812;Parent=gene864;Name=YP_002344314.1;Dbxref=InterPro:IPR007423 UniProtKB FTrEMBL:Q0P9Y3 Genbank:YP_002344314.1 GeneID:905180;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0916c 2C unknown 2C len: 65 aa 3B similar to two hypothetical E. coli proteins 3B YBDD_ECOLI 2865 aa 29 2C fasta scores 3B opt: 154 z-score: 227.0 E 28 29: 2.5e-05 2C 41.3 25 identity in 46 aa overlap 2C and YJIX_ECOLI 2867 aa 29 2C fasta scores 3B opt: 141 z-score: 209.5 E 28 29: 0.00023 2C 35.8 25 identity in 67 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF04328 Protein of unknown function 28DUF466 29 identified within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 852181 852378 . - . ID=gene864;Name=Cj0916c;locus_tag=Cj0916c;Dbxref=GeneID:905180;gbkey=Gene NC_002163.1 RefSeq region 852184 852378 . - . ID=id1697;Name=id1697;Dbxref=GeneID:905180;gbkey=misc_feature;Note=HMMPfam hit to PF04328 2C Protein of unknown function 28DUF466 29 2C score 1.2e-39 NC_002163.1 RefSeq gene 852359 854470 . - . ID=gene865;gene=cstA;Name=cstA;locus_tag=Cj0917c;Dbxref=GeneID:905216;gbkey=Gene NC_002163.1 RefSeq CDS 852359 854470 . - 0 ID=cds813;Parent=gene865;gene=cstA;Name=YP_002344315.1;Dbxref=GOA:Q0P9Y2 InterPro:IPR003706 UniProtKB FTrEMBL:Q0P9Y2 Genbank:YP_002344315.1 GeneID:905216;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0917c 2C cstA 2C integral membrane protein 2C homolog of carbon starvation protein A 2Clen: 703 aa 3B highly similar to e.g. CSTA_ECOLI carbon starvation protein A 28701 aa 29 2C fasta scores 3B opt: 2523 z-score: 2823.2 E 28 29: 0 2C 56.0 25 identity in 707 aa overlap. 65.6 25 identity to HP1168 7EUpdated 282006 29 note: Pfam domain PF02554 Carbon starvation protein CstA identified within CDS. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Membranes 2C lipoproteins and porins 7EPMID:1848300 NC_002163.1 RefSeq region 852422 852490 . - . ID=id64;gene=cstA;Name=id64;Dbxref=GeneID:905216;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0917c by TMHMM2.0 at aa 7-26 2C 36-58 2C 87-109 2C 119-138 2C159-181 2C 191-213 2C 218-240 2C 255-277 2C 284-306 2C 321-343 2C364-386 2C 465-487 2C 508-530 2C 540-562 2C 575-594 and 661-683 NC_002163.1 RefSeq region 852440 852472 . - . ID=id1698;gene=cstA;Name=id1698;Dbxref=GeneID:905216;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 852689 852748 . - . ID=id64;gene=cstA;Name=id64;Dbxref=GeneID:905216;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0917c by TMHMM2.0 at aa 7-26 2C 36-58 2C 87-109 2C 119-138 2C159-181 2C 191-213 2C 218-240 2C 255-277 2C 284-306 2C 321-343 2C364-386 2C 465-487 2C 508-530 2C 540-562 2C 575-594 and 661-683 NC_002163.1 RefSeq region 852785 852853 . - . ID=id64;gene=cstA;Name=id64;Dbxref=GeneID:905216;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0917c by TMHMM2.0 at aa 7-26 2C 36-58 2C 87-109 2C 119-138 2C159-181 2C 191-213 2C 218-240 2C 255-277 2C 284-306 2C 321-343 2C364-386 2C 465-487 2C 508-530 2C 540-562 2C 575-594 and 661-683 NC_002163.1 RefSeq region 852881 852949 . - . ID=id64;gene=cstA;Name=id64;Dbxref=GeneID:905216;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0917c by TMHMM2.0 at aa 7-26 2C 36-58 2C 87-109 2C 119-138 2C159-181 2C 191-213 2C 218-240 2C 255-277 2C 284-306 2C 321-343 2C364-386 2C 465-487 2C 508-530 2C 540-562 2C 575-594 and 661-683 NC_002163.1 RefSeq region 853010 853078 . - . ID=id64;gene=cstA;Name=id64;Dbxref=GeneID:905216;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0917c by TMHMM2.0 at aa 7-26 2C 36-58 2C 87-109 2C 119-138 2C159-181 2C 191-213 2C 218-240 2C 255-277 2C 284-306 2C 321-343 2C364-386 2C 465-487 2C 508-530 2C 540-562 2C 575-594 and 661-683 NC_002163.1 RefSeq region 853175 854377 . - . ID=id1699;gene=cstA;Name=id1699;Dbxref=GeneID:905216;gbkey=misc_feature;Note=HMMPfam hit to PF02554 2C Carbon starvation protein CstA 2C score 3.2e-248 NC_002163.1 RefSeq region 853313 853381 . - . ID=id64;gene=cstA;Name=id64;Dbxref=GeneID:905216;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0917c by TMHMM2.0 at aa 7-26 2C 36-58 2C 87-109 2C 119-138 2C159-181 2C 191-213 2C 218-240 2C 255-277 2C 284-306 2C 321-343 2C364-386 2C 465-487 2C 508-530 2C 540-562 2C 575-594 and 661-683 NC_002163.1 RefSeq region 853319 853351 . - . ID=id1700;gene=cstA;Name=id1700;Dbxref=GeneID:905216;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 853442 853510 . - . ID=id64;gene=cstA;Name=id64;Dbxref=GeneID:905216;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0917c by TMHMM2.0 at aa 7-26 2C 36-58 2C 87-109 2C 119-138 2C159-181 2C 191-213 2C 218-240 2C 255-277 2C 284-306 2C 321-343 2C364-386 2C 465-487 2C 508-530 2C 540-562 2C 575-594 and 661-683 NC_002163.1 RefSeq region 853463 853495 . - . ID=id1701;gene=cstA;Name=id1701;Dbxref=GeneID:905216;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 853553 853621 . - . ID=id64;gene=cstA;Name=id64;Dbxref=GeneID:905216;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0917c by TMHMM2.0 at aa 7-26 2C 36-58 2C 87-109 2C 119-138 2C159-181 2C 191-213 2C 218-240 2C 255-277 2C 284-306 2C 321-343 2C364-386 2C 465-487 2C 508-530 2C 540-562 2C 575-594 and 661-683 NC_002163.1 RefSeq region 853640 853708 . - . ID=id64;gene=cstA;Name=id64;Dbxref=GeneID:905216;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0917c by TMHMM2.0 at aa 7-26 2C 36-58 2C 87-109 2C 119-138 2C159-181 2C 191-213 2C 218-240 2C 255-277 2C 284-306 2C 321-343 2C364-386 2C 465-487 2C 508-530 2C 540-562 2C 575-594 and 661-683 NC_002163.1 RefSeq region 853751 853819 . - . ID=id64;gene=cstA;Name=id64;Dbxref=GeneID:905216;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0917c by TMHMM2.0 at aa 7-26 2C 36-58 2C 87-109 2C 119-138 2C159-181 2C 191-213 2C 218-240 2C 255-277 2C 284-306 2C 321-343 2C364-386 2C 465-487 2C 508-530 2C 540-562 2C 575-594 and 661-683 NC_002163.1 RefSeq region 853832 853900 . - . ID=id64;gene=cstA;Name=id64;Dbxref=GeneID:905216;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0917c by TMHMM2.0 at aa 7-26 2C 36-58 2C 87-109 2C 119-138 2C159-181 2C 191-213 2C 218-240 2C 255-277 2C 284-306 2C 321-343 2C364-386 2C 465-487 2C 508-530 2C 540-562 2C 575-594 and 661-683 NC_002163.1 RefSeq region 853928 853996 . - . ID=id64;gene=cstA;Name=id64;Dbxref=GeneID:905216;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0917c by TMHMM2.0 at aa 7-26 2C 36-58 2C 87-109 2C 119-138 2C159-181 2C 191-213 2C 218-240 2C 255-277 2C 284-306 2C 321-343 2C364-386 2C 465-487 2C 508-530 2C 540-562 2C 575-594 and 661-683 NC_002163.1 RefSeq region 854057 854116 . - . ID=id64;gene=cstA;Name=id64;Dbxref=GeneID:905216;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0917c by TMHMM2.0 at aa 7-26 2C 36-58 2C 87-109 2C 119-138 2C159-181 2C 191-213 2C 218-240 2C 255-277 2C 284-306 2C 321-343 2C364-386 2C 465-487 2C 508-530 2C 540-562 2C 575-594 and 661-683 NC_002163.1 RefSeq region 854144 854212 . - . ID=id64;gene=cstA;Name=id64;Dbxref=GeneID:905216;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0917c by TMHMM2.0 at aa 7-26 2C 36-58 2C 87-109 2C 119-138 2C159-181 2C 191-213 2C 218-240 2C 255-277 2C 284-306 2C 321-343 2C364-386 2C 465-487 2C 508-530 2C 540-562 2C 575-594 and 661-683 NC_002163.1 RefSeq region 854297 854365 . - . ID=id64;gene=cstA;Name=id64;Dbxref=GeneID:905216;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0917c by TMHMM2.0 at aa 7-26 2C 36-58 2C 87-109 2C 119-138 2C159-181 2C 191-213 2C 218-240 2C 255-277 2C 284-306 2C 321-343 2C364-386 2C 465-487 2C 508-530 2C 540-562 2C 575-594 and 661-683 NC_002163.1 RefSeq region 854393 854452 . - . ID=id64;gene=cstA;Name=id64;Dbxref=GeneID:905216;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj0917c by TMHMM2.0 at aa 7-26 2C 36-58 2C 87-109 2C 119-138 2C159-181 2C 191-213 2C 218-240 2C 255-277 2C 284-306 2C 321-343 2C364-386 2C 465-487 2C 508-530 2C 540-562 2C 575-594 and 661-683 ### NC_002163.1 RefSeq CDS 854637 855566 . - 0 ID=cds814;Parent=gene866;gene=prsA;Name=YP_002344316.1;Dbxref=GOA:Q9PP15 HSSP:P14193 InterPro:IPR000836 InterPro:IPR000842 InterPro:IPR005946 UniProtKB FSwiss-Prot:Q9PP15 Genbank:YP_002344316.1 GeneID:905217;gbkey=CDS;product=ribose-phosphate pyrophosphokinase;Note=catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP NC_002163.1 RefSeq gene 854637 855566 . - . ID=gene866;gene=prsA;Name=prsA;locus_tag=Cj0918c;Dbxref=GeneID:905217;gbkey=Gene NC_002163.1 RefSeq region 854760 855152 . - . ID=id1702;gene=prsA;Name=id1702;Dbxref=GeneID:905217;gbkey=misc_feature;Note=HMMPfam hit to PF00156 2C Phosphoribosyl transferase domain 2C score 2.6e-35 NC_002163.1 RefSeq region 854889 854927 . - . ID=id1703;gene=prsA;Name=id1703;Dbxref=GeneID:905217;gbkey=misc_feature;Note=PS00103 Purine 2Fpyrimidine phosphoribosyl transferases signature NC_002163.1 RefSeq region 855138 855185 . - . ID=id1704;gene=prsA;Name=id1704;Dbxref=GeneID:905217;gbkey=misc_feature;Note=PS00114 Phosphoribosyl pyrophosphate synthetase signature NC_002163.1 RefSeq region 855186 855215 . - . ID=id1705;gene=prsA;Name=id1705;Dbxref=GeneID:905217;gbkey=misc_feature;Note=PS00339 Aminoacyl-transfer RNA synthetases class-II signature 2 ### NC_002163.1 UTR_Extractor 5'-UTR 855567 855599 . - . ID=utr325;locus_tag=Cj0918c;product=ribose-phosphate pyrophosphokinase NC_002163.1 RefSeq CDS 855674 856333 . - 0 ID=cds815;Parent=gene867;Name=YP_002344317.1;Dbxref=GOA:Q0P9Y0 InterPro:IPR000515 InterPro:IPR010065 UniProtKB FTrEMBL:Q0P9Y0 Genbank:YP_002344317.1 GeneID:904985;gbkey=CDS;product=amino acid ABC transporter permease;Note=Original 282000 29 note: Cj0919c 2C probable ABC-type amino-acid transporter permease 2C len: 219 aa 3B similar to many e.g. GLTK_ECOLI glutamate 2Faspartate transport system permease 28224 aa 29 2C fasta scores 3B opt: 380 z-score: 457.9 E 28 29: 3.3e-18 2C 32.6 25 identity in 221 aa overlap. No Hp ortholog. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp sign. 2C and Pfam match to entry PF00528 BPD_transp 2CBinding-protein-dependent transport systems inner membrane component 7EUpdated 282006 29 note: Three probable transmembrane helices predicted by TMHMM2.0. No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification - Transport 2Fbinding proteins - Amino acids and amines 7EPMID:16689801 NC_002163.1 RefSeq gene 855674 856333 . - . ID=gene867;Name=Cj0919c;locus_tag=Cj0919c;Dbxref=GeneID:904985;gbkey=Gene NC_002163.1 RefSeq region 855683 856297 . - . ID=id1706;Name=id1706;Dbxref=GeneID:904985;gbkey=misc_feature;Note=HMMPfam hit to PF00528 2C Binding-protein-dependent transport syst 2C score 7.4e-18 NC_002163.1 RefSeq region 855710 855778 . - . ID=id65;Name=id65;Dbxref=GeneID:904985;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0919c by TMHMM2.0 at aa 23-45 2C 66-88 and 186-208 NC_002163.1 RefSeq region 855923 856009 . - . ID=id1707;Name=id1707;Dbxref=GeneID:904985;gbkey=misc_feature;Note=PS00402 Binding-protein-dependent transport systems inner membrane comp. sign NC_002163.1 RefSeq region 856070 856138 . - . ID=id65;Name=id65;Dbxref=GeneID:904985;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0919c by TMHMM2.0 at aa 23-45 2C 66-88 and 186-208 NC_002163.1 RefSeq region 856115 856147 . - . ID=id1708;Name=id1708;Dbxref=GeneID:904985;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 856199 856267 . - . ID=id65;Name=id65;Dbxref=GeneID:904985;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0919c by TMHMM2.0 at aa 23-45 2C 66-88 and 186-208 ### NC_002163.1 RefSeq CDS 856344 857096 . - 0 ID=cds816;Parent=gene868;Name=YP_002344318.1;Dbxref=GOA:Q0P9X9 InterPro:IPR000515 InterPro:IPR010065 UniProtKB FTrEMBL:Q0P9X9 Genbank:YP_002344318.1 GeneID:905218;gbkey=CDS;product=amino acid ABC transporter permease;Note=Original 282000 29 note: Cj0920c 2C probable ABC-type amino-acid transporter permease 2C len: 250 aa 3B similar to many e.g. YCKA_BACSU probable amino-acid ABC transporter permease 28226 aa 29 2C fasta scores 3B opt: 448 z-score: 560.9 E 28 29: 6e-24 2C 32.0 25 identity in 219 aa overlap. No Hp ortholog. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp sign. 2C and Pfam match to entry PF00528 BPD_transp 2CBinding-protein-dependent transport systems inner membrane component 7EUpdated 282006 29 note: Three probable transmembrane helices predicted by TMHMM2.0. No specific characterisation has been carried out yet. kept within product function. Functional classification -Transport 2Fbinding proteins - Amino acids and amines 7EPMID:16689801 NC_002163.1 RefSeq gene 856344 857096 . - . ID=gene868;Name=Cj0920c;locus_tag=Cj0920c;Dbxref=GeneID:905218;gbkey=Gene NC_002163.1 RefSeq region 856362 856967 . - . ID=id1709;Name=id1709;Dbxref=GeneID:905218;gbkey=misc_feature;Note=HMMPfam hit to PF00528 2C Binding-protein-dependent transport syst 2C score 1.2e-24 NC_002163.1 RefSeq region 856389 856457 . - . ID=id66;Name=id66;Dbxref=GeneID:905218;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0920c by TMHMM2.0 at aa 47-69 2C 90-112 and 214-236 NC_002163.1 RefSeq region 856593 856679 . - . ID=id1710;Name=id1710;Dbxref=GeneID:905218;gbkey=misc_feature;Note=PS00402 Binding-protein-dependent transport systems inner membrane comp. sign NC_002163.1 RefSeq region 856761 856829 . - . ID=id66;Name=id66;Dbxref=GeneID:905218;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0920c by TMHMM2.0 at aa 47-69 2C 90-112 and 214-236 NC_002163.1 RefSeq region 856890 856958 . - . ID=id66;Name=id66;Dbxref=GeneID:905218;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0920c by TMHMM2.0 at aa 47-69 2C 90-112 and 214-236 ### NC_002163.1 RefSeq CDS 857098 857877 . - 0 ID=cds817;Parent=gene869;gene=peb1A;Name=YP_002344319.1;Dbxref=GOA:Q0P9X8 InterPro:IPR001638 InterPro:IPR015683 PDB:2V25 UniProtKB FSwiss-Prot:Q0P9X8 Genbank:YP_002344319.1 GeneID:906008;gbkey=CDS;product=bifunctional adhesin 2FABC transporter aspartate 2Fglutamate-binding protein;Note=PEB1 NC_002163.1 RefSeq gene 857098 857877 . - . ID=gene869;gene=peb1A;Name=peb1A;locus_tag=Cj0921c;Dbxref=GeneID:906008;gbkey=Gene NC_002163.1 RefSeq region 857101 857760 . - . ID=id1711;gene=peb1A;Name=id1711;Dbxref=GeneID:906008;gbkey=misc_feature;Note=HMMPfam hit to PF00497 2C Bacterial extracellular solute-binding prot 2C score 5.3e-41 NC_002163.1 RefSeq region 857650 857691 . - . ID=id1712;gene=peb1A;Name=id1712;Dbxref=GeneID:906008;gbkey=misc_feature;Note=PS01039 Bacterial extracellular solute-binding proteins 2C family 3 signature ### NC_002163.1 RefSeq CDS 857899 858627 . - 0 ID=cds818;Parent=gene870;gene=pebC;Name=YP_002344320.1;Dbxref=GOA:Q0P9X7 HSSP:P02915 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FSwiss-Prot:Q0P9X7 Genbank:YP_002344320.1 GeneID:905220;gbkey=CDS;product=amino acid ABC transporter ATP-binding protein;Note=Original 282000 29 note: Cj0922c 2C pebC 2C probable ABC-type amino-acid transporter ATP-binding protein 2C len: 242 aa 3B 98.8 25 identical to PEBC_CAMJE 2C and similar to many e.g. GLNQ_BACST glutamine transport ATP-binding protein 28242 aa 29 2C fasta scores 3B opt: 1013 z-score: 1161.8 E 28 29: 0 2C64.6 25 identity in 243 aa overlap. No Hp ortholog. Contains PS00211 ABC transporters family signature 2C PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C and Pfam match to entry PF00005 ABC_tran 2C ABC transporters 7EUpdated 282006 29 note: Characterised within Campylobacter jejuni. not added to product function. Functional classification - Transport 2Fbinding proteins - Amino acids and amines 7EPMID:16689801 NC_002163.1 RefSeq gene 857899 858627 . - . ID=gene870;gene=pebC;Name=pebC;locus_tag=Cj0922c;Dbxref=GeneID:905220;gbkey=Gene NC_002163.1 RefSeq region 857992 858549 . - . ID=id1713;gene=pebC;Name=id1713;Dbxref=GeneID:905220;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 1.3e-64 NC_002163.1 RefSeq region 858178 858222 . - . ID=id1714;gene=pebC;Name=id1714;Dbxref=GeneID:905220;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq region 858505 858528 . - . ID=id1715;gene=pebC;Name=id1715;Dbxref=GeneID:905220;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 UTR_Extractor 5'-UTR 858628 858665 . - . ID=utr326;locus_tag=Cj0922c;product=amino-acid ABC transporter ATP-binding protein NC_002163.1 RefSeq CDS 858763 859551 . - 0 ID=cds819;Parent=gene871;gene=cheR;Name=YP_002344321.1;Dbxref=GOA:Q0P9X6 InterPro:IPR000780 UniProtKB FSwiss-Prot:Q0P9X6 Genbank:YP_002344321.1 GeneID:905222;gbkey=CDS;product=MCP protein methyltransferase;Note=Original 282000 29 note: Cj0923c 2C cheR 2C probable MCP protein methyltransferase 2C len: 262 aa 3B identical to YPEB_CAMJE 2C and similar to e.g. CHER_BACSU chemotaxis protein methyltransferase 28EC 2.1.1.80 29 28256 aa 29 2C fasta scores 3B opt: 357 z-score: 432.6 E 28 29: 8.5e-17 2C 31.6 25 identity in 231 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domains PF01739 CheR methyltransferase 2C SAM binding domain and PF03705 CheR methyltransferase 2C all-alpha domain were identified within CDS. Further support given to product function. Characterised in more than one genus 2C however 2C identity scores were marginal. kept within product function. Functional classification - Chemotaxis and mobility 7EPMID:8244966 2C PMID:8360165 2C PMID:3510184 2CPMID:11669626 NC_002163.1 RefSeq gene 858763 859551 . - . ID=gene871;gene=cheR;Name=cheR;locus_tag=Cj0923c;Dbxref=GeneID:905222;gbkey=Gene NC_002163.1 RefSeq region 858778 859332 . - . ID=id1716;gene=cheR;Name=id1716;Dbxref=GeneID:905222;gbkey=misc_feature;Note=HMMPfam hit to PF01739 2C CheR methyltransferase 2C SAM binding domain 2C score 5.3e-73 NC_002163.1 RefSeq region 859363 859530 . - . ID=id1717;gene=cheR;Name=id1717;Dbxref=GeneID:905222;gbkey=misc_feature;Note=HMMPfam hit to PF03705 2C CheR methyltransferase 2Call-alpha domain 2C score 3e-12 ### NC_002163.1 RefSeq gene 859567 860121 . - . ID=gene872;gene=cheB';Name=cheB';locus_tag=Cj0924c;Dbxref=GeneID:904926;gbkey=Gene NC_002163.1 RefSeq CDS 859567 860121 . - 0 ID=cds820;Parent=gene872;gene=cheB';Name=YP_002344322.1;Dbxref=GOA:Q0P9X5 InterPro:IPR000673 UniProtKB FTrEMBL:Q0P9X5 Genbank:YP_002344322.1 GeneID:904926;gbkey=CDS;product=MCP protein-glutamate methylesterase;Note=Original 282000 29 note: Cj0924c 2C cheB 27 probable MCP protein-glutamate methylesterase 2C len: 184 aa 3B similar to the methylesterase domain of e.g. CHEB_ECOLI protein-glutamate methylesterase 28EC 3.1.1.61 29 28349 aa 29 2Cfasta scores 3B opt: 339 z-score: 430.2 E 28 29: 1.1e-16 2C 34.4 25 identity in 183 aa overlap. Note that the 27response reciever domain 27 normally found in cheB is not present. No Hp match 7EUpdated 282006 29 note: Characterised within Escherichia coli 2C however 2C identity scores were marginal. Possible truncated protein as missing receiver domain of CheB protein. kept within product function. Functional classification - Chemotaxis and mobility 7EPMID:3280143 2C PMID:3510184 2C PMID:2188960 2CPMID:8244966 NC_002163.1 RefSeq region 859582 860115 . - . ID=id1718;gene=cheB';Name=id1718;Dbxref=GeneID:904926;gbkey=misc_feature;Note=HMMPfam hit to PF01339 2C CheB methylesterase 2C score 7.1e-18 ### NC_002163.1 UTR_Extractor 5'-UTR 860122 860162 . - . ID=utr327;locus_tag=Cj0924c;product=putative MCP protein-glutamate methylesterase NC_002163.1 UTR_Extractor 5'-UTR 860252 860286 . + . ID=utr328;locus_tag=Cj0925;product=ribose 5-phosphate isomerase NC_002163.1 RefSeq CDS 860287 860724 . + 0 ID=cds821;Parent=gene873;gene=rpiB;Name=YP_002344323.1;Dbxref=GOA:Q0P9X4 InterPro:IPR000276 InterPro:IPR003500 InterPro:IPR004785 UniProtKB FTrEMBL:Q0P9X4 Genbank:YP_002344323.1 GeneID:905223;gbkey=CDS;product=ribose 5-phosphate isomerase;Note=Original 282000 29 note: Cj0925 2C rpiB 2C probable ribose 5-phosphate isomerase 2C len: 145 aa 3B highly similar to e.g. RPIB_ECOLI ribose 5-phosphate isomerase B 28EC 5.3.1.6 29 28149 aa 29 2C fasta scores 3B opt: 399 z-score: 505.9 E 28 29: 7e-21 2C 45.0 25 identity in 140 aa overlap. 45.0 25 identity to HP0574 2C misannotated as galactosidase acetyltransferase 28lacA 29 7EUpdated 282006 29 note: Prosite domain PS00237 G_PROTEIN_RECEP_F1_1 2C Rhodopsin-like GPCR superfamily and Pfam domain PF02502 Ribose 2FGalactose Isomerase were identified within CDS. Further support given to product function. Characterised in Escherichia coli with acceptable identity score. removed from product funtion. Functional classification - Energy metabolism -Pentose phosphate pathway - Non-oxidative branch 7EPMID:8576032 2CPMID:14499611 NC_002163.1 RefSeq gene 860287 860724 . + . ID=gene873;gene=rpiB;Name=rpiB;locus_tag=Cj0925;Dbxref=GeneID:905223;gbkey=Gene NC_002163.1 RefSeq region 860470 860712 . + . ID=id1719;gene=rpiB;Name=id1719;Dbxref=GeneID:905223;gbkey=misc_feature;Note=HMMPfam hit to PF02502 2C Ribose 2FGalactose Isomerase 2Cscore 2.4e-46 NC_002163.1 RefSeq region 860482 860532 . + . ID=id1720;gene=rpiB;Name=id1720;Dbxref=GeneID:905223;gbkey=misc_feature;Note=PS00237 G-protein coupled receptors signature NC_002163.1 RefSeq region 860536 860553 . + . ID=id1721;gene=rpiB;Name=id1721;Dbxref=GeneID:905223;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature NC_002163.1 RefSeq gene 860724 861056 . + . ID=gene874;gene=Cj0926;Name=Cj0926;locus_tag=Cj0926;Dbxref=GeneID:905225;gbkey=Gene NC_002163.1 RefSeq CDS 860724 861056 . + 0 ID=cds822;Parent=gene874;Name=YP_002344324.1;Dbxref=GOA:Q0P9X3 UniProtKB FTrEMBL:Q0P9X3 Genbank:YP_002344324.1 GeneID:905225;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0926 2C possible membrane protein 2C len: 110 aa 3B 50.0 25 identity to HP0573. Contains possible transmembrane domain at N-terminus 7EUpdated 282006 29 note: One probable transmembrane helix predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 860736 860795 . + . ID=id1722;Name=id1722;Dbxref=GeneID:905225;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0926 by TMHMM2.0 at aa 5-24 NC_002163.1 RefSeq gene 861053 861601 . + . ID=gene875;gene=apt;Name=apt;locus_tag=Cj0927;Dbxref=GeneID:905205;gbkey=Gene NC_002163.1 RefSeq CDS 861053 861601 . + 0 ID=cds823;Parent=gene875;gene=apt;Name=YP_002344325.1;Dbxref=GOA:Q9PP06 HSSP:P49435 InterPro:IPR000836 InterPro:IPR002375 InterPro:IPR005764 UniProtKB FSwiss-Prot:Q9PP06 Genbank:YP_002344325.1 GeneID:905205;gbkey=CDS;product=adenine phosphoribosyltransferase;Note=catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis NC_002163.1 RefSeq region 861143 861559 . + . ID=id1723;gene=apt;Name=id1723;Dbxref=GeneID:905205;gbkey=misc_feature;Note=HMMPfam hit to PF00156 2C Phosphoribosyl transferase domain 2C score 1.6e-41 NC_002163.1 RefSeq region 861251 861274 . + . ID=id1724;gene=apt;Name=id1724;Dbxref=GeneID:905205;gbkey=misc_feature;Note=PS00030 Eukaryotic RNA-binding region RNP-1 signature NC_002163.1 RefSeq region 861425 861463 . + . ID=id1725;gene=apt;Name=id1725;Dbxref=GeneID:905205;gbkey=misc_feature;Note=PS00103 Purine 2Fpyrimidine phosphoribosyl transferases signature ### NC_002163.1 RefSeq CDS 861620 862216 . + 0 ID=cds824;Parent=gene876;Name=YP_002344326.1;Dbxref=GOA:Q0P9X1 UniProtKB FTrEMBL:Q0P9X1 Genbank:YP_002344326.1 GeneID:905226;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0928 2C probable integral membrane protein 2C len: 198 aa 3B similar to members of the dedA family of hypothetical integral membrane proteins e.g. YOHD_ECOLI 28192 aa 29 2C fasta scores 3B opt: 303 z-score: 394.8 E 28 29: 1.1e-14 2C 29.1 25 identity in 172 aa overlap 2C and DEDA_ECOLI DEDA protein 28219 aa 29 2C fasta scores 3B opt: 169 z-score: 224.4 E 28 29: 3.3e-05 2C 25.3 25 identity in 162 aa overlap. 61.4 25 identity to HP0571. Contains Pfam match to entry PF00597 DedA 2C DedA family. Also similar to Cj1210 2827.1 25 identity in 177 aa overlap 29 7EUpdated 282006 29 note: Five probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 861620 862216 . + . ID=gene876;Name=Cj0928;locus_tag=Cj0928;Dbxref=GeneID:905226;gbkey=Gene NC_002163.1 RefSeq region 861662 861730 . + . ID=id1726;Name=id1726;Dbxref=GeneID:905226;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0928 by TMHMM2.0 at aa 15-37 2C 44-66 2C 86-108 2C 128-150 and 165-183 NC_002163.1 RefSeq region 861671 862114 . + . ID=id1727;Name=id1727;Dbxref=GeneID:905226;gbkey=misc_feature;Note=HMMPfam hit to PF00597 2C DedA family 2C score 2.4e-10 NC_002163.1 RefSeq region 861749 861817 . + . ID=id1726;Name=id1726;Dbxref=GeneID:905226;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0928 by TMHMM2.0 at aa 15-37 2C 44-66 2C 86-108 2C 128-150 and 165-183 NC_002163.1 RefSeq region 861875 861943 . + . ID=id1726;Name=id1726;Dbxref=GeneID:905226;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0928 by TMHMM2.0 at aa 15-37 2C 44-66 2C 86-108 2C 128-150 and 165-183 NC_002163.1 RefSeq region 862001 862069 . + . ID=id1726;Name=id1726;Dbxref=GeneID:905226;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0928 by TMHMM2.0 at aa 15-37 2C 44-66 2C 86-108 2C 128-150 and 165-183 NC_002163.1 RefSeq region 862112 862168 . + . ID=id1726;Name=id1726;Dbxref=GeneID:905226;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0928 by TMHMM2.0 at aa 15-37 2C 44-66 2C 86-108 2C 128-150 and 165-183 NC_002163.1 RefSeq CDS 862213 863664 . + 0 ID=cds825;Parent=gene877;gene=pepA;Name=YP_002344327.1;Dbxref=GOA:Q9PP04 HSSP:P11648 InterPro:IPR000819 InterPro:IPR008283 InterPro:IPR011356 UniProtKB FSwiss-Prot:Q9PP04 Genbank:YP_002344327.1 GeneID:904492;gbkey=CDS;product=leucyl aminopeptidase;Note=catalyzes the removal of N-terminal amino acids preferably leucine from various peptides NC_002163.1 RefSeq gene 862213 863664 . + . ID=gene877;gene=pepA;Name=pepA;locus_tag=Cj0929;Dbxref=GeneID:904492;gbkey=Gene NC_002163.1 RefSeq region 862666 862713 . + . ID=id1728;gene=pepA;Name=id1728;Dbxref=GeneID:904492;gbkey=misc_feature;Note=PS00038 Myc-type 2C 27helix-loop-helix 27 dimerization domain signature NC_002163.1 RefSeq region 862693 863631 . + . ID=id1729;gene=pepA;Name=id1729;Dbxref=GeneID:904492;gbkey=misc_feature;Note=HMMPfam hit to PF00883 2C Cytosol aminopeptidase family 2C catalyti 2C score 5.3e-159 NC_002163.1 RefSeq region 863182 863205 . + . ID=id1730;gene=pepA;Name=id1730;Dbxref=GeneID:904492;gbkey=misc_feature;Note=PS00631 Cytosol aminopeptidase signature NC_002163.1 UTR_Extractor 5'-UTR 863452 863660 . + . ID=utr329;locus_tag=Cj0930;product=GTP-dependent nucleic acid-binding protein EngD NC_002163.1 RefSeq CDS 863661 864764 . + 0 ID=cds826;Parent=gene878;Name=YP_002344328.1;Dbxref=GOA:Q0P9W9 InterPro:IPR002917 InterPro:IPR004396 InterPro:IPR006073 InterPro:IPR012675 InterPro:IPR013029 UniProtKB FTrEMBL:Q0P9W9 Genbank:YP_002344328.1 GeneID:904351;gbkey=CDS;product=GTP-dependent nucleic acid-binding protein EngD;Note=translation-associated GTPase 3B the crystal structure of the Haemophilus influenzae YchF protein showed similarity to the yeast structure 28PDB: 1NI3 29 3B fluorescence spectroscopy revealed nucleic acid binding 3B the yeast protein YBR025c interacts with the translation elongation factor eEF1 NC_002163.1 RefSeq gene 863661 864764 . + . ID=gene878;gene=Cj0930;Name=Cj0930;locus_tag=Cj0930;Dbxref=GeneID:904351;gbkey=Gene NC_002163.1 RefSeq region 863667 864098 . + . ID=id1731;Name=id1731;Dbxref=GeneID:904351;gbkey=misc_feature;Note=HMMPfam hit to PF01926 2C GTPase of unknown function 2Cscore 2.2e-34 NC_002163.1 RefSeq region 863685 863708 . + . ID=id1732;Name=id1732;Dbxref=GeneID:904351;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 864507 864758 . + . ID=id1733;Name=id1733;Dbxref=GeneID:904351;gbkey=misc_feature;Note=HMMPfam hit to PF06071 2C Protein of unknown function 28DUF933 29 2C score 8.1e-60 ### NC_002163.1 RefSeq CDS 864786 866168 . - 0 ID=cds827;Parent=gene879;gene=argH;Name=YP_002344329.1;Dbxref=GOA:Q46104 HSSP:P24058 InterPro:IPR000362 InterPro:IPR003031 InterPro:IPR009049 UniProtKB FSwiss-Prot:Q46104 Genbank:YP_002344329.1 GeneID:905111;gbkey=CDS;product=argininosuccinate lyase;Note=catalyzes the formation of arginine from 28N-L-arginino 29succinate NC_002163.1 RefSeq gene 864786 866168 . - . ID=gene879;gene=argH;Name=argH;locus_tag=Cj0931c;Dbxref=GeneID:905111;gbkey=Gene NC_002163.1 RefSeq region 865260 866147 . - . ID=id1734;gene=argH;Name=id1734;Dbxref=GeneID:905111;gbkey=misc_feature;Note=HMMPfam hit to PF00206 2C Lyase 2C score 5.1e-88 NC_002163.1 RefSeq region 865308 865337 . - . ID=id1735;gene=argH;Name=id1735;Dbxref=GeneID:905111;gbkey=misc_feature;Note=PS00163 Fumarate lyases signature ### NC_002163.1 RefSeq CDS 866178 867752 . - 0 ID=cds828;Parent=gene880;gene=pckA;Name=YP_002344330.1;Dbxref=GOA:Q9PP01 HSSP:P22259 InterPro:IPR001272 InterPro:IPR008210 InterPro:IPR013035 InterPro:IPR015994 UniProtKB FSwiss-Prot:Q9PP01 Genbank:YP_002344330.1 GeneID:905227;gbkey=CDS;product=phosphoenolpyruvate carboxykinase;Note=PEP carboxykinase 3B PEP carboxylase 3B PEPCK 3B catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP NC_002163.1 RefSeq gene 866178 867752 . - . ID=gene880;gene=pckA;Name=pckA;locus_tag=Cj0932c;Dbxref=GeneID:905227;gbkey=Gene NC_002163.1 RefSeq region 866322 867716 . - . ID=id1736;gene=pckA;Name=id1736;Dbxref=GeneID:905227;gbkey=misc_feature;Note=HMMPfam hit to PF01293 2C Phosphoenolpyruvate carboxykinase 2C score 1.7e-302 NC_002163.1 RefSeq region 866970 867017 . - . ID=id1737;gene=pckA;Name=id1737;Dbxref=GeneID:905227;gbkey=misc_feature;Note=PS00532 Phosphoenolpyruvate carboxykinase 28ATP 29 signature NC_002163.1 RefSeq region 867045 867068 . - . ID=id1738;gene=pckA;Name=id1738;Dbxref=GeneID:905227;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 RefSeq CDS 867765 869564 . - 0 ID=cds829;Parent=gene881;gene=pycB;Name=YP_002344331.1;Dbxref=GOA:Q0P9W6 InterPro:IPR000089 InterPro:IPR000891 InterPro:IPR001882 InterPro:IPR013785 UniProtKB FTrEMBL:Q0P9W6 Genbank:YP_002344331.1 GeneID:905229;gbkey=CDS;product=pyruvate carboxylase B subunit;Note=Original 282000 29 note: Cj0933c 2C pycB 2C possible possible pyruvate carboxylase B subunit 2C len: 599 aa 3B similar to TR:O27179 28EMBL:AE000942 29 Methanobacterium thermoautotrophicum characterised pyruvate carboxylase B 28EC 6.4.1.1 29 28568 aa 29 2C fasta scores 3B opt: 425 z-score: 482.7 E 28 29: 1.4e-19 2C 29.1 25 identity in 601 aa overlap. Also similar to other biotin-requiring decarboxlases e.g. DCOA_SALTY oxaloacetate decarboxylase alpha chain 28590 aa 29 2C fasta scores 3B opt: 515 z-score: 584.5 E 28 29: 2.9e-25 2C27.3 25 identity in 605 aa overlap 2C and C-terminus of PYC1_YEAST pyruvate carboxylase 1 281178 aa 29 2C fasta scores 3B opt: 434 z-score: 488.3 E 28 29: 6.7e-20 2C 24.2 25 identity in 631 aa overlap. No Hp match. Contains S00188 Biotin-requiring enzymes attachment site and Pfam match to entry PF00364 biotin_req_enzy 2C Biotin-requiring enzymes 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification -Central intermediary metabolism - Gluconeogenesis NC_002163.1 RefSeq gene 867765 869564 . - . ID=gene881;gene=pycB;Name=pycB;locus_tag=Cj0933c;Dbxref=GeneID:905229;gbkey=Gene NC_002163.1 RefSeq region 867774 867977 . - . ID=id1739;gene=pycB;Name=id1739;Dbxref=GeneID:905229;gbkey=misc_feature;Note=HMMPfam hit to PF00364 2C Biotin-requiring enzyme 2Cscore 2e-19 NC_002163.1 RefSeq region 867852 867905 . - . ID=id1740;gene=pycB;Name=id1740;Dbxref=GeneID:905229;gbkey=misc_feature;Note=PS00188 Biotin-requiring enzymes attachment site ### NC_002163.1 RefSeq CDS 869596 870936 . - 0 ID=cds830;Parent=gene882;Name=YP_002344332.1;Dbxref=GOA:Q0P9W5 InterPro:IPR000175 UniProtKB FTrEMBL:Q0P9W5 Genbank:YP_002344332.1 GeneID:905237;gbkey=CDS;product=sodium:amino-acid symporter family protein;Note=Original 282000 29 note: Cj0934c 2C probable transmembrane transport protein 2C len: 446 aa 3B similar to members of the sodium:neurotransmitter symporter family e.g. YD19_METJA hypothetical sodium-dependent transporter MJ1319 28492 aa 29 2C fasta scores 3B opt: 628 z-score: 711.7 E 28 29: 2.4e-32 2C 27.4 25 identity in 457 aa overlap. 42.6 25 identity to HP0498. Also similar to Cj0935c 2851.0 25 identity in 441 aa overlap 29 and Cj0601c 2828.2 25 identity in 454 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF00209 Sodium:neurotransmitter symporter family identified within CDS. Also 2C eleven probable transmembrane helices predicted by TMHMM2.0. Product function modified to more specfific family member based on motif identification. No specific characterisation has been carried out 2C so has kept within product function. Functional classification -Transport 2Fbinding proteins - Other NC_002163.1 RefSeq gene 869596 870936 . - . ID=gene882;Name=Cj0934c;locus_tag=Cj0934c;Dbxref=GeneID:905237;gbkey=Gene NC_002163.1 RefSeq region 869602 869670 . - . ID=id67;Name=id67;Dbxref=GeneID:905237;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0934c by TMHMM2.0 at aa 7-25 2C 35-57 2C 87-109 2C 133-155 2C167-189 2C 216-238 2C 251-273 2C 298-320 2C 341-363 2C 383-402 and 423-445 NC_002163.1 RefSeq region 869608 870930 . - . ID=id1741;Name=id1741;Dbxref=GeneID:905237;gbkey=misc_feature;Note=HMMPfam hit to PF00209 2C Sodium:neurotransmitter symporter family 2C score 3.5e-08 NC_002163.1 RefSeq region 869731 869790 . - . ID=id67;Name=id67;Dbxref=GeneID:905237;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0934c by TMHMM2.0 at aa 7-25 2C 35-57 2C 87-109 2C 133-155 2C167-189 2C 216-238 2C 251-273 2C 298-320 2C 341-363 2C 383-402 and 423-445 NC_002163.1 RefSeq region 869848 869916 . - . ID=id67;Name=id67;Dbxref=GeneID:905237;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0934c by TMHMM2.0 at aa 7-25 2C 35-57 2C 87-109 2C 133-155 2C167-189 2C 216-238 2C 251-273 2C 298-320 2C 341-363 2C 383-402 and 423-445 NC_002163.1 RefSeq region 869977 870045 . - . ID=id67;Name=id67;Dbxref=GeneID:905237;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0934c by TMHMM2.0 at aa 7-25 2C 35-57 2C 87-109 2C 133-155 2C167-189 2C 216-238 2C 251-273 2C 298-320 2C 341-363 2C 383-402 and 423-445 NC_002163.1 RefSeq region 870118 870186 . - . ID=id67;Name=id67;Dbxref=GeneID:905237;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0934c by TMHMM2.0 at aa 7-25 2C 35-57 2C 87-109 2C 133-155 2C167-189 2C 216-238 2C 251-273 2C 298-320 2C 341-363 2C 383-402 and 423-445 NC_002163.1 RefSeq region 870223 870291 . - . ID=id67;Name=id67;Dbxref=GeneID:905237;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0934c by TMHMM2.0 at aa 7-25 2C 35-57 2C 87-109 2C 133-155 2C167-189 2C 216-238 2C 251-273 2C 298-320 2C 341-363 2C 383-402 and 423-445 NC_002163.1 RefSeq region 870247 870279 . - . ID=id1742;Name=id1742;Dbxref=GeneID:905237;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 870370 870438 . - . ID=id67;Name=id67;Dbxref=GeneID:905237;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0934c by TMHMM2.0 at aa 7-25 2C 35-57 2C 87-109 2C 133-155 2C167-189 2C 216-238 2C 251-273 2C 298-320 2C 341-363 2C 383-402 and 423-445 NC_002163.1 RefSeq region 870472 870540 . - . ID=id67;Name=id67;Dbxref=GeneID:905237;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0934c by TMHMM2.0 at aa 7-25 2C 35-57 2C 87-109 2C 133-155 2C167-189 2C 216-238 2C 251-273 2C 298-320 2C 341-363 2C 383-402 and 423-445 NC_002163.1 RefSeq region 870610 870678 . - . ID=id67;Name=id67;Dbxref=GeneID:905237;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0934c by TMHMM2.0 at aa 7-25 2C 35-57 2C 87-109 2C 133-155 2C167-189 2C 216-238 2C 251-273 2C 298-320 2C 341-363 2C 383-402 and 423-445 NC_002163.1 RefSeq region 870766 870834 . - . ID=id67;Name=id67;Dbxref=GeneID:905237;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0934c by TMHMM2.0 at aa 7-25 2C 35-57 2C 87-109 2C 133-155 2C167-189 2C 216-238 2C 251-273 2C 298-320 2C 341-363 2C 383-402 and 423-445 NC_002163.1 RefSeq region 870862 870918 . - . ID=id67;Name=id67;Dbxref=GeneID:905237;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0934c by TMHMM2.0 at aa 7-25 2C 35-57 2C 87-109 2C 133-155 2C167-189 2C 216-238 2C 251-273 2C 298-320 2C 341-363 2C 383-402 and 423-445 ### NC_002163.1 RefSeq CDS 870949 872283 . - 0 ID=cds831;Parent=gene883;Name=YP_002344333.1;Dbxref=GOA:Q0P9W4 InterPro:IPR000175 UniProtKB FTrEMBL:Q0P9W4 Genbank:YP_002344333.1 GeneID:906006;gbkey=CDS;product=sodium:amino-acid symporter family protein;Note=Original 282000 29 note: Cj0935c 2C probable transmembrane transport protein 2C len: 444 aa 3B similar to members of the sodium:neurotransmitter symporter family e.g. YG90_HAEIN hypothetical sodium-dependent transporter HI1690 28457 aa 29 2C fasta scores 3B opt: 694 z-score: 771.9 E 28 29: 0 2C 33.0 25 identity in 449 aa overlap. 40.4 25 identity to HP0497. Pfam match to entry PF00209 SNF 2CSodium:neurotransmitter symporter family. Also similar to Cj0934c 2851.0 25 identity in 441 aa overlap 29 and Cj0601c 2832.6 25 identity in 451 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF00209 Sodium:neurotransmitter symporter family identified within CDS. Also 2C eleven probable transmembrane helices predicted by TMHMM2.0. Product function modified to more specfific family member based on motif identification. No specific characterisation has been carried out 2C so has kept within product function. Functional classification -Transport 2Fbinding proteins - Other NC_002163.1 RefSeq gene 870949 872283 . - . ID=gene883;Name=Cj0935c;locus_tag=Cj0935c;Dbxref=GeneID:906006;gbkey=Gene NC_002163.1 RefSeq region 870955 871023 . - . ID=id68;Name=id68;Dbxref=GeneID:906006;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0935c by TMHMM2.0 at aa 7-25 2C 40-62 2C 83-105 2C 139-161 2C174-196 2C 216-238 2C 251-273 2C 299-321 2C 342-364 2C 384-401 and 421-443 NC_002163.1 RefSeq region 870961 872268 . - . ID=id1743;Name=id1743;Dbxref=GeneID:906006;gbkey=misc_feature;Note=HMMPfam hit to PF00209 2C Sodium:neurotransmitter symporter family 2C score 2.2e-10 NC_002163.1 RefSeq region 871081 871134 . - . ID=id68;Name=id68;Dbxref=GeneID:906006;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0935c by TMHMM2.0 at aa 7-25 2C 40-62 2C 83-105 2C 139-161 2C174-196 2C 216-238 2C 251-273 2C 299-321 2C 342-364 2C 384-401 and 421-443 NC_002163.1 RefSeq region 871192 871260 . - . ID=id68;Name=id68;Dbxref=GeneID:906006;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0935c by TMHMM2.0 at aa 7-25 2C 40-62 2C 83-105 2C 139-161 2C174-196 2C 216-238 2C 251-273 2C 299-321 2C 342-364 2C 384-401 and 421-443 NC_002163.1 RefSeq region 871321 871389 . - . ID=id68;Name=id68;Dbxref=GeneID:906006;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0935c by TMHMM2.0 at aa 7-25 2C 40-62 2C 83-105 2C 139-161 2C174-196 2C 216-238 2C 251-273 2C 299-321 2C 342-364 2C 384-401 and 421-443 NC_002163.1 RefSeq region 871465 871533 . - . ID=id68;Name=id68;Dbxref=GeneID:906006;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0935c by TMHMM2.0 at aa 7-25 2C 40-62 2C 83-105 2C 139-161 2C174-196 2C 216-238 2C 251-273 2C 299-321 2C 342-364 2C 384-401 and 421-443 NC_002163.1 RefSeq region 871570 871638 . - . ID=id68;Name=id68;Dbxref=GeneID:906006;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0935c by TMHMM2.0 at aa 7-25 2C 40-62 2C 83-105 2C 139-161 2C174-196 2C 216-238 2C 251-273 2C 299-321 2C 342-364 2C 384-401 and 421-443 NC_002163.1 RefSeq region 871696 871764 . - . ID=id68;Name=id68;Dbxref=GeneID:906006;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0935c by TMHMM2.0 at aa 7-25 2C 40-62 2C 83-105 2C 139-161 2C174-196 2C 216-238 2C 251-273 2C 299-321 2C 342-364 2C 384-401 and 421-443 NC_002163.1 RefSeq region 871801 871869 . - . ID=id68;Name=id68;Dbxref=GeneID:906006;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0935c by TMHMM2.0 at aa 7-25 2C 40-62 2C 83-105 2C 139-161 2C174-196 2C 216-238 2C 251-273 2C 299-321 2C 342-364 2C 384-401 and 421-443 NC_002163.1 RefSeq region 871969 872037 . - . ID=id68;Name=id68;Dbxref=GeneID:906006;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0935c by TMHMM2.0 at aa 7-25 2C 40-62 2C 83-105 2C 139-161 2C174-196 2C 216-238 2C 251-273 2C 299-321 2C 342-364 2C 384-401 and 421-443 NC_002163.1 RefSeq region 872098 872166 . - . ID=id68;Name=id68;Dbxref=GeneID:906006;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0935c by TMHMM2.0 at aa 7-25 2C 40-62 2C 83-105 2C 139-161 2C174-196 2C 216-238 2C 251-273 2C 299-321 2C 342-364 2C 384-401 and 421-443 NC_002163.1 RefSeq region 872209 872265 . - . ID=id68;Name=id68;Dbxref=GeneID:906006;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0935c by TMHMM2.0 at aa 7-25 2C 40-62 2C 83-105 2C 139-161 2C174-196 2C 216-238 2C 251-273 2C 299-321 2C 342-364 2C 384-401 and 421-443 ### NC_002163.1 UTR_Extractor 5'-UTR 872284 872318 . - . ID=utr330;locus_tag=Cj0935c;product=putative sodium:amino-acid symporter family protein NC_002163.1 UTR_Extractor 5'-UTR 872432 872515 . + . ID=utr331;locus_tag=Cj0936;product=F0F1 ATP synthase subunit C NC_002163.1 RefSeq CDS 872516 872854 . + 0 ID=cds832;Parent=gene884;gene=atpE;Name=YP_002344334.1;Dbxref=GOA:Q0P9W3 InterPro:IPR000454 InterPro:IPR002379 InterPro:IPR005953 UniProtKB FTrEMBL:Q0P9W3 Genbank:YP_002344334.1 GeneID:905243;gbkey=CDS;product=F0F1 ATP synthase subunit C;Note=Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit C is part of the membrane proton channel F0 NC_002163.1 RefSeq gene 872516 872854 . + . ID=gene884;gene=atpE;Name=atpE;locus_tag=Cj0936;Dbxref=GeneID:905243;gbkey=Gene NC_002163.1 RefSeq region 872528 872587 . + . ID=id1744;gene=atpE;Name=id1744;Dbxref=GeneID:905243;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0936 by TMHMM2.0 at aa 5-24 2C 39-61 and 82-104 NC_002163.1 RefSeq region 872621 872830 . + . ID=id1745;gene=atpE;Name=id1745;Dbxref=GeneID:905243;gbkey=misc_feature;Note=HMMPfam hit to PF00137 2C ATP synthase subunit C 2Cscore 3.8e-19 NC_002163.1 RefSeq region 872630 872698 . + . ID=id1744;gene=atpE;Name=id1744;Dbxref=GeneID:905243;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0936 by TMHMM2.0 at aa 5-24 2C 39-61 and 82-104 NC_002163.1 RefSeq region 872717 872782 . + . ID=id1746;gene=atpE;Name=id1746;Dbxref=GeneID:905243;gbkey=misc_feature;Note=PS00605 ATP synthase c subunit signature NC_002163.1 RefSeq region 872759 872827 . + . ID=id1744;gene=atpE;Name=id1744;Dbxref=GeneID:905243;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj0936 by TMHMM2.0 at aa 5-24 2C 39-61 and 82-104 ### NC_002163.1 RefSeq gene 872889 872974 . + . ID=gene885;gene=tRNALeu;Name=tRNALeu;locus_tag=Cjt01;Dbxref=GeneID:3245043;gbkey=Gene NC_002163.1 RefSeq tRNA 872889 872974 . + . ID=rna29;Parent=gene885;gene=tRNALeu;Name=rna29;Dbxref=GeneID:3245043;gbkey=tRNA;product=tRNA-Leu;Note=tRNA Leu anticodon GAG 2C Cove score 55.92 NC_002163.1 RefSeq exon 872889 872974 . + . ID=id1747;Parent=rna29;gene=tRNALeu;Name=id1747;Dbxref=GeneID:3245043;gbkey=tRNA;product=tRNA-Leu;Note=tRNA Leu anticodon GAG 2C Cove score 55.92 NC_002163.1 RefSeq CDS 873171 874082 . + 0 ID=cds833;Parent=gene886;Name=YP_002344335.1;Dbxref=GOA:Q0P9W2 InterPro:IPR004776 UniProtKB FTrEMBL:Q0P9W2 Genbank:YP_002344335.1 GeneID:905231;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0937 2C probable integral membrane protein 2C len: 303 aa 3B simimlar to hypothetical membrane proteins e.g. YA31_METJA MJ1031 28308 aa 29 2C fasta scores 3B opt: 379 z-score: 446.4 E 28 29: 1.4e-17 2C 26.1 25 identity in 318 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF03547 Auxin Efflux Carrier identified within CDS. Also 2C ten probable transmembrane helices predicted by TMHMM2.0. PProteins in this group are mostly uncharacterised and of unknown function. Functional classification - Membranes 2Clipoproteins and porins NC_002163.1 RefSeq gene 873171 874082 . + . ID=gene886;Name=Cj0937;locus_tag=Cj0937;Dbxref=GeneID:905231;gbkey=Gene NC_002163.1 RefSeq region 873174 874067 . + . ID=id1748;Name=id1748;Dbxref=GeneID:905231;gbkey=misc_feature;Note=HMMPfam hit to PF03547 2C Auxin Efflux Carrier 2C score 1.1e-81 NC_002163.1 RefSeq region 873180 873248 . + . ID=id1749;Name=id1749;Dbxref=GeneID:905231;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0937 by TMHMM2.0 at aa 4-26 2C 31-48 2C 58-80 2C 93-115 2C125-147 2C 168-187 2C 192-214 2C 221-243 2C 253-271 and 278-300 NC_002163.1 RefSeq region 873261 873314 . + . ID=id1749;Name=id1749;Dbxref=GeneID:905231;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0937 by TMHMM2.0 at aa 4-26 2C 31-48 2C 58-80 2C 93-115 2C125-147 2C 168-187 2C 192-214 2C 221-243 2C 253-271 and 278-300 NC_002163.1 RefSeq region 873342 873410 . + . ID=id1749;Name=id1749;Dbxref=GeneID:905231;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0937 by TMHMM2.0 at aa 4-26 2C 31-48 2C 58-80 2C 93-115 2C125-147 2C 168-187 2C 192-214 2C 221-243 2C 253-271 and 278-300 NC_002163.1 RefSeq region 873351 873383 . + . ID=id1750;Name=id1750;Dbxref=GeneID:905231;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 873438 873470 . + . ID=id1751;Name=id1751;Dbxref=GeneID:905231;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 873447 873515 . + . ID=id1749;Name=id1749;Dbxref=GeneID:905231;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0937 by TMHMM2.0 at aa 4-26 2C 31-48 2C 58-80 2C 93-115 2C125-147 2C 168-187 2C 192-214 2C 221-243 2C 253-271 and 278-300 NC_002163.1 RefSeq region 873543 873611 . + . ID=id1749;Name=id1749;Dbxref=GeneID:905231;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0937 by TMHMM2.0 at aa 4-26 2C 31-48 2C 58-80 2C 93-115 2C125-147 2C 168-187 2C 192-214 2C 221-243 2C 253-271 and 278-300 NC_002163.1 RefSeq region 873672 873731 . + . ID=id1749;Name=id1749;Dbxref=GeneID:905231;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0937 by TMHMM2.0 at aa 4-26 2C 31-48 2C 58-80 2C 93-115 2C125-147 2C 168-187 2C 192-214 2C 221-243 2C 253-271 and 278-300 NC_002163.1 RefSeq region 873744 873812 . + . ID=id1749;Name=id1749;Dbxref=GeneID:905231;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0937 by TMHMM2.0 at aa 4-26 2C 31-48 2C 58-80 2C 93-115 2C125-147 2C 168-187 2C 192-214 2C 221-243 2C 253-271 and 278-300 NC_002163.1 RefSeq region 873831 873899 . + . ID=id1749;Name=id1749;Dbxref=GeneID:905231;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0937 by TMHMM2.0 at aa 4-26 2C 31-48 2C 58-80 2C 93-115 2C125-147 2C 168-187 2C 192-214 2C 221-243 2C 253-271 and 278-300 NC_002163.1 RefSeq region 873927 873983 . + . ID=id1749;Name=id1749;Dbxref=GeneID:905231;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0937 by TMHMM2.0 at aa 4-26 2C 31-48 2C 58-80 2C 93-115 2C125-147 2C 168-187 2C 192-214 2C 221-243 2C 253-271 and 278-300 NC_002163.1 RefSeq region 874002 874070 . + . ID=id1749;Name=id1749;Dbxref=GeneID:905231;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj0937 by TMHMM2.0 at aa 4-26 2C 31-48 2C 58-80 2C 93-115 2C125-147 2C 168-187 2C 192-214 2C 221-243 2C 253-271 and 278-300 ### NC_002163.1 RefSeq CDS 874090 877602 . - 0 ID=cds834;Parent=gene887;gene=aas;Name=YP_002344336.1;Dbxref=GOA:Q0P9W1 InterPro:IPR000873 InterPro:IPR002123 InterPro:IPR011701 UniProtKB FTrEMBL:Q0P9W1 Genbank:YP_002344336.1 GeneID:905232;gbkey=CDS;product=2-acylglycerophosphoethanolamine acyltransferase;Note=Original 282000 29 note: Cj0938c 2C aas 2C probable 2-acylglycerophosphoethanolamine acyltransferase 2F acyl-acyl carrier protein synthetase 2C len: 1170 aa 3B contains 2 domains 3B C-terminal domain 28420 aa to end 29 is simlar to the bifunctional enzyme AAS_ECOLI 2-acylglycerophosphoethanolamine acyltransferase 2F acyl-acyl carrier protein synthetase 28719 aa 29 2C fasta scores 3B opt: 438 z-score: 471.6 E 28 29: 5.7e-19 2C 31.0 25 identity in 762 aa overlap 3B N-terminal domain contains approx 12 transmembrane domains 2C and is similar to the hypothetical membrane protein immediately upstreram of the E. coli aas 3B YGED_ECOLI 3B wublastp scores E 3D 3.5e-12 2C 25 25 in 192 aa overlap and 31 25 identity in 146 aa overlap. No Hp match. Contains PS00455 AMP-binding domain signature 2C and Pfam match to entry PF00501 AMP-binding 2CAMP-binding enzyme 7EUpdated 282006 29 note: Now contains additional Pfam domains in centre of CDS 2C PF01553 Acyltransferase and N-terminal domain PF07690 Major Facilitator Superfamily. Characterisation has been carried out within Escherichia coli 2C however 2C sequence alignment is only partial. kept within product function. Functional classification - Fatty acid biosynthesis 7EPMID:10733890 NC_002163.1 RefSeq gene 874090 877602 . - . ID=gene887;gene=aas;Name=aas;locus_tag=Cj0938c;Dbxref=GeneID:905232;gbkey=Gene NC_002163.1 RefSeq region 874306 875652 . - . ID=id1752;gene=aas;Name=id1752;Dbxref=GeneID:905232;gbkey=misc_feature;Note=HMMPfam hit to PF00501 2C AMP-binding enzyme 2C score 1e-63 NC_002163.1 RefSeq region 875140 875175 . - . ID=id1753;gene=aas;Name=id1753;Dbxref=GeneID:905232;gbkey=misc_feature;Note=PS00455 AMP-binding domain signature NC_002163.1 RefSeq region 875200 875268 . - . ID=id69;gene=aas;Name=id69;Dbxref=GeneID:905232;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0938c by TMHMM2.0 at aa 7-29 2C 49-71 2C 84-103 2C 107-129 2C142-164 2C 179-201 2C 239-258 2C 273-295 2C 304-326 2C 330-352 2C365-387 2C 391-413 and 779-801 NC_002163.1 RefSeq region 875923 876306 . - . ID=id1754;gene=aas;Name=id1754;Dbxref=GeneID:905232;gbkey=misc_feature;Note=HMMPfam hit to PF01553 2C Acyltransferase 2C score 3.3e-22 NC_002163.1 RefSeq region 876364 876432 . - . ID=id69;gene=aas;Name=id69;Dbxref=GeneID:905232;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0938c by TMHMM2.0 at aa 7-29 2C 49-71 2C 84-103 2C 107-129 2C142-164 2C 179-201 2C 239-258 2C 273-295 2C 304-326 2C 330-352 2C365-387 2C 391-413 and 779-801 NC_002163.1 RefSeq region 876439 877560 . - . ID=id1755;gene=aas;Name=id1755;Dbxref=GeneID:905232;gbkey=misc_feature;Note=HMMPfam hit to PF07690 2C Major Facilitator Superfamily 2C score 3e-18 NC_002163.1 RefSeq region 876442 876510 . - . ID=id69;gene=aas;Name=id69;Dbxref=GeneID:905232;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0938c by TMHMM2.0 at aa 7-29 2C 49-71 2C 84-103 2C 107-129 2C142-164 2C 179-201 2C 239-258 2C 273-295 2C 304-326 2C 330-352 2C365-387 2C 391-413 and 779-801 NC_002163.1 RefSeq region 876547 876615 . - . ID=id69;gene=aas;Name=id69;Dbxref=GeneID:905232;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0938c by TMHMM2.0 at aa 7-29 2C 49-71 2C 84-103 2C 107-129 2C142-164 2C 179-201 2C 239-258 2C 273-295 2C 304-326 2C 330-352 2C365-387 2C 391-413 and 779-801 NC_002163.1 RefSeq region 876625 876693 . - . ID=id69;gene=aas;Name=id69;Dbxref=GeneID:905232;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0938c by TMHMM2.0 at aa 7-29 2C 49-71 2C 84-103 2C 107-129 2C142-164 2C 179-201 2C 239-258 2C 273-295 2C 304-326 2C 330-352 2C365-387 2C 391-413 and 779-801 NC_002163.1 RefSeq region 876718 876786 . - . ID=id69;gene=aas;Name=id69;Dbxref=GeneID:905232;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0938c by TMHMM2.0 at aa 7-29 2C 49-71 2C 84-103 2C 107-129 2C142-164 2C 179-201 2C 239-258 2C 273-295 2C 304-326 2C 330-352 2C365-387 2C 391-413 and 779-801 NC_002163.1 RefSeq region 876829 876888 . - . ID=id69;gene=aas;Name=id69;Dbxref=GeneID:905232;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0938c by TMHMM2.0 at aa 7-29 2C 49-71 2C 84-103 2C 107-129 2C142-164 2C 179-201 2C 239-258 2C 273-295 2C 304-326 2C 330-352 2C365-387 2C 391-413 and 779-801 NC_002163.1 RefSeq region 877000 877068 . - . ID=id69;gene=aas;Name=id69;Dbxref=GeneID:905232;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0938c by TMHMM2.0 at aa 7-29 2C 49-71 2C 84-103 2C 107-129 2C142-164 2C 179-201 2C 239-258 2C 273-295 2C 304-326 2C 330-352 2C365-387 2C 391-413 and 779-801 NC_002163.1 RefSeq region 877021 877053 . - . ID=id1756;gene=aas;Name=id1756;Dbxref=GeneID:905232;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 877111 877179 . - . ID=id69;gene=aas;Name=id69;Dbxref=GeneID:905232;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0938c by TMHMM2.0 at aa 7-29 2C 49-71 2C 84-103 2C 107-129 2C142-164 2C 179-201 2C 239-258 2C 273-295 2C 304-326 2C 330-352 2C365-387 2C 391-413 and 779-801 NC_002163.1 RefSeq region 877216 877284 . - . ID=id69;gene=aas;Name=id69;Dbxref=GeneID:905232;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0938c by TMHMM2.0 at aa 7-29 2C 49-71 2C 84-103 2C 107-129 2C142-164 2C 179-201 2C 239-258 2C 273-295 2C 304-326 2C 330-352 2C365-387 2C 391-413 and 779-801 NC_002163.1 RefSeq region 877294 877353 . - . ID=id69;gene=aas;Name=id69;Dbxref=GeneID:905232;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0938c by TMHMM2.0 at aa 7-29 2C 49-71 2C 84-103 2C 107-129 2C142-164 2C 179-201 2C 239-258 2C 273-295 2C 304-326 2C 330-352 2C365-387 2C 391-413 and 779-801 NC_002163.1 RefSeq region 877390 877458 . - . ID=id69;gene=aas;Name=id69;Dbxref=GeneID:905232;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0938c by TMHMM2.0 at aa 7-29 2C 49-71 2C 84-103 2C 107-129 2C142-164 2C 179-201 2C 239-258 2C 273-295 2C 304-326 2C 330-352 2C365-387 2C 391-413 and 779-801 NC_002163.1 RefSeq region 877516 877584 . - . ID=id69;gene=aas;Name=id69;Dbxref=GeneID:905232;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj0938c by TMHMM2.0 at aa 7-29 2C 49-71 2C 84-103 2C 107-129 2C142-164 2C 179-201 2C 239-258 2C 273-295 2C 304-326 2C 330-352 2C365-387 2C 391-413 and 779-801 ### NC_002163.1 RefSeq gene 877647 878027 . - . ID=gene888;Name=Cj0939c;locus_tag=Cj0939c;Dbxref=GeneID:905233;gbkey=Gene NC_002163.1 RefSeq CDS 877647 878027 . - 0 ID=cds835;Parent=gene888;Name=YP_002344337.1;Dbxref=GOA:Q0P9W0 UniProtKB FTrEMBL:Q0P9W0 Genbank:YP_002344337.1 GeneID:905233;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0939c 2C unknown 2C len: 126 aa 3B 29.5 25 identity to HP1065. Functional classification -Conserved hypothetical proteins NC_002163.1 UTR_Extractor 5'-UTR 878028 878057 . - . ID=utr332;locus_tag=Cj0939c;product=hypothetical protein NC_002163.1 RefSeq gene 878095 878171 . - . ID=gene889;gene=tRNAAsp;Name=tRNAAsp;locus_tag=Cjt02;Dbxref=GeneID:3245040;gbkey=Gene NC_002163.1 RefSeq tRNA 878095 878171 . - . ID=rna30;Parent=gene889;gene=tRNAAsp;Name=rna30;Dbxref=GeneID:3245040;gbkey=tRNA;product=tRNA-Asp;Note=tRNA Asp anticodon GTC 2C Cove score 91.78 NC_002163.1 RefSeq exon 878095 878171 . - . ID=id1757;Parent=rna30;gene=tRNAAsp;Name=id1757;Dbxref=GeneID:3245040;gbkey=tRNA;product=tRNA-Asp;Note=tRNA Asp anticodon GTC 2C Cove score 91.78 NC_002163.1 RefSeq gene 878223 878298 . - . ID=gene890;gene=tRNAVal;Name=tRNAVal;locus_tag=Cjp19;Dbxref=GeneID:905029;gbkey=Gene NC_002163.1 RefSeq tRNA 878223 878298 . - . ID=rna31;Parent=gene890;gene=tRNAVal;Name=rna31;Dbxref=GeneID:905029;gbkey=tRNA;product=tRNA-Val;Note=tRNA Val anticodon TAC 2C Cove score 90.03 NC_002163.1 RefSeq exon 878223 878298 . - . ID=id1758;Parent=rna31;gene=tRNAVal;Name=id1758;Dbxref=GeneID:905029;gbkey=tRNA;product=tRNA-Val;Note=tRNA Val anticodon TAC 2C Cove score 90.03 NC_002163.1 RefSeq gene 878400 878475 . - . ID=gene891;gene=tRNALys;Name=tRNALys;locus_tag=Cjp20;Dbxref=GeneID:905235;gbkey=Gene NC_002163.1 RefSeq tRNA 878400 878475 . - . ID=rna32;Parent=gene891;gene=tRNALys;Name=rna32;Dbxref=GeneID:905235;gbkey=tRNA;product=tRNA-Lys;Note=tRNA Lys anticodon TTT 2C Cove score 81.97 NC_002163.1 RefSeq exon 878400 878475 . - . ID=id1759;Parent=rna32;gene=tRNALys;Name=id1759;Dbxref=GeneID:905235;gbkey=tRNA;product=tRNA-Lys;Note=tRNA Lys anticodon TTT 2C Cove score 81.97 NC_002163.1 RefSeq gene 878480 878556 . - . ID=gene892;gene=tRNAAsp;Name=tRNAAsp;locus_tag=Cjt2;Dbxref=GeneID:3245055;gbkey=Gene NC_002163.1 RefSeq tRNA 878480 878556 . - . ID=rna33;Parent=gene892;gene=tRNAAsp;Name=rna33;Dbxref=GeneID:3245055;gbkey=tRNA;product=tRNA-Asp;Note=tRNA Asp anticodon GTC 2C Cove score 91.78 NC_002163.1 RefSeq exon 878480 878556 . - . ID=id1760;Parent=rna33;gene=tRNAAsp;Name=id1760;Dbxref=GeneID:3245055;gbkey=tRNA;product=tRNA-Asp;Note=tRNA Asp anticodon GTC 2C Cove score 91.78 NC_002163.1 RefSeq gene 878608 878683 . - . ID=gene893;gene=tRNAVal;Name=tRNAVal;locus_tag=Cjt03;Dbxref=GeneID:3245044;gbkey=Gene NC_002163.1 RefSeq tRNA 878608 878683 . - . ID=rna34;Parent=gene893;gene=tRNAVal;Name=rna34;Dbxref=GeneID:3245044;gbkey=tRNA;product=tRNA-Val;Note=tRNA Val anticodon TAC 2C Cove score 90.03 NC_002163.1 RefSeq exon 878608 878683 . - . ID=id1761;Parent=rna34;gene=tRNAVal;Name=id1761;Dbxref=GeneID:3245044;gbkey=tRNA;product=tRNA-Val;Note=tRNA Val anticodon TAC 2C Cove score 90.03 NC_002163.1 RefSeq gene 878691 878766 . - . ID=gene894;gene=tRNALys;Name=tRNALys;locus_tag=Cjt04;Dbxref=GeneID:3245048;gbkey=Gene NC_002163.1 RefSeq tRNA 878691 878766 . - . ID=rna35;Parent=gene894;gene=tRNALys;Name=rna35;Dbxref=GeneID:3245048;gbkey=tRNA;product=tRNA-Lys;Note=tRNA Lys anticodon TTT 2C Cove score 81.97 NC_002163.1 RefSeq exon 878691 878766 . - . ID=id1762;Parent=rna35;gene=tRNALys;Name=id1762;Dbxref=GeneID:3245048;gbkey=tRNA;product=tRNA-Lys;Note=tRNA Lys anticodon TTT 2C Cove score 81.97 NC_002163.1 RefSeq CDS 878828 879613 . - 0 ID=cds836;Parent=gene895;gene=glnP;Name=YP_002344338.1;Dbxref=GOA:Q0P9V9 InterPro:IPR000515 InterPro:IPR010065 UniProtKB FTrEMBL:Q0P9V9 Genbank:YP_002344338.1 GeneID:905236;gbkey=CDS;product=glutamine transporter permease;Note=Original 282000 29 note: Cj0940c 2C glnP 2C probable glutamine transport system permease 2C len: 261 aa 3B similar to many e.g. GLNP_ECOLI glutamine transport system permease 28219 aa 29 2C fasta scores 3B opt: 414 z-score: 509.0 E 28 29: 4.7e-21 2C 37.5 25 identity in 216 aa overlap. No Hp otholog. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp sign. 2C and Pfam match to entry PF00528 BPD_transp 2CBinding-protein-dependent transport systems inner membrane component 7EUpdated 282006 29 note: Six probable transmembrane helices predicted by TMHMM2.0. Not fully characterised 2C so kept in product function. Functional classification - Transport 2Fbinding proteins - Amino acids and amines NC_002163.1 RefSeq gene 878828 879613 . - . ID=gene895;gene=glnP;Name=glnP;locus_tag=Cj0940c;Dbxref=GeneID:905236;gbkey=Gene NC_002163.1 RefSeq region 878831 879436 . - . ID=id1763;gene=glnP;Name=id1763;Dbxref=GeneID:905236;gbkey=misc_feature;Note=HMMPfam hit to PF00528 2C Binding-protein-dependent transport syst 2C score 4.8e-27 NC_002163.1 RefSeq region 878849 878917 . - . ID=id70;gene=glnP;Name=id70;Dbxref=GeneID:905236;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0940c by TMHMM2.0 at aa 26-48 2C 68-90 2C 102-124 2C 134-156 2C177-199 and 233-255 NC_002163.1 RefSeq region 879017 879085 . - . ID=id70;gene=glnP;Name=id70;Dbxref=GeneID:905236;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0940c by TMHMM2.0 at aa 26-48 2C 68-90 2C 102-124 2C 134-156 2C177-199 and 233-255 NC_002163.1 RefSeq region 879062 879148 . - . ID=id1764;gene=glnP;Name=id1764;Dbxref=GeneID:905236;gbkey=misc_feature;Note=PS00402 Binding-protein-dependent transport systems inner membrane comp. sign NC_002163.1 RefSeq region 879146 879214 . - . ID=id70;gene=glnP;Name=id70;Dbxref=GeneID:905236;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0940c by TMHMM2.0 at aa 26-48 2C 68-90 2C 102-124 2C 134-156 2C177-199 and 233-255 NC_002163.1 RefSeq region 879242 879310 . - . ID=id70;gene=glnP;Name=id70;Dbxref=GeneID:905236;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0940c by TMHMM2.0 at aa 26-48 2C 68-90 2C 102-124 2C 134-156 2C177-199 and 233-255 NC_002163.1 RefSeq region 879344 879412 . - . ID=id70;gene=glnP;Name=id70;Dbxref=GeneID:905236;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0940c by TMHMM2.0 at aa 26-48 2C 68-90 2C 102-124 2C 134-156 2C177-199 and 233-255 NC_002163.1 RefSeq region 879470 879538 . - . ID=id70;gene=glnP;Name=id70;Dbxref=GeneID:905236;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0940c by TMHMM2.0 at aa 26-48 2C 68-90 2C 102-124 2C 134-156 2C177-199 and 233-255 ### NC_002163.1 RefSeq CDS 879636 880841 . - 0 ID=cds837;Parent=gene896;Name=YP_002344339.1;Dbxref=GOA:Q0P9V8 InterPro:IPR003838 UniProtKB FTrEMBL:Q0P9V8 Genbank:YP_002344339.1 GeneID:904433;gbkey=CDS;product=permease;Note=Original 282000 29 note: Cj0941c 2C probable integral membrane protein 2C len: 401 aa 3B similar to many hypothetical membrane proteins e.g. YCFU_ECOLI 28399 aa 29 2Cfasta scores 3B opt: 414 z-score: 478.9 E 28 29: 2.2e-19 2C 22.1 25 identity in 408 aa overlap. 53.5 25 identity to HP0787 7EUpdated 282006 29 note: Pfam domain PF02687 Predicted permease identified within CDS. Also 2C four probable transmembrane helices predicted by TMHMM2.0. Product modified to more specific family member based on motif match. Not specific characterisation has been carried out yet 2C so kept within product function. Functional classification - Transport 2Fbinding proteins - Other NC_002163.1 RefSeq gene 879636 880841 . - . ID=gene896;Name=Cj0941c;locus_tag=Cj0941c;Dbxref=GeneID:904433;gbkey=Gene NC_002163.1 RefSeq region 879660 880187 . - . ID=id1765;Name=id1765;Dbxref=GeneID:904433;gbkey=misc_feature;Note=HMMPfam hit to PF02687 2C Predicted permease 2C score 7.2e-44 NC_002163.1 RefSeq region 879690 879758 . - . ID=id71;Name=id71;Dbxref=GeneID:904433;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0941c by TMHMM2.0 at aa 21-43 2C 266-288 2C 314-336 and 362-384 NC_002163.1 RefSeq region 879834 879902 . - . ID=id71;Name=id71;Dbxref=GeneID:904433;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0941c by TMHMM2.0 at aa 21-43 2C 266-288 2C 314-336 and 362-384 NC_002163.1 RefSeq region 879978 880046 . - . ID=id71;Name=id71;Dbxref=GeneID:904433;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0941c by TMHMM2.0 at aa 21-43 2C 266-288 2C 314-336 and 362-384 NC_002163.1 RefSeq region 880713 880781 . - . ID=id71;Name=id71;Dbxref=GeneID:904433;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj0941c by TMHMM2.0 at aa 21-43 2C 266-288 2C 314-336 and 362-384 NC_002163.1 RefSeq CDS 880838 883426 . - 0 ID=cds838;Parent=gene897;gene=secA;Name=YP_002344340.1;Dbxref=GOA:Q0P9V7 InterPro:IPR000185 InterPro:IPR001650 InterPro:IPR004027 InterPro:IPR011115 InterPro:IPR011116 InterPro:IPR011130 InterPro:IPR014018 UniProtKB FSwiss-Prot:Q0P9V7 Genbank:YP_002344340.1 GeneID:905172;gbkey=CDS;product=preprotein translocase subunit SecA;Note=functions in protein export 3B can interact with acidic membrane phospholipids and the SecYEG protein complex 3B binds to preproteins 3B binds to ATP and undergoes a conformational change to promote membrane insertion of SecA 2Fbound preprotein 3B ATP hydrolysis appears to drive release of the preprotein from SecA and deinsertion of SecA from the membrane 3B additional proteins SecD 2FF 2FYajC aid SecA recycling 3B exists in an equilibrium between monomers and dimers 3B may possibly form higher order oligomers 3B proteins in this cluster correspond SecA1 3B SecA2 is not essential and seems to play a role in secretion of a subset of proteins NC_002163.1 RefSeq gene 880838 883426 . - . ID=gene897;gene=secA;Name=secA;locus_tag=Cj0942c;Dbxref=GeneID:905172;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 880842 880909 . - . ID=utr333;locus_tag=Cj0941c;product=putative permease NC_002163.1 RefSeq region 880862 880924 . - . ID=id1766;gene=secA;Name=id1766;Dbxref=GeneID:905172;gbkey=misc_feature;Note=HMMPfam hit to PF02810 2C SEC-C motif 2C score 3.7e-09 NC_002163.1 RefSeq region 881051 881683 . - . ID=id1767;gene=secA;Name=id1767;Dbxref=GeneID:905172;gbkey=misc_feature;Note=HMMPfam hit to PF07516 2C SecA Wing and Scaffold domain 2C score 2.8e-73 NC_002163.1 RefSeq region 881795 882043 . - . ID=id1768;gene=secA;Name=id1768;Dbxref=GeneID:905172;gbkey=misc_feature;Note=HMMPfam hit to PF00271 2C Helicase conserved C-terminal domain 2C score 0.002 NC_002163.1 RefSeq region 882239 883411 . - . ID=id1769;gene=secA;Name=id1769;Dbxref=GeneID:905172;gbkey=misc_feature;Note=HMMPfam hit to PF07517 2C SecA DEAD-like domain 2Cscore 5.8e-153 NC_002163.1 RefSeq region 882371 882739 . - . ID=id1770;gene=secA;Name=id1770;Dbxref=GeneID:905172;gbkey=misc_feature;Note=HMMPfam hit to PF01043 2C SecA preprotein cross-linking domain 2C score 6.2e-69 ### NC_002163.1 UTR_Extractor 5'-UTR 883427 883451 . - . ID=utr334;locus_tag=Cj0942c;product=preprotein translocase subunit SecA NC_002163.1 RefSeq gene 883526 884035 . + . ID=gene898;gene=lolA;Name=lolA;locus_tag=Cj0943;Dbxref=GeneID:905238;gbkey=Gene NC_002163.1 RefSeq CDS 883526 884035 . + 0 ID=cds839;Parent=gene898;gene=lolA;Name=YP_002344341.1;Dbxref=GOA:Q9PNZ0 InterPro:IPR004564 UniProtKB FSwiss-Prot:Q9PNZ0 Genbank:YP_002344341.1 GeneID:905238;gbkey=CDS;product=outer-membrane lipoprotein carrier protein;Note=participates with LolB in the incorporation of lipoprotein into the outer membrane NC_002163.1 RefSeq gene 884032 884766 . - . ID=gene899;gene=Cj0944c;Name=Cj0944c;locus_tag=Cj0944c;Dbxref=GeneID:904376;gbkey=Gene NC_002163.1 RefSeq CDS 884032 884766 . - 0 ID=cds840;Parent=gene899;Name=YP_002344342.1;Dbxref=UniProtKB FTrEMBL:Q0P9V5 Genbank:YP_002344342.1 GeneID:904376;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0944c 2C probable periplasmic protein 2C len: 244 aa 3B no Hp match 7EUpdated 282006 29 note: Paper identified linking protein to glycoprotein. Functional classification -Miscellaneous periplasmic proteins 7EPMID:12186869 ### NC_002163.1 RefSeq CDS 884776 886119 . - 0 ID=cds841;Parent=gene900;Name=YP_002344343.1;Dbxref=GOA:Q0P9V4 InterPro:IPR003593 UniProtKB FTrEMBL:Q0P9V4 Genbank:YP_002344343.1 GeneID:905207;gbkey=CDS;product=helicase;Note=Original 282000 29 note: Cj0945c 2C possible helicase 2Clen: 447 aa 3B similar to the C-terminus of members of the eukaryotic RAD3 2FXPD helicase subfamily 2C e.g. PIF1_YEAST mitochondrial DNA repair and recombination protein 28857 aa 29 2C fasta scores 3B opt: 193 z-score: 220.7 E 28 29: 5.4e-05 2C29.6 25 identity in 324 aa overlap. No Hp match. Contains S00017 ATP 2FGTP-binding site motif A 28P-loop 29 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification -DNA replication 2C restriction 2Fmodification 2C recombination and repair NC_002163.1 RefSeq gene 884776 886119 . - . ID=gene900;Name=Cj0945c;locus_tag=Cj0945c;Dbxref=GeneID:905207;gbkey=Gene NC_002163.1 RefSeq region 885931 885999 . - . ID=id1771;Name=id1771;Dbxref=GeneID:905207;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0945c by TMHMM2.0 at aa 41-63 NC_002163.1 RefSeq region 886045 886068 . - . ID=id1772;Name=id1772;Dbxref=GeneID:905207;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 UTR_Extractor 5'-UTR 886146 886167 . + . ID=utr335;locus_tag=Cj0946;product=putative lipoprotein NC_002163.1 RefSeq gene 886168 887514 . + . ID=gene901;Name=Cj0946;locus_tag=Cj0946;Dbxref=GeneID:905239;gbkey=Gene NC_002163.1 RefSeq CDS 886168 887514 . + 0 ID=cds842;Parent=gene901;Name=YP_002344344.1;Dbxref=InterPro:IPR000064 UniProtKB FTrEMBL:Q0P9V3 Genbank:YP_002344344.1 GeneID:905239;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj0946 2C probable lipoprotein 2Clen: 448 aa 3B 29.0 25 identity to HP0087. Contains probable N-terminal signal sequence with appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site 2C and Pfam match to entry PF00877 NLPC_P60 2C NLP 2FP60 family. Functional classification - Membranes 2Clipoproteins and porins NC_002163.1 RefSeq region 886186 886218 . + . ID=id1773;Name=id1773;Dbxref=GeneID:905239;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq CDS 887526 888398 . - 0 ID=cds843;Parent=gene902;Name=YP_002344345.1;Dbxref=GOA:Q0P9V2 InterPro:IPR003010 UniProtKB FTrEMBL:Q0P9V2 Genbank:YP_002344345.1 GeneID:905240;gbkey=CDS;product=carbon-nitrogen hydrolase;Note=Original 282000 29 note: Cj0947c 2C probable hydrolase 2Clen: 290 aa 3B similar to prokaryotic hypothetical hydrolases 2C and to e.g. BUP_RAT beta-ureidopropionase 28393 aa 29 2C fasta scores 3B opt: 319 z-score: 392.0 E 28 29: 1.6e-14 2C26.0 25 identity in 304 aa overlap. 60.9 25 identity to HP0757 7EUpdated 282006 29 note: Pfam domain PF00795 Carbon-nitrogen hydrolase identified within CDS. Product modified to more specific family member based on motif match. Specific characterisation has been carried out yet 2Cso kept in product funciton. Functional classification - Misc NC_002163.1 RefSeq gene 887526 888398 . - . ID=gene902;Name=Cj0947c;locus_tag=Cj0947c;Dbxref=GeneID:905240;gbkey=Gene NC_002163.1 RefSeq region 887877 888395 . - . ID=id1774;Name=id1774;Dbxref=GeneID:905240;gbkey=misc_feature;Note=HMMPfam hit to PF00795 2C Carbon-nitrogen hydrolase 2Cscore 2.2e-59 NC_002163.1 RefSeq gene 888395 889282 . - . ID=gene903;Name=Cj0948c;locus_tag=Cj0948c;Dbxref=GeneID:905780;gbkey=Gene NC_002163.1 RefSeq CDS 888395 889282 . - 0 ID=cds844;Parent=gene903;Name=YP_002344346.1;Dbxref=GOA:Q0P9V1 InterPro:IPR002524 UniProtKB FTrEMBL:Q0P9V1 Genbank:YP_002344346.1 GeneID:905780;gbkey=CDS;product=cation efflux family protein;Note=Original 282000 29 note: Cj0948c 2C possible transmembrane transport protein 2C len: 295 aa 3B similar to members of the UPF0018 family 2C e.g. YIIP_ECOLI 28300 aa 29 2Cfasta scores 3B opt: 564 z-score: 671.3 E 28 29: 4.3e-30 2C 31.8 25 identity in 292 aa overlap 2C and to cation efflux proteins e.g. CZCD_ALCEU cation efflux system protein CZCD 28316 aa 29 2C fasta scores 3B opt: 262 z-score: 316.4 E 28 29: 2.5e-10 2C22.3 25 identity in 273 aa overlap. No Hp match. Also similar to Cj1163c 2824.7 25 identity in 279 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01545 Cation efflux family identified within CDS. Six probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterisation within more than one species e.g. Klebsiella pneumoniae and some Escherichia coli. kept in product function. Functional classification - Drug 2Fanalogue sensitivity 7EPMID:12019132 2C PMID:15549269 NC_002163.1 RefSeq region 888422 889261 . - . ID=id1775;Name=id1775;Dbxref=GeneID:905780;gbkey=misc_feature;Note=HMMPfam hit to PF01545 2C Cation efflux family 2C score 5.9e-101 NC_002163.1 RefSeq region 888701 888769 . - . ID=id72;Name=id72;Dbxref=GeneID:905780;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0948c by TMHMM2.0 at aa 7-29 2C 33-55 2C 75-97 2C 112-134 2C146-168 and 172-194 NC_002163.1 RefSeq region 888779 888847 . - . ID=id72;Name=id72;Dbxref=GeneID:905780;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0948c by TMHMM2.0 at aa 7-29 2C 33-55 2C 75-97 2C 112-134 2C146-168 and 172-194 NC_002163.1 RefSeq region 888881 888949 . - . ID=id72;Name=id72;Dbxref=GeneID:905780;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0948c by TMHMM2.0 at aa 7-29 2C 33-55 2C 75-97 2C 112-134 2C146-168 and 172-194 NC_002163.1 RefSeq region 888992 889060 . - . ID=id72;Name=id72;Dbxref=GeneID:905780;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0948c by TMHMM2.0 at aa 7-29 2C 33-55 2C 75-97 2C 112-134 2C146-168 and 172-194 NC_002163.1 RefSeq region 889118 889186 . - . ID=id72;Name=id72;Dbxref=GeneID:905780;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0948c by TMHMM2.0 at aa 7-29 2C 33-55 2C 75-97 2C 112-134 2C146-168 and 172-194 NC_002163.1 RefSeq region 889196 889264 . - . ID=id72;Name=id72;Dbxref=GeneID:905780;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj0948c by TMHMM2.0 at aa 7-29 2C 33-55 2C 75-97 2C 112-134 2C146-168 and 172-194 NC_002163.1 RefSeq gene 889279 890256 . - . ID=gene904;Name=Cj0949c;locus_tag=Cj0949c;Dbxref=GeneID:905241;gbkey=Gene NC_002163.1 RefSeq CDS 889279 890256 . - 0 ID=cds845;Parent=gene904;Name=YP_002344347.1;Dbxref=InterPro:IPR007466 UniProtKB FTrEMBL:Q0P9V0 Genbank:YP_002344347.1 GeneID:905241;gbkey=CDS;product=peptidyl-arginine deiminase family protein;Note=Original 282000 29 note: Cj0949c 2C unknown 2C len: 325 aa 3B similar to hypothetical proteins e.g. TR:O86509 28EMBL:AL031124 29 Streptomyces coelicolor SC1C2.08 28339 aa 29 2Cfasta scores 3B opt: 283 z-score: 328.5 E 28 29: 5.3e-11 2C 24.3 25 identity in 333 aa overlap. 45.5 25 identity to HP0049 7EUpdated 282006 29 note: Pfam domain PF04371 Porphyromonas-type peptidyl-arginine deiminase identified within CDS. Product modified to more specific family member based on motif match. Not fully characterised yet 2Cso kept within product function. Functional classification - Misc NC_002163.1 RefSeq region 889294 890253 . - . ID=id1776;Name=id1776;Dbxref=GeneID:905241;gbkey=misc_feature;Note=HMMPfam hit to PF04371 2C Porphyromonas-type peptidyl-arginine deimin 2C score 6.5e-166 ### NC_002163.1 UTR_Extractor 5'-UTR 890257 890284 . - . ID=utr336;locus_tag=Cj0949c;product=putative peptidyl-arginine deiminase family protein NC_002163.1 RefSeq CDS 890355 890789 . - 0 ID=cds846;Parent=gene905;Name=YP_002344348.1;Dbxref=GOA:Q0P9U9 InterPro:IPR005184 UniProtKB FTrEMBL:Q0P9U9 Genbank:YP_002344348.1 GeneID:905242;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj0950c 2C probable lipoprotein 2C len: 144 aa 3B some similarity to HSLJ_ECOLI heat shock protein HSLJ 28140 aa 29 2C fasta scores 3B opt: 152 z-score: 202.3 E 28 29: 0.00057 2C 26.2 25 identity in 145 aa overlap. 33.3 25 identity to HP1462 28secreted protein involved in flagellar motility 29. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site 7EUpdated 282006 29 note: Pfam domain PF03724 Domain of unknown function 28306 29 identified within CDS. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 890355 890789 . - . ID=gene905;Name=Cj0950c;locus_tag=Cj0950c;Dbxref=GeneID:905242;gbkey=Gene NC_002163.1 RefSeq region 890382 890693 . - . ID=id1777;Name=id1777;Dbxref=GeneID:905242;gbkey=misc_feature;Note=HMMPfam hit to PF03724 2C Domain of unknown function 28306 29 2C score 1.5e-33 NC_002163.1 RefSeq region 890739 890771 . - . ID=id1778;Name=id1778;Dbxref=GeneID:905242;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 UTR_Extractor 5'-UTR 890790 890826 . - . ID=utr337;locus_tag=Cj0950c;product=putative lipoprotein NC_002163.1 RefSeq pseudogene 890799 892379 . - . ID=gene906;Name=Cj0951c;locus_tag=Cj0951c;Dbxref=GeneID:905244;gbkey=Gene NC_002163.1 RefSeq region 891792 891860 . - . ID=id73;Name=id73;Dbxref=GeneID:905244;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0952c by TMHMM2.0 at aa 10-32 and 175-197 NC_002163.1 RefSeq region 892287 892355 . - . ID=id73;Name=id73;Dbxref=GeneID:905244;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0952c by TMHMM2.0 at aa 10-32 and 175-197 ### NC_002163.1 UTR_Extractor 5'-UTR 892383 892406 . - . ID=utr338;locus_tag=Cj0952c;product=putative HAMP containing membrane protein NC_002163.1 RefSeq CDS 892478 894010 . - 0 ID=cds847;Parent=gene907;gene=purH;Name=YP_002344351.1;Dbxref=GOA:Q9PNY2 HSSP:P31335 InterPro:IPR002695 InterPro:IPR011607 InterPro:IPR013982 UniProtKB FSwiss-Prot:Q9PNY2 Genbank:YP_002344351.1 GeneID:905247;gbkey=CDS;product=bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase 2FIMP cyclohydrolase;Note=involved in de novo purine biosynthesis NC_002163.1 RefSeq gene 892478 894010 . - . ID=gene907;gene=purH;Name=purH;locus_tag=Cj0953c;Dbxref=GeneID:905247;gbkey=Gene NC_002163.1 RefSeq region 892685 893620 . - . ID=id1779;gene=purH;Name=id1779;Dbxref=GeneID:905247;gbkey=misc_feature;Note=HMMPfam hit to PF01808 2C AICARFT 2FIMPCHase bienzyme 2Cscore 1.3e-86 NC_002163.1 RefSeq region 893633 893977 . - . ID=id1780;gene=purH;Name=id1780;Dbxref=GeneID:905247;gbkey=misc_feature;Note=HMMPfam hit to PF02142 2C MGS-like domain 2C score 3.8e-53 ### NC_002163.1 RefSeq CDS 894013 894783 . - 0 ID=cds848;Parent=gene908;Name=YP_002344352.1;Dbxref=GOA:Q0P9U5 InterPro:IPR001623 InterPro:IPR015609 UniProtKB FTrEMBL:Q0P9U5 Genbank:YP_002344352.1 GeneID:905248;gbkey=CDS;product=DnaJ-like protein;Note=Original 282000 29 note: Cj0954c 2C possible dnaJ-like protein 2C len: 256 aa 3B weak similarity to e.g. DJLA_COXBU DNAJ-like protein DJLA 28270 aa 29 2C fasta scores 3B opt: 167 z-score: 193.0 E 28 29: 0.0019 2C 26.9 25 identity in 201 aa overlap. No Hp match. Contains Pfam match to entry PF00226 DnaJ 2C DnaJ domain 7EUpdated 282006 29 note: No specific characterisation with acceptable identity scores carried out yet. kept within product function. Functional classification -Chaperones 2C chaperonins 2C heat shock NC_002163.1 RefSeq gene 894013 894783 . - . ID=gene908;Name=Cj0954c;locus_tag=Cj0954c;Dbxref=GeneID:905248;gbkey=Gene NC_002163.1 RefSeq region 894022 894213 . - . ID=id1781;Name=id1781;Dbxref=GeneID:905248;gbkey=misc_feature;Note=HMMPfam hit to PF00226 2C DnaJ domain 2C score 9e-11 NC_002163.1 RefSeq gene 894780 896966 . - . ID=gene909;gene=purL;Name=purL;locus_tag=Cj0955c;Dbxref=GeneID:904957;gbkey=Gene NC_002163.1 RefSeq CDS 894780 896966 . - 0 ID=cds849;Parent=gene909;gene=purL;Name=YP_002344353.1;Dbxref=GOA:Q9PNY0 InterPro:IPR000728 InterPro:IPR010074 InterPro:IPR010918 UniProtKB FSwiss-Prot:Q9PNY0 Genbank:YP_002344353.1 GeneID:904957;gbkey=CDS;product=phosphoribosylformylglycinamidine synthase II;Note=catalyzes the formation of 2- 28formamido 29-N1- 285-phospho-D-ribosyl 29acetamidine from N2-formyl-N1- 285-phospho-D-ribosyl 29glycinamide and L-glutamine in purine biosynthesis NC_002163.1 UTR_Extractor 5'-UTR 894784 894951 . - . ID=utr339;locus_tag=Cj0954c;product=putative DnaJ-like protein NC_002163.1 RefSeq region 894843 895271 . - . ID=id1782;gene=purL;Name=id1782;Dbxref=GeneID:904957;gbkey=misc_feature;Note=HMMPfam hit to PF02769 2C AIR synthase related protein 2C C-terminal dom 2C score 2.5e-09 NC_002163.1 RefSeq region 895305 895781 . - . ID=id1783;gene=purL;Name=id1783;Dbxref=GeneID:904957;gbkey=misc_feature;Note=HMMPfam hit to PF00586 2C AIR synthase related protein 2C N-terminal dom 2C score 6.5e-29 NC_002163.1 RefSeq region 895905 896375 . - . ID=id1784;gene=purL;Name=id1784;Dbxref=GeneID:904957;gbkey=misc_feature;Note=HMMPfam hit to PF02769 2C AIR synthase related protein 2C C-terminal dom 2C score 6.6e-47 NC_002163.1 RefSeq region 896406 896867 . - . ID=id1785;gene=purL;Name=id1785;Dbxref=GeneID:904957;gbkey=misc_feature;Note=HMMPfam hit to PF00586 2C AIR synthase related protein 2C N-terminal dom 2C score 4.9e-39 ### NC_002163.1 RefSeq CDS 896977 898305 . - 0 ID=cds850;Parent=gene910;gene=trmE;Name=YP_002344354.1;Dbxref=GOA:Q9PNX9 HSSP:Q9X1F8 InterPro:IPR001806 InterPro:IPR002917 InterPro:IPR004520 InterPro:IPR005225 InterPro:IPR005289 UniProtKB FSwiss-Prot:Q9PNX9 Genbank:YP_002344354.1 GeneID:905249;gbkey=CDS;product=tRNA modification GTPase TrmE;Note=in Escherichia coli this protein is involved in the biosynthesis of the hypermodified nucleoside 5-methylaminomethyl-2-thiouridine 2C which is found in the wobble position of some tRNAs and affects ribosomal frameshifting 3B shows potassium-dependent dimerization and GTP hydrolysis 3B also involved in regulation of glutamate-dependent acid resistance and activation of gadE NC_002163.1 RefSeq gene 896977 898305 . - . ID=gene910;gene=trmE;Name=trmE;locus_tag=Cj0956c;Dbxref=GeneID:905249;gbkey=Gene NC_002163.1 RefSeq region 897307 897663 . - . ID=id1786;gene=trmE;Name=id1786;Dbxref=GeneID:905249;gbkey=misc_feature;Note=HMMPfam hit to PF01926 2C GTPase of unknown function 2Cscore 1.7e-44 NC_002163.1 RefSeq region 897622 897645 . - . ID=id1787;gene=trmE;Name=id1787;Dbxref=GeneID:905249;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq gene 898298 899116 . - . ID=gene911;gene=Cj0957c;Name=Cj0957c;locus_tag=Cj0957c;Dbxref=GeneID:906015;gbkey=Gene NC_002163.1 RefSeq CDS 898298 899116 . - 0 ID=cds851;Parent=gene911;Name=YP_002344355.1;Dbxref=UniProtKB FTrEMBL:Q0P9U2 Genbank:YP_002344355.1 GeneID:906015;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0957c 2C unknown 2C len: 272 aa 3B 42.5 25 identity to HP1451. Functional classification -Conserved hypothetical proteins ### NC_002163.1 RefSeq CDS 899120 900706 . - 0 ID=cds852;Parent=gene912;Name=YP_002344356.1;Dbxref=GOA:Q9PNX7 InterPro:IPR001708 InterPro:IPR013308 UniProtKB FSwiss-Prot:Q9PNX7 Genbank:YP_002344356.1 GeneID:904358;gbkey=CDS;product=inner membrane protein translocase component YidC;Note=functions to insert inner membrane proteins into the IM in Escherichia coli 3B interacts with transmembrane segments 3B functions in both Sec-dependent and -independent membrane insertion 3B similar to Oxa1p in mitochondria NC_002163.1 RefSeq gene 899120 900706 . - . ID=gene912;Name=Cj0958c;locus_tag=Cj0958c;Dbxref=GeneID:904358;gbkey=Gene NC_002163.1 RefSeq region 899153 899707 . - . ID=id1788;Name=id1788;Dbxref=GeneID:904358;gbkey=misc_feature;Note=HMMPfam hit to PF02096 2C 60Kd inner membrane protein 2C score 1.1e-110 NC_002163.1 RefSeq region 899204 899272 . - . ID=id74;Name=id74;Dbxref=GeneID:904358;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0958c by TMHMM2.0 at aa 13-32 2C 332-354 2C 400-422 2C 442-459 and 479-501 NC_002163.1 RefSeq region 899330 899383 . - . ID=id74;Name=id74;Dbxref=GeneID:904358;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0958c by TMHMM2.0 at aa 13-32 2C 332-354 2C 400-422 2C 442-459 and 479-501 NC_002163.1 RefSeq region 899441 899509 . - . ID=id74;Name=id74;Dbxref=GeneID:904358;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0958c by TMHMM2.0 at aa 13-32 2C 332-354 2C 400-422 2C 442-459 and 479-501 NC_002163.1 RefSeq region 899645 899713 . - . ID=id74;Name=id74;Dbxref=GeneID:904358;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0958c by TMHMM2.0 at aa 13-32 2C 332-354 2C 400-422 2C 442-459 and 479-501 NC_002163.1 RefSeq region 900611 900670 . - . ID=id74;Name=id74;Dbxref=GeneID:904358;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj0958c by TMHMM2.0 at aa 13-32 2C 332-354 2C 400-422 2C 442-459 and 479-501 NC_002163.1 RefSeq gene 900703 901044 . - . ID=gene913;Name=Cj0959c;locus_tag=Cj0959c;Dbxref=GeneID:905228;gbkey=Gene NC_002163.1 RefSeq CDS 900703 901044 . - 0 ID=cds853;Parent=gene913;Name=YP_002344357.1;Dbxref=InterPro:IPR002696 UniProtKB FSwiss-Prot:Q9PNX6 Genbank:YP_002344357.1 GeneID:905228;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0959c 2C unknown 2C len: 113 aa 3B similar to hypothetical proteins from a wide range of organisms 2C e.g. YIDD_BUCAP 2885 aa 29 2C fasta scores 3B opt: 168 z-score: 234.3 E 28 29: 9.5e-06 2C 32.3 25 identity in 65 aa overlap 2C and YIDD_ECOLI 2885 aa 29 2C fasta scores 3B opt: 156 z-score: 218.9 E 28 29: 6.8e-05 2C 31.7 25 identity in 63 aa overlap. Also similar to TR:Q44066 28EMBL:L36462 29 Aeromonas hydrophila ALPHA-HEMOLYSIN 2885 aa 29 2C fasta scores 3B opt: 156 z-score: 218.9 E 28 29: 6.8e-05 2C 31.7 25 identity in 63 aa overlap. 34.2 25 identity to HP1449 7EUpdated 282006 29 note: Pfam domain PF01809 Domain of unknown function DUF37 identified within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq region 900847 901044 . - . ID=id1789;Name=id1789;Dbxref=GeneID:905228;gbkey=misc_feature;Note=HMMPfam hit to PF01809 2C Domain of unknown function DUF37 2C score 6e-25 NC_002163.1 RefSeq gene 901041 901367 . - . ID=gene914;gene=rnpA;Name=rnpA;locus_tag=Cj0960c;Dbxref=GeneID:905252;gbkey=Gene NC_002163.1 RefSeq CDS 901041 901367 . - 0 ID=cds854;Parent=gene914;gene=rnpA;Name=YP_002344358.1;Dbxref=GOA:Q9PNX5 InterPro:IPR000100 InterPro:IPR014721 UniProtKB FSwiss-Prot:Q9PNX5 Genbank:YP_002344358.1 GeneID:905252;gbkey=CDS;product=ribonuclease P protein component;Note=Original 282000 29 note: Cj0960c 2C rnpA 2C probable ribonuclease P protein component 2C len: 108 aa 3B similar to e.g. RNPA_BACSU ribonuclease P protein component 28EC 3.1.26.5 29 28116 aa 29 2C fasta scores 3B opt: 195 z-score: 280.1 E 28 29: 2.6e-08 2C 27.9 25 identity in 111 aa overlap. 31.9 25 identity to HP1448. Contains Pfam match to entry PF00825 Ribonuclease_P 2C Ribonuclease P 7EUpdated 282006 29 note: Prosite domain PS00648 RIBONUCLEASE_P 2C Bacterial ribonuclease P protein identified within CDS. Further support given to product function. Characterised in Bacillus subtilis 2C however 2Cidentity score was marginal. not added to product function. Functional classification - RNA synthesis 2C RNA modification and DNA transcription 7EPMID:9628904 NC_002163.1 RefSeq region 901053 901367 . - . ID=id1790;gene=rnpA;Name=id1790;Dbxref=GeneID:905252;gbkey=misc_feature;Note=HMMPfam hit to PF00825 2C Ribonuclease P 2C score 2.6e-15 NC_002163.1 RefSeq CDS 901364 901498 . - 0 ID=cds855;Parent=gene915;gene=rpmH;Name=YP_002344359.1;Dbxref=GOA:Q9PNX4 InterPro:IPR000271 UniProtKB FSwiss-Prot:Q9PNX4 Genbank:YP_002344359.1 GeneID:905034;gbkey=CDS;product=50S ribosomal protein L34;Note=in Escherichia coli transcription of this gene is enhanced by polyamines NC_002163.1 RefSeq gene 901364 901498 . - . ID=gene915;gene=rpmH;Name=rpmH;locus_tag=Cj0961c;Dbxref=GeneID:905034;gbkey=Gene NC_002163.1 RefSeq region 901367 901498 . - . ID=id1791;gene=rpmH;Name=id1791;Dbxref=GeneID:905034;gbkey=misc_feature;Note=HMMPfam hit to PF00468 2C Ribosomal protein L34 2Cscore 2.7e-18 NC_002163.1 RefSeq region 901436 901495 . - . ID=id1792;gene=rpmH;Name=id1792;Dbxref=GeneID:905034;gbkey=misc_feature;Note=PS00784 Ribosomal protein L34 signature ### NC_002163.1 UTR_Extractor 5'-UTR 901499 901529 . - . ID=utr340;locus_tag=Cj0961c;product=50S ribosomal protein L34 NC_002163.1 UTR_Extractor 5'-UTR 901608 901628 . + . ID=utr341;locus_tag=Cj0962;product=putative acetyltransferase NC_002163.1 RefSeq CDS 901629 902108 . + 0 ID=cds856;Parent=gene916;Name=YP_002344360.1;Dbxref=GOA:Q0P9T7 InterPro:IPR000182 InterPro:IPR016181 UniProtKB FTrEMBL:Q0P9T7 Genbank:YP_002344360.1 GeneID:905253;gbkey=CDS;product=acetyltransferase;Note=Original 282000 29 note: Cj0962 2C possible acetyltransferase 2C len: 159 aa 3B most similar to eukaryotic acetyltransferases 2C e.g. TR:P79081 28EMBL:U82218 29 Schizosaccharomyces pombe acetyltransferase ATS1 28168 aa 29 2C fasta scores 3B opt: 317 z-score: 406.2 E 28 29: 2.5e-15 2C 34.6 25 identity in 162 aa overlap 2C and ATDA_MOUSE diamine acetyltransferase 28171 aa 29 2C fasta scores 3B opt: 211 z-score: 274.9 E 28 29: 5.2e-08 2C 27.4 25 identity in 168 aa overlap. No Hp match. Contains Pfam match to entry PF00583 Acetyltransf 2C Acetyltransferase 28GNAT 29 family 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification -Misc NC_002163.1 RefSeq gene 901629 902108 . + . ID=gene916;Name=Cj0962;locus_tag=Cj0962;Dbxref=GeneID:905253;gbkey=Gene NC_002163.1 RefSeq region 901788 902042 . + . ID=id1793;Name=id1793;Dbxref=GeneID:905253;gbkey=misc_feature;Note=HMMPfam hit to PF00583 2C Acetyltransferase 28GNAT 29 family 2C score 1.8e-13 NC_002163.1 RefSeq gene 902105 902713 . + . ID=gene917;Name=Cj0963;locus_tag=Cj0963;Dbxref=GeneID:905142;gbkey=Gene NC_002163.1 RefSeq CDS 902105 902713 . + 0 ID=cds857;Parent=gene917;Name=YP_002344361.1;Dbxref=GOA:Q0P9T6 InterPro:IPR005122 UniProtKB FTrEMBL:Q0P9T6 Genbank:YP_002344361.1 GeneID:905142;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0963 2C unknown 2C len: 202 aa 3B similar to hypothetical proteins e.g. TR:O67598 28EMBL:AE000751 29 Aquifex aeolicus DPLF 28195 aa 29 2C fasta scores 3B opt: 234 z-score: 301.4 E 28 29: 1.7e-09 2C 27.2 25 identity in 184 aa overlap. 21.4 25 identity to HP0650. Functional classification - Conserved hypothetical proteins NC_002163.1 UTR_Extractor 5'-UTR 902482 902709 . + . ID=utr342;locus_tag=Cj0964;product=putative periplasmic protein NC_002163.1 RefSeq gene 902710 903900 . + . ID=gene918;Name=Cj0964;locus_tag=Cj0964;Dbxref=GeneID:905256;gbkey=Gene NC_002163.1 RefSeq CDS 902710 903900 . + 0 ID=cds858;Parent=gene918;Name=YP_002344362.1;Dbxref=UniProtKB FTrEMBL:Q0P9T5 Genbank:YP_002344362.1 GeneID:905256;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0964 2C probable periplasmic protein 2C len: 396 aa 3B 26.6 25 identity to HP0781. Contains probable N-terminal signal sequence. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq CDS 903892 904266 . - 0 ID=cds859;Parent=gene919;Name=YP_002344363.1;Dbxref=GOA:Q0P9T4 InterPro:IPR006683 InterPro:IPR006684 InterPro:IPR008272 UniProtKB FTrEMBL:Q0P9T4 Genbank:YP_002344363.1 GeneID:905257;gbkey=CDS;product=acyl-CoA thioester hydrolase;Note=Original 282000 29 note: Cj0965c 2C unknown 2C len: 124 aa 3B similar to hypothetical proteins e.g. YBGC_ECOLI 28134 aa 29 2C fasta scores 3B opt: 235 z-score: 313.7 E 28 29: 3.5e-10 2C38.1 25 identity in 113 aa overlap. 40.6 25 identity to HP0496 7EUpdated 282006 29 note: Pfam domain PF03061 Thioesterase superfamily and Prosite domain PS01328 4HBCOA_THIOESTERASE 2C 4-hydroxybenzoyl-CoA thioesterase 2Cactive site identified within CDS. Product modified to more specific family member based on motif match. Some characterisation carried out in Escerichia coli with acceptable identity score. kept in product function. Functional classification - Misc 7EPMID:15808744 NC_002163.1 RefSeq gene 903892 904266 . - . ID=gene919;Name=Cj0965c;locus_tag=Cj0965c;Dbxref=GeneID:905257;gbkey=Gene NC_002163.1 RefSeq region 903979 904230 . - . ID=id1794;Name=id1794;Dbxref=GeneID:905257;gbkey=misc_feature;Note=HMMPfam hit to PF03061 2C Thioesterase superfamily 2Cscore 1.4e-18 NC_002163.1 RefSeq region 904204 904257 . - . ID=id1795;Name=id1795;Dbxref=GeneID:905257;gbkey=misc_feature;Note=PS01328 4-hydroxybenzoyl-CoA thioesterase family active site ### NC_002163.1 UTR_Extractor 5'-UTR 904267 904302 . - . ID=utr343;locus_tag=Cj0965c;product=putative acyl-CoA thioester hydrolase NC_002163.1 RefSeq CDS 904409 906697 . + 0 ID=cds860;Parent=gene920;Name=YP_002344364.1;Dbxref=InterPro:IPR000169 InterPro:IPR000834 UniProtKB FTrEMBL:Q0P9T3 Genbank:YP_002344364.1 GeneID:905258;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0967 2C possible periplasmic protein 2C len: 762 aa 3B no Hp match. N- and C- termini are similar to two consecutive genes Cj0735 2837.8 25 identity in 214 aa overlap 29 and Cj0736 2842.3 25 identity in 562 aa overlap 29. Contains probable N-terminal signal sequence. Note that an ATA initiation codon has been used: this is consistent with the RBS 2C the similarity to Cj0735 2C and measures of coding likelyhood based on aa usage. Contains S00639 Eukaryotic thiol 28cysteine 29 proteases histidine active site 2C PS00133 Zinc carboxypeptidases 2C zinc-binding region 2 signature 2C and PS00017 ATP 2FGTP-binding site motif A 28P-loop 29. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 904409 906697 . + . ID=gene920;Name=Cj0967;locus_tag=Cj0967;Dbxref=GeneID:905258;gbkey=Gene NC_002163.1 RefSeq region 904736 904768 . + . ID=id1796;Name=id1796;Dbxref=GeneID:905258;gbkey=misc_feature;Note=PS00639 Eukaryotic thiol 28cysteine 29 proteases histidine active site NC_002163.1 RefSeq region 904763 904795 . + . ID=id1797;Name=id1797;Dbxref=GeneID:905258;gbkey=misc_feature;Note=PS00133 Zinc carboxypeptidases 2C zinc-binding region 2 signature NC_002163.1 RefSeq region 905468 905491 . + . ID=id1798;Name=id1798;Dbxref=GeneID:905258;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 RefSeq sRNA 906748 907066 . - . ID=NC_002163.1:Intergenic_906748_907066:unknown_transcript_1;Parent=NC_002163.1:Intergenic_906748_907066;Name=NC_002163.1:Intergenic_906748_907066:unknown_transcript_1;locus_tag=Intergenic_906748_907066;gbkey=misc_RNA;product=Intergenic_906748_907066 NC_002163.1 RefSeq gene 906748 907066 . - . ID=NC_002163.1:Intergenic_906748_907066;Name=NC_002163.1:Intergenic_906748_907066;locus_tag=Intergenic_906748_907066 NC_002163.1 RefSeq stem_loop 906964 907004 . + . ID=id1799;Name=id1799;gbkey=stem_loop NC_002163.1 UTR_Extractor 5'-UTR 906973 907116 . + . ID=utr344;locus_tag=Cj0969;product=pseudo ### NC_002163.1 RefSeq region 907117 907305 . + . ID=id1800;Name=id1800;Dbxref=GeneID:905260;gbkey=misc_feature;Note=Original 282000 29 note: Cj0968 2C probable periplasmic protein 2C len: 80 aa 3B no Hp match. Contains probable N-terminal signal sequence. Similar to N-terminus of Cj0737 2853.3 25 identity in 92 aa overlap 29. The similarity continues in Cj0968 2C suggesting that this may be the start of a pseudogene 7EOriginal 282000 29 note: Cj0969 2C probable pseudogene 2Clen 132 bp 3B 65.4 25 identical to part of Cj0737 2C similarity continues from upstream ORF. No Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity scores has been carried out yet. Thus 2C kept within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq pseudogene 907117 907396 . + . ID=gene921;Name=Cj0969;locus_tag=Cj0969;Dbxref=GeneID:905260;gbkey=Gene NC_002163.1 RefSeq region 907289 907396 . + . ID=id1800;Name=id1800;Dbxref=GeneID:905260;gbkey=misc_feature;Note=Original 282000 29 note: Cj0968 2C probable periplasmic protein 2C len: 80 aa 3B no Hp match. Contains probable N-terminal signal sequence. Similar to N-terminus of Cj0737 2853.3 25 identity in 92 aa overlap 29. The similarity continues in Cj0968 2C suggesting that this may be the start of a pseudogene 7EOriginal 282000 29 note: Cj0969 2C probable pseudogene 2Clen 132 bp 3B 65.4 25 identical to part of Cj0737 2C similarity continues from upstream ORF. No Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity scores has been carried out yet. Thus 2C kept within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Miscellaneous periplasmic proteins ### NC_002163.1 RefSeq gene 907408 907710 . + . ID=gene922;Name=Cj0970;locus_tag=Cj0970;Dbxref=GeneID:905261;gbkey=Gene NC_002163.1 RefSeq CDS 907408 907710 . + 0 ID=cds861;Parent=gene922;Name=YP_002344365.1;Dbxref=UniProtKB FTrEMBL:Q0P9T2 Genbank:YP_002344365.1 GeneID:905261;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0970 2C unknown 2C len: 100 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 RefSeq gene 907713 908105 . + . ID=gene923;Name=Cj0971;locus_tag=Cj0971;Dbxref=GeneID:905262;gbkey=Gene NC_002163.1 RefSeq CDS 907713 908105 . + 0 ID=cds862;Parent=gene923;Name=YP_002344366.1;Dbxref=UniProtKB FTrEMBL:Q0P9T1 Genbank:YP_002344366.1 GeneID:905262;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0971 2C unknown 2C len: 130 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 RefSeq gene 908107 908430 . + . ID=gene924;Name=Cj0972;locus_tag=Cj0972;Dbxref=GeneID:905263;gbkey=Gene NC_002163.1 RefSeq CDS 908107 908430 . + 0 ID=cds863;Parent=gene924;Name=YP_002344367.1;Dbxref=UniProtKB FTrEMBL:Q0P9T0 Genbank:YP_002344367.1 GeneID:905263;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0972 2C unknown 2C len: 107 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 RefSeq pseudogene 908554 908705 . + . ID=gene925;Name=Cj0973;locus_tag=Cj0973;Dbxref=GeneID:905264;gbkey=Gene NC_002163.1 RefSeq gene 908693 908833 . + . ID=gene926;Name=Cj0974;locus_tag=Cj0974;Dbxref=GeneID:905265;gbkey=Gene NC_002163.1 RefSeq CDS 908693 908833 . + 0 ID=cds864;Parent=gene926;Name=YP_002344369.1;Dbxref=UniProtKB FTrEMBL:Q0P9S8 Genbank:YP_002344369.1 GeneID:905265;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0974 2C questionable CDS 2C len 46 aa 3B no Hp match. Functional classification - Unknown ### NC_002163.1 RefSeq gene 908891 910615 . + . ID=gene927;Name=Cj0975;locus_tag=Cj0975;Dbxref=GeneID:905266;gbkey=Gene NC_002163.1 RefSeq CDS 908891 910615 . + 0 ID=cds865;Parent=gene927;Name=YP_002344370.1;Dbxref=InterPro:IPR013686 UniProtKB FTrEMBL:Q0P9S7 Genbank:YP_002344370.1 GeneID:905266;gbkey=CDS;product=outer-membrane protein;Note=Original 282000 29 note: Cj0975 2C probable outer-membrane protein 2C len: 584 aa 3B similar to OM proteins involved in specific protein secretion 2Factivation e.g. HXB1_HAEIN heme-hemopexin utilization protein B precursor 28565 aa 29 2C fasta scores 3B opt: 489 z-score: 539.9 E 28 29: 9e-23 2C 23.9 25 identity in 570 aa overlap 2C and HLYB_PROMI hemolysin activator protein precursor 28561 aa 29 2Cfasta scores 3B opt: 220 z-score: 244.2 E 28 29: 2.7e-06 2C 21.0 25 identity in 539 aa overlap. No Hp match. Apparently a complete copy of pseudogene Cj0742 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification -Protein and peptide secretion NC_002163.1 UTR_Extractor 5'-UTR 910700 910710 . + . ID=utr345;locus_tag=Cj0976;product=putative methyltransferase NC_002163.1 RefSeq gene 910711 911601 . + . ID=gene928;Name=Cj0976;locus_tag=Cj0976;Dbxref=GeneID:905267;gbkey=Gene NC_002163.1 RefSeq CDS 910711 911601 . + 0 ID=cds866;Parent=gene928;Name=YP_002344371.1;Dbxref=GOA:Q0P9S6 UniProtKB FSwiss-Prot:Q0P9S6 Genbank:YP_002344371.1 GeneID:905267;gbkey=CDS;product=methyltransferase;Note=Original 282000 29 note: Cj0976 2C unknown 2C len: 296 aa 3B similar to hypothetical proteins e.g. YECP_ECOLI 28323 aa 29 2Cfatsta scores 3B opt: 649 z-score: 775.1 E 28 29: 0 2C 35.7 25 identity in 291 aa overlap. 51.2 25 identity to HP0419 7EUpdated 282006 29 note: Prosite domain PS50124 methyltransferase identified within CDS. Product modified to more specific family member based on motif match. kept within product function. Functional classification - Misc NC_002163.1 UTR_Extractor 5'-UTR 911633 911673 . + . ID=utr346;locus_tag=Cj0977;product=hypothetical protein NC_002163.1 RefSeq gene 911674 912252 . + . ID=gene929;Name=Cj0977;locus_tag=Cj0977;Dbxref=GeneID:905268;gbkey=Gene NC_002163.1 RefSeq CDS 911674 912252 . + 0 ID=cds867;Parent=gene929;Name=YP_002344372.1;Dbxref=UniProtKB FTrEMBL:Q0P9S5 Genbank:YP_002344372.1 GeneID:905268;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0977 2C unknown 2C len: 192 aa 3B 29.2 25 identity to HP0420 7EUpdated 282006 29 note: Literature search identified paper linking product function to be involved with invasion of intestinal epithelial cells. Functional classification - Conserved hypothetical proteins 7EPMID:16369037 NC_002163.1 RefSeq gene 912253 912426 . - . ID=gene930;Name=Cj0978c;locus_tag=Cj0978c;Dbxref=GeneID:905269;gbkey=Gene NC_002163.1 RefSeq CDS 912253 912426 . - 0 ID=cds868;Parent=gene930;Name=YP_002344373.1;Dbxref=UniProtKB FTrEMBL:Q0P9S4 Genbank:YP_002344373.1 GeneID:905269;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj0978c 2C probable lipoprotein 2C len: 57 aa 3B no Hp match. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 912376 912408 . - . ID=id1801;Name=id1801;Dbxref=GeneID:905269;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 UTR_Extractor 5'-UTR 912427 912620 . - . ID=utr347;locus_tag=Cj0978c;product=putative lipoprotein NC_002163.1 RefSeq CDS 912435 912962 . - 0 ID=cds869;Parent=gene931;Name=YP_002344374.1;Dbxref=GOA:Q0P9S3 InterPro:IPR006021 UniProtKB FTrEMBL:Q0P9S3 Genbank:YP_002344374.1 GeneID:905270;gbkey=CDS;product=nuclease;Note=Original 282000 29 note: Cj0979c 2C probable secreted nuclease 2C len: 175 aa 3B similar to many e.g. NUC_STAHY thermonuclease precursor 28EC 3.1.31.1 29 28169 aa 29 2C fasta scores 3B opt: 206 z-score: 261.7 E 28 29: 2.8e-07 2C 36.9 25 identity in 122 aa overlap. No Hp match. Contains possible N-terminal signal sequence and Pfam match to entry PF00565 SNase 2C Staphylococcal nuclease homologues 7EUpdated 282006 29 note: Some characterisation work in Staphylococcus spp. kept in product function. Functional classification - Degradation of macromolecules - DNA 7EPMID:67041918 NC_002163.1 RefSeq gene 912435 912962 . - . ID=gene931;Name=Cj0979c;locus_tag=Cj0979c;Dbxref=GeneID:905270;gbkey=Gene NC_002163.1 RefSeq region 912483 912839 . - . ID=id1802;Name=id1802;Dbxref=GeneID:905270;gbkey=misc_feature;Note=HMMPfam hit to PF00565 2C Staphylococcal nuclease homologue 2C score 1.3e-34 NC_002163.1 RefSeq region 912846 912902 . - . ID=id1803;Name=id1803;Dbxref=GeneID:905270;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0979c by TMHMM2.0 at aa 21-39 ### NC_002163.1 UTR_Extractor 5'-UTR 912963 912998 . - . ID=utr348;locus_tag=Cj0979c;product=putative secreted nuclease NC_002163.1 UTR_Extractor 5'-UTR 913013 913029 . + . ID=utr349;locus_tag=Cj0980;product=putative peptidase NC_002163.1 RefSeq CDS 913030 914298 . + 0 ID=cds870;Parent=gene932;Name=YP_002344375.1;Dbxref=GOA:Q0P9S2 InterPro:IPR001160 UniProtKB FTrEMBL:Q0P9S2 Genbank:YP_002344375.1 GeneID:905271;gbkey=CDS;product=peptidase;Note=Original 282000 29 note: Cj0980 2C possible peptidase 2Clen: 422 aa 3B similar to e.g. PEPD_ECOLI aminoacyl-histidine dipeptidase 28484 aa 29 2C fasta scores 3B opt: 175 z-score: 206.9 E 28 29: 0.00032 2C 31.1 25 identity in 476 aa overlap. No Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification -Degradation of macromolecules - Proteins 2C peptides and glycopeptides 7EPMID:2651887 NC_002163.1 RefSeq gene 913030 914298 . + . ID=gene932;Name=Cj0980;locus_tag=Cj0980;Dbxref=GeneID:905271;gbkey=Gene NC_002163.1 RefSeq CDS 914281 915528 . - 0 ID=cds871;Parent=gene933;gene=cjaB;Name=YP_002344376.1;Dbxref=GOA:Q0P9S1 InterPro:IPR007114 InterPro:IPR011701 UniProtKB FTrEMBL:Q0P9S1 Genbank:YP_002344376.1 GeneID:905272;gbkey=CDS;product=MFS transport protein;Note=Original 282000 29 note: Cj0981c 2C transmembrane transport protein 2C len: 415 aa 3B similar to many members of the sugar transporter family e.g. YHJE_ECOLI hypothetical metabolite transport protein I 28440 aa 29 2C fasta scores 3B opt: 548 z-score: 610.3 E 28 29: 1.1e-26 2C 30.4 25 identity in 418 aa overlap 2C and PROP_ECOLI proline 2Fbetaine transporter 28500 aa 29 2C fasta scores 3B opt: 474 z-score: 528.2 E 28 29: 4e-22 2C 28.0 25 identity in 421 aa overlap. No Hp ortholog. Contains PS00216 Sugar transport protein 7EUpdated 282006 29 note: Pfam domains PF07690 Major Facilitator Superfamily and PF00083 Sugar 28and other 29 transporter 2C were identified within CDS. Twelve probable transmembrane helices predicted by TMHMM2.0. Product modified to more specific family member based on motif match. Not specifically characterised yet 2C so kept in product function. Some characterisation work carried out within Campylobacter jejuni. Gene name has been added. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:9395059 NC_002163.1 RefSeq gene 914281 915528 . - . ID=gene933;gene=cjaB;Name=cjaB;locus_tag=Cj0981c;Dbxref=GeneID:905272;gbkey=Gene NC_002163.1 RefSeq region 914284 915513 . - . ID=id1804;gene=cjaB;Name=id1804;Dbxref=GeneID:905272;gbkey=misc_feature;Note=HMMPfam hit to PF00083 2C Sugar 28and other 29 transporter 2C score 6.5e-10 NC_002163.1 RefSeq region 914332 914391 . - . ID=id75;gene=cjaB;Name=id75;Dbxref=GeneID:905272;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0981c by TMHMM2.0 at aa 7-29 2C 44-66 2C 79-98 2C 103-122 2C142-164 2C 179-198 2C 232-254 2C 269-291 2C 298-315 2C 320-342 2C354-376 and 380-399 NC_002163.1 RefSeq region 914356 914388 . - . ID=id1805;gene=cjaB;Name=id1805;Dbxref=GeneID:905272;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 914395 915498 . - . ID=id1806;gene=cjaB;Name=id1806;Dbxref=GeneID:905272;gbkey=misc_feature;Note=HMMPfam hit to PF07690 2C Major Facilitator Superfamily 2C score 2.8e-19 NC_002163.1 RefSeq region 914401 914469 . - . ID=id75;gene=cjaB;Name=id75;Dbxref=GeneID:905272;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0981c by TMHMM2.0 at aa 7-29 2C 44-66 2C 79-98 2C 103-122 2C142-164 2C 179-198 2C 232-254 2C 269-291 2C 298-315 2C 320-342 2C354-376 and 380-399 NC_002163.1 RefSeq region 914503 914571 . - . ID=id75;gene=cjaB;Name=id75;Dbxref=GeneID:905272;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0981c by TMHMM2.0 at aa 7-29 2C 44-66 2C 79-98 2C 103-122 2C142-164 2C 179-198 2C 232-254 2C 269-291 2C 298-315 2C 320-342 2C354-376 and 380-399 NC_002163.1 RefSeq region 914584 914637 . - . ID=id75;gene=cjaB;Name=id75;Dbxref=GeneID:905272;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0981c by TMHMM2.0 at aa 7-29 2C 44-66 2C 79-98 2C 103-122 2C142-164 2C 179-198 2C 232-254 2C 269-291 2C 298-315 2C 320-342 2C354-376 and 380-399 NC_002163.1 RefSeq region 914656 914724 . - . ID=id75;gene=cjaB;Name=id75;Dbxref=GeneID:905272;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0981c by TMHMM2.0 at aa 7-29 2C 44-66 2C 79-98 2C 103-122 2C142-164 2C 179-198 2C 232-254 2C 269-291 2C 298-315 2C 320-342 2C354-376 and 380-399 NC_002163.1 RefSeq region 914767 914835 . - . ID=id75;gene=cjaB;Name=id75;Dbxref=GeneID:905272;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0981c by TMHMM2.0 at aa 7-29 2C 44-66 2C 79-98 2C 103-122 2C142-164 2C 179-198 2C 232-254 2C 269-291 2C 298-315 2C 320-342 2C354-376 and 380-399 NC_002163.1 RefSeq region 914935 914994 . - . ID=id75;gene=cjaB;Name=id75;Dbxref=GeneID:905272;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0981c by TMHMM2.0 at aa 7-29 2C 44-66 2C 79-98 2C 103-122 2C142-164 2C 179-198 2C 232-254 2C 269-291 2C 298-315 2C 320-342 2C354-376 and 380-399 NC_002163.1 RefSeq region 915037 915105 . - . ID=id75;gene=cjaB;Name=id75;Dbxref=GeneID:905272;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0981c by TMHMM2.0 at aa 7-29 2C 44-66 2C 79-98 2C 103-122 2C142-164 2C 179-198 2C 232-254 2C 269-291 2C 298-315 2C 320-342 2C354-376 and 380-399 NC_002163.1 RefSeq region 915163 915222 . - . ID=id75;gene=cjaB;Name=id75;Dbxref=GeneID:905272;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0981c by TMHMM2.0 at aa 7-29 2C 44-66 2C 79-98 2C 103-122 2C142-164 2C 179-198 2C 232-254 2C 269-291 2C 298-315 2C 320-342 2C354-376 and 380-399 NC_002163.1 RefSeq region 915235 915294 . - . ID=id75;gene=cjaB;Name=id75;Dbxref=GeneID:905272;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0981c by TMHMM2.0 at aa 7-29 2C 44-66 2C 79-98 2C 103-122 2C142-164 2C 179-198 2C 232-254 2C 269-291 2C 298-315 2C 320-342 2C354-376 and 380-399 NC_002163.1 RefSeq region 915280 915330 . - . ID=id1807;gene=cjaB;Name=id1807;Dbxref=GeneID:905272;gbkey=misc_feature;Note=PS00216 Sugar transport proteins signature 1 NC_002163.1 RefSeq region 915331 915399 . - . ID=id75;gene=cjaB;Name=id75;Dbxref=GeneID:905272;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0981c by TMHMM2.0 at aa 7-29 2C 44-66 2C 79-98 2C 103-122 2C142-164 2C 179-198 2C 232-254 2C 269-291 2C 298-315 2C 320-342 2C354-376 and 380-399 NC_002163.1 RefSeq region 915442 915510 . - . ID=id75;gene=cjaB;Name=id75;Dbxref=GeneID:905272;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj0981c by TMHMM2.0 at aa 7-29 2C 44-66 2C 79-98 2C 103-122 2C142-164 2C 179-198 2C 232-254 2C 269-291 2C 298-315 2C 320-342 2C354-376 and 380-399 ### NC_002163.1 RefSeq CDS 915568 916407 . - 0 ID=cds872;Parent=gene934;gene=cjaA;Name=YP_002344377.1;Dbxref=GOA:Q0P9S0 InterPro:IPR001638 UniProtKB FTrEMBL:Q0P9S0 Genbank:YP_002344377.1 GeneID:905273;gbkey=CDS;product=amino acid transporter substrate-binding protein;Note=Original 282000 29 note: Cj0982c 2C probable amino-acid transporter periplasmic solute-binding protein 2C len: 279 aa 3B similar to e.g. GLNH_BACST glutamine-binding protein precursor 28262 aa 29 2C fasta scores 3B opt: 410 z-score: 484.3 E 28 29: 1.1e-19 2C 32.4 25 identity in 253 aa overlap. 98.2 25 identical to TR:O05414 28EMBL:U93169 29 C. jejuni OMPH1 2C and 89.2 25 identical to TR:P94643 28EMBL:U93169 29 C. jejuni CjaA. 56.1 25 identity to HP1172. Contains Pfam match to entry PF00497 SBP_bac_3 2C Bacterial extracellular solute-binding proteins 2C N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site 7EUpdated 282006 29 note: Similar to more than one genus with marginal identity scores. kept within product function. Some characterisation work carried out within Campylobacter jejuni. Gene name has been added. Functional classification - Transport 2Fbinding proteins -Other 7EPMID:9395059 NC_002163.1 RefSeq gene 915568 916407 . - . ID=gene934;gene=cjaA;Name=cjaA;locus_tag=Cj0982c;Dbxref=GeneID:905273;gbkey=Gene NC_002163.1 RefSeq region 915625 916287 . - . ID=id1808;gene=cjaA;Name=id1808;Dbxref=GeneID:905273;gbkey=misc_feature;Note=HMMPfam hit to PF00497 2C Bacterial extracellular solute-binding prot 2C score 4.6e-53 NC_002163.1 RefSeq region 916348 916380 . - . ID=id1809;gene=cjaA;Name=id1809;Dbxref=GeneID:905273;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 UTR_Extractor 5'-UTR 916408 916464 . - . ID=utr350;locus_tag=Cj0982c;product=putative amino-acid transporter periplasmic solute-binding protein NC_002163.1 UTR_Extractor 5'-UTR 916602 916625 . + . ID=utr351;locus_tag=Cj0983;product=putative lipoprotein NC_002163.1 RefSeq gene 916626 917744 . + . ID=gene935;Name=Cj0983;locus_tag=Cj0983;Dbxref=GeneID:905274;gbkey=Gene NC_002163.1 RefSeq CDS 916626 917744 . + 0 ID=cds873;Parent=gene935;Name=YP_002344378.1;Dbxref=GOA:P45492 UniProtKB FSwiss-Prot:P45492 Genbank:YP_002344378.1 GeneID:905274;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj0983 2C probable lipoprotein 2Clen: 372 aa 3B 97.0 25 identical to YHI4_CAMJE. No Hp match. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 916647 916679 . + . ID=id1810;Name=id1810;Dbxref=GeneID:905274;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq region 917836 918573 . + . ID=id1811;Name=id1811;Dbxref=GeneID:905275;gbkey=misc_feature;Note=HMMPfam hit to PF03883 2C Protein of unknown function 28DUF328 29 2C score 1.8e-128 NC_002163.1 RefSeq gene 917836 918576 . + . ID=gene936;Name=Cj0984;locus_tag=Cj0984;Dbxref=GeneID:905275;gbkey=Gene NC_002163.1 RefSeq CDS 917836 918576 . + 0 ID=cds874;Parent=gene936;Name=YP_002344379.1;Dbxref=InterPro:IPR005583 UniProtKB FSwiss-Prot:P45491 Genbank:YP_002344379.1 GeneID:905275;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0984 2C unknown 2C len: 246 aa 3B 97.2 25 identical to YHI3_CAMJE. No Hp match. Weak similarity to TR:O66885 28EMBL:AE000700 29 Aquifex aeolicus AQ_644 28227 aa 29 2C fasta scores 3B opt: 154 z-score: 190.3 E 28 29: 0.0027 2C 23.6 25 identity in 212 aa overlap 7EUpdated 282006 29 note: Pfam domain PF03883 Protein of unknown function 28DUF328 29 identified within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins ### NC_002163.1 RefSeq CDS 918580 919731 . - 0 ID=cds875;Parent=gene937;gene=hipO;Name=YP_002344380.1;Dbxref=GOA:P45493 InterPro:IPR002933 InterPro:IPR010168 InterPro:IPR011650 InterPro:IPR017439 UniProtKB FSwiss-Prot:P45493 Genbank:YP_002344380.1 GeneID:905276;gbkey=CDS;product=hippurate hydrolase;Note=Original 282000 29 note: Cj0985c 2C hipO 2C hippurate hydrolase 2C len: 383 aa 3B 99.0 25 identical to HIPO_CAMJE hippurate hydrolase 28EC 3.5.1.32 29 2C and similar to other hydrolases belinging to the peptidase M40 family 28AMA 2FHIPO 2FHYUC hydrolase family 29 e.g. CBPX_SULSO thermostable carboxypeptidase 28393 aa 29 2C fasta scores 3B opt: 805 z-score: 949.5 E 28 29: 0 2C 38.2 25 identity in 398 aa overlap 7EUpdated 282006 29 note: Pfam domains PF01546 Peptidase family M20 2FM25 2FM40 and PF07687 Peptidase dimerisation domain identified within CDS. Characterised in Campylobacter jejuni 2C so not added to product function. Functional classification - Misc 7EPMID:7730270 NC_002163.1 RefSeq gene 918580 919731 . - . ID=gene937;gene=hipO;Name=hipO;locus_tag=Cj0985c;Dbxref=GeneID:905276;gbkey=Gene NC_002163.1 RefSeq region 918592 919518 . - . ID=id1812;gene=hipO;Name=id1812;Dbxref=GeneID:905276;gbkey=misc_feature;Note=HMMPfam hit to PF01546 2C Peptidase family M20 2FM25 2FM40 2C score 8.8e-44 NC_002163.1 RefSeq region 918658 918681 . - . ID=id1813;gene=hipO;Name=id1813;Dbxref=GeneID:905276;gbkey=misc_feature;Note=PS00881 Protein splicing signature NC_002163.1 RefSeq region 918883 919203 . - . ID=id1814;gene=hipO;Name=id1814;Dbxref=GeneID:905276;gbkey=misc_feature;Note=HMMPfam hit to PF07687 2C Peptidase dimerisation domain 2C score 3.8e-12 ### NC_002163.1 UTR_Extractor 5'-UTR 919732 919874 . - . ID=utr352;locus_tag=Cj0985c;product=hippurate hydrolase NC_002163.1 RefSeq pseudogene 919733 920953 . - . ID=gene938;Name=Cj0986c;locus_tag=Cj0986c;Dbxref=GeneID:905277;gbkey=Gene NC_002163.1 RefSeq region 919769 919837 . - . ID=id76;Name=id76;Dbxref=GeneID:905277;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0986c by TMHMM2.0 at aa 2-19 and 29-51 NC_002163.1 RefSeq region 919865 919918 . - . ID=id76;Name=id76;Dbxref=GeneID:905277;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj0986c by TMHMM2.0 at aa 2-19 and 29-51 NC_002163.1 RefSeq region 920033 920101 . - . ID=id77;Name=id77;Dbxref=GeneID:905277;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0987c by TMHMM2.0 at aa 12-31 2C 51-73 2C 80-97 2C 103-125 2C134-156 2C 171-188 2C 212-234 2C 256-273 and 285-307 NC_002163.1 RefSeq region 920135 920188 . - . ID=id77;Name=id77;Dbxref=GeneID:905277;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0987c by TMHMM2.0 at aa 12-31 2C 51-73 2C 80-97 2C 103-125 2C134-156 2C 171-188 2C 212-234 2C 256-273 and 285-307 NC_002163.1 RefSeq region 920252 920320 . - . ID=id77;Name=id77;Dbxref=GeneID:905277;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0987c by TMHMM2.0 at aa 12-31 2C 51-73 2C 80-97 2C 103-125 2C134-156 2C 171-188 2C 212-234 2C 256-273 and 285-307 NC_002163.1 RefSeq region 920390 920443 . - . ID=id77;Name=id77;Dbxref=GeneID:905277;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0987c by TMHMM2.0 at aa 12-31 2C 51-73 2C 80-97 2C 103-125 2C134-156 2C 171-188 2C 212-234 2C 256-273 and 285-307 NC_002163.1 RefSeq region 920486 920554 . - . ID=id77;Name=id77;Dbxref=GeneID:905277;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0987c by TMHMM2.0 at aa 12-31 2C 51-73 2C 80-97 2C 103-125 2C134-156 2C 171-188 2C 212-234 2C 256-273 and 285-307 NC_002163.1 RefSeq region 920579 920647 . - . ID=id77;Name=id77;Dbxref=GeneID:905277;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0987c by TMHMM2.0 at aa 12-31 2C 51-73 2C 80-97 2C 103-125 2C134-156 2C 171-188 2C 212-234 2C 256-273 and 285-307 NC_002163.1 RefSeq region 920663 920716 . - . ID=id77;Name=id77;Dbxref=GeneID:905277;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0987c by TMHMM2.0 at aa 12-31 2C 51-73 2C 80-97 2C 103-125 2C134-156 2C 171-188 2C 212-234 2C 256-273 and 285-307 NC_002163.1 RefSeq region 920735 920803 . - . ID=id77;Name=id77;Dbxref=GeneID:905277;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0987c by TMHMM2.0 at aa 12-31 2C 51-73 2C 80-97 2C 103-125 2C134-156 2C 171-188 2C 212-234 2C 256-273 and 285-307 NC_002163.1 RefSeq region 920861 920920 . - . ID=id77;Name=id77;Dbxref=GeneID:905277;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj0987c by TMHMM2.0 at aa 12-31 2C 51-73 2C 80-97 2C 103-125 2C134-156 2C 171-188 2C 212-234 2C 256-273 and 285-307 ### NC_002163.1 UTR_Extractor 5'-UTR 920954 920979 . - . ID=utr353;locus_tag=Cj0987c;product=putative MFS transport protein NC_002163.1 RefSeq CDS 920967 921203 . - 0 ID=cds876;Parent=gene939;Name=YP_002344383.1;Dbxref=UniProtKB FTrEMBL:Q0P9R4 Genbank:YP_002344383.1 GeneID:905279;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0988c 2C questionable CDS 2Clen: 78 aa 3B 98.3 25 identical to TR:Q46117 28EMBL:Z36940 29 C. jejuni hypothetical protein. No Hp match 7EUpdated 282006 29 note: One probable transmembrane helix predicted by TMHMM2.0. Functional classification -Unknown NC_002163.1 RefSeq gene 920967 921203 . - . ID=gene939;Name=Cj0988c;locus_tag=Cj0988c;Dbxref=GeneID:905279;gbkey=Gene NC_002163.1 RefSeq region 921078 921131 . - . ID=id1815;Name=id1815;Dbxref=GeneID:905279;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0988c by TMHMM2.0 at aa 25-42 NC_002163.1 UTR_Extractor 5'-UTR 921165 921187 . + . ID=utr354;locus_tag=Cj0989;product=hypothetical protein NC_002163.1 RefSeq gene 921188 921394 . + . ID=gene940;Name=Cj0989;locus_tag=Cj0989;Dbxref=GeneID:905280;gbkey=Gene NC_002163.1 RefSeq CDS 921188 921394 . + 0 ID=cds877;Parent=gene940;Name=YP_002344384.1;Dbxref=GOA:Q46118 UniProtKB FTrEMBL:Q46118 Genbank:YP_002344384.1 GeneID:905280;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0989 2C possible membrane protein 2C len: 68 aa 3B identical to TR:Q46118 28EMBL:Z36940 29 C. jejuni hypothetical protein. No Hp match 7EUpdated 282006 29 note: One probable transmembrane helix predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 921197 921250 . + . ID=id1816;Name=id1816;Dbxref=GeneID:905280;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj0989 by TMHMM2.0 at aa 4-21 ### NC_002163.1 RefSeq CDS 921397 922158 . - 0 ID=cds878;Parent=gene941;Name=YP_002344385.1;Dbxref=GOA:P45489 UniProtKB FSwiss-Prot:P45489 Genbank:YP_002344385.1 GeneID:905281;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0990c 2C unknown 2C len: 253 aa 3B identical in C-terminus to YHI1_CAMJE C. jejuni hypothetical protein fragment 2894 aa 29. No Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 RefSeq gene 921397 922158 . - . ID=gene941;Name=Cj0990c;locus_tag=Cj0990c;Dbxref=GeneID:905281;gbkey=Gene NC_002163.1 RefSeq CDS 922155 923420 . - 0 ID=cds879;Parent=gene942;Name=YP_002344386.1;Dbxref=GOA:Q0P9R1 InterPro:IPR001450 InterPro:IPR004017 InterPro:IPR012257 InterPro:IPR012285 UniProtKB FTrEMBL:Q0P9R1 Genbank:YP_002344386.1 GeneID:905282;gbkey=CDS;product=oxidoreductase ferredoxin-type electron transport protein;Note=Original 282000 29 note: Cj0991c 2C probable oxidoreductase ferredoxin-type electron transport protein 2Clen: 421 3B weak similarity to e.g. GLPC_ECOLI anaerobic glycerol-3-phosphate dehydrogenase subunit C 28396 aa 29 2Cfasta scores 3B opt: 280 z-score: 323.3 E 28 29: 1e-10 2C 23.3 25 identity in 425 aa overlap 2C and GLCF_ECOLI glycolate oxidase iron-sulfur subunit 28407 aa 29 2C fasta scores 3B opt: 199 z-score: 231.5 E 28 29: 1.4e-05 2C 22.3 25 identity in 413 aa overlap. 44.7 25 identity to HP0666 28annotated as glpC 2C but there are no homologs of glpA or glpB in Hp or Cj 29. Contains PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature 2C and 2x Pfam match to entry PF00037 fer4 2C4Fe-4S ferredoxins and related iron-sulfur cluster binding domains 7EUpdated 282006 29 note: Pfam domain PF02754 Cysteine-rich domain identified within CDS. No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification - Energy metabolism - Electron transport NC_002163.1 RefSeq gene 922155 923420 . - . ID=gene942;Name=Cj0991c;locus_tag=Cj0991c;Dbxref=GeneID:905282;gbkey=Gene NC_002163.1 RefSeq region 922227 922418 . - . ID=id1817;Name=id1817;Dbxref=GeneID:905282;gbkey=misc_feature;Note=HMMPfam hit to PF02754 2C Cysteine-rich domain 2C score 2.4e-11 NC_002163.1 RefSeq region 922638 922826 . - . ID=id1818;Name=id1818;Dbxref=GeneID:905282;gbkey=misc_feature;Note=HMMPfam hit to PF02754 2C Cysteine-rich domain 2C score 6.7e-10 NC_002163.1 RefSeq region 923190 923261 . - . ID=id1819;Name=id1819;Dbxref=GeneID:905282;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 0.0013 NC_002163.1 RefSeq region 923205 923240 . - . ID=id1820;Name=id1820;Dbxref=GeneID:905282;gbkey=misc_feature;Note=PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature ### NC_002163.1 RefSeq CDS 923422 924777 . - 0 ID=cds880;Parent=gene943;gene=hemN;Name=YP_002344387.1;Dbxref=GOA:Q0P9R0 InterPro:IPR004558 InterPro:IPR006638 InterPro:IPR007197 InterPro:IPR010723 UniProtKB FTrEMBL:Q0P9R0 Genbank:YP_002344387.1 GeneID:905283;gbkey=CDS;product=coproporphyrinogen III oxidase;Note=catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III NC_002163.1 RefSeq gene 923422 924777 . - . ID=gene943;gene=hemN;Name=hemN;locus_tag=Cj0992c;Dbxref=GeneID:905283;gbkey=Gene NC_002163.1 RefSeq region 923506 923862 . - . ID=id1821;gene=hemN;Name=id1821;Dbxref=GeneID:905283;gbkey=misc_feature;Note=HMMPfam hit to PF06969 2C HemN C-terminal region 2Cscore 6.8e-41 NC_002163.1 RefSeq region 924106 924633 . - . ID=id1822;gene=hemN;Name=id1822;Dbxref=GeneID:905283;gbkey=misc_feature;Note=HMMPfam hit to PF04055 2C Radical SAM superfamily 2Cscore 3.5e-26 NC_002163.1 RefSeq gene 924764 925255 . - . ID=gene944;gene=Cj0993c;Name=Cj0993c;locus_tag=Cj0993c;Dbxref=GeneID:905284;gbkey=Gene NC_002163.1 RefSeq CDS 924764 925255 . - 0 ID=cds881;Parent=gene944;Name=YP_002344388.1;Dbxref=GOA:Q0P9Q9 UniProtKB FTrEMBL:Q0P9Q9 Genbank:YP_002344388.1 GeneID:905284;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0993c 2C unknown 2C len: 163 aa 3B 30.1 25 identity to HP0664. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 925252 926172 . - . ID=gene945;gene=argF;Name=argF;locus_tag=Cj0994c;Dbxref=GeneID:905285;gbkey=Gene NC_002163.1 RefSeq CDS 925252 926172 . - 0 ID=cds882;Parent=gene945;gene=argF;Name=YP_002344389.1;Dbxref=GOA:Q9PNU6 HSSP:Q51742 InterPro:IPR002292 InterPro:IPR006130 InterPro:IPR006131 InterPro:IPR006132 UniProtKB FSwiss-Prot:Q9PNU6 Genbank:YP_002344389.1 GeneID:905285;gbkey=CDS;product=ornithine carbamoyltransferase;Note=catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation NC_002163.1 RefSeq region 925276 925749 . - . ID=id1823;gene=argF;Name=id1823;Dbxref=GeneID:905285;gbkey=misc_feature;Note=HMMPfam hit to PF00185 2C Aspartate 2Fornithine carbamoyltransferase 2C As 2C score 4.8e-46 NC_002163.1 RefSeq region 925756 926169 . - . ID=id1824;gene=argF;Name=id1824;Dbxref=GeneID:905285;gbkey=misc_feature;Note=HMMPfam hit to PF02729 2C Aspartate 2Fornithine carbamoyltransferase 2C ca 2C score 3.9e-67 NC_002163.1 RefSeq region 926026 926049 . - . ID=id1825;gene=argF;Name=id1825;Dbxref=GeneID:905285;gbkey=misc_feature;Note=PS00097 Aspartate and ornithine carbamoyltransferases signature NC_002163.1 RefSeq CDS 926169 927152 . - 0 ID=cds883;Parent=gene946;gene=hemB;Name=YP_002344390.1;Dbxref=GOA:Q0P9Q7 InterPro:IPR001731 InterPro:IPR013785 UniProtKB FTrEMBL:Q0P9Q7 Genbank:YP_002344390.1 GeneID:905286;gbkey=CDS;product=delta-aminolevulinic acid dehydratase;Note=catalyzes the formation of porphobilinogen from 5-aminolevulinate NC_002163.1 RefSeq gene 926169 927152 . - . ID=gene946;gene=hemB;Name=hemB;locus_tag=Cj0995c;Dbxref=GeneID:905286;gbkey=Gene NC_002163.1 RefSeq region 926184 927152 . - . ID=id1826;gene=hemB;Name=id1826;Dbxref=GeneID:905286;gbkey=misc_feature;Note=HMMPfam hit to PF00490 2C Delta-aminolevulinic acid dehydratase 2C score 2e-176 NC_002163.1 RefSeq region 926391 926429 . - . ID=id1827;gene=hemB;Name=id1827;Dbxref=GeneID:905286;gbkey=misc_feature;Note=PS00169 Delta-aminolevulinic acid dehydratase active site ### NC_002163.1 UTR_Extractor 5'-UTR 927184 927209 . + . ID=utr355;locus_tag=Cj0996;product=GTP cyclohydrolase II NC_002163.1 RefSeq region 927210 927698 . + . ID=id1828;gene=ribA;Name=id1828;Dbxref=GeneID:905287;gbkey=misc_feature;Note=HMMPfam hit to PF00925 2C GTP cyclohydrolase II 2Cscore 7e-67 NC_002163.1 RefSeq gene 927210 927770 . + . ID=gene947;gene=ribA;Name=ribA;locus_tag=Cj0996;Dbxref=GeneID:905287;gbkey=Gene NC_002163.1 RefSeq CDS 927210 927770 . + 0 ID=cds884;Parent=gene947;gene=ribA;Name=YP_002344391.1;Dbxref=GOA:Q0P9Q6 InterPro:IPR000926 UniProtKB FTrEMBL:Q0P9Q6 Genbank:YP_002344391.1 GeneID:905287;gbkey=CDS;product=GTP cyclohydrolase II;Note=catalyzes the conversion of GTP to formate and 2 2C5-diamino-6-hydroxy-4- 285-phosphoribosylamino 29pyrimidine and diphosphate ### NC_002163.1 RefSeq CDS 927771 928337 . + 0 ID=cds885;Parent=gene948;Name=YP_002344392.1;Dbxref=GOA:Q9PNU3 InterPro:IPR003682 UniProtKB FSwiss-Prot:Q9PNU3 Genbank:YP_002344392.1 GeneID:905288;gbkey=CDS;product=methyltransferase;Note=Original 282000 29 note: Cj0997 2C probable gidB homolog. len: 188 aa 3B similar to gidB proteins from many organisms e.g. GIDB_ECOLI glucose inhibited division protein B 28207 aa 29 2C fasta scores 3B opt: 212 z-score: 265.9 E 28 29: 1.6e-07 2C 24.7 25 identity in 182 aa overlap. 37.3 25 identity to HP1063 7EUpdated 282006 29 note: Pfam domain PF02527 Glucose inhibited division protein identified within CDS. Further support given to product function. Recent characterisation within Escherichia coli has identified GidB containing a methyltransferase fold 28PMID:12001236 29. Thus 2C product function has now been modified to more specific family member. Functional classification - Misc 7EPMID:12001236 NC_002163.1 RefSeq gene 927771 928337 . + . ID=gene948;Name=Cj0997;locus_tag=Cj0997;Dbxref=GeneID:905288;gbkey=Gene NC_002163.1 RefSeq region 927819 928325 . + . ID=id1829;Name=id1829;Dbxref=GeneID:905288;gbkey=misc_feature;Note=HMMPfam hit to PF02527 2C Glucose inhibited division protein 2C score 1.4e-21 NC_002163.1 RefSeq region 928323 928334 . + . ID=id1830;Name=id1830;Dbxref=GeneID:905288;gbkey=misc_feature;Note=PS00294 Prenyl group binding site 28CAAX box 29 ### NC_002163.1 RefSeq gene 928353 928925 . - . ID=gene949;Name=Cj0998c;locus_tag=Cj0998c;Dbxref=GeneID:905289;gbkey=Gene NC_002163.1 RefSeq CDS 928353 928925 . - 0 ID=cds886;Parent=gene949;Name=YP_002344393.1;Dbxref=UniProtKB FTrEMBL:Q0P9Q4 Genbank:YP_002344393.1 GeneID:905289;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj0998c 2C probable periplasmic protein 2C len: 190 aa 3B 33.9 25 identity to HP0305. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Paper identified linking protein to glycoprotein. Functional classification -Miscellaneous periplasmic proteins 7EPMID:12186869 NC_002163.1 UTR_Extractor 5'-UTR 928926 928956 . - . ID=utr356;locus_tag=Cj0998c;product=putative periplasmic protein NC_002163.1 RefSeq CDS 929020 930117 . - 0 ID=cds887;Parent=gene950;Name=YP_002344394.1;Dbxref=GOA:Q9PNU1 InterPro:IPR004630 UniProtKB FSwiss-Prot:Q9PNU1 Genbank:YP_002344394.1 GeneID:905290;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj0999c 2C probable integral membrane protein 2C len: 365 aa 3B similar to hypothetical membrane proteins e.g. YEIH_ECOLI 28349 aa 29 2C fasta scores 3B opt: 631 z-score: 729.2 E 28 29: 0 2C 35.7 25 identity in 347 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF03601 Conserved hypothetical protein identified within CDS. Also 2C eleven probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 929020 930117 . - . ID=gene950;Name=Cj0999c;locus_tag=Cj0999c;Dbxref=GeneID:905290;gbkey=Gene NC_002163.1 RefSeq region 929038 929106 . - . ID=id78;Name=id78;Dbxref=GeneID:905290;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0999c by TMHMM2.0 at aa 12-34 2C 44-63 2C 83-100 2C 105-127 2C134-153 2C 163-185 2C 197-219 2C 234-256 2C 269-288 2C 303-325 and 338-360 NC_002163.1 RefSeq region 929092 930066 . - . ID=id1831;Name=id1831;Dbxref=GeneID:905290;gbkey=misc_feature;Note=HMMPfam hit to PF03601 2C Conserved hypothetical protein 2C score 3.7e-156 NC_002163.1 RefSeq region 929143 929211 . - . ID=id78;Name=id78;Dbxref=GeneID:905290;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0999c by TMHMM2.0 at aa 12-34 2C 44-63 2C 83-100 2C 105-127 2C134-153 2C 163-185 2C 197-219 2C 234-256 2C 269-288 2C 303-325 and 338-360 NC_002163.1 RefSeq region 929254 929313 . - . ID=id78;Name=id78;Dbxref=GeneID:905290;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0999c by TMHMM2.0 at aa 12-34 2C 44-63 2C 83-100 2C 105-127 2C134-153 2C 163-185 2C 197-219 2C 234-256 2C 269-288 2C 303-325 and 338-360 NC_002163.1 RefSeq region 929350 929418 . - . ID=id78;Name=id78;Dbxref=GeneID:905290;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0999c by TMHMM2.0 at aa 12-34 2C 44-63 2C 83-100 2C 105-127 2C134-153 2C 163-185 2C 197-219 2C 234-256 2C 269-288 2C 303-325 and 338-360 NC_002163.1 RefSeq region 929461 929529 . - . ID=id78;Name=id78;Dbxref=GeneID:905290;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0999c by TMHMM2.0 at aa 12-34 2C 44-63 2C 83-100 2C 105-127 2C134-153 2C 163-185 2C 197-219 2C 234-256 2C 269-288 2C 303-325 and 338-360 NC_002163.1 RefSeq region 929563 929631 . - . ID=id78;Name=id78;Dbxref=GeneID:905290;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0999c by TMHMM2.0 at aa 12-34 2C 44-63 2C 83-100 2C 105-127 2C134-153 2C 163-185 2C 197-219 2C 234-256 2C 269-288 2C 303-325 and 338-360 NC_002163.1 RefSeq region 929659 929718 . - . ID=id78;Name=id78;Dbxref=GeneID:905290;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0999c by TMHMM2.0 at aa 12-34 2C 44-63 2C 83-100 2C 105-127 2C134-153 2C 163-185 2C 197-219 2C 234-256 2C 269-288 2C 303-325 and 338-360 NC_002163.1 RefSeq region 929737 929805 . - . ID=id78;Name=id78;Dbxref=GeneID:905290;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0999c by TMHMM2.0 at aa 12-34 2C 44-63 2C 83-100 2C 105-127 2C134-153 2C 163-185 2C 197-219 2C 234-256 2C 269-288 2C 303-325 and 338-360 NC_002163.1 RefSeq region 929818 929871 . - . ID=id78;Name=id78;Dbxref=GeneID:905290;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0999c by TMHMM2.0 at aa 12-34 2C 44-63 2C 83-100 2C 105-127 2C134-153 2C 163-185 2C 197-219 2C 234-256 2C 269-288 2C 303-325 and 338-360 NC_002163.1 RefSeq region 929929 929988 . - . ID=id78;Name=id78;Dbxref=GeneID:905290;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0999c by TMHMM2.0 at aa 12-34 2C 44-63 2C 83-100 2C 105-127 2C134-153 2C 163-185 2C 197-219 2C 234-256 2C 269-288 2C 303-325 and 338-360 NC_002163.1 RefSeq region 930016 930084 . - . ID=id78;Name=id78;Dbxref=GeneID:905290;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj0999c by TMHMM2.0 at aa 12-34 2C 44-63 2C 83-100 2C 105-127 2C134-153 2C 163-185 2C 197-219 2C 234-256 2C 269-288 2C 303-325 and 338-360 ### NC_002163.1 RefSeq CDS 930230 931111 . + 0 ID=cds888;Parent=gene951;Name=YP_002344395.1;Dbxref=GOA:Q0P9Q2 InterPro:IPR000847 InterPro:IPR005119 InterPro:IPR011991 UniProtKB FTrEMBL:Q0P9Q2 Genbank:YP_002344395.1 GeneID:905291;gbkey=CDS;product=transcriptional regulator;Note=Original 282000 29 note: Cj1000 2C probable transcriptional regulator 2C len: 293 aa 3B similar to members of the lysR family e.g. YEIE_ECOLI hypothetical transcriptional regulator 28293 aa 29 2C fasta scores 3B opt: 332 z-score: 390.5 E 28 29: 1.9e-14 2C 24.3 25 identity in 288 aa overlap. No Hp match. Contains Pfam match to entry PF00126 HTH_1 2C Bacterial regulatory helix-turn-helix proteins 2ClysR family 2C and probable helix-turn-helix motif at aa 17-38 28Score 1147 2C 2B3.09 SD 29 7EUpdated 282006 29 note: Pfam domain PF03466 LysR substrate binding domain identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score carried out yet 2C so kept in product function. Functional classification - Broad regulatory functions NC_002163.1 RefSeq gene 930230 931111 . + . ID=gene951;Name=Cj1000;locus_tag=Cj1000;Dbxref=GeneID:905291;gbkey=Gene NC_002163.1 RefSeq region 930236 930415 . + . ID=id1832;Name=id1832;Dbxref=GeneID:905291;gbkey=misc_feature;Note=HMMPfam hit to PF00126 2C Bacterial regulatory helix-turn-helix 2C score 7e-15 NC_002163.1 RefSeq region 930482 931108 . + . ID=id1833;Name=id1833;Dbxref=GeneID:905291;gbkey=misc_feature;Note=HMMPfam hit to PF03466 2C LysR substrate binding domain 2C score 7.7e-23 ### NC_002163.1 UTR_Extractor 5'-UTR 931132 931190 . + . ID=utr357;locus_tag=Cj1001;product=RNA polymerase sigma factor RpoD NC_002163.1 RefSeq CDS 931191 933059 . + 0 ID=cds889;Parent=gene952;gene=rpoD;Name=YP_002344396.1;Dbxref=GOA:Q0P9Q1 InterPro:IPR000943 InterPro:IPR007624 InterPro:IPR007627 InterPro:IPR007630 InterPro:IPR009042 InterPro:IPR011991 InterPro:IPR012760 InterPro:IPR014284 UniProtKB FTrEMBL:Q0P9Q1 Genbank:YP_002344396.1 GeneID:905292;gbkey=CDS;product=RNA polymerase sigma factor RpoD;Note=sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released 3B this is the primary sigma factor of bacteria NC_002163.1 RefSeq gene 931191 933059 . + . ID=gene952;gene=rpoD;Name=rpoD;locus_tag=Cj1001;Dbxref=GeneID:905292;gbkey=Gene NC_002163.1 RefSeq region 931497 931607 . + . ID=id1834;gene=rpoD;Name=id1834;Dbxref=GeneID:905292;gbkey=misc_feature;Note=HMMPfam hit to PF00140 2C Sigma-70 factor 2C region 2Cscore 8.5e-15 NC_002163.1 RefSeq region 931626 932168 . + . ID=id1835;gene=rpoD;Name=id1835;Dbxref=GeneID:905292;gbkey=misc_feature;Note=HMMPfam hit to PF04546 2C Sigma-70 2C non-essential region 2C score 0.01 NC_002163.1 RefSeq region 932343 932555 . + . ID=id1836;gene=rpoD;Name=id1836;Dbxref=GeneID:905292;gbkey=misc_feature;Note=HMMPfam hit to PF04542 2C Sigma-70 region 2C score 6.2e-28 NC_002163.1 RefSeq region 932415 932456 . + . ID=id1837;gene=rpoD;Name=id1837;Dbxref=GeneID:905292;gbkey=misc_feature;Note=PS00715 Sigma-70 factors family signature 1 NC_002163.1 RefSeq region 932565 932813 . + . ID=id1838;gene=rpoD;Name=id1838;Dbxref=GeneID:905292;gbkey=misc_feature;Note=HMMPfam hit to PF04539 2C Sigma-70 region 2C score 5.3e-35 NC_002163.1 RefSeq region 932847 933011 . + . ID=id1839;gene=rpoD;Name=id1839;Dbxref=GeneID:905292;gbkey=misc_feature;Note=HMMPfam hit to PF04545 2C Sigma-70 2C region 2C score 7.3e-19 NC_002163.1 RefSeq region 932925 933005 . + . ID=id1840;gene=rpoD;Name=id1840;Dbxref=GeneID:905292;gbkey=misc_feature;Note=PS00716 Sigma-70 factors family signature 2 ### NC_002163.1 RefSeq CDS 933075 933587 . - 0 ID=cds890;Parent=gene953;Name=YP_002344397.1;Dbxref=GOA:Q0P9Q0 InterPro:IPR013078 UniProtKB FTrEMBL:Q0P9Q0 Genbank:YP_002344397.1 GeneID:905293;gbkey=CDS;product=phosphoglycerate 2Fbisphosphoglycerate mutase;Note=Original 282000 29 note: Cj1002c 2C unknown 2C len: 170 aa 3B similar to hypothetical proteins e.g. TR:O67234 28EMBL:AE000727 29 Aquifex aeolicus AQ_1173 28149 aa 29 2C fasta scores 3B opt: 185 z-score: 235.0 E 28 29: 8.6e-06 2C 34.2 25 identity in 117 aa overlap. No Hp match 7EUpdated 282006 29 note: Running own Pfam search allowed identification of Pfam domain PF00300 Phosphoglycerate mutase family. This is an enzyme that catalyses reactions involving the transfer of phospho groups between the 3 carbon atoms of phosphoglycerate. Not specifically characterised 2C so kept in product function. Functional classification - Energy metabolism -Glycolysis NC_002163.1 RefSeq gene 933075 933587 . - . ID=gene953;Name=Cj1002c;locus_tag=Cj1002c;Dbxref=GeneID:905293;gbkey=Gene NC_002163.1 RefSeq CDS 933584 934102 . - 0 ID=cds891;Parent=gene954;Name=YP_002344398.1;Dbxref=GOA:Q0P9P9 InterPro:IPR002610 UniProtKB FTrEMBL:Q0P9P9 Genbank:YP_002344398.1 GeneID:905294;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj1003c 2C probable integral membrane protein 2C len: 172 aa 3B similar to hypothetical proteins e.g. TR:O59166 28EMBL:AP000006 29 Pyrococcus horikoshii PH1497 28197 aa 29 2C fasta scores 3B opt: 233 z-score: 292.8 E 28 29: 5.2e-09 2C 30.8 25 identity in 172 aa overlap. No Hp ortholog 7EUpdated 282006 29 note: Pfam domain PF01694 Rhomboid family identified within CDS. Also 2C five probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific charactersation carried out yet 2C so kept in product function. Functional classification - Membranes 2Clipoproteins and porins NC_002163.1 RefSeq gene 933584 934102 . - . ID=gene954;Name=Cj1003c;locus_tag=Cj1003c;Dbxref=GeneID:905294;gbkey=Gene NC_002163.1 RefSeq region 933587 934012 . - . ID=id1841;Name=id1841;Dbxref=GeneID:905294;gbkey=misc_feature;Note=HMMPfam hit to PF01694 2C Rhomboid family 2C score 2.2e-38 NC_002163.1 RefSeq region 933644 933712 . - . ID=id79;Name=id79;Dbxref=GeneID:905294;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1003c by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-95 2C 105-124 and 131-153 NC_002163.1 RefSeq region 933731 933790 . - . ID=id79;Name=id79;Dbxref=GeneID:905294;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1003c by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-95 2C 105-124 and 131-153 NC_002163.1 RefSeq region 933818 933886 . - . ID=id79;Name=id79;Dbxref=GeneID:905294;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1003c by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-95 2C 105-124 and 131-153 NC_002163.1 RefSeq region 933905 933973 . - . ID=id79;Name=id79;Dbxref=GeneID:905294;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1003c by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-95 2C 105-124 and 131-153 NC_002163.1 RefSeq region 934016 934084 . - . ID=id79;Name=id79;Dbxref=GeneID:905294;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1003c by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-95 2C 105-124 and 131-153 ### NC_002163.1 RefSeq gene 934201 934617 . + . ID=gene955;Name=Cj1004;locus_tag=Cj1004;Dbxref=GeneID:905295;gbkey=Gene NC_002163.1 RefSeq CDS 934201 934617 . + 0 ID=cds892;Parent=gene955;Name=YP_002344399.1;Dbxref=GOA:Q0P9P8 UniProtKB FTrEMBL:Q0P9P8 Genbank:YP_002344399.1 GeneID:905295;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1004 2C probable periplasmic protein 2C len: 138 aa 3B very weak similarity to TR:P75137 28EMBL:AE000019 29 Mycoplasma pneumoniae lipoprotein E09_orf129 28129 aa 29 2C fasta scores 3B opt: 110 z-score: 147.3 E 28 29: 0.66 2C 34.9 25 identity in 129 aa overlap. No Hp match. Also similar to Cj1626c 2838.6 25 identity in 140 aa overlap 29 7EUpdated 282006 29 note: Literature search identified paper giving further clues on product funciton. Functional classification - Miscellaneous periplasmic proteins 7EPMID:15554967 NC_002163.1 RefSeq CDS 934626 936242 . - 0 ID=cds893;Parent=gene956;Name=YP_002344400.1;Dbxref=GOA:Q0P9P7 InterPro:IPR000642 InterPro:IPR003593 InterPro:IPR003959 InterPro:IPR003960 InterPro:IPR011546 UniProtKB FTrEMBL:Q0P9P7 Genbank:YP_002344400.1 GeneID:905296;gbkey=CDS;product=membrane bound ATPase;Note=Original 282000 29 note: Cj1005c 2C probable membrane bound ATPase 2C len: 538 aa 3B similar to many members of the AAA family e.g. FTSH_BACSU cell division protein FTSH homolog 28EC 3.4.24.- 29 28637 aa 29 2C fasta scores 3B opt: 901 z-score: 909.6 E 28 29: 0 2C 36.3 25 identity in 518 aa overlap. 43.8 25 identity to HP0286. Also similar to ftsH Cj1116c 2836.2 25 identity in 578 aa overlap 29. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00674 AAA-protein family signature 2C and Pfam match to entry PF00004 AAA 2CATPases associated with various cellular activities 28AAA 29 7EUpdated 282006 29 note: Pfam domain PF06480 FtsH Extracellular protein. This domain is found in FtsH family proteins. FtsH is the only membrane-bound ATP-dependent protease universally conserved in prokaryotes. kept within product function. Functional classification -Misc 7EPMID:8892813 2C PMID:9244252 and PMID:96132941 NC_002163.1 RefSeq gene 934626 936242 . - . ID=gene956;Name=Cj1005c;locus_tag=Cj1005c;Dbxref=GeneID:905296;gbkey=Gene NC_002163.1 RefSeq region 934638 935120 . - . ID=id1842;Name=id1842;Dbxref=GeneID:905296;gbkey=misc_feature;Note=HMMPfam hit to PF01434 2C Peptidase family M41 2C score 0.00033 NC_002163.1 RefSeq region 935136 935684 . - . ID=id1843;Name=id1843;Dbxref=GeneID:905296;gbkey=misc_feature;Note=HMMPfam hit to PF00004 2C ATPase family associated with various c 2C score 3.2e-83 NC_002163.1 RefSeq region 935325 935381 . - . ID=id1844;Name=id1844;Dbxref=GeneID:905296;gbkey=misc_feature;Note=PS00674 AAA-protein family signature NC_002163.1 RefSeq region 935646 935669 . - . ID=id1845;Name=id1845;Dbxref=GeneID:905296;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 935760 936161 . - . ID=id1846;Name=id1846;Dbxref=GeneID:905296;gbkey=misc_feature;Note=HMMPfam hit to PF06480 2C FtsH Extracellular 2C score 5e-36 NC_002163.1 RefSeq region 935913 935981 . - . ID=id80;Name=id80;Dbxref=GeneID:905296;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1005c by TMHMM2.0 at aa 6-23 and 88-110 NC_002163.1 RefSeq region 936174 936227 . - . ID=id80;Name=id80;Dbxref=GeneID:905296;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1005c by TMHMM2.0 at aa 6-23 and 88-110 ### NC_002163.1 RefSeq CDS 936246 937496 . - 0 ID=cds894;Parent=gene957;Name=YP_002344401.1;Dbxref=GOA:Q0P9P6 InterPro:IPR005839 InterPro:IPR006467 InterPro:IPR006638 InterPro:IPR007197 InterPro:IPR013848 UniProtKB FTrEMBL:Q0P9P6 Genbank:YP_002344401.1 GeneID:905297;gbkey=CDS;product=MiaB-like tRNA modifying enzyme;Note=Original 282000 29 note: Cj1006c 2C unknown 2C len: 416 aa 3B similar to hypothetical proteins belonging to the UPF0004 family e.g. Y16R_MYCIO 28438 aa 29 2C fasta scores 3B opt: 580 z-score: 664.7 E 28 29: 1e-29 2C 30.5 25 identity in 413 aa overlap. 50.1 25 identity to HP0285. Also similar to Cj0458c 2828.6 25 identity in 391 aa overlap 29 and Cj1454c 2828.4 25 identity in 419 aa overlap 29. Contains PS01278 Uncharacterized protein family UPF0004 signature and Pfam match to entry PF00919 UPF0004 7EUpdated 282006 29 note: Pfam domain PF04055 Radical SAM superfamily identified within CDS. TIGRFAM TIGR01579 MiaB-like tRNA modifying enzyme has also been identified. Characterisation papers have also been attached. Product modified based on motif match and supporting literature. Some characterisation in Escherichia coli 2C however 2C kept within product function. Functional classification - RNA synthesis 2C RNA modification and DNA transcription 7EPMID:10572129 2C PMID:11882645 and PMID:11313137 NC_002163.1 RefSeq gene 936246 937496 . - . ID=gene957;Name=Cj1006c;locus_tag=Cj1006c;Dbxref=GeneID:905297;gbkey=Gene NC_002163.1 RefSeq region 936585 937088 . - . ID=id1847;Name=id1847;Dbxref=GeneID:905297;gbkey=misc_feature;Note=HMMPfam hit to PF04055 2C Radical SAM superfamily 2Cscore 1.5e-18 NC_002163.1 RefSeq region 937026 937088 . - . ID=id1848;Name=id1848;Dbxref=GeneID:905297;gbkey=misc_feature;Note=PS01278 Uncharacterized protein family UPF0004 signature NC_002163.1 RefSeq region 937212 937487 . - . ID=id1849;Name=id1849;Dbxref=GeneID:905297;gbkey=misc_feature;Note=HMMPfam hit to PF00919 2C Uncharacterized protein family UPF0004 2C score 8.5e-21 NC_002163.1 RefSeq CDS 937493 939064 . - 0 ID=cds895;Parent=gene958;Name=YP_002344402.1;Dbxref=GOA:Q0P9P5 InterPro:IPR006685 UniProtKB FTrEMBL:Q0P9P5 Genbank:YP_002344402.1 GeneID:905298;gbkey=CDS;product=mechanosensitive ion channel family protein;Note=Original 282000 29 note: Cj1007c 2C probable membrane protein 2C len: 523 aa 3B similar in C-terminus to hypothetical proteins e.g. Y700_METJA hypothetical protein MJ0700 28324 aa 29 2C fasta scores 3B opt: 281 z-score: 300.2 E 28 29: 2e-09 2C 29.0 25 identity in 276 aa overlap. 37.4 25 identity to HP0284 7EUpdated 282006 29 note: Pfam domain PF00924 Mechanosensitive ion channel identified within CDS. Also 2Cthree probable transmembrane helices predicted by TMHMM2.0. Product modified to more specific family member based on motif match. No specific characterisation has been carried out yet. kept within product function. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:12446901 NC_002163.1 RefSeq gene 937493 939064 . - . ID=gene958;Name=Cj1007c;locus_tag=Cj1007c;Dbxref=GeneID:905298;gbkey=Gene NC_002163.1 RefSeq region 937589 938293 . - . ID=id1850;Name=id1850;Dbxref=GeneID:905298;gbkey=misc_feature;Note=HMMPfam hit to PF00924 2C Mechanosensitive ion channel 2C score 1.1e-24 NC_002163.1 RefSeq region 938105 938164 . - . ID=id81;Name=id81;Dbxref=GeneID:905298;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1007c by TMHMM2.0 at aa 221-243 2C 264-286 and 301-320 NC_002163.1 RefSeq region 938207 938275 . - . ID=id81;Name=id81;Dbxref=GeneID:905298;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1007c by TMHMM2.0 at aa 221-243 2C 264-286 and 301-320 NC_002163.1 RefSeq region 938336 938404 . - . ID=id81;Name=id81;Dbxref=GeneID:905298;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1007c by TMHMM2.0 at aa 221-243 2C 264-286 and 301-320 NC_002163.1 RefSeq gene 939061 940116 . - . ID=gene959;gene=aroB;Name=aroB;locus_tag=Cj1008c;Dbxref=GeneID:905299;gbkey=Gene NC_002163.1 RefSeq CDS 939061 940116 . - 0 ID=cds896;Parent=gene959;gene=aroB;Name=YP_002344403.1;Dbxref=GOA:Q9PNT2 HSSP:P07547 InterPro:IPR002658 InterPro:IPR016037 InterPro:IPR016303 UniProtKB FSwiss-Prot:Q9PNT2 Genbank:YP_002344403.1 GeneID:905299;gbkey=CDS;product=3-dehydroquinate synthase;Note=catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate 3B functions in aromatic amino acid biosynthesis NC_002163.1 UTR_Extractor 5'-UTR 939065 939210 . - . ID=utr358;locus_tag=Cj1007c;product=putative mechanosensitive ion channel family protein NC_002163.1 RefSeq region 939166 940098 . - . ID=id1851;gene=aroB;Name=id1851;Dbxref=GeneID:905299;gbkey=misc_feature;Note=HMMPfam hit to PF01761 2C 3-dehydroquinate synthase 2Cscore 7.1e-147 NC_002163.1 RefSeq region 939748 939780 . - . ID=id1852;gene=aroB;Name=id1852;Dbxref=GeneID:905299;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq CDS 940162 941562 . - 0 ID=cds897;Parent=gene960;Name=YP_002344404.1;Dbxref=GOA:Q0P9P3 InterPro:IPR006037 UniProtKB FTrEMBL:Q0P9P3 Genbank:YP_002344404.1 GeneID:905300;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1009c 2C unknown 2C len: 466 aa 3B 29.1 25 identity to HP0282 7EUpdated 282006 29 note: Pfam domain PF02080 TrkA-C domain identified within CDS. The TrkA-C domain is typically found next to the -N domain. Currently unknown function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 940162 941562 . - . ID=gene960;Name=Cj1009c;locus_tag=Cj1009c;Dbxref=GeneID:905300;gbkey=Gene NC_002163.1 RefSeq region 940918 941121 . - . ID=id1853;Name=id1853;Dbxref=GeneID:905300;gbkey=misc_feature;Note=HMMPfam hit to PF02080 2C TrkA-C domain 2C score 2.6e-11 NC_002163.1 UTR_Extractor 5'-UTR 941540 941591 . + . ID=utr359;locus_tag=Cj1010;product=queuine tRNA-ribosyltransferase NC_002163.1 UTR_Extractor 5'-UTR 941563 941582 . - . ID=utr360;locus_tag=Cj1009c;product=hypothetical protein ### NC_002163.1 RefSeq gene 941592 942713 . + . ID=gene961;gene=tgt;Name=tgt;locus_tag=Cj1010;Dbxref=GeneID:905301;gbkey=Gene NC_002163.1 RefSeq CDS 941592 942713 . + 0 ID=cds898;Parent=gene961;gene=tgt;Name=YP_002344405.1;Dbxref=GOA:Q9PNT0 HSSP:P28720 InterPro:IPR002616 InterPro:IPR004803 UniProtKB FSwiss-Prot:Q9PNT0 Genbank:YP_002344405.1 GeneID:905301;gbkey=CDS;product=queuine tRNA-ribosyltransferase;Note=Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU 28N 29 anticodons 28tRNA-Asp 2C -Asn 2C -His and -Tyr 29 NC_002163.1 RefSeq region 941967 942698 . + . ID=id1854;gene=tgt;Name=id1854;Dbxref=GeneID:905301;gbkey=misc_feature;Note=HMMPfam hit to PF01702 2C Queuine tRNA-ribosyltransferase 2C score 4.9e-110 ### NC_002163.1 RefSeq gene 942715 943482 . + . ID=gene962;Name=Cj1011;locus_tag=Cj1011;Dbxref=GeneID:905302;gbkey=Gene NC_002163.1 RefSeq CDS 942715 943482 . + 0 ID=cds899;Parent=gene962;Name=YP_002344406.1;Dbxref=GOA:Q0P9P1 InterPro:IPR002523 UniProtKB FTrEMBL:Q0P9P1 Genbank:YP_002344406.1 GeneID:905302;gbkey=CDS;product=CorA-like Mg2 2B transporter protein;Note=Original 282000 29 note: Cj1011 2C probable membrane protein 2C len: 255 aa 3B no Hp match 7EUpdated 282006 29 note: Two probable transmembrane helices predicted by TMHMM2.0. Running own Pfam search identified PF01544 CorA-like Mg2 2B transporter protein. Product modified to more specific family member based on motif match. No specific characterisation has been carried out yet. kept in product function. Functional classification - Transport 2Fbinding proteins - Cations NC_002163.1 RefSeq region 943252 943320 . + . ID=id1855;Name=id1855;Dbxref=GeneID:905302;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1011 by TMHMM2.0 at aa 180-202 and 217-236 NC_002163.1 RefSeq region 943363 943422 . + . ID=id1855;Name=id1855;Dbxref=GeneID:905302;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1011 by TMHMM2.0 at aa 180-202 and 217-236 ### NC_002163.1 RefSeq gene 943535 943611 . + . ID=gene963;gene=tRNAArg;Name=tRNAArg;locus_tag=Cjp21;Dbxref=GeneID:905303;gbkey=Gene NC_002163.1 RefSeq tRNA 943535 943611 . + . ID=rna36;Parent=gene963;gene=tRNAArg;Name=rna36;Dbxref=GeneID:905303;gbkey=tRNA;product=tRNA-Arg;Note=tRNA Arg anticodon GCG 2C Cove score 83.29 NC_002163.1 RefSeq exon 943535 943611 . + . ID=id1856;Parent=rna36;gene=tRNAArg;Name=id1856;Dbxref=GeneID:905303;gbkey=tRNA;product=tRNA-Arg;Note=tRNA Arg anticodon GCG 2C Cove score 83.29 NC_002163.1 RefSeq gene 943614 944063 . - . ID=gene964;Name=Cj1012c;locus_tag=Cj1012c;Dbxref=GeneID:905304;gbkey=Gene NC_002163.1 RefSeq CDS 943614 944063 . - 0 ID=cds900;Parent=gene964;Name=YP_002344407.1;Dbxref=GOA:Q0P9P0 UniProtKB FTrEMBL:Q0P9P0 Genbank:YP_002344407.1 GeneID:905304;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1012c 2C possible membrane protein 2C len: 149 aa 3B no Hp match 7EUpdated 282006 29 note: One probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 943995 944054 . - . ID=id1857;Name=id1857;Dbxref=GeneID:905304;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1012c by TMHMM2.0 at aa 4-23 ### NC_002163.1 RefSeq CDS 944080 947325 . - 0 ID=cds901;Parent=gene965;Name=YP_002344408.1;Dbxref=GOA:Q0P9N9 InterPro:IPR002541 UniProtKB FTrEMBL:Q0P9N9 Genbank:YP_002344408.1 GeneID:905305;gbkey=CDS;product=cytochrome C biogenesis protein;Note=Original 282000 29 note: Cj1013c 2C probable membrane protein 2C len: 1081 aa 3B contains three domains 3B aa 1-90 contains three membrane spanning domains 3B aa 90-780 is non-membrane 2C and aa 780-1081 contains ten possible membrane spanning domains. Some similarity in C-teminal membrane domain to eukaryotic proteins e.g. CCSA_CHLRE cytochrome C biogenesis protein CCSA 28353 aa 29 2C fasta scores 3B opt: 459 z-score: 515.4 E 28 29: 2.1e-21 2C 36.0 25 identity in 267 aa overlap 2C and to prokaryotic equivalents e.g. CCMF_ECOLI cytochrome C-type biogenesis protein CCMF 28647 aa 29 3B BLASTP scores 3B E 3D 0.20 2C 24 25 identity in 293 aa overlap. 39.0 25 identity to HP0378 28domains 2 2B3 only 29 7EUpdated 282006 29 note: Twelve probable transmembrane helices predicted by TMHMM2.0. Pfam domain PF01578 Cytochrome C assembly protein identified within CDS. Product function modified based on motif match. Some characterisation within Wolinella succinogenes and Escherichia coli 2C however 2C identity scores were marginal. kept within product function. Functional classification - Energy metabolism - Electron transport 7EPMID:10672190 2C PMID:11069671 2C PMID:16629661 NC_002163.1 RefSeq gene 944080 947325 . - . ID=gene965;Name=Cj1013c;locus_tag=Cj1013c;Dbxref=GeneID:905305;gbkey=Gene NC_002163.1 RefSeq region 944113 944172 . - . ID=id82;Name=id82;Dbxref=GeneID:905305;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1013c by TMHMM2.0 at aa 13-32 2C 47-66 2C 78-100 2C 771-793 2C805-827 2C 837-859 2C 864-883 2C 910-932 2C 953-975 2C 990-1008 2C1015-1037 and 1052-1071 NC_002163.1 RefSeq region 944197 944817 . - . ID=id1858;Name=id1858;Dbxref=GeneID:905305;gbkey=misc_feature;Note=HMMPfam hit to PF01578 2C Cytochrome C assembly protein 2C score 3.8e-49 NC_002163.1 RefSeq region 944215 944283 . - . ID=id82;Name=id82;Dbxref=GeneID:905305;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1013c by TMHMM2.0 at aa 13-32 2C 47-66 2C 78-100 2C 771-793 2C805-827 2C 837-859 2C 864-883 2C 910-932 2C 953-975 2C 990-1008 2C1015-1037 and 1052-1071 NC_002163.1 RefSeq region 944302 944358 . - . ID=id82;Name=id82;Dbxref=GeneID:905305;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1013c by TMHMM2.0 at aa 13-32 2C 47-66 2C 78-100 2C 771-793 2C805-827 2C 837-859 2C 864-883 2C 910-932 2C 953-975 2C 990-1008 2C1015-1037 and 1052-1071 NC_002163.1 RefSeq region 944401 944469 . - . ID=id82;Name=id82;Dbxref=GeneID:905305;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1013c by TMHMM2.0 at aa 13-32 2C 47-66 2C 78-100 2C 771-793 2C805-827 2C 837-859 2C 864-883 2C 910-932 2C 953-975 2C 990-1008 2C1015-1037 and 1052-1071 NC_002163.1 RefSeq region 944530 944598 . - . ID=id82;Name=id82;Dbxref=GeneID:905305;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1013c by TMHMM2.0 at aa 13-32 2C 47-66 2C 78-100 2C 771-793 2C805-827 2C 837-859 2C 864-883 2C 910-932 2C 953-975 2C 990-1008 2C1015-1037 and 1052-1071 NC_002163.1 RefSeq region 944677 944736 . - . ID=id82;Name=id82;Dbxref=GeneID:905305;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1013c by TMHMM2.0 at aa 13-32 2C 47-66 2C 78-100 2C 771-793 2C805-827 2C 837-859 2C 864-883 2C 910-932 2C 953-975 2C 990-1008 2C1015-1037 and 1052-1071 NC_002163.1 RefSeq region 944749 944817 . - . ID=id82;Name=id82;Dbxref=GeneID:905305;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1013c by TMHMM2.0 at aa 13-32 2C 47-66 2C 78-100 2C 771-793 2C805-827 2C 837-859 2C 864-883 2C 910-932 2C 953-975 2C 990-1008 2C1015-1037 and 1052-1071 NC_002163.1 RefSeq region 944845 944913 . - . ID=id82;Name=id82;Dbxref=GeneID:905305;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1013c by TMHMM2.0 at aa 13-32 2C 47-66 2C 78-100 2C 771-793 2C805-827 2C 837-859 2C 864-883 2C 910-932 2C 953-975 2C 990-1008 2C1015-1037 and 1052-1071 NC_002163.1 RefSeq region 944947 945015 . - . ID=id82;Name=id82;Dbxref=GeneID:905305;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1013c by TMHMM2.0 at aa 13-32 2C 47-66 2C 78-100 2C 771-793 2C805-827 2C 837-859 2C 864-883 2C 910-932 2C 953-975 2C 990-1008 2C1015-1037 and 1052-1071 NC_002163.1 RefSeq region 947026 947094 . - . ID=id82;Name=id82;Dbxref=GeneID:905305;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1013c by TMHMM2.0 at aa 13-32 2C 47-66 2C 78-100 2C 771-793 2C805-827 2C 837-859 2C 864-883 2C 910-932 2C 953-975 2C 990-1008 2C1015-1037 and 1052-1071 NC_002163.1 RefSeq region 947128 947187 . - . ID=id82;Name=id82;Dbxref=GeneID:905305;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1013c by TMHMM2.0 at aa 13-32 2C 47-66 2C 78-100 2C 771-793 2C805-827 2C 837-859 2C 864-883 2C 910-932 2C 953-975 2C 990-1008 2C1015-1037 and 1052-1071 NC_002163.1 RefSeq region 947230 947289 . - . ID=id82;Name=id82;Dbxref=GeneID:905305;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1013c by TMHMM2.0 at aa 13-32 2C 47-66 2C 78-100 2C 771-793 2C805-827 2C 837-859 2C 864-883 2C 910-932 2C 953-975 2C 990-1008 2C1015-1037 and 1052-1071 ### NC_002163.1 RefSeq gene 947343 948038 . - . ID=gene966;gene=livF;Name=livF;locus_tag=Cj1014c;Dbxref=GeneID:905306;gbkey=Gene NC_002163.1 RefSeq CDS 947343 948038 . - 0 ID=cds902;Parent=gene966;gene=livF;Name=YP_002344409.1;Dbxref=GOA:Q0P9N8 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FTrEMBL:Q0P9N8 Genbank:YP_002344409.1 GeneID:905306;gbkey=CDS;product=branched-chain amino acid ABC transporter ATP-binding protein;Note=Original 282000 29 note: Cj1014c 2C livF 2C probable branched-chain amino-acid ABC transport system ATP-binding protein 2C len: 231 aa 3B similar to e.g. LIVF_ECOLI high-affinity branched-chain amino acid transport ATP-binding protein 28237 aa 29 2C fasta scores 3B opt: 686 z-score: 797.6 E 28 29: 0 2C 46.4 25 identity in 233 aa overlap. No Hp ortholog. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00211 ABC transporters family signature 2C and Pfam match to entry PF00005 ABC_tran 7EUpdated 282006 29 note: Characterised within Pseudomonas aeruginosa and Escherichia coli with acceptable identity scores. not added to product function. Functional classification - Transport 2Fbinding proteins - Amino acids and amines 7EPMID:2120183 2C PMID:1429514 2C PMID:2195019 NC_002163.1 RefSeq region 947418 947960 . - . ID=id1859;gene=livF;Name=id1859;Dbxref=GeneID:905306;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 1.7e-42 NC_002163.1 RefSeq region 947601 947645 . - . ID=id1860;gene=livF;Name=id1860;Dbxref=GeneID:905306;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq region 947916 947939 . - . ID=id1861;gene=livF;Name=id1861;Dbxref=GeneID:905306;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 948025 948795 . - 0 ID=cds903;Parent=gene967;gene=livG;Name=YP_002344410.1;Dbxref=GOA:Q0P9N7 InterPro:IPR001395 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FTrEMBL:Q0P9N7 Genbank:YP_002344410.1 GeneID:905307;gbkey=CDS;product=branched-chain amino acid ABC transporter ATP-binding protein;Note=Original 282000 29 note: Cj1015c 2C livG 2C probable branched-chain amino-acid ABC transport system ATP-binding protein 2C len: 256 aa 3B similar to e.g. LIVG_ECOLI high-affinity branched-chain amino acid transport ATP-binding protein 28255 aa 29 2C fasta scores 3B opt: 680 z-score: 800.2 E 28 29: 0 2C 41.2 25 identity in 250 aa overlap. No Hp ortholog. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00211 ABC transporters family signature 2C and Pfam match to entry PF00005 ABC_tran 7EUpdated 282006 29 note: Characterised within Pseudomonas aeruginosa and Escherichia coli with acceptable identity scores. not added to product function. Functional classification - Transport 2Fbinding proteins - Amino acids and amines 7EPMID:2120183 2C PMID:1429514 2C PMID:2195019 NC_002163.1 RefSeq gene 948025 948795 . - . ID=gene967;gene=livG;Name=livG;locus_tag=Cj1015c;Dbxref=GeneID:905307;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 948039 948272 . - . ID=utr361;locus_tag=Cj1014c;product=branched-chain amino-acid ABC transporter ATP-binding protein NC_002163.1 RefSeq region 948115 948714 . - . ID=id1862;gene=livG;Name=id1862;Dbxref=GeneID:905307;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 1.5e-57 NC_002163.1 RefSeq region 948301 948345 . - . ID=id1863;gene=livG;Name=id1863;Dbxref=GeneID:905307;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq region 948514 948561 . - . ID=id1864;gene=livG;Name=id1864;Dbxref=GeneID:905307;gbkey=misc_feature;Note=PS00063 Aldo 2Fketo reductase family active site signature NC_002163.1 RefSeq region 948670 948693 . - . ID=id1865;gene=livG;Name=id1865;Dbxref=GeneID:905307;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 948792 949844 . - 0 ID=cds904;Parent=gene968;gene=livM;Name=YP_002344411.1;Dbxref=GOA:Q0P9N6 InterPro:IPR001851 UniProtKB FTrEMBL:Q0P9N6 Genbank:YP_002344411.1 GeneID:905308;gbkey=CDS;product=branched-chain amino acid ABC transporter permease;Note=Original 282000 29 note: Cj1016c 2C livM 2C probable branched-chain amino-acid ABC transport system permease 2C len: 350 aa 3B similar to e.g. LIVM_ECOLI high-affinity branched-chain amino acid transport permease 28425 aa 29 fasta scores 3B opt: 239 z-score: 284.9 E 28 29: 1.4e-08 2C 31.5 25 identity in 321 aa overlap. No Hp ortholog 7EUpdated 282006 29 note: Eight probable transmembrane helices predicted by TMHMM2.0. Pfam domain PF02653 Branched-chain amino acid transport system 2F permease component. Characterised in Escherichia coli with marginal identity score. Appropriate motifs present. removed from product function. Functional classification - Transport 2Fbinding proteins - Amino acids and amines 7EPMID:2120183 2C PMID:1429514 2C PMID:2195019 NC_002163.1 RefSeq gene 948792 949844 . - . ID=gene968;gene=livM;Name=livM;locus_tag=Cj1016c;Dbxref=GeneID:905308;gbkey=Gene NC_002163.1 RefSeq region 948873 948926 . - . ID=id83;gene=livM;Name=id83;Dbxref=GeneID:905308;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1016c by TMHMM2.0 at aa 7-29 2C 34-51 2C 58-80 2C 104-126 2C133-155 2C 170-191 2C 257-279 and 307-324 NC_002163.1 RefSeq region 948882 949757 . - . ID=id1866;gene=livM;Name=id1866;Dbxref=GeneID:905308;gbkey=misc_feature;Note=HMMPfam hit to PF02653 2C Branched-chain amino acid transport syst 2C score 1.8e-32 NC_002163.1 RefSeq region 949008 949076 . - . ID=id83;gene=livM;Name=id83;Dbxref=GeneID:905308;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1016c by TMHMM2.0 at aa 7-29 2C 34-51 2C 58-80 2C 104-126 2C133-155 2C 170-191 2C 257-279 and 307-324 NC_002163.1 RefSeq region 949272 949337 . - . ID=id83;gene=livM;Name=id83;Dbxref=GeneID:905308;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1016c by TMHMM2.0 at aa 7-29 2C 34-51 2C 58-80 2C 104-126 2C133-155 2C 170-191 2C 257-279 and 307-324 NC_002163.1 RefSeq region 949380 949448 . - . ID=id83;gene=livM;Name=id83;Dbxref=GeneID:905308;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1016c by TMHMM2.0 at aa 7-29 2C 34-51 2C 58-80 2C 104-126 2C133-155 2C 170-191 2C 257-279 and 307-324 NC_002163.1 RefSeq region 949467 949535 . - . ID=id83;gene=livM;Name=id83;Dbxref=GeneID:905308;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1016c by TMHMM2.0 at aa 7-29 2C 34-51 2C 58-80 2C 104-126 2C133-155 2C 170-191 2C 257-279 and 307-324 NC_002163.1 RefSeq region 949605 949673 . - . ID=id83;gene=livM;Name=id83;Dbxref=GeneID:905308;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1016c by TMHMM2.0 at aa 7-29 2C 34-51 2C 58-80 2C 104-126 2C133-155 2C 170-191 2C 257-279 and 307-324 NC_002163.1 RefSeq region 949692 949745 . - . ID=id83;gene=livM;Name=id83;Dbxref=GeneID:905308;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1016c by TMHMM2.0 at aa 7-29 2C 34-51 2C 58-80 2C 104-126 2C133-155 2C 170-191 2C 257-279 and 307-324 NC_002163.1 RefSeq region 949758 949826 . - . ID=id83;gene=livM;Name=id83;Dbxref=GeneID:905308;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1016c by TMHMM2.0 at aa 7-29 2C 34-51 2C 58-80 2C 104-126 2C133-155 2C 170-191 2C 257-279 and 307-324 NC_002163.1 RefSeq gene 949844 950740 . - . ID=gene969;gene=livH;Name=livH;locus_tag=Cj1017c;Dbxref=GeneID:905309;gbkey=Gene NC_002163.1 RefSeq CDS 949844 950740 . - 0 ID=cds905;Parent=gene969;gene=livH;Name=YP_002344412.1;Dbxref=GOA:Q0P9N5 InterPro:IPR001851 UniProtKB FTrEMBL:Q0P9N5 Genbank:YP_002344412.1 GeneID:905309;gbkey=CDS;product=branched-chain amino acid ABC transporter permease;Note=Original 282000 29 note: Cj1017c 2C livH 2C probable branched-chain amino-acid ABC transport system permease 2C len: 298 aa 3B similar to e.g. LIVH_ECOLI high-affinity branched-chain amino acid transport permease 28308 aa 29 fasta scores 3B opt: 538 z-score: 595.2 E 28 29: 7.4e-26 2C 40.8 25 identity in 299 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02653 Branched-chain amino acid transport system 2F permease component identified within CDS. Also 2C seven probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised in Escherichia coli with marginal identity score. Appropriate motifs present. removed from product function. Functional classification - Transport 2Fbinding proteins -Amino acids and amines 7EPMID:2120183 2C PMID:1429514 2C PMID:2195019 NC_002163.1 RefSeq region 949862 949930 . - . ID=id84;gene=livH;Name=id84;Dbxref=GeneID:905309;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1017c by TMHMM2.0 at aa 15-37 2C 58-80 2C 95-117 2C 138-160 2C191-213 2C 234-256 and 271-293 NC_002163.1 RefSeq region 949898 950716 . - . ID=id1867;gene=livH;Name=id1867;Dbxref=GeneID:905309;gbkey=misc_feature;Note=HMMPfam hit to PF02653 2C Branched-chain amino acid transport syst 2C score 1e-38 NC_002163.1 RefSeq region 949973 950041 . - . ID=id84;gene=livH;Name=id84;Dbxref=GeneID:905309;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1017c by TMHMM2.0 at aa 15-37 2C 58-80 2C 95-117 2C 138-160 2C191-213 2C 234-256 and 271-293 NC_002163.1 RefSeq region 950102 950170 . - . ID=id84;gene=livH;Name=id84;Dbxref=GeneID:905309;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1017c by TMHMM2.0 at aa 15-37 2C 58-80 2C 95-117 2C 138-160 2C191-213 2C 234-256 and 271-293 NC_002163.1 RefSeq region 950261 950329 . - . ID=id84;gene=livH;Name=id84;Dbxref=GeneID:905309;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1017c by TMHMM2.0 at aa 15-37 2C 58-80 2C 95-117 2C 138-160 2C191-213 2C 234-256 and 271-293 NC_002163.1 RefSeq region 950390 950458 . - . ID=id84;gene=livH;Name=id84;Dbxref=GeneID:905309;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1017c by TMHMM2.0 at aa 15-37 2C 58-80 2C 95-117 2C 138-160 2C191-213 2C 234-256 and 271-293 NC_002163.1 RefSeq region 950501 950569 . - . ID=id84;gene=livH;Name=id84;Dbxref=GeneID:905309;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1017c by TMHMM2.0 at aa 15-37 2C 58-80 2C 95-117 2C 138-160 2C191-213 2C 234-256 and 271-293 NC_002163.1 RefSeq region 950513 950545 . - . ID=id1868;gene=livH;Name=id1868;Dbxref=GeneID:905309;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 950630 950698 . - . ID=id84;gene=livH;Name=id84;Dbxref=GeneID:905309;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1017c by TMHMM2.0 at aa 15-37 2C 58-80 2C 95-117 2C 138-160 2C191-213 2C 234-256 and 271-293 ### NC_002163.1 RefSeq gene 950759 951868 . - . ID=gene970;gene=livK;Name=livK;locus_tag=Cj1018c;Dbxref=GeneID:905310;gbkey=Gene NC_002163.1 RefSeq CDS 950759 951868 . - 0 ID=cds906;Parent=gene970;gene=livK;Name=YP_002344413.1;Dbxref=InterPro:IPR001828 UniProtKB FTrEMBL:Q0P9N4 Genbank:YP_002344413.1 GeneID:905310;gbkey=CDS;product=branched-chain amino acid ABC transporter substrate-binding protein;Note=Original 282000 29 note: Cj1018c 2C livK 2C probable branched-chain amino-acid ABC transport system periplasmic binding protein 2C len: 369 aa 3B similar to e.g. LIVK_ECOLI LEU 2FILE 2FVAL-binding protein precursor 28367 aa 29 2C fasta scores 3B opt: 386 z-score: 436.5 E 28 29: 5.1e-17 2C 28.3 25 identity in 272 aa overlap. No Hp match. Highly similar to Cj1019c 2862.0 25 identity in 371 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01094 Receptor family ligand binding region identified within CDS. Further support given to product function. Paper identified linking protein to glycoprotein 28PMID:12186869 29. Characterised in Escherichia coli with marginal identity score. Appropriate motifs present. removed from product function. Functional classification - Transport 2Fbinding proteins - Amino acids and amines 7EPMID:2649683 2C PMID:2195019 NC_002163.1 RefSeq region 950789 951769 . - . ID=id1869;gene=livK;Name=id1869;Dbxref=GeneID:905310;gbkey=misc_feature;Note=HMMPfam hit to PF01094 2C Receptor family ligand binding region 2C score 3.8e-49 ### NC_002163.1 RefSeq CDS 951890 953005 . - 0 ID=cds907;Parent=gene971;gene=livJ;Name=YP_002344414.1;Dbxref=InterPro:IPR001828 UniProtKB FTrEMBL:Q0P9N3 Genbank:YP_002344414.1 GeneID:905311;gbkey=CDS;product=branched-chain amino acid ABC transporter substrate-binding protein;Note=Original 282000 29 note: Cj1019c 2C livJ 2C probable branched-chain amino-acid ABC transport system periplasmic binding protein 2C len: 369 aa 3B similar to e.g. LIVJ_ECOLI LEU 2FILE 2FVAL-binding protein precursor 28367 aa 29 2C fasta scores 3B opt: 419 z-score: 465.8 E 28 29: 1.2e-18 2C 27.8 25 identity in 352 aa overlap. No Hp match. Highly similar to Cj1018c 2862.0 25 identity in 371 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01094 Receptor family ligand binding region identified within CDS. Further support given to producnt fucntion. Characterised in Escherichia coli with marginal identity score. Appropriate motifs present. not added to product function. Functional classification - Transport 2Fbinding proteins - Amino acids and amines 7EPMID:15850393 2C PMID:2195019 NC_002163.1 RefSeq gene 951890 953005 . - . ID=gene971;gene=livJ;Name=livJ;locus_tag=Cj1019c;Dbxref=GeneID:905311;gbkey=Gene NC_002163.1 RefSeq region 951920 952888 . - . ID=id1870;gene=livJ;Name=id1870;Dbxref=GeneID:905311;gbkey=misc_feature;Note=HMMPfam hit to PF01094 2C Receptor family ligand binding region 2C score 1.3e-52 NC_002163.1 RefSeq region 952907 952924 . - . ID=id1871;gene=livJ;Name=id1871;Dbxref=GeneID:905311;gbkey=misc_feature;Note=PS00343 Gram-positive cocci surface proteins 27anchoring 27 hexapeptide ### NC_002163.1 RefSeq CDS 953036 953470 . - 0 ID=cds908;Parent=gene972;Name=YP_002344415.1;Dbxref=GOA:Q0P9N2 InterPro:IPR009056 UniProtKB FTrEMBL:Q0P9N2 Genbank:YP_002344415.1 GeneID:905312;gbkey=CDS;product=cytochrome C;Note=Original 282000 29 note: Cj1020c 2C probable cytochrome C 2C len: 144 aa 3B similar to e.g.C553_DESDN cytochrome C-553 2880 aa 29 2C fasta scores 3B opt: 142 z-score: 184.4 E 28 29: 0.0056 2C 30.8 25 identity in 78 aa overlap. Also similar to Cj1153 2827.6 25 identity in 76 aa overlap 29. No Hp ortholog. Contains N-terminal signal sequence 2C PS00190 Cytochrome c family heme-binding site signature 2C and Pfam match to entry PF00034 cytochrome_c 7EUpdated 282006 29 note: kept in product function as no specific characterisation has been carried out. Functional classification - Energy metabolism -Electron transport NC_002163.1 RefSeq gene 953036 953470 . - . ID=gene972;Name=Cj1020c;locus_tag=Cj1020c;Dbxref=GeneID:905312;gbkey=Gene NC_002163.1 RefSeq region 953117 953359 . - . ID=id1872;Name=id1872;Dbxref=GeneID:905312;gbkey=misc_feature;Note=HMMPfam hit to PF00034 2C Cytochrome c 2C score 0.0087 NC_002163.1 RefSeq region 953309 953326 . - . ID=id1873;Name=id1873;Dbxref=GeneID:905312;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature NC_002163.1 RefSeq region 953390 953458 . - . ID=id1874;Name=id1874;Dbxref=GeneID:905312;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1020c by TMHMM2.0 at aa 5-27 ### NC_002163.1 RefSeq gene 953479 953670 . - . ID=gene973;Name=Cj1021c;locus_tag=Cj1021c;Dbxref=GeneID:905313;gbkey=Gene NC_002163.1 RefSeq CDS 953479 953670 . - 0 ID=cds909;Parent=gene973;Name=YP_002344416.1;Dbxref=InterPro:IPR008439 UniProtKB FTrEMBL:Q0P9N1 Genbank:YP_002344416.1 GeneID:905313;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1021c 2C probable periplasmic protein 2C len: 63 aa 3B similar to the N-terminus of C. jejuni major outer membrane protein TR:G2529699 28EMBL:U96452 29 28MOMP_CAMJE 29 momp 2C porA 2C Cj1259 28424 aa 29 2Cfasta scores 3B opt: 110 z-score: 165.3 E 28 29: 0.066 2C 36.4 25 identity in 55 aa overlap. No Hp match. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF05538 Campylobacter major outer membrane protein identified when running own Pfam search. Some characterisation work within Cj1259 2C however 2C alignment was only partial. kept within product function. Psort was also ran with no additional results. Functional classification -Miscellaneous periplasmic proteins 7EPMID:10992471 2C PMID:754346 2C PMID:99163918 NC_002163.1 UTR_Extractor 5'-UTR 953671 953694 . - . ID=utr362;locus_tag=Cj1021c;product=putative periplasmic protein NC_002163.1 RefSeq CDS 953723 954229 . - 0 ID=cds910;Parent=gene974;Name=YP_002344417.1;Dbxref=InterPro:IPR005134 UniProtKB FTrEMBL:Q0P9N0 Genbank:YP_002344417.1 GeneID:905314;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj1022c 2C probable integral membrane protein 2C len: 168 aa 3B similar to e.g. TR:O66639 28EMBL:AE000682 29 Aquifex aeolicus AQ_286 28175 aa 29 2C fasta scores 3B opt: 354 z-score: 451.1 E 28 29: 7.9e-18 2C 34.3 25 identity in 166 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF07053 Protein of unknown function 28DUF1334 29 identified within CDS. Also 2Cfour probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 953723 954229 . - . ID=gene974;Name=Cj1022c;locus_tag=Cj1022c;Dbxref=GeneID:905314;gbkey=Gene NC_002163.1 RefSeq region 953741 953794 . - . ID=id85;Name=id85;Dbxref=GeneID:905314;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1022c by TMHMM2.0 at aa 13-35 2C 63-85 2C 119-136 and 146-163 NC_002163.1 RefSeq region 953750 954202 . - . ID=id1875;Name=id1875;Dbxref=GeneID:905314;gbkey=misc_feature;Note=HMMPfam hit to PF07053 2C Protein of unknown function 28DUF1334 29 2C score 3e-81 NC_002163.1 RefSeq region 953822 953875 . - . ID=id85;Name=id85;Dbxref=GeneID:905314;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1022c by TMHMM2.0 at aa 13-35 2C 63-85 2C 119-136 and 146-163 NC_002163.1 RefSeq region 953975 954043 . - . ID=id85;Name=id85;Dbxref=GeneID:905314;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1022c by TMHMM2.0 at aa 13-35 2C 63-85 2C 119-136 and 146-163 NC_002163.1 RefSeq region 954125 954193 . - . ID=id85;Name=id85;Dbxref=GeneID:905314;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1022c by TMHMM2.0 at aa 13-35 2C 63-85 2C 119-136 and 146-163 ### NC_002163.1 RefSeq CDS 954238 955269 . - 0 ID=cds911;Parent=gene975;gene=asd;Name=YP_002344418.1;Dbxref=GOA:Q59291 HSSP:P00353 InterPro:IPR000319 InterPro:IPR000534 InterPro:IPR005986 InterPro:IPR012080 InterPro:IPR012280 UniProtKB FSwiss-Prot:Q59291 Genbank:YP_002344418.1 GeneID:905315;gbkey=CDS;product=aspartate-semialdehyde dehydrogenase;Note=catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde NC_002163.1 RefSeq gene 954238 955269 . - . ID=gene975;gene=asd;Name=asd;locus_tag=Cj1023c;Dbxref=GeneID:905315;gbkey=Gene NC_002163.1 RefSeq region 954298 954843 . - . ID=id1876;gene=asd;Name=id1876;Dbxref=GeneID:905315;gbkey=misc_feature;Note=HMMPfam hit to PF02774 2C Semialdehyde dehydrogenase 2Cdimerisat 2C score 6.2e-88 NC_002163.1 RefSeq region 954523 954567 . - . ID=id1877;gene=asd;Name=id1877;Dbxref=GeneID:905315;gbkey=misc_feature;Note=PS01103 Aspartate-semialdehyde dehydrogenase signature NC_002163.1 RefSeq region 954880 955260 . - . ID=id1878;gene=asd;Name=id1878;Dbxref=GeneID:905315;gbkey=misc_feature;Note=HMMPfam hit to PF01118 2C Semialdehyde dehydrogenase 2CNAD bindi 2C score 5.8e-59 NC_002163.1 RefSeq gene 955269 956570 . - . ID=gene976;gene=flgR;Name=flgR;locus_tag=Cj1024c;Dbxref=GeneID:905316;gbkey=Gene NC_002163.1 RefSeq CDS 955269 956570 . - 0 ID=cds912;Parent=gene976;gene=flgR;Name=YP_002344419.1;Dbxref=GOA:Q0P9M8 InterPro:IPR001789 InterPro:IPR002078 InterPro:IPR002197 InterPro:IPR003593 UniProtKB FTrEMBL:Q0P9M8 Genbank:YP_002344419.1 GeneID:905316;gbkey=CDS;product=sigma-54 associated transcriptional activator;Note=Original 282000 29 note: Cj1024c 2C probable signal-transduction regulatory protein 2C len: 433 aa 3B similar to e.g. NTRC_PROVU nitrogen regulation protein NR 28I 29 28473 aa 29 2C fasta scores 3B opt: 957 z-score: 1002.5 E 28 29: 0 2C 38.8 25 identity in 397 aa overlap 2C and ATOC_ECOLI acetoacetate metabolism regulatory protein 28461 aa 29 2C fasta scores 3B opt: 929 z-score: 973.5 E 28 29: 0 2C 38.2 25 identity in 453 aa overlap. 57.1 25 identity to HP0703. Contains Pfam match to entry PF00072 response_reg 2C Response regulator receiver domain 2C PS00675 and PS00676 Sigma-54 interaction domain ATP-binding regions A and B signatures 2C and Pfam match to entry PF00158 sigma54 2C Sigma-54 transcription factors 7EUpdated 282006 29 note: Characterised within Campylobacter jejuni and Helicobacter pylori. not added to product function. Literature search identified papers linking Cj0793 and Cj1024 to a two-component signal transduction system 28FlgS 2FFlgR 29 that regulates the fla regulon in Campylobacter jejuni. Similar to that found in Helicobacter pylori. Functional classification - Signal transduction 7EPMID:11292815 2C PMID:14617189 2C PMID:14960570 NC_002163.1 UTR_Extractor 5'-UTR 955270 955506 . - . ID=utr363;locus_tag=Cj1023c;product=aspartate-semialdehyde dehydrogenase NC_002163.1 RefSeq region 955500 956165 . - . ID=id1879;gene=flgR;Name=id1879;Dbxref=GeneID:905316;gbkey=misc_feature;Note=HMMPfam hit to PF00158 2C Sigma-54 interaction domain 2C score 9.7e-136 NC_002163.1 RefSeq region 955860 955907 . - . ID=id1880;gene=flgR;Name=id1880;Dbxref=GeneID:905316;gbkey=misc_feature;Note=PS00676 Sigma-54 interaction domain ATP-binding region B signature NC_002163.1 RefSeq region 956052 956093 . - . ID=id1881;gene=flgR;Name=id1881;Dbxref=GeneID:905316;gbkey=misc_feature;Note=PS00675 Sigma-54 interaction domain ATP-binding region A signature NC_002163.1 RefSeq region 956220 956570 . - . ID=id1882;gene=flgR;Name=id1882;Dbxref=GeneID:905316;gbkey=misc_feature;Note=HMMPfam hit to PF00072 2C Response regulator receiver domain 2C score 9.1e-27 ### NC_002163.1 UTR_Extractor 5'-UTR 956571 956593 . - . ID=utr364;locus_tag=Cj1024c;product=sigma-54 associated transcriptional activator NC_002163.1 RefSeq CDS 956627 957076 . - 0 ID=cds913;Parent=gene977;Name=YP_002344420.1;Dbxref=GOA:Q0P9M7 UniProtKB FTrEMBL:Q0P9M7 Genbank:YP_002344420.1 GeneID:905317;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1025c 2C unknown 2C len: 149 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 RefSeq gene 956627 957076 . - . ID=gene977;Name=Cj1025c;locus_tag=Cj1025c;Dbxref=GeneID:905317;gbkey=Gene NC_002163.1 RefSeq CDS 957052 957567 . - 0 ID=cds914;Parent=gene978;Name=YP_002344421.1;Dbxref=InterPro:IPR007293 UniProtKB FTrEMBL:Q0P9M6 Genbank:YP_002344421.1 GeneID:905318;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj1026c 2C probable lipoprotein 2C len: 171 aa 3B 51.0 25 identity in N-terminus to HP0837 28102 aa 29. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site 7EUpdated 282006 29 note: Pfam domain PF04164 Protein of unknown function 2C DUF400 identified within CDS. Literature search identified paper linking product to motility. Functional classification - Membranes 2C lipoproteins and porins 7EPMID:14985343 NC_002163.1 RefSeq gene 957052 957567 . - . ID=gene978;Name=Cj1026c;locus_tag=Cj1026c;Dbxref=GeneID:905318;gbkey=Gene NC_002163.1 RefSeq region 957055 957351 . - . ID=id1883;Name=id1883;Dbxref=GeneID:905318;gbkey=misc_feature;Note=HMMPfam hit to PF04164 2C Protein of unknown function 2C DUF400 2C score 3.2e-61 NC_002163.1 RefSeq region 957517 957549 . - . ID=id1884;Name=id1884;Dbxref=GeneID:905318;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 UTR_Extractor 5'-UTR 957568 957593 . - . ID=utr365;locus_tag=Cj1026c;product=putative lipoprotein NC_002163.1 RefSeq CDS 957631 960222 . - 0 ID=cds915;Parent=gene979;gene=gyrA;Name=YP_002344422.1;Dbxref=GOA:Q03470 HSSP:P09097 InterPro:IPR002205 InterPro:IPR005743 InterPro:IPR006691 InterPro:IPR013757 InterPro:IPR013758 UniProtKB FSwiss-Prot:Q03470 Genbank:YP_002344422.1 GeneID:905319;gbkey=CDS;product=DNA gyrase subunit A;Note=negatively supercoils closed circular double-stranded DNA NC_002163.1 RefSeq gene 957631 960222 . - . ID=gene979;gene=gyrA;Name=gyrA;locus_tag=Cj1027c;Dbxref=GeneID:905319;gbkey=Gene NC_002163.1 RefSeq region 957688 957834 . - . ID=id1885;gene=gyrA;Name=id1885;Dbxref=GeneID:905319;gbkey=misc_feature;Note=HMMPfam hit to PF03989 2C DNA gyrase C-terminal domain 2C beta-prop 2C score 9.4e-11 NC_002163.1 RefSeq region 957835 957987 . - . ID=id1886;gene=gyrA;Name=id1886;Dbxref=GeneID:905319;gbkey=misc_feature;Note=HMMPfam hit to PF03989 2C DNA gyrase C-terminal domain 2C beta-prop 2C score 1.4e-15 NC_002163.1 RefSeq region 957991 958143 . - . ID=id1887;gene=gyrA;Name=id1887;Dbxref=GeneID:905319;gbkey=misc_feature;Note=HMMPfam hit to PF03989 2C DNA gyrase C-terminal domain 2C beta-prop 2C score 2.1e-15 NC_002163.1 RefSeq region 958252 958395 . - . ID=id1888;gene=gyrA;Name=id1888;Dbxref=GeneID:905319;gbkey=misc_feature;Note=HMMPfam hit to PF03989 2C DNA gyrase C-terminal domain 2C beta-prop 2C score 2.4e-14 NC_002163.1 RefSeq region 958405 958563 . - . ID=id1889;gene=gyrA;Name=id1889;Dbxref=GeneID:905319;gbkey=misc_feature;Note=HMMPfam hit to PF03989 2C DNA gyrase C-terminal domain 2C beta-prop 2C score 5.4e-15 NC_002163.1 RefSeq region 958564 958713 . - . ID=id1890;gene=gyrA;Name=id1890;Dbxref=GeneID:905319;gbkey=misc_feature;Note=HMMPfam hit to PF03989 2C DNA gyrase C-terminal domain 2C beta-prop 2C score 4.8e-14 NC_002163.1 RefSeq region 958780 960120 . - . ID=id1891;gene=gyrA;Name=id1891;Dbxref=GeneID:905319;gbkey=misc_feature;Note=HMMPfam hit to PF00521 2C DNA gyrase 2Ftopoisomerase IV 2C subunit A 2C score 0 ### NC_002163.1 UTR_Extractor 5'-UTR 960223 960246 . - . ID=utr366;locus_tag=Cj1027c;product=DNA gyrase subunit A NC_002163.1 RefSeq CDS 960263 960838 . - 0 ID=cds916;Parent=gene980;Name=YP_002344423.1;Dbxref=GOA:Q0P9M4 InterPro:IPR000836 InterPro:IPR002375 UniProtKB FTrEMBL:Q0P9M4 Genbank:YP_002344423.1 GeneID:905320;gbkey=CDS;product=purine 2Fpyrimidine phosphoribosyltransferase;Note=Original 282000 29 note: Cj1028c 2C possible purine 2Fpyrimidine phosphoribosyltransferase 2C len: 191 aa 3B weak similarity to e.g. orotate phosphoribosyltransferase domain of PYR5_HUMAN uridine 5 27-monophosphate synthase 28480 aa 29 2C fasta scores 3B opt: 114 z-score: 145.4 E 28 29: 0.85 2C25.5 25 identity in 149 aa overlap. 37.3 25 identity to HP1473. Contains PS00103 Purine 2Fpyrimidine phosphoribosyl transferases signature 7EUpdated 282006 29 note: Pfam domain PF00156 Phosphoribosyl transferase domain identified within CDS. Further support given to product function. Product kept the same as no specific characterisation has been carried out. Possible was changed to . Literature search identified two papers giving further clues to product function. Functional classification - Miscellaneous nucleoside 2Fnucleotide reactions 7EPMID:16048946 2C PMID:12949093 NC_002163.1 RefSeq gene 960263 960838 . - . ID=gene980;Name=Cj1028c;locus_tag=Cj1028c;Dbxref=GeneID:905320;gbkey=Gene NC_002163.1 RefSeq region 960344 960382 . - . ID=id1892;Name=id1892;Dbxref=GeneID:905320;gbkey=misc_feature;Note=PS00103 Purine 2Fpyrimidine phosphoribosyl transferases signature NC_002163.1 RefSeq gene 960835 961479 . - . ID=gene981;gene=mapA;Name=mapA;locus_tag=Cj1029c;Dbxref=GeneID:905321;gbkey=Gene NC_002163.1 RefSeq CDS 960835 961479 . - 0 ID=cds917;Parent=gene981;gene=mapA;Name=YP_002344424.1;Dbxref=GOA:P0C633 UniProtKB FSwiss-Prot:P0C633 Genbank:YP_002344424.1 GeneID:905321;gbkey=CDS;product=liproprotein;Note=Original 282000 29 note: Cj1029c 2C mapA 2C probable lipoprotein 2C len: 214 aa 3B identical to TR:Q46122 28EMBL:X80135 29 C. jeuni species specific mapA gene 28214 aa 29. No Hp match. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site 7EUpdated 282006 29 note: Studied in Campylobacter jejuni. No specific characterisation has been carried out yet. Functional classification - Membranes 2C lipoproteins and porins 7EPMID:7790451 NC_002163.1 RefSeq region 961426 961458 . - . ID=id1893;gene=mapA;Name=id1893;Dbxref=GeneID:905321;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 UTR_Extractor 5'-UTR 961480 961500 . - . ID=utr367;locus_tag=Cj1029c;product=putative liproprotein NC_002163.1 RefSeq CDS 961556 963352 . - 0 ID=cds918;Parent=gene982;gene=lepA;Name=YP_002344425.1;Dbxref=GOA:Q9PNR1 HSSP:P32324 InterPro:IPR000640 InterPro:IPR000795 InterPro:IPR004161 InterPro:IPR005225 InterPro:IPR006297 InterPro:IPR013842 UniProtKB FSwiss-Prot:Q9PNR1 Genbank:YP_002344425.1 GeneID:905322;gbkey=CDS;product=GTP-binding protein LepA;Note=binds to the ribosome on the universally-conserved alpha-sarcin loop NC_002163.1 RefSeq gene 961556 963352 . - . ID=gene982;gene=lepA;Name=lepA;locus_tag=Cj1030c;Dbxref=GeneID:905322;gbkey=Gene NC_002163.1 RefSeq region 961559 961885 . - . ID=id1894;gene=lepA;Name=id1894;Dbxref=GeneID:905322;gbkey=misc_feature;Note=HMMPfam hit to PF06421 2C GTP-binding protein LepA C-terminus 2C score 1.2e-74 NC_002163.1 RefSeq region 961886 962155 . - . ID=id1895;gene=lepA;Name=id1895;Dbxref=GeneID:905322;gbkey=misc_feature;Note=HMMPfam hit to PF00679 2C Elongation factor G C-terminus 2C score 3.7e-39 NC_002163.1 RefSeq region 962522 962737 . - . ID=id1896;gene=lepA;Name=id1896;Dbxref=GeneID:905322;gbkey=misc_feature;Note=HMMPfam hit to PF03144 2C Elongation factor Tu domain 2C score 1.2e-10 NC_002163.1 RefSeq region 962798 963343 . - . ID=id1897;gene=lepA;Name=id1897;Dbxref=GeneID:905322;gbkey=misc_feature;Note=HMMPfam hit to PF00009 2C Elongation factor Tu GTP binding domain 2C score 5.1e-73 NC_002163.1 RefSeq region 963176 963223 . - . ID=id1898;gene=lepA;Name=id1898;Dbxref=GeneID:905322;gbkey=misc_feature;Note=PS00301 GTP-binding elongation factors signature NC_002163.1 RefSeq region 963293 963316 . - . ID=id1899;gene=lepA;Name=id1899;Dbxref=GeneID:905322;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 UTR_Extractor 5'-UTR 963479 963479 . + . ID=utr368;locus_tag=Cj1031;product=multidrug efflux system outer membrane protein NC_002163.1 RefSeq CDS 963479 964753 . + 0 ID=cds919;Parent=gene983;gene=cmeD;Name=YP_002344426.1;Dbxref=GOA:Q0P9M1 InterPro:IPR003423 UniProtKB FTrEMBL:Q0P9M1 Genbank:YP_002344426.1 GeneID:905323;gbkey=CDS;product=multidrug efflux system outer membrane protein;Note=Original 282000 29 note: Cj1031 2C possible outer membrane component of efflux system 2C len: 424 aa 3B similar to members of the PRTF family of secretion proteins e.g. TR:O68960 28EMBL:AF059041 29 outer membrane pore protein hefA 28 3DHP0605 29 28477 aa 29 2C fasta scores 3B opt: 238 z-score: 261.5 E 28 29: 2.9e-07 2C 25.2 25 identity in 409 aa overlap 2C and TOLC_SALEN outer membrane protein TOLC precursor 28491 aa 29 2C fasta scores 3B opt: 174 z-score: 192.9 E 28 29: 0.0019 2C 21.5 25 identity in 437 aa overlap. 24.8 25 identity to HP0605. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domains x2 PF02321 Outer membrane efflux protein were identified within CDS. Further support given to product function. Characterised in Campylobacter jejuni 2C so removed from product function. Functional classification - Antibiotic resistance 7EPMID:16048946 2C PMID:15793099 2C PMID:12069964 2CPMID:15201231 2C PMID:16303882 NC_002163.1 RefSeq gene 963479 964753 . + . ID=gene983;gene=cmeD;Name=cmeD;locus_tag=Cj1031;Dbxref=GeneID:905323;gbkey=Gene NC_002163.1 RefSeq region 963548 964096 . + . ID=id1900;gene=cmeD;Name=id1900;Dbxref=GeneID:905323;gbkey=misc_feature;Note=HMMPfam hit to PF02321 2C Outer membrane efflux protein 2C score 3.8e-05 NC_002163.1 RefSeq region 964139 964723 . + . ID=id1901;gene=cmeD;Name=id1901;Dbxref=GeneID:905323;gbkey=misc_feature;Note=HMMPfam hit to PF02321 2C Outer membrane efflux protein 2C score 1.3e-11 NC_002163.1 RefSeq gene 964750 965490 . + . ID=gene984;gene=cmeE;Name=cmeE;locus_tag=Cj1032;Dbxref=GeneID:905324;gbkey=Gene NC_002163.1 RefSeq CDS 964750 965490 . + 0 ID=cds920;Parent=gene984;gene=cmeE;Name=YP_002344427.1;Dbxref=UniProtKB FTrEMBL:Q0P9M0 Genbank:YP_002344427.1 GeneID:905324;gbkey=CDS;product=mutlidrug efflux system membrane fusion protein;Note=Original 282000 29 note: Cj1032 2C possible membrane fusion component of efflux system 2C len: 246 aa 3B similar to e.g. TR:O68961 EMBL:AF059041 29 H. pylori membrane fusion protein hefB 28 3DHP0606 29 28241 aa 29 2C fasta scores 3B opt: 318 z-score: 369.4 E 28 29: 2.8e-13 2C 35.5 25 identity in 248 aa overlap 2C and part of CZCB_ALCSP cation efflux system protein CZCB 28520 aa 29 2C fasta scores 3B opt: 224 z-score: 258.9 E 28 29: 4e-07 2C 28.6 25 identity in 213 aa overlap. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain identified by running own Pfam search 2C PF00529 HlyD family secretion protein. Further support given to product function. Characterised in Campylobacter jejuni 2C so removed from product function. Functional classification -Antibiotic resistance 7EPMID:16048946 2C PMID:15793099 2C PMID:12069964 2CPMID:15201231 2C PMID:16303882 ### NC_002163.1 RefSeq region 965493 968459 . + . ID=id1902;gene=cmeF;Name=id1902;Dbxref=GeneID:905325;gbkey=misc_feature;Note=HMMPfam hit to PF00873 2C AcrB 2FAcrD 2FAcrF family 2Cscore 5.6e-198 NC_002163.1 RefSeq CDS 965493 968510 . + 0 ID=cds921;Parent=gene985;gene=cmeF;Name=YP_002344428.1;Dbxref=InterPro:IPR001036 UniProtKB FTrEMBL:Q0P9L9 Genbank:YP_002344428.1 GeneID:905325;gbkey=CDS;product=multidrug efflux system membrane protein;Note=Original 282000 29 note: Cj1033 2C probable integral membrane component of efflux system 2C len: 1005 aa 3B similar to members of the ACRB 2FACRD 2FACRF family e.g. TR:O68962 28EMBL:AF059041 29 H. pylori RND pump protein hefC 28 3DHP0607 29 281026 aa 29 2C fasta scores 3B opt: 1372 z-score: 1439.0 E 28 29: 0 2C 36.9 25 identity in 1027 aa overlap 2C and ACRD_ECOLI acriflavin resistance protein D 281037 aa 29 2Cfasta scores 3B opt: 571 z-score: 598.0 E 28 29: 5.2e-26 2C 25.7 25 identity in 1033 aa overlap. 37.1 25 identity to HP0607. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2Cand Pfam match to entry PF00873 ACR_tran 2C AcrB 2FAcrD 2FAcrF family 7EUpdated 282006 29 note: Twelve probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised in Campylobacter jejuni 2Cso removed from product function. Functional classification - Antibiotic resistance 7EPMID:16048946 2C PMID:15793099 2C PMID:12069964 2CPMID:15201231 2C PMID:16303882 NC_002163.1 RefSeq gene 965493 968510 . + . ID=gene985;gene=cmeF;Name=cmeF;locus_tag=Cj1033;Dbxref=GeneID:905325;gbkey=Gene NC_002163.1 RefSeq region 965526 965594 . + . ID=id1903;gene=cmeF;Name=id1903;Dbxref=GeneID:905325;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1033 by TMHMM2.0 at aa 12-34 2C 319-338 2C 345-367 2C 372-394 2C415-437 2C 452-474 2C 508-530 2C 829-851 2C 856-878 2C 883-905 2C931-953 and 963-985 NC_002163.1 RefSeq region 966447 966506 . + . ID=id1903;gene=cmeF;Name=id1903;Dbxref=GeneID:905325;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1033 by TMHMM2.0 at aa 12-34 2C 319-338 2C 345-367 2C 372-394 2C415-437 2C 452-474 2C 508-530 2C 829-851 2C 856-878 2C 883-905 2C931-953 and 963-985 NC_002163.1 RefSeq region 966525 966593 . + . ID=id1903;gene=cmeF;Name=id1903;Dbxref=GeneID:905325;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1033 by TMHMM2.0 at aa 12-34 2C 319-338 2C 345-367 2C 372-394 2C415-437 2C 452-474 2C 508-530 2C 829-851 2C 856-878 2C 883-905 2C931-953 and 963-985 NC_002163.1 RefSeq region 966606 966674 . + . ID=id1903;gene=cmeF;Name=id1903;Dbxref=GeneID:905325;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1033 by TMHMM2.0 at aa 12-34 2C 319-338 2C 345-367 2C 372-394 2C415-437 2C 452-474 2C 508-530 2C 829-851 2C 856-878 2C 883-905 2C931-953 and 963-985 NC_002163.1 RefSeq region 966735 966803 . + . ID=id1903;gene=cmeF;Name=id1903;Dbxref=GeneID:905325;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1033 by TMHMM2.0 at aa 12-34 2C 319-338 2C 345-367 2C 372-394 2C415-437 2C 452-474 2C 508-530 2C 829-851 2C 856-878 2C 883-905 2C931-953 and 963-985 NC_002163.1 RefSeq region 966846 966914 . + . ID=id1903;gene=cmeF;Name=id1903;Dbxref=GeneID:905325;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1033 by TMHMM2.0 at aa 12-34 2C 319-338 2C 345-367 2C 372-394 2C415-437 2C 452-474 2C 508-530 2C 829-851 2C 856-878 2C 883-905 2C931-953 and 963-985 NC_002163.1 RefSeq region 967014 967082 . + . ID=id1903;gene=cmeF;Name=id1903;Dbxref=GeneID:905325;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1033 by TMHMM2.0 at aa 12-34 2C 319-338 2C 345-367 2C 372-394 2C415-437 2C 452-474 2C 508-530 2C 829-851 2C 856-878 2C 883-905 2C931-953 and 963-985 NC_002163.1 RefSeq region 967977 968045 . + . ID=id1903;gene=cmeF;Name=id1903;Dbxref=GeneID:905325;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1033 by TMHMM2.0 at aa 12-34 2C 319-338 2C 345-367 2C 372-394 2C415-437 2C 452-474 2C 508-530 2C 829-851 2C 856-878 2C 883-905 2C931-953 and 963-985 NC_002163.1 RefSeq region 968058 968126 . + . ID=id1903;gene=cmeF;Name=id1903;Dbxref=GeneID:905325;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1033 by TMHMM2.0 at aa 12-34 2C 319-338 2C 345-367 2C 372-394 2C415-437 2C 452-474 2C 508-530 2C 829-851 2C 856-878 2C 883-905 2C931-953 and 963-985 NC_002163.1 RefSeq region 968139 968207 . + . ID=id1903;gene=cmeF;Name=id1903;Dbxref=GeneID:905325;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1033 by TMHMM2.0 at aa 12-34 2C 319-338 2C 345-367 2C 372-394 2C415-437 2C 452-474 2C 508-530 2C 829-851 2C 856-878 2C 883-905 2C931-953 and 963-985 NC_002163.1 RefSeq region 968256 968279 . + . ID=id1904;gene=cmeF;Name=id1904;Dbxref=GeneID:905325;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 968283 968351 . + . ID=id1903;gene=cmeF;Name=id1903;Dbxref=GeneID:905325;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1033 by TMHMM2.0 at aa 12-34 2C 319-338 2C 345-367 2C 372-394 2C415-437 2C 452-474 2C 508-530 2C 829-851 2C 856-878 2C 883-905 2C931-953 and 963-985 NC_002163.1 RefSeq region 968379 968447 . + . ID=id1903;gene=cmeF;Name=id1903;Dbxref=GeneID:905325;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1033 by TMHMM2.0 at aa 12-34 2C 319-338 2C 345-367 2C 372-394 2C415-437 2C 452-474 2C 508-530 2C 829-851 2C 856-878 2C 883-905 2C931-953 and 963-985 ### NC_002163.1 RefSeq gene 968534 969340 . - . ID=gene986;Name=Cj1034c;locus_tag=Cj1034c;Dbxref=GeneID:905326;gbkey=Gene NC_002163.1 RefSeq CDS 968534 969340 . - 0 ID=cds922;Parent=gene986;Name=YP_002344429.1;Dbxref=GOA:Q0P9L8 InterPro:IPR001623 UniProtKB FTrEMBL:Q0P9L8 Genbank:YP_002344429.1 GeneID:905326;gbkey=CDS;product=adenylosuccinate lyase;Note=Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide NC_002163.1 RefSeq region 968537 968734 . - . ID=id1905;Name=id1905;Dbxref=GeneID:905326;gbkey=misc_feature;Note=HMMPfam hit to PF00226 2C DnaJ domain 2C score 1.5e-05 ### NC_002163.1 UTR_Extractor 5'-UTR 969341 969400 . - . ID=utr369;locus_tag=Cj1034c;product=adenylosuccinate lyase NC_002163.1 RefSeq CDS 969341 970060 . - 0 ID=cds923;Parent=gene987;Name=YP_002344430.1;Dbxref=GOA:Q9PNQ6 InterPro:IPR007471 InterPro:IPR007472 InterPro:IPR017138 UniProtKB FSwiss-Prot:Q9PNQ6 Genbank:YP_002344430.1 GeneID:905327;gbkey=CDS;product=arginyl-tRNA-protein transferase;Note=Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate NC_002163.1 RefSeq gene 969341 970060 . - . ID=gene987;Name=Cj1035c;locus_tag=Cj1035c;Dbxref=GeneID:905327;gbkey=Gene NC_002163.1 RefSeq region 969362 969781 . - . ID=id1906;Name=id1906;Dbxref=GeneID:905327;gbkey=misc_feature;Note=HMMPfam hit to PF04377 2C Arginine-tRNA-protein transferase 2C C terminu 2C score 7.3e-72 NC_002163.1 RefSeq region 969797 970060 . - . ID=id1907;Name=id1907;Dbxref=GeneID:905327;gbkey=misc_feature;Note=HMMPfam hit to PF04376 2C Arginine-tRNA-protein transferase 2C N terminu 2C score 1.9e-42 NC_002163.1 RefSeq gene 970060 970311 . - . ID=gene988;Name=Cj1036c;locus_tag=Cj1036c;Dbxref=GeneID:905328;gbkey=Gene NC_002163.1 RefSeq CDS 970060 970311 . - 0 ID=cds924;Parent=gene988;Name=YP_002344431.1;Dbxref=GOA:Q0P9L6 UniProtKB FTrEMBL:Q0P9L6 Genbank:YP_002344431.1 GeneID:905328;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1036c 2C possible transcriptional regulator 2C len: 83 aa 3B no Hp match. Contains probable helix-turn-helix motif at aa 19-40 28Score 1070 2C 2B2.83 SD 29 7EUpdated 282006 29 note: Conserved added to product function. Functional classification - Broad regulatory functions ### NC_002163.1 RefSeq CDS 970315 971760 . - 0 ID=cds925;Parent=gene989;gene=pycA;Name=YP_002344432.1;Dbxref=GOA:Q0P9L5 InterPro:IPR004549 InterPro:IPR005479 InterPro:IPR005481 InterPro:IPR005482 InterPro:IPR011761 InterPro:IPR011764 InterPro:IPR013816 InterPro:IPR013817 UniProtKB FTrEMBL:Q0P9L5 Genbank:YP_002344432.1 GeneID:905329;gbkey=CDS;product=acetyl-CoA carboxylase subunit A;Note=biotin carboxylase 3B catalyses the carboxylation of the carrier protein which then transfers the carboxyl group to form malonyl-CoA 2C which in turn controls the rate of fatty acid metabolism NC_002163.1 RefSeq gene 970315 971760 . - . ID=gene989;gene=pycA;Name=pycA;locus_tag=Cj1037c;Dbxref=GeneID:905329;gbkey=Gene NC_002163.1 RefSeq region 970429 970749 . - . ID=id1908;gene=pycA;Name=id1908;Dbxref=GeneID:905329;gbkey=misc_feature;Note=HMMPfam hit to PF02785 2C Biotin carboxylase C-terminal domain 2C score 7.6e-49 NC_002163.1 RefSeq region 970768 971415 . - . ID=id1909;gene=pycA;Name=id1909;Dbxref=GeneID:905329;gbkey=misc_feature;Note=HMMPfam hit to PF02786 2C Carbamoyl-phosphate synthase L chain 2C 2C score 2.9e-98 NC_002163.1 RefSeq region 970876 970899 . - . ID=id1910;gene=pycA;Name=id1910;Dbxref=GeneID:905329;gbkey=misc_feature;Note=PS00867 Carbamoyl-phosphate synthase subdomain signature 2 NC_002163.1 RefSeq region 971254 971298 . - . ID=id1911;gene=pycA;Name=id1911;Dbxref=GeneID:905329;gbkey=misc_feature;Note=PS00866 Carbamoyl-phosphate synthase subdomain signature 1 NC_002163.1 RefSeq region 971419 971754 . - . ID=id1912;gene=pycA;Name=id1912;Dbxref=GeneID:905329;gbkey=misc_feature;Note=HMMPfam hit to PF00289 2C Carbamoyl-phosphate synthase L chain 2C 2C score 1.3e-42 ### NC_002163.1 UTR_Extractor 5'-UTR 971761 971788 . - . ID=utr370;locus_tag=Cj1037c;product=acetyl-CoA carboxylase subunit A NC_002163.1 UTR_Extractor 5'-UTR 971858 971899 . + . ID=utr371;locus_tag=Cj1038;product=putative cell division 2Fpeptidoglycan biosynthesis protein NC_002163.1 RefSeq CDS 971900 973063 . + 0 ID=cds926;Parent=gene990;Name=YP_002344433.1;Dbxref=GOA:Q0P9L4 InterPro:IPR001182 InterPro:IPR013437 UniProtKB FTrEMBL:Q0P9L4 Genbank:YP_002344433.1 GeneID:905330;gbkey=CDS;product=cell division 2Fpeptidoglycan biosynthesis protein;Note=Original 282000 29 note: Cj1038 2C probable cell division 2Fpeptidoglycan biosynthesis protein 2C len: 387 aa 3B similar to members of the FTSW 2FRODA 2FSPOVE family e.g. RODA_ECOLi rod shape-determining protein RODA 28370 aa 29 2Cfasta scores 3B opt: 297 z-score: 358.2 E 28 29: 1.2e-12 2C 27.1 25 identity in 388 aa overlap 2C and FTSW_ECOLI cell division protein FTSW 28414 aa 29 2C fasta scores 3B opt: 288 z-score: 346.8 E 28 29: 5.1e-12 2C 28.4 25 identity in 394 aa overlap. 46.4 25 identity to HP1560. Contains Pfam match to entry PF01098 FTSW_RODA_SPOVE 2C Cell cycle protein 7EUpdated 282006 29 note: Ten probable transmembrane helices predicted by TMHMM2.0. Specific characterisation not yet carried out 2C so kept in product function. Functional classification - Cell division NC_002163.1 RefSeq gene 971900 973063 . + . ID=gene990;Name=Cj1038;locus_tag=Cj1038;Dbxref=GeneID:905330;gbkey=Gene NC_002163.1 RefSeq region 971912 973060 . + . ID=id1913;Name=id1913;Dbxref=GeneID:905330;gbkey=misc_feature;Note=HMMPfam hit to PF01098 2C Cell cycle protein 2C score 6e-78 NC_002163.1 RefSeq region 971918 971986 . + . ID=id1914;Name=id1914;Dbxref=GeneID:905330;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1038 by TMHMM2.0 at aa 7-29 2C 39-58 2C 71-93 2C 103-125 2C145-164 2C 168-186 2C 191-208 2C 294-314 2C 326-348 and 358-380 NC_002163.1 RefSeq region 972014 972073 . + . ID=id1914;Name=id1914;Dbxref=GeneID:905330;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1038 by TMHMM2.0 at aa 7-29 2C 39-58 2C 71-93 2C 103-125 2C145-164 2C 168-186 2C 191-208 2C 294-314 2C 326-348 and 358-380 NC_002163.1 RefSeq region 972110 972178 . + . ID=id1914;Name=id1914;Dbxref=GeneID:905330;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1038 by TMHMM2.0 at aa 7-29 2C 39-58 2C 71-93 2C 103-125 2C145-164 2C 168-186 2C 191-208 2C 294-314 2C 326-348 and 358-380 NC_002163.1 RefSeq region 972206 972274 . + . ID=id1914;Name=id1914;Dbxref=GeneID:905330;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1038 by TMHMM2.0 at aa 7-29 2C 39-58 2C 71-93 2C 103-125 2C145-164 2C 168-186 2C 191-208 2C 294-314 2C 326-348 and 358-380 NC_002163.1 RefSeq region 972332 972391 . + . ID=id1914;Name=id1914;Dbxref=GeneID:905330;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1038 by TMHMM2.0 at aa 7-29 2C 39-58 2C 71-93 2C 103-125 2C145-164 2C 168-186 2C 191-208 2C 294-314 2C 326-348 and 358-380 NC_002163.1 RefSeq region 972401 972457 . + . ID=id1914;Name=id1914;Dbxref=GeneID:905330;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1038 by TMHMM2.0 at aa 7-29 2C 39-58 2C 71-93 2C 103-125 2C145-164 2C 168-186 2C 191-208 2C 294-314 2C 326-348 and 358-380 NC_002163.1 RefSeq region 972470 972523 . + . ID=id1914;Name=id1914;Dbxref=GeneID:905330;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1038 by TMHMM2.0 at aa 7-29 2C 39-58 2C 71-93 2C 103-125 2C145-164 2C 168-186 2C 191-208 2C 294-314 2C 326-348 and 358-380 NC_002163.1 RefSeq region 972779 972841 . + . ID=id1914;Name=id1914;Dbxref=GeneID:905330;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1038 by TMHMM2.0 at aa 7-29 2C 39-58 2C 71-93 2C 103-125 2C145-164 2C 168-186 2C 191-208 2C 294-314 2C 326-348 and 358-380 NC_002163.1 RefSeq region 972875 972943 . + . ID=id1914;Name=id1914;Dbxref=GeneID:905330;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1038 by TMHMM2.0 at aa 7-29 2C 39-58 2C 71-93 2C 103-125 2C145-164 2C 168-186 2C 191-208 2C 294-314 2C 326-348 and 358-380 NC_002163.1 UTR_Extractor 5'-UTR 972950 973059 . + . ID=utr372;locus_tag=Cj1039;product=undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase NC_002163.1 RefSeq region 972971 973039 . + . ID=id1914;Name=id1914;Dbxref=GeneID:905330;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1038 by TMHMM2.0 at aa 7-29 2C 39-58 2C 71-93 2C 103-125 2C145-164 2C 168-186 2C 191-208 2C 294-314 2C 326-348 and 358-380 NC_002163.1 RefSeq CDS 973060 974088 . + 0 ID=cds927;Parent=gene991;gene=murG;Name=YP_002344434.1;Dbxref=GOA:Q9PNQ2 InterPro:IPR004276 InterPro:IPR006009 InterPro:IPR007235 UniProtKB FSwiss-Prot:Q9PNQ2 Genbank:YP_002344434.1 GeneID:905331;gbkey=CDS;product=UDP-diphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase;Note=UDP-N-acetylglucosamine--N-acetylmuramyl- 28pentapeptide 29 pyrophosphoryl-undecaprenol N-acetylglucosamine transferase 3B involved in cell wall formation 3B inner membrane-associated 3B last step of peptidoglycan synthesis NC_002163.1 RefSeq gene 973060 974088 . + . ID=gene991;gene=murG;Name=murG;locus_tag=Cj1039;Dbxref=GeneID:905331;gbkey=Gene NC_002163.1 RefSeq region 973066 973488 . + . ID=id1915;gene=murG;Name=id1915;Dbxref=GeneID:905331;gbkey=misc_feature;Note=HMMPfam hit to PF03033 2C Glycosyltransferase family 2Cscore 1.4e-14 NC_002163.1 RefSeq region 973567 974058 . + . ID=id1916;gene=murG;Name=id1916;Dbxref=GeneID:905331;gbkey=misc_feature;Note=HMMPfam hit to PF04101 2C Glycosyltransferase family 2Cscore 1.2e-40 NC_002163.1 RefSeq gene 974059 975222 . - . ID=gene992;Name=Cj1040c;locus_tag=Cj1040c;Dbxref=GeneID:905332;gbkey=Gene NC_002163.1 RefSeq CDS 974059 975222 . - 0 ID=cds928;Parent=gene992;Name=YP_002344435.1;Dbxref=InterPro:IPR011701 UniProtKB FTrEMBL:Q0P9L2 Genbank:YP_002344435.1 GeneID:905332;gbkey=CDS;product=MFS transport protein;Note=Original 282000 29 note: Cj1040c 2C probable transmembrane transport protein 2C len: 387 aa 3B simlar to hypothetical membrane proteins e.g. YEAN_ECOLI 28393 aa 29 2Cfasta scores 3B opt: 641 z-score: 726.5 E 28 29: 0 2C 31.2 25 identity in 381 aa overlap 2C and to CYNX_ECOLI cyanate transport protein CYNX 28384 aa 29 2C fasta scores 3B opt: 421 z-score: 480.1 E 28 29: 1.9e-19 2C 23.9 25 identity in 368 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF07690 Major Facilitator Superfamily 28MFS 29 protein identified within CDS. Also 2C Twelve probable transmembrane helices predicted by TMHMM2.0. Specific characterisation has not been carried out yet 2C so kept in product function. Functional classification - Transport 2Fbinding proteins -Other NC_002163.1 RefSeq region 974080 974148 . - . ID=id86;Name=id86;Dbxref=GeneID:905332;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1040c by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-92 2C 96-118 2C131-153 2C 157-179 2C 206-228 2C 238-260 2C 267-289 2C 295-317 2C330-349 and 359-381 NC_002163.1 RefSeq region 974161 975180 . - . ID=id1917;Name=id1917;Dbxref=GeneID:905332;gbkey=misc_feature;Note=HMMPfam hit to PF07690 2C Major Facilitator Superfamily 2C score 4.2e-14 NC_002163.1 RefSeq region 974176 974235 . - . ID=id86;Name=id86;Dbxref=GeneID:905332;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1040c by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-92 2C 96-118 2C131-153 2C 157-179 2C 206-228 2C 238-260 2C 267-289 2C 295-317 2C330-349 and 359-381 NC_002163.1 RefSeq region 974272 974340 . - . ID=id86;Name=id86;Dbxref=GeneID:905332;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1040c by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-92 2C 96-118 2C131-153 2C 157-179 2C 206-228 2C 238-260 2C 267-289 2C 295-317 2C330-349 and 359-381 NC_002163.1 RefSeq region 974356 974424 . - . ID=id86;Name=id86;Dbxref=GeneID:905332;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1040c by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-92 2C 96-118 2C131-153 2C 157-179 2C 206-228 2C 238-260 2C 267-289 2C 295-317 2C330-349 and 359-381 NC_002163.1 RefSeq region 974443 974511 . - . ID=id86;Name=id86;Dbxref=GeneID:905332;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1040c by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-92 2C 96-118 2C131-153 2C 157-179 2C 206-228 2C 238-260 2C 267-289 2C 295-317 2C330-349 and 359-381 NC_002163.1 RefSeq region 974539 974607 . - . ID=id86;Name=id86;Dbxref=GeneID:905332;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1040c by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-92 2C 96-118 2C131-153 2C 157-179 2C 206-228 2C 238-260 2C 267-289 2C 295-317 2C330-349 and 359-381 NC_002163.1 RefSeq region 974686 974754 . - . ID=id86;Name=id86;Dbxref=GeneID:905332;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1040c by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-92 2C 96-118 2C131-153 2C 157-179 2C 206-228 2C 238-260 2C 267-289 2C 295-317 2C330-349 and 359-381 NC_002163.1 RefSeq region 974764 974832 . - . ID=id86;Name=id86;Dbxref=GeneID:905332;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1040c by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-92 2C 96-118 2C131-153 2C 157-179 2C 206-228 2C 238-260 2C 267-289 2C 295-317 2C330-349 and 359-381 NC_002163.1 RefSeq region 974869 974937 . - . ID=id86;Name=id86;Dbxref=GeneID:905332;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1040c by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-92 2C 96-118 2C131-153 2C 157-179 2C 206-228 2C 238-260 2C 267-289 2C 295-317 2C330-349 and 359-381 NC_002163.1 RefSeq region 974908 974940 . - . ID=id1918;Name=id1918;Dbxref=GeneID:905332;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 974947 975006 . - . ID=id86;Name=id86;Dbxref=GeneID:905332;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1040c by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-92 2C 96-118 2C131-153 2C 157-179 2C 206-228 2C 238-260 2C 267-289 2C 295-317 2C330-349 and 359-381 NC_002163.1 RefSeq region 975025 975093 . - . ID=id86;Name=id86;Dbxref=GeneID:905332;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1040c by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-92 2C 96-118 2C131-153 2C 157-179 2C 206-228 2C 238-260 2C 267-289 2C 295-317 2C330-349 and 359-381 NC_002163.1 RefSeq region 975136 975204 . - . ID=id86;Name=id86;Dbxref=GeneID:905332;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1040c by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-92 2C 96-118 2C131-153 2C 157-179 2C 206-228 2C 238-260 2C 267-289 2C 295-317 2C330-349 and 359-381 ### NC_002163.1 UTR_Extractor 5'-UTR 975223 975248 . - . ID=utr373;locus_tag=Cj1040c;product=putative MFS transport protein NC_002163.1 RefSeq gene 975230 976081 . - . ID=gene993;Name=Cj1041c;locus_tag=Cj1041c;Dbxref=GeneID:905333;gbkey=Gene NC_002163.1 RefSeq CDS 975230 976081 . - 0 ID=cds929;Parent=gene993;Name=YP_002344436.1;Dbxref=GOA:Q0P9L1 InterPro:IPR011042 UniProtKB FTrEMBL:Q0P9L1 Genbank:YP_002344436.1 GeneID:905333;gbkey=CDS;product=ATP 2FGTP-binding protein;Note=Original 282000 29 note: Cj1041c 2C probable periplasmic ATP 2FGTP-binding protein 2C len: 283 aa 3B no Hp match. Contains probable N-terminal signal sequence and PS00017 ATP 2FGTP-binding site motif A 28P-loop 29. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 975809 975832 . - . ID=id1919;Name=id1919;Dbxref=GeneID:905333;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 RefSeq CDS 976144 977034 . - 0 ID=cds930;Parent=gene994;Name=YP_002344437.1;Dbxref=GOA:Q0P9L0 InterPro:IPR000005 InterPro:IPR012287 UniProtKB FTrEMBL:Q0P9L0 Genbank:YP_002344437.1 GeneID:905334;gbkey=CDS;product=transcriptional regulator;Note=Original 282000 29 note: Cj1042c 2C probable transcriptional regulatory protein 2C len: 296 aa 3B similar to many members of the ARAC 2FXYLS family e.g. VIRF_YEREN VIRULENCE regulon transcriptional activator 28271 aa 29 2Cfasta scores 3B opt: 220 z-score: 270.6 E 28 29: 9e-08 2C 23.9 25 identity in 247 aa overlap 2C and LCRF_YERPE thermoregulatory protein LCRF 28271 aa 29 2C fasta scores 3B opt: 219 z-score: 269.4 E 28 29: 1e-07 2C 23.5 25 identity in 247 aa overlap. No Hp match. Contains PS00041 Bacterial regulatory proteins 2C araC family signature 2C and Pfam match to entry PF00165 HTH_2 2C Bacterial regulatory helix-turn-helix proteins 2C araC family 7EUpdated 282006 29 note: No characterisation with acceptable identity score has been identified 2C so kept in product function. Literature search identified paper giving further clues to product function. Functional classification - Broad regulatory functions 7EPMID:15201231 NC_002163.1 RefSeq gene 976144 977034 . - . ID=gene994;Name=Cj1042c;locus_tag=Cj1042c;Dbxref=GeneID:905334;gbkey=Gene NC_002163.1 RefSeq region 976177 976311 . - . ID=id1920;Name=id1920;Dbxref=GeneID:905334;gbkey=misc_feature;Note=HMMPfam hit to PF00165 2C Bacterial regulatory helix-turn-helix protei 2C score 3.3e-11 NC_002163.1 RefSeq region 976192 976320 . - . ID=id1921;Name=id1921;Dbxref=GeneID:905334;gbkey=misc_feature;Note=PS00041 Bacterial regulatory proteins 2C araC family signature NC_002163.1 RefSeq region 976327 976446 . - . ID=id1922;Name=id1922;Dbxref=GeneID:905334;gbkey=misc_feature;Note=HMMPfam hit to PF00165 2C Bacterial regulatory helix-turn-helix protei 2C score 0.096 NC_002163.1 RefSeq gene 977031 977636 . - . ID=gene995;Name=Cj1043c;locus_tag=Cj1043c;Dbxref=GeneID:905335;gbkey=Gene NC_002163.1 RefSeq CDS 977031 977636 . - 0 ID=cds931;Parent=gene995;Name=YP_002344438.1;Dbxref=GOA:Q0P9K9 InterPro:IPR003733 InterPro:IPR013785 UniProtKB FTrEMBL:Q0P9K9 Genbank:YP_002344438.1 GeneID:905335;gbkey=CDS;product=thiamine-phosphate pyrophosphorylase;Note=Original 282000 29 note: Cj1043c 2C possible transferase 2C len: 201 aa 3B similar to e.g. TENI_BACSU regulatory protein TENI 28205 aa 29 2C fasta scores 3B opt: 217 z-score: 277.4 E 28 29: 3.8e-08 2C 26.3 25 identity in 171 aa overlap 2C and THIE_ECOLI thiamin-phosphate pyrophosphorylase 28211 aa 29 2C fasta scores 3B opt: 146 z-score: 190.3 E 28 29: 0.0026 2C 27.9 25 identity in 154 aa overlap. No Hp ortholog. Also similar to Cj1081c 2830.0 25 identity in 190 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF02581 Thiamine monophosphate synthase 2FTENI identified by running own Pfam search. Product modified to more specific family member based on motif matches. Specific characterisation with acceptable identity score has not been carried out yet 2C so kept in product function. Functional classification - Biosynthesis of cofactors 2C prosthetic groups and carriers - Thiamine NC_002163.1 RefSeq CDS 977626 978771 . - 0 ID=cds932;Parent=gene996;gene=thiH;Name=YP_002344439.1;Dbxref=GOA:Q0P9K8 InterPro:IPR006638 InterPro:IPR007197 InterPro:IPR010722 InterPro:IPR012726 InterPro:IPR013785 UniProtKB FTrEMBL:Q0P9K8 Genbank:YP_002344439.1 GeneID:905336;gbkey=CDS;product=thiamine biosynthesis protein ThiH;Note=in Escherichia coli this enzyme functions in thiamine biosynthesis along with thiFSGI and iscS 3B with ThiFSG catalyzes the formation of thiazole phosphate from tyrosine 2C cysteine and 1-deoxy-D-xylulose-5-phosphate 3B forms a complex with ThiG 3B contains an iron-sulfur center NC_002163.1 RefSeq gene 977626 978771 . - . ID=gene996;gene=thiH;Name=thiH;locus_tag=Cj1044c;Dbxref=GeneID:905336;gbkey=Gene NC_002163.1 RefSeq region 977656 977976 . - . ID=id1923;gene=thiH;Name=id1923;Dbxref=GeneID:905336;gbkey=misc_feature;Note=HMMPfam hit to PF06968 2C Biotin and Thiamin Synthesis associated d 2C score 1.4e-41 NC_002163.1 RefSeq STS 977842 978621 . + . ID=id1924;gene=thiH;Name=id1924;Dbxref=UniSTS:515532;gbkey=STS NC_002163.1 RefSeq region 978013 978504 . - . ID=id1925;gene=thiH;Name=id1925;Dbxref=GeneID:905336;gbkey=misc_feature;Note=HMMPfam hit to PF04055 2C Radical SAM superfamily 2Cscore 2.4e-10 NC_002163.1 RefSeq region 978064 978087 . - . ID=id1926;gene=thiH;Name=id1926;Dbxref=GeneID:905336;gbkey=misc_feature;Note=PS00030 Eukaryotic RNA-binding region RNP-1 signature ### NC_002163.1 RefSeq gene 978774 979550 . - . ID=gene997;gene=thiG;Name=thiG;locus_tag=Cj1045c;Dbxref=GeneID:905337;gbkey=Gene NC_002163.1 RefSeq CDS 978774 979550 . - 0 ID=cds933;Parent=gene997;gene=thiG;Name=YP_002344440.1;Dbxref=GOA:Q9PNP6 InterPro:IPR008867 InterPro:IPR013785 UniProtKB FSwiss-Prot:Q9PNP6 Genbank:YP_002344440.1 GeneID:905337;gbkey=CDS;product=thiazole synthase;Note=functions in thiamine 28vitamin B1 29 biosynthesis 3B in Bacillus subtilis this enzyme catalyzes the formation of thiazole from dehydroxyglycine and 1-deoxy-D-xylulose-5-phosphate and ThiS-thiocarboxylate NC_002163.1 RefSeq region 978780 979526 . - . ID=id1927;gene=thiG;Name=id1927;Dbxref=GeneID:905337;gbkey=misc_feature;Note=HMMPfam hit to PF05690 2C Thiazole biosynthesis protein ThiG 2C score 8.9e-158 ### NC_002163.1 RefSeq CDS 979553 980356 . - 0 ID=cds934;Parent=gene998;gene=moeB;Name=YP_002344441.1;Dbxref=GOA:Q0P9K6 InterPro:IPR000594 InterPro:IPR012729 InterPro:IPR016040 UniProtKB FTrEMBL:Q0P9K6 Genbank:YP_002344441.1 GeneID:905338;gbkey=CDS;product=thiamine biosynthesis protein ThiF;Note=catalyzes the adenylation of ThiS which is involved in the formation of 5-methyl-4- 28beta-hydroxyethyl 29thiazole phosphate NC_002163.1 RefSeq gene 979553 980356 . - . ID=gene998;gene=moeB;Name=moeB;locus_tag=Cj1046c;Dbxref=GeneID:905338;gbkey=Gene NC_002163.1 RefSeq region 979703 980110 . - . ID=id1928;gene=moeB;Name=id1928;Dbxref=GeneID:905338;gbkey=misc_feature;Note=HMMPfam hit to PF00899 2C ThiF family 2C score 4.1e-30 NC_002163.1 RefSeq gene 980353 980544 . - . ID=gene999;gene=thiS;Name=thiS;locus_tag=Cj1047c;Dbxref=GeneID:905339;gbkey=Gene NC_002163.1 RefSeq CDS 980353 980544 . - 0 ID=cds935;Parent=gene999;gene=thiS;Name=YP_002344442.1;Dbxref=GOA:Q0P9K5 InterPro:IPR003749 InterPro:IPR010035 InterPro:IPR012675 UniProtKB FTrEMBL:Q0P9K5 Genbank:YP_002344442.1 GeneID:905339;gbkey=CDS;product=thiamine biosynthesis protein;Note=Original 282000 29 note: Cj1047c 2C unknown 2C len: 63 aa 3B similar to hypothetical proteins e.g. YC40_ODOSI 2873 aa 29 2Cfasta scores 3B opt: 131 z-score: 200.4 E 28 29: 0.00072 2C 37.1 25 identity in 62 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02597 ThiS family identified within CDS. Product modified to a more specific family member based on motif match. Characterisation has been carried out within Escherichia coli and Bacillus subtilis with marginal simlilarity score. Putativae kept in product function. Functional classification - Biosynthesis of cofactors 2C prosthetic groups and carriers - Thiamine 7EPMID:15489164 2C PMID:15362849 NC_002163.1 RefSeq region 980356 980544 . - . ID=id1929;gene=thiS;Name=id1929;Dbxref=GeneID:905339;gbkey=misc_feature;Note=HMMPfam hit to PF02597 2C ThiS family 2C score 1.4e-12 ### NC_002163.1 UTR_Extractor 5'-UTR 980545 980628 . - . ID=utr374;locus_tag=Cj1047c;product=putative thiamine biosynthesis protein NC_002163.1 RefSeq CDS 980554 981651 . - 0 ID=cds936;Parent=gene1000;gene=dapE;Name=YP_002344443.1;Dbxref=GOA:Q0P9K4 InterPro:IPR001261 InterPro:IPR002933 InterPro:IPR005941 InterPro:IPR011650 UniProtKB FTrEMBL:Q0P9K4 Genbank:YP_002344443.1 GeneID:905340;gbkey=CDS;product=succinyl-diaminopimelate desuccinylase;Note=dapE-encoded N-succinyl-L 2CL-diaminopimelic acid desuccinylase 28DapE 29 2C catalyzes the hydrolysis of N-succinyl-L 2CLdiaminopimelate L 2CL-SDAP to L 2CL-diaminopimelate and succinate. It is a metalloprotease containing dinuclear active sites. Its structure is similar to the carboxypeptidase G2 from Pseudomonas sp. strain RS-16 and the aminopeptidase from Aeromonas proteolytica. NC_002163.1 RefSeq gene 980554 981651 . - . ID=gene1000;gene=dapE;Name=dapE;locus_tag=Cj1048c;Dbxref=GeneID:905340;gbkey=Gene NC_002163.1 RefSeq region 980560 981471 . - . ID=id1930;gene=dapE;Name=id1930;Dbxref=GeneID:905340;gbkey=misc_feature;Note=HMMPfam hit to PF01546 2C Peptidase family M20 2FM25 2FM40 2C score 1.5e-35 NC_002163.1 RefSeq region 980824 981150 . - . ID=id1931;gene=dapE;Name=id1931;Dbxref=GeneID:905340;gbkey=misc_feature;Note=HMMPfam hit to PF07687 2C Peptidase dimerisation domain 2C score 9.4e-17 NC_002163.1 RefSeq region 981445 981474 . - . ID=id1932;gene=dapE;Name=id1932;Dbxref=GeneID:905340;gbkey=misc_feature;Note=PS00758 ArgE 2F dapE 2F ACY1 2F CPG2 2F yscS family signature 1 ### NC_002163.1 UTR_Extractor 5'-UTR 981652 981697 . - . ID=utr375;locus_tag=Cj1048c;product=succinyl-diaminopimelate desuccinylase NC_002163.1 RefSeq CDS 981655 982254 . - 0 ID=cds937;Parent=gene1001;Name=YP_002344444.1;Dbxref=GOA:Q0P9K3 InterPro:IPR001123 UniProtKB FTrEMBL:Q0P9K3 Genbank:YP_002344444.1 GeneID:905341;gbkey=CDS;product=LysE family transporter protein;Note=Original 282000 29 note: Cj1049c 2C probable integral membrane protein 2C len: 199 aa 3B similar to hypothetical membrane proteins belonging to the UPF0056 28MARC 29 family e.g. YVBG_BACSU 28211 aa 29 2C fasta scores 3B opt: 173 z-score: 220.6 E 28 29: 5.4e-05 2C 32.8 25 identity in 189 aa overlap. No Hp match 7EUpdated 282006 29 note: Six probable transmembrane helices predicted by TMHMM2.0. Also 2C Pfam domain PF01810 LysE type translocator identified within CDS. Lysine exporter protein is involved in the efflux of excess L-lysine as a control for intracellular levels of L-lysine. Product modified to more specific family member based on motif match. Characterisation has not been specifically carried out 2C so kept in product function. Functional classification - Transport 2Fbinding proteins - Other NC_002163.1 RefSeq gene 981655 982254 . - . ID=gene1001;Name=Cj1049c;locus_tag=Cj1049c;Dbxref=GeneID:905341;gbkey=Gene NC_002163.1 RefSeq region 981667 982218 . - . ID=id1933;Name=id1933;Dbxref=GeneID:905341;gbkey=misc_feature;Note=HMMPfam hit to PF01810 2C LysE type translocator 2Cscore 3.1e-59 NC_002163.1 RefSeq region 981685 981753 . - . ID=id87;Name=id87;Dbxref=GeneID:905341;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1049c by TMHMM2.0 at aa 5-27 2C 40-62 2C 66-88 2C 109-131 2C141-163 and 168-190 NC_002163.1 RefSeq region 981766 981834 . - . ID=id87;Name=id87;Dbxref=GeneID:905341;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1049c by TMHMM2.0 at aa 5-27 2C 40-62 2C 66-88 2C 109-131 2C141-163 and 168-190 NC_002163.1 RefSeq region 981862 981930 . - . ID=id87;Name=id87;Dbxref=GeneID:905341;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1049c by TMHMM2.0 at aa 5-27 2C 40-62 2C 66-88 2C 109-131 2C141-163 and 168-190 NC_002163.1 RefSeq region 981991 982059 . - . ID=id87;Name=id87;Dbxref=GeneID:905341;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1049c by TMHMM2.0 at aa 5-27 2C 40-62 2C 66-88 2C 109-131 2C141-163 and 168-190 NC_002163.1 RefSeq region 982069 982137 . - . ID=id87;Name=id87;Dbxref=GeneID:905341;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1049c by TMHMM2.0 at aa 5-27 2C 40-62 2C 66-88 2C 109-131 2C141-163 and 168-190 NC_002163.1 RefSeq region 982174 982242 . - . ID=id87;Name=id87;Dbxref=GeneID:905341;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1049c by TMHMM2.0 at aa 5-27 2C 40-62 2C 66-88 2C 109-131 2C141-163 and 168-190 NC_002163.1 RefSeq CDS 982247 982948 . - 0 ID=cds938;Parent=gene1002;gene=npdA;Name=YP_002344445.1;Dbxref=GOA:Q9JN05 HSSP:O28597 InterPro:IPR003000 UniProtKB FSwiss-Prot:Q9JN05 Genbank:YP_002344445.1 GeneID:905342;gbkey=CDS;product=NAD-dependent deacetylase;Note=Original 282000 29 note: Cj1050c 2C possible transferase 2C len: 233 aa 3B similar to hypothetical proteins and to TR:G2996605 28EMBL:U89687 29 nicotinic acid mononucleotide:5 2C6-dimethylbenzimidazole 28DMB 29 phosphoribosyltransferase 28cobB 29 gene 28237 aa 29 2C fasta scores 3B opt: 486 z-score: 586.6 E 28 29: 2.2e-25 2C 37.7 25 identity in 207 aa overlap. 42.4 25 identity to HP1259 7EUpdated 282006 29 note: Pfam domain PF02146 Sir2 family identified within CDS. These sequences represent the Sir2 family of NAD 2B-dependent deacetylases. Characterisation has been carried out in Escherichia coli and this matches up with acceptable identity score and appropriate motifs. Product modified to more specific family member. not added to product function. Functional classification - Misc 7EPMID:10811920 2C PMID:15019790 NC_002163.1 RefSeq gene 982247 982948 . - . ID=gene1002;gene=npdA;Name=npdA;locus_tag=Cj1050c;Dbxref=GeneID:905342;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 982255 982319 . - . ID=utr376;locus_tag=Cj1049c;product=putative LysE family transporter protein NC_002163.1 RefSeq region 982412 982924 . - . ID=id1934;gene=npdA;Name=id1934;Dbxref=GeneID:905342;gbkey=misc_feature;Note=HMMPfam hit to PF02146 2C Sir2 family 2C score 4.1e-40 ### NC_002163.1 UTR_Extractor 5'-UTR 982949 982968 . - . ID=utr377;locus_tag=Cj1050c;product=NAD-dependent deacetylase NC_002163.1 RefSeq CDS 982991 987010 . - 0 ID=cds939;Parent=gene1003;gene=cjeI;Name=YP_002344446.1;Dbxref=GOA:Q0P9K1 InterPro:IPR000055 InterPro:IPR002052 InterPro:IPR002296 InterPro:IPR003356 UniProtKB FTrEMBL:Q0P9K1 Genbank:YP_002344446.1 GeneID:905343;gbkey=CDS;product=restriction modification enzyme;Note=Original 282000 29 note: Cj1051c 2C probable restriction modification enzyme 2C len: 1339 aa 3B similar in N-terminal 70 25 to TR:O85299 28EMBL:AF060542 29 Haemophilus influenzae biogroup aegyptius HaeIV restriction 2Fmodification system 28953 aa 29 2C fasta scores 3B opt: 1818 z-score: 1949.8 E 28 29: 0 42.7 25 identity in 976 aa overlap 2C and in extreme C-terminus to e.g. T1SA_ECOLI type I restriction enzyme ECOAI specificity protein 28589 aa 29 2C fasta scores 3B opt: 393 z-score: 422.5 E 28 29: 3.1e-16 2C 40.4 25 identity in 178 aa overlap. No Hp ortholog. Contains PS00092 N-6 Adenine-specific DNA methylases signature 7EUpdated 282006 29 note: Pfam domains PF01420 x2 Type I restriction modification DNA specificity domain was identified within CDS. Prosite domain PS00290 IG_MHC 2CImmunoglobulins and major histocompatibility complex proteins signature was also identified within CDS. Further support given to product function. Characterised in Escherichia coli with acceptable identity score. not added to product function. Functional classification -DNA replication 2C restriction 2Fmodification 2C recombination and repair 7EPMID:2642743 2C PMID:12879741 2C PMID:15699185 NC_002163.1 RefSeq gene 982991 987010 . - . ID=gene1003;gene=cjeI;Name=cjeI;locus_tag=Cj1051c;Dbxref=GeneID:905343;gbkey=Gene NC_002163.1 RefSeq region 983072 983575 . - . ID=id1935;gene=cjeI;Name=id1935;Dbxref=GeneID:905343;gbkey=misc_feature;Note=HMMPfam hit to PF01420 2C Type I restriction modification DNA speci 2C score 8.2e-06 NC_002163.1 RefSeq region 983888 984340 . - . ID=id1936;gene=cjeI;Name=id1936;Dbxref=GeneID:905343;gbkey=misc_feature;Note=HMMPfam hit to PF01420 2C Type I restriction modification DNA speci 2C score 4.8e-08 NC_002163.1 RefSeq region 985373 985393 . - . ID=id1937;gene=cjeI;Name=id1937;Dbxref=GeneID:905343;gbkey=misc_feature;Note=PS00092 N-6 Adenine-specific DNA methylases signature NC_002163.1 RefSeq region 985649 985669 . - . ID=id1938;gene=cjeI;Name=id1938;Dbxref=GeneID:905343;gbkey=misc_feature;Note=PS00290 Immunoglobulins and major histocompatibility complex proteins signature ### NC_002163.1 RefSeq CDS 987019 989229 . - 0 ID=cds940;Parent=gene1004;gene=mutS;Name=YP_002344447.1;Dbxref=GOA:Q0P9K0 InterPro:IPR000432 InterPro:IPR002625 InterPro:IPR005747 InterPro:IPR007696 UniProtKB FTrEMBL:Q0P9K0 Genbank:YP_002344447.1 GeneID:905344;gbkey=CDS;product=recombination and DNA strand exchange inhibitor protein;Note=MutS2 3B MutS-II 3B involved in blocking homologous and homeologous recombination 3B has ATPase activity stimulated by recombination intermediates 3B inhibits DNA strand exchange NC_002163.1 RefSeq gene 987019 989229 . - . ID=gene1004;gene=mutS;Name=mutS;locus_tag=Cj1052c;Dbxref=GeneID:905344;gbkey=Gene NC_002163.1 RefSeq region 987022 987246 . - . ID=id1939;gene=mutS;Name=id1939;Dbxref=GeneID:905344;gbkey=misc_feature;Note=HMMPfam hit to PF01713 2C Smr domain 2C score 2.2e-31 NC_002163.1 RefSeq region 988273 988296 . - . ID=id1940;gene=mutS;Name=id1940;Dbxref=GeneID:905344;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq gene 989219 989569 . - . ID=gene1005;Name=Cj1053c;locus_tag=Cj1053c;Dbxref=GeneID:905345;gbkey=Gene NC_002163.1 RefSeq CDS 989219 989569 . - 0 ID=cds941;Parent=gene1005;Name=YP_002344448.1;Dbxref=GOA:Q0P9J9 UniProtKB FTrEMBL:Q0P9J9 Genbank:YP_002344448.1 GeneID:905345;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj1053c 2C possible integral membrane protein 2C len: 116 aa 3B 25.4 25 identity to HP0622 7EUpdated 282006 29 note: Two probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 UTR_Extractor 5'-UTR 989230 989338 . - . ID=utr378;locus_tag=Cj1052c;product=recombination and DNA strand exchange inhibitor protein NC_002163.1 RefSeq region 989423 989476 . - . ID=id88;Name=id88;Dbxref=GeneID:905345;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1053c by TMHMM2.0 at aa 5-22 and 32-49 NC_002163.1 RefSeq region 989504 989557 . - . ID=id88;Name=id88;Dbxref=GeneID:905345;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1053c by TMHMM2.0 at aa 5-22 and 32-49 NC_002163.1 RefSeq gene 989562 990860 . - . ID=gene1006;gene=murC;Name=murC;locus_tag=Cj1054c;Dbxref=GeneID:905346;gbkey=Gene NC_002163.1 RefSeq CDS 989562 990860 . - 0 ID=cds942;Parent=gene1006;gene=murC;Name=YP_002344449.1;Dbxref=GOA:Q9PNN7 HSSP:P45066 InterPro:IPR000713 InterPro:IPR004101 InterPro:IPR005758 InterPro:IPR013221 InterPro:IPR016040 UniProtKB FSwiss-Prot:Q9PNN7 Genbank:YP_002344449.1 GeneID:905346;gbkey=CDS;product=UDP-N-acetylmuramate--L-alanine ligase;Note=Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis NC_002163.1 RefSeq region 989712 989990 . - . ID=id1941;gene=murC;Name=id1941;Dbxref=GeneID:905346;gbkey=misc_feature;Note=HMMPfam hit to PF02875 2C Mur ligase family 2Cglutamate ligase doma 2C score 1.1e-24 NC_002163.1 RefSeq region 990015 990749 . - . ID=id1942;gene=murC;Name=id1942;Dbxref=GeneID:905346;gbkey=misc_feature;Note=HMMPfam hit to PF01225 2C Mur ligase family 2Ccatalytic domain 2C score 6.5e-27 ### NC_002163.1 UTR_Extractor 5'-UTR 990861 990881 . - . ID=utr379;locus_tag=Cj1054c;product=UDP-N-acetylmuramate--L-alanine ligase NC_002163.1 RefSeq CDS 990924 992897 . - 0 ID=cds943;Parent=gene1007;Name=YP_002344450.1;Dbxref=GOA:Q0P9J7 InterPro:IPR000917 InterPro:IPR017849 UniProtKB FTrEMBL:Q0P9J7 Genbank:YP_002344450.1 GeneID:905347;gbkey=CDS;product=sulfatase family protein;Note=Original 282000 29 note: Cj1055c 2C probable integral membrane protein 2C len: 657 aa 3B weakly similar to hypothetical proteins 2C e.g. YQGS_BACSU 28638 aa 29 2C fasta scores 3B opt: 197 z-score: 215.2 E 28 29: 0.00011 2C 22.1 25 identity in 602 aa overlap. 24.3 25 identity to HP0578. Contains PS00044 Bacterial regulatory proteins 2C lysR family signature 2C though this may be spurious 7EUpdated 282006 29 note: Pfam domain PF00884 Sulfatase identified within CDS. Sulfatases are enzymes that hydrolyze various sulphate esters. Five probable transmembrane helices predicted by TMHMM2.0. Product function modified to more specific family member based on motif match. No specific characterisation has been carried out yet 2C so kept in product function. Functional classification - Transport 2Fbinding proteins - Other NC_002163.1 RefSeq gene 990924 992897 . - . ID=gene1007;Name=Cj1055c;locus_tag=Cj1055c;Dbxref=GeneID:905347;gbkey=Gene NC_002163.1 RefSeq region 990975 992069 . - . ID=id1943;Name=id1943;Dbxref=GeneID:905347;gbkey=misc_feature;Note=HMMPfam hit to PF00884 2C Sulfatase 2C score 1.4e-94 NC_002163.1 RefSeq region 992298 992366 . - . ID=id89;Name=id89;Dbxref=GeneID:905347;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1055c by TMHMM2.0 at aa 5-27 2C 55-77 2C 90-112 2C 149-171 and 178-200 NC_002163.1 RefSeq region 992385 992453 . - . ID=id89;Name=id89;Dbxref=GeneID:905347;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1055c by TMHMM2.0 at aa 5-27 2C 55-77 2C 90-112 2C 149-171 and 178-200 NC_002163.1 RefSeq region 992562 992630 . - . ID=id89;Name=id89;Dbxref=GeneID:905347;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1055c by TMHMM2.0 at aa 5-27 2C 55-77 2C 90-112 2C 149-171 and 178-200 NC_002163.1 RefSeq region 992586 992618 . - . ID=id1944;Name=id1944;Dbxref=GeneID:905347;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 992643 992735 . - . ID=id1945;Name=id1945;Dbxref=GeneID:905347;gbkey=misc_feature;Note=PS00044 Bacterial regulatory proteins 2C lysR family signature NC_002163.1 RefSeq region 992667 992735 . - . ID=id89;Name=id89;Dbxref=GeneID:905347;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1055c by TMHMM2.0 at aa 5-27 2C 55-77 2C 90-112 2C 149-171 and 178-200 NC_002163.1 RefSeq region 992817 992885 . - . ID=id89;Name=id89;Dbxref=GeneID:905347;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1055c by TMHMM2.0 at aa 5-27 2C 55-77 2C 90-112 2C 149-171 and 178-200 ### NC_002163.1 RefSeq CDS 992909 993685 . - 0 ID=cds944;Parent=gene1008;Name=YP_002344451.1;Dbxref=GOA:Q0P9J6 InterPro:IPR003010 UniProtKB FTrEMBL:Q0P9J6 Genbank:YP_002344451.1 GeneID:905348;gbkey=CDS;product=carbon-nitrogen hydrolase family protein;Note=Original 282000 29 note: Cj1056c 2C unknown 2C len: 258 aa 3B similar to hypothetical proteins e.g. TR:O59829 28EMBL:AL023590 29 Schizosaccharomyces pombe nitrilase SPCC965.09 28272 aa 29 2C fasta scores 3B opt: 175 z-score: 224.3 E 28 29: 3.4e-05 2C 25.1 25 identity in 187 aa overlap. 38.8 25 identity to HP1481 7EUpdated 282006 29 note: Prosite domain PS50263 CN_HYDROLASE 2C Carbon-nitrogen hydrolase domain 2CNitrilase 2Fcyanide hydratase and apolipoprotein N-acyltransferase identified within CDS. Product modified to more specific family member due to motif match. No specific characterisation yet 2C so kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 992909 993685 . - . ID=gene1008;Name=Cj1056c;locus_tag=Cj1056c;Dbxref=GeneID:905348;gbkey=Gene NC_002163.1 RefSeq CDS 993678 993851 . - 0 ID=cds945;Parent=gene1009;Name=YP_002344452.1;Dbxref=GOA:Q0P9J5 UniProtKB FTrEMBL:Q0P9J5 Genbank:YP_002344452.1 GeneID:905349;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1057c 2C probable coiled-coil protein 2C len: 57 aa 3B 31.5 25 identity to HP1482. Contains coiled-coil prediction for entire length. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 993678 993851 . - . ID=gene1009;Name=Cj1057c;locus_tag=Cj1057c;Dbxref=GeneID:905349;gbkey=Gene NC_002163.1 RefSeq gene 993848 995305 . - . ID=gene1010;gene=guaB;Name=guaB;locus_tag=Cj1058c;Dbxref=GeneID:905350;gbkey=Gene NC_002163.1 RefSeq CDS 993848 995305 . - 0 ID=cds946;Parent=gene1010;gene=guaB;Name=YP_002344453.1;Dbxref=GOA:Q0P9J4 InterPro:IPR000644 InterPro:IPR001093 InterPro:IPR005990 InterPro:IPR013785 InterPro:IPR015875 UniProtKB FTrEMBL:Q0P9J4 Genbank:YP_002344453.1 GeneID:905350;gbkey=CDS;product=inosine 5 27-monophosphate dehydrogenase;Note=catalyzes the synthesis of xanthosine monophosphate by the NAD 2B dependent oxidation of inosine monophosphate NC_002163.1 RefSeq region 993899 995290 . - . ID=id1946;gene=guaB;Name=id1946;Dbxref=GeneID:905350;gbkey=misc_feature;Note=HMMPfam hit to PF00478 2C IMP dehydrogenase 2F GMP reductase domain 2C score 4.6e-211 NC_002163.1 RefSeq region 994397 994435 . - . ID=id1947;gene=guaB;Name=id1947;Dbxref=GeneID:905350;gbkey=misc_feature;Note=PS00487 IMP dehydrogenase 2F GMP reductase signature NC_002163.1 RefSeq region 994694 994855 . - . ID=id1948;gene=guaB;Name=id1948;Dbxref=GeneID:905350;gbkey=misc_feature;Note=HMMPfam hit to PF00571 2C CBS domain 2C score 4.4e-11 NC_002163.1 RefSeq region 994877 995038 . - . ID=id1949;gene=guaB;Name=id1949;Dbxref=GeneID:905350;gbkey=misc_feature;Note=HMMPfam hit to PF00571 2C CBS domain 2C score 1.3e-17 ### NC_002163.1 RefSeq CDS 995315 996676 . - 0 ID=cds947;Parent=gene1011;gene=gatA;Name=YP_002344454.1;Dbxref=GOA:Q9PNN2 InterPro:IPR000120 InterPro:IPR004412 UniProtKB FSwiss-Prot:Q9PNN2 Genbank:YP_002344454.1 GeneID:905351;gbkey=CDS;product=aspartyl 2Fglutamyl-tRNA amidotransferase subunit A;Note=allows the formation of correctly charged Asn-tRNA 28Asn 29 or Gln-tRNA 28Gln 29 through the transamidation of misacylated Asp-tRNA 28Asn 29 or Glu-tRNA 28Gln 29 in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases 3B reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA 28Asn 29 or phospho-Glu-tRNA NC_002163.1 RefSeq gene 995315 996676 . - . ID=gene1011;gene=gatA;Name=gatA;locus_tag=Cj1059c;Dbxref=GeneID:905351;gbkey=Gene NC_002163.1 RefSeq region 995354 996661 . - . ID=id1950;gene=gatA;Name=id1950;Dbxref=GeneID:905351;gbkey=misc_feature;Note=HMMPfam hit to PF01425 2C Amidase 2C score 4.2e-161 NC_002163.1 RefSeq region 996197 996292 . - . ID=id1951;gene=gatA;Name=id1951;Dbxref=GeneID:905351;gbkey=misc_feature;Note=PS00571 Amidases signature NC_002163.1 RefSeq region 996323 996346 . - . ID=id1952;gene=gatA;Name=id1952;Dbxref=GeneID:905351;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 996335 996367 . - . ID=id1953;gene=gatA;Name=id1953;Dbxref=GeneID:905351;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq gene 996673 996783 . - . ID=gene1012;gene=Cj1060c;Name=Cj1060c;locus_tag=Cj1060c;Dbxref=GeneID:905352;gbkey=Gene NC_002163.1 RefSeq CDS 996673 996783 . - 0 ID=cds948;Parent=gene1012;Name=YP_002344455.1;Dbxref=UniProtKB FTrEMBL:Q0P9J2 Genbank:YP_002344455.1 GeneID:905352;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1060c 2C small hydrophobic protein 2C len: 36 aa. No Hp match 7EUpdated 282006 29 note: One probable transmembrane helix predicted for TMHMM2.0. Also 2C one signal peptide predicted by SignalP 2.0 HMM. Product function modified to more specific family member. kept within product function. Functional classification - Membranes 2Clipoproteins and porins NC_002163.1 RefSeq region 996697 996756 . - . ID=id1954;Name=id1954;Dbxref=GeneID:905352;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1060c by TMHMM2.0 at aa 10-29 NC_002163.1 RefSeq gene 996777 999530 . - . ID=gene1013;gene=ileS;Name=ileS;locus_tag=Cj1061c;Dbxref=GeneID:905353;gbkey=Gene NC_002163.1 RefSeq CDS 996777 999530 . - 0 ID=cds949;Parent=gene1013;gene=ileS;Name=YP_002344456.1;Dbxref=GOA:P41257 HSSP:P41972 InterPro:IPR001412 InterPro:IPR002300 InterPro:IPR002301 InterPro:IPR010663 InterPro:IPR013155 InterPro:IPR014729 InterPro:IPR015905 UniProtKB FSwiss-Prot:P41257 Genbank:YP_002344456.1 GeneID:905353;gbkey=CDS;product=isoleucyl-tRNA synthetase;Note=IleRS 3B catalyzes the formation of isoleucyl-tRNA 28Ile 29 from isoleucine and tRNA 28Ile 29 3B since isoleucine and other amino acids such as valine are similar 2C there are additional editing function in this enzyme 3B one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA 28Ile 29 3B there are two active sites 2C one for aminoacylation and one for editing 3B class-I aminoacyl-tRNA synthetase family type 1 subfamily 3B some organisms carry two different copies of this enzyme NC_002163.1 UTR_Extractor 5'-UTR 996784 997029 . - . ID=utr380;locus_tag=Cj1060c;product=hypothetical protein NC_002163.1 RefSeq region 996798 996872 . - . ID=id1955;gene=ileS;Name=id1955;Dbxref=GeneID:905353;gbkey=misc_feature;Note=HMMPfam hit to PF06827 2C Zinc finger found in FPG and IleRS 2C score 0.0023 NC_002163.1 RefSeq region 997584 999455 . - . ID=id1956;gene=ileS;Name=id1956;Dbxref=GeneID:905353;gbkey=misc_feature;Note=HMMPfam hit to PF00133 2C tRNA synthetases class I 28I 2C L 2C M and V 29 2C score 0 NC_002163.1 RefSeq region 998319 998351 . - . ID=id1957;gene=ileS;Name=id1957;Dbxref=GeneID:905353;gbkey=misc_feature;Note=PS00133 Zinc carboxypeptidases 2C zinc-binding region 2 signature NC_002163.1 RefSeq region 999321 999356 . - . ID=id1958;gene=ileS;Name=id1958;Dbxref=GeneID:905353;gbkey=misc_feature;Note=PS00178 Aminoacyl-transfer RNA synthetases class-I signature ### NC_002163.1 UTR_Extractor 5'-UTR 999531 999554 . - . ID=utr381;locus_tag=Cj1061c;product=isoleucyl-tRNA synthetase NC_002163.1 RefSeq gene 999629 1000717 . + . ID=gene1014;Name=Cj1062;locus_tag=Cj1062;Dbxref=GeneID:905354;gbkey=Gene NC_002163.1 RefSeq CDS 999629 1000717 . + 0 ID=cds950;Parent=gene1014;Name=YP_002344457.1;Dbxref=GOA:Q0P9J0 InterPro:IPR008136 UniProtKB FTrEMBL:Q0P9J0 Genbank:YP_002344457.1 GeneID:905354;gbkey=CDS;product=CinA-like protein;Note=Original 282000 29 note: Cj1062 2C unknown 2C len: 362 aa 3B C-terminus is similar to hypothetical proteins e.g. YGAD_ENTAG 28164 aa 29 2C fasta scores 3B opt: 326 z-score: 399.0 E 28 29: 6.3e-15 2C 39.9 25 identity in 153 aa overlap. 33.5 25 identity in C-terminus to HP0952 7EUpdated 282006 29 note: Pfam domain PF02464 Competence-damaged protein 28CinA 29 identified within CDS. Product modified to more specific family member based on motif match. Specific characterisation not yet carried out 2C so kept within product function. Literature search identified paper 28PMID:11895937 29 2C giving further clues to product function. Functional classification -Pathogenicity 7EPMID:11895937 NC_002163.1 RefSeq region 1000232 1000696 . + . ID=id1959;Name=id1959;Dbxref=GeneID:905354;gbkey=misc_feature;Note=HMMPfam hit to PF02464 2C Competence-damaged protein 2Cscore 1.5e-28 ### NC_002163.1 RefSeq gene 1000729 1001154 . + . ID=gene1015;Name=Cj1063;locus_tag=Cj1063;Dbxref=GeneID:905355;gbkey=Gene NC_002163.1 RefSeq CDS 1000729 1001154 . + 0 ID=cds951;Parent=gene1015;Name=YP_002344458.1;Dbxref=GOA:Q0P9I9 InterPro:IPR000182 InterPro:IPR016181 UniProtKB FTrEMBL:Q0P9I9 Genbank:YP_002344458.1 GeneID:905355;gbkey=CDS;product=acetyltransferase;Note=Original 282000 29 note: Cj1063 2C possible acetyltransferase 2C len: 141 aa 3B very weak similarity to PHNO_ECOLI PHNO protein 28involved in alkylphosphonate uptake 29 28144 aa 29 2C fasta scores 3B opt: 135 z-score: 184.7 E 28 29: 0.0054 2C 26.8 25 identity in 138 aa overlap. No Hp match. Contains Pfam match to entry PF00583 Acetyltransf 2CAcetyltransferase 28GNAT 29 family 7EUpdated 282006 29 note: Specific characterisation with acceptable identity score has not been carried out yet 2C so was kept within product function. Functional classification - Misc NC_002163.1 RefSeq region 1000861 1001115 . + . ID=id1960;Name=id1960;Dbxref=GeneID:905355;gbkey=misc_feature;Note=HMMPfam hit to PF00583 2C Acetyltransferase 28GNAT 29 family 2C score 1.1e-12 ### NC_002163.1 UTR_Extractor 5'-UTR 1001190 1001217 . + . ID=utr382;locus_tag=Cj1064;product=pseudo NC_002163.1 RefSeq region 1001218 1001520 . + . ID=id1961;Name=id1961;Dbxref=PSEUDO:CAL35182.1 GeneID:905356;gbkey=misc_feature;Note=Original 282000 29 note: Cj1064 2C possible nitroreductase pseudogene 2C len: 617 bp 3B similar to many e.g. YFKO_BACSU NAD 28P 29H nitroreductase YFKO 28221 aa 29. Contains single frasemhift. Equivalent to HP0642 2C and similar to downstream 28intact 29 gene Cj1066. Contains Pfam match to entry PF00881 Nitroreductase 7EUpdated 282006 29 note: Characterised within Escherichia coli and Bacillus subtilus with acceptable identity scores. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Misc 7EPMID:8947835 2C PMID:7813889 NC_002163.1 RefSeq pseudogene 1001218 1001837 . + . ID=gene1016;Name=Cj1064;locus_tag=Cj1064;Dbxref=GeneID:905356;gbkey=Gene NC_002163.1 RefSeq region 1001236 1001520 . + . ID=id1962;Name=id1962;Dbxref=GeneID:905356;gbkey=misc_feature;Note=HMMPfam hit to PF00881 2C Nitroreductase family 2Cscore 1.3e-32 NC_002163.1 RefSeq region 1001523 1001762 . + . ID=id1962;Name=id1962;Dbxref=GeneID:905356;gbkey=misc_feature;Note=HMMPfam hit to PF00881 2C Nitroreductase family 2Cscore 1.3e-32 NC_002163.1 RefSeq region 1001523 1001837 . + . ID=id1961;Name=id1961;Dbxref=PSEUDO:CAL35182.1 GeneID:905356;gbkey=misc_feature;Note=Original 282000 29 note: Cj1064 2C possible nitroreductase pseudogene 2C len: 617 bp 3B similar to many e.g. YFKO_BACSU NAD 28P 29H nitroreductase YFKO 28221 aa 29. Contains single frasemhift. Equivalent to HP0642 2C and similar to downstream 28intact 29 gene Cj1066. Contains Pfam match to entry PF00881 Nitroreductase 7EUpdated 282006 29 note: Characterised within Escherichia coli and Bacillus subtilus with acceptable identity scores. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Misc 7EPMID:8947835 2C PMID:7813889 NC_002163.1 RefSeq CDS 1001837 1002442 . + 0 ID=cds952;Parent=gene1017;gene=rdxA;Name=YP_002344459.1;Dbxref=GOA:Q0P9I8 InterPro:IPR000415 UniProtKB FTrEMBL:Q0P9I8 Genbank:YP_002344459.1 GeneID:905357;gbkey=CDS;product=nitroreductase;Note=Original 282000 29 note: Cj1066 2C rdxA 2C probable nitroreductase 2C len: 201 aa 3B similar to TR:O30585 28EMBL:AF012552 29 H. pylori NADPH-linked flavin nitroreductase RDXA 28 3DHP0954 29 28210 aa 29 2C fasta scores 3B opt: 261 z-score: 325.6 E 28 29: 7.8e-11 2C 29.1 25 identity in 199 aa overlap. 28.3 25 identity to HP0954. Also similar to upstream pseudogene Cj1064. Contains Pfam match to entry PF00881 Nitroreductase 2C Nitroreductase family 7EUpdated 282006 29 note: Some characterisation in Helicobacter pylori. Appropriate motifs present. not added to product function. Functional classification -Misc NC_002163.1 RefSeq gene 1001837 1002442 . + . ID=gene1017;gene=rdxA;Name=rdxA;locus_tag=Cj1066;Dbxref=GeneID:905357;gbkey=Gene NC_002163.1 RefSeq region 1001858 1002376 . + . ID=id1963;gene=rdxA;Name=id1963;Dbxref=GeneID:905357;gbkey=misc_feature;Note=HMMPfam hit to PF00881 2C Nitroreductase family 2Cscore 2e-33 NC_002163.1 RefSeq stem_loop 1002434 1002471 . + . ID=id1964;gene=rdxA;Name=id1964;gbkey=stem_loop ### NC_002163.1 UTR_Extractor 5'-UTR 1002532 1002566 . + . ID=utr383;locus_tag=Cj1067;product=CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase NC_002163.1 RefSeq CDS 1002567 1003103 . + 0 ID=cds953;Parent=gene1018;gene=pgsA;Name=YP_002344460.1;Dbxref=GOA:Q0P9I7 InterPro:IPR000462 InterPro:IPR004570 UniProtKB FTrEMBL:Q0P9I7 Genbank:YP_002344460.1 GeneID:905358;gbkey=CDS;product=CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase;Note=Original 282000 29 note: Cj1067 2C pgsA 2C probable CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase 2C len: 201 aa 3B similar to many e.g. PGSA_ECOLI CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase 28EC 2.7.8.5 29 28181 aa 29 2C fasta scores 3B opt: 320 z-score: 405.9 E 28 29: 2.6e-15 2C 35.8 25 identity in 176 aa overlap. 43.9 25 identity to HP1016. Contains PS00379 CDP-alcohol phosphatidyltransferases signature 2C and Pfam match to entry PF01066 CDP-OH_P_transf 2C CDP-alcohol phosphatidyltransferase 7EUpdated 282006 29 note: Four probable transmembrane helices predicted by TMHMM2.0. Characterised in Escherichia coli with acceptable identity score 2C so not added to product function. Functional classification - Synthesis and modification of macromolecules - Phospholipids 7EPMID:6267013 2C PMID:9853401 NC_002163.1 RefSeq gene 1002567 1003103 . + . ID=gene1018;gene=pgsA;Name=pgsA;locus_tag=Cj1067;Dbxref=GeneID:905358;gbkey=Gene NC_002163.1 RefSeq region 1002585 1002638 . + . ID=id1965;gene=pgsA;Name=id1965;Dbxref=GeneID:905358;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1067 by TMHMM2.0 at aa 7-24 2C 34-56 2C 77-99 and 141-163 NC_002163.1 RefSeq region 1002666 1002734 . + . ID=id1965;gene=pgsA;Name=id1965;Dbxref=GeneID:905358;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1067 by TMHMM2.0 at aa 7-24 2C 34-56 2C 77-99 and 141-163 NC_002163.1 RefSeq region 1002681 1003070 . + . ID=id1966;gene=pgsA;Name=id1966;Dbxref=GeneID:905358;gbkey=misc_feature;Note=HMMPfam hit to PF01066 2C CDP-alcohol phosphatidyltransferase 2C score 6.5e-30 NC_002163.1 RefSeq region 1002720 1002788 . + . ID=id1967;gene=pgsA;Name=id1967;Dbxref=GeneID:905358;gbkey=misc_feature;Note=PS00379 CDP-alcohol phosphatidyltransferases signature NC_002163.1 RefSeq region 1002795 1002863 . + . ID=id1965;gene=pgsA;Name=id1965;Dbxref=GeneID:905358;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1067 by TMHMM2.0 at aa 7-24 2C 34-56 2C 77-99 and 141-163 NC_002163.1 RefSeq region 1002987 1003055 . + . ID=id1965;gene=pgsA;Name=id1965;Dbxref=GeneID:905358;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1067 by TMHMM2.0 at aa 7-24 2C 34-56 2C 77-99 and 141-163 NC_002163.1 RefSeq CDS 1003100 1004206 . + 0 ID=cds954;Parent=gene1019;Name=YP_002344461.1;Dbxref=GOA:Q9PNM6 InterPro:IPR001478 InterPro:IPR004387 InterPro:IPR006025 InterPro:IPR008915 UniProtKB FSwiss-Prot:Q9PNM6 Genbank:YP_002344461.1 GeneID:905359;gbkey=CDS;product=peptidase M50 family protein;Note=Original 282000 29 note: Cj1068 2C probable integral membrane protein 2C len: 368 aa 3B similar to hypothetical proteins e.g. YAEL_ECOLI 28450 aa 29 2C fasta scores 3B opt: 341 z-score: 399.4 E 28 29: 6e-15 2C 29.0 25 identity in 445 aa overlap. 39.6 25 identity to HP0258. Contains PS00142 Neutral zinc metallopeptidases 2C zinc-binding region signature 2C and Pfam match to entry PF00595 PDZ 2C PDZ domain 28Also known as DHR or GLGF 29 7EUpdated 282006 29 note: Pfam domain PF02163 Peptidase family M50 identified within CDS. Also 2C four probable transmembrane helices predicted by TMHMM2.0. Product modified to more specific family member due to motif match. No specific characterisation has been carried out yet. kept within product function. Functional classification - Degradation of macromolecules - Proteins 2Cpeptides and glycopeptides NC_002163.1 RefSeq gene 1003100 1004206 . + . ID=gene1019;gene=Cj1068;Name=Cj1068;locus_tag=Cj1068;Dbxref=GeneID:905359;gbkey=Gene NC_002163.1 RefSeq region 1003118 1003186 . + . ID=id1968;Name=id1968;Dbxref=GeneID:905359;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1068 by TMHMM2.0 at aa 7-29 2C 112-134 2C 291-313 and 338-360 NC_002163.1 RefSeq region 1003169 1004182 . + . ID=id1969;Name=id1969;Dbxref=GeneID:905359;gbkey=misc_feature;Note=HMMPfam hit to PF02163 2C Peptidase family M50 2C score 1.2e-61 NC_002163.1 RefSeq region 1003196 1003225 . + . ID=id1970;Name=id1970;Dbxref=GeneID:905359;gbkey=misc_feature;Note=PS00142 Neutral zinc metallopeptidases 2Czinc-binding region signature NC_002163.1 RefSeq region 1003433 1003501 . + . ID=id1968;Name=id1968;Dbxref=GeneID:905359;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1068 by TMHMM2.0 at aa 7-29 2C 112-134 2C 291-313 and 338-360 NC_002163.1 RefSeq region 1003970 1004038 . + . ID=id1968;Name=id1968;Dbxref=GeneID:905359;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1068 by TMHMM2.0 at aa 7-29 2C 112-134 2C 291-313 and 338-360 NC_002163.1 RefSeq region 1004111 1004179 . + . ID=id1968;Name=id1968;Dbxref=GeneID:905359;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1068 by TMHMM2.0 at aa 7-29 2C 112-134 2C 291-313 and 338-360 NC_002163.1 RefSeq gene 1004199 1005065 . + . ID=gene1020;Name=Cj1069;locus_tag=Cj1069;Dbxref=GeneID:905360;gbkey=Gene NC_002163.1 RefSeq CDS 1004199 1005065 . + 0 ID=cds955;Parent=gene1020;Name=YP_002344462.1;Dbxref=InterPro:IPR007488 UniProtKB FTrEMBL:Q0P9I5 Genbank:YP_002344462.1 GeneID:905360;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1069 2C unknown 2C len: 288 aa 3B similar to hypothetical proteins e.g. YB19_HAEIN HI1119 28292 aa 29 2C fasta scores 3B opt: 428 z-score: 534.0 E 28 29: 1.9e-22 2C 34.1 25 identity in 290 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF04393 Protein of unknown function 28DUF535 29 identified within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq region 1004229 1005050 . + . ID=id1971;Name=id1971;Dbxref=GeneID:905360;gbkey=misc_feature;Note=HMMPfam hit to PF04393 2C Protein of unknown function 28DUF535 29 2C score 6.6e-134 ### NC_002163.1 UTR_Extractor 5'-UTR 1005092 1005151 . + . ID=utr384;locus_tag=Cj1070;product=30S ribosomal protein S6 NC_002163.1 RefSeq gene 1005152 1005529 . + . ID=gene1021;gene=rpsF;Name=rpsF;locus_tag=Cj1070;Dbxref=GeneID:905361;gbkey=Gene NC_002163.1 RefSeq CDS 1005152 1005529 . + 0 ID=cds956;Parent=gene1021;gene=rpsF;Name=YP_002344463.1;Dbxref=GOA:Q9ZAH3 HSSP:P23370 InterPro:IPR000529 InterPro:IPR014717 UniProtKB FSwiss-Prot:Q9ZAH3 Genbank:YP_002344463.1 GeneID:905361;gbkey=CDS;product=30S ribosomal protein S6;Note=binds cooperatively with S18 to the S15-16S complex 2C allowing platform assembly to continue with S11 and S21 NC_002163.1 RefSeq region 1005155 1005430 . + . ID=id1972;gene=rpsF;Name=id1972;Dbxref=GeneID:905361;gbkey=misc_feature;Note=HMMPfam hit to PF01250 2C Ribosomal protein S6 2C score 3.5e-37 ### NC_002163.1 RefSeq CDS 1005538 1006089 . + 0 ID=cds957;Parent=gene1022;gene=ssb;Name=YP_002344464.1;Dbxref=GOA:O69302 HSSP:P02339 InterPro:IPR000424 InterPro:IPR011344 InterPro:IPR012340 UniProtKB FSwiss-Prot:O69302 Genbank:YP_002344464.1 GeneID:905362;gbkey=CDS;product=single-stranded DNA-binding protein;Note=binds to single stranded DNA and may facilitate the binding and interaction of other proteins to DNA NC_002163.1 RefSeq gene 1005538 1006089 . + . ID=gene1022;gene=ssb;Name=ssb;locus_tag=Cj1071;Dbxref=GeneID:905362;gbkey=Gene NC_002163.1 RefSeq region 1005541 1005579 . + . ID=id1974;gene=ssb;Name=id1974;Dbxref=GeneID:905362;gbkey=misc_feature;Note=PS00735 Single-strand binding protein family signature 1 NC_002163.1 RefSeq region 1005541 1005852 . + . ID=id1973;gene=ssb;Name=id1973;Dbxref=GeneID:905362;gbkey=misc_feature;Note=HMMPfam hit to PF00436 2C Single-strand binding protein family 2C score 6.3e-33 ### NC_002163.1 RefSeq gene 1006100 1006360 . + . ID=gene1023;gene=rpsR;Name=rpsR;locus_tag=Cj1072;Dbxref=GeneID:905363;gbkey=Gene NC_002163.1 RefSeq CDS 1006100 1006360 . + 0 ID=cds958;Parent=gene1023;gene=rpsR;Name=YP_002344465.1;Dbxref=GOA:O69301 InterPro:IPR001648 UniProtKB FSwiss-Prot:O69301 Genbank:YP_002344465.1 GeneID:905363;gbkey=CDS;product=30S ribosomal protein S18;Note=binds as a heterodimer with protein S6 to the central domain of the 16S rRNA 3B helps stabilize the platform of the 30S subunit NC_002163.1 RefSeq region 1006145 1006306 . + . ID=id1975;gene=rpsR;Name=id1975;Dbxref=GeneID:905363;gbkey=misc_feature;Note=HMMPfam hit to PF01084 2C Ribosomal protein S18 2Cscore 5.9e-25 ### NC_002163.1 RefSeq CDS 1006421 1008796 . - 0 ID=cds959;Parent=gene1024;gene=lon;Name=YP_002344466.1;Dbxref=GOA:O69300 InterPro:IPR001984 InterPro:IPR003111 InterPro:IPR003593 InterPro:IPR003959 InterPro:IPR004815 InterPro:IPR008268 InterPro:IPR008269 UniProtKB FSwiss-Prot:O69300 Genbank:YP_002344466.1 GeneID:905364;gbkey=CDS;product=ATP-dependent protease La;Note=Original 282000 29 note: Cj1073c 2C lon 2C ATP-dependent protease La 2C len: 791 aa 3B 99.7 25 identical to LON_CAMJE ATP-dependent protease La 28EC 3.4.21.53 29 28791 aa 29 2C and similar to many e.g. LON_ECOLI 28784 aa 29 2C fasta scores 3B opt: 1394 z-score: 1373.0 E 28 29: 0 2C 39.9 25 identity in 782 aa overlap. 55.6 25 identity to HP1379. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS01046 ATP-dependent serine proteases 2C lon family 2C serine active site 2C and Pfam match to entry PF00004 AAA 2C ATPases associated with various cellular activities 7EUpdated 282006 29 note: Characterised in Campylobacter jejuni 2C so not added to product function. Functional classification - Degradation of macromolecules - Proteins 2C peptides and glycopeptides 7EPMID:9742705 NC_002163.1 RefSeq gene 1006421 1008796 . - . ID=gene1024;gene=lon;Name=lon;locus_tag=Cj1073c;Dbxref=GeneID:905364;gbkey=Gene NC_002163.1 RefSeq region 1006424 1007068 . - . ID=id1976;gene=lon;Name=id1976;Dbxref=GeneID:905364;gbkey=misc_feature;Note=HMMPfam hit to PF05362 2C Lon protease 28S16 29 C-terminal proteolytic do 2C score 3.7e-98 NC_002163.1 RefSeq region 1006691 1006717 . - . ID=id1977;gene=lon;Name=id1977;Dbxref=GeneID:905364;gbkey=misc_feature;Note=PS01046 ATP-dependent serine proteases 2C lon family 2Cserine active site NC_002163.1 RefSeq region 1007135 1007722 . - . ID=id1978;gene=lon;Name=id1978;Dbxref=GeneID:905364;gbkey=misc_feature;Note=HMMPfam hit to PF00004 2C ATPase family associated with various cellul 2C score 6.4e-49 NC_002163.1 RefSeq region 1007684 1007707 . - . ID=id1979;gene=lon;Name=id1979;Dbxref=GeneID:905364;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 1008194 1008763 . - . ID=id1980;gene=lon;Name=id1980;Dbxref=GeneID:905364;gbkey=misc_feature;Note=HMMPfam hit to PF02190 2C ATP-dependent protease La 28LON 29 domain 2C score 1.9e-06 ### NC_002163.1 RefSeq gene 1008813 1009460 . - . ID=gene1025;Name=Cj1074c;locus_tag=Cj1074c;Dbxref=GeneID:905365;gbkey=Gene NC_002163.1 RefSeq CDS 1008813 1009460 . - 0 ID=cds960;Parent=gene1025;Name=YP_002344467.1;Dbxref=UniProtKB FTrEMBL:Q0P9I0 Genbank:YP_002344467.1 GeneID:905365;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj1074c 2C probable lipoprotein 2C len: 215 aa 3B identical to partial TR:O69299 28EMBL:Y17166 29 C. jejuni 28called comL 29 2C 34.1 25 identity to HP1378 28called comL 2C on basis of weak match to N. gonorrhoeae comL 29. This gene has no detectable similarity to N.g. comL. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 1009407 1009439 . - . ID=id1981;Name=id1981;Dbxref=GeneID:905365;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 UTR_Extractor 5'-UTR 1009461 1009492 . - . ID=utr385;locus_tag=Cj1074c;product=putative lipoprotein NC_002163.1 UTR_Extractor 5'-UTR 1009588 1009620 . + . ID=utr386;locus_tag=Cj1075;product=flagellar assembly protein FliW NC_002163.1 RefSeq region 1009621 1009989 . + . ID=id1982;Name=id1982;Dbxref=GeneID:905366;gbkey=misc_feature;Note=HMMPfam hit to PF02623 2C Uncharacterized BCR 2CCOG1699 2C score 1.2e-36 NC_002163.1 RefSeq gene 1009621 1010010 . + . ID=gene1026;Name=Cj1075;locus_tag=Cj1075;Dbxref=GeneID:905366;gbkey=Gene NC_002163.1 RefSeq CDS 1009621 1010010 . + 0 ID=cds961;Parent=gene1026;Name=YP_002344468.1;Dbxref=GOA:Q0P9H9 InterPro:IPR003775 UniProtKB FSwiss-Prot:Q0P9H9 Genbank:YP_002344468.1 GeneID:905366;gbkey=CDS;product=flagellar assembly protein FliW;Note=binds to flagellin and appears to stabilize flagellin during flagella assembly NC_002163.1 RefSeq gene 1010010 1010741 . + . ID=gene1027;gene=proC;Name=proC;locus_tag=Cj1076;Dbxref=GeneID:905367;gbkey=Gene NC_002163.1 RefSeq CDS 1010010 1010741 . + 0 ID=cds962;Parent=gene1027;gene=proC;Name=YP_002344469.1;Dbxref=GOA:Q0P9H8 InterPro:IPR000304 InterPro:IPR004455 UniProtKB FTrEMBL:Q0P9H8 Genbank:YP_002344469.1 GeneID:905367;gbkey=CDS;product=pyrroline-5-carboxylate reductase;Note=catalyzes the formation of L-proline from pyrroline-5-carboxylate NC_002163.1 RefSeq region 1010019 1010705 . + . ID=id1983;gene=proC;Name=id1983;Dbxref=GeneID:905367;gbkey=misc_feature;Note=HMMPfam hit to PF01089 2C Delta 1-pyrroline-5-carboxylate reductase 2C score 2.4e-44 NC_002163.1 RefSeq region 1010448 1010480 . + . ID=id1984;gene=proC;Name=id1984;Dbxref=GeneID:905367;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1010616 1010684 . + . ID=id1985;gene=proC;Name=id1985;Dbxref=GeneID:905367;gbkey=misc_feature;Note=PS00521 Delta 1-pyrroline-5-carboxylate reductase signature NC_002163.1 RefSeq CDS 1010738 1011040 . + 0 ID=cds963;Parent=gene1028;gene=ctsT;Name=YP_002344470.1;Dbxref=UniProtKB FTrEMBL:Q0P9H7 Genbank:YP_002344470.1 GeneID:905368;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1077 2C probable periplasmic protein 2C len: 100 aa 3B no Hp match. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Some characterisation work carried out within Campylobacter jejuni. Product unchanged 2C but gene name added. Functional classification - Miscellaneous periplasmic proteins 7EPMID:12949093 NC_002163.1 RefSeq gene 1010738 1011040 . + . ID=gene1028;gene=ctsT;Name=ctsT;locus_tag=Cj1077;Dbxref=GeneID:905368;gbkey=Gene NC_002163.1 RefSeq region 1010756 1010824 . + . ID=id1986;gene=ctsT;Name=id1986;Dbxref=GeneID:905368;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1077 by TMHMM2.0 at aa 7-29 NC_002163.1 RefSeq gene 1011037 1011699 . + . ID=gene1029;gene=Cj1078;Name=Cj1078;locus_tag=Cj1078;Dbxref=GeneID:905369;gbkey=Gene NC_002163.1 RefSeq CDS 1011037 1011699 . + 0 ID=cds964;Parent=gene1029;Name=YP_002344471.1;Dbxref=InterPro:IPR001360 InterPro:IPR012902 UniProtKB FTrEMBL:Q0P9H6 Genbank:YP_002344471.1 GeneID:905369;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1078 2C probable periplasmic protein 2C len: 220 aa 3B no Hp match. Contains probable N-terminal signal sequence and PS00572 Glycosyl hydrolases family 1 active site 7EUpdated 282006 29 note: Some research carried out within Campylobacter jejuni. Product unchanged. Functional classification - Miscellaneous periplasmic proteins 7EPMID:12949093 NC_002163.1 RefSeq region 1011049 1011108 . + . ID=id1987;Name=id1987;Dbxref=GeneID:905369;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1078 by TMHMM2.0 at aa 5-24 NC_002163.1 RefSeq region 1011451 1011477 . + . ID=id1988;Name=id1988;Dbxref=GeneID:905369;gbkey=misc_feature;Note=PS00572 Glycosyl hydrolases family 1 active site NC_002163.1 RefSeq CDS 1011696 1012148 . + 0 ID=cds965;Parent=gene1030;Name=YP_002344472.1;Dbxref=GOA:Q0P9H5 UniProtKB FTrEMBL:Q0P9H5 Genbank:YP_002344472.1 GeneID:905370;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1079 2C probable periplasmic protein 2C len: 150 aa 3B no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 1011696 1012148 . + . ID=gene1030;Name=Cj1079;locus_tag=Cj1079;Dbxref=GeneID:905370;gbkey=Gene NC_002163.1 RefSeq region 1011708 1011776 . + . ID=id1989;Name=id1989;Dbxref=GeneID:905370;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1079 by TMHMM2.0 at aa 5-27 NC_002163.1 RefSeq CDS 1012145 1012774 . - 0 ID=cds966;Parent=gene1031;gene=hemD;Name=YP_002344473.1;Dbxref=GOA:Q0P9H4 InterPro:IPR003754 UniProtKB FTrEMBL:Q0P9H4 Genbank:YP_002344473.1 GeneID:905371;gbkey=CDS;product=uroporphyrinogen-III synthase;Note=catalyzes the formation of uroporphyrinogen-III from hydroxymethylbilane 3B functions in tetrapyrrole and heme biosynthesis NC_002163.1 RefSeq gene 1012145 1012774 . - . ID=gene1031;gene=hemD;Name=hemD;locus_tag=Cj1080c;Dbxref=GeneID:905371;gbkey=Gene NC_002163.1 RefSeq region 1012166 1012774 . - . ID=id1990;gene=hemD;Name=id1990;Dbxref=GeneID:905371;gbkey=misc_feature;Note=HMMPfam hit to PF02602 2C Uroporphyrinogen-III synthase HemD 2C score 1.6e-06 NC_002163.1 RefSeq CDS 1012752 1013384 . - 0 ID=cds967;Parent=gene1032;gene=thiE;Name=YP_002344474.1;Dbxref=GOA:Q9PNL3 HSSP:P39594 InterPro:IPR003733 InterPro:IPR013785 UniProtKB FSwiss-Prot:Q9PNL3 Genbank:YP_002344474.1 GeneID:905372;gbkey=CDS;product=thiamin-phosphate pyrophosphorylase;Note=Original 282000 29 note: Cj1081c 2C thiE 2C probale thiamin-phosphate pyrophosphorylase 2C len: 210 aa 3B similar to many e.g. THIE_BACSU thiamin-phosphate pyrophosphorylase 28EC 2.5.1.3 29 28222 aa 29 2C fasta scores 3B opt: 342 z-score: 426.6 E 28 29: 1.8e-16 2C 31.6 25 identity in 206 aa overlap. 38.9 25 identity to HP0843. Also similar to Cj1043c 2829.5 25 identity in 190 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF02581 Thiamine monophosphate synthase 2FTENI identified within CDS. Further support given to product function. Characterised in Bacillus subtilis with marginal identity score. Appropriate motifs present. not added to product function. Functional classification - Biosynthesis of cofactors 2C prosthetic groups and carriers - Thiamine 7EPMID:10350464 NC_002163.1 RefSeq gene 1012752 1013384 . - . ID=gene1032;gene=thiE;Name=thiE;locus_tag=Cj1081c;Dbxref=GeneID:905372;gbkey=Gene NC_002163.1 RefSeq region 1012776 1013369 . - . ID=id1991;gene=thiE;Name=id1991;Dbxref=GeneID:905372;gbkey=misc_feature;Note=HMMPfam hit to PF02581 2C Thiamine monophosphate synthase 2FTENI 2C score 1.5e-63 NC_002163.1 RefSeq CDS 1013374 1014186 . - 0 ID=cds968;Parent=gene1033;gene=thiD;Name=YP_002344475.1;Dbxref=GOA:Q0P9H2 InterPro:IPR004399 InterPro:IPR013749 UniProtKB FTrEMBL:Q0P9H2 Genbank:YP_002344475.1 GeneID:905373;gbkey=CDS;product=phosphomethylpyrimidine kinase;Note=Original 282000 29 note: Cj1082c 2C thiD 2C probable phosphomethylpyrimidine kinase 2C len: 270 aa 3B similar to many e.g. THID_ECOLI phosphomethylpyrimidine kinase 28EC 2.7.4.7 29 28266 aa 29 2C fasta scores 3B opt: 582 z-score: 703.6 E 28 29: 6.8e-32 2C 41.0 25 identity in 261 aa overlap. 43.4 25 identity to HP0844 7EUpdated 282006 29 note: Characterised in Escherichia coli with acceptable identity score 2C so not added to product function. Functional classification -Biosynthesis of cofactors 2C prosthetic groups and carriers - Thiamine 7EPMID:10075431 NC_002163.1 RefSeq gene 1013374 1014186 . - . ID=gene1033;gene=thiD;Name=thiD;locus_tag=Cj1082c;Dbxref=GeneID:905373;gbkey=Gene NC_002163.1 RefSeq gene 1014183 1014869 . - . ID=gene1034;gene=Cj1083c;Name=Cj1083c;locus_tag=Cj1083c;Dbxref=GeneID:905374;gbkey=Gene NC_002163.1 RefSeq CDS 1014183 1014869 . - 0 ID=cds969;Parent=gene1034;Name=YP_002344476.1;Dbxref=GOA:Q0P9H1 InterPro:IPR003265 UniProtKB FTrEMBL:Q0P9H1 Genbank:YP_002344476.1 GeneID:905374;gbkey=CDS;product=nuclease;Note=Original 282000 29 note: Cj1083c 2C possible nuclease 2Clen: 228 aa 3B some similarity with predicted proteins showing similarity to endonucleases e.g. END3_RICPR endonuclease III 28EC 4.2.99.18 29 28212 aa 29 2C fasta scores 3B opt: 147 z-score: 181.9 E 28 29: 0.0078 2C 25.7 25 identity in 152 aa overlap. 43.0 25 identity to HP0602 28annotated as endonuclease III 29. No detectable similarity to C. jejuni endonuclease III 28Cj0595c 2C equivalent to HP0585 29 7EUpdated 282006 29 note: Pfam domain PF00730 HhH-GPD superfamily base excision DNA repair identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score carried out yet. Possible changed to . Functional classification - DNA replication 2Crestriction 2Fmodification 2C recombination and repair NC_002163.1 RefSeq region 1014348 1014767 . - . ID=id1992;Name=id1992;Dbxref=GeneID:905374;gbkey=misc_feature;Note=HMMPfam hit to PF00730 2C HhH-GPD superfamily base excision DNA repair 2C score 2.7e-11 NC_002163.1 RefSeq CDS 1014866 1015627 . - 0 ID=cds970;Parent=gene1035;Name=YP_002344477.1;Dbxref=InterPro:IPR008533 UniProtKB FTrEMBL:Q0P9H0 Genbank:YP_002344477.1 GeneID:905375;gbkey=CDS;product=ATP 2FGTP-binding protein;Note=Original 282000 29 note: Cj1084c 2C possible ATP 2FGTP-binding protein 2C len: 253 aa 3B similar to part of hypothetical proteins from Synechocystis TR:Q55502 28EMBL:D64006 29 28436 aa 29 2C fasta scores 3B opt: 586 z-score: 675.2 E 28 29: 2.6e-30 2C 42.4 25 identity in 236 aa overlap 2C and Aquifex aeolicus TR:O66668 28EMBL:AE000684 29 AQ_336 28196 aa 29 2C fasta scores 3B opt: 383 z-score: 449.2 E 28 29: 1e-17 2C40.4 25 identity in 136 aa overlap. No Hp match. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 7EUpdated 282006 29 note: Pfam domain PF05673 Protein of unknown function 28DUF815 29 identified within CDS. No specific characterisation has been carried out yet. kept within product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 1014866 1015627 . - . ID=gene1035;Name=Cj1084c;locus_tag=Cj1084c;Dbxref=GeneID:905375;gbkey=Gene NC_002163.1 RefSeq region 1014893 1015183 . - . ID=id1993;Name=id1993;Dbxref=GeneID:905375;gbkey=misc_feature;Note=HMMPfam hit to PF05673 2C Protein of unknown function 28DUF815 29 2C score 3.3e-60 NC_002163.1 RefSeq region 1015421 1015444 . - . ID=id1994;Name=id1994;Dbxref=GeneID:905375;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 RefSeq gene 1015629 1018565 . - . ID=gene1036;gene=mfd;Name=mfd;locus_tag=Cj1085c;Dbxref=GeneID:905376;gbkey=Gene NC_002163.1 RefSeq CDS 1015629 1018565 . - 0 ID=cds971;Parent=gene1036;gene=mfd;Name=YP_002344478.1;Dbxref=GOA:Q0P9G9 InterPro:IPR001650 InterPro:IPR003711 InterPro:IPR004576 InterPro:IPR005118 InterPro:IPR011545 InterPro:IPR014001 InterPro:IPR014021 UniProtKB FTrEMBL:Q0P9G9 Genbank:YP_002344478.1 GeneID:905376;gbkey=CDS;product=transcription-repair coupling factor;Note=Original 282000 29 note: Cj1085c 2C mfd 2C probable transcription-repair coupling factor 2C len: 978 aa 3B similar to many e.g. MFD_ECOLI transcription-repair coupling factor 281148 aa 29 2C fasta scores 3B opt: 1474 z-score: 1608.2 E 28 29: 0 2C 31.5 25 identity in 967 aa overlap. 48.3 25 identity to HP1541. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C and Pfam match to entry PF00271 helicase_C 2CHelicases conserved C-terminal domain 7EUpdated 282006 29 note: Pfam domains PF03461 TRCF domain 2C PF00270 DEAD 2FDEAH box helicase and PF02559 CarD-like 2FTRCF domain were all identified within CDS. Further support given to product function. Characterised within Escherichia coli with marginal identity score. Appropriate motifs present. not added to product funciton. Functional classification - DNA replication 2Crestriction 2Fmodification 2C recombination and repair 7EPMID:16511235 2C PMID:12658334 2C PMID:12086674 NC_002163.1 RefSeq region 1015656 1015970 . - . ID=id1995;gene=mfd;Name=id1995;Dbxref=GeneID:905376;gbkey=misc_feature;Note=HMMPfam hit to PF03461 2C TRCF domain 2C score 5.5e-31 NC_002163.1 RefSeq region 1016250 1016480 . - . ID=id1996;gene=mfd;Name=id1996;Dbxref=GeneID:905376;gbkey=misc_feature;Note=HMMPfam hit to PF00271 2C Helicase conserved C-terminal domain 2C score 1.3e-15 NC_002163.1 RefSeq region 1016673 1017164 . - . ID=id1997;gene=mfd;Name=id1997;Dbxref=GeneID:905376;gbkey=misc_feature;Note=HMMPfam hit to PF00270 2C DEAD 2FDEAH box helicase 2Cscore 1.7e-25 NC_002163.1 RefSeq region 1017060 1017083 . - . ID=id1998;gene=mfd;Name=id1998;Dbxref=GeneID:905376;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 1017246 1017539 . - . ID=id1999;gene=mfd;Name=id1999;Dbxref=GeneID:905376;gbkey=misc_feature;Note=HMMPfam hit to PF02559 2C CarD-like 2FTRCF domain 2Cscore 4.1e-42 NC_002163.1 RefSeq CDS 1018565 1018960 . - 0 ID=cds972;Parent=gene1037;Name=YP_002344479.1;Dbxref=InterPro:IPR007607 InterPro:IPR010916 UniProtKB FTrEMBL:Q0P9G8 Genbank:YP_002344479.1 GeneID:905377;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1086c 2C unknown 2C len: 131 aa 3B some similarity to hypothetical proteins e.g. TR:O51261 28EMBL:AE001134 29 Borrelia burgdorferi BB0245 28184 aa 29 2C fasta scores 3B opt: 197 z-score: 255.1 E 28 29: 6.6e-07 2C30.0 25 identity in 110 aa overlap. 39.8 25 identity to HP1542 7EUpdated 282006 29 note: Pfam domain PF04519 Protein of unknown function 2C DUF583 are identified within CDS. Prosite domain PS00430 TONB_DEPENDENT_REC_1 2CTonB-dependent receptor proteins signature 1 was also identified. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 1018565 1018960 . - . ID=gene1037;gene=Cj1086c;Name=Cj1086c;locus_tag=Cj1086c;Dbxref=GeneID:905377;gbkey=Gene NC_002163.1 RefSeq region 1018598 1018933 . - . ID=id2000;Name=id2000;Dbxref=GeneID:905377;gbkey=misc_feature;Note=HMMPfam hit to PF04519 2C Protein of unknown function 2C DUF583 2C score 2.2e-48 NC_002163.1 RefSeq region 1018787 1018960 . - . ID=id2001;Name=id2001;Dbxref=GeneID:905377;gbkey=misc_feature;Note=PS00430 TonB-dependent receptor proteins signature 1 NC_002163.1 RefSeq gene 1018897 1019799 . - . ID=gene1038;Name=Cj1087c;locus_tag=Cj1087c;Dbxref=GeneID:905378;gbkey=Gene NC_002163.1 RefSeq CDS 1018897 1019799 . - 0 ID=cds973;Parent=gene1038;Name=YP_002344480.1;Dbxref=GOA:Q0P9G7 InterPro:IPR002886 InterPro:IPR016047 UniProtKB FTrEMBL:Q0P9G7 Genbank:YP_002344480.1 GeneID:905378;gbkey=CDS;product=peptidase;Note=Original 282000 29 note: Cj1087c 2C possible periplasmic protein 2C len: 300 aa 3B similar to TR:Q57503 28EMBL:U39068 29 Vibrio cholerae ToxR activated gene 28302 aa 29 2C fasta scores 3B opt: 575 z-score: 642.1 E 28 29: 1.8e-28 2C 34.4 25 identity in 305 aa overlap. Also contains a segment of similarity to e.g. LSTP_STASI lysostaphin precursor 28493 aa 29 2C fasta scores 3B opt: 262 z-score: 294.5 E 28 29: 4.2e-09 2C28.8 25 identity in 208 aa overlap. 36.9 25 identity to HP1543. Also similar to Cj1215 2840.6 25 identity in 133 aa overlap 29 2C and Cj1235 2840.7 25 identity in 123 aa overlap 29. Contains possible N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF01551 Peptidase family M23 identified within CDS. Product modified to more specific family member based on motif match. No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification - Degradation of macromolecules - Proteins 2Cpeptides and glycopeptides NC_002163.1 RefSeq region 1019026 1019319 . - . ID=id2002;Name=id2002;Dbxref=GeneID:905378;gbkey=misc_feature;Note=HMMPfam hit to PF01551 2C Peptidase family M23 2C score 1.8e-47 NC_002163.1 RefSeq region 1019659 1019718 . - . ID=id2003;Name=id2003;Dbxref=GeneID:905378;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1087c by TMHMM2.0 at aa 28-47 NC_002163.1 RefSeq gene 1019786 1020970 . - . ID=gene1039;gene=folC;Name=folC;locus_tag=Cj1088c;Dbxref=GeneID:905379;gbkey=Gene NC_002163.1 RefSeq CDS 1019786 1020970 . - 0 ID=cds974;Parent=gene1039;gene=folC;Name=YP_002344481.1;Dbxref=GOA:Q0P9G6 InterPro:IPR001645 InterPro:IPR004101 InterPro:IPR013221 UniProtKB FTrEMBL:Q0P9G6 Genbank:YP_002344481.1 GeneID:905379;gbkey=CDS;product=bifunctional folylpolyglutamate synthase 2Fdihydrofolate synthase;Note=Original 282000 29 note: Cj1088c 2C folC 2C probable folylpolyglutamate synthase 2Fdihydrofolate synthase 2C len: 394 aa 3B similar to many e.g. FOLC_ECOLI folylpolyglutamate synthase 28EC 6.3.2.17 29 2F dihydrofolate synthase 28EC 6.3.2.12 29 28422 aa 29 2C fasta sores 3B opt: 315 z-score: 360.4 E 28 29: 8.9e-13 2C 30.7 25 identity in 313 aa overlap. 42.7 25 identity to HP1545. Contains Pfam match to entry PF01225 FPGS 2C Folylpolyglutamate synthase 7EUpdated 282006 29 note: Characterised in Escherichia coli with marginal identity score. Appropriate motifs present. not added to product function. Functional classification - Biosynthesis of cofactors 2Cprosthetic groups and carriers - Heme 7EPMID:3040739 2C PMID:1939056 NC_002163.1 UTR_Extractor 5'-UTR 1019800 1019963 . - . ID=utr387;locus_tag=Cj1087c;product=putative peptidase NC_002163.1 RefSeq gene 1020936 1022333 . - . ID=gene1040;gene=Cj1089c;Name=Cj1089c;locus_tag=Cj1089c;Dbxref=GeneID:905380;gbkey=Gene NC_002163.1 RefSeq CDS 1020936 1022333 . - 0 ID=cds975;Parent=gene1040;Name=YP_002344482.1;Dbxref=GOA:Q0P9G5 UniProtKB FTrEMBL:Q0P9G5 Genbank:YP_002344482.1 GeneID:905380;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1089c 2C unknown 2C len: 65 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 RefSeq gene 1022317 1022829 . - . ID=gene1041;Name=Cj1090c;locus_tag=Cj1090c;Dbxref=GeneID:905381;gbkey=Gene NC_002163.1 RefSeq CDS 1022317 1022829 . - 0 ID=cds976;Parent=gene1041;Name=YP_002344483.1;Dbxref=UniProtKB FTrEMBL:Q0P9G4 Genbank:YP_002344483.1 GeneID:905381;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj1090c 2C probable lipoprotein 2C len: 170 aa 3B 26.5 25 identity to HP1546. Contains N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes 2Clipoproteins and porins NC_002163.1 UTR_Extractor 5'-UTR 1022334 1022585 . - . ID=utr388;locus_tag=Cj1089c;product=hypothetical protein NC_002163.1 RefSeq region 1022782 1022814 . - . ID=id2004;Name=id2004;Dbxref=GeneID:905381;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq CDS 1022826 1025255 . - 0 ID=cds977;Parent=gene1042;gene=leuS;Name=YP_002344484.1;Dbxref=GOA:Q9PNK3 InterPro:IPR001412 InterPro:IPR002300 InterPro:IPR002302 InterPro:IPR014729 UniProtKB FSwiss-Prot:Q9PNK3 Genbank:YP_002344484.1 GeneID:905382;gbkey=CDS;product=leucyl-tRNA synthetase;Note=leucine--tRNA ligase 3B LeuRS 3B class-I aminoacyl-tRNA synthetase 3B charges leucine by linking carboxyl group to alpha-phosphate of ATP and then transfers aminoacyl-adenylate to its tRNA 3B due to the large number of codons that tRNA 28Leu 29 recognizes 2C the leucyl-tRNA synthetase does not recognize the anticodon loop of the tRNA 2C but instead recognition is dependent on a conserved discriminator base A37 and a long arm 3B an editing domain hydrolyzes misformed products 3B in Methanothermobacter thermautotrophicus this enzyme associates with prolyl-tRNA synthetase NC_002163.1 RefSeq gene 1022826 1025255 . - . ID=gene1042;gene=leuS;Name=leuS;locus_tag=Cj1091c;Dbxref=GeneID:905382;gbkey=Gene NC_002163.1 RefSeq region 1022880 1022903 . - . ID=id2005;gene=leuS;Name=id2005;Dbxref=GeneID:905382;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 1023192 1023224 . - . ID=id2006;gene=leuS;Name=id2006;Dbxref=GeneID:905382;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1023399 1025225 . - . ID=id2007;gene=leuS;Name=id2007;Dbxref=GeneID:905382;gbkey=misc_feature;Note=HMMPfam hit to PF00133 2C tRNA synthetases class I 28I 2C L 2C M and V 29 2C score 7.4e-139 NC_002163.1 RefSeq region 1025103 1025138 . - . ID=id2008;gene=leuS;Name=id2008;Dbxref=GeneID:905382;gbkey=misc_feature;Note=PS00178 Aminoacyl-transfer RNA synthetases class-I signature ### NC_002163.1 RefSeq CDS 1025265 1026236 . - 0 ID=cds978;Parent=gene1043;gene=secF;Name=YP_002344485.1;Dbxref=GOA:Q0P9G2 InterPro:IPR003335 InterPro:IPR005665 UniProtKB FTrEMBL:Q0P9G2 Genbank:YP_002344485.1 GeneID:905383;gbkey=CDS;product=preprotein translocase subunit SecF;Note=forms a complex with SecD and YajC 3B SecDFyajC stimulates the proton motive force-driven protein translocation 3B seems to modulate the cycling of SecA by stabilizing its membrane-inserted state and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane 3B in some organisms 2C such as Bacillus subtilis 2C SecD is fused to SecF NC_002163.1 RefSeq gene 1025265 1026236 . - . ID=gene1043;gene=secF;Name=secF;locus_tag=Cj1092c;Dbxref=GeneID:905383;gbkey=Gene NC_002163.1 RefSeq region 1025358 1025921 . - . ID=id2009;gene=secF;Name=id2009;Dbxref=GeneID:905383;gbkey=misc_feature;Note=HMMPfam hit to PF02355 2C Protein export membrane protein 2C score 9.9e-82 NC_002163.1 RefSeq region 1025367 1025435 . - . ID=id90;gene=secF;Name=id90;Dbxref=GeneID:905383;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1092c by TMHMM2.0 at aa 13-35 2C 137-154 2C 236-258 and 268-290 NC_002163.1 RefSeq region 1025463 1025531 . - . ID=id90;gene=secF;Name=id90;Dbxref=GeneID:905383;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1092c by TMHMM2.0 at aa 13-35 2C 137-154 2C 236-258 and 268-290 NC_002163.1 RefSeq region 1025775 1025828 . - . ID=id90;gene=secF;Name=id90;Dbxref=GeneID:905383;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1092c by TMHMM2.0 at aa 13-35 2C 137-154 2C 236-258 and 268-290 NC_002163.1 RefSeq region 1026054 1026140 . - . ID=id2010;gene=secF;Name=id2010;Dbxref=GeneID:905383;gbkey=misc_feature;Note=HMMPfam hit to PF07549 2C SecD 2FSecF GG Motif 2C score 0.00022 NC_002163.1 RefSeq region 1026132 1026200 . - . ID=id90;gene=secF;Name=id90;Dbxref=GeneID:905383;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1092c by TMHMM2.0 at aa 13-35 2C 137-154 2C 236-258 and 268-290 NC_002163.1 RefSeq CDS 1026236 1027816 . - 0 ID=cds979;Parent=gene1044;gene=secD;Name=YP_002344486.1;Dbxref=GOA:Q0P9G1 InterPro:IPR001036 InterPro:IPR003335 InterPro:IPR005791 UniProtKB FTrEMBL:Q0P9G1 Genbank:YP_002344486.1 GeneID:905384;gbkey=CDS;product=preprotein translocase subunit SecD;Note=part of the preprotein secretory system 3B when complexed with proteins SecF and YajC 2C SecDFyajC stimulates the proton motive force-driven protein translocation 2C and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane NC_002163.1 RefSeq gene 1026236 1027816 . - . ID=gene1044;gene=secD;Name=secD;locus_tag=Cj1093c;Dbxref=GeneID:905384;gbkey=Gene NC_002163.1 RefSeq region 1026287 1026832 . - . ID=id2011;gene=secD;Name=id2011;Dbxref=GeneID:905384;gbkey=misc_feature;Note=HMMPfam hit to PF02355 2C Protein export membrane protein 2C score 3.4e-06 NC_002163.1 RefSeq region 1026305 1026373 . - . ID=id91;gene=secD;Name=id91;Dbxref=GeneID:905384;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1093c by TMHMM2.0 at aa 7-29 2C 359-381 2C 388-410 and 482-504 NC_002163.1 RefSeq region 1026587 1026655 . - . ID=id91;gene=secD;Name=id91;Dbxref=GeneID:905384;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1093c by TMHMM2.0 at aa 7-29 2C 359-381 2C 388-410 and 482-504 NC_002163.1 RefSeq region 1026674 1026742 . - . ID=id91;gene=secD;Name=id91;Dbxref=GeneID:905384;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1093c by TMHMM2.0 at aa 7-29 2C 359-381 2C 388-410 and 482-504 NC_002163.1 RefSeq region 1027640 1027735 . - . ID=id2012;gene=secD;Name=id2012;Dbxref=GeneID:905384;gbkey=misc_feature;Note=HMMPfam hit to PF07549 2C SecD 2FSecF GG Motif 2C score 0.00025 NC_002163.1 RefSeq region 1027730 1027798 . - . ID=id91;gene=secD;Name=id91;Dbxref=GeneID:905384;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1093c by TMHMM2.0 at aa 7-29 2C 359-381 2C 388-410 and 482-504 NC_002163.1 RefSeq gene 1027809 1028081 . - . ID=gene1045;gene=yajC;Name=yajC;locus_tag=Cj1094c;Dbxref=GeneID:905385;gbkey=Gene NC_002163.1 RefSeq CDS 1027809 1028081 . - 0 ID=cds980;Parent=gene1045;gene=yajC;Name=YP_002344487.1;Dbxref=GOA:Q0P9G0 InterPro:IPR003849 UniProtKB FTrEMBL:Q0P9G0 Genbank:YP_002344487.1 GeneID:905385;gbkey=CDS;product=preprotein translocase subunit YajC;Note=member of preprotein translocase 3B forms a heterotrimer with SecD and SecF 3B links the SecD 2FSecF 2FYajC 2FYidC complex with the SecY 2FSecE 2FSecG complex NC_002163.1 UTR_Extractor 5'-UTR 1027817 1027931 . - . ID=utr389;locus_tag=Cj1093c;product=preprotein translocase subunit SecD NC_002163.1 RefSeq region 1027818 1028069 . - . ID=id2013;gene=yajC;Name=id2013;Dbxref=GeneID:905385;gbkey=misc_feature;Note=HMMPfam hit to PF02699 2C Preprotein translocase subunit 2C score 8.3e-40 NC_002163.1 UTR_Extractor 5'-UTR 1027898 1028053 . + . ID=utr390;locus_tag=Cj1095;product=apolipoprotein N-acyltransferase NC_002163.1 RefSeq region 1028010 1028069 . - . ID=id2014;gene=yajC;Name=id2014;Dbxref=GeneID:905385;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1094c by TMHMM2.0 at aa 5-24 NC_002163.1 RefSeq gene 1028054 1029379 . + . ID=gene1046;gene=Cj1095;Name=Cj1095;locus_tag=Cj1095;Dbxref=GeneID:905386;gbkey=Gene NC_002163.1 RefSeq CDS 1028054 1029379 . + 0 ID=cds981;Parent=gene1046;Name=YP_002344488.1;Dbxref=GOA:Q9PNJ9 InterPro:IPR003010 InterPro:IPR004563 UniProtKB FSwiss-Prot:Q9PNJ9 Genbank:YP_002344488.1 GeneID:905386;gbkey=CDS;product=apolipoprotein N-acyltransferase;Note=Transfers the fatty acyl group on membrane lipoproteins NC_002163.1 UTR_Extractor 5'-UTR 1028082 1028111 . - . ID=utr391;locus_tag=Cj1094c;product=preprotein translocase subunit YajC NC_002163.1 RefSeq region 1028120 1028188 . + . ID=id2015;Name=id2015;Dbxref=GeneID:905386;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1095 by TMHMM2.0 at aa 23-45 2C 49-68 2C 75-97 2C 101-123 2C128-145 2C 155-177 and 184-201 NC_002163.1 RefSeq region 1028198 1028257 . + . ID=id2015;Name=id2015;Dbxref=GeneID:905386;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1095 by TMHMM2.0 at aa 23-45 2C 49-68 2C 75-97 2C 101-123 2C128-145 2C 155-177 and 184-201 NC_002163.1 RefSeq region 1028276 1028344 . + . ID=id2015;Name=id2015;Dbxref=GeneID:905386;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1095 by TMHMM2.0 at aa 23-45 2C 49-68 2C 75-97 2C 101-123 2C128-145 2C 155-177 and 184-201 NC_002163.1 RefSeq region 1028354 1028422 . + . ID=id2015;Name=id2015;Dbxref=GeneID:905386;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1095 by TMHMM2.0 at aa 23-45 2C 49-68 2C 75-97 2C 101-123 2C128-145 2C 155-177 and 184-201 NC_002163.1 RefSeq region 1028435 1028488 . + . ID=id2015;Name=id2015;Dbxref=GeneID:905386;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1095 by TMHMM2.0 at aa 23-45 2C 49-68 2C 75-97 2C 101-123 2C128-145 2C 155-177 and 184-201 NC_002163.1 RefSeq region 1028516 1028584 . + . ID=id2015;Name=id2015;Dbxref=GeneID:905386;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1095 by TMHMM2.0 at aa 23-45 2C 49-68 2C 75-97 2C 101-123 2C128-145 2C 155-177 and 184-201 NC_002163.1 RefSeq region 1028603 1028656 . + . ID=id2015;Name=id2015;Dbxref=GeneID:905386;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1095 by TMHMM2.0 at aa 23-45 2C 49-68 2C 75-97 2C 101-123 2C128-145 2C 155-177 and 184-201 ### NC_002163.1 RefSeq CDS 1029616 1030812 . - 0 ID=cds982;Parent=gene1047;gene=metK;Name=YP_002344489.1;Dbxref=GOA:Q0P9F8 InterPro:IPR002133 UniProtKB FTrEMBL:Q0P9F8 Genbank:YP_002344489.1 GeneID:905387;gbkey=CDS;product=S-adenosylmethionine synthetase;Note=catalyzes the formation of S-adenosylmethionine from methionine and ATP 3B methionine adenosyltransferase NC_002163.1 RefSeq gene 1029616 1030812 . - . ID=gene1047;gene=metK;Name=metK;locus_tag=Cj1096c;Dbxref=GeneID:905387;gbkey=Gene NC_002163.1 RefSeq region 1029652 1030083 . - . ID=id2016;gene=metK;Name=id2016;Dbxref=GeneID:905387;gbkey=misc_feature;Note=HMMPfam hit to PF02773 2C S-adenosylmethionine synthetase 2C C-te 2C score 9e-51 NC_002163.1 RefSeq region 1030087 1030461 . - . ID=id2017;gene=metK;Name=id2017;Dbxref=GeneID:905387;gbkey=misc_feature;Note=HMMPfam hit to PF02772 2C S-adenosylmethionine synthetase 2C cent 2C score 1e-22 NC_002163.1 RefSeq region 1030420 1030452 . - . ID=id2018;gene=metK;Name=id2018;Dbxref=GeneID:905387;gbkey=misc_feature;Note=PS00376 S-adenosylmethionine synthetase signature 1 NC_002163.1 RefSeq region 1030489 1030812 . - . ID=id2019;gene=metK;Name=id2019;Dbxref=GeneID:905387;gbkey=misc_feature;Note=HMMPfam hit to PF00438 2C S-adenosylmethionine synthetase 2C N-te 2C score 7.3e-25 ### NC_002163.1 UTR_Extractor 5'-UTR 1030813 1030836 . - . ID=utr392;locus_tag=Cj1096c;product=S-adenosylmethionine synthetase NC_002163.1 RefSeq CDS 1030953 1032176 . + 0 ID=cds983;Parent=gene1048;Name=YP_002344490.1;Dbxref=GOA:Q0P9F7 InterPro:IPR001991 UniProtKB FSwiss-Prot:Q0P9F7 Genbank:YP_002344490.1 GeneID:905388;gbkey=CDS;product=serine 2Fthreonine transporter SstT;Note=involved in the import of serine and threonine coupled with the import of sodium NC_002163.1 RefSeq gene 1030953 1032176 . + . ID=gene1048;Name=Cj1097;locus_tag=Cj1097;Dbxref=GeneID:905388;gbkey=Gene NC_002163.1 RefSeq region 1030986 1031045 . + . ID=id2020;Name=id2020;Dbxref=GeneID:905388;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1097 by TMHMM2.0 at aa 12-31 2C 41-63 2C 83-105 2C 139-161 2C182-201 2C 216-238 2C 245-267 2C 287-309 and 322-344 NC_002163.1 RefSeq region 1030992 1032140 . + . ID=id2021;Name=id2021;Dbxref=GeneID:905388;gbkey=misc_feature;Note=HMMPfam hit to PF00375 2C Sodium:dicarboxylate symporter family 2C score 4e-101 NC_002163.1 RefSeq region 1031073 1031141 . + . ID=id2020;Name=id2020;Dbxref=GeneID:905388;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1097 by TMHMM2.0 at aa 12-31 2C 41-63 2C 83-105 2C 139-161 2C182-201 2C 216-238 2C 245-267 2C 287-309 and 322-344 NC_002163.1 RefSeq region 1031199 1031267 . + . ID=id2020;Name=id2020;Dbxref=GeneID:905388;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1097 by TMHMM2.0 at aa 12-31 2C 41-63 2C 83-105 2C 139-161 2C182-201 2C 216-238 2C 245-267 2C 287-309 and 322-344 NC_002163.1 RefSeq region 1031205 1031237 . + . ID=id2022;Name=id2022;Dbxref=GeneID:905388;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1031367 1031435 . + . ID=id2020;Name=id2020;Dbxref=GeneID:905388;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1097 by TMHMM2.0 at aa 12-31 2C 41-63 2C 83-105 2C 139-161 2C182-201 2C 216-238 2C 245-267 2C 287-309 and 322-344 NC_002163.1 RefSeq region 1031496 1031555 . + . ID=id2020;Name=id2020;Dbxref=GeneID:905388;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1097 by TMHMM2.0 at aa 12-31 2C 41-63 2C 83-105 2C 139-161 2C182-201 2C 216-238 2C 245-267 2C 287-309 and 322-344 NC_002163.1 RefSeq region 1031598 1031666 . + . ID=id2020;Name=id2020;Dbxref=GeneID:905388;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1097 by TMHMM2.0 at aa 12-31 2C 41-63 2C 83-105 2C 139-161 2C182-201 2C 216-238 2C 245-267 2C 287-309 and 322-344 NC_002163.1 RefSeq region 1031685 1031753 . + . ID=id2020;Name=id2020;Dbxref=GeneID:905388;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1097 by TMHMM2.0 at aa 12-31 2C 41-63 2C 83-105 2C 139-161 2C182-201 2C 216-238 2C 245-267 2C 287-309 and 322-344 NC_002163.1 RefSeq region 1031811 1031879 . + . ID=id2020;Name=id2020;Dbxref=GeneID:905388;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1097 by TMHMM2.0 at aa 12-31 2C 41-63 2C 83-105 2C 139-161 2C182-201 2C 216-238 2C 245-267 2C 287-309 and 322-344 NC_002163.1 RefSeq region 1031916 1031984 . + . ID=id2020;Name=id2020;Dbxref=GeneID:905388;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1097 by TMHMM2.0 at aa 12-31 2C 41-63 2C 83-105 2C 139-161 2C182-201 2C 216-238 2C 245-267 2C 287-309 and 322-344 NC_002163.1 RefSeq region 1031931 1031963 . + . ID=id2023;Name=id2023;Dbxref=GeneID:905388;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq CDS 1032186 1033073 . + 0 ID=cds984;Parent=gene1049;gene=pyrB;Name=YP_002344491.1;Dbxref=GOA:Q9PNJ6 HSSP:P04391 InterPro:IPR002082 InterPro:IPR006130 InterPro:IPR006131 InterPro:IPR006132 UniProtKB FSwiss-Prot:Q9PNJ6 Genbank:YP_002344491.1 GeneID:905389;gbkey=CDS;product=aspartate carbamoyltransferase;Note=catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis NC_002163.1 RefSeq gene 1032186 1033073 . + . ID=gene1049;gene=pyrB;Name=pyrB;locus_tag=Cj1098;Dbxref=GeneID:905389;gbkey=Gene NC_002163.1 RefSeq region 1032189 1032611 . + . ID=id2024;gene=pyrB;Name=id2024;Dbxref=GeneID:905389;gbkey=misc_feature;Note=HMMPfam hit to PF02729 2C Aspartate 2Fornithine carbamoyltransferase 2C ca 2C score 2.7e-47 NC_002163.1 RefSeq region 1032312 1032335 . + . ID=id2025;gene=pyrB;Name=id2025;Dbxref=GeneID:905389;gbkey=misc_feature;Note=PS00097 Aspartate and ornithine carbamoyltransferases signature NC_002163.1 RefSeq region 1032621 1033055 . + . ID=id2026;gene=pyrB;Name=id2026;Dbxref=GeneID:905389;gbkey=misc_feature;Note=HMMPfam hit to PF00185 2C Aspartate 2Fornithine carbamoyltransferase 2C As 2C score 8.3e-14 ### NC_002163.1 RefSeq gene 1033077 1034798 . + . ID=gene1050;Name=Cj1099;locus_tag=Cj1099;Dbxref=GeneID:905390;gbkey=Gene NC_002163.1 RefSeq CDS 1033077 1034798 . + 0 ID=cds985;Parent=gene1050;Name=YP_002344492.1;Dbxref=GOA:Q0P9F5 InterPro:IPR001567 InterPro:IPR006025 InterPro:IPR011977 InterPro:IPR013647 UniProtKB FTrEMBL:Q0P9F5 Genbank:YP_002344492.1 GeneID:905390;gbkey=CDS;product=peptidase;Note=Original 282000 29 note: Cj1099 2C probable peptidase 2Clen: 573 aa 3B similar to many members of the peptidase family M3 28zinc metalloprotease 29 e.g. PEPF_LACLA oligoendopeptidase F 28601 aa 29 2C fasta scores 3B opt: 603 z-score: 673.0 E 28 29: 3.4e-30 2C 25.9 25 identity in 595 aa overlap. 53.5 25 identity to HP0470. Contains PS00142 Neutral zinc metallopeptidases 2C zinc-binding region signature 7EUpdated 282006 29 note: Pfam domain PF01432 Peptidase family M3 identified within CDS. Further support given to product function. Specific characterisation has not been carried out yet. not added to product function. Functional classification - Degradation of macromolecules - Proteins 2C peptides and glycopeptides NC_002163.1 RefSeq region 1033617 1034753 . + . ID=id2027;Name=id2027;Dbxref=GeneID:905390;gbkey=misc_feature;Note=HMMPfam hit to PF01432 2C Peptidase family M3 2C score 1.3e-73 NC_002163.1 RefSeq region 1034163 1034192 . + . ID=id2028;Name=id2028;Dbxref=GeneID:905390;gbkey=misc_feature;Note=PS00142 Neutral zinc metallopeptidases 2Czinc-binding region signature NC_002163.1 RefSeq gene 1034792 1035229 . + . ID=gene1051;Name=Cj1100;locus_tag=Cj1100;Dbxref=GeneID:905391;gbkey=Gene NC_002163.1 RefSeq CDS 1034792 1035229 . + 0 ID=cds986;Parent=gene1051;Name=YP_002344493.1;Dbxref=UniProtKB FTrEMBL:Q0P9F4 Genbank:YP_002344493.1 GeneID:905391;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1100 2C unknown 2C len: 145 aa 3B 34.7 25 identity to HP0469. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 1035226 1037301 . + . ID=gene1052;Name=Cj1101;locus_tag=Cj1101;Dbxref=GeneID:905392;gbkey=Gene NC_002163.1 RefSeq CDS 1035226 1037301 . + 0 ID=cds987;Parent=gene1052;Name=YP_002344494.1;Dbxref=GOA:Q0P9F3 InterPro:IPR000212 InterPro:IPR014016 InterPro:IPR014017 UniProtKB FTrEMBL:Q0P9F3 Genbank:YP_002344494.1 GeneID:905392;gbkey=CDS;product=ATP-dependent DNA helicase;Note=Original 282000 29 note: Cj1101 2C probable ATP-dependent DNA helicase 2C len: 691 aa 3B similar to many e.g REP_ECOLI ATP-dependent DNA helicase REP 28EC 3.6.1.- 29 28673 aa 29 2C fasta scores 3B opt: 977 z-score: 1067.3 E 28 29: 0 2C36.9 25 identity in 640 aa overlap 2C and UVRD_ECOLI DNA helicase II 28EC 3.6.1.- 29 28720 aa 29 2C fasta scores 3B opt: 1129 z-score: 1232.6 E 28 29: 0 2C 35.2 25 identity in 714 aa overlap. 43.7 25 identity to HP1478. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C and Pfam match to entry PF00580 UvrD-helicase 2C UvrD 2FREP helicase 7EUpdated 282006 29 note: Similar to more than one helicase with acceptable identity scores. not added to product function. Functional classification - DNA replication 2C restriction 2Fmodification 2C recombination and repair 7EPMID:9288744 2C PMID:8419285 NC_002163.1 RefSeq region 1035244 1036707 . + . ID=id2029;Name=id2029;Dbxref=GeneID:905392;gbkey=misc_feature;Note=HMMPfam hit to PF00580 2C UvrD 2FREP helicase 2C score 2.6e-149 NC_002163.1 RefSeq region 1035301 1035324 . + . ID=id2030;Name=id2030;Dbxref=GeneID:905392;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 UTR_Extractor 5'-UTR 1037268 1037297 . + . ID=utr393;locus_tag=Cj1102;product=tRNA pseudouridine synthase B NC_002163.1 RefSeq CDS 1037298 1038116 . + 0 ID=cds988;Parent=gene1053;gene=truB;Name=YP_002344495.1;Dbxref=GOA:Q9PNJ2 InterPro:IPR002501 InterPro:IPR014780 UniProtKB FSwiss-Prot:Q9PNJ2 Genbank:YP_002344495.1 GeneID:905393;gbkey=CDS;product=tRNA pseudouridine synthase B;Note=catalyzes isomerization of specific uridines in RNA to pseudouridine 3B responsible for residues in T loops of many tRNAs NC_002163.1 RefSeq gene 1037298 1038116 . + . ID=gene1053;gene=truB;Name=truB;locus_tag=Cj1102;Dbxref=GeneID:905393;gbkey=Gene NC_002163.1 RefSeq region 1037364 1037807 . + . ID=id2031;gene=truB;Name=id2031;Dbxref=GeneID:905393;gbkey=misc_feature;Note=HMMPfam hit to PF01509 2C TruB family pseudouridylate synthase 28N term 2C score 1.1e-25 NC_002163.1 UTR_Extractor 5'-UTR 1037935 1038109 . + . ID=utr394;locus_tag=Cj1103;product=carbon storage regulator NC_002163.1 RefSeq region 1038110 1038298 . + . ID=id2032;gene=csrA;Name=id2032;Dbxref=GeneID:905394;gbkey=misc_feature;Note=HMMPfam hit to PF02599 2C Global regulator protein family 2C score 1.1e-31 NC_002163.1 RefSeq gene 1038110 1038337 . + . ID=gene1054;gene=csrA;Name=csrA;locus_tag=Cj1103;Dbxref=GeneID:905394;gbkey=Gene NC_002163.1 RefSeq CDS 1038110 1038337 . + 0 ID=cds989;Parent=gene1054;gene=csrA;Name=YP_002344496.1;Dbxref=GOA:Q0P9F1 InterPro:IPR003751 UniProtKB FTrEMBL:Q0P9F1 Genbank:YP_002344496.1 GeneID:905394;gbkey=CDS;product=carbon storage regulator;Note=Original 282000 29 note: Cj1103 2C csrA 2C probable carbon storage regulator homolog 2C len: 75 aa 3B similar to many e.g. CSRA_ECOLI carbon storage regulator 2861 aa 29 2C fasta scores 3B opt: 133 z-score: 202.6 E 28 29: 0.00055 2C 33.3 25 identity in 54 aa overlap. 46.7 25 identity to HP1442 7EUpdated 282006 29 note: Pfam domain PF02599 Global regulator protein family was identified within CDS. Further support given to product function. Characterised in Escherichia coli with marginal identity score. Homolog designation kept in product function. Functional classification - Broad regulatory functions 7EPMID:9211896 2C PMID:8393005 NC_002163.1 RefSeq gene 1038334 1039101 . + . ID=gene1055;gene=Cj1104;Name=Cj1104;locus_tag=Cj1104;Dbxref=GeneID:905395;gbkey=Gene NC_002163.1 RefSeq CDS 1038334 1039101 . + 0 ID=cds990;Parent=gene1055;Name=YP_002344497.1;Dbxref=GOA:Q9PNJ0 InterPro:IPR004424 InterPro:IPR006204 InterPro:IPR014721 UniProtKB FSwiss-Prot:Q9PNJ0 Genbank:YP_002344497.1 GeneID:905395;gbkey=CDS;product=4-diphosphocytidyl-2-C-methyl-D-erythritol kinase;Note=catalyzes the phosphorylation of 4-diphosphocytidyl-2-C-methyl-D-erythritol in the nonmevalonate pathway of isoprenoid biosynthesis NC_002163.1 RefSeq region 1038589 1039098 . + . ID=id2033;Name=id2033;Dbxref=GeneID:905395;gbkey=misc_feature;Note=HMMPfam hit to PF00288 2C GHMP kinases ATP-binding protei 2C score 1.2e-17 NC_002163.1 UTR_Extractor 5'-UTR 1039038 1039097 . + . ID=utr395;locus_tag=Cj1105;product=SsrA-binding protein NC_002163.1 RefSeq CDS 1039098 1039550 . + 0 ID=cds991;Parent=gene1056;gene=smpB;Name=YP_002344498.1;Dbxref=GOA:Q9PNI9 HSSP:O66640 InterPro:IPR000037 UniProtKB FSwiss-Prot:Q9PNI9 Genbank:YP_002344498.1 GeneID:905396;gbkey=CDS;product=SsrA-binding protein;Note=binds to ssrA RNA 28tmRNA 29 and is required for its successful binding to ribosomes 3B also appears to function in the trans-translation step by promoting accommodation of tmRNA into the ribosomal A site 3B SmpB protects the tmRNA from RNase R degradation in Caulobacter crescentus 3B both the tmRNA and SmpB are regulated in cell cycle-dependent manner 3B functions in release of stalled ribosomes from damaged mRNAs and targeting proteins for degradation NC_002163.1 RefSeq gene 1039098 1039550 . + . ID=gene1056;gene=smpB;Name=smpB;locus_tag=Cj1105;Dbxref=GeneID:905396;gbkey=Gene NC_002163.1 RefSeq region 1039101 1039307 . + . ID=id2034;gene=smpB;Name=id2034;Dbxref=GeneID:905396;gbkey=misc_feature;Note=HMMPfam hit to PF01668 2C SmpB protein 2C score 1.8e-35 NC_002163.1 UTR_Extractor 5'-UTR 1039404 1039560 . + . ID=utr396;locus_tag=Cj1106;product=putative periplasmic thioredoxin ### NC_002163.1 RefSeq CDS 1039561 1040163 . + 0 ID=cds992;Parent=gene1057;Name=YP_002344499.1;Dbxref=GOA:Q0P9E8 InterPro:IPR012335 UniProtKB FTrEMBL:Q0P9E8 Genbank:YP_002344499.1 GeneID:905397;gbkey=CDS;product=thioredoxin;Note=Original 282000 29 note: Cj1106 2C possible periplasmic thioredoxin 2C len: 200 aa 3B similar to active site region of thioredoxins e.g. THIO_BACSU thioredoxin 28103 aa 29 2C fasta scores 3B opt: 112 z-score: 150.6 E 28 29: 0.43 2C 37.7 25 identity in 69 aa overlap. Contains probable N-terminal signal sequence. No Hp match. Also similar to Cj1207c 2829.4 25 identity in 201 aa overlap 29 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score has been carried out yet 2Cso kept in product function. Functional classification - Energy metabolism - Electron transport NC_002163.1 RefSeq gene 1039561 1040163 . + . ID=gene1057;Name=Cj1106;locus_tag=Cj1106;Dbxref=GeneID:905397;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 1040086 1040162 . + . ID=utr397;locus_tag=Cj1107;product=ATP-dependent Clp protease adaptor protein NC_002163.1 RefSeq gene 1040163 1040453 . + . ID=gene1058;gene=clpS;Name=clpS;locus_tag=Cj1107;Dbxref=GeneID:905398;gbkey=Gene NC_002163.1 RefSeq CDS 1040163 1040453 . + 0 ID=cds993;Parent=gene1058;gene=clpS;Name=YP_002344500.1;Dbxref=GOA:Q9PNI7 HSSP:P75832 InterPro:IPR003769 InterPro:IPR014719 UniProtKB FSwiss-Prot:Q9PNI7 Genbank:YP_002344500.1 GeneID:905398;gbkey=CDS;product=ATP-dependent Clp protease adaptor protein;Note=Original 282000 29 note: Cj1107 2C unknown 2C len: 96 aa 3B similar to hypothetical proteins e.g. YLJA_ECOLI 28also upstream of clpA 29 28106 aa 29 2C fasta scores 3B opt: 255 z-score: 354.9 E 28 29: 1.8e-12 2C 44.0 25 identity in 84 aa overlap. 38.2 25 identity to HP0032 7EUpdated 282006 29 note: Pfam domain PF02617 ATP-dependent Clp protease adaptor protein Clps 2Cidentified within CDS. Product function modified to more specific family member based on motif match. Characterised in Escherichia coli with acceptable identity score. Appropriate motifs present. not added to product function. Functional classification - Chaperones 2Cchaperonins 2C heat shock 7EPMID:12426582 2C PMID:12235156 2C PMID:9278503 NC_002163.1 RefSeq region 1040196 1040441 . + . ID=id2035;gene=clpS;Name=id2035;Dbxref=GeneID:905398;gbkey=misc_feature;Note=HMMPfam hit to PF02617 2C ATP-dependent Clp protease adaptor protein C 2C score 2.9e-43 NC_002163.1 RefSeq gene 1040450 1042579 . + . ID=gene1059;gene=clpA;Name=clpA;locus_tag=Cj1108;Dbxref=GeneID:905399;gbkey=Gene NC_002163.1 RefSeq CDS 1040450 1042579 . + 0 ID=cds994;Parent=gene1059;gene=clpA;Name=YP_002344501.1;Dbxref=GOA:Q0P9E6 InterPro:IPR001270 InterPro:IPR003593 InterPro:IPR003959 InterPro:IPR004176 InterPro:IPR013093 InterPro:IPR013461 UniProtKB FTrEMBL:Q0P9E6 Genbank:YP_002344501.1 GeneID:905399;gbkey=CDS;product=ATP-dependent Clp protease ATP-binding subunit;Note=Original 282000 29 note: Cj1108 2C clpA 2C probable ATP-dependent CLP protease ATP-binding subunit 2C len: CLPA_ECOLI ATP-dependent CLP protease ATP-binding subunit 28758 aa 29 2C fasta scores 3B opt: 1730 z-score: 1803.9 E 28 29: 0 2C41.2 25 identity in 748 aa overlap. 41.7 25 identity to HP0033. Contains 2x PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00871 Chaperonins clpA 2FB signature 2 2C and Pfam match to entry PF00495 clpA_B 2C Chaperonins clpA 2FB. Also similar to clpB Cj0509c 2836.5 25 identity in 835 aa overlap 29 7EUpdated 282006 29 note: Pfam domains PF02861 Clp amino terminal domain and PF00004 ATPase family associated with various cellular activities 28AAA 29 were identified within CDS. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification - Chaperones 2C chaperonins 2C heat shock 7EPMID:11344323 2C PMID:11274130 NC_002163.1 RefSeq region 1040489 1040647 . + . ID=id2036;gene=clpA;Name=id2036;Dbxref=GeneID:905399;gbkey=misc_feature;Note=HMMPfam hit to PF02861 2C Clp amino terminal domain 2Cscore 3.7e-05 NC_002163.1 RefSeq region 1040990 1041574 . + . ID=id2037;gene=clpA;Name=id2037;Dbxref=GeneID:905399;gbkey=misc_feature;Note=HMMPfam hit to PF00004 2C ATPase family associated with various cellul 2C score 9e-08 NC_002163.1 RefSeq region 1041005 1041028 . + . ID=id2038;gene=clpA;Name=id2038;Dbxref=GeneID:905399;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 1041812 1042288 . + . ID=id2039;gene=clpA;Name=id2039;Dbxref=GeneID:905399;gbkey=misc_feature;Note=HMMPfam hit to PF07724 2C ATPase family associated with various cellul 2C score 6e-80 NC_002163.1 RefSeq region 1041824 1042480 . + . ID=id2040;gene=clpA;Name=id2040;Dbxref=GeneID:905399;gbkey=misc_feature;Note=HMMPfam hit to PF00004 2C ATPase family associated with various cellul 2C score 3.8e-05 NC_002163.1 RefSeq region 1041839 1041862 . + . ID=id2041;gene=clpA;Name=id2041;Dbxref=GeneID:905399;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 1041908 1041964 . + . ID=id2042;gene=clpA;Name=id2042;Dbxref=GeneID:905399;gbkey=misc_feature;Note=PS00871 Chaperonins clpA 2FB signature 2 NC_002163.1 UTR_Extractor 5'-UTR 1042435 1042553 . + . ID=utr398;locus_tag=Cj1109;product=leucyl 2Fphenylalanyl-tRNA--protein transferase NC_002163.1 RefSeq gene 1042554 1043201 . + . ID=gene1060;gene=aat;Name=aat;locus_tag=Cj1109;Dbxref=GeneID:905400;gbkey=Gene NC_002163.1 RefSeq CDS 1042554 1043201 . + 0 ID=cds995;Parent=gene1060;gene=aat;Name=YP_002344502.1;Dbxref=GOA:Q9PNI5 InterPro:IPR004616 UniProtKB FSwiss-Prot:Q9PNI5 Genbank:YP_002344502.1 GeneID:905400;gbkey=CDS;product=leucyl 2Fphenylalanyl-tRNA--protein transferase;Note=leucyltransferase 3B phenylalanyltransferse 3B functions in the N-end rule pathway 3B transfers Leu 2C Phe 2C Met 2C from aminoacyl-tRNAs to N-terminal of proteins with Arg or Lys NC_002163.1 RefSeq region 1042629 1043123 . + . ID=id2043;gene=aat;Name=id2043;Dbxref=GeneID:905400;gbkey=misc_feature;Note=HMMPfam hit to PF03588 2C Leucyl 2Fphenylalanyl-tRNA protein transf 2C score 9.3e-105 ### NC_002163.1 RefSeq CDS 1043223 1044512 . - 0 ID=cds996;Parent=gene1061;Name=YP_002344503.1;Dbxref=GOA:Q0P9E4 InterPro:IPR000014 InterPro:IPR000700 InterPro:IPR001610 InterPro:IPR004089 InterPro:IPR004090 InterPro:IPR013655 UniProtKB FTrEMBL:Q0P9E4 Genbank:YP_002344503.1 GeneID:905401;gbkey=CDS;product=MCP-type signal transduction protein;Note=Original 282000 29 note: Cj1110c 2C probable MCP-type signal transduction protein 2C len: 429 aa 3B similar to TR:O68016 28EMBL:AF010180 29 Agrobacterium tumefaciens plasmid pTiC58 MCPA 28579 aa 29 2C fasta scores 3B opt: 749 z-score: 785.2 E 28 29: 0 2C 34.5 25 identity in 496 aa overlap 2Cand to many other proteins with MCP domains e.g. PILJ_PSEAE PILJ protein 28682 aa 29 2C fasta scores 3B opt: 379 z-score: 399.1 E 28 29: 6.3e-15 2C 26.9 25 identity in 443 aa overlap 2C and HLYB_VIBCH hemolysin secretion protein precursor 28548 aa 29 2C fasta scores 3B opt: 357 z-score: 377.6 E 28 29: 9.8e-14 2C 37.0 25 identity in 173 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00015 MCPsignal 2CMethyl-accepting chemotaxis protein 28MCP 29 signaling domain 7EUpdated 282006 29 note: Specific characterisation with acceptable identity score has not been carried out yet 2C so kept in product function. Functional classification - Signal transduction NC_002163.1 RefSeq gene 1043223 1044512 . - . ID=gene1061;Name=Cj1110c;locus_tag=Cj1110c;Dbxref=GeneID:905401;gbkey=Gene NC_002163.1 RefSeq region 1043226 1043786 . - . ID=id2044;Name=id2044;Dbxref=GeneID:905401;gbkey=misc_feature;Note=HMMPfam hit to PF00015 2C Methyl-accepting chemotaxis protein 28MCP 29 s 2C score 2.9e-15 NC_002163.1 RefSeq region 1043736 1043864 . - . ID=id2045;Name=id2045;Dbxref=GeneID:905401;gbkey=misc_feature;Note=HMMPfam hit to PF00785 2C PAC motif 2C score 5.7e-06 NC_002163.1 RefSeq region 1044102 1044230 . - . ID=id2046;Name=id2046;Dbxref=GeneID:905401;gbkey=misc_feature;Note=HMMPfam hit to PF00785 2C PAC motif 2C score 0.11 ### NC_002163.1 RefSeq CDS 1044593 1045219 . - 0 ID=cds997;Parent=gene1062;Name=YP_002344504.1;Dbxref=InterPro:IPR002771 UniProtKB FTrEMBL:Q0P9E3 Genbank:YP_002344504.1 GeneID:905402;gbkey=CDS;product=MarC family integral membrane protein;Note=Original 282000 29 note: Cj1111c 2C probable integral membrane protein 2C len: 208 aa 3B similar to many hypothetical membrane proteoins 2C e.g. YVBG_BACSU 28211 aa 29 2Cfasta scores 3B opt: 324 z-score: 391.8 E 28 29: 1.6e-14 2C 28.8 25 identity in 198 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF01914 MarC family integral membrane protein identified within CDS. Also 2C six probable transmembrane helices predicted by TMHMM2.0. Product modified to more specific family member based on Pfam match. Specific characterisation has not yet been carried out 2C so kept within product function. Functional classification - Membranes 2Clipoproteins and porins NC_002163.1 RefSeq gene 1044593 1045219 . - . ID=gene1062;Name=Cj1111c;locus_tag=Cj1111c;Dbxref=GeneID:905402;gbkey=Gene NC_002163.1 RefSeq region 1044602 1045207 . - . ID=id2047;Name=id2047;Dbxref=GeneID:905402;gbkey=misc_feature;Note=HMMPfam hit to PF01914 2C MarC family integral membrane protein 2C score 1.4e-15 NC_002163.1 RefSeq region 1044614 1044667 . - . ID=id92;Name=id92;Dbxref=GeneID:905402;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1111c by TMHMM2.0 at aa 7-29 2C 44-66 2C 79-101 2C 119-141 2C148-170 and 185-202 NC_002163.1 RefSeq region 1044710 1044778 . - . ID=id92;Name=id92;Dbxref=GeneID:905402;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1111c by TMHMM2.0 at aa 7-29 2C 44-66 2C 79-101 2C 119-141 2C148-170 and 185-202 NC_002163.1 RefSeq region 1044797 1044865 . - . ID=id92;Name=id92;Dbxref=GeneID:905402;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1111c by TMHMM2.0 at aa 7-29 2C 44-66 2C 79-101 2C 119-141 2C148-170 and 185-202 NC_002163.1 RefSeq region 1044917 1044985 . - . ID=id92;Name=id92;Dbxref=GeneID:905402;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1111c by TMHMM2.0 at aa 7-29 2C 44-66 2C 79-101 2C 119-141 2C148-170 and 185-202 NC_002163.1 RefSeq region 1045022 1045090 . - . ID=id92;Name=id92;Dbxref=GeneID:905402;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1111c by TMHMM2.0 at aa 7-29 2C 44-66 2C 79-101 2C 119-141 2C148-170 and 185-202 NC_002163.1 RefSeq region 1045133 1045201 . - . ID=id92;Name=id92;Dbxref=GeneID:905402;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1111c by TMHMM2.0 at aa 7-29 2C 44-66 2C 79-101 2C 119-141 2C148-170 and 185-202 ### NC_002163.1 RefSeq gene 1045234 1045593 . - . ID=gene1063;Name=Cj1112c;locus_tag=Cj1112c;Dbxref=GeneID:905403;gbkey=Gene NC_002163.1 RefSeq CDS 1045234 1045593 . - 0 ID=cds998;Parent=gene1063;Name=YP_002344505.1;Dbxref=GOA:Q0P9E2 InterPro:IPR002579 UniProtKB FTrEMBL:Q0P9E2 Genbank:YP_002344505.1 GeneID:905403;gbkey=CDS;product=methionine sulfoxide reductase B;Note=this stereospecific enzymes reduces the R isomer of methionine sulfoxide while MsrA reduces the S form 3B a fusion protein of this enzyme with MsrA and thioredoxin provides protection against oxidative stress in Neisseria gonorrhoeae NC_002163.1 RefSeq region 1045243 1045590 . - . ID=id2048;Name=id2048;Dbxref=GeneID:905403;gbkey=misc_feature;Note=HMMPfam hit to PF01641 2C SelR domain 2C score 1.8e-58 ### NC_002163.1 UTR_Extractor 5'-UTR 1045594 1045614 . - . ID=utr399;locus_tag=Cj1112c;product=methionine sulfoxide reductase B NC_002163.1 UTR_Extractor 5'-UTR 1045637 1045682 . + . ID=utr400;locus_tag=Cj1113;product=hypothetical protein NC_002163.1 RefSeq CDS 1045683 1046480 . + 0 ID=cds999;Parent=gene1064;Name=YP_002344506.1;Dbxref=InterPro:IPR007402 InterPro:IPR011197 UniProtKB FTrEMBL:Q0P9E1 Genbank:YP_002344506.1 GeneID:905404;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1113 2C unknown 2C len: 265 aa 3B similar to a hypothetical protein from Haemophilus Y077_HAEIN HI0077 28288 aa 29 2C fasta scores 3B opt: 441 z-score: 521.9 E 28 29: 9.1e-22 2C 34.5 25 identity in 275 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF04305 Protein of unknown function 28DUF455 29 identified within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 1045683 1046480 . + . ID=gene1064;Name=Cj1113;locus_tag=Cj1113;Dbxref=GeneID:905404;gbkey=Gene NC_002163.1 RefSeq region 1045719 1046477 . + . ID=id2049;Name=id2049;Dbxref=GeneID:905404;gbkey=misc_feature;Note=HMMPfam hit to PF04305 2C Protein of unknown function 28DUF455 29 2C score 4.6e-167 NC_002163.1 RefSeq gene 1046471 1047199 . - . ID=gene1065;gene=pssA;Name=pssA;locus_tag=Cj1114c;Dbxref=GeneID:905405;gbkey=Gene NC_002163.1 RefSeq CDS 1046471 1047199 . - 0 ID=cds1000;Parent=gene1065;gene=pssA;Name=YP_002344507.1;Dbxref=GOA:Q0P9E0 InterPro:IPR000462 InterPro:IPR004533 UniProtKB FTrEMBL:Q0P9E0 Genbank:YP_002344507.1 GeneID:905405;gbkey=CDS;product=CDP-diacylglycerol--serine O-phosphatidyltransferase;Note=Original 282000 29 note: Cj1114c 2C pssA 2C probable CDP-diacylglycerol--serine O-phosphatidyltransferase 2C len: 242 aa 3B similar to the characterised PSS_HELPY CDP-diacylglycerol--serine O-phosphatidyltransferase 28EC 2.7.8.8 29 28HP1071 29 28237 aa 29 2C fasta scores 3B opt: 754 z-score: 933.2 E 28 29: 0 2C 50.9 25 identity in 226 aa overlap 2Cand to others e.g. PSS_YEAST 28275 aa 29 2C fasta scores 3B opt: 287 z-score: 360.8 E 28 29: 8.5e-13 2C 38.2 25 identity in 165 aa overlap. Contains PS00379 CDP-alcohol phosphatidyltransferases signature 7EUpdated 282006 29 note: Characterised within Helicobacter pylori with acceptable identity score. not added to product function. Functional classification - Synthesis and modification of macromolecules - Phospholipids 7EPMID:9244252 2C PMID:9260935 NC_002163.1 RefSeq region 1046501 1046569 . - . ID=id93;gene=pssA;Name=id93;Dbxref=GeneID:905405;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1114c by TMHMM2.0 at aa 7-29 2C 33-55 2C 75-92 2C 97-114 2C126-148 2C 158-175 2C 188-207 and 211-233 NC_002163.1 RefSeq region 1046579 1046638 . - . ID=id93;gene=pssA;Name=id93;Dbxref=GeneID:905405;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1114c by TMHMM2.0 at aa 7-29 2C 33-55 2C 75-92 2C 97-114 2C126-148 2C 158-175 2C 188-207 and 211-233 NC_002163.1 RefSeq region 1046666 1047085 . - . ID=id2050;gene=pssA;Name=id2050;Dbxref=GeneID:905405;gbkey=misc_feature;Note=HMMPfam hit to PF01066 2C CDP-alcohol phosphatidyltransferase 2C score 3.4e-23 NC_002163.1 RefSeq region 1046675 1046728 . - . ID=id93;gene=pssA;Name=id93;Dbxref=GeneID:905405;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1114c by TMHMM2.0 at aa 7-29 2C 33-55 2C 75-92 2C 97-114 2C126-148 2C 158-175 2C 188-207 and 211-233 NC_002163.1 RefSeq region 1046756 1046824 . - . ID=id93;gene=pssA;Name=id93;Dbxref=GeneID:905405;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1114c by TMHMM2.0 at aa 7-29 2C 33-55 2C 75-92 2C 97-114 2C126-148 2C 158-175 2C 188-207 and 211-233 NC_002163.1 RefSeq region 1046858 1046911 . - . ID=id93;gene=pssA;Name=id93;Dbxref=GeneID:905405;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1114c by TMHMM2.0 at aa 7-29 2C 33-55 2C 75-92 2C 97-114 2C126-148 2C 158-175 2C 188-207 and 211-233 NC_002163.1 RefSeq region 1046924 1046977 . - . ID=id93;gene=pssA;Name=id93;Dbxref=GeneID:905405;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1114c by TMHMM2.0 at aa 7-29 2C 33-55 2C 75-92 2C 97-114 2C126-148 2C 158-175 2C 188-207 and 211-233 NC_002163.1 RefSeq region 1046978 1047046 . - . ID=id2051;gene=pssA;Name=id2051;Dbxref=GeneID:905405;gbkey=misc_feature;Note=PS00379 CDP-alcohol phosphatidyltransferases signature NC_002163.1 RefSeq region 1047035 1047103 . - . ID=id93;gene=pssA;Name=id93;Dbxref=GeneID:905405;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1114c by TMHMM2.0 at aa 7-29 2C 33-55 2C 75-92 2C 97-114 2C126-148 2C 158-175 2C 188-207 and 211-233 NC_002163.1 RefSeq region 1047113 1047181 . - . ID=id93;gene=pssA;Name=id93;Dbxref=GeneID:905405;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1114c by TMHMM2.0 at aa 7-29 2C 33-55 2C 75-92 2C 97-114 2C126-148 2C 158-175 2C 188-207 and 211-233 ### NC_002163.1 UTR_Extractor 5'-UTR 1047200 1047260 . - . ID=utr401;locus_tag=Cj1114c;product=CDP-diacylglycerol--serine O-phosphatidyltransferase NC_002163.1 RefSeq CDS 1047209 1047826 . - 0 ID=cds1001;Parent=gene1066;Name=YP_002344508.1;Dbxref=GOA:Q0P9D9 UniProtKB FTrEMBL:Q0P9D9 Genbank:YP_002344508.1 GeneID:905406;gbkey=CDS;product=phosphatidylserine decarboxylase-like protein;Note=Original 282000 29 note: Cj1115c 2C probable membrane protein 2C len: 205 aa 3B simimlar to hypothetical proteins e.g. TR:Q50967 28EMBL:U34760 29 Neisseria gonorrhoeae ORF259 28259 aa 29 2C fasta scores 3B opt: 223 z-score: 281.2 E 28 29: 2.3e-08 2C 24.6 25 identity in 191 aa overlap. No Hp match 7EUpdated 282006 29 note: One probable transmembrane helix predicted by TMHMM2.0. Characterised within Escherichia coli and Bacillus subtilis with identity scores marginal identity scores. kept within product function. Functional classification - Misc 7EPMID:361737 2C PMID:3042771 NC_002163.1 RefSeq gene 1047209 1047826 . - . ID=gene1066;Name=Cj1115c;locus_tag=Cj1115c;Dbxref=GeneID:905406;gbkey=Gene NC_002163.1 RefSeq region 1047695 1047799 . - . ID=id2052;Name=id2052;Dbxref=GeneID:905406;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1115c by TMHMM2.0 at aa 10-44 NC_002163.1 RefSeq gene 1047823 1049760 . - . ID=gene1067;gene=ftsH;Name=ftsH;locus_tag=Cj1116c;Dbxref=GeneID:905407;gbkey=Gene NC_002163.1 RefSeq CDS 1047823 1049760 . - 0 ID=cds1002;Parent=gene1067;gene=ftsH;Name=YP_002344509.1;Dbxref=GOA:Q0P9D8 InterPro:IPR000642 InterPro:IPR003593 InterPro:IPR003959 InterPro:IPR003960 InterPro:IPR005936 InterPro:IPR011546 UniProtKB FTrEMBL:Q0P9D8 Genbank:YP_002344509.1 GeneID:905407;gbkey=CDS;product=membrane bound zinc metallopeptidase;Note=Original 282000 29 note: Cj1116c 2C ftsH 2C probable membrane bound zinc metallopeptidase 2C len: 645 aa 3B similar to many e.g. FTSH_ECOLI cell division protein FTSH 28EC 3.4.24.- 29 28644 aa 29 2C fasta scores 3B opt: 1598 z-score: 1665.6 E 28 29: 0 2C 43.3 25 identity in 609 aa overlap. 67.4 25 identity to HP1069. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00674 AAA-protein family signature 2Cand Pfam match to entry PF00004 AAA 2C ATPases associated with various cellular activities 28AAA 29 7EUpdated 282006 29 note: Two probable transmembrane helices predicted by TMHMM2.0. Additional Pfam domains PF06480 FtsH Extracellular and PF01434 Peptidase family M41 were also identified within CDS. Further support given to product function. Characterised in Escherichia coli and others with acceptable identity score 2C so not added to product function. Functional classification -Degradation of macromolecules - Proteins 2C peptides and glycopeptides 7EPMID:8892813 2C PMID:12037319 2C PMID:1925026 2CPMID:8444796 NC_002163.1 RefSeq region 1047910 1048539 . - . ID=id2053;gene=ftsH;Name=id2053;Dbxref=GeneID:905407;gbkey=misc_feature;Note=HMMPfam hit to PF01434 2C Peptidase family M41 2C score 1.1e-86 NC_002163.1 RefSeq region 1048555 1049124 . - . ID=id2054;gene=ftsH;Name=id2054;Dbxref=GeneID:905407;gbkey=misc_feature;Note=HMMPfam hit to PF00004 2C ATPase family associated with various c 2C score 3e-87 NC_002163.1 RefSeq region 1048750 1048806 . - . ID=id2055;gene=ftsH;Name=id2055;Dbxref=GeneID:905407;gbkey=misc_feature;Note=PS00674 AAA-protein family signature NC_002163.1 RefSeq region 1049086 1049109 . - . ID=id2056;gene=ftsH;Name=id2056;Dbxref=GeneID:905407;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 1049200 1049589 . - . ID=id2057;gene=ftsH;Name=id2057;Dbxref=GeneID:905407;gbkey=misc_feature;Note=HMMPfam hit to PF06480 2C FtsH Extracellular 2C score 4.9e-38 NC_002163.1 RefSeq region 1049320 1049379 . - . ID=id94;gene=ftsH;Name=id94;Dbxref=GeneID:905407;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1116c by TMHMM2.0 at aa 22-41 and 128-147 NC_002163.1 RefSeq region 1049638 1049697 . - . ID=id94;gene=ftsH;Name=id94;Dbxref=GeneID:905407;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1116c by TMHMM2.0 at aa 22-41 and 128-147 ### NC_002163.1 UTR_Extractor 5'-UTR 1049761 1049887 . - . ID=utr402;locus_tag=Cj1116c;product=membrane bound zinc metallopeptidase NC_002163.1 RefSeq gene 1049764 1050609 . - . ID=gene1068;gene=prmA;Name=prmA;locus_tag=Cj1117c;Dbxref=GeneID:905408;gbkey=Gene NC_002163.1 RefSeq CDS 1049764 1050609 . - 0 ID=cds1003;Parent=gene1068;gene=prmA;Name=YP_002344510.1;Dbxref=GOA:Q9PNH7 InterPro:IPR010456 UniProtKB FSwiss-Prot:Q9PNH7 Genbank:YP_002344510.1 GeneID:905408;gbkey=CDS;product=50S ribosomal protein L11 methyltransferase;Note=methylates ribosomal protein L11 at multiple amino acid positions 3B mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype NC_002163.1 RefSeq region 1049776 1050600 . - . ID=id2058;gene=prmA;Name=id2058;Dbxref=GeneID:905408;gbkey=misc_feature;Note=HMMPfam hit to PF06325 2C Ribosomal protein L11 methyltransferase 28Prm 2C score 1.6e-22 ### NC_002163.1 RefSeq gene 1050632 1051024 . - . ID=gene1069;gene=cheY;Name=cheY;locus_tag=Cj1118c;Dbxref=GeneID:905409;gbkey=Gene NC_002163.1 RefSeq CDS 1050632 1051024 . - 0 ID=cds1004;Parent=gene1069;gene=cheY;Name=YP_002344511.1;Dbxref=GOA:P0C635 HSSP:P06143 InterPro:IPR001789 UniProtKB FSwiss-Prot:P0C635 Genbank:YP_002344511.1 GeneID:905409;gbkey=CDS;product=chemotaxis regulatory protein;Note=Original 282000 29 note: Cj1118c 2C cheY 2C chemotaxis regulatory protein 2C len: 130 aa 3B identical to CHEY_CAMJE 2Cand highly similar to e.g. CHEY_ECOLI 28128 aa 29 2C fasta scores 3B opt: 376 z-score: 468.7 E 28 29: 8.2e-19 2C 48.3 25 identity in 120 aa overlap. 82.8 25 identity to HP1067. Contains Pfam match to entry PF00072 response_reg 2CResponse regulator receiver domain 7EUpdated 282006 29 note: Characterised within Campylobacter jejuni. not added to product function. Functional classification - Chemotaxis and mobility 7EPMID:9076738 2C PMID:11912013 NC_002163.1 RefSeq region 1050653 1051024 . - . ID=id2059;gene=cheY;Name=id2059;Dbxref=GeneID:905409;gbkey=misc_feature;Note=HMMPfam hit to PF00072 2C Response regulator receiver domain 2C score 3.7e-32 ### NC_002163.1 UTR_Extractor 5'-UTR 1051025 1051105 . - . ID=utr403;locus_tag=Cj1118c;product=chemotaxis regulatory protein NC_002163.1 RefSeq CDS 1051137 1052030 . - 0 ID=cds1005;Parent=gene1070;gene=pglG;Name=YP_002344512.1;Dbxref=GOA:Q0P9D5 InterPro:IPR004010 UniProtKB FTrEMBL:Q0P9D5 Genbank:YP_002344512.1 GeneID:905410;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj1119c 2C wlaM 2C pglG 2C probable integral membrane protein 2C len: 297 aa 3B 99.3 25 identical to TR:O86160 28EMBL:Y11648 29 C. jejuni 81116 wlaM 28297 aa 29. Also contains short section of similarity to TR:Q56633 28EMBL:L25660 29 Vibrio cholerae accessory colonization factor 28ACFB 29 28626 aa 29 2C fasta scores 3B opt: 165 z-score: 202.6 E 28 29: 0.00055 2C 34.0 25 identity in 103 aa overlap. 37.6 25 identity to HP0158 7EUpdated 282006 29 note: Four probable transmembrane helices predicted by TMHMM2.0. Characterised in Campylobacter jejuni. The integral membrane protein shows no known role in N-linked glycosylation. Identifed as part of Campylobacter jejuni N-linked glycosylation locus 28Cj1119c - Cj1130c 29. Functional classification - Membranes 2C lipoproteins and porins 7EPMID:15752194 2C PMID:16186480 2C PMID:16618123 2CPMID:16547029 NC_002163.1 RefSeq gene 1051137 1052030 . - . ID=gene1070;gene=pglG;Name=pglG;locus_tag=Cj1119c;Dbxref=GeneID:905410;gbkey=Gene NC_002163.1 RefSeq region 1051167 1051235 . - . ID=id95;gene=pglG;Name=id95;Dbxref=GeneID:905410;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1119c by TMHMM2.0 at aa 161-183 2C 196-218 2C 239-261 and 266-288 NC_002163.1 RefSeq region 1051248 1051316 . - . ID=id95;gene=pglG;Name=id95;Dbxref=GeneID:905410;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1119c by TMHMM2.0 at aa 161-183 2C 196-218 2C 239-261 and 266-288 NC_002163.1 RefSeq region 1051377 1051445 . - . ID=id95;gene=pglG;Name=id95;Dbxref=GeneID:905410;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1119c by TMHMM2.0 at aa 161-183 2C 196-218 2C 239-261 and 266-288 NC_002163.1 RefSeq region 1051482 1051550 . - . ID=id95;gene=pglG;Name=id95;Dbxref=GeneID:905410;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1119c by TMHMM2.0 at aa 161-183 2C 196-218 2C 239-261 and 266-288 NC_002163.1 RefSeq gene 1052030 1053802 . - . ID=gene1071;gene=pglF;Name=pglF;locus_tag=Cj1120c;Dbxref=GeneID:905411;gbkey=Gene NC_002163.1 RefSeq CDS 1052030 1053802 . - 0 ID=cds1006;Parent=gene1071;gene=pglF;Name=YP_002344513.1;Dbxref=GOA:Q0P9D4 InterPro:IPR003869 InterPro:IPR016040 UniProtKB FTrEMBL:Q0P9D4 Genbank:YP_002344513.1 GeneID:905411;gbkey=CDS;product=UDP-GlcNAc C4 2C6 dehydratase;Note=Original 282000 29 note: Cj1120c 2C wlaL 2C pglF 2C possible sugar epimerase 2Fdehydratase 2C len: 590 aa 3B 99.5 25 identical to TR:O86159 28EMBL:Y11648 29 C. jejuni 81116 wlaL 28590 aa 29 2Cand similar to e.g. CAPD_STAAU Staphylococcus aureus capsular polysaccharide biosynthesis CAPD protein 28599 aa 29 2C fasta scores 3B opt: 1051 z-score: 1218.6 E 28 29: 0 2C 38.4 25 identity in 614 aa overlap 2C and TR:O69130 28EMBL:AF064070 29 Burkholderia pseudomallei epimerase 2Fdehydratase WBII 28637 aa 29 2C fasta scores 3B opt: 961 z-score: 1113.9 E 28 29: 0 2C 36.0 25 identity in 605 aa overlap. No Hp ortholog. Contains probable integral membrane domain at N-terminus 7EUpdated 282006 29 note: Pfam domain PF02719 Polysaccharide biosynthesis protein identified within CDS. Characterised in Campylobacter jejuni. Product function modified to more specific family member. This dehydratase forms EDP-2-acetamido-2 2C6-dideoxy-alpha-D-xylo-hexos-4-ulose. Identifed as part of Campylobacter jejuni N-linked glycosylation locus 28Cj1119c - Cj1130c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:16421095 PMID:15752194 2C PMID:16186480 2CPMID:16618123 2C PMID:16547029 2C PMID:16286454 NC_002163.1 RefSeq region 1052057 1053562 . - . ID=id2060;gene=pglF;Name=id2060;Dbxref=GeneID:905411;gbkey=misc_feature;Note=HMMPfam hit to PF02719 2C Polysaccharide biosynthesis protein 2C score 4e-140 NC_002163.1 RefSeq region 1053497 1053565 . - . ID=id96;gene=pglF;Name=id96;Dbxref=GeneID:905411;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1120c by TMHMM2.0 at aa 9-28 2C 38-60 and 80-102 NC_002163.1 RefSeq region 1053623 1053691 . - . ID=id96;gene=pglF;Name=id96;Dbxref=GeneID:905411;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1120c by TMHMM2.0 at aa 9-28 2C 38-60 and 80-102 NC_002163.1 RefSeq region 1053719 1053778 . - . ID=id96;gene=pglF;Name=id96;Dbxref=GeneID:905411;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1120c by TMHMM2.0 at aa 9-28 2C 38-60 and 80-102 ### NC_002163.1 RefSeq gene 1053804 1054964 . - . ID=gene1072;gene=pglE;Name=pglE;locus_tag=Cj1121c;Dbxref=GeneID:905412;gbkey=Gene NC_002163.1 RefSeq CDS 1053804 1054964 . - 0 ID=cds1007;Parent=gene1072;gene=pglE;Name=YP_002344514.1;Dbxref=GOA:Q0P9D3 InterPro:IPR000653 InterPro:IPR015421 InterPro:IPR015422 UniProtKB FTrEMBL:Q0P9D3 Genbank:YP_002344514.1 GeneID:905412;gbkey=CDS;product=UDP-4-keto-6-deoxy-GlcNAc C4 aminotransferase;Note=Original 282000 29 note: Cj1121c 2C wlaK 2C pglE 2C possible aminotransferase 2C len: 386 aa 3B 98.7 25 identical to TR:O86158 28EMBL:Y11648 29 C. jejuni 81116 wlaK 28386 aa 29 2C and similar to e.g. TR:O68392 28EMBL:AF036614 29 Brucella melitensis perosamine synthetase rfbE 28367 aa 29 2C fasta scores 3B opt: 621 z-score: 742.5 E 28 29: 0 2C 31.5 25 identity in 375 aa overlap 2C and TR:P72452 28EMBL:Y00459 29 Streptomyces griseus aminotransferase strS 28378 aa 29 2C fasta scores 3B opt: 426 z-score: 510.6 E 28 29: 3.8e- 2C 32.2 25 identity in 264 aa overlap. No Hp ortholog. Contains Pfam match to entry PF01041 DegT_DnrJ_EryC1 2C DegT 2FDnrJ 2FEryC1 2FStrS family 7EUpdated 282006 29 note: Characterised in Campylobacter jejuni. Product function modified to more specific family member. This protein acts to form 2 2C4-diacetamido bacillosamine. Identifed as part of Campylobacter jejuni N-linked glycosylation locus 28Cj1119c - Cj1130c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:15752194 2C PMID:16186480 2C PMID:16618123 2CPMID:16547029 2C PMID:16286454 2C PMID:16690622 NC_002163.1 RefSeq region 1053825 1054943 . - . ID=id2061;gene=pglE;Name=id2061;Dbxref=GeneID:905412;gbkey=misc_feature;Note=HMMPfam hit to PF01041 2C DegT 2FDnrJ 2FEryC1 2FStrS aminotransferase 2C score 2e-75 ### NC_002163.1 UTR_Extractor 5'-UTR 1054965 1055001 . - . ID=utr404;locus_tag=Cj1121c;product=UDP-4-keto-6-deoxy-GlcNAc C4 aminotransferase NC_002163.1 RefSeq CDS 1055060 1055713 . - 0 ID=cds1008;Parent=gene1073;Name=YP_002344515.1;Dbxref=GOA:Q0P9D2 UniProtKB FTrEMBL:Q0P9D2 Genbank:YP_002344515.1 GeneID:905413;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj1122c 2C wlaJ 2C possible integral membrane protein 2C len: 217 aa 3B 99.5 25 identical to TR:G4100601 28EMBL:AF001497 29 C. jejuni 11168 orfE 28217 aa 29. Not present in C. jejuni 81116. No Hp match 7EUpdated 282006 29 note: Three probable transmembrane helices predicted by TMHMM2.0 NC_002163.1 RefSeq gene 1055060 1055713 . - . ID=gene1073;Name=Cj1122c;locus_tag=Cj1122c;Dbxref=GeneID:905413;gbkey=Gene NC_002163.1 RefSeq region 1055303 1055371 . - . ID=id97;Name=id97;Dbxref=GeneID:905413;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1122c by TMHMM2.0 at aa 33-52 2C 73-95 and 115-137 NC_002163.1 RefSeq region 1055429 1055497 . - . ID=id97;Name=id97;Dbxref=GeneID:905413;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1122c by TMHMM2.0 at aa 33-52 2C 73-95 and 115-137 NC_002163.1 RefSeq region 1055558 1055617 . - . ID=id97;Name=id97;Dbxref=GeneID:905413;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1122c by TMHMM2.0 at aa 33-52 2C 73-95 and 115-137 NC_002163.1 RefSeq gene 1055670 1056257 . - . ID=gene1074;gene=pglD;Name=pglD;locus_tag=Cj1123c;Dbxref=GeneID:905414;gbkey=Gene NC_002163.1 RefSeq CDS 1055670 1056257 . - 0 ID=cds1009;Parent=gene1074;gene=pglD;Name=YP_002344516.1;Dbxref=GOA:Q0P9D1 PDB:2NPO UniProtKB FTrEMBL:Q0P9D1 Genbank:YP_002344516.1 GeneID:905414;gbkey=CDS;product=acetyltransferase;Note=Original 282000 29 note: Cj1123c 2C wlaI 2C pglD 2C possible transferase 2C len: 195 aa 3B 98.0 25 identical to TR:O86157 28EMBL:Y11648 29 C. jejuni 81116 wlaI 28203 aa 29 2C and similar to e.g. TR:Q46674 28EMBL:U05248 29 E. coli polysialic acid gene cluster region 2 neuD 28207 aa 29 2C fasta scores 3B opt: 287 z-score: 358.6 E 28 29: 1.1e-12 2C 28.6 25 identity in 203 aa overlap 2C and in the N-terminus to several acetyltransferases 2C e.g. LPXD_ECOLI UDP-3-O- 5B3-hydroxymyristoyl 5D glucosamine N-acyltransferase 28340 aa 29 2C fasta scores 3B opt: 149 z-score: 188.9 E 28 29: 0.0032 2C 31.7 25 identity in 82 aa overlap. No hp match. Also similar to Cj1321 2830.2 25 identity in 179 aa overlap 29. Contains 2x Pfam match to entry PF00132 hexapep 2C Bacterial transferase hexapeptide 28four repeats 29 7EUpdated 282006 29 note: Characterised in Campylobacter jejuni. Product function modified to more specific family member. This protein acts as an acetyltransferase to form 2 2C4-diacetamido bacillosamine. Identifed as part of Campylobacter jejuni N-linked glycosylation locus 28Cj1119c - Cj1130c 29. Functional classification - Surface polysaccharides 2C lipopolysaccharides and antigens 7EPMID:15752194 2C PMID:16186480 2C PMID:16618123 2CPMID:16547029 NC_002163.1 RefSeq region 1055775 1055828 . - . ID=id2062;gene=pglD;Name=id2062;Dbxref=GeneID:905414;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C no description 2C score 4 NC_002163.1 RefSeq region 1055865 1055918 . - . ID=id2063;gene=pglD;Name=id2063;Dbxref=GeneID:905414;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C no description 2C score 20 NC_002163.1 RefSeq region 1055919 1055972 . - . ID=id2064;gene=pglD;Name=id2064;Dbxref=GeneID:905414;gbkey=misc_feature;Note=HMMPfam hit to PF00132 2C no description 2C score 65 NC_002163.1 RefSeq gene 1056244 1056846 . - . ID=gene1075;gene=pglC;Name=pglC;locus_tag=Cj1124c;Dbxref=GeneID:905415;gbkey=Gene NC_002163.1 RefSeq CDS 1056244 1056846 . - 0 ID=cds1010;Parent=gene1075;gene=pglC;Name=YP_002344517.1;Dbxref=GOA:Q0P9D0 InterPro:IPR003362 UniProtKB FTrEMBL:Q0P9D0 Genbank:YP_002344517.1 GeneID:905415;gbkey=CDS;product=galactosyltransferase;Note=Original 282000 29 note: Cj1124c 2C wlaH 2C pglC 2C probable galactosyltransferase 2C len: 200 aa 3B 99.0 25 identical to TR:O86156 28EMBL:Y11648 29 C. jejuni 81116 wlaH 28200 aa 29 2C96.5 25 identical to TR:P71124 28EMBL:X91081 29 C. hyoilei galactosyltransferase RFBP 28200 aa 29 2C and similar to e.g. RFBP_SALTY UDP-phosphate galactosephosphotransferase 28476 aa 29 2C fasta scores 3B opt: 330 z-score: 406.2 E 28 29: 2.5e-15 2C 38.0 25 identity in 200 aa overlap. No Hp match. Contains one possible transmembrane domain 7EUpdated 282006 29 note: Pfam domain PF02397 2C Bacterial sugar transferase 2C identified within CDS. Characterised in Campylobacter jejuni. Product function modified to more specific family member. This protein transfers UDP bacillosamine to UndP. not added to product function. Identifed as part of Campylobacter jejuni N-linked glycosylation locus 28Cj1119c - Cj1130c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:15752194 2C PMID:16186480 2C PMID:16618123 2CPMID:16547029 NC_002163.1 RefSeq region 1056289 1056828 . - . ID=id2065;gene=pglC;Name=id2065;Dbxref=GeneID:905415;gbkey=misc_feature;Note=HMMPfam hit to PF02397 2C Bacterial sugar transferase 2C score 1.8e-42 NC_002163.1 RefSeq region 1056748 1056813 . - . ID=id2066;gene=pglC;Name=id2066;Dbxref=GeneID:905415;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1124c by TMHMM2.0 at aa 12-33 NC_002163.1 RefSeq CDS 1056839 1057969 . - 0 ID=cds1011;Parent=gene1076;gene=pglA;Name=YP_002344518.1;Dbxref=GOA:Q0P9C9 InterPro:IPR001296 UniProtKB FTrEMBL:Q0P9C9 Genbank:YP_002344518.1 GeneID:905416;gbkey=CDS;product=GalNAc transferase;Note=Original 282000 29 note: Cj1125c 2C wlaG 2C pglA 2C probable galactosyltransferase 2C len: 376 aa 3B 98.4 25 identical to TR:O86155 28EMBL:Y11648 29 C. jejuni 81116 wlaG 28376 aa 29 2C82.7 25 identical to TR:P71123 28EMBL:X91081 29 C. hyoileigalactosyltransferase RFBF 28376 aa 29 2C and similar to e.g. TR:O87893 28EMBL:U73942 29 NEISSERIA MENINGITIDIS GLYCOSYLTRANSFERASE PGLA 28376 aa 29 2C fasta scores 3B opt: 549 z-score: 651.7 E 28 29: 5.3e-29 2C 29.5 25 identity in 387 aa overlap. No Hp match. Contains Pfam match to entry PF00534 Glycos_transf_1 7EUpdated 282006 29 note: Pfam domain PF00534 2C Glycosyl transferase group 2C identified within CDS. Characterised in Campylobacter jejuni. Product function modified to more specific family member. This protein acts as the GalNAc transferase of the first GalNAc to bacillosamine. not added to product function. Identifed as part of Campylobacter jejuni N-linked glycosylation locus 28Cj1119c - Cj1130c 29. Functional classification - Surface polysaccharides 2C lipopolysaccharides and antigens 7EPMID:15752194 2C PMID:16186480 2C PMID:16618123 2CPMID:16547029 NC_002163.1 RefSeq gene 1056839 1057969 . - . ID=gene1076;gene=pglA;Name=pglA;locus_tag=Cj1125c;Dbxref=GeneID:905416;gbkey=Gene NC_002163.1 RefSeq region 1056914 1057402 . - . ID=id2067;gene=pglA;Name=id2067;Dbxref=GeneID:905416;gbkey=misc_feature;Note=HMMPfam hit to PF00534 2C Glycosyl transferases group 2C score 3.3e-48 ### NC_002163.1 RefSeq CDS 1057979 1060120 . - 0 ID=cds1012;Parent=gene1077;gene=pglB;Name=YP_002344519.1;Dbxref=GOA:Q0P9C8 InterPro:IPR003674 UniProtKB FTrEMBL:Q0P9C8 Genbank:YP_002344519.1 GeneID:905417;gbkey=CDS;product=general glycosylation pathway protein;Note=Original 282000 29 note: Cj1126c 2C wlaF 2C pglB 2C probable integral membrane protein 2C possible oligosaccharyl transferase 2C len: 713 aa 3B 98.9 25 identical to TR:O86154 28EMBL:Y11648 29 C. jejuni 81116 wlaF 28713 aa 29 2C very weak simlarity to e.g. STT3_HUMAN P46977 oligosaccharyl transferase STT3 subunit homolog 28705 aa 29 2C blastp scores 3B E 3D 6.7e-05 2C 22 25 identity in 233 aa overlap and 32 25 identity in 56 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02516 2COligosaccharyl transferase STT3 subunit 2C identified within CDS. Characterised in Campylobacter jejuni. Product function modified to more specific family member. This protein acts as the oligosaccharyl transferase to N-glycosylate proteins. not added to product function. Identifed as part of Campylobacter jejuni N-linked glycosylation locus 28Cj1119c - Cj1130c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:15752194 2C PMID:16186480 2C PMID:16618123 2CPMID:16547029 2C PMID:16356848 2C PMID:16641107 NC_002163.1 RefSeq gene 1057979 1060120 . - . ID=gene1077;gene=pglB;Name=pglB;locus_tag=Cj1126c;Dbxref=GeneID:905417;gbkey=Gene NC_002163.1 RefSeq region 1058195 1060096 . - . ID=id2068;gene=pglB;Name=id2068;Dbxref=GeneID:905417;gbkey=misc_feature;Note=HMMPfam hit to PF02516 2C Oligosaccharyl transferase STT3 subunit 2C score 1e-204 NC_002163.1 RefSeq region 1058846 1058914 . - . ID=id98;gene=pglB;Name=id98;Dbxref=GeneID:905417;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1126c by TMHMM2.0 at aa 12-34 2C 97-119 2C 126-143 2C 153-170 2C177-194 2C 198-215 2C 222-244 2C 259-281 2C 329-347 2C 373-390 and 403-425 NC_002163.1 RefSeq region 1058951 1059004 . - . ID=id98;gene=pglB;Name=id98;Dbxref=GeneID:905417;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1126c by TMHMM2.0 at aa 12-34 2C 97-119 2C 126-143 2C 153-170 2C177-194 2C 198-215 2C 222-244 2C 259-281 2C 329-347 2C 373-390 and 403-425 NC_002163.1 RefSeq region 1059080 1059136 . - . ID=id98;gene=pglB;Name=id98;Dbxref=GeneID:905417;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1126c by TMHMM2.0 at aa 12-34 2C 97-119 2C 126-143 2C 153-170 2C177-194 2C 198-215 2C 222-244 2C 259-281 2C 329-347 2C 373-390 and 403-425 NC_002163.1 RefSeq region 1059278 1059346 . - . ID=id98;gene=pglB;Name=id98;Dbxref=GeneID:905417;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1126c by TMHMM2.0 at aa 12-34 2C 97-119 2C 126-143 2C 153-170 2C177-194 2C 198-215 2C 222-244 2C 259-281 2C 329-347 2C 373-390 and 403-425 NC_002163.1 RefSeq region 1059389 1059457 . - . ID=id98;gene=pglB;Name=id98;Dbxref=GeneID:905417;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1126c by TMHMM2.0 at aa 12-34 2C 97-119 2C 126-143 2C 153-170 2C177-194 2C 198-215 2C 222-244 2C 259-281 2C 329-347 2C 373-390 and 403-425 NC_002163.1 RefSeq region 1059476 1059529 . - . ID=id98;gene=pglB;Name=id98;Dbxref=GeneID:905417;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1126c by TMHMM2.0 at aa 12-34 2C 97-119 2C 126-143 2C 153-170 2C177-194 2C 198-215 2C 222-244 2C 259-281 2C 329-347 2C 373-390 and 403-425 NC_002163.1 RefSeq region 1059539 1059592 . - . ID=id98;gene=pglB;Name=id98;Dbxref=GeneID:905417;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1126c by TMHMM2.0 at aa 12-34 2C 97-119 2C 126-143 2C 153-170 2C177-194 2C 198-215 2C 222-244 2C 259-281 2C 329-347 2C 373-390 and 403-425 NC_002163.1 RefSeq region 1059611 1059664 . - . ID=id98;gene=pglB;Name=id98;Dbxref=GeneID:905417;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1126c by TMHMM2.0 at aa 12-34 2C 97-119 2C 126-143 2C 153-170 2C177-194 2C 198-215 2C 222-244 2C 259-281 2C 329-347 2C 373-390 and 403-425 NC_002163.1 RefSeq region 1059692 1059745 . - . ID=id98;gene=pglB;Name=id98;Dbxref=GeneID:905417;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1126c by TMHMM2.0 at aa 12-34 2C 97-119 2C 126-143 2C 153-170 2C177-194 2C 198-215 2C 222-244 2C 259-281 2C 329-347 2C 373-390 and 403-425 NC_002163.1 RefSeq region 1059764 1059832 . - . ID=id98;gene=pglB;Name=id98;Dbxref=GeneID:905417;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1126c by TMHMM2.0 at aa 12-34 2C 97-119 2C 126-143 2C 153-170 2C177-194 2C 198-215 2C 222-244 2C 259-281 2C 329-347 2C 373-390 and 403-425 NC_002163.1 RefSeq region 1060019 1060087 . - . ID=id98;gene=pglB;Name=id98;Dbxref=GeneID:905417;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1126c by TMHMM2.0 at aa 12-34 2C 97-119 2C 126-143 2C 153-170 2C177-194 2C 198-215 2C 222-244 2C 259-281 2C 329-347 2C 373-390 and 403-425 ### NC_002163.1 RefSeq gene 1060124 1061221 . - . ID=gene1078;gene=pglJ;Name=pglJ;locus_tag=Cj1127c;Dbxref=GeneID:905418;gbkey=Gene NC_002163.1 RefSeq CDS 1060124 1061221 . - 0 ID=cds1013;Parent=gene1078;gene=pglJ;Name=YP_002344520.1;Dbxref=GOA:Q0P9C7 InterPro:IPR001296 UniProtKB FTrEMBL:Q0P9C7 Genbank:YP_002344520.1 GeneID:905418;gbkey=CDS;product=GalNAc transferase;Note=Original 282000 29 note: Cj1127c 2C wlaE 2C probable glycosyltransferase 2C len: 365 aa 3B 98.6 25 identical to TR:O86153 28EMBL:Y11648 29 C. jejuni 81116 wlaE 28365 aa 29 2C and similar to e.g. AMSD_ERWAM amylovoran biosynthesis glycosyl transerase AMSD 28351 aa 29 2C fasta scores 3B opt: 250 z-score: 309.4 E 28 29: 6.2e-10 2C 27.1 25 identity in 351 aa overlap. No Hp match. Contains Pfam match to entry PF00534 Glycos_transf_1 7EUpdated 282006 29 note: Characterised in Campylobacter jejuni. Product function modified to more specific family member. This protein acts as the GalNAc transferase for the next GalNAc to bacillosamine. not added to product function. Identifed as part of Campylobacter jejuni N-linked glycosylation locus 28Cj1119c - Cj1130c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:15752194 2C PMID:16186480 2C PMID:16618123 2CPMID:16547029 NC_002163.1 RefSeq region 1060184 1060681 . - . ID=id2069;gene=pglJ;Name=id2069;Dbxref=GeneID:905418;gbkey=misc_feature;Note=HMMPfam hit to PF00534 2C Glycosyl transferases group 2C score 4.1e-42 NC_002163.1 RefSeq gene 1061209 1062138 . - . ID=gene1079;gene=pglI;Name=pglI;locus_tag=Cj1128c;Dbxref=GeneID:905419;gbkey=Gene NC_002163.1 RefSeq CDS 1061209 1062138 . - 0 ID=cds1014;Parent=gene1079;gene=pglI;Name=YP_002344521.1;Dbxref=GOA:Q0P9C6 InterPro:IPR001173 UniProtKB FTrEMBL:Q0P9C6 Genbank:YP_002344521.1 GeneID:905419;gbkey=CDS;product=glucosyl transferase;Note=Original 282000 29 note: Cj1128c 2C wlaD 2C epsI 2C probable glycosyltransferase 2C len: 309 aa 3B 99.7 25 identical to TR:O86152 28EMBL:Y11648 29 C. jejuni 81116 wlaD 28309 aa 29 2C99.7 25 identical to TR:O52906 28EMBL:AJ000854 29 C. jejuni 11168 epsI 28309 aa 29 2C and similar to e.g. TR:O87182 28EMBL:AB017355 29 Streptococcus agalactiae N-acetylglucosaminyltransferase CPSH 28333 aa 29 2C fasta scores 3B opt: 281 z-score: 324.3 E 28 29: 9.1e-11 2C 23.5 25 identity in 281 aa overlap. No Hp match. Contains Pfam match to entry PF00535 Glycos_transf_2 7EUpdated 282006 29 note: Characterised in Campylobacter jejuni. Product function modified to more specific family member. This protein is responsible for adding the glucose branch to the maturing glycan. not added to product function. Identifed as part of Campylobacter jejuni N-linked glycosylation locus 28Cj1119c - Cj1130c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:15752194 2C PMID:16186480 2C PMID:16618123 2CPMID:16547029 NC_002163.1 UTR_Extractor 5'-UTR 1061222 1061262 . - . ID=utr405;locus_tag=Cj1127c;product=GalNAc transferase NC_002163.1 RefSeq region 1061647 1062126 . - . ID=id2070;gene=pglI;Name=id2070;Dbxref=GeneID:905419;gbkey=misc_feature;Note=HMMPfam hit to PF00535 2C Glycosyl transferase 2C score 1.2e-41 NC_002163.1 RefSeq CDS 1062131 1063210 . - 0 ID=cds1015;Parent=gene1080;gene=pglH;Name=YP_002344522.1;Dbxref=GOA:Q0P9C5 InterPro:IPR001296 UniProtKB FTrEMBL:Q0P9C5 Genbank:YP_002344522.1 GeneID:905420;gbkey=CDS;product=GalNAc transferase 2Fpolymerase;Note=Original 282000 29 note: Cj1129c 2C wlaC 2C capM 2C probable glycosyltransferase 2C len: 359 aa 3B identical to TR:O52905 28EMBL:AJ000854 29 C. jejuni 11168 capM 28358 aa 29 2C 97.2 25 identical to TR:O86151 28EMBL:Y11648 29 C. jejuni 81116 wlaC 28358 aa 29 2C and similar to e.g. AMSD_ERWAM amylovoran biosynthesis glycosyl transerase 28351 aa 29 2C fasta scores 3B opt: 360 z-score: 445.6 E 28 29: 1.6e-17 2C 27.3 25 identity in 362 aa overlap. No Hp match. Contains Pfam match to entry PF00534 Glycos_transf_1 7EUpdated 282006 29 note: Characterised in Campylobacter jejuni. Product function modified to more specific family member. This protein acts as the transferase 2Fpolymerase of GalNAc 28s 29 to bacillosamine. not added to product function. Identifed as part of Campylobacter jejuni N-linked glycosylation locus 28Cj1119c - Cj1130c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:15752194 2C PMID:16498400 2C PMID:15184581 2CPMID:16186480 2C PMID:16618123 2C PMID:16547029 NC_002163.1 RefSeq gene 1062131 1063210 . - . ID=gene1080;gene=pglH;Name=pglH;locus_tag=Cj1129c;Dbxref=GeneID:905420;gbkey=Gene NC_002163.1 RefSeq region 1062203 1062703 . - . ID=id2071;gene=pglH;Name=id2071;Dbxref=GeneID:905420;gbkey=misc_feature;Note=HMMPfam hit to PF00534 2C Glycosyl transferases group 2C score 1e-47 NC_002163.1 RefSeq gene 1063207 1064901 . - . ID=gene1081;gene=pglK;Name=pglK;locus_tag=Cj1130c;Dbxref=GeneID:905421;gbkey=Gene NC_002163.1 RefSeq CDS 1063207 1064901 . - 0 ID=cds1016;Parent=gene1081;gene=pglK;Name=YP_002344523.1;Dbxref=GOA:Q6TG26 HSSP:P08716 InterPro:IPR001140 InterPro:IPR003439 InterPro:IPR003593 InterPro:IPR011527 UniProtKB FTrEMBL:Q6TG26 Genbank:YP_002344523.1 GeneID:905421;gbkey=CDS;product=flippase;Note=Original 282000 29 note: Cj1130c 2C wlaB 2C ABC-type transport protein 2C len: 564 aa 3B 98.2 25 identical to TR:O86150 28EMBL:Y11648 29 C. jejuni 81116 wlaB 28564 aa 29 2C and similar to e.g. HLY2_ECOLI hemolysin secretion atp-binding protein 28707 aa 29 2C fasta scores 3B opt: 655 z-score: 715.2 E 28 29: 1.5e-32 2C 29.0 25 identity in 572 aa overlap. Integral membrane domain in N-term contains Pfam match to entry PF00664 ABC_membrane 2C ABC transporter transmembrane region 2C ATP-binding domain in C-term contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00211 ABC transporters family signature 2C and Pfam match to entry PF00005 ABC_tran 2C ABC transporters. 38.3 25 identity to HP1206 28called multidrug resistance protein 28hetA 29 29 7EUpdated 282006 29 note: Characterised in Campylobacter jejuni. Product function modified to more specific family member. This protein flips the glycan across the inner membrane. not added to product function. Identifed as part of Campylobacter jejuni N-linked glycosylation locus 28Cj1119c - Cj1130c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:15752194 2C PMID:16547029 2C PMID:16498400 2CPMID:16481326 NC_002163.1 RefSeq region 1063228 1063779 . - . ID=id2072;gene=pglK;Name=id2072;Dbxref=GeneID:905421;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 2e-60 NC_002163.1 RefSeq region 1063405 1063449 . - . ID=id2073;gene=pglK;Name=id2073;Dbxref=GeneID:905421;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq region 1063735 1063758 . - . ID=id2074;gene=pglK;Name=id2074;Dbxref=GeneID:905421;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 1063990 1064043 . - . ID=id99;gene=pglK;Name=id99;Dbxref=GeneID:905421;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1130c by TMHMM2.0 at aa 20-42 2C 63-85 2C 146-168 2C 175-197 2C261-280 and 287-304 NC_002163.1 RefSeq region 1063993 1064862 . - . ID=id2075;gene=pglK;Name=id2075;Dbxref=GeneID:905421;gbkey=misc_feature;Note=HMMPfam hit to PF00664 2C ABC transporter transmembrane region 2C score 1.9e-07 NC_002163.1 RefSeq region 1064062 1064121 . - . ID=id99;gene=pglK;Name=id99;Dbxref=GeneID:905421;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1130c by TMHMM2.0 at aa 20-42 2C 63-85 2C 146-168 2C 175-197 2C261-280 and 287-304 NC_002163.1 RefSeq region 1064311 1064379 . - . ID=id99;gene=pglK;Name=id99;Dbxref=GeneID:905421;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1130c by TMHMM2.0 at aa 20-42 2C 63-85 2C 146-168 2C 175-197 2C261-280 and 287-304 NC_002163.1 RefSeq region 1064398 1064466 . - . ID=id99;gene=pglK;Name=id99;Dbxref=GeneID:905421;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1130c by TMHMM2.0 at aa 20-42 2C 63-85 2C 146-168 2C 175-197 2C261-280 and 287-304 NC_002163.1 RefSeq region 1064647 1064715 . - . ID=id99;gene=pglK;Name=id99;Dbxref=GeneID:905421;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1130c by TMHMM2.0 at aa 20-42 2C 63-85 2C 146-168 2C 175-197 2C261-280 and 287-304 NC_002163.1 RefSeq region 1064659 1064706 . - . ID=id2076;gene=pglK;Name=id2076;Dbxref=GeneID:905421;gbkey=misc_feature;Note=PS00225 Crystallins beta and gamma 27Greek key 27 motif signature NC_002163.1 RefSeq region 1064776 1064844 . - . ID=id99;gene=pglK;Name=id99;Dbxref=GeneID:905421;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1130c by TMHMM2.0 at aa 20-42 2C 63-85 2C 146-168 2C 175-197 2C261-280 and 287-304 NC_002163.1 RefSeq gene 1064895 1065881 . - . ID=gene1082;gene=gne;Name=gne;locus_tag=Cj1131c;Dbxref=GeneID:905422;gbkey=Gene NC_002163.1 RefSeq CDS 1064895 1065881 . - 0 ID=cds1017;Parent=gene1082;gene=gne;Name=YP_002344524.1;Dbxref=GOA:Q0P9C3 InterPro:IPR001509 InterPro:IPR005886 InterPro:IPR016040 UniProtKB FTrEMBL:Q0P9C3 Genbank:YP_002344524.1 GeneID:905422;gbkey=CDS;product=UDP-GlcNAc 2FGlc 4-epimerase;Note=Original 282000 29 note: Cj1131c 2C galE 2C probable UDP-glucose 4-epimerase 2C len: 328 aa 3B 98.2 25 identical to TR:O86149 28EMBL:Y11648 29 C. jejuni 81116 galE 28328 aa 29 2C and similar to e.g. GALE_STRMU UDP-glucose 4-epimerase 28EC 5.1.3.2 29 28333 aa 29 2C fasta scores 3B opt: 887 z-score: 1056.0 E 28 29: 0 2C 43.7 25 identity in 327 aa overlap. 50.0 25 identity to HP0360 7EUpdated 282006 29 note: Pfam domain PF01370 2C NAD dependent epimerase 2Fdehydratase family identified within CDS. Characterised within Campylobacter jejuni with recent evidence allowing product function and gene name to be updated. This protein acts as the UDP-GlcNAc 2FGlc 4-epimerase for the LOS 2C capsule and N-linked glycan in 11168. Identifed as part of Campylobacter jejuni lipooligosaccharide locus 28Cj1131c - Cj1152c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:9720026 2C PMID:14742567 2C PMID:10768949 2CPMID:15509570 NC_002163.1 RefSeq region 1064901 1065875 . - . ID=id2077;gene=gne;Name=id2077;Dbxref=GeneID:905422;gbkey=misc_feature;Note=HMMPfam hit to PF01370 2C NAD dependent epimerase 2Fdehydratase family 2C score 2.2e-109 ### NC_002163.1 UTR_Extractor 5'-UTR 1065882 1065911 . - . ID=utr406;locus_tag=Cj1131c;product=UDP-GlcNAc 2FGlc 4-epimerase NC_002163.1 RefSeq gene 1065939 1066733 . - . ID=gene1083;Name=Cj1132c;locus_tag=Cj1132c;Dbxref=GeneID:905423;gbkey=Gene NC_002163.1 RefSeq CDS 1065939 1066733 . - 0 ID=cds1018;Parent=gene1083;Name=YP_002344525.1;Dbxref=GOA:Q0P9C2 UniProtKB FTrEMBL:Q0P9C2 Genbank:YP_002344525.1 GeneID:905423;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1132c 2C unknown 2C len: 264 aa 3B some similarity to part of DNA polymerases e.g. DPOL_PYRFU DNA polymerase 28775 aa 29 2C fasta scores 3B opt: 168 z-score: 197.4 E 28 29: 0.0011 2C 29.6 25 identity in 247 aa overlap. Similar in N- and C-termini to sequential Hp CDSs 3B HP0688 2846.7 25 identity in 169 aa overlap 29 2C and HP0689 2847.4 25 identity in 95 aa overlap 29. Contains Pfam match to entry PF00136 DNA_pol_B 2C DNA polymerase family B 7EUpdated 282006 29 note: Literature search identified paper giving further clues about product function. Conserved added to product function. Identifed as part of Campylobacter jejuni lipooligosaccharide locus 28Cj1131c -Cj1152c 29. Functional classification - Conserved hypothetical proteins 7EPMID:15509570 NC_002163.1 RefSeq region 1066230 1066733 . - . ID=id2078;Name=id2078;Dbxref=GeneID:905423;gbkey=misc_feature;Note=HMMPfam hit to PF03104 2C DNA polymerase family B 2Cexonuclease do 2C score 0.0038 ### NC_002163.1 RefSeq CDS 1066799 1067827 . + 0 ID=cds1019;Parent=gene1084;gene=waaC;Name=YP_002344526.1;Dbxref=GOA:Q0P9C1 InterPro:IPR002201 InterPro:IPR011908 UniProtKB FTrEMBL:Q0P9C1 Genbank:YP_002344526.1 GeneID:905424;gbkey=CDS;product=heptosyltransferase I;Note=Original 282000 29 note: Cj1133 2C waaC 2C probable lipopolysaccharide heptosyltransferase 2C len: 342 aa 3B 98.2 25 identical to TR:O87585 28EMBL:AF086705 29 C. jejuni heptosyltransferase WaaC 28342 aa 29 2C and similar to e.g. RFAC_ECOLI lipopolysaccharide heptosyltransferase-1 28319 aa 29 2C fasta scores 3B opt: 212 z-score: 252.9 E 28 29: 8.6e-07 2C26.2 25 identity in 302 aa overlap. 38.5 25 identity to HP0279. Contains Pfam match to entry PF01075 Heptosyltranf 2C Heptosyltransferase 7EUpdated 282006 29 note: Characterised within Campylobacter jejuni. Product function further updated. not added to product function. Identifed as part of Campylobacter jejuni lipooligosaccharide locus 28Cj1131c - Cj1152c 29. Functional classification - Surface polysaccharides 2C lipopolysaccharides and antigens 7EPMID:16621820 2C PMID:9831648 2C PMID:11689567 2CPMID:15808749 2C PMID:11083778 2C PMID:10660542 NC_002163.1 RefSeq gene 1066799 1067827 . + . ID=gene1084;gene=waaC;Name=waaC;locus_tag=Cj1133;Dbxref=GeneID:905424;gbkey=Gene NC_002163.1 RefSeq region 1066991 1067758 . + . ID=id2079;gene=waaC;Name=id2079;Dbxref=GeneID:905424;gbkey=misc_feature;Note=HMMPfam hit to PF01075 2C Glycosyltransferase family 2Cscore 3e-20 NC_002163.1 RefSeq region 1067817 1068671 . + . ID=id2080;gene=htrB;Name=id2080;Dbxref=GeneID:905425;gbkey=misc_feature;Note=HMMPfam hit to PF03279 2C Bacterial lipid A biosynthesis acyltr 2C score 7e-34 NC_002163.1 RefSeq CDS 1067817 1068704 . + 0 ID=cds1020;Parent=gene1085;gene=htrB;Name=YP_002344527.1;Dbxref=GOA:Q7BC57 InterPro:IPR004960 UniProtKB FTrEMBL:Q7BC57 Genbank:YP_002344527.1 GeneID:905425;gbkey=CDS;product=lipid A biosynthesis lauroyl acyltransferase;Note=acylates the intermediate 28KDO 292-lipid IVA to form 28KDO 292- 28lauroyl 29-lipid IVA 3B essential for survival 3B plays a role in cell responses to environmental changes NC_002163.1 RefSeq gene 1067817 1068704 . + . ID=gene1085;gene=htrB;Name=htrB;locus_tag=Cj1134;Dbxref=GeneID:905425;gbkey=Gene NC_002163.1 RefSeq region 1067853 1067921 . + . ID=id2081;gene=htrB;Name=id2081;Dbxref=GeneID:905425;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1134 by TMHMM2.0 at aa 13-35 NC_002163.1 RefSeq region 1068697 1080900 . + . ID=id2082;gene=htrB;Name=id2082;gbkey=misc_feature;Note=region with low G 2BC: 25.4 25 NC_002163.1 RefSeq gene 1068701 1070248 . + . ID=gene1086;gene=Cj1135;Name=Cj1135;locus_tag=Cj1135;Dbxref=GeneID:905426;gbkey=Gene NC_002163.1 RefSeq CDS 1068701 1070248 . + 0 ID=cds1021;Parent=gene1086;Name=YP_002344528.1;Dbxref=GOA:Q7BC56 InterPro:IPR001173 UniProtKB FTrEMBL:Q7BC56 Genbank:YP_002344528.1 GeneID:905426;gbkey=CDS;product=glucosyltransferase;Note=Original 282000 29 note: Cj1135 2C probable two-domain glycosyltransferase 2C len: 515 aa 3B contains similarities in N- and C-termini to glycosyltransferases e.g. TR:P95373 28EMBL:U58765 29 Neisseria meningitidis beta 1 2C4 glucosyltransferase lgtF 28252 aa 29 2C fatsa scores 3B opt: 380 z-score: 453.4 E 28 29: 5.9e-18 2C 30.9 25 identity in 262 aa overlap 2C and TR:O85457 Pasteurella multocida glycosyl transferase hyaD 28864 aa 29 2C fasta scores 3B opt: 259 z-score: 302.8 E 28 29: 1.4e-09 2C 28.0 25 identity in 239 aa overlap. No Hp match. Contains 2x Pfam match to entry PF00535 Glycos_transf_2 2C Glycosyl transferases 7EUpdated 282006 29 note: Some characterisation within Neisseria meningitidis 2Chowever 2C identity score was marginal. Appropriate motifs present. Product function modified to more specific family member. This protein is most likely responsible for transferring the two glucose residues to the heptoses. Gilbert 28Michel.Gilbert@nrc-cnrc.gc.ca 29 personal communication. Identifed as part of Campylobacter jejuni lipooligosaccharide locus 28Cj1131c - Cj1152c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:11689567 2C PMID:15808749 2C PMID:11083778 2CPMID:10660542 NC_002163.1 RefSeq region 1068719 1069219 . + . ID=id2083;Name=id2083;Dbxref=GeneID:905426;gbkey=misc_feature;Note=HMMPfam hit to PF00535 2C Glycosyl transferase 2C score 4.7e-21 NC_002163.1 RefSeq region 1069475 1069978 . + . ID=id2084;Name=id2084;Dbxref=GeneID:905426;gbkey=misc_feature;Note=HMMPfam hit to PF00535 2C Glycosyl transferase 2C score 9.4e-25 NC_002163.1 RefSeq CDS 1070252 1071424 . + 0 ID=cds1022;Parent=gene1087;Name=YP_002344529.1;Dbxref=GOA:Q7BC55 InterPro:IPR001173 InterPro:IPR002035 UniProtKB FTrEMBL:Q7BC55 Genbank:YP_002344529.1 GeneID:905427;gbkey=CDS;product=glycosyltransferase;Note=Original 282000 29 note: Cj1136 2C probable galactosyltransferase 2C len: 390 aa 3B similar to e.g. TR:O07340 28EMBL:X85787 29 Streptococcus pneumoniae SS-1 2C4-galactosyltransferase CPS14J 28318 aa 29 2C fasta scores 3B opt: 309 z-score: 361.4 E 28 29: 7.8e-13 2C 29.0 25 identity in 290 aa overlap. No Hp match. Contains Pfam match to entry PF00535 Glycos_transf_2 2C Glycosyl transferases 7EUpdated 282006 29 note: Pfam domain PF00535 Glycosyl transferase identified within CDS. Product function updated based on motif match. No specific characterisation has been carried out yet 2C so kept within product function. Identifed as part of Campylobacter jejuni lipooligosaccharide locus 28Cj1131c - Cj1152c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:11689567 2C PMID:15808749 2C PMID:11083778 2CPMID:10660542 2C PMID:16594990 NC_002163.1 RefSeq gene 1070252 1071424 . + . ID=gene1087;Name=Cj1136;locus_tag=Cj1136;Dbxref=GeneID:905427;gbkey=Gene NC_002163.1 RefSeq region 1070264 1070926 . + . ID=id2085;Name=id2085;Dbxref=GeneID:905427;gbkey=misc_feature;Note=HMMPfam hit to PF00535 2C Glycosyl transferase 2C score 9.9e-28 NC_002163.1 RefSeq CDS 1071408 1072403 . - 0 ID=cds1023;Parent=gene1088;Name=YP_002344530.1;Dbxref=GOA:Q7BC54 InterPro:IPR008441 UniProtKB FTrEMBL:Q7BC54 Genbank:YP_002344530.1 GeneID:905428;gbkey=CDS;product=glycosyltransferase;Note=Original 282000 29 note: Cj1137c 2C unknown 2C len: 331 aa 3B similar to hypothetcal proteins in polysaccharide biosynthesis operons e.g. TR:O86892 28EMBL:AJ006986 29 Streptococcus pneumoniae CAPP33FI protein 28322 aa 29 2C fasta scores 3B opt: 295 z-score: 346.5 E 28 29: 5.3e-12 2C 26.5 25 identity in 294 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF05704 Capsular polysaccharide synthesis protein identified within CDS. Product function modified to more specific family member. No specific characterisation has been carried out yet. kept within product function. Gilbert 28Michel.Gilbert@nrc-cnrc.gc.ca 29 personal communication. Identifed as part of Campylobacter jejuni lipooligosaccharide locus 28Cj1131c - Cj1152c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:11689567 2C PMID:14742567 2C PMID:11083778 2CPMID:10660542 NC_002163.1 RefSeq gene 1071408 1072403 . - . ID=gene1088;Name=Cj1137c;locus_tag=Cj1137c;Dbxref=GeneID:905428;gbkey=Gene NC_002163.1 RefSeq region 1071423 1072325 . - . ID=id2086;Name=id2086;Dbxref=GeneID:905428;gbkey=misc_feature;Note=HMMPfam hit to PF05704 2C Capsular polysaccharide synthesis protein 2C score 5.2e-160 NC_002163.1 RefSeq CDS 1072461 1073630 . + 0 ID=cds1024;Parent=gene1089;Name=YP_002344531.1;Dbxref=GOA:Q7BC53 InterPro:IPR001173 UniProtKB FTrEMBL:Q7BC53 Genbank:YP_002344531.1 GeneID:905429;gbkey=CDS;product=glycosyltransferase;Note=Original 282000 29 note: Cj1138 2C probable galactosyltransferase 2C len: 389 aa 3B similar to e.g. TR:O07340 28EMBL:X85787 29 Streptococcus pneumoniae SS-1 2C4-galactosyltransferase CPS14J 28318 aa 29 2C fasta scores 3B opt: 304 z-score: 361.2 E 28 29: 8e-13 2C 25.8 25 identity in 383 aa overlap. No Hp match. Contains Pfam match to entry PF00535 Glycos_transf_2 2C Glycosyl transferases 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score has been carried out yet. kept within product function. Product function modified to more specific family member. Identifed as part of Campylobacter jejuni lipooligosaccharide locus 28Cj1131c - Cj1152c 29. Functional classification - Surface polysaccharides 2C lipopolysaccharides and antigens 7EPMID:16594990 2C PMID:11083778 2C PMID:10660542 NC_002163.1 RefSeq gene 1072461 1073630 . + . ID=gene1089;Name=Cj1138;locus_tag=Cj1138;Dbxref=GeneID:905429;gbkey=Gene NC_002163.1 RefSeq region 1072473 1073108 . + . ID=id2087;Name=id2087;Dbxref=GeneID:905429;gbkey=misc_feature;Note=HMMPfam hit to PF00535 2C Glycosyl transferase 2C score 5.6e-28 NC_002163.1 RefSeq gene 1073619 1074530 . - . ID=gene1090;gene=wlaN;Name=wlaN;locus_tag=Cj1139c;Dbxref=GeneID:905430;gbkey=Gene NC_002163.1 RefSeq CDS 1073619 1074530 . - 0 ID=cds1025;Parent=gene1090;gene=wlaN;Name=YP_002344532.1;Dbxref=GOA:Q0P9B5 InterPro:IPR001173 UniProtKB FTrEMBL:Q0P9B5 Genbank:YP_002344532.1 GeneID:905430;gbkey=CDS;product=beta-1 2C3 galactosyltransferase;Note=Original 282000 29 note: Cj1139c 2C probable galactosyltransferase 2C len: 303 aa 3B similar to e.g. TR:O07340 28EMBL:X85787 29 Streptococcus pneumoniae SS-1 2C4-galactosyltransferase CPS14J 28318 aa 29 2C fasta scores 3B opt: 309 z-score: 362.2 E 28 29: 7.1e-13 2C 26.1 25 identity in 249 aa overlap. No Hp match. Contains Pfam match to entry PF00535 Glycos_transf_2 2C Glycosyl transferases. Contains C 288-9 29 polymorphic region at aa 111. C 288 29 2C the consensus 2C allows translation of the full length protein. C 289 29 would cause a premature truncation after a further 20 aa 7EUpdated 282006 29 note: Characterised within Campylobacter jejuni. Product function modified to more specific family member. not added to product function. This protein carries out the beta-1 2C3 galactosyltransferase addition of terminal galactose to LOS. Identifed as part of Campylobacter jejuni lipooligosaccharide locus 28Cj1131c - Cj1152c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:10931344 2C PMID:11083778 2C PMID:10660542 NC_002163.1 RefSeq region 1074009 1074518 . - . ID=id2088;gene=wlaN;Name=id2088;Dbxref=GeneID:905430;gbkey=misc_feature;Note=HMMPfam hit to PF00535 2C Glycosyl transferase 2C score 3.7e-39 NC_002163.1 UTR_Extractor 5'-UTR 1074566 1074584 . + . ID=utr407;locus_tag=Cj1140;product=alpha-2 2C3 sialyltransferase NC_002163.1 RefSeq gene 1074585 1075469 . + . ID=gene1091;gene=cstIII;Name=cstIII;locus_tag=Cj1140;Dbxref=GeneID:905431;gbkey=Gene NC_002163.1 RefSeq CDS 1074585 1075469 . + 0 ID=cds1026;Parent=gene1091;gene=cstIII;Name=YP_002344533.1;Dbxref=GOA:Q7BP25 InterPro:IPR009251 UniProtKB FTrEMBL:Q7BP25 Genbank:YP_002344533.1 GeneID:905431;gbkey=CDS;product=alpha-2 2C3 sialyltransferase;Note=Original 282000 29 note: Cj1140 2C unknown 2C len: 294 aa 3B similar to H. influenzae hypothetical protein in lipopolysaccharide biosynthesis gene cluster Y352_HAEIN HI0352 28ORF1 29 28231 aa 29 2C fasta scores 3B opt: 558 z-score: 672.8 E 28 29: 3.5e-30 2C 41.5 25 identity in 229 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF06002 Alpha-2 2C3-sialyltransferase 28CST-I 29 identified within CDS. Characterisation work carried out within Campylobacter jejuni 2C so product function modified to new family member. not added to product function. This protein transfers sialic acid from cytidine-5 27-monophospho-N-acetyl-neuraminic acid 28CMP-NeuAc 29 to LOS. Gilbert 28Michel.Gilbert@nrc-cnrc.gc.ca 29 personal communication. Identifed as part of Campylobacter jejuni lipooligosaccharide locus 28Cj1131c - Cj1152c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:11083778 2C PMID:11689567 2C PMID:10660542 2CPMID:14730352 2C PMID:16620397 NC_002163.1 RefSeq region 1074594 1075448 . + . ID=id2089;gene=cstIII;Name=id2089;Dbxref=GeneID:905431;gbkey=misc_feature;Note=HMMPfam hit to PF06002 2C Alpha-2 2C3-sialyltransferase 28CST-I 29 2C score 7.4e-239 NC_002163.1 RefSeq CDS 1075450 1076481 . + 0 ID=cds1027;Parent=gene1092;gene=neuB1;Name=YP_002344534.1;Dbxref=GOA:Q7BC51 InterPro:IPR006190 InterPro:IPR013132 InterPro:IPR013785 InterPro:IPR013974 UniProtKB FTrEMBL:Q7BC51 Genbank:YP_002344534.1 GeneID:905432;gbkey=CDS;product=sialic acid synthase;Note=Original 282000 29 note: Cj1141 2C neuB1 2C probable N-acetylneuraminic acid synthetase 2C len: 343 aa 3B highly similar to e.g. TR:Q57265 28EMBL:U40740 29 N-acetylneuraminic acid synthetase 28EC 4.1.3.- 29 28349 aa 29 2C fasta scores 3B opt: 1327 z-score: 1554.1 E 28 29: 0 2C 59.0 25 identity in 344 aa overlap. No Hp ortholog. Also similar to Cj1327 2837.1 25 identity in 329 aa overlap 29 and Cj1317 2834.4 25 identity in 340 aa overlap 29 7EUpdated 282006 29 note: Pfam domains PF03102 NeuB family and PF01354 Antifreeze-like domain were identified within CDS. Characterisation work carried out within Campylobacter jejuni. Product function further modified to more specific family member. not added to product function. This protein acts in the condensation of N-acetyl-D-mannosamine and phosphoenolpyruvate to N-acetylneuraminic acid. Identifed as part of Campylobacter jejuni lipooligosaccharide locus 28Cj1131c -Cj1152c 29. Functional classification - Surface polysaccharides 2C lipopolysaccharides and antigens 7EPMID:10712693 2C PMID:11689567 2C PMID:10660542 2CPMID:14742567 2C PMID:16567003 NC_002163.1 RefSeq gene 1075450 1076481 . + . ID=gene1092;gene=neuB1;Name=neuB1;locus_tag=Cj1141;Dbxref=GeneID:905432;gbkey=Gene NC_002163.1 RefSeq region 1075552 1076259 . + . ID=id2090;gene=neuB1;Name=id2090;Dbxref=GeneID:905432;gbkey=misc_feature;Note=HMMPfam hit to PF03102 2C NeuB family 2C score 9.2e-91 NC_002163.1 RefSeq region 1076305 1076478 . + . ID=id2091;gene=neuB1;Name=id2091;Dbxref=GeneID:905432;gbkey=misc_feature;Note=HMMPfam hit to PF01354 2C Antifreeze-like domain 2Cscore 1.8e-30 NC_002163.1 RefSeq gene 1076478 1077593 . + . ID=gene1093;gene=neuC1;Name=neuC1;locus_tag=Cj1142;Dbxref=GeneID:905433;gbkey=Gene NC_002163.1 RefSeq CDS 1076478 1077593 . + 0 ID=cds1028;Parent=gene1093;gene=neuC1;Name=YP_002344535.1;Dbxref=GOA:Q7BP23 InterPro:IPR003331 UniProtKB FTrEMBL:Q7BP23 Genbank:YP_002344535.1 GeneID:905433;gbkey=CDS;product=UDP-N-acetylglucosamine 2-epimerase;Note=Original 282000 29 note: Cj1142 2C neuC1 2C probable N-acetylglucosamine-6-phosphate 2-epimerase 2FN-acetylglucosamine-6-phosphatase 2C len: 371 aa 3B similar to e.g. TR:Q57141 28EMBL:X78068 29 Neisseria meningitidis N-acetylglucosamine-6-phosphate 2-epimerase 28EC 5.1.3.- 29 2F N-acetylglucosamine-6-phosphatase 28EC 3.1.3.- 29 28377 aa 29 2Cfatsta scores 3B opt: 1029 z-score: 1162.4 E 28 29: 0 2C 44.0 25 identity in 377 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02350 UDP-N-acetylglucosamine 2-epimerase identified within CDS. Further support given to product function. Product function updated based on characterisation work within Neisseria meningitidis 28PMID:15518580 29. kept within product function. This protein plays a role in sialic acid biosysthesis. Gilbert 28Michel.Gilbert@nrc-cnrc.gc.ca 29 personal communication. Identifed as part of Campylobacter jejuni lipooligosaccharide locus 28Cj1131c - Cj1152c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:15518580 2C PMID:11083778 2C PMID:11689567 2CPMID:10688204 2C PMID:11796612 NC_002163.1 RefSeq region 1076541 1077539 . + . ID=id2092;gene=neuC1;Name=id2092;Dbxref=GeneID:905433;gbkey=misc_feature;Note=HMMPfam hit to PF02350 2C UDP-N-acetylglucosamine 2-epimerase 2C score 5.7e-149 NC_002163.1 RefSeq region 1077590 1078522 . + . ID=id2093;gene=neuA1;Name=id2093;Dbxref=GeneID:905434;gbkey=misc_feature;Note=HMMPfam hit to PF06306 2CBeta-1 2C4-N-acetylgalactosaminyltransfera 2C score 6.3e-101 NC_002163.1 RefSeq CDS 1077590 1079200 . + 0 ID=cds1029;Parent=gene1094;gene=neuA1;Name=YP_002344536.1;Dbxref=GOA:Q0P9B1 InterPro:IPR003329 InterPro:IPR010446 UniProtKB FTrEMBL:Q0P9B1 Genbank:YP_002344536.1 GeneID:905434;gbkey=CDS;product=bifunctional beta-1 2C4-N-acetylgalactosaminyltransferase 2FCMP-Neu5Ac synthase;Note=Original 282000 29 note: Cj1143 2C neuA1 2C probable acylneuraminate cytidylyltransferase 28CMP-N-acetylneuraminic acid synthetase 29 2C len: 536 aa 3B N-terminus is similar to HP0217 2849.1 25 identity in 279 aa overlap 29 2C C-traminus is similar to NEUA_NEIME acylneuraminate cytidylyltransferase 28EC 2.7.7.43 29 28228 aa 29 2C fasta scores 3B opt: 471 z-score: 550.3 E 28 29: 2.3e-23 2C39.4 25 identity in 221 aa overlap 2C and to Cj1311 2831.6 25 identity in 215 aa overlap 29 and Cj1331 2834.7 25 identity in 219 aa overlap 29 7EUpdated 282006 29 note: Pfam domains PF06306 Beta-1 2C4-N-acetylgalactosaminylt transferase and PF02348 Cytidylyltransferase were identified within CDS. Further support given to product function. Product function modified to more specific family member based on recent characterisation papers. This protein converts N-acetylneuraminic acid to CMP N-acetylneuraminic acid. Identifed as part of Campylobacter jejuni lipooligosaccharide locus 28Cj1131c - Cj1152c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:15808749 2C PMID:11083778 2C PMID:16481326 2CPMID:12044670 2C PMID:10660542 2C PMID:11796612 NC_002163.1 RefSeq gene 1077590 1079200 . + . ID=gene1094;gene=neuA1;Name=neuA1;locus_tag=Cj1143;Dbxref=GeneID:905434;gbkey=Gene NC_002163.1 RefSeq region 1078544 1079194 . + . ID=id2094;gene=neuA1;Name=id2094;Dbxref=GeneID:905434;gbkey=misc_feature;Note=HMMPfam hit to PF02348 2C Cytidylyltransferase 2C score 9.4e-24 NC_002163.1 RefSeq CDS 1079195 1079743 . - 0 ID=cds1030a;Parent=gene1095;Name=YP_002344537.1;Dbxref=InterPro:IPR007577 UniProtKB FTrEMBL:Q0P9B0 Genbank:YP_002344537.1 GeneID:905436;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1144c 2C unknown 2C len: 197 aa 3B no Hp match. Contains C 288-9 29 polymorphism at aa 15 3B C 288 29 2C the consnsus gives this CDS 3B C 289 29 would cause truncation after 4 aa 2C although a Met at aa 23 would allow translation to re-initiate. C 287 29 or C 2810 29 2C although not seen in shotgun 2C would allow translation from upstream CDS Cj1145c 7EOriginal 282000 29 note: Cj1145c 2C unknown 2C len: 105 aa 3B no Hp match. Contains C 288-9 29 polymorphism at aa 99 3B C 288 29 2C the consnsus gives this CDS 3B C 289 29 would cause truncation after4 aa 3B C 287 29 or C 2810 29 2C although not seen in shotgun 2C would allow translation into downstream CDS Cj1144c 7EUpdated 282006 29 note: Coding sequences have been merged to reflect the complete amino acid sequence for this gene regardless of phase. Previous annotation gave Cj1144c and Cj1145c as seperate CDS. Merging of these CDSs has lead to loss of the downstream CDS. Functional classification - Unknown NC_002163.1 RefSeq gene 1079195 1080041 . - . ID=gene1095;Name=Cj1145c;locus_tag=Cj1145c;Dbxref=GeneID:905436;gbkey=Gene NC_002163.1 RefSeq CDS 1079745 1080041 . - 0 ID=cds1030b;Parent=gene1095;Name=YP_002344537.1;Dbxref=InterPro:IPR007577 UniProtKB FTrEMBL:Q0P9B0 Genbank:YP_002344537.1 GeneID:905436;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1144c 2C unknown 2C len: 197 aa 3B no Hp match. Contains C 288-9 29 polymorphism at aa 15 3B C 288 29 2C the consnsus gives this CDS 3B C 289 29 would cause truncation after 4 aa 2C although a Met at aa 23 would allow translation to re-initiate. C 287 29 or C 2810 29 2C although not seen in shotgun 2C would allow translation from upstream CDS Cj1145c 7EOriginal 282000 29 note: Cj1145c 2C unknown 2C len: 105 aa 3B no Hp match. Contains C 288-9 29 polymorphism at aa 99 3B C 288 29 2C the consnsus gives this CDS 3B C 289 29 would cause truncation after4 aa 3B C 287 29 or C 2810 29 2C although not seen in shotgun 2C would allow translation into downstream CDS Cj1144c 7EUpdated 282006 29 note: Coding sequences have been merged to reflect the complete amino acid sequence for this gene regardless of phase. Previous annotation gave Cj1144c and Cj1145c as seperate CDS. Merging of these CDSs has lead to loss of the downstream CDS. Functional classification - Unknown NC_002163.1 RefSeq CDS 1080025 1080849 . - 0 ID=cds1031;Parent=gene1096;gene=waaV;Name=YP_002344538.1;Dbxref=GOA:Q7BC48 InterPro:IPR001173 UniProtKB FTrEMBL:Q7BC48 Genbank:YP_002344538.1 GeneID:905437;gbkey=CDS;product=glucosyltransferase;Note=Original 282000 29 note: Cj1146c 2C waaV 2C possible glucosyltransferase 2C len: 274 aa 3B similar to e.g. TR:O87182 28EMBL:AB017355 29 Streptococcus agalactiae N-acetylglucosaminyltransferase CPSH 28333 aa 29 2C fasta scores 3B opt: 339 z-score: 402.4 E 28 29: 4.1e-15 2C 31.4 25 identity in 274 aa overlap. No Hp match. Contains Pfam match to entry PF00535 Glycos_transf_2 2C Glycosyl transferases 7EUpdated 282006 29 note: Some characterisation within Escherichia coli 2C however 2C identity score was marginal. kept within product function. Identifed as part of Campylobacter jejuni lipooligosaccharide locus 28Cj1131c - Cj1152c 29. Functional classification - Surface polysaccharides 2C lipopolysaccharides and antigens 7EPMID:9792656 NC_002163.1 RefSeq gene 1080025 1080849 . - . ID=gene1096;gene=waaV;Name=waaV;locus_tag=Cj1146c;Dbxref=GeneID:905437;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 1080042 1080162 . - . ID=utr408;locus_tag=Cj1145c;product=hypothetical protein NC_002163.1 RefSeq region 1080340 1080837 . - . ID=id2095;gene=waaV;Name=id2095;Dbxref=GeneID:905437;gbkey=misc_feature;Note=HMMPfam hit to PF00535 2C Glycosyl transferase 2C score 4.8e-39 NC_002163.1 UTR_Extractor 5'-UTR 1080850 1080879 . - . ID=utr409;locus_tag=Cj1146c;product=putative glucosyltransferase NC_002163.1 UTR_Extractor 5'-UTR 1080877 1080907 . + . ID=utr410;locus_tag=Cj1148;product=heptosyltransferase II ### NC_002163.1 RefSeq CDS 1080908 1081867 . + 0 ID=cds1032;Parent=gene1097;gene=waaF;Name=YP_002344539.1;Dbxref=GOA:Q0P9A8 InterPro:IPR002201 InterPro:IPR011910 UniProtKB FTrEMBL:Q0P9A8 Genbank:YP_002344539.1 GeneID:905438;gbkey=CDS;product=heptosyltransferase II;Note=Original 282000 29 note: Cj1148 2C waaF 2C probable ADP-heptose--LPS heptosyltransferase 2C len: 319 aa 3B similar to e.g. TR:Q51063 28EMBL:Z37141 29 Neisseria gonorrhoeae ADP-heptose:LPS heptosyltransferase II 28336 aa 29 2C fasta scores 3B opt: 384 z-score: 447.0 E 28 29: 1.3e-17 2C 29.7 25 identity in 333 aa overlap 2C and RFAF_ECOLI ADP-heptose--LPS heptosyltransferase II 28348 aa 29 2C fasta scores 3B opt: 292 z-score: 341.5 E 28 29: 1e-11 2C 24.1 25 identity in 348 aa overlap. 37.6 25 identity to HP1191. Also similar to Cj1133 2824.8 25 identity in 351 aa overlap 29. Contains Pfam match to entry PF01075 Heptosyltranf 2CHeptosyltransferase 7EUpdated 282006 29 note: Pfam domain now modified to Glycosyltransferase family 9 28heptosyltransferase 29. Characterisation work carried out within Campylobacter jejuni 2C so not added to product function. Identifed as part of Campylobacter jejuni lipooligosaccharide locus 28Cj1131c - Cj1152c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:9446588 2C PMID:11054112 2C PMID:11914340 NC_002163.1 RefSeq gene 1080908 1081867 . + . ID=gene1097;gene=waaF;Name=waaF;locus_tag=Cj1148;Dbxref=GeneID:905438;gbkey=Gene NC_002163.1 RefSeq region 1081100 1081795 . + . ID=id2096;gene=waaF;Name=id2096;Dbxref=GeneID:905438;gbkey=misc_feature;Note=HMMPfam hit to PF01075 2C Glycosyltransferase family 2Cscore 6.3e-22 NC_002163.1 RefSeq gene 1081848 1082408 . - . ID=gene1098;gene=gmhA;Name=gmhA;locus_tag=Cj1149c;Dbxref=GeneID:905439;gbkey=Gene NC_002163.1 RefSeq CDS 1081848 1082408 . - 0 ID=cds1033;Parent=gene1098;gene=gmhA;Name=YP_002344540.1;Dbxref=GOA:Q9PNE6 InterPro:IPR001347 InterPro:IPR004515 PDB:1TK9 UniProtKB FSwiss-Prot:Q9PNE6 Genbank:YP_002344540.1 GeneID:905439;gbkey=CDS;product=phosphoheptose isomerase;Note=catalyzes the isomerization of sedoheptulose 7-phosphate to D-glycero-D-manno-heptose 7-phosphate NC_002163.1 RefSeq region 1081860 1082309 . - . ID=id2097;gene=gmhA;Name=id2097;Dbxref=GeneID:905439;gbkey=misc_feature;Note=HMMPfam hit to PF01380 2C SIS domain 2C score 2.5e-19 NC_002163.1 RefSeq region 1082046 1082069 . - . ID=id2098;gene=gmhA;Name=id2098;Dbxref=GeneID:905439;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq gene 1082405 1083790 . - . ID=gene1099;gene=hldE;Name=hldE;locus_tag=Cj1150c;Dbxref=GeneID:905440;gbkey=Gene NC_002163.1 RefSeq CDS 1082405 1083790 . - 0 ID=cds1034;Parent=gene1099;gene=hldE;Name=YP_002344541.1;Dbxref=GOA:Q6TG09 HSSP:P27623 InterPro:IPR002173 InterPro:IPR004820 InterPro:IPR004821 InterPro:IPR011611 InterPro:IPR011913 InterPro:IPR011914 InterPro:IPR014729 UniProtKB FSwiss-Prot:Q6TG09 Genbank:YP_002344541.1 GeneID:905440;gbkey=CDS;product=bifunctional D-beta-D-heptose 7-phosphate kinase 2FD-beta-D-heptose 1-phosphate adenylyltransferase;Note=Original 282000 29 note: Cj1150c 2C waaE 2C possible ADP-heptose synthase 2C len: 461 aa 3B similar to TR:Q48046 28EMBL:U17642 29 Haemophilus influenzae ADP-heptose synthase 28342 aa 29 2C fasta scores 3B opt: 687 z-score: 784.6 E 28 29: 0 2C40.8 25 identity in 306 aa overlap. Similar in N-term to RBSK_BACSU ribokinase 28286 aa 29 2C fasta scores 3B opt: 204 z-score: 238.0 E 28 29: 5.9e-06 2C 28.1 25 identity in 295 aa overlap 2C and in C-term to TAGD_BACSU glycerol-3-phosphate cytidylyltransferase 28129 aa 29 2C fasta scores 3B opt: 208 z-score: 247.5 E 28 29: 1.7e-06 2C 34.9 25 identity in 129 aa overlap. 50.8 25 identity to HP0858. Contains 2x Pfam match to entry PF00294 pfkB 2C pfkB family carbohydrate kinase 7EUpdated 282006 29 note: Pfam domain PF01467 Cytidylyltransferase identified within CDS. Characterised within Escherichia coli with acceptable identity score. Product function updated to more specific family member. Gene name was formerly designated as waaE. not added to product function. Identifed as part of Campylobacter jejuni lipooligosaccharide locus 28Cj1131c -Cj1152c 29. Functional classification - Surface polysaccharides 2C lipopolysaccharides and antigens 7EPMID:10629197 2C PMID:11751812 2C PMID:16030223 2CPMID:11751812 2C PMID:12101286 NC_002163.1 RefSeq region 1082423 1082791 . - . ID=id2099;gene=hldE;Name=id2099;Dbxref=GeneID:905440;gbkey=misc_feature;Note=HMMPfam hit to PF01467 2C Cytidylyltransferase 2C score 4.7e-19 NC_002163.1 RefSeq region 1082882 1083760 . - . ID=id2100;gene=hldE;Name=id2100;Dbxref=GeneID:905440;gbkey=misc_feature;Note=HMMPfam hit to PF00294 2C pfkB family carbohydrate kinase 2C score 7.8e-26 NC_002163.1 RefSeq gene 1083783 1084736 . - . ID=gene1100;gene=hldD;Name=hldD;locus_tag=Cj1151c;Dbxref=GeneID:905441;gbkey=Gene NC_002163.1 RefSeq CDS 1083783 1084736 . - 0 ID=cds1035;Parent=gene1100;gene=hldD;Name=YP_002344542.1;Dbxref=GOA:Q0P9A5 InterPro:IPR001509 InterPro:IPR011912 InterPro:IPR016040 UniProtKB FTrEMBL:Q0P9A5 Genbank:YP_002344542.1 GeneID:905441;gbkey=CDS;product=ADP-glyceromanno-heptose 6-epimerase;Note=Original 282000 29 note: Cj1151c 2C waaD 2C probable ADP-L-glycero-D-manno-heptose-6-epimerase 2C len: 317 aa 3B similar to e.g. RFAD_ECOLI ADP-L-glycero-D-manno-heptose-6-epimerase 28EC 5.1.3.20 29 28310 aa 29 2C fasta scores 3B opt: 533 z-score: 600.5 E 28 29: 3.8e-26. 32.9 25 identity in 319 aa overlap. 48.3 25 identity to HP0859 7EUpdated 282006 29 note: Pfam domain PF01370 NAD dependent epimerase 2Fdehydratase family identified within CDS. Further support given to product function. Characterised within Escherichia coli with marginal identity score. Product function has been updated. Gene name was formerly waaD. not added to product function. Identifed as part of Campylobacter jejuni lipooligosaccharide locus 28Cj1131c - Cj1152c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:10896473 2C PMID:11751812 2C PMID:16481326 2CPMID:12101286 NC_002163.1 RefSeq region 1083804 1084730 . - . ID=id2101;gene=hldD;Name=id2101;Dbxref=GeneID:905441;gbkey=misc_feature;Note=HMMPfam hit to PF01370 2C NAD dependent epimerase 2Fdehydratase family 2C score 1.5e-14 ### NC_002163.1 UTR_Extractor 5'-UTR 1084737 1084990 . - . ID=utr411;locus_tag=Cj1151c;product=ADP-glyceromanno-heptose 6-epimerase NC_002163.1 RefSeq gene 1084737 1085297 . - . ID=gene1101;gene=gmhB;Name=gmhB;locus_tag=Cj1152c;Dbxref=GeneID:905442;gbkey=Gene NC_002163.1 RefSeq CDS 1084737 1085297 . - 0 ID=cds1036;Parent=gene1101;gene=gmhB;Name=YP_002344543.1;Dbxref=GOA:Q6TG07 InterPro:IPR004446 InterPro:IPR005834 InterPro:IPR006543 InterPro:IPR006549 UniProtKB FSwiss-Prot:Q6TG07 Genbank:YP_002344543.1 GeneID:905442;gbkey=CDS;product=D 2CD-heptose 1 2C7-bisphosphate phosphatase;Note=Original 282000 29 note: Cj1152c 2C possible phosphatase 2C len: 186 aa 3B similar to hypothetical proteins e.g. YAED_ECOLI 28191 aa 29 2C fasta scores 3B opt: 295 z-score: 372.3 E 28 29: 1.9e-13 2C 45.1 25 identity in 153 aa overlap. 46.2 25 identity to HP0860. Some similarity to N-terminal histidinol-phosphatase domain of hisB proteins e.g. HIS7_ECOLI imidazoleglycerol-phosphate dehydratase 2Fhistidinol-phosphatase 28355 aa 29 2C fasta scores 3B opt: 266 z-score: 332.8 E 28 29: 3.1e-11 2C 30.8 25 identity in 146 aa overlap 7EUpdated 282006 29 note: Pfam domain PF00702 haloacid dehalogenase-like hydrolase identified within CDS. Characterisation work carried out within Escherichia coli and Campylobacter jejuni with acceptable identity scores. GmhB is required for the formation of ADP-D-beta-D-heptose. Product function modified to more specific family member. not added to product function. Identifed as part of Campylobacter jejuni lipooligosaccharide locus 28Cj1131c - Cj1152c 29. Functional classification - Misc 7EPMID:11751812 2C PMID:12101286 ### NC_002163.1 UTR_Extractor 5'-UTR 1085349 1085378 . + . ID=utr412;locus_tag=Cj1153;product=putative periplasmic cytochrome C NC_002163.1 RefSeq CDS 1085379 1085681 . + 0 ID=cds1037;Parent=gene1102;Name=YP_002344544.1;Dbxref=GOA:Q7BPS0 InterPro:IPR003088 InterPro:IPR009056 UniProtKB FTrEMBL:Q7BPS0 Genbank:YP_002344544.1 GeneID:905443;gbkey=CDS;product=cytochrome C;Note=Original 282000 29 note: Cj1153 2C probable periplasmic cytochrome C 2C len: 100 aa 3B similar to many e.g. 553_DESVH cytochrome C-553 precursor 28103 aa 29 2C fasta scores 3B opt: 187 z-score: 243.8 E 28 29: 2.8e-06 2C 34.6 25 identity in 107 aa overlap. 31.0 25 identity to HP1227. Contains PS00190 Cytochrome c family heme-binding site signature 2C and Pfam match to entry PF00034 cytochrome_c 7EUpdated 282006 29 note: Characterisation work has been carried out in Helicobacter pylori 2C however 2C identity searches were marginal. kept in product function. Functional classification - Energy metabolism - Electron transport 7EPMID:10965034 NC_002163.1 RefSeq gene 1085379 1085681 . + . ID=gene1102;Name=Cj1153;locus_tag=Cj1153;Dbxref=GeneID:905443;gbkey=Gene NC_002163.1 RefSeq region 1085388 1085456 . + . ID=id2102;Name=id2102;Dbxref=GeneID:905443;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1153 by TMHMM2.0 at aa 4-26 NC_002163.1 RefSeq region 1085436 1085678 . + . ID=id2103;Name=id2103;Dbxref=GeneID:905443;gbkey=misc_feature;Note=HMMPfam hit to PF00034 2C Cytochrome c 2C score 5.8e-09 NC_002163.1 RefSeq region 1085463 1085480 . + . ID=id2104;Name=id2104;Dbxref=GeneID:905443;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature ### NC_002163.1 RefSeq CDS 1085704 1085910 . - 0 ID=cds1038;Parent=gene1103;Name=YP_002344545.1;Dbxref=InterPro:IPR004714 UniProtKB FTrEMBL:Q7BPR9 Genbank:YP_002344545.1 GeneID:905444;gbkey=CDS;product=cbb3-type cytochrome oxidase maturation protein;Note=Original 282000 29 note: Cj1154c 2C small hydrophobic protein 2C len: 68 aa 3B 38.7 25 identity to HP1163 7EUpdated 282006 29 note: Pfam domain PF03597 Cytochrome oxidase maturation protein cbb3-type identified within CDS. Also 2C one probable transmembrane helix predicted by TMHMM2.0. Product modified to more specific family member based on motif match. Specific characterisation has not been carried out yet 2C so kept within product function. Functional classification - Protein translation and modification NC_002163.1 RefSeq gene 1085704 1085910 . - . ID=gene1103;Name=Cj1154c;locus_tag=Cj1154c;Dbxref=GeneID:905444;gbkey=Gene NC_002163.1 RefSeq region 1085761 1085907 . - . ID=id2105;Name=id2105;Dbxref=GeneID:905444;gbkey=misc_feature;Note=HMMPfam hit to PF03597 2C Cytochrome oxidase maturation protein cbb3-t 2C score 4.7e-21 NC_002163.1 RefSeq region 1085830 1085898 . - . ID=id2106;Name=id2106;Dbxref=GeneID:905444;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1154c by TMHMM2.0 at aa 5-27 NC_002163.1 RefSeq gene 1085907 1088264 . - . ID=gene1104;Name=Cj1155c;locus_tag=Cj1155c;Dbxref=GeneID:905445;gbkey=Gene NC_002163.1 RefSeq CDS 1085907 1088264 . - 0 ID=cds1039;Parent=gene1104;Name=YP_002344546.1;Dbxref=GOA:Q0P9A1 InterPro:IPR000150 InterPro:IPR001756 InterPro:IPR001757 InterPro:IPR005834 InterPro:IPR006121 InterPro:IPR006416 InterPro:IPR008250 UniProtKB FTrEMBL:Q0P9A1 Genbank:YP_002344546.1 GeneID:905445;gbkey=CDS;product=cation-transporting ATPase;Note=Original 282000 29 note: Cj1155c 2C probable cation-transporting ATPase 2C len: 785 aa 3B similar to members of the E1-E2 ATPase family e.g. ATCU_ECOLI probable copper-transporting ATPase 28834 aa 29 2C fasta scores 3B opt: 708 z-score: 767.6 E 28 29: 0 2C 28.9 25 identity in 830 aa overlap. 36.5 25 identity to HP1503. Contains 2x Pfam match to entry PF00122 E1-E2_ATPase 7EUpdated 282006 29 note: Pfam domains PF00702 haloacid dehalogenase-like hydrolase and PF00403 Heavy-metal-associated domain were identified within CDS. Eight probable transmembrane helices predicted by TMHMM2.0. Some characterisation within Escherichia coli and others with marginal identity scores. kept within product function. Functional classification -Transport 2Fbinding proteins - Cations NC_002163.1 RefSeq region 1085922 1085975 . - . ID=id100;Name=id100;Dbxref=GeneID:905445;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1155c by TMHMM2.0 at aa 166-188 2C 198-215 2C 235-254 2C259-277 2C 410-432 2C 447-469 2C 741-760 and 764-781 NC_002163.1 RefSeq region 1085985 1086044 . - . ID=id100;Name=id100;Dbxref=GeneID:905445;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1155c by TMHMM2.0 at aa 166-188 2C 198-215 2C 235-254 2C259-277 2C 410-432 2C 447-469 2C 741-760 and 764-781 NC_002163.1 RefSeq region 1086153 1086794 . - . ID=id2107;Name=id2107;Dbxref=GeneID:905445;gbkey=misc_feature;Note=HMMPfam hit to PF00702 2C haloacid dehalogenase-like hydrolase 2C score 2.8e-17 NC_002163.1 RefSeq region 1086156 1086224 . - . ID=id2108;Name=id2108;Dbxref=GeneID:905445;gbkey=misc_feature;Note=PS01229 Hypothetical cof family signature 2 NC_002163.1 RefSeq region 1086804 1087469 . - . ID=id2109;Name=id2109;Dbxref=GeneID:905445;gbkey=misc_feature;Note=HMMPfam hit to PF00122 2C E1-E2 ATPase 2C score 1.2e-42 NC_002163.1 RefSeq region 1086858 1086926 . - . ID=id100;Name=id100;Dbxref=GeneID:905445;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1155c by TMHMM2.0 at aa 166-188 2C 198-215 2C 235-254 2C259-277 2C 410-432 2C 447-469 2C 741-760 and 764-781 NC_002163.1 RefSeq region 1086906 1086938 . - . ID=id2110;Name=id2110;Dbxref=GeneID:905445;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1086969 1087037 . - . ID=id100;Name=id100;Dbxref=GeneID:905445;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1155c by TMHMM2.0 at aa 166-188 2C 198-215 2C 235-254 2C259-277 2C 410-432 2C 447-469 2C 741-760 and 764-781 NC_002163.1 RefSeq region 1087434 1087490 . - . ID=id100;Name=id100;Dbxref=GeneID:905445;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1155c by TMHMM2.0 at aa 166-188 2C 198-215 2C 235-254 2C259-277 2C 410-432 2C 447-469 2C 741-760 and 764-781 NC_002163.1 RefSeq region 1087503 1087562 . - . ID=id100;Name=id100;Dbxref=GeneID:905445;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1155c by TMHMM2.0 at aa 166-188 2C 198-215 2C 235-254 2C259-277 2C 410-432 2C 447-469 2C 741-760 and 764-781 NC_002163.1 RefSeq region 1087620 1087673 . - . ID=id100;Name=id100;Dbxref=GeneID:905445;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1155c by TMHMM2.0 at aa 166-188 2C 198-215 2C 235-254 2C259-277 2C 410-432 2C 447-469 2C 741-760 and 764-781 NC_002163.1 RefSeq region 1087701 1087769 . - . ID=id100;Name=id100;Dbxref=GeneID:905445;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1155c by TMHMM2.0 at aa 166-188 2C 198-215 2C 235-254 2C259-277 2C 410-432 2C 447-469 2C 741-760 and 764-781 NC_002163.1 RefSeq region 1087830 1088024 . - . ID=id2111;Name=id2111;Dbxref=GeneID:905445;gbkey=misc_feature;Note=HMMPfam hit to PF00403 2C Heavy-metal-associated domain 2C score 0.031 ### NC_002163.1 UTR_Extractor 5'-UTR 1088265 1088330 . - . ID=utr413;locus_tag=Cj1155c;product=putative cation-transporting ATPase NC_002163.1 UTR_Extractor 5'-UTR 1088335 1088372 . + . ID=utr414;locus_tag=Cj1156;product=transcription termination factor Rho NC_002163.1 RefSeq CDS 1088373 1089671 . + 0 ID=cds1040;Parent=gene1105;gene=rho;Name=YP_002344547.1;Dbxref=GOA:Q0P9A0 InterPro:IPR000194 InterPro:IPR003593 InterPro:IPR004665 InterPro:IPR011112 InterPro:IPR011113 InterPro:IPR011129 UniProtKB FTrEMBL:Q0P9A0 Genbank:YP_002344547.1 GeneID:905446;gbkey=CDS;product=transcription termination factor Rho;Note=An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes NC_002163.1 RefSeq gene 1088373 1089671 . + . ID=gene1105;gene=rho;Name=rho;locus_tag=Cj1156;Dbxref=GeneID:905446;gbkey=Gene NC_002163.1 RefSeq region 1088436 1088564 . + . ID=id2112;gene=rho;Name=id2112;Dbxref=GeneID:905446;gbkey=misc_feature;Note=HMMPfam hit to PF07498 2C Rho termination factor 2CN-terminal domai 2C score 4.9e-18 NC_002163.1 RefSeq region 1088568 1088801 . + . ID=id2113;gene=rho;Name=id2113;Dbxref=GeneID:905446;gbkey=misc_feature;Note=HMMPfam hit to PF07497 2C Rho termination factor 2CRNA-binding doma 2C score 2.5e-47 NC_002163.1 RefSeq region 1088883 1089509 . + . ID=id2114;gene=rho;Name=id2114;Dbxref=GeneID:905446;gbkey=misc_feature;Note=HMMPfam hit to PF00006 2C ATP synthase alpha 2Fbeta family 2C nucleoti 2C score 4.3e-68 NC_002163.1 RefSeq region 1088946 1088969 . + . ID=id2115;gene=rho;Name=id2115;Dbxref=GeneID:905446;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 RefSeq CDS 1089675 1091204 . + 0 ID=cds1041;Parent=gene1106;gene=dnaX;Name=YP_002344548.1;Dbxref=GOA:Q0P999 InterPro:IPR003593 InterPro:IPR003959 InterPro:IPR012763 UniProtKB FTrEMBL:Q0P999 Genbank:YP_002344548.1 GeneID:905447;gbkey=CDS;product=DNA polymerase III subunits gamma and tau;Note=catalyzes the DNA-template-directed extension of the 3 27-end of a DNA strand 3B the tau chain serves as a scaffold to help in the dimerizaton of the alpha 2Cepsilon and theta core complex 3B the gamma chain seems to interact with the delta and delta 27 subunits to transfer the beta subunit on the DNA NC_002163.1 RefSeq gene 1089675 1091204 . + . ID=gene1106;gene=dnaX;Name=dnaX;locus_tag=Cj1157;Dbxref=GeneID:905447;gbkey=Gene NC_002163.1 RefSeq region 1089789 1090361 . + . ID=id2116;gene=dnaX;Name=id2116;Dbxref=GeneID:905447;gbkey=misc_feature;Note=HMMPfam hit to PF00004 2C ATPase family associated with various cellul 2C score 3.1e-07 NC_002163.1 RefSeq region 1089804 1089827 . + . ID=id2117;gene=dnaX;Name=id2117;Dbxref=GeneID:905447;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 1091201 1091428 . - 0 ID=cds1042;Parent=gene1107;Name=YP_002344549.1;Dbxref=UniProtKB FTrEMBL:Q0P998 Genbank:YP_002344549.1 GeneID:905448;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1158c 2C small hydrophobic protein 2C len: 75 aa 3B no Hp match 7EUpdated 282006 29 note: Two probable transmembrane helices predicted by TMHMM2.0. Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 RefSeq gene 1091201 1091428 . - . ID=gene1107;Name=Cj1158c;locus_tag=Cj1158c;Dbxref=GeneID:905448;gbkey=Gene NC_002163.1 RefSeq region 1091216 1091272 . - . ID=id101;Name=id101;Dbxref=GeneID:905448;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1158c by TMHMM2.0 at aa 21-43 and 53-71 NC_002163.1 RefSeq region 1091300 1091368 . - . ID=id101;Name=id101;Dbxref=GeneID:905448;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1158c by TMHMM2.0 at aa 21-43 and 53-71 NC_002163.1 RefSeq gene 1091407 1091529 . - . ID=gene1108;Name=Cj1159c;locus_tag=Cj1159c;Dbxref=GeneID:905449;gbkey=Gene NC_002163.1 RefSeq CDS 1091407 1091529 . - 0 ID=cds1043;Parent=gene1108;Name=YP_002344550.1;Dbxref=UniProtKB FTrEMBL:Q0P997 Genbank:YP_002344550.1 GeneID:905449;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1159c 2C small hydrophobic protein 2C len: 40 aa 3B no Hp match 7EUpdated 282006 29 note: One probable transmembrane helices predicted by TMHMM2.0. Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 RefSeq region 1091446 1091511 . - . ID=id2118;Name=id2118;Dbxref=GeneID:905449;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1159c by TMHMM2.0 at aa 7-28 ### NC_002163.1 RefSeq gene 1091544 1091723 . - . ID=gene1109;Name=Cj1160c;locus_tag=Cj1160c;Dbxref=GeneID:905450;gbkey=Gene NC_002163.1 RefSeq CDS 1091544 1091723 . - 0 ID=cds1044;Parent=gene1109;Name=YP_002344551.1;Dbxref=UniProtKB FTrEMBL:Q0P996 Genbank:YP_002344551.1 GeneID:905450;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1160c 2C small hydrophobic protein 2C len: 59 aa 3B no Hp match 7EUpdated 282006 29 note: One probable transmembrane helix predicted for TMHMM2.0. Also 2C one signal peptide predicted by SignalP 2.0 HMM. Product function modified to more specific family member. kept within product function. Functional classification - Membranes 2Clipoproteins and porins NC_002163.1 RefSeq region 1091619 1091687 . - . ID=id2119;Name=id2119;Dbxref=GeneID:905450;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1160c by TMHMM2.0 at aa 13-35 ### NC_002163.1 UTR_Extractor 5'-UTR 1091724 1091751 . - . ID=utr415;locus_tag=Cj1160c;product=hypothetical protein NC_002163.1 RefSeq CDS 1091795 1093894 . - 0 ID=cds1045;Parent=gene1110;Name=YP_002344552.1;Dbxref=GOA:Q0P995 InterPro:IPR001756 InterPro:IPR001757 InterPro:IPR005834 InterPro:IPR006121 InterPro:IPR006403 InterPro:IPR006416 InterPro:IPR008250 UniProtKB FTrEMBL:Q0P995 Genbank:YP_002344552.1 GeneID:905451;gbkey=CDS;product=cation-transporting ATPase;Note=Original 282000 29 note: Cj1161c 2C probable cation-transporting ATPase 2C len: 699 aa 3B similar to members of the E1-E2 ATPase family e.g. COPA_HELFE copper-transporting ATPase 28732 aa 29 2C fasta scores 3B opt: 1106 z-score: 1124.4 E 28 29: 0 2C 32.8 25 identity in 729 aa overlap. 33.2 25 identity to HP1072. Contains Pfam match to entry PF00403 HMA 2C Heavy-metal-associated domain containing proteins 2C 2x Pfam match to entry PF00122 E1-E2_ATPase 2C and PS00154 E1-E2 ATPases phosphorylation site 7EUpdated 282006 29 note: Characterisation in more than one bacteria with marginal identity scores. kept within product function. Functional classification -Transport 2Fbinding proteins - Cations 7EPMID:9440521 NC_002163.1 RefSeq gene 1091795 1093894 . - . ID=gene1110;Name=Cj1161c;locus_tag=Cj1161c;Dbxref=GeneID:905451;gbkey=Gene NC_002163.1 RefSeq region 1091813 1091866 . - . ID=id102;Name=id102;Dbxref=GeneID:905451;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1161c by TMHMM2.0 at aa 88-105 2C 115-137 2C 144-166 2C171-190 2C 328-345 2C 360-382 2C 650-672 and 677-694 NC_002163.1 RefSeq region 1091879 1091947 . - . ID=id102;Name=id102;Dbxref=GeneID:905451;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1161c by TMHMM2.0 at aa 88-105 2C 115-137 2C 144-166 2C171-190 2C 328-345 2C 360-382 2C 650-672 and 677-694 NC_002163.1 RefSeq region 1092056 1092688 . - . ID=id2120;Name=id2120;Dbxref=GeneID:905451;gbkey=misc_feature;Note=HMMPfam hit to PF00702 2C haloacid dehalogenase-like hydrolase 2C score 2.3e-14 NC_002163.1 RefSeq region 1092650 1092670 . - . ID=id2121;Name=id2121;Dbxref=GeneID:905451;gbkey=misc_feature;Note=PS00154 E1-E2 ATPases phosphorylation site NC_002163.1 RefSeq region 1092698 1093360 . - . ID=id2122;Name=id2122;Dbxref=GeneID:905451;gbkey=misc_feature;Note=HMMPfam hit to PF00122 2C E1-E2 ATPase 2C score 1.5e-61 NC_002163.1 RefSeq region 1092749 1092817 . - . ID=id102;Name=id102;Dbxref=GeneID:905451;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1161c by TMHMM2.0 at aa 88-105 2C 115-137 2C 144-166 2C171-190 2C 328-345 2C 360-382 2C 650-672 and 677-694 NC_002163.1 RefSeq region 1092800 1092832 . - . ID=id2123;Name=id2123;Dbxref=GeneID:905451;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1092860 1092913 . - . ID=id102;Name=id102;Dbxref=GeneID:905451;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1161c by TMHMM2.0 at aa 88-105 2C 115-137 2C 144-166 2C171-190 2C 328-345 2C 360-382 2C 650-672 and 677-694 NC_002163.1 RefSeq region 1093325 1093384 . - . ID=id102;Name=id102;Dbxref=GeneID:905451;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1161c by TMHMM2.0 at aa 88-105 2C 115-137 2C 144-166 2C171-190 2C 328-345 2C 360-382 2C 650-672 and 677-694 NC_002163.1 RefSeq region 1093397 1093465 . - . ID=id102;Name=id102;Dbxref=GeneID:905451;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1161c by TMHMM2.0 at aa 88-105 2C 115-137 2C 144-166 2C171-190 2C 328-345 2C 360-382 2C 650-672 and 677-694 NC_002163.1 RefSeq region 1093484 1093552 . - . ID=id102;Name=id102;Dbxref=GeneID:905451;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1161c by TMHMM2.0 at aa 88-105 2C 115-137 2C 144-166 2C171-190 2C 328-345 2C 360-382 2C 650-672 and 677-694 NC_002163.1 RefSeq region 1093580 1093633 . - . ID=id102;Name=id102;Dbxref=GeneID:905451;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1161c by TMHMM2.0 at aa 88-105 2C 115-137 2C 144-166 2C171-190 2C 328-345 2C 360-382 2C 650-672 and 677-694 NC_002163.1 RefSeq region 1093691 1093882 . - . ID=id2124;Name=id2124;Dbxref=GeneID:905451;gbkey=misc_feature;Note=HMMPfam hit to PF00403 2C Heavy-metal-associated domain 2C score 0.00017 NC_002163.1 RefSeq gene 1093894 1094088 . - . ID=gene1111;Name=Cj1162c;locus_tag=Cj1162c;Dbxref=GeneID:905452;gbkey=Gene NC_002163.1 RefSeq CDS 1093894 1094088 . - 0 ID=cds1046;Parent=gene1111;Name=YP_002344553.1;Dbxref=GOA:Q0P994 InterPro:IPR006121 UniProtKB FTrEMBL:Q0P994 Genbank:YP_002344553.1 GeneID:905452;gbkey=CDS;product=heavy-metal-associated domain-containing protein;Note=Original 282000 29 note: Cj1162c 2C unknown 2C len: 64 aa 3B no Hp match 7EUpdated 282006 29 note: Prosite domain PS50846 HMA_2 2CHeavy metal transport 2Fdetoxification protein within CDS. Product modified to more specific family member based on motif match. No specific characterisation carried out yet 2Cso kept within product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq CDS 1094078 1095028 . - 0 ID=cds1047;Parent=gene1112;Name=YP_002344554.1;Dbxref=GOA:Q0P993 InterPro:IPR002524 UniProtKB FTrEMBL:Q0P993 Genbank:YP_002344554.1 GeneID:905453;gbkey=CDS;product=cation transport protein;Note=Original 282000 29 note: Cj1163c 2C possible cation transport protein 2C len: 316 aa 3B similar to e.g. CZCD_ALCEU cobalt-zinc-cadmium resistance protein CZCD 28316 aa 29 2Cfasta scores 3B opt: 609 z-score: 699.8 E 28 29: 1.1e-31 2C 36.2 25 identity in 287 aa overlap. No Hp match. Contains His-rich regin at N-terminus. Also similar to Cj0948c 2825.7 25 identity in 280 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01545 Cation efflux family domain identified within CDS. Also 2C six probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterisation has been carried out in more than one bacteria with marginal identity scores. kept within product function. Functional classification -Transport 2Fbinding proteins - Cations 7EPMID:9044283 NC_002163.1 RefSeq gene 1094078 1095028 . - . ID=gene1112;Name=Cj1163c;locus_tag=Cj1163c;Dbxref=GeneID:905453;gbkey=Gene NC_002163.1 RefSeq region 1094081 1094908 . - . ID=id2125;Name=id2125;Dbxref=GeneID:905453;gbkey=misc_feature;Note=HMMPfam hit to PF01545 2C Cation efflux family 2C score 1.3e-97 NC_002163.1 RefSeq region 1094357 1094425 . - . ID=id103;Name=id103;Dbxref=GeneID:905453;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1163c by TMHMM2.0 at aa 40-62 2C 72-91 2C 104-126 2C 141-163 2C176-198 and 202-224 NC_002163.1 RefSeq region 1094435 1094503 . - . ID=id103;Name=id103;Dbxref=GeneID:905453;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1163c by TMHMM2.0 at aa 40-62 2C 72-91 2C 104-126 2C 141-163 2C176-198 and 202-224 NC_002163.1 RefSeq region 1094540 1094608 . - . ID=id103;Name=id103;Dbxref=GeneID:905453;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1163c by TMHMM2.0 at aa 40-62 2C 72-91 2C 104-126 2C 141-163 2C176-198 and 202-224 NC_002163.1 RefSeq region 1094651 1094719 . - . ID=id103;Name=id103;Dbxref=GeneID:905453;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1163c by TMHMM2.0 at aa 40-62 2C 72-91 2C 104-126 2C 141-163 2C176-198 and 202-224 NC_002163.1 RefSeq region 1094756 1094815 . - . ID=id103;Name=id103;Dbxref=GeneID:905453;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1163c by TMHMM2.0 at aa 40-62 2C 72-91 2C 104-126 2C 141-163 2C176-198 and 202-224 NC_002163.1 RefSeq region 1094843 1094911 . - . ID=id103;Name=id103;Dbxref=GeneID:905453;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1163c by TMHMM2.0 at aa 40-62 2C 72-91 2C 104-126 2C 141-163 2C176-198 and 202-224 ### NC_002163.1 RefSeq stem_loop 1095030 1095081 . + . ID=id2126;Name=id2126;gbkey=stem_loop NC_002163.1 RefSeq gene 1095104 1095367 . - . ID=gene1113;Name=Cj1164c;locus_tag=Cj1164c;Dbxref=GeneID:905454;gbkey=Gene NC_002163.1 RefSeq CDS 1095104 1095367 . - 0 ID=cds1048;Parent=gene1113;Name=YP_002344555.1;Dbxref=GOA:Q0P992 UniProtKB FTrEMBL:Q0P992 Genbank:YP_002344555.1 GeneID:905454;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1164c 2C unknown 2C len: 87 aa 3B no Hp match. Contains two Cys pairs 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 UTR_Extractor 5'-UTR 1095368 1095393 . - . ID=utr416;locus_tag=Cj1164c;product=hypothetical protein NC_002163.1 RefSeq CDS 1095437 1095931 . - 0 ID=cds1049;Parent=gene1114;Name=YP_002344556.1;Dbxref=UniProtKB FTrEMBL:Q0P991 Genbank:YP_002344556.1 GeneID:905455;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj1165c 2C probable integral membrane protein 2C len: 164 aa 3B some similarity to hypothetical proteins e.g. YJJB_ECOLI 28128 aa 29 2C fasta scores 3B opt: 171 z-score: 229.8 E 28 29: 1.7e-05 2C 29.2 25 identity in 106 aa overlap. No Hp match. Contains one Cys pair 7EUpdated 282006 29 note: Five probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 1095437 1095931 . - . ID=gene1114;Name=Cj1165c;locus_tag=Cj1165c;Dbxref=GeneID:905455;gbkey=Gene NC_002163.1 RefSeq region 1095479 1095547 . - . ID=id104;Name=id104;Dbxref=GeneID:905455;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1165c by TMHMM2.0 at aa 4-23 2C 30-48 2C 53-75 2C 87-109 and 129-151 NC_002163.1 RefSeq region 1095605 1095673 . - . ID=id104;Name=id104;Dbxref=GeneID:905455;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1165c by TMHMM2.0 at aa 4-23 2C 30-48 2C 53-75 2C 87-109 and 129-151 NC_002163.1 RefSeq region 1095707 1095775 . - . ID=id104;Name=id104;Dbxref=GeneID:905455;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1165c by TMHMM2.0 at aa 4-23 2C 30-48 2C 53-75 2C 87-109 and 129-151 NC_002163.1 RefSeq region 1095788 1095844 . - . ID=id104;Name=id104;Dbxref=GeneID:905455;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1165c by TMHMM2.0 at aa 4-23 2C 30-48 2C 53-75 2C 87-109 and 129-151 NC_002163.1 RefSeq region 1095863 1095895 . - . ID=id2127;Name=id2127;Dbxref=GeneID:905455;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1095863 1095922 . - . ID=id104;Name=id104;Dbxref=GeneID:905455;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1165c by TMHMM2.0 at aa 4-23 2C 30-48 2C 53-75 2C 87-109 and 129-151 NC_002163.1 RefSeq CDS 1095928 1096704 . - 0 ID=cds1050;Parent=gene1115;Name=YP_002344557.1;Dbxref=InterPro:IPR010619 UniProtKB FTrEMBL:Q0P990 Genbank:YP_002344557.1 GeneID:905456;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj1166c 2C probable integral membrane protein 2C len: 258 aa 3B some similarity to hypothetical proteins e.g. YJJP_ECOLI 28277 aa 29 2C fasta scores 3B opt: 292 z-score: 367.7 E 28 29: 3.5e-13 2C 25.8 25 identity in 236 aa overlap. No Hp match. Contains one Cys pair 7EUpdated 282006 29 note: Pfam domain PF06738 Protein of unknown function 28DUF1212 29 identified within CDS. Five probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 1095928 1096704 . - . ID=gene1115;Name=Cj1166c;locus_tag=Cj1166c;Dbxref=GeneID:905456;gbkey=Gene NC_002163.1 RefSeq region 1095952 1096020 . - . ID=id105;Name=id105;Dbxref=GeneID:905456;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1166c by TMHMM2.0 at aa 120-139 2C 144-161 2C 168-187 2C197-216 and 229-251 NC_002163.1 RefSeq region 1096057 1096116 . - . ID=id105;Name=id105;Dbxref=GeneID:905456;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1166c by TMHMM2.0 at aa 120-139 2C 144-161 2C 168-187 2C197-216 and 229-251 NC_002163.1 RefSeq region 1096078 1096659 . - . ID=id2128;Name=id2128;Dbxref=GeneID:905456;gbkey=misc_feature;Note=HMMPfam hit to PF06738 2C Protein of unknown function 28DUF1212 29 2C score 9.3e-61 NC_002163.1 RefSeq region 1096144 1096203 . - . ID=id105;Name=id105;Dbxref=GeneID:905456;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1166c by TMHMM2.0 at aa 120-139 2C 144-161 2C 168-187 2C197-216 and 229-251 NC_002163.1 RefSeq region 1096222 1096275 . - . ID=id105;Name=id105;Dbxref=GeneID:905456;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1166c by TMHMM2.0 at aa 120-139 2C 144-161 2C 168-187 2C197-216 and 229-251 NC_002163.1 RefSeq region 1096288 1096347 . - . ID=id105;Name=id105;Dbxref=GeneID:905456;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1166c by TMHMM2.0 at aa 120-139 2C 144-161 2C 168-187 2C197-216 and 229-251 ### NC_002163.1 RefSeq CDS 1096771 1097697 . + 0 ID=cds1051;Parent=gene1116;gene=ldh;Name=YP_002344558.1;Dbxref=GOA:Q0P989 InterPro:IPR001236 InterPro:IPR001557 InterPro:IPR011304 InterPro:IPR015955 InterPro:IPR016040 UniProtKB FTrEMBL:Q0P989 Genbank:YP_002344558.1 GeneID:905457;gbkey=CDS;product=L-lactate dehydrogenase;Note=Original 282000 29 note: Cj1167 2C ldh 2C probable L-lactate dehydrogenase 2C len: LDH_LACLA L-lactate dehydrogenase 28EC 1.1.1.27 29 28324 aa 29 2C fasta scores 3B opt: 579 z-score: 683.7 E 28 29: 8.8e-31 2C 33.7 25 identity in 306 aa overlap. No Hp match. Also similar to Cj0532 mdh 2825.4 25 identity in 311 aa overlap 29. Contains 7EUpdated 282006 29 note: Pfam domains PF00056 lactate 2Fmalate dehydrogenase 2C NAD binding domain and PF02866 lactate 2Fmalate dehydrogenase 2C alpha 2Fbeta C-terminal were identified within CDS. Also 2C Prosite PS00064 L_LDH 2C L-lactate dehydrogenase active site was identified within CDS. Further support given to product function. Characterisation work has been carried out in Lactococcus lactis with marginal identity score. Appropriate motifs present. removed from product function. Functional classification - Energy metabolism -Respiration - Aerobic 7EPMID:8081494 2C PMID:15644899 NC_002163.1 RefSeq gene 1096771 1097697 . + . ID=gene1116;gene=ldh;Name=ldh;locus_tag=Cj1167;Dbxref=GeneID:905457;gbkey=Gene NC_002163.1 RefSeq region 1096774 1097202 . + . ID=id2129;gene=ldh;Name=id2129;Dbxref=GeneID:905457;gbkey=misc_feature;Note=HMMPfam hit to PF00056 2C lactate 2Fmalate dehydrogenase 2C NAD binding do 2C score 2.2e-21 NC_002163.1 RefSeq region 1097206 1097694 . + . ID=id2130;gene=ldh;Name=id2130;Dbxref=GeneID:905457;gbkey=misc_feature;Note=HMMPfam hit to PF02866 2C lactate 2Fmalate dehydrogenase 2C alpha 2Fbeta C-t 2C score 7.5e-40 NC_002163.1 RefSeq region 1097287 1097307 . + . ID=id2131;gene=ldh;Name=id2131;Dbxref=GeneID:905457;gbkey=misc_feature;Note=PS00064 L-lactate dehydrogenase active site NC_002163.1 RefSeq gene 1097694 1098296 . - . ID=gene1117;Name=Cj1168c;locus_tag=Cj1168c;Dbxref=GeneID:905458;gbkey=Gene NC_002163.1 RefSeq CDS 1097694 1098296 . - 0 ID=cds1052;Parent=gene1117;Name=YP_002344559.1;Dbxref=GOA:Q0P988 InterPro:IPR015414 UniProtKB FTrEMBL:Q0P988 Genbank:YP_002344559.1 GeneID:905458;gbkey=CDS;product=integral membrane protein;Note=Updated 282006 29 note: Four probable transmembrane helices predicted by TMHMM2.0 7EOriginal 282000 29 note: Cj1168c 2C probable integral membrane protein 28dedA homolog 29 2C len: 200 aa 3B similar to many members of the dedA family e.g. APL_LACLA alkaline phosphatase like protein 28242 aa 29 2C fasta scores 3B opt: 424 z-score: 531.1 E 28 29: 2.8e-22 2C 37.5 25 identity in 208 aa overlap 2C and DEDA_ECOLI DEDA protein 28219 aa 29 2C fasta scores 3B opt: 240 z-score: 306.1 E 28 29: 9.5e-10 2C 24.7 25 identity in 190 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00597 DedA. Also similar to Cj1210 2824.5 25 identity in 200 aa overlap 29. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 1097718 1097786 . - . ID=id106;Name=id106;Dbxref=GeneID:905458;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1168c by TMHMM2.0 at aa 13-35 2C 55-77 2C 139-161 and 171-193 NC_002163.1 RefSeq region 1097766 1098242 . - . ID=id2132;Name=id2132;Dbxref=GeneID:905458;gbkey=misc_feature;Note=HMMPfam hit to PF00597 2C DedA family 2C score 7.9e-14 NC_002163.1 RefSeq region 1097814 1097882 . - . ID=id106;Name=id106;Dbxref=GeneID:905458;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1168c by TMHMM2.0 at aa 13-35 2C 55-77 2C 139-161 and 171-193 NC_002163.1 RefSeq region 1098045 1098092 . - . ID=id2133;Name=id2133;Dbxref=GeneID:905458;gbkey=misc_feature;Note=PS00225 Crystallins beta and gamma 27Greek key 27 motif signature NC_002163.1 RefSeq region 1098066 1098134 . - . ID=id106;Name=id106;Dbxref=GeneID:905458;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1168c by TMHMM2.0 at aa 13-35 2C 55-77 2C 139-161 and 171-193 NC_002163.1 RefSeq region 1098192 1098260 . - . ID=id106;Name=id106;Dbxref=GeneID:905458;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1168c by TMHMM2.0 at aa 13-35 2C 55-77 2C 139-161 and 171-193 ### NC_002163.1 UTR_Extractor 5'-UTR 1098297 1098322 . - . ID=utr417;locus_tag=Cj1168c;product=putative integral membrane protein NC_002163.1 RefSeq gene 1098377 1098604 . - . ID=gene1118;Name=Cj1169c;locus_tag=Cj1169c;Dbxref=GeneID:905459;gbkey=Gene NC_002163.1 RefSeq CDS 1098377 1098604 . - 0 ID=cds1053;Parent=gene1118;Name=YP_002344560.1;Dbxref=UniProtKB FTrEMBL:Q0P987 Genbank:YP_002344560.1 GeneID:905459;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1169c 2C probable periplasmic protein 2C len: 75 aa 3B no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 UTR_Extractor 5'-UTR 1098605 1098619 . - . ID=utr418;locus_tag=Cj1169c;product=putative periplasmic protein NC_002163.1 RefSeq gene 1098615 1100036 . - . ID=gene1119;gene=omp50;Name=omp50;locus_tag=Cj1170c;Dbxref=GeneID:905460;gbkey=Gene NC_002163.1 RefSeq CDS 1098615 1100036 . - 0 ID=cds1054;Parent=gene1119;gene=omp50;Name=YP_002344561.1;Dbxref=UniProtKB FTrEMBL:Q0P986 Genbank:YP_002344561.1 GeneID:905460;gbkey=CDS;product=outer membrane protein;Note=Original 282000 29 note: Cj1170c 2C omp50 2C outer membrane protein 2C len: 473 aa 3B no Hp match. Contains N-terminal signal sequence and coiled-coil region between aa 60-90. Identification as an outer membrane protein by M-J. Bolla 28Jean-Michel.Bolla@medicine.univ-mrs.fr 29 personal communication 7EUpdated 282006 29 note: Further characterisation with attached papers give more information on protein naming. Functional classification - Membranes 2C lipoproteins and porins 7EPMID:11104668 2C PMID:15131219 ### NC_002163.1 UTR_Extractor 5'-UTR 1100037 1100081 . - . ID=utr419;locus_tag=Cj1170c;product=50 kda outer membrane protein precursor NC_002163.1 RefSeq CDS 1100192 1100674 . - 0 ID=cds1055;Parent=gene1120;gene=ppi;Name=YP_002344562.1;Dbxref=GOA:Q0P985 InterPro:IPR002130 UniProtKB FTrEMBL:Q0P985 Genbank:YP_002344562.1 GeneID:905461;gbkey=CDS;product=peptidyl-prolyl cis-trans isomerase;Note=Original 282000 29 note: Cj1171c 2C ppi 2C probable peptidyl-prolyl cis-trans isomerase 2C len: 480 aa 3B similar to many e.g. YPB_BACSU peptidyl-prolyl cis-trans isomerase B 28EC 5.2.1.8 29 28143 aa 29 2C fasta scores 3B opt: 537 z-score: 643.2 E 28 29: 1.6e-28 2C 56.2 25 identity in 137 aa overlap. 55.3 25 identity to HP1441. Contains PS00170 Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature 2C and Pfam match to entry PF00160 pro_isomerase 2CPeptidyl-prolyl cis-trans isomerases 7EUpdated 282006 29 note: Characterised in Bacillus subtilis with acceptable identity score 2C so not added to product function. Functional classification -Protein translation and modification 7EPMID:8022278 NC_002163.1 RefSeq gene 1100192 1100674 . - . ID=gene1120;gene=ppi;Name=ppi;locus_tag=Cj1171c;Dbxref=GeneID:905461;gbkey=Gene NC_002163.1 RefSeq region 1100195 1100632 . - . ID=id2134;gene=ppi;Name=id2134;Dbxref=GeneID:905461;gbkey=misc_feature;Note=HMMPfam hit to PF00160 2C Cyclophilin type peptidyl-prolyl cis-tr 2C score 7.2e-55 NC_002163.1 RefSeq region 1100474 1100527 . - . ID=id2135;gene=ppi;Name=id2135;Dbxref=GeneID:905461;gbkey=misc_feature;Note=PS00170 Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature ### NC_002163.1 RefSeq gene 1100684 1101391 . - . ID=gene1121;Name=Cj1172c;locus_tag=Cj1172c;Dbxref=GeneID:905462;gbkey=Gene NC_002163.1 RefSeq CDS 1100684 1101391 . - 0 ID=cds1056;Parent=gene1121;Name=YP_002344563.1;Dbxref=GOA:Q9PNC3 HSSP:P24237 InterPro:IPR002876 InterPro:IPR017856 UniProtKB FSwiss-Prot:Q9PNC3 Genbank:YP_002344563.1 GeneID:905462;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1172c 2C unknown 2C len: 235 aa 3B similar to hypothetical proteins e.g. YEBC_ECOLI 28246 aa 29 2C fasta scores 3B opt: 508 z-score: 579.3 E 28 29: 5.7e-25 2C37.1 25 identity in 229 aa overlap. 58.1 25 identity to HP0162 7EUpdated 282006 29 note: Pfam domain PF01709 Domain of unknown function DUF28 identified within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq region 1100687 1101385 . - . ID=id2136;Name=id2136;Dbxref=GeneID:905462;gbkey=misc_feature;Note=HMMPfam hit to PF01709 2C Domain of unknown function DUF28 2C score 2.1e-118 ### NC_002163.1 UTR_Extractor 5'-UTR 1101392 1101422 . - . ID=utr420;locus_tag=Cj1172c;product=hypothetical protein NC_002163.1 RefSeq CDS 1101500 1101841 . + 0 ID=cds1057;Parent=gene1122;Name=YP_002344564.1;Dbxref=GOA:Q0P983 InterPro:IPR000390 UniProtKB FTrEMBL:Q0P983 Genbank:YP_002344564.1 GeneID:905463;gbkey=CDS;product=multidrug resistance protein;Note=Original 282000 29 note: Cj1173 2C possible efflux protein 2C len: 113 aa 3B similar to many e.g. EBR_STAAU ethidium bromide resistance protein 28107 aa 29 2C fasta scores 3B opt: 232 z-score: 309.2 E 28 29: 6.3e-10 2C 38.0 25 identity in 100 aa overlap. No Hp match. Contains Pfam match to entry PF00893 DUF7 2C Integral membrane protein. Also similar to Cj0310c 2827.1 25 identity in 107 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF00893 Small Multidrug Resistance protein identified within CDS. Also 2Cfour probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Some characterisation in Escherichia coli with acceptable identity score. kept within product function. Additional paper 28PMID:16048946 29 giving further information within Campylobacter spp. Functional classification - Drug 2Fanalogue sensitivity 7EPMID:11566977 2C PMID:15919996 2C PMID:16048946 NC_002163.1 RefSeq gene 1101500 1101841 . + . ID=gene1122;Name=Cj1173;locus_tag=Cj1173;Dbxref=GeneID:905463;gbkey=Gene NC_002163.1 RefSeq region 1101518 1101586 . + . ID=id2137;Name=id2137;Dbxref=GeneID:905463;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1173 by TMHMM2.0 at aa 7-29 2C 34-53 2C 62-84 and 89-111 NC_002163.1 RefSeq region 1101527 1101796 . + . ID=id2138;Name=id2138;Dbxref=GeneID:905463;gbkey=misc_feature;Note=HMMPfam hit to PF00893 2C Small Multidrug Resistance protein 2C score 8.6e-17 NC_002163.1 RefSeq region 1101599 1101658 . + . ID=id2137;Name=id2137;Dbxref=GeneID:905463;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1173 by TMHMM2.0 at aa 7-29 2C 34-53 2C 62-84 and 89-111 NC_002163.1 RefSeq region 1101683 1101751 . + . ID=id2137;Name=id2137;Dbxref=GeneID:905463;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1173 by TMHMM2.0 at aa 7-29 2C 34-53 2C 62-84 and 89-111 NC_002163.1 RefSeq region 1101764 1101832 . + . ID=id2137;Name=id2137;Dbxref=GeneID:905463;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1173 by TMHMM2.0 at aa 7-29 2C 34-53 2C 62-84 and 89-111 NC_002163.1 RefSeq region 1101841 1102119 . + . ID=id2139;Name=id2139;Dbxref=GeneID:905464;gbkey=misc_feature;Note=HMMPfam hit to PF00893 2C Small Multidrug Resistance protein 2C score 1.5e-21 NC_002163.1 RefSeq gene 1101841 1102149 . + . ID=gene1123;Name=Cj1174;locus_tag=Cj1174;Dbxref=GeneID:905464;gbkey=Gene NC_002163.1 RefSeq CDS 1101841 1102149 . + 0 ID=cds1058;Parent=gene1123;Name=YP_002344565.1;Dbxref=GOA:Q0P982 InterPro:IPR000390 UniProtKB FTrEMBL:Q0P982 Genbank:YP_002344565.1 GeneID:905464;gbkey=CDS;product=multidrug resistance protein;Note=Original 282000 29 note: Cj1174 2C possible efflux protein 2C len: 102 aa 3B similar to many e.g. EBR_STAAU ethidium bromide resistance protein 28107 aa 29 2C fasta scores 3B opt: 228 z-score: 302.9 E 28 29: 1.4e-09 2C 33.0 25 identity in 100 aa overlap. No Hp match. Contains Pfam match to entry PF00893 DUF7 2C Integral membrane protein. Also similar to Cj0309c 2828.7 25 identity in 94 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF00893 Small Multidrug Resistance protein identified within CDS. Also 2Cfour probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Some characterisation in Escherichia coli with acceptable identity score. kept within product function. Additional paper 28PMID:16048946 29 giving further information within Campylobacter spp. Functional classification - Drug 2Fanalogue sensitivity 7EPMID:11566977 2C PMID:15919996 2C PMID:16048946 NC_002163.1 RefSeq region 1101844 1101900 . + . ID=id2140;Name=id2140;Dbxref=GeneID:905464;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1174 by TMHMM2.0 at aa 2-20 2C 30-48 2C 55-77 and 82-101 NC_002163.1 RefSeq region 1101928 1101984 . + . ID=id2140;Name=id2140;Dbxref=GeneID:905464;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1174 by TMHMM2.0 at aa 2-20 2C 30-48 2C 55-77 and 82-101 NC_002163.1 RefSeq region 1102003 1102071 . + . ID=id2140;Name=id2140;Dbxref=GeneID:905464;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1174 by TMHMM2.0 at aa 2-20 2C 30-48 2C 55-77 and 82-101 NC_002163.1 RefSeq region 1102084 1102143 . + . ID=id2140;Name=id2140;Dbxref=GeneID:905464;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1174 by TMHMM2.0 at aa 2-20 2C 30-48 2C 55-77 and 82-101 ### NC_002163.1 RefSeq CDS 1102167 1103759 . - 0 ID=cds1059;Parent=gene1124;gene=argS;Name=YP_002344566.1;Dbxref=GOA:Q9PNC0 InterPro:IPR001278 InterPro:IPR001412 InterPro:IPR005148 InterPro:IPR008909 InterPro:IPR014729 InterPro:IPR015945 UniProtKB FSwiss-Prot:Q9PNC0 Genbank:YP_002344566.1 GeneID:905465;gbkey=CDS;product=arginyl-tRNA synthetase;Note=catalyzes a two-step reaction 2C first charging an arginine molecule by linking its carboxyl group to the alpha-phosphate of ATP 2C followed by transfer of the aminoacyl-adenylate to its tRNA 3B class-I aminoacyl-tRNA synthetase NC_002163.1 RefSeq gene 1102167 1103759 . - . ID=gene1124;gene=argS;Name=argS;locus_tag=Cj1175c;Dbxref=GeneID:905465;gbkey=Gene NC_002163.1 RefSeq region 1102176 1102520 . - . ID=id2141;gene=argS;Name=id2141;Dbxref=GeneID:905465;gbkey=misc_feature;Note=HMMPfam hit to PF05746 2C DALR anticodon binding domain 2C score 9e-34 NC_002163.1 RefSeq region 1102563 1103507 . - . ID=id2142;gene=argS;Name=id2142;Dbxref=GeneID:905465;gbkey=misc_feature;Note=HMMPfam hit to PF00750 2C tRNA synthetases class I 28R 29 2C score 4.9e-73 NC_002163.1 RefSeq region 1103388 1103417 . - . ID=id2143;gene=argS;Name=id2143;Dbxref=GeneID:905465;gbkey=misc_feature;Note=PS00178 Aminoacyl-transfer RNA synthetases class-I signature NC_002163.1 RefSeq region 1103529 1103759 . - . ID=id2144;gene=argS;Name=id2144;Dbxref=GeneID:905465;gbkey=misc_feature;Note=HMMPfam hit to PF03485 2C Arginyl tRNA synthetase N terminal do 2C score 1.6e-26 ### NC_002163.1 RefSeq CDS 1103771 1104010 . - 0 ID=cds1060;Parent=gene1125;gene=tatA;Name=YP_002344567.1;Dbxref=GOA:Q9PNB9 InterPro:IPR003369 InterPro:IPR006312 UniProtKB FSwiss-Prot:Q9PNB9 Genbank:YP_002344567.1 GeneID:905466;gbkey=CDS;product=Sec-independent protein translocase;Note=Original 282000 29 note: Cj1176c 2C unknown 2C len: 79 aa 3B similar to hypothetical proteins e.g. YY34_MYCTU MTCY49.34C 2883 aa 29 2C fasta scores 3B opt: 162 z-score: 221.6 E 28 29: 4.8e-05 2C 42.9 25 identity in 56 aa overlap. 49.4 25 identity to HP0320 7EUpdated 282006 29 note: Pfam domain PF02416 mttA 2FHcf106 family identified within CDS. Members of this protein family are involved in Sec independent translocation mechanism. Product function modified to more specific family member based on motif match. Characterisation has been carried out in Escherichia coli 2Cwith acceptable identity score. Product function uses homolog description. Functional classification - Protein and peptide secretion 7EPMID:9649434 2C PMID:12427031 2C PMID:15571732 2CPMID:9546395 2C PMID:16027357 NC_002163.1 RefSeq gene 1103771 1104010 . - . ID=gene1125;gene=tatA;Name=tatA;locus_tag=Cj1176c;Dbxref=GeneID:905466;gbkey=Gene NC_002163.1 RefSeq region 1103822 1103998 . - . ID=id2145;gene=tatA;Name=id2145;Dbxref=GeneID:905466;gbkey=misc_feature;Note=HMMPfam hit to PF02416 2C mttA 2FHcf106 family 2C score 3.9e-19 NC_002163.1 RefSeq region 1103942 1104001 . - . ID=id2146;gene=tatA;Name=id2146;Dbxref=GeneID:905466;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1176c by TMHMM2.0 at aa 4-23 ### NC_002163.1 UTR_Extractor 5'-UTR 1104011 1104199 . - . ID=utr421;locus_tag=Cj1176c;product=Sec-independent protein translocase NC_002163.1 RefSeq CDS 1104012 1104635 . - 0 ID=cds1061;Parent=gene1126;gene=gmk;Name=YP_002344568.1;Dbxref=GOA:Q9PNB8 HSSP:P15454 InterPro:IPR008144 InterPro:IPR008145 InterPro:IPR017665 UniProtKB FSwiss-Prot:Q9PNB8 Genbank:YP_002344568.1 GeneID:905467;gbkey=CDS;product=guanylate kinase;Note=Essential for recycling GMP and indirectly 2C cGMP NC_002163.1 RefSeq gene 1104012 1104635 . - . ID=gene1126;gene=gmk;Name=gmk;locus_tag=Cj1177c;Dbxref=GeneID:905467;gbkey=Gene NC_002163.1 RefSeq region 1104198 1104515 . - . ID=id2147;gene=gmk;Name=id2147;Dbxref=GeneID:905467;gbkey=misc_feature;Note=HMMPfam hit to PF00625 2C Guanylate kinase 2C score 2.1e-36 NC_002163.1 RefSeq region 1104465 1104518 . - . ID=id2148;gene=gmk;Name=id2148;Dbxref=GeneID:905467;gbkey=misc_feature;Note=PS00856 Guanylate kinase signature NC_002163.1 RefSeq region 1104579 1104602 . - . ID=id2149;gene=gmk;Name=id2149;Dbxref=GeneID:905467;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 1104632 1106260 . - 0 ID=cds1062;Parent=gene1127;Name=YP_002344569.1;Dbxref=UniProtKB FTrEMBL:Q0P978 Genbank:YP_002344569.1 GeneID:905468;gbkey=CDS;product=highly acidic protein;Note=Original 282000 29 note: Cj1178c 2C highly acidic protein 2C len: 542 aa 3B no Hp match. Very Asp- Glu- rich 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 RefSeq gene 1104632 1106260 . - . ID=gene1127;gene=Cj1178c;Name=Cj1178c;locus_tag=Cj1178c;Dbxref=GeneID:905468;gbkey=Gene ### NC_002163.1 UTR_Extractor 5'-UTR 1106261 1106283 . - . ID=utr422;locus_tag=Cj1178c;product=highly acidic protein NC_002163.1 RefSeq CDS 1106317 1107084 . - 0 ID=cds1063;Parent=gene1128;gene=fliR;Name=YP_002344570.1;Dbxref=GOA:Q0P977 InterPro:IPR002010 InterPro:IPR006303 UniProtKB FTrEMBL:Q0P977 Genbank:YP_002344570.1 GeneID:905469;gbkey=CDS;product=flagellar biosynthesis protein FliR;Note=FliR 2C with proteins FliP and FliQ 2C forms the core of the central channel in the flagella export apparatus NC_002163.1 RefSeq gene 1106317 1107084 . - . ID=gene1128;gene=fliR;Name=fliR;locus_tag=Cj1179c;Dbxref=GeneID:905469;gbkey=Gene NC_002163.1 RefSeq region 1106335 1107057 . - . ID=id2150;gene=fliR;Name=id2150;Dbxref=GeneID:905469;gbkey=misc_feature;Note=HMMPfam hit to PF01311 2C Bacterial export proteins 2Cfamily 2C score 9e-53 NC_002163.1 RefSeq region 1106386 1106454 . - . ID=id107;gene=fliR;Name=id107;Dbxref=GeneID:905469;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1179c by TMHMM2.0 at aa 13-32 2C 37-59 2C 72-94 2C 116-138 2C143-162 2C 177-199 and 211-233 NC_002163.1 RefSeq region 1106488 1106556 . - . ID=id107;gene=fliR;Name=id107;Dbxref=GeneID:905469;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1179c by TMHMM2.0 at aa 13-32 2C 37-59 2C 72-94 2C 116-138 2C143-162 2C 177-199 and 211-233 NC_002163.1 RefSeq region 1106599 1106658 . - . ID=id107;gene=fliR;Name=id107;Dbxref=GeneID:905469;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1179c by TMHMM2.0 at aa 13-32 2C 37-59 2C 72-94 2C 116-138 2C143-162 2C 177-199 and 211-233 NC_002163.1 RefSeq region 1106671 1106739 . - . ID=id107;gene=fliR;Name=id107;Dbxref=GeneID:905469;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1179c by TMHMM2.0 at aa 13-32 2C 37-59 2C 72-94 2C 116-138 2C143-162 2C 177-199 and 211-233 NC_002163.1 RefSeq region 1106803 1106871 . - . ID=id107;gene=fliR;Name=id107;Dbxref=GeneID:905469;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1179c by TMHMM2.0 at aa 13-32 2C 37-59 2C 72-94 2C 116-138 2C143-162 2C 177-199 and 211-233 NC_002163.1 RefSeq region 1106908 1106976 . - . ID=id107;gene=fliR;Name=id107;Dbxref=GeneID:905469;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1179c by TMHMM2.0 at aa 13-32 2C 37-59 2C 72-94 2C 116-138 2C143-162 2C 177-199 and 211-233 NC_002163.1 RefSeq region 1106989 1107048 . - . ID=id107;gene=fliR;Name=id107;Dbxref=GeneID:905469;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1179c by TMHMM2.0 at aa 13-32 2C 37-59 2C 72-94 2C 116-138 2C143-162 2C 177-199 and 211-233 NC_002163.1 RefSeq gene 1107071 1107706 . - . ID=gene1129;gene=Cj1180c;Name=Cj1180c;locus_tag=Cj1180c;Dbxref=GeneID:905470;gbkey=Gene NC_002163.1 RefSeq CDS 1107071 1107706 . - 0 ID=cds1064;Parent=gene1129;Name=YP_002344571.1;Dbxref=GOA:Q0P976 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FTrEMBL:Q0P976 Genbank:YP_002344571.1 GeneID:905470;gbkey=CDS;product=ABC transporter ATP-binding protein;Note=Original 282000 29 note: Cj1180c 2C probable ABC transporter ATP binding protein 2C len: 211 aa 3B similar to many e.g. YBBA_ECOLI hypothetical ABC transporter ATP-binding protein 28228 aa 29 2C fasta scores 3B opt: 457 z-score: 554.6 E 28 29: 1.4e-23 2C 39.7 25 identity in 199 aa overlap. 49.5 25 identity to HP0179. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00211 ABC transporters family signature 2C and Pfam match to entry PF00005 ABC_tran 2C ABC transporters 7EUpdated 282006 29 note: Similar to many identified as lipoprotein-releasing system ATP-binding protein. kept within product function. Functional classification -Transport 2Fbinding proteins - Other 7EPMID:10783239 2C PMID:11844772 2C PMID:12823819 NC_002163.1 RefSeq region 1107083 1107625 . - . ID=id2151;Name=id2151;Dbxref=GeneID:905470;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 5.1e-46 NC_002163.1 RefSeq region 1107266 1107310 . - . ID=id2152;Name=id2152;Dbxref=GeneID:905470;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq region 1107581 1107604 . - . ID=id2153;Name=id2153;Dbxref=GeneID:905470;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 RefSeq CDS 1107719 1108792 . - 0 ID=cds1065;Parent=gene1130;gene=tsf;Name=YP_002344572.1;Dbxref=GOA:Q9PNB4 HSSP:P02997 InterPro:IPR000449 InterPro:IPR001816 InterPro:IPR014039 UniProtKB FSwiss-Prot:Q9PNB4 Genbank:YP_002344572.1 GeneID:905471;gbkey=CDS;product=elongation factor Ts;Note=EF-Ts 3B functions during elongation stage of protein translation 3B forms a dimer 3B associates with EF-Tu-GDP complex and promotes exchange of GDP to GTP resulting in regeneration of the active form of EF-Tu NC_002163.1 RefSeq gene 1107719 1108792 . - . ID=gene1130;gene=tsf;Name=tsf;locus_tag=Cj1181c;Dbxref=GeneID:905471;gbkey=Gene NC_002163.1 RefSeq region 1107773 1108624 . - . ID=id2154;gene=tsf;Name=id2154;Dbxref=GeneID:905471;gbkey=misc_feature;Note=HMMPfam hit to PF00889 2C Elongation factor TS 2C score 2.1e-78 NC_002163.1 RefSeq region 1108532 1108564 . - . ID=id2155;gene=tsf;Name=id2155;Dbxref=GeneID:905471;gbkey=misc_feature;Note=PS01127 Elongation factor Ts signature 2 NC_002163.1 RefSeq region 1108661 1108783 . - . ID=id2156;gene=tsf;Name=id2156;Dbxref=GeneID:905471;gbkey=misc_feature;Note=HMMPfam hit to PF00627 2C UBA 2FTS-N domain 2C score 3e-11 NC_002163.1 RefSeq region 1108712 1108759 . - . ID=id2157;gene=tsf;Name=id2157;Dbxref=GeneID:905471;gbkey=misc_feature;Note=PS01126 Elongation factor Ts signature 1 NC_002163.1 RefSeq CDS 1108792 1109583 . - 0 ID=cds1066;Parent=gene1131;gene=rpsB;Name=YP_002344573.1;Dbxref=GOA:Q9PNB3 InterPro:IPR001865 InterPro:IPR005706 UniProtKB FSwiss-Prot:Q9PNB3 Genbank:YP_002344573.1 GeneID:905472;gbkey=CDS;product=30S ribosomal protein S2;Note=one of the last subunits in the assembly of the 30S subunit 3B absence of S2 does not inhibit assembly but results in an inactive subunit NC_002163.1 RefSeq gene 1108792 1109583 . - . ID=gene1131;gene=rpsB;Name=rpsB;locus_tag=Cj1182c;Dbxref=GeneID:905472;gbkey=Gene NC_002163.1 RefSeq region 1108915 1109565 . - . ID=id2158;gene=rpsB;Name=id2158;Dbxref=GeneID:905472;gbkey=misc_feature;Note=HMMPfam hit to PF00318 2C Ribosomal protein S2 2C score 1.3e-104 NC_002163.1 RefSeq region 1109044 1109118 . - . ID=id2159;gene=rpsB;Name=id2159;Dbxref=GeneID:905472;gbkey=misc_feature;Note=PS00963 Ribosomal protein S2 signature 2 NC_002163.1 RefSeq region 1109539 1109574 . - . ID=id2160;gene=rpsB;Name=id2160;Dbxref=GeneID:905472;gbkey=misc_feature;Note=PS00962 Ribosomal protein S2 signature 1 ### NC_002163.1 UTR_Extractor 5'-UTR 1109584 1109667 . - . ID=utr423;locus_tag=Cj1182c;product=30S ribosomal protein S2 NC_002163.1 RefSeq gene 1109699 1110862 . - . ID=gene1132;gene=cfa;Name=cfa;locus_tag=Cj1183c;Dbxref=GeneID:905473;gbkey=Gene NC_002163.1 RefSeq CDS 1109699 1110862 . - 0 ID=cds1067;Parent=gene1132;gene=cfa;Name=YP_002344574.1;Dbxref=GOA:Q0P973 InterPro:IPR003333 UniProtKB FTrEMBL:Q0P973 Genbank:YP_002344574.1 GeneID:905473;gbkey=CDS;product=cyclopropane-fatty-acyl-phospholipid synthase;Note=Original 282000 29 note: Cj1183c 2C cfa 2C probable cyclopropane-fatty-acyl-phospholipid synthase 2C len: 387 aa 3B CFA_ECOLI cyclopropane-fatty-acyl-phospholipid synthase 28EC 2.1.1.79 29 28381 aa 29 2C fasta scores 3B opt: 721 z-score: 802.3 E 28 29: 0 2C 38.7 25 identity in 362 aa overlap. 62.1 25 identity to HP0416 7EUpdated 282006 29 note: Pfam domain PF02353 Cyclopropane-fatty-acyl-phosphol lipid synthase identified within CDS. Further support given to product function. Characterised in Escherichia coli with acceptable identity score. Appropiate motifs present. removed from product function. Functional classification - Fatty acid biosynthesis 7EPMID:1445840 NC_002163.1 RefSeq region 1109747 1110226 . - . ID=id2161;gene=cfa;Name=id2161;Dbxref=GeneID:905473;gbkey=misc_feature;Note=HMMPfam hit to PF02353 2CCyclopropane-fatty-acyl-phospholipid synthas 2C score 7.3e-83 ### NC_002163.1 UTR_Extractor 5'-UTR 1110863 1111049 . - . ID=utr424;locus_tag=Cj1183c;product=cyclopropane-fatty-acyl-phospholipid synthase NC_002163.1 RefSeq CDS 1110990 1112114 . - 0 ID=cds1068;Parent=gene1133;gene=petC;Name=YP_002344575.1;Dbxref=GOA:Q0P972 InterPro:IPR003088 InterPro:IPR009056 InterPro:IPR013838 UniProtKB FTrEMBL:Q0P972 Genbank:YP_002344575.1 GeneID:905474;gbkey=CDS;product=ubiquinol-cytochrome C reductase cytochrome C subunit;Note=Original 282000 29 note: Cj1184c 2C petC 2C possible ubiquinol-cytochrome C reductase cytochrome C subunit 2Clen: 374 aa 3B some similarity to e.g. CYC_TETPY cytochrome C 28109 aa 29 2C fasta scores 3B opt: 124 z-score: 145.5 E 28 29: 0.83 2C 25.6 25 identity in 121 aa overlap. 36.4 25 identity to HP1538. Contains Pfam match to entry PF00034 cytochrome_c 2CCytochrome c 2C probable N-terminal signal sequence 2C and possible membrane anchor at C-terminus 7EUpdated 282006 29 note: Two probable transmembrane helices predicted by TMHMM2.0. Specific characterisation with acceptable identity score not carried out yet 2C so kept in product function. Literature search identified paper giving further clues to functionality within Campylobacter. Functional classification - Energy metabolism - Electron transport 7EPMID:16041056 NC_002163.1 RefSeq gene 1110990 1112114 . - . ID=gene1133;gene=petC;Name=petC;locus_tag=Cj1184c;Dbxref=GeneID:905474;gbkey=Gene NC_002163.1 RefSeq region 1111020 1111079 . - . ID=id108;gene=petC;Name=id108;Dbxref=GeneID:905474;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1184c by TMHMM2.0 at aa 7-29 and 346-365 NC_002163.1 RefSeq region 1111491 1111799 . - . ID=id2162;gene=petC;Name=id2162;Dbxref=GeneID:905474;gbkey=misc_feature;Note=HMMPfam hit to PF00034 2C Cytochrome c 2C score 0.0076 NC_002163.1 RefSeq region 1112028 1112096 . - . ID=id108;gene=petC;Name=id108;Dbxref=GeneID:905474;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1184c by TMHMM2.0 at aa 7-29 and 346-365 NC_002163.1 RefSeq region 1112103 1112114 . - . ID=id2163;gene=petC;Name=id2163;Dbxref=GeneID:905474;gbkey=misc_feature;Note=PS00228 Tubulin-beta mRNA autoregulation signal NC_002163.1 RefSeq gene 1112111 1113361 . - . ID=gene1134;gene=petB;Name=petB;locus_tag=Cj1185c;Dbxref=GeneID:905475;gbkey=Gene NC_002163.1 RefSeq CDS 1112111 1113361 . - 0 ID=cds1069;Parent=gene1134;gene=petB;Name=YP_002344576.1;Dbxref=GOA:Q0P971 InterPro:IPR005797 InterPro:IPR005798 InterPro:IPR016175 UniProtKB FTrEMBL:Q0P971 Genbank:YP_002344576.1 GeneID:905475;gbkey=CDS;product=ubiquinol-cytochrome C reductase cytochrome B subunit;Note=Original 282000 29 note: Cj1185c 2C petB 2C probable ubiquinol-cytochrome C reductase cytochrome B subunit 2Clen: 416 aa 3B similar to e.g. CYB_RHOSH cytochrome B 28EC 1.10.2.2 29 28444 aa 29 2C fasta scores 3B opt: 1023 z-score: 1190.8 E 28 29: 0 2C 40.4 25 identity in 416 aa overlap. 70.9 25 identity to HP1539 3B Contains PS00193 Cytochrome b 2Fb6 Qo site signature 2C Pfam match to entry PF00033 cytochrome_b_N 2C Cytochrome b 28N-terminal 29 2Fb6 2FpetB 2C and Pfam match to entry PF00032 cytochrome_b_C 2C Cytochrome b 28C-terminal 29 2Fb6 2FpetD 7EUpdated 282006 29 note: Ten probable transmembrane helices predicted by TMHMM2.0. Specific characterisation with acceptable identity score carried out in Rhodobacter sphaeroides. kept within product function. Literature search identified paper 28PMID:16041056 29 giving further clues to functionality within Campylobacter. Functional classification - Energy metabolism - Electron transport 7EPMID:2176595 2C PMID:1645718 2C PMID:16041056 NC_002163.1 RefSeq region 1112138 1112206 . - . ID=id109;gene=petB;Name=id109;Dbxref=GeneID:905475;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1185c by TMHMM2.0 at aa 39-61 2C 95-117 2C 124-146 2C 156-178 2C191-213 2C 258-280 2C 301-320 2C 325-344 2C 357-376 and 386-408 NC_002163.1 RefSeq region 1112192 1112503 . - . ID=id2164;gene=petB;Name=id2164;Dbxref=GeneID:905475;gbkey=misc_feature;Note=HMMPfam hit to PF00032 2C Cytochrome b 28C-terminal 29 2Fb6 2FpetD 2C score 2.5e-06 NC_002163.1 RefSeq region 1112213 1112230 . - . ID=id2165;gene=petB;Name=id2165;Dbxref=GeneID:905475;gbkey=misc_feature;Note=PS00343 Gram-positive cocci surface proteins 27anchoring 27 hexapeptide NC_002163.1 RefSeq region 1112234 1112293 . - . ID=id109;gene=petB;Name=id109;Dbxref=GeneID:905475;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1185c by TMHMM2.0 at aa 39-61 2C 95-117 2C 124-146 2C 156-178 2C191-213 2C 258-280 2C 301-320 2C 325-344 2C 357-376 and 386-408 NC_002163.1 RefSeq region 1112330 1112389 . - . ID=id109;gene=petB;Name=id109;Dbxref=GeneID:905475;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1185c by TMHMM2.0 at aa 39-61 2C 95-117 2C 124-146 2C 156-178 2C191-213 2C 258-280 2C 301-320 2C 325-344 2C 357-376 and 386-408 NC_002163.1 RefSeq region 1112402 1112461 . - . ID=id109;gene=petB;Name=id109;Dbxref=GeneID:905475;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1185c by TMHMM2.0 at aa 39-61 2C 95-117 2C 124-146 2C 156-178 2C191-213 2C 258-280 2C 301-320 2C 325-344 2C 357-376 and 386-408 NC_002163.1 RefSeq region 1112450 1112467 . - . ID=id2166;gene=petB;Name=id2166;Dbxref=GeneID:905475;gbkey=misc_feature;Note=PS00193 Cytochrome b 2Fb6 Qo site signature NC_002163.1 RefSeq region 1112522 1112590 . - . ID=id109;gene=petB;Name=id109;Dbxref=GeneID:905475;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1185c by TMHMM2.0 at aa 39-61 2C 95-117 2C 124-146 2C 156-178 2C191-213 2C 258-280 2C 301-320 2C 325-344 2C 357-376 and 386-408 NC_002163.1 RefSeq region 1112708 1113319 . - . ID=id2167;gene=petB;Name=id2167;Dbxref=GeneID:905475;gbkey=misc_feature;Note=HMMPfam hit to PF00033 2C Cytochrome b 28N-terminal 29 2Fb6 2FpetB 2C score 2.9e-61 NC_002163.1 RefSeq region 1112723 1112791 . - . ID=id109;gene=petB;Name=id109;Dbxref=GeneID:905475;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1185c by TMHMM2.0 at aa 39-61 2C 95-117 2C 124-146 2C 156-178 2C191-213 2C 258-280 2C 301-320 2C 325-344 2C 357-376 and 386-408 NC_002163.1 RefSeq region 1112828 1112896 . - . ID=id109;gene=petB;Name=id109;Dbxref=GeneID:905475;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1185c by TMHMM2.0 at aa 39-61 2C 95-117 2C 124-146 2C 156-178 2C191-213 2C 258-280 2C 301-320 2C 325-344 2C 357-376 and 386-408 NC_002163.1 RefSeq region 1112924 1112992 . - . ID=id109;gene=petB;Name=id109;Dbxref=GeneID:905475;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1185c by TMHMM2.0 at aa 39-61 2C 95-117 2C 124-146 2C 156-178 2C191-213 2C 258-280 2C 301-320 2C 325-344 2C 357-376 and 386-408 NC_002163.1 RefSeq region 1113011 1113079 . - . ID=id109;gene=petB;Name=id109;Dbxref=GeneID:905475;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1185c by TMHMM2.0 at aa 39-61 2C 95-117 2C 124-146 2C 156-178 2C191-213 2C 258-280 2C 301-320 2C 325-344 2C 357-376 and 386-408 NC_002163.1 RefSeq region 1113179 1113247 . - . ID=id109;gene=petB;Name=id109;Dbxref=GeneID:905475;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1185c by TMHMM2.0 at aa 39-61 2C 95-117 2C 124-146 2C 156-178 2C191-213 2C 258-280 2C 301-320 2C 325-344 2C 357-376 and 386-408 ### NC_002163.1 RefSeq CDS 1113363 1113866 . - 0 ID=cds1070;Parent=gene1135;gene=petA;Name=YP_002344577.1;Dbxref=GOA:Q0P970 InterPro:IPR005805 InterPro:IPR005806 InterPro:IPR006317 InterPro:IPR014349 UniProtKB FTrEMBL:Q0P970 Genbank:YP_002344577.1 GeneID:905476;gbkey=CDS;product=ubiquinol-cytochrome C reductase iron-sulfur subunit;Note=Original 282000 29 note: Cj1186c 2C petA 2C probable ubiquinol-cytochrome C reductase iron-sulfur subunit 2C len: 167 aa 3B similar to e.g. UCRI_BRAJA ubiquinol-cytochrome C reductase iron-sulfur subunit 28EC 1.10.2.2 29 28176 aa 29 2Cfatsa scores 3B opt: 236 z-score: 291.2 E 28 29: 6.4e-09 2C 39.2 25 identity in 171 aa overlap. 56.8 25 identity to HP1540. Contains PS00199 Rieske iron-sulfur protein signature 1 2Cand Pfam match to entry PF00355 Rieske 2C Rieske iron-sulfur protein 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score 2C so kept within product function. Literature search identified paper giving further clues to functionality within Campylobacter. Functional classification - Energy metabolism - Electron transport 7EPMID:16041056 NC_002163.1 RefSeq gene 1113363 1113866 . - . ID=gene1135;gene=petA;Name=petA;locus_tag=Cj1186c;Dbxref=GeneID:905476;gbkey=Gene NC_002163.1 RefSeq region 1113420 1113671 . - . ID=id2168;gene=petA;Name=id2168;Dbxref=GeneID:905476;gbkey=misc_feature;Note=HMMPfam hit to PF00355 2C Rieske 5B2Fe-2S 5D domain 2Cscore 7.4e-08 NC_002163.1 RefSeq region 1113552 1113572 . - . ID=id2169;gene=petA;Name=id2169;Dbxref=GeneID:905476;gbkey=misc_feature;Note=PS00199 Rieske iron-sulfur protein signature 1 NC_002163.1 RefSeq region 1113780 1113839 . - . ID=id2170;gene=petA;Name=id2170;Dbxref=GeneID:905476;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1186c by TMHMM2.0 at aa 10-29 ### NC_002163.1 UTR_Extractor 5'-UTR 1113867 1113898 . - . ID=utr425;locus_tag=Cj1186c;product=putative ubiquinol-cytochrome C reductase iron-sulfur subunit NC_002163.1 RefSeq CDS 1113956 1115242 . - 0 ID=cds1071;Parent=gene1136;gene=arsB;Name=YP_002344578.1;Dbxref=GOA:Q0P969 InterPro:IPR000802 UniProtKB FTrEMBL:Q0P969 Genbank:YP_002344578.1 GeneID:905477;gbkey=CDS;product=arsenical pump membrane protein;Note=Original 282000 29 note: Cj1187c 2C arsB 2C possible arsenical pump membrane protein 2C len: 428 aa 3B simlar to many e.g. ARSB_ECOLI arsenical pump membrane protein 28429 aa 29 2C fasta scores 3B opt: 805 z-score: 920.7 E 28 29: 0 2C 33.5 25 identity in 433 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02040 Arsenical pump membrane protein identified within CDS. Also 2C eleven probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised in Escherichia coli with marginal identity score. Appropriate motifs present. removed from product function. Functional classification - Drug 2Fanalogue sensitivity 7EPMID:7721697 2C PMID:1688427 NC_002163.1 RefSeq gene 1113956 1115242 . - . ID=gene1136;gene=arsB;Name=arsB;locus_tag=Cj1187c;Dbxref=GeneID:905477;gbkey=Gene NC_002163.1 RefSeq region 1113959 1115239 . - . ID=id2171;gene=arsB;Name=id2171;Dbxref=GeneID:905477;gbkey=misc_feature;Note=HMMPfam hit to PF02040 2C Arsenical pump membrane protein 2C score 7.3e-69 NC_002163.1 RefSeq region 1113962 1114021 . - . ID=id110;gene=arsB;Name=id110;Dbxref=GeneID:905477;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1187c by TMHMM2.0 at aa 20-42 2C 57-79 2C 103-134 2C 144-166 2C189-211 2C 226-248 2C 255-271 2C 281-303 2C 324-346 2C 366-395 and 408-427 NC_002163.1 RefSeq region 1114058 1114147 . - . ID=id110;gene=arsB;Name=id110;Dbxref=GeneID:905477;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1187c by TMHMM2.0 at aa 20-42 2C 57-79 2C 103-134 2C 144-166 2C189-211 2C 226-248 2C 255-271 2C 281-303 2C 324-346 2C 366-395 and 408-427 NC_002163.1 RefSeq region 1114205 1114273 . - . ID=id110;gene=arsB;Name=id110;Dbxref=GeneID:905477;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1187c by TMHMM2.0 at aa 20-42 2C 57-79 2C 103-134 2C 144-166 2C189-211 2C 226-248 2C 255-271 2C 281-303 2C 324-346 2C 366-395 and 408-427 NC_002163.1 RefSeq region 1114334 1114402 . - . ID=id110;gene=arsB;Name=id110;Dbxref=GeneID:905477;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1187c by TMHMM2.0 at aa 20-42 2C 57-79 2C 103-134 2C 144-166 2C189-211 2C 226-248 2C 255-271 2C 281-303 2C 324-346 2C 366-395 and 408-427 NC_002163.1 RefSeq region 1114430 1114480 . - . ID=id110;gene=arsB;Name=id110;Dbxref=GeneID:905477;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1187c by TMHMM2.0 at aa 20-42 2C 57-79 2C 103-134 2C 144-166 2C189-211 2C 226-248 2C 255-271 2C 281-303 2C 324-346 2C 366-395 and 408-427 NC_002163.1 RefSeq region 1114499 1114567 . - . ID=id110;gene=arsB;Name=id110;Dbxref=GeneID:905477;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1187c by TMHMM2.0 at aa 20-42 2C 57-79 2C 103-134 2C 144-166 2C189-211 2C 226-248 2C 255-271 2C 281-303 2C 324-346 2C 366-395 and 408-427 NC_002163.1 RefSeq region 1114610 1114678 . - . ID=id110;gene=arsB;Name=id110;Dbxref=GeneID:905477;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1187c by TMHMM2.0 at aa 20-42 2C 57-79 2C 103-134 2C 144-166 2C189-211 2C 226-248 2C 255-271 2C 281-303 2C 324-346 2C 366-395 and 408-427 NC_002163.1 RefSeq region 1114745 1114813 . - . ID=id110;gene=arsB;Name=id110;Dbxref=GeneID:905477;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1187c by TMHMM2.0 at aa 20-42 2C 57-79 2C 103-134 2C 144-166 2C189-211 2C 226-248 2C 255-271 2C 281-303 2C 324-346 2C 366-395 and 408-427 NC_002163.1 RefSeq region 1114841 1114936 . - . ID=id110;gene=arsB;Name=id110;Dbxref=GeneID:905477;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1187c by TMHMM2.0 at aa 20-42 2C 57-79 2C 103-134 2C 144-166 2C189-211 2C 226-248 2C 255-271 2C 281-303 2C 324-346 2C 366-395 and 408-427 NC_002163.1 RefSeq region 1115006 1115074 . - . ID=id110;gene=arsB;Name=id110;Dbxref=GeneID:905477;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1187c by TMHMM2.0 at aa 20-42 2C 57-79 2C 103-134 2C 144-166 2C189-211 2C 226-248 2C 255-271 2C 281-303 2C 324-346 2C 366-395 and 408-427 NC_002163.1 RefSeq region 1115117 1115185 . - . ID=id110;gene=arsB;Name=id110;Dbxref=GeneID:905477;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1187c by TMHMM2.0 at aa 20-42 2C 57-79 2C 103-134 2C 144-166 2C189-211 2C 226-248 2C 255-271 2C 281-303 2C 324-346 2C 366-395 and 408-427 ### NC_002163.1 UTR_Extractor 5'-UTR 1115243 1115470 . - . ID=utr426;locus_tag=Cj1187c;product=arsenical pump membrane protein NC_002163.1 RefSeq CDS 1115243 1117102 . - 0 ID=cds1072;Parent=gene1137;gene=gidA;Name=YP_002344579.1;Dbxref=GOA:Q9PNA7 InterPro:IPR002218 InterPro:IPR004416 InterPro:IPR013027 UniProtKB FSwiss-Prot:Q9PNA7 Genbank:YP_002344579.1 GeneID:905478;gbkey=CDS;product=tRNA uridine 5-carboxymethylaminomethyl modification protein GidA;Note=GidA 3B glucose-inhibited cell division protein A 3B involved in the 5-carboxymethylaminomethyl modification 28mnm 285 29s 282 29U 29 of the wobble uridine base in some tRNAs NC_002163.1 RefSeq gene 1115243 1117102 . - . ID=gene1137;gene=gidA;Name=gidA;locus_tag=Cj1188c;Dbxref=GeneID:905478;gbkey=Gene NC_002163.1 RefSeq region 1115903 1117096 . - . ID=id2172;gene=gidA;Name=id2172;Dbxref=GeneID:905478;gbkey=misc_feature;Note=HMMPfam hit to PF01134 2C Glucose inhibited division protein A 2C score 4e-226 NC_002163.1 RefSeq region 1116260 1116304 . - . ID=id2173;gene=gidA;Name=id2173;Dbxref=GeneID:905478;gbkey=misc_feature;Note=PS01280 Glucose inhibited division protein A family signature 1 ### NC_002163.1 UTR_Extractor 5'-UTR 1117103 1117137 . - . ID=utr427;locus_tag=Cj1188c;product=tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA NC_002163.1 RefSeq gene 1117190 1117687 . - . ID=gene1138;gene=cetB;Name=cetB;locus_tag=Cj1189c;Dbxref=GeneID:905479;gbkey=Gene NC_002163.1 RefSeq CDS 1117190 1117687 . - 0 ID=cds1073;Parent=gene1138;gene=cetB;Name=YP_002344580.1;Dbxref=GOA:Q0P967 InterPro:IPR000014 InterPro:IPR013655 UniProtKB FTrEMBL:Q0P967 Genbank:YP_002344580.1 GeneID:905479;gbkey=CDS;product=bipartate energy taxis response protein CetB;Note=Original 282000 29 note: Cj1189c 2C possible signal-transduction sensor protein 2C len: 165 aa 3B similar to N-terminus of genes involved in oxygen-sensing e.g. AER_ECOLI aerotaxis receptor 28506 aa 29 2C fasta scores 3B opt: 342 z-score: 407.5 E 28 29: 2.1e-15 2C 36.4 25 identity in 140 aa overlap 2C and NIFL_AZOVI nitrogen fixation regulatory protein 28519 aa 29 2C fasta scores 3B opt: 175 z-score: 212.5 E 28 29: 0.00015 2C 33.6 25 identity in 110 aa overlap. No Hp match. Also similar to Cj1191c 2863.4 25 identity in 161 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF00989 PAS fold identified within CDS. PAS domains are involved in many signalling proteins where they are used as a signal sensor domain. Prosite domain PS50112 PAS 2C PAS repeat profile identified within CDS. Further support given to product function. Characterisation work carried out in Campylobacter jejuni. Product function updated. Literature search identified paper giving further information on product functionality 28PMID:11298288 29. Gene name added. Functional classification - Signal transduction 7EPMID:9380671 2C PMID:11298288 NC_002163.1 RefSeq CDS 1117705 1119084 . - 0 ID=cds1074;Parent=gene1139;gene=cetA;Name=YP_002344581.1;Dbxref=GOA:Q0P966 InterPro:IPR004089 UniProtKB FTrEMBL:Q0P966 Genbank:YP_002344581.1 GeneID:905480;gbkey=CDS;product=bipartate energy taxis response protein CetA;Note=Original 282000 29 note: Cj1190c 2C probable MCP-domain signal transduction protein 2C len: 459 aa 3B similar to many e.g. TLPC_BACSU methyl-accepting chemotaxis protein TLPC 28573 aa 29 2C fasta scores 3B opt: 371 z-score: 397.9 E 28 29: 7.3e-15 2C 26.2 25 identity in 404 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00015 MCPsignal 2CMethyl-accepting chemotaxis protein 28MCP 29 signaling domain 2C and probable membrane spanning domain at N-terminus 7EUpdated 282006 29 note: Characterisation work carried out in Campylobacter jejuni. Product function updated. Literature search identified paper giving further information to product functionality 28PMID:11298288 29. New gene name has been added. Functional classification -Signal transduction 7EPMID:8188684 2C PMID:11298288 NC_002163.1 RefSeq gene 1117705 1119084 . - . ID=gene1139;gene=cetA;Name=cetA;locus_tag=Cj1190c;Dbxref=GeneID:905480;gbkey=Gene NC_002163.1 RefSeq region 1118005 1118595 . - . ID=id2174;gene=cetA;Name=id2174;Dbxref=GeneID:905480;gbkey=misc_feature;Note=HMMPfam hit to PF00015 2C Methyl-accepting chemotaxis protein 28MCP 29 s 2C score 2.6e-19 NC_002163.1 RefSeq region 1118962 1119066 . - . ID=id2175;gene=cetA;Name=id2175;Dbxref=GeneID:905480;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1190c by TMHMM2.0 at aa 7-41 ### NC_002163.1 UTR_Extractor 5'-UTR 1119085 1119165 . - . ID=utr428;locus_tag=Cj1190c;product=bipartate energy taxis response protein CetA NC_002163.1 RefSeq gene 1119205 1119699 . - . ID=gene1140;Name=Cj1191c;locus_tag=Cj1191c;Dbxref=GeneID:905481;gbkey=Gene NC_002163.1 RefSeq CDS 1119205 1119699 . - 0 ID=cds1075;Parent=gene1140;Name=YP_002344582.1;Dbxref=GOA:Q0P965 InterPro:IPR000014 InterPro:IPR013655 UniProtKB FTrEMBL:Q0P965 Genbank:YP_002344582.1 GeneID:905481;gbkey=CDS;product=PAS domain-containing signal-transduction sensor protein;Note=Original 282000 29 note: Cj1191c 2C possible signal-transduction sensor protein 2C len: 164 aa 3B similar to N-terminus of genes involved in oxygen-sensing e.g. AER_ECOLI aerotaxis receptor 28506 aa 29 2C fasta scores 3B opt: 297 z-score: 373.5 E 28 29: 1.7e-13 2C 34.3 25 identity in 134 aa overlap 2C and NIFL_AZOVI nitrogen fixation regulatory protein 28519 aa 29 2C fasta scores 3B opt: 178 z-score: 226.6 E 28 29: 2.5e-05 2C 33.0 25 identity in 103 aa overlap. No Hp match. Also similar to Cj1189c 2863.4 25 identity in 161 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF00989 PAS fold identified within CDS. PAS domains are involved in many signalling proteins where they are used as a signal sensor domain. Prosite domain PS50112 PAS 2C PAS repeat profile identified within CDS. Further support given to product function. Product function modified to include motif information. Literature search identified paper giving further clues to product functionality 28PMID:11298288 29. Functional classification - Signal transduction 7EPMID:9380671 2C PMID:11298288 NC_002163.1 UTR_Extractor 5'-UTR 1119700 1119738 . - . ID=utr429;locus_tag=Cj1191c;product=putative PAS domain containing signal-transduction sensor protein NC_002163.1 RefSeq CDS 1119968 1121344 . + 0 ID=cds1076;Parent=gene1141;gene=dctA;Name=YP_002344583.1;Dbxref=GOA:Q0P964 InterPro:IPR001991 UniProtKB FTrEMBL:Q0P964 Genbank:YP_002344583.1 GeneID:905482;gbkey=CDS;product=C4-dicarboxylate transport protein;Note=Original 282000 29 note: Cj1192 2C dctA 2C probable C4-dicarboxylate transport protein 2C len: 458 aa 3B similar to many e.g. DCTA_ECOLI C4-dicarboxylate transport protein 28428 aa 29 2C fasta scores 3B opt: 1073 z-score: 1222.5 E 28 29: 0 2C45.3 25 identity in 433 aa overlap. No Hp match. Contains Pfam match to entry PF00375 SDF 2C Sodium:dicarboxylate symporter family 7EUpdated 282006 29 note: Eight probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised in Escherichia coli with acceptable identity score. kept within product function. Functional classification - Carbohydrates 2Corganic acids and alcohols 7EPMID:8955389 2C PMID:10482502 2C PMID:15919996 2CPMID:11803016 NC_002163.1 RefSeq gene 1119968 1121344 . + . ID=gene1141;gene=dctA;Name=dctA;locus_tag=Cj1192;Dbxref=GeneID:905482;gbkey=Gene NC_002163.1 RefSeq region 1120022 1120090 . + . ID=id2176;gene=dctA;Name=id2176;Dbxref=GeneID:905482;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1192 by TMHMM2.0 at aa 19-41 2C 56-78 2C 91-113 2C 168-187 2C210-232 2C 242-264 2C 351-373 and 388-407 NC_002163.1 RefSeq region 1120034 1121266 . + . ID=id2177;gene=dctA;Name=id2177;Dbxref=GeneID:905482;gbkey=misc_feature;Note=HMMPfam hit to PF00375 2C Sodium:dicarboxylate symporter family 2C score 3.4e-93 NC_002163.1 RefSeq region 1120133 1120201 . + . ID=id2176;gene=dctA;Name=id2176;Dbxref=GeneID:905482;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1192 by TMHMM2.0 at aa 19-41 2C 56-78 2C 91-113 2C 168-187 2C210-232 2C 242-264 2C 351-373 and 388-407 NC_002163.1 RefSeq region 1120238 1120306 . + . ID=id2176;gene=dctA;Name=id2176;Dbxref=GeneID:905482;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1192 by TMHMM2.0 at aa 19-41 2C 56-78 2C 91-113 2C 168-187 2C210-232 2C 242-264 2C 351-373 and 388-407 NC_002163.1 RefSeq region 1120469 1120528 . + . ID=id2176;gene=dctA;Name=id2176;Dbxref=GeneID:905482;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1192 by TMHMM2.0 at aa 19-41 2C 56-78 2C 91-113 2C 168-187 2C210-232 2C 242-264 2C 351-373 and 388-407 NC_002163.1 RefSeq region 1120595 1120663 . + . ID=id2176;gene=dctA;Name=id2176;Dbxref=GeneID:905482;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1192 by TMHMM2.0 at aa 19-41 2C 56-78 2C 91-113 2C 168-187 2C210-232 2C 242-264 2C 351-373 and 388-407 NC_002163.1 RefSeq region 1120682 1120714 . + . ID=id2178;gene=dctA;Name=id2178;Dbxref=GeneID:905482;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1120691 1120759 . + . ID=id2176;gene=dctA;Name=id2176;Dbxref=GeneID:905482;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1192 by TMHMM2.0 at aa 19-41 2C 56-78 2C 91-113 2C 168-187 2C210-232 2C 242-264 2C 351-373 and 388-407 NC_002163.1 RefSeq region 1121018 1121086 . + . ID=id2176;gene=dctA;Name=id2176;Dbxref=GeneID:905482;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1192 by TMHMM2.0 at aa 19-41 2C 56-78 2C 91-113 2C 168-187 2C210-232 2C 242-264 2C 351-373 and 388-407 NC_002163.1 RefSeq region 1121129 1121188 . + . ID=id2176;gene=dctA;Name=id2176;Dbxref=GeneID:905482;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1192 by TMHMM2.0 at aa 19-41 2C 56-78 2C 91-113 2C 168-187 2C210-232 2C 242-264 2C 351-373 and 388-407 NC_002163.1 RefSeq CDS 1121341 1122147 . - 0 ID=cds1077;Parent=gene1142;Name=YP_002344584.1;Dbxref=UniProtKB FTrEMBL:Q0P963 Genbank:YP_002344584.1 GeneID:905483;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1193c 2C probable periplasmic protein 2C len: 268 aa 3B no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 1121341 1122147 . - . ID=gene1142;gene=Cj1193c;Name=Cj1193c;locus_tag=Cj1193c;Dbxref=GeneID:905483;gbkey=Gene ### NC_002163.1 UTR_Extractor 5'-UTR 1122148 1122179 . - . ID=utr430;locus_tag=Cj1193c;product=putative periplasmic protein NC_002163.1 RefSeq CDS 1122289 1123815 . + 0 ID=cds1078;Parent=gene1143;Name=YP_002344585.1;Dbxref=GOA:Q0P962 InterPro:IPR001204 UniProtKB FTrEMBL:Q0P962 Genbank:YP_002344585.1 GeneID:905484;gbkey=CDS;product=phosphate permease;Note=Original 282000 29 note: Cj1194 2C possible phosphate permease 2C len: 508 aa 3B similar to many predicted phosphate permeases e.g. TR:Q50684 Mycobacterium tuberculosis phosphate permease Rv2281 MTCY339.29C 28552 aa 29 2Cfasta scores 3B opt: 900 z-score: 971.5 E 28 29: 0 2C 46.6 25 identity in 511 aa overlap. 32.7 25 identity to HP1491 7EUpdated 282006 29 note: Pfam domain PF01384 Phosphate transporter family identified within CDS. Also 2C thirteen probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation has been carried out yet 2C so kept within product function. Functional classification -Transport 2Fbinding proteins - Anions NC_002163.1 RefSeq gene 1122289 1123815 . + . ID=gene1143;Name=Cj1194;locus_tag=Cj1194;Dbxref=GeneID:905484;gbkey=Gene NC_002163.1 RefSeq region 1122301 1122369 . + . ID=id2179;Name=id2179;Dbxref=GeneID:905484;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1194 by TMHMM2.0 at aa 5-27 2C 32-51 2C 72-89 2C 109-128 2C133-155 2C 175-197 2C 276-298 2C 313-334 2C 346-368 2C 388-410 2C423-445 2C 449-468 and 480-502 NC_002163.1 RefSeq region 1122382 1122441 . + . ID=id2179;Name=id2179;Dbxref=GeneID:905484;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1194 by TMHMM2.0 at aa 5-27 2C 32-51 2C 72-89 2C 109-128 2C133-155 2C 175-197 2C 276-298 2C 313-334 2C 346-368 2C 388-410 2C423-445 2C 449-468 and 480-502 NC_002163.1 RefSeq region 1122433 1123773 . + . ID=id2180;Name=id2180;Dbxref=GeneID:905484;gbkey=misc_feature;Note=HMMPfam hit to PF01384 2C Phosphate transporter family 2C score 9.5e-139 NC_002163.1 RefSeq region 1122502 1122555 . + . ID=id2179;Name=id2179;Dbxref=GeneID:905484;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1194 by TMHMM2.0 at aa 5-27 2C 32-51 2C 72-89 2C 109-128 2C133-155 2C 175-197 2C 276-298 2C 313-334 2C 346-368 2C 388-410 2C423-445 2C 449-468 and 480-502 NC_002163.1 RefSeq region 1122613 1122672 . + . ID=id2179;Name=id2179;Dbxref=GeneID:905484;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1194 by TMHMM2.0 at aa 5-27 2C 32-51 2C 72-89 2C 109-128 2C133-155 2C 175-197 2C 276-298 2C 313-334 2C 346-368 2C 388-410 2C423-445 2C 449-468 and 480-502 NC_002163.1 RefSeq region 1122685 1122753 . + . ID=id2179;Name=id2179;Dbxref=GeneID:905484;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1194 by TMHMM2.0 at aa 5-27 2C 32-51 2C 72-89 2C 109-128 2C133-155 2C 175-197 2C 276-298 2C 313-334 2C 346-368 2C 388-410 2C423-445 2C 449-468 and 480-502 NC_002163.1 RefSeq region 1122811 1122879 . + . ID=id2179;Name=id2179;Dbxref=GeneID:905484;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1194 by TMHMM2.0 at aa 5-27 2C 32-51 2C 72-89 2C 109-128 2C133-155 2C 175-197 2C 276-298 2C 313-334 2C 346-368 2C 388-410 2C423-445 2C 449-468 and 480-502 NC_002163.1 RefSeq region 1123114 1123182 . + . ID=id2179;Name=id2179;Dbxref=GeneID:905484;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1194 by TMHMM2.0 at aa 5-27 2C 32-51 2C 72-89 2C 109-128 2C133-155 2C 175-197 2C 276-298 2C 313-334 2C 346-368 2C 388-410 2C423-445 2C 449-468 and 480-502 NC_002163.1 RefSeq region 1123225 1123290 . + . ID=id2179;Name=id2179;Dbxref=GeneID:905484;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1194 by TMHMM2.0 at aa 5-27 2C 32-51 2C 72-89 2C 109-128 2C133-155 2C 175-197 2C 276-298 2C 313-334 2C 346-368 2C 388-410 2C423-445 2C 449-468 and 480-502 NC_002163.1 RefSeq region 1123324 1123392 . + . ID=id2179;Name=id2179;Dbxref=GeneID:905484;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1194 by TMHMM2.0 at aa 5-27 2C 32-51 2C 72-89 2C 109-128 2C133-155 2C 175-197 2C 276-298 2C 313-334 2C 346-368 2C 388-410 2C423-445 2C 449-468 and 480-502 NC_002163.1 RefSeq region 1123450 1123518 . + . ID=id2179;Name=id2179;Dbxref=GeneID:905484;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1194 by TMHMM2.0 at aa 5-27 2C 32-51 2C 72-89 2C 109-128 2C133-155 2C 175-197 2C 276-298 2C 313-334 2C 346-368 2C 388-410 2C423-445 2C 449-468 and 480-502 NC_002163.1 RefSeq region 1123555 1123623 . + . ID=id2179;Name=id2179;Dbxref=GeneID:905484;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1194 by TMHMM2.0 at aa 5-27 2C 32-51 2C 72-89 2C 109-128 2C133-155 2C 175-197 2C 276-298 2C 313-334 2C 346-368 2C 388-410 2C423-445 2C 449-468 and 480-502 NC_002163.1 RefSeq region 1123633 1123692 . + . ID=id2179;Name=id2179;Dbxref=GeneID:905484;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1194 by TMHMM2.0 at aa 5-27 2C 32-51 2C 72-89 2C 109-128 2C133-155 2C 175-197 2C 276-298 2C 313-334 2C 346-368 2C 388-410 2C423-445 2C 449-468 and 480-502 NC_002163.1 RefSeq region 1123726 1123794 . + . ID=id2179;Name=id2179;Dbxref=GeneID:905484;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1194 by TMHMM2.0 at aa 5-27 2C 32-51 2C 72-89 2C 109-128 2C133-155 2C 175-197 2C 276-298 2C 313-334 2C 346-368 2C 388-410 2C423-445 2C 449-468 and 480-502 ### NC_002163.1 RefSeq CDS 1123823 1125001 . - 0 ID=cds1079;Parent=gene1144;gene=pyrC2;Name=YP_002344586.1;Dbxref=GOA:Q0P961 InterPro:IPR002048 InterPro:IPR006680 UniProtKB FTrEMBL:Q0P961 Genbank:YP_002344586.1 GeneID:905485;gbkey=CDS;product=dihydroorotase;Note=Catalyzes the reversible hydrolysis of the amide bond within dihydroorotate. This metabolic intermediate is required for the biosynthesis of pyrimidine nucleotides NC_002163.1 RefSeq gene 1123823 1125001 . - . ID=gene1144;gene=pyrC2;Name=pyrC2;locus_tag=Cj1195c;Dbxref=GeneID:905485;gbkey=Gene NC_002163.1 RefSeq region 1123931 1124878 . - . ID=id2181;gene=pyrC2;Name=id2181;Dbxref=GeneID:905485;gbkey=misc_feature;Note=HMMPfam hit to PF01979 2C Amidohydrolase family 2Cscore 0.096 NC_002163.1 RefSeq region 1124468 1124506 . - . ID=id2182;gene=pyrC2;Name=id2182;Dbxref=GeneID:905485;gbkey=misc_feature;Note=PS00018 EF-hand calcium-binding domain ### NC_002163.1 RefSeq CDS 1125011 1125907 . - 0 ID=cds1080;Parent=gene1145;gene=gpsA;Name=YP_002344587.1;Dbxref=GOA:Q9PN99 HSSP:P90551 InterPro:IPR006109 InterPro:IPR006168 InterPro:IPR011128 InterPro:IPR013328 InterPro:IPR016040 UniProtKB FSwiss-Prot:Q9PN99 Genbank:YP_002344587.1 GeneID:905486;gbkey=CDS;product=NAD 28P 29H-dependent glycerol-3-phosphate dehydrogenase;Note=catalyzes the NAD 28P 29H-dependent reduction of glycerol 3-phosphate to glycerone phosphate NC_002163.1 RefSeq gene 1125011 1125907 . - . ID=gene1145;gene=gpsA;Name=gpsA;locus_tag=Cj1196c;Dbxref=GeneID:905486;gbkey=Gene NC_002163.1 RefSeq region 1125029 1125460 . - . ID=id2183;gene=gpsA;Name=id2183;Dbxref=GeneID:905486;gbkey=misc_feature;Note=HMMPfam hit to PF07479 2C NAD-dependent glycerol-3-phosphate deh 2C score 6.7e-64 NC_002163.1 RefSeq region 1125461 1125907 . - . ID=id2184;gene=gpsA;Name=id2184;Dbxref=GeneID:905486;gbkey=misc_feature;Note=HMMPfam hit to PF01210 2C NAD-dependent glycerol-3-phosphate deh 2C score 2.4e-14 NC_002163.1 RefSeq gene 1125904 1127322 . - . ID=gene1146;gene=gatB;Name=gatB;locus_tag=Cj1197c;Dbxref=GeneID:905487;gbkey=Gene NC_002163.1 RefSeq CDS 1125904 1127322 . - 0 ID=cds1081;Parent=gene1146;gene=gatB;Name=YP_002344588.1;Dbxref=GOA:Q9PN98 InterPro:IPR003789 InterPro:IPR004413 InterPro:IPR006075 InterPro:IPR006107 UniProtKB FSwiss-Prot:Q9PN98 Genbank:YP_002344588.1 GeneID:905487;gbkey=CDS;product=aspartyl 2Fglutamyl-tRNA amidotransferase subunit B;Note=allows the formation of correctly charged Asn-tRNA 28Asn 29 or Gln-tRNA 28Gln 29 through the transamidation of misacylated Asp-tRNA 28Asn 29 or Glu-tRNA 28Gln 29 in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases 3B reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA 28Asn 29 or phospho-Glu-tRNA NC_002163.1 RefSeq region 1125910 1126353 . - . ID=id2185;gene=gatB;Name=id2185;Dbxref=GeneID:905487;gbkey=misc_feature;Note=HMMPfam hit to PF02637 2C GatB 2FYqey domain 2C score 2.1e-54 NC_002163.1 RefSeq region 1126357 1126554 . - . ID=id2186;gene=gatB;Name=id2186;Dbxref=GeneID:905487;gbkey=misc_feature;Note=HMMPfam hit to PF01162 2C PET112 family 2C C terminal region 2C score 5e-24 NC_002163.1 RefSeq region 1126612 1127322 . - . ID=id2187;gene=gatB;Name=id2187;Dbxref=GeneID:905487;gbkey=misc_feature;Note=HMMPfam hit to PF02934 2C PET112 family 2C N terminal region 2C score 7.9e-155 NC_002163.1 RefSeq region 1126861 1126908 . - . ID=id2188;gene=gatB;Name=id2188;Dbxref=GeneID:905487;gbkey=misc_feature;Note=PS01234 PET112 family signature ### NC_002163.1 UTR_Extractor 5'-UTR 1127323 1127345 . - . ID=utr431;locus_tag=Cj1197c;product=aspartyl 2Fglutamyl-tRNA amidotransferase subunit B NC_002163.1 UTR_Extractor 5'-UTR 1127413 1127436 . + . ID=utr432;locus_tag=Cj1198;product=S-ribosylhomocysteinase NC_002163.1 RefSeq gene 1127437 1127931 . + . ID=gene1147;Name=Cj1198;locus_tag=Cj1198;Dbxref=GeneID:905488;gbkey=Gene NC_002163.1 RefSeq CDS 1127437 1127931 . + 0 ID=cds1082;Parent=gene1147;Name=YP_002344589.1;Dbxref=GOA:Q9PN97 HSSP:P44007 InterPro:IPR003815 UniProtKB FSwiss-Prot:Q9PN97 Genbank:YP_002344589.1 GeneID:905488;gbkey=CDS;product=S-ribosylhomocysteinase;Note=catalyzes the hydrolysis of S-ribosylhomocysteine to homocysteine and autoinducer-2 NC_002163.1 RefSeq region 1127440 1127922 . + . ID=id2189;Name=id2189;Dbxref=GeneID:905488;gbkey=misc_feature;Note=HMMPfam hit to PF02664 2C S-Ribosylhomocysteinase 28LuxS 29 2C score 2.5e-98 ### NC_002163.1 RefSeq gene 1127994 1128130 . + . ID=NC_002163.1:CJnc110;Name=NC_002163.1:CJnc110;locus_tag=CJnc110 NC_002163.1 RefSeq sRNA 1127994 1128130 . + . ID=NC_002163.1:CJnc110:unknown_transcript_1;Parent=NC_002163.1:CJnc110;Name=NC_002163.1:CJnc110:unknown_transcript_1;locus_tag=CJnc110;gbkey=misc_RNA;product=CJnc110 NC_002163.1 RefSeq CDS 1128243 1129235 . + 0 ID=cds1083;Parent=gene1148;Name=YP_002344590.1;Dbxref=GOA:Q0P957 InterPro:IPR002283 InterPro:IPR005123 UniProtKB FTrEMBL:Q0P957 Genbank:YP_002344590.1 GeneID:905489;gbkey=CDS;product=iron 2Fascorbate-dependent oxidoreductase;Note=Original 282000 29 note: Cj1199 2C probable iron 2Fascorbate-dependent oxidoreductase 2C len: 330 aa 3B similar to many eukaryotic oxidoreductases e.g. LDOX_MALSP Malus sp. 28crab apple 29 leucoanthocyanidin dioxygenase 28EC 1.-.-.- 29 28357 aa 29 2C fasta scores 3B opt: 334 z-score: 386.2 E 28 29: 3.3e-14 2C 25.2 25 identity in 313 aa overlap 2C and ACCO_MALDO Malus domesticus 28apple 29 1-aminocyclopropane-1-carboxylate oxidase 28314 aa 29 2C fasta scores 3B opt: 301 z-score: 349.6 E 28 29: 3.6e-12 2C 26.7 25 identity in 303 aa overlap. No Hp match. Contains Pfam match to entry PF00671 Fe_Asc_oxidored 2C Iron 2FAscorbate family of oxidoreductases 7EUpdated 282006 29 note: Pfam domain PF03171 2OG-Fe 28II 29 oxygenase superfamily identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score has been carried out yet. kept in product function. Functional classification - Misc NC_002163.1 RefSeq gene 1128243 1129235 . + . ID=gene1148;Name=Cj1199;locus_tag=Cj1199;Dbxref=GeneID:905489;gbkey=Gene NC_002163.1 RefSeq region 1128747 1129040 . + . ID=id2190;Name=id2190;Dbxref=GeneID:905489;gbkey=misc_feature;Note=HMMPfam hit to PF03171 2C 2OG-Fe 28II 29 oxygenase superfamily 2C score 1.9e-25 NC_002163.1 RefSeq gene 1129228 1130016 . + . ID=gene1149;Name=Cj1200;locus_tag=Cj1200;Dbxref=GeneID:905490;gbkey=Gene NC_002163.1 RefSeq CDS 1129228 1130016 . + 0 ID=cds1084;Parent=gene1149;Name=YP_002344591.1;Dbxref=InterPro:IPR004872 UniProtKB FTrEMBL:Q0P956 Genbank:YP_002344591.1 GeneID:905490;gbkey=CDS;product=NLPA family lipoprotein;Note=Original 282000 29 note: Cj1200 2C probable periplasmic protein 2C len: 262 aa 3B similar to members of the nlpA family of outem membrane lipoproteins 2C e.g. NLPA_ECOLI lipoprotein-28 precursor 28272 aa 29 2C fasta scores 3B opt: 560 z-score: 650.6 E 28 29: 6.1e-29 2C 39.7 25 identity in 239 aa overlap 2C and PLPC_PASHA outer membrane lipoprotein 3 precursor 28263 aa 29 2C fasta scores 3B opt: 564 z-score: 655.4 E 28 29: 3.3e-29 2C 38.6 25 identity in 259 aa overlap. No Hp ortholog. Contains probable N-terminal signal sequence. Also similar to Cj0772c 2857.5 25 identity in 254 aa overlap 29 2C Cj0771c 2845.6 25 identity in 259 aa overlap 29 2C and Cj0770c 2844.9 25 identity in 256 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF03180 NLPA lipoprotein identified within CDS. Characterised in Escherichia coli as lipoprotein-28 precursor. Recent work has led to classification of some similar CDS 27s as D-methionine-binding lipoprotein metQ precursor. Product function modified to more specific family member. kept within product function. Functional classification -Miscellaneous periplasmic proteins 7EPMID:3003106 2C PMID:12169620 NC_002163.1 RefSeq region 1129315 1130013 . + . ID=id2191;Name=id2191;Dbxref=GeneID:905490;gbkey=misc_feature;Note=HMMPfam hit to PF03180 2C NLPA lipoprotein 2C score 3.8e-131 ### NC_002163.1 RefSeq CDS 1130028 1132292 . + 0 ID=cds1085;Parent=gene1150;gene=metE;Name=YP_002344592.1;Dbxref=GOA:Q9PN94 InterPro:IPR002629 InterPro:IPR006276 InterPro:IPR013215 UniProtKB FSwiss-Prot:Q9PN94 Genbank:YP_002344592.1 GeneID:905491;gbkey=CDS;product=5-methyltetrahydropteroyltriglutamate 2Fhomocysteine S-methyltransferase;Note=catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine to form methionine NC_002163.1 RefSeq gene 1130028 1132292 . + . ID=gene1150;gene=metE;Name=metE;locus_tag=Cj1201;Dbxref=GeneID:905491;gbkey=Gene NC_002163.1 RefSeq region 1131300 1132274 . + . ID=id2192;gene=metE;Name=id2192;Dbxref=GeneID:905491;gbkey=misc_feature;Note=HMMPfam hit to PF01717 2C Methionine synthase 2Cvitamin-B12 inde 2C score 6.4e-187 NC_002163.1 UTR_Extractor 5'-UTR 1132203 1132301 . + . ID=utr433;locus_tag=Cj1202;product=5 2C10-methylenetetrahydrofolate reductase ### NC_002163.1 RefSeq gene 1132302 1133150 . + . ID=gene1151;gene=metF;Name=metF;locus_tag=Cj1202;Dbxref=GeneID:905492;gbkey=Gene NC_002163.1 RefSeq CDS 1132302 1133150 . + 0 ID=cds1086;Parent=gene1151;gene=metF;Name=YP_002344593.1;Dbxref=GOA:Q0P954 InterPro:IPR003171 InterPro:IPR004620 UniProtKB FTrEMBL:Q0P954 Genbank:YP_002344593.1 GeneID:905492;gbkey=CDS;product=5 2C10-methylenetetrahydrofolate reductase;Note=Original 282000 29 note: Cj1202 2C metF 2C probable 5 2C10-methylenetetrahydrofolate reductase 2C len: 282 aa 3B similar to e.g. METF_ECOLI 5 2C10-methylenetetrahydrofolate reductase 28EC 1.7.99.5 29 28296 aa 29 2C fasta scores 3B opt: 529 z-score: 613.4 E 28 29: 7.2e-27 33.0 25 identity in 264 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02219 Methylenetetrahydrofolate reductase was identified within CDS. Characterised in Escherichia coli with marginal identity score. Appropriate motifs present. not added to product function. Functional classification -Central intermediary metabolism - General 7EPMID:6356036 2C PMID:10201405 NC_002163.1 RefSeq region 1132308 1133120 . + . ID=id2193;gene=metF;Name=id2193;Dbxref=GeneID:905492;gbkey=misc_feature;Note=HMMPfam hit to PF02219 2C Methylenetetrahydrofolate reductase 2C score 3.9e-72 ### NC_002163.1 RefSeq CDS 1133172 1133363 . - 0 ID=cds1087;Parent=gene1152;Name=YP_002344594.1;Dbxref=UniProtKB FTrEMBL:Q0P953 Genbank:YP_002344594.1 GeneID:905493;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj1203c 2C probable integral membrane protein 2C len: 63 aa 3B no Hp match 7EUpdated 282006 29 note: Two probable transmembrane helices predicted by TMHMM2.0. Functional classification -Central intermediary metabolism - General NC_002163.1 RefSeq gene 1133172 1133363 . - . ID=gene1152;Name=Cj1203c;locus_tag=Cj1203c;Dbxref=GeneID:905493;gbkey=Gene NC_002163.1 RefSeq region 1133211 1133279 . - . ID=id111;Name=id111;Dbxref=GeneID:905493;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1203c by TMHMM2.0 at aa 2-24 and 29-51 NC_002163.1 RefSeq region 1133292 1133360 . - . ID=id111;Name=id111;Dbxref=GeneID:905493;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1203c by TMHMM2.0 at aa 2-24 and 29-51 NC_002163.1 RefSeq CDS 1133360 1134040 . - 0 ID=cds1088;Parent=gene1153;gene=atpB;Name=YP_002344595.1;Dbxref=GOA:Q0P952 InterPro:IPR000568 UniProtKB FTrEMBL:Q0P952 Genbank:YP_002344595.1 GeneID:905494;gbkey=CDS;product=F0F1 ATP synthase subunit A;Note=Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit A is part of the membrane proton channel F0 NC_002163.1 RefSeq gene 1133360 1134040 . - . ID=gene1153;gene=atpB;Name=atpB;locus_tag=Cj1204c;Dbxref=GeneID:905494;gbkey=Gene NC_002163.1 RefSeq region 1133375 1133428 . - . ID=id112;gene=atpB;Name=id112;Dbxref=GeneID:905494;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1204c by TMHMM2.0 at aa 15-37 2C 76-98 2C 103-122 2C 134-156 2C176-198 and 205-222 NC_002163.1 RefSeq region 1133387 1133824 . - . ID=id2194;gene=atpB;Name=id2194;Dbxref=GeneID:905494;gbkey=misc_feature;Note=HMMPfam hit to PF00119 2C ATP synthase A chain 2C score 1.5e-29 NC_002163.1 RefSeq region 1133447 1133515 . - . ID=id112;gene=atpB;Name=id112;Dbxref=GeneID:905494;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1204c by TMHMM2.0 at aa 15-37 2C 76-98 2C 103-122 2C 134-156 2C176-198 and 205-222 NC_002163.1 RefSeq region 1133528 1133557 . - . ID=id2195;gene=atpB;Name=id2195;Dbxref=GeneID:905494;gbkey=misc_feature;Note=PS00449 ATP synthase a subunit signature NC_002163.1 RefSeq region 1133573 1133641 . - . ID=id112;gene=atpB;Name=id112;Dbxref=GeneID:905494;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1204c by TMHMM2.0 at aa 15-37 2C 76-98 2C 103-122 2C 134-156 2C176-198 and 205-222 NC_002163.1 RefSeq region 1133675 1133734 . - . ID=id112;gene=atpB;Name=id112;Dbxref=GeneID:905494;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1204c by TMHMM2.0 at aa 15-37 2C 76-98 2C 103-122 2C 134-156 2C176-198 and 205-222 NC_002163.1 RefSeq region 1133747 1133815 . - . ID=id112;gene=atpB;Name=id112;Dbxref=GeneID:905494;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1204c by TMHMM2.0 at aa 15-37 2C 76-98 2C 103-122 2C 134-156 2C176-198 and 205-222 NC_002163.1 RefSeq region 1133930 1133998 . - . ID=id112;gene=atpB;Name=id112;Dbxref=GeneID:905494;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1204c by TMHMM2.0 at aa 15-37 2C 76-98 2C 103-122 2C 134-156 2C176-198 and 205-222 ### NC_002163.1 UTR_Extractor 5'-UTR 1134041 1134067 . - . ID=utr434;locus_tag=Cj1204c;product=F0F1 ATP synthase subunit A NC_002163.1 RefSeq CDS 1134109 1135449 . - 0 ID=cds1089;Parent=gene1154;gene=radA;Name=YP_002344596.1;Dbxref=GOA:Q9PN90 InterPro:IPR001984 InterPro:IPR003593 InterPro:IPR004504 InterPro:IPR007694 UniProtKB FSwiss-Prot:Q9PN90 Genbank:YP_002344596.1 GeneID:905495;gbkey=CDS;product=DNA repair protein RadA;Note=Sms 3B stabilizes the strand-invasion intermediate during the DNA repair 3B involved in recombination of donor DNA and plays an important role in DNA damage repair after exposure to mutagenic agents NC_002163.1 RefSeq gene 1134109 1135449 . - . ID=gene1154;gene=radA;Name=radA;locus_tag=Cj1205c;Dbxref=GeneID:905495;gbkey=Gene NC_002163.1 RefSeq region 1134793 1135251 . - . ID=id2196;gene=radA;Name=id2196;Dbxref=GeneID:905495;gbkey=misc_feature;Note=HMMPfam hit to PF03796 2C DnaB-like helicase C terminal domain 2C score 0.00015 NC_002163.1 RefSeq region 1135141 1135164 . - . ID=id2197;gene=radA;Name=id2197;Dbxref=GeneID:905495;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 1135449 1136315 . - 0 ID=cds1090;Parent=gene1155;gene=ftsY;Name=YP_002344597.1;Dbxref=GOA:Q0P950 InterPro:IPR000897 InterPro:IPR003593 InterPro:IPR004390 UniProtKB FTrEMBL:Q0P950 Genbank:YP_002344597.1 GeneID:905496;gbkey=CDS;product=signal recognition particle protein;Note=Original 282000 29 note: Cj1206c 2C ftsY 2C probable signal recognition particle protein 2C len: 288 aa 3B similar to e.g. FTSY_ECOLI cell division protein FTSY 28497 aa 29 2Cfasta scores 3B opt: 663 z-score: 759.0 E 28 29: 0 2C 43.3 25 identity in 298 aa overlap 2C and PILA_NEIME probable signal recognition particle protein 28421 aa 29 2C fasta scores 3B opt: 633 z-score: 726.0 E 28 29: 3.8e-33 2C 39.9 25 identity in 298 aa overlap. 48.6 25 identity to HP0763. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00300 SRP54-type proteins GTP-binding domain signature 2C and Pfam match to entry PF00448 SRP54 2C SRP54-type protein. Also similar to Cj0709 ffh 2831.4 25 identity in 271 aa overlap 29 7EUpdated 282006 29 note: Similar to more than one bacteria with acceptable identity score. kept within product function. Functional classification -Protein and peptide secretion 7EPMID:10048040 2C PMID:9188744 2C PMID:8194520 NC_002163.1 RefSeq gene 1135449 1136315 . - . ID=gene1155;gene=ftsY;Name=ftsY;locus_tag=Cj1206c;Dbxref=GeneID:905496;gbkey=Gene NC_002163.1 RefSeq region 1135464 1136072 . - . ID=id2198;gene=ftsY;Name=id2198;Dbxref=GeneID:905496;gbkey=misc_feature;Note=HMMPfam hit to PF00448 2C SRP54-type protein 2C GTPase domain 2C score 1.4e-102 NC_002163.1 RefSeq region 1135506 1135547 . - . ID=id2199;gene=ftsY;Name=id2199;Dbxref=GeneID:905496;gbkey=misc_feature;Note=PS00300 SRP54-type proteins GTP-binding domain signature NC_002163.1 RefSeq region 1136025 1136048 . - . ID=id2200;gene=ftsY;Name=id2200;Dbxref=GeneID:905496;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 1136315 1136872 . - 0 ID=cds1091;Parent=gene1156;Name=YP_002344598.1;Dbxref=GOA:Q0P949 InterPro:IPR006662 InterPro:IPR012335 InterPro:IPR013740 InterPro:IPR015467 UniProtKB FTrEMBL:Q0P949 Genbank:YP_002344598.1 GeneID:905497;gbkey=CDS;product=lipoprotein thiredoxin;Note=Original 282000 29 note: Cj1207c 2C possible lipoprotein thiredoxin 2C len: 185 aa 3B some similarity to TR:G4100188 28EMBL:U95250 29 Treponema pallidum predicted thioredoxin 28185 aa 29 2C fasta scores 3B opt: 196 z-score: 242.3 E 28 29: 3.4e-06 2C 31.5 25 identity in 111 aa overlap 2C and HELX_RHOCA thiol:disulfide interchange protein 28176 aa 29 2C fatsa scores 3B opt: 153 z-score: 192.6 E 28 29: 0.002 2C 23.2 25 identity in 142 aa overlap. 23.7 25 identity to HP0762. Also similar to Cj1106 2829.4 25 identity in 201 aa overlap 29. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site 7EUpdated 282006 29 note: Prosite domain PS50223 THIOREDOXIN_2 2C Thioredoxin domain 2 was identified within CDS. Further support given to product function. kept within product function. Functional classification -Energy metabolism - Electron transport NC_002163.1 RefSeq gene 1136315 1136872 . - . ID=gene1156;gene=Cj1207c;Name=Cj1207c;locus_tag=Cj1207c;Dbxref=GeneID:905497;gbkey=Gene NC_002163.1 RefSeq region 1136816 1136848 . - . ID=id2201;Name=id2201;Dbxref=GeneID:905497;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 UTR_Extractor 5'-UTR 1136873 1136906 . - . ID=utr435;locus_tag=Cj1207c;product=putative lipoprotein thiredoxin NC_002163.1 UTR_Extractor 5'-UTR 1136921 1136954 . + . ID=utr436;locus_tag=Cj1208;product=putative 5-formyltetrahydrofolate cyclo-ligase family protein NC_002163.1 RefSeq CDS 1136955 1137581 . + 0 ID=cds1092;Parent=gene1157;Name=YP_002344599.1;Dbxref=GOA:Q0P948 InterPro:IPR002698 UniProtKB FTrEMBL:Q0P948 Genbank:YP_002344599.1 GeneID:905498;gbkey=CDS;product=5-formyltetrahydrofolate cyclo-ligase;Note=Original 282000 29 note: Cj1208 2C unknown 2C len: 208 aa 3B similar to hypothetical proteins e.g. YGFA_HAEIN HI0858 28187 aa 29 2C fasta scores 3B opt: 150 z-score: 196.6 E 28 29: 0.0012 2C 26.8 25 identity in 164 aa overlap. 27.8 25 identity to HP0761 7EUpdated 282006 29 note: One probable transmembrane helix predicted by TMHMM2.0. Pfam domain PF01812 5-formyltetrahydrofolate cyclo-ligase family identified within CDS. Product modified to more specific family member based on motif match. No specific characterisation has been carried out in related bacteria 2C so kept within product function. Functional classification -Purine ribonucleotide biosynthesis NC_002163.1 RefSeq gene 1136955 1137581 . + . ID=gene1157;Name=Cj1208;locus_tag=Cj1208;Dbxref=GeneID:905498;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 1137210 1137501 . + . ID=utr437;locus_tag=Cj1209;product=phosphodiesterase NC_002163.1 RefSeq gene 1137502 1139055 . + . ID=gene1158;Name=Cj1209;locus_tag=Cj1209;Dbxref=GeneID:905499;gbkey=Gene NC_002163.1 RefSeq CDS 1137502 1139055 . + 0 ID=cds1093;Parent=gene1158;Name=YP_002344600.1;Dbxref=GOA:Q9PN86 InterPro:IPR003607 InterPro:IPR004087 InterPro:IPR004088 InterPro:IPR006674 InterPro:IPR006675 InterPro:IPR017705 UniProtKB FSwiss-Prot:Q9PN86 Genbank:YP_002344600.1 GeneID:905499;gbkey=CDS;product=phosphodiesterase;Note=protein from Staphylococcus aureus has phosphodiesterase activity against 2 27-3 27-cAMP and 2 27-3 27-cGMP NC_002163.1 RefSeq region 1137514 1137567 . + . ID=id2202;Name=id2202;Dbxref=GeneID:905498;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1209 by TMHMM2.0 at aa 5-22 NC_002163.1 RefSeq region 1138123 1138302 . + . ID=id2203;Name=id2203;Dbxref=GeneID:905499;gbkey=misc_feature;Note=HMMPfam hit to PF00013 2C KH domain 2C score 3.5e-05 NC_002163.1 RefSeq region 1138498 1138779 . + . ID=id2204;Name=id2204;Dbxref=GeneID:905499;gbkey=misc_feature;Note=HMMPfam hit to PF01966 2C HD domain 2C score 7.9e-20 ### NC_002163.1 RefSeq CDS 1139064 1139621 . + 0 ID=cds1094;Parent=gene1159;Name=YP_002344601.1;Dbxref=GOA:Q0P946 InterPro:IPR015414 UniProtKB FTrEMBL:Q0P946 Genbank:YP_002344601.1 GeneID:905500;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj1210 2C probable integral membrane protein 2C len: 185 aa 3B similar to members of the dedA family e.g. DEDA_ECOLI DEDA protein 28219 aa 29 2C fasta scores 3B opt: 193 z-score: 248.3 E 28 29: 1.6e-06 2C 26.7 25 identity in 172 aa overlap. 35.6 25 identity to HP1162. Also similar to Cj0928 2827.7 25 identity in 177 aa overlap 29 2C and Cj1168c 2823.0 25 identity in 200 aa overlap 29. Contains Pfam match to entry PF00597 DedA 2C DedA family 7EUpdated 282006 29 note: Four probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 1139064 1139621 . + . ID=gene1159;Name=Cj1210;locus_tag=Cj1210;Dbxref=GeneID:905500;gbkey=Gene NC_002163.1 RefSeq region 1139100 1139168 . + . ID=id2205;Name=id2205;Dbxref=GeneID:905500;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1210 by TMHMM2.0 at aa 13-35 2C 45-67 2C 124-146 and 161-180 NC_002163.1 RefSeq region 1139103 1139552 . + . ID=id2206;Name=id2206;Dbxref=GeneID:905500;gbkey=misc_feature;Note=HMMPfam hit to PF00597 2C DedA family 2C score 2.4e-05 NC_002163.1 RefSeq region 1139196 1139264 . + . ID=id2205;Name=id2205;Dbxref=GeneID:905500;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1210 by TMHMM2.0 at aa 13-35 2C 45-67 2C 124-146 and 161-180 NC_002163.1 RefSeq region 1139433 1139501 . + . ID=id2205;Name=id2205;Dbxref=GeneID:905500;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1210 by TMHMM2.0 at aa 13-35 2C 45-67 2C 124-146 and 161-180 NC_002163.1 RefSeq region 1139544 1139603 . + . ID=id2205;Name=id2205;Dbxref=GeneID:905500;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1210 by TMHMM2.0 at aa 13-35 2C 45-67 2C 124-146 and 161-180 NC_002163.1 RefSeq gene 1139621 1140880 . + . ID=gene1160;Name=Cj1211;locus_tag=Cj1211;Dbxref=GeneID:905501;gbkey=Gene NC_002163.1 RefSeq CDS 1139621 1140880 . + 0 ID=cds1095;Parent=gene1160;Name=YP_002344602.1;Dbxref=InterPro:IPR004477 UniProtKB FTrEMBL:Q0P945 Genbank:YP_002344602.1 GeneID:905501;gbkey=CDS;product=competence family protein;Note=Original 282000 29 note: Cj1211 2C probable integral membrane protein 2C len: 419 aa 3B similar to hypothetical membrane proteins e.g. TR:O51537 28EMBL:AE001160 29 BB0591 28416 aa 29 2C fasta scores 3B opt: 222 z-score: 251.2 E 28 29: 1.1e-06 2C 26.4 25 identity in 405 aa overlap. 33.9 25 identity to HP1361 28called competence locus E 28comE3 29 29 7EUpdated 282006 29 note: Pfam motif PF03772 Competence protein was identified within CDS. Nine probable transmembrane helices predicted by TMHMM2.0. Product function modified to more specific family member based on motif match. No specific characterisation with acceptable identity score carried out yet 2C so kept in product function. Functional classification - Membranes 2Clipoproteins and porins 7EPMID:7968523 NC_002163.1 RefSeq region 1139663 1139731 . + . ID=id2207;Name=id2207;Dbxref=GeneID:905501;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1211 by TMHMM2.0 at aa 15-37 2C 176-198 2C 213-235 2C 242-264 2C274-294 2C 307-329 2C 334-356 2C 369-391 and 401-418 NC_002163.1 RefSeq region 1140071 1140850 . + . ID=id2208;Name=id2208;Dbxref=GeneID:905501;gbkey=misc_feature;Note=HMMPfam hit to PF03772 2C Competence protein 2C score 5.4e-67 NC_002163.1 RefSeq region 1140146 1140214 . + . ID=id2207;Name=id2207;Dbxref=GeneID:905501;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1211 by TMHMM2.0 at aa 15-37 2C 176-198 2C 213-235 2C 242-264 2C274-294 2C 307-329 2C 334-356 2C 369-391 and 401-418 NC_002163.1 RefSeq region 1140257 1140325 . + . ID=id2207;Name=id2207;Dbxref=GeneID:905501;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1211 by TMHMM2.0 at aa 15-37 2C 176-198 2C 213-235 2C 242-264 2C274-294 2C 307-329 2C 334-356 2C 369-391 and 401-418 NC_002163.1 RefSeq region 1140266 1140298 . + . ID=id2209;Name=id2209;Dbxref=GeneID:905501;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1140344 1140412 . + . ID=id2207;Name=id2207;Dbxref=GeneID:905501;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1211 by TMHMM2.0 at aa 15-37 2C 176-198 2C 213-235 2C 242-264 2C274-294 2C 307-329 2C 334-356 2C 369-391 and 401-418 NC_002163.1 RefSeq region 1140440 1140502 . + . ID=id2207;Name=id2207;Dbxref=GeneID:905501;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1211 by TMHMM2.0 at aa 15-37 2C 176-198 2C 213-235 2C 242-264 2C274-294 2C 307-329 2C 334-356 2C 369-391 and 401-418 NC_002163.1 RefSeq region 1140539 1140607 . + . ID=id2207;Name=id2207;Dbxref=GeneID:905501;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1211 by TMHMM2.0 at aa 15-37 2C 176-198 2C 213-235 2C 242-264 2C274-294 2C 307-329 2C 334-356 2C 369-391 and 401-418 NC_002163.1 RefSeq region 1140620 1140688 . + . ID=id2207;Name=id2207;Dbxref=GeneID:905501;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1211 by TMHMM2.0 at aa 15-37 2C 176-198 2C 213-235 2C 242-264 2C274-294 2C 307-329 2C 334-356 2C 369-391 and 401-418 NC_002163.1 RefSeq region 1140725 1140793 . + . ID=id2207;Name=id2207;Dbxref=GeneID:905501;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1211 by TMHMM2.0 at aa 15-37 2C 176-198 2C 213-235 2C 242-264 2C274-294 2C 307-329 2C 334-356 2C 369-391 and 401-418 NC_002163.1 RefSeq region 1140821 1140874 . + . ID=id2207;Name=id2207;Dbxref=GeneID:905501;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1211 by TMHMM2.0 at aa 15-37 2C 176-198 2C 213-235 2C 242-264 2C274-294 2C 307-329 2C 334-356 2C 369-391 and 401-418 NC_002163.1 RefSeq gene 1140824 1141630 . - . ID=gene1161;gene=rbn;Name=rbn;locus_tag=Cj1212c;Dbxref=GeneID:905502;gbkey=Gene NC_002163.1 RefSeq CDS 1140824 1141630 . - 0 ID=cds1096;Parent=gene1161;gene=rbn;Name=YP_002344603.1;Dbxref=GOA:Q0P944 InterPro:IPR004664 InterPro:IPR017039 UniProtKB FTrEMBL:Q0P944 Genbank:YP_002344603.1 GeneID:905502;gbkey=CDS;product=ribonuclease BN;Note=Original 282000 29 note: Cj1212c 2C rbn 2C possible ribonuclease BN 2C len: RBN_ECOLI ribonuclease BN 28EC 3.1.-.- 29 28290 aa 29 2C fasta scores 3B opt: 365 z-score: 430.3 E 28 29: 1.1e-16 2C 28.5 25 identity in 242 aa overlap. 29.2 25 identity to HP1407 7EUpdated 282006 29 note: Six probable transmembrane helices predicted by TMHMM2.0. Characterised in Escherichia coli with marginal identity score. kept within product function. Functional classification -Aminoacyl tRNA synthetases and their modification 7EPMID:8955422 NC_002163.1 RefSeq region 1140866 1141597 . - . ID=id2210;gene=rbn;Name=id2210;Dbxref=GeneID:905502;gbkey=misc_feature;Note=HMMPfam hit to PF03631 2C Ribonuclease BN-like family 2C score 1.1e-66 NC_002163.1 RefSeq region 1140905 1140973 . - . ID=id113;gene=rbn;Name=id113;Dbxref=GeneID:905502;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1212c by TMHMM2.0 at aa 20-42 2C 86-108 2C 123-145 2C 157-176 2C191-213 and 220-242 NC_002163.1 RefSeq region 1140992 1141060 . - . ID=id113;gene=rbn;Name=id113;Dbxref=GeneID:905502;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1212c by TMHMM2.0 at aa 20-42 2C 86-108 2C 123-145 2C 157-176 2C191-213 and 220-242 NC_002163.1 RefSeq region 1141103 1141162 . - . ID=id113;gene=rbn;Name=id113;Dbxref=GeneID:905502;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1212c by TMHMM2.0 at aa 20-42 2C 86-108 2C 123-145 2C 157-176 2C191-213 and 220-242 NC_002163.1 RefSeq region 1141196 1141264 . - . ID=id113;gene=rbn;Name=id113;Dbxref=GeneID:905502;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1212c by TMHMM2.0 at aa 20-42 2C 86-108 2C 123-145 2C 157-176 2C191-213 and 220-242 NC_002163.1 RefSeq region 1141307 1141375 . - . ID=id113;gene=rbn;Name=id113;Dbxref=GeneID:905502;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1212c by TMHMM2.0 at aa 20-42 2C 86-108 2C 123-145 2C 157-176 2C191-213 and 220-242 NC_002163.1 RefSeq region 1141505 1141573 . - . ID=id113;gene=rbn;Name=id113;Dbxref=GeneID:905502;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1212c by TMHMM2.0 at aa 20-42 2C 86-108 2C 123-145 2C 157-176 2C191-213 and 220-242 ### NC_002163.1 RefSeq CDS 1141634 1143016 . - 0 ID=cds1097;Parent=gene1162;gene=glcD;Name=YP_002344604.1;Dbxref=GOA:Q0P943 InterPro:IPR004113 InterPro:IPR006094 InterPro:IPR016167 InterPro:IPR016168 UniProtKB FTrEMBL:Q0P943 Genbank:YP_002344604.1 GeneID:905503;gbkey=CDS;product=glycolate oxidase subunit D;Note=Original 282000 29 note: Cj1213c 2C glcD 2C probable glycolate oxidase subunit D 2C len: 460 aa 3B similar to e.g. GLCD_ECOLI glycolate oxidase subunit GLCD 28499 aa 29 2C fasta scores 3B opt: 952 z-score: 1099.5 E 28 29: 0 2C 37.0 25 identity in 419 aa overlap. 64.8 25 identity to HP0509 7EUpdated 282006 29 note: Pfam domains PF02913 FAD linked oxidases 2C C-terminal domain and PF01565 FAD binding domain were identified within CDS. Further support given to product function. Characterised in Escherichia coli with marginal identity score. kept in product function. Functional classification - Degradation - Carbon compounds 7EPMID:8606183 2C PMID:11283302 NC_002163.1 RefSeq gene 1141634 1143016 . - . ID=gene1162;gene=glcD;Name=glcD;locus_tag=Cj1213c;Dbxref=GeneID:905503;gbkey=Gene NC_002163.1 RefSeq region 1141643 1142374 . - . ID=id2211;gene=glcD;Name=id2211;Dbxref=GeneID:905503;gbkey=misc_feature;Note=HMMPfam hit to PF02913 2C FAD linked oxidases 2CC-terminal domain 2C score 1.4e-99 NC_002163.1 RefSeq region 1142414 1142902 . - . ID=id2212;gene=glcD;Name=id2212;Dbxref=GeneID:905503;gbkey=misc_feature;Note=HMMPfam hit to PF01565 2C FAD binding domain 2C score 3.5e-71 ### NC_002163.1 RefSeq gene 1143019 1143744 . - . ID=gene1163;Name=Cj1214c;locus_tag=Cj1214c;Dbxref=GeneID:905504;gbkey=Gene NC_002163.1 RefSeq CDS 1143019 1143744 . - 0 ID=cds1098;Parent=gene1163;Name=YP_002344605.1;Dbxref=UniProtKB FTrEMBL:Q0P942 Genbank:YP_002344605.1 GeneID:905504;gbkey=CDS;product=exporting protein;Note=Original 282000 29 note: Cj1214c 2C unknown 2C len: 241 aa 3B similar to N-terminal half of HP0508 28452 aa 29 2824.9 25 identity in 245 aa overlap 29 7EUpdated 282006 29 note: One signal peptide predicted by SignalP 2.0 HMM. Product function modified to more specific family member. kept within product function. Paper identified linking protein to glycoprotein 28PMID:12186869 29. Functional classification -Transport 2Fbinding proteins - Other 7EPMID:12186869 NC_002163.1 UTR_Extractor 5'-UTR 1143745 1143791 . - . ID=utr438;locus_tag=Cj1214c;product=putative exporting protein NC_002163.1 UTR_Extractor 5'-UTR 1143826 1143865 . + . ID=utr439;locus_tag=Cj1215;product=putative peptidase M23 family protein NC_002163.1 RefSeq CDS 1143866 1145026 . + 0 ID=cds1099;Parent=gene1164;Name=YP_002344606.1;Dbxref=GOA:Q0P941 InterPro:IPR002886 InterPro:IPR016047 UniProtKB FTrEMBL:Q0P941 Genbank:YP_002344606.1 GeneID:905505;gbkey=CDS;product=peptidase M23 family protein;Note=Original 282000 29 note: Cj1215 2C probable periplasmic protein 2C len: 386 aa 3B similar to hypothetical proteins e.g. YEBA_ECOLI 28419 aa 29 2C fasta scores 3B opt: 491 z-score: 556.7 E 28 29: 1e-23 2C 30.2 25 identity in 338 aa overlap. 44.0 25 identity to HP0506. Also similar 2C in part 2C to Cj1087c 2840.6 25 identity in 133 aa overlap 29 2C and Cj1235 2829.6 25 identity in 206 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01551 Peptidase family M23 identified within CDS. Further support given to product function. Product modified to more specific family member based on motif results. No specific characterisation has been carried out yet 2C so kept within product function. Functional classification -Degradation of macromolecules - Proteins 2C peptides and glycopeptides NC_002163.1 RefSeq gene 1143866 1145026 . + . ID=gene1164;Name=Cj1215;locus_tag=Cj1215;Dbxref=GeneID:905505;gbkey=Gene NC_002163.1 RefSeq region 1144574 1144864 . + . ID=id2213;Name=id2213;Dbxref=GeneID:905505;gbkey=misc_feature;Note=HMMPfam hit to PF01551 2C Peptidase family M23 2C score 3.6e-53 NC_002163.1 RefSeq gene 1145023 1145226 . - . ID=gene1165;Name=Cj1216c;locus_tag=Cj1216c;Dbxref=GeneID:905506;gbkey=Gene NC_002163.1 RefSeq CDS 1145023 1145226 . - 0 ID=cds1100;Parent=gene1165;Name=YP_002344607.1;Dbxref=UniProtKB FTrEMBL:Q0P940 Genbank:YP_002344607.1 GeneID:905506;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1216c 2C unknown 2C len: 67 aa 3B no Hp match. Functional classification - Unknown ### NC_002163.1 RefSeq CDS 1145228 1145908 . - 0 ID=cds1101;Parent=gene1166;Name=YP_002344608.1;Dbxref=InterPro:IPR003730 UniProtKB FSwiss-Prot:Q9PN78 Genbank:YP_002344608.1 GeneID:905507;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1217c 2C unknown 2C len: 226 aa 3B similar to hypothetical proteins e.g. YFIH_ECOLI 28243 aa 29 2C fasta scores 3B opt: 262 z-score: 319.9 E 28 29: 1.6e-10 2C30.3 25 identity in 185 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02578 Uncharacterised ACR 2C YfiH family COG1496 identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 1145228 1145908 . - . ID=gene1166;Name=Cj1217c;locus_tag=Cj1217c;Dbxref=GeneID:905507;gbkey=Gene NC_002163.1 RefSeq region 1145234 1145893 . - . ID=id2214;Name=id2214;Dbxref=GeneID:905507;gbkey=misc_feature;Note=HMMPfam hit to PF02578 2C Uncharacterised ACR 2C YfiH family COG1496 2C score 2.3e-21 NC_002163.1 RefSeq gene 1145872 1146483 . - . ID=gene1167;gene=ribA;Name=ribA;locus_tag=Cj1218c;Dbxref=GeneID:905508;gbkey=Gene NC_002163.1 RefSeq CDS 1145872 1146483 . - 0 ID=cds1102;Parent=gene1167;gene=ribA;Name=YP_002344609.1;Dbxref=GOA:Q0P938 InterPro:IPR001783 UniProtKB FTrEMBL:Q0P938 Genbank:YP_002344609.1 GeneID:905508;gbkey=CDS;product=riboflavin synthase subunit alpha;Note=catalyzes the formation of riboflavin from 6 2C7-dimethyl-8- 281-D-ribityl 29lumazine NC_002163.1 RefSeq region 1145962 1146216 . - . ID=id2215;gene=ribA;Name=id2215;Dbxref=GeneID:905508;gbkey=misc_feature;Note=HMMPfam hit to PF00677 2C Lumazine binding domain 2Cscore 2.3e-25 ### NC_002163.1 RefSeq gene 1146492 1149032 . - . ID=gene1168;Name=Cj1219c;locus_tag=Cj1219c;Dbxref=GeneID:905509;gbkey=Gene NC_002163.1 RefSeq CDS 1146492 1149032 . - 0 ID=cds1103;Parent=gene1168;Name=YP_002344610.1;Dbxref=UniProtKB FTrEMBL:Q0P937 Genbank:YP_002344610.1 GeneID:905509;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1219c 2C probable periplasmic protein 2C len: 846 aa 3B 27.3 25 identity to HP0358. Weak similarity to FLID_ECOLI flagellar hook-associated protein 2 28467 aa 29 2C fasta scores 3B opt: 168 z-score: 180.0 E 28 29: 0.0099 2C 24.2 25 identity in 446 aa overlap 2C and to Cj0530 2822.1 25 identity in 891 aa overlap 29. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 1148952 1149020 . - . ID=id2216;Name=id2216;Dbxref=GeneID:905509;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1219c by TMHMM2.0 at aa 5-27 ### NC_002163.1 UTR_Extractor 5'-UTR 1149033 1149261 . - . ID=utr440;locus_tag=Cj1219c;product=putative periplasmic protein NC_002163.1 RefSeq minus_35_signal 1149110 1149115 . + . ID=id2217;Name=id2217;gbkey=-35_signal NC_002163.1 RefSeq minus_10_signal 1149133 1149138 . + . ID=id2218;Name=id2218;gbkey=-10_signal NC_002163.1 UTR_Extractor 5'-UTR 1149145 1149193 . + . ID=utr441;locus_tag=Cj1220;product=co-chaperonin GroES NC_002163.1 RefSeq gene 1149194 1149454 . + . ID=gene1169;gene=groES;Name=groES;locus_tag=Cj1220;Dbxref=GeneID:905510;gbkey=Gene NC_002163.1 RefSeq CDS 1149194 1149454 . + 0 ID=cds1104;Parent=gene1169;gene=groES;Name=YP_002344611.1;Dbxref=GOA:P56970 HSSP:P09621 InterPro:IPR001476 UniProtKB FSwiss-Prot:P56970 Genbank:YP_002344611.1 GeneID:905510;gbkey=CDS;product=co-chaperonin GroES;Note=10 kDa chaperonin 3B Cpn10 3B GroES 3B forms homoheptameric ring 3B binds to one or both ends of the GroEL double barrel in the presence of adenine nucleotides capping it 3B folding of unfolded substrates initiates in a GroEL-substrate bound and capped by GroES 3B release of the folded substrate is dependent on ATP binding and hydrolysis in the trans ring NC_002163.1 RefSeq region 1149197 1149451 . + . ID=id2219;gene=groES;Name=id2219;Dbxref=GeneID:905510;gbkey=misc_feature;Note=HMMPfam hit to PF00166 2C Chaperonin 10 Kd subunit 2Cscore 5.4e-35 ### NC_002163.1 RefSeq CDS 1149475 1151112 . + 0 ID=cds1105;Parent=gene1170;gene=groEL;Name=YP_002344612.1;Dbxref=GOA:O69289 HSSP:Q9Z462 InterPro:IPR001844 InterPro:IPR002423 InterPro:IPR012723 UniProtKB FSwiss-Prot:O69289 Genbank:YP_002344612.1 GeneID:905511;gbkey=CDS;product=molecular chaperone GroEL;Note=60 kDa chaperone family 3B promotes refolding of misfolded polypeptides especially under stressful conditions 3B forms two stacked rings of heptamers to form a barrel-shaped 14mer 3B ends can be capped by GroES 3B misfolded proteins enter the barrel where they are refolded when GroES binds 3B many bacteria have multiple copies of the groEL gene which are active under different environmental conditions 3B the B.japonicum protein in this cluster is expressed constitutively 3B in Rhodobacter 2C Corynebacterium and Rhizobium this protein is essential for growth NC_002163.1 RefSeq gene 1149475 1151112 . + . ID=gene1170;gene=groEL;Name=groEL;locus_tag=Cj1221;Dbxref=GeneID:905511;gbkey=Gene NC_002163.1 RefSeq region 1149538 1151043 . + . ID=id2220;gene=groEL;Name=id2220;Dbxref=GeneID:905511;gbkey=misc_feature;Note=HMMPfam hit to PF00118 2C TCP-1 2Fcpn60 chaperonin family 2C score 5.5e-196 NC_002163.1 RefSeq region 1150684 1150719 . + . ID=id2221;gene=groEL;Name=id2221;Dbxref=GeneID:905511;gbkey=misc_feature;Note=PS00296 Chaperonins cpn60 signature NC_002163.1 RefSeq gene 1151053 1151149 . + . ID=NC_002163.1:CJnc120;Name=NC_002163.1:CJnc120;locus_tag=CJnc120 NC_002163.1 RefSeq sRNA 1151053 1151149 . + . ID=NC_002163.1:CJnc120:unknown_transcript_1;Parent=NC_002163.1:CJnc120;Name=NC_002163.1:CJnc120:unknown_transcript_1;locus_tag=CJnc120;gbkey=misc_RNA;product=CJnc120 ### NC_002163.1 RefSeq CDS 1151155 1152345 . - 0 ID=cds1106;Parent=gene1171;gene=dccS;Name=YP_002344613.1;Dbxref=GOA:Q0P934 InterPro:IPR003594 InterPro:IPR003661 InterPro:IPR004358 InterPro:IPR005467 UniProtKB FTrEMBL:Q0P934 Genbank:YP_002344613.1 GeneID:905512;gbkey=CDS;product=two-component sensor histidine kinase;Note=Original 282000 29 note: Cj1222c 2C probable two-component sensor 28histidine kinase 29 2C len: 396 aa 3B similar to many sensor proteins e.g. RSTB_ECOLI sensor protein RSTB 28433 aa 29 2C fasta scores 3B opt: 226 z-score: 267.7 E 28 29: 1.3e-07 2C 24.5 25 identity in 237 aa overlap. 28.5 25 identity to HP1364. Contains Pfam match to entry PF00512 signal 2C Signal carboxyl-terminal domain 2C and two possible membrane spanning domains 7EUpdated 282006 29 note: Pfam domains PF02518 Histidine kinase- 2C DNA gyrase B- 2C and HSP90-like ATPase motif and PF00512 His Kinase A 28phosphoacceptor 29 domain were identified within CDS. Prosite domain PS50109 HIS_KIN 2CHistidine kinase domain profile was also identified within CDS. Also 2C two probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised in Campylobacter jejuni. Literature search identified characterisation paper where Cj1222c and Cj1223c were shown to be required for optimal colonization and were termed dccRS 28diminished capacity to colonize 29 two-component system. Functional classification - Signal transduction 7EPMID:15554967 NC_002163.1 RefSeq gene 1151155 1152345 . - . ID=gene1171;gene=dccS;Name=dccS;locus_tag=Cj1222c;Dbxref=GeneID:905512;gbkey=Gene NC_002163.1 RefSeq region 1151161 1151460 . - . ID=id2222;gene=dccS;Name=id2222;Dbxref=GeneID:905512;gbkey=misc_feature;Note=HMMPfam hit to PF02518 2C Histidine kinase- 2C DNA gyrase B- 2C and HSP90 2C score 6e-20 NC_002163.1 RefSeq region 1151584 1151775 . - . ID=id2223;gene=dccS;Name=id2223;Dbxref=GeneID:905512;gbkey=misc_feature;Note=HMMPfam hit to PF00512 2C His Kinase A 28phosphoacceptor 29 domain 2C score 9.6e-05 NC_002163.1 RefSeq region 1151812 1151871 . - . ID=id114;gene=dccS;Name=id114;Dbxref=GeneID:905512;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1222c by TMHMM2.0 at aa 5-27 and 159-178 NC_002163.1 RefSeq region 1152265 1152333 . - . ID=id114;gene=dccS;Name=id114;Dbxref=GeneID:905512;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1222c by TMHMM2.0 at aa 5-27 and 159-178 NC_002163.1 RefSeq gene 1152338 1153003 . - . ID=gene1172;gene=dccR;Name=dccR;locus_tag=Cj1223c;Dbxref=GeneID:905513;gbkey=Gene NC_002163.1 RefSeq CDS 1152338 1153003 . - 0 ID=cds1107;Parent=gene1172;gene=dccR;Name=YP_002344614.1;Dbxref=GOA:Q0P933 InterPro:IPR001789 InterPro:IPR001867 UniProtKB FTrEMBL:Q0P933 Genbank:YP_002344614.1 GeneID:905513;gbkey=CDS;product=two-component regulator;Note=Original 282000 29 note: Cj1223c 2C probable two-component regulator 2C len: 221 aa 3B similar to many e.g. CIAR_STRPN transcriptional regulatory protein CIAR 28224 aa 29 2C fasta scores 3B opt: 426 z-score: 522.6 E 28 29: 8.2e-22 2C37.0 25 identity in 219 aa overlap. 39.4 25 identity to HP1365. Contains Pfam match to entry PF00072 response_reg 2CResponse regulator receiver domain 2C and Pfam match to entry PF00486 trans_reg_C 2C Transcriptional regulatory protein 2C C terminal 7EUpdated 282006 29 note: Characterised in Campylobacter jejuni. Literature search identified characterisation paper where Cj1222c and Cj1223c were shown to required for optimal colonization and were termed dccRS 28diminished capacity to colonize 29 two-component system. Functional classification - Signal transduction 7EPMID:15554967 NC_002163.1 RefSeq region 1152344 1152559 . - . ID=id2224;gene=dccR;Name=id2224;Dbxref=GeneID:905513;gbkey=misc_feature;Note=HMMPfam hit to PF00486 2C Transcriptional regulatory protein 2C C te 2C score 2.7e-18 NC_002163.1 RefSeq region 1152638 1152997 . - . ID=id2225;gene=dccR;Name=id2225;Dbxref=GeneID:905513;gbkey=misc_feature;Note=HMMPfam hit to PF00072 2C Response regulator receiver domain 2C score 3e-25 ### NC_002163.1 UTR_Extractor 5'-UTR 1153004 1153039 . - . ID=utr442;locus_tag=Cj1223c;product=two-component regulator NC_002163.1 UTR_Extractor 5'-UTR 1153120 1153150 . + . ID=utr443;locus_tag=Cj1224;product=putative iron-binding protein NC_002163.1 RefSeq CDS 1153151 1153750 . + 0 ID=cds1108;Parent=gene1173;Name=YP_002344615.1;Dbxref=GOA:Q0P932 InterPro:IPR012312 InterPro:IPR012827 InterPro:IPR016131 UniProtKB FTrEMBL:Q0P932 Genbank:YP_002344615.1 GeneID:905514;gbkey=CDS;product=iron-binding protein;Note=Original 282000 29 note: Cj1224 2C possible iron-binding protein 2C len: 199 aa 3B some simlarity to TR:Q58157 28EMBL:U67520 29 Methanococcus jannaschii MJ0747 28169 aa 29 2Cfasta scores 3B opt: 230 z-score: 274.3 E 28 29: 5.6e-08 2C 33.9 25 identity in 127 aa overlap. Weak similarity to members of the eukaryotic oxygen-binding hemerythrin family 2C e.g. HEMM_THEZO myohemerythrin 28118 aa 29 2C fasta scores 3B opt: 159 z-score: 196.6 E 28 29: 0.0012 2C 30.5 25 identity in 118 aa overlap. Note that all of the iron-binding residues are conserved. No Hp match. Also similar to Cj0045c 2829.2 25 identity in 202 aa overlap 29 2C Cj0072c 28pseudogene 29 2C and Cj0241c 2834.7 25 identity in 118 aa overlap 29 7EUpdated 282006 29 note: Pfam domain 28x2 29 PF01814 Hemerythrin HHE cation binding domain identified within CDS. Prosite domain PS00550 HEMERYTHRINS 2C Hemerythrin family signature also identified within CDS. Further support given to product function. Specific characterisation has not been carried out yet 2C so kept within product function. Functional classification -Transport 2Fbinding proteins - Cations NC_002163.1 RefSeq gene 1153151 1153750 . + . ID=gene1173;Name=Cj1224;locus_tag=Cj1224;Dbxref=GeneID:905514;gbkey=Gene NC_002163.1 RefSeq region 1153184 1153354 . + . ID=id2226;Name=id2226;Dbxref=GeneID:905514;gbkey=misc_feature;Note=HMMPfam hit to PF01814 2C Hemerythrin HHE cation binding domain 2C score 1.1e-05 NC_002163.1 RefSeq region 1153364 1153528 . + . ID=id2227;Name=id2227;Dbxref=GeneID:905514;gbkey=misc_feature;Note=HMMPfam hit to PF01814 2C Hemerythrin HHE cation binding domain 2C score 0.00038 ### NC_002163.1 RefSeq gene 1153761 1154009 . + . ID=gene1174;Name=Cj1225;locus_tag=Cj1225;Dbxref=GeneID:905515;gbkey=Gene NC_002163.1 RefSeq CDS 1153761 1154009 . + 0 ID=cds1109;Parent=gene1174;Name=YP_002344616.1;Dbxref=GOA:Q0P931 UniProtKB FTrEMBL:Q0P931 Genbank:YP_002344616.1 GeneID:905515;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1225 2C unknown 2C len: 82 aa 3B weak similarity to CDS from Borrelia burgdorferi repeated DNA element TR:Q45025 28EMBL:X87127 29 28210 aa 29 2C fasta scores 3B opt: 117 z-score: 159.0 E 28 29: 0.15 2C 33.3 25 identity in 78 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF01402 Ribbon-helix-helix protein 2C copG family identified within CDS. No specific characterisation has yet been carried out yet. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 1154100 1154174 . - . ID=gene1175;gene=tRNAAsn;Name=tRNAAsn;locus_tag=Cjp22;Dbxref=GeneID:905516;gbkey=Gene NC_002163.1 RefSeq tRNA 1154100 1154174 . - . ID=rna37;Parent=gene1175;gene=tRNAAsn;Name=rna37;Dbxref=GeneID:905516;gbkey=tRNA;product=tRNA-Asn;Note=tRNA Asn anticodon GTT 2C Cove score 84.50 NC_002163.1 RefSeq exon 1154100 1154174 . - . ID=id2228;Parent=rna37;gene=tRNAAsn;Name=id2228;Dbxref=GeneID:905516;gbkey=tRNA;product=tRNA-Asn;Note=tRNA Asn anticodon GTT 2C Cove score 84.50 NC_002163.1 RefSeq CDS 1154267 1155514 . - 0 ID=cds1110;Parent=gene1176;Name=YP_002344617.1;Dbxref=GOA:Q0P930 InterPro:IPR003594 InterPro:IPR003660 InterPro:IPR003661 InterPro:IPR005467 UniProtKB FTrEMBL:Q0P930 Genbank:YP_002344617.1 GeneID:905517;gbkey=CDS;product=two-component sensor;Note=Original 282000 29 note: Cj1226c 2C probable two-component sensor 28histidine kinase 29 2C len: 415 aa 3B similar to many sensor proteins e.g. CPXA_ECOLI sensor protein CPXA 28457 aa 29 2C fasta scores 3B opt: 205 z-score: 241.7 E 28 29: 3.7e-06 2C 25.2 25 identity in 270 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00512 signal 2CSignal carboxyl-terminal domain 2C and two possible membrane spanning domains. Also similar to Cj1262 2831.0 25 identity in 410 aa overlap 29 7EUpdated 282006 29 note: Pfam domains PF02518 Histidine kinase- 2C DNA gyrase B- 2C and HSP90-like ATPase motifs 2CPF00512 His Kinase A 28phosphoacceptor 29 domain and PF00672 HAMP domain were all identified within CDS. Also 2C PS50109 HIS_KIN 2C Histidine kinase domain profile was identified within CDS. Further support given to product function. Product function modified to include motif information. Specific characterisation has not been carried out yet 2C so kept within product function. Functional classification - Signal transduction NC_002163.1 RefSeq gene 1154267 1155514 . - . ID=gene1176;Name=Cj1226c;locus_tag=Cj1226c;Dbxref=GeneID:905517;gbkey=Gene NC_002163.1 RefSeq region 1154285 1154587 . - . ID=id2229;Name=id2229;Dbxref=GeneID:905517;gbkey=misc_feature;Note=HMMPfam hit to PF02518 2C Histidine kinase- 2C DNA gyrase B- 2C and HSP90 2C score 3.2e-07 NC_002163.1 RefSeq region 1154708 1154884 . - . ID=id2230;Name=id2230;Dbxref=GeneID:905517;gbkey=misc_feature;Note=HMMPfam hit to PF00512 2C His Kinase A 28phosphoacceptor 29 domain 2C score 3.7e-05 NC_002163.1 RefSeq region 1154894 1155106 . - . ID=id2231;Name=id2231;Dbxref=GeneID:905517;gbkey=misc_feature;Note=HMMPfam hit to PF00672 2C HAMP domain 2C score 7.2e-08 NC_002163.1 RefSeq region 1155044 1155112 . - . ID=id115;Name=id115;Dbxref=GeneID:905517;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1226c by TMHMM2.0 at aa 6-28 and 135-157 NC_002163.1 RefSeq region 1155431 1155499 . - . ID=id115;Name=id115;Dbxref=GeneID:905517;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1226c by TMHMM2.0 at aa 6-28 and 135-157 NC_002163.1 RefSeq CDS 1155511 1156185 . - 0 ID=cds1111;Parent=gene1177;Name=YP_002344618.1;Dbxref=GOA:Q0P929 InterPro:IPR001789 InterPro:IPR001867 InterPro:IPR011991 UniProtKB FTrEMBL:Q0P929 Genbank:YP_002344618.1 GeneID:905518;gbkey=CDS;product=two-component regulator;Note=Original 282000 29 note: Cj1227c 2C probable two-component regulator 2C len: 224 aa 3B identical to TR:Q46095 28EMBL:U27271 29 C. jejuni CDS 28called ompR 29 28198 aa 29 2C and similar to many e.g. YYCF_BACSU hypothetical 27.2 kd sensory transduction protein 28235 aa 29 2C fasta scores 3B opt: 490 z-score: 561.1 E 28 29: 5.9e-24 2C 36.4 25 identity in 225 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00072 response_reg 2C Response regulator receiver domain 2C and Pfam match to entry PF00486 trans_reg_C 2CTranscriptional regulatory protein 2C C terminal. Also similar to Cj1261 2850.7 25 identity in 223 aa overlap 29 7EUpdated 282006 29 note: Similar to more than one type of two-component regulator with acceptable identity scores 2C so kept within product function. Literature search identified paper giving further clues to product function. Functional classification - Signal transduction 7EPMID:15901688 2C PMID:2402249 NC_002163.1 RefSeq gene 1155511 1156185 . - . ID=gene1177;Name=Cj1227c;locus_tag=Cj1227c;Dbxref=GeneID:905518;gbkey=Gene NC_002163.1 RefSeq region 1155520 1155750 . - . ID=id2232;Name=id2232;Dbxref=GeneID:905518;gbkey=misc_feature;Note=HMMPfam hit to PF00486 2C Transcriptional regulatory protein 2C C te 2C score 6.9e-19 NC_002163.1 RefSeq region 1155826 1156182 . - . ID=id2233;Name=id2233;Dbxref=GeneID:905518;gbkey=misc_feature;Note=HMMPfam hit to PF00072 2C Response regulator receiver domain 2C score 2.9e-31 ### NC_002163.1 UTR_Extractor 5'-UTR 1156186 1156207 . - . ID=utr444;locus_tag=Cj1227c;product=putative two-component regulator NC_002163.1 RefSeq CDS 1156261 1157679 . - 0 ID=cds1112;Parent=gene1178;gene=htrA;Name=YP_002344619.1;Dbxref=GOA:Q0P928 InterPro:IPR001254 InterPro:IPR001478 InterPro:IPR001940 InterPro:IPR011782 UniProtKB FTrEMBL:Q0P928 Genbank:YP_002344619.1 GeneID:905519;gbkey=CDS;product=serine protease;Note=Original 282000 29 note: Cj1228c 2C htrA 2C probable serine protease 28protease DO 29 2C len: 472 aa 3B 99.2 25 identical to TR:Q46120 28EMBL:X82628 29 C. jejuni serine protease htrA 28472 aa 29 2C and similar to e.g. HTRA_ECOLI protease DO precursor 28EC 3.4.21.- 29 28474 aa 29 2C fasta scores 3B opt: 965 z-score: 1004.5 E 28 29: 0 2C 39.5 25 identity in 461 aa overlap. 50.5 25 identity to HP1019. Contains Pfam match to entry PF00089 trypsin 2C and 2x Pfam match to entry PF00595 PDZ 2C PDZ domain 7EUpdated 282006 29 note: Characterised in Escherichia coli and Campylobacter jejuni 2C so not added to product function. Functional classification - Degradation of macromolecules - Proteins 2C peptides and glycopeptides 7EPMID:15933023 2C PMID:16041056 NC_002163.1 RefSeq gene 1156261 1157679 . - . ID=gene1178;gene=htrA;Name=htrA;locus_tag=Cj1228c;Dbxref=GeneID:905519;gbkey=Gene NC_002163.1 RefSeq region 1156297 1156590 . - . ID=id2234;gene=htrA;Name=id2234;Dbxref=GeneID:905519;gbkey=misc_feature;Note=HMMPfam hit to PF00595 2C PDZ domain 28Also known as DHR or GLGF 29 2C score 0.03 NC_002163.1 RefSeq region 1156615 1156875 . - . ID=id2235;gene=htrA;Name=id2235;Dbxref=GeneID:905519;gbkey=misc_feature;Note=HMMPfam hit to PF00595 2C PDZ domain 28Also known as DHR or GLGF 29 2C score 1.7e-08 NC_002163.1 RefSeq region 1156882 1157412 . - . ID=id2236;gene=htrA;Name=id2236;Dbxref=GeneID:905519;gbkey=misc_feature;Note=HMMPfam hit to PF00089 2C Trypsin 2C score 1.2e-20 ### NC_002163.1 UTR_Extractor 5'-UTR 1157680 1157731 . - . ID=utr445;locus_tag=Cj1228c;product=serine protease NC_002163.1 UTR_Extractor 5'-UTR 1157840 1157878 . + . ID=utr446;locus_tag=Cj1229;product=putative curved-DNA binding protein NC_002163.1 RefSeq CDS 1157879 1158772 . + 0 ID=cds1113;Parent=gene1179;gene=cbpA;Name=YP_002344620.1;Dbxref=GOA:Q0P927 InterPro:IPR001623 InterPro:IPR002939 InterPro:IPR003095 InterPro:IPR015609 UniProtKB FTrEMBL:Q0P927 Genbank:YP_002344620.1 GeneID:905520;gbkey=CDS;product=curved-DNA binding protein;Note=Original 282000 29 note: Cj1229 2C cbpA 2C probable curved-DNA binding protein 2C len: 297 aa 3B similar to e.g. CBPA_ECOLI curved DNA-binding protein 28306 aa 29 2C fatsa scores 3B opt: 514 z-score: 550.9 E 28 29: 2.2e-23 2C 32.8 25 identity in 287 aa overlap. 52.0 25 identity to HP1024. Contains S00636 Nt-dnaJ domain signature 2C and Pfam match to entry PF00226 DnaJ 2C DnaJ domain 7EUpdated 282006 29 note: Pfam domain PF01556 DnaJ C terminal region identified within CDS. Further support given to product function. Characterised in Escherichia coli with marginal identity score. kept within product function. Functional classification - Chaperones 2Cchaperonins 2C heat shock 7EPMID:15184371 2C PMID:10947847 2C PMID:10551881 NC_002163.1 RefSeq gene 1157879 1158772 . + . ID=gene1179;gene=cbpA;Name=cbpA;locus_tag=Cj1229;Dbxref=GeneID:905520;gbkey=Gene NC_002163.1 RefSeq region 1157885 1158079 . + . ID=id2237;gene=cbpA;Name=id2237;Dbxref=GeneID:905520;gbkey=misc_feature;Note=HMMPfam hit to PF00226 2C DnaJ domain 2C score 1.2e-40 NC_002163.1 RefSeq region 1158008 1158067 . + . ID=id2238;gene=cbpA;Name=id2238;Dbxref=GeneID:905520;gbkey=misc_feature;Note=PS00636 Nt-dnaJ domain signature NC_002163.1 RefSeq region 1158389 1158766 . + . ID=id2239;gene=cbpA;Name=id2239;Dbxref=GeneID:905520;gbkey=misc_feature;Note=HMMPfam hit to PF01556 2C DnaJ C terminal region 2Cscore 6.2e-22 ### NC_002163.1 RefSeq CDS 1158788 1159162 . + 0 ID=cds1114;Parent=gene1180;gene=hspR;Name=YP_002344621.1;Dbxref=GOA:Q0P926 InterPro:IPR000551 UniProtKB FTrEMBL:Q0P926 Genbank:YP_002344621.1 GeneID:905521;gbkey=CDS;product=heat shock transcriptional regulator;Note=Original 282000 29 note: Cj1230 2C hspR 2C possible heat shock transcriptional regulator 2C len: 124 aa 3B similar to SPR_STRCO heat shock protein HSPR 28151 aa 29 2C fatsa scores 3B opt: 309 z-score: 385.2 E 28 29: 3.7e-14 2C 42.4 25 identity in 118 aa overlap 2C and to other members of the MerR family of transcriptional regulators. 63.3 25 identity to HP1025. Contains PS00552 Bacterial regulatory proteins 2CmerR family signature 2C Pfam match to entry PF00376 merR 2Cand probable helix-turn-helix motif at aa 11-32 28Score 1333 2C 2B3.73 SD 29 7EUpdated 282006 29 note: Characterised in Campylobacter jejuni 28PMID:15758235 29. removed from product function. Functional classification - Chaperones 2Cchaperonins 2C heat shock 7EPMID: PMID:8801421 2C PMID:15758235 2CPMID:10564507 2C PMID:15720562 NC_002163.1 RefSeq gene 1158788 1159162 . + . ID=gene1180;gene=hspR;Name=hspR;locus_tag=Cj1230;Dbxref=GeneID:905521;gbkey=Gene NC_002163.1 RefSeq region 1158818 1158928 . + . ID=id2240;gene=hspR;Name=id2240;Dbxref=GeneID:905521;gbkey=misc_feature;Note=HMMPfam hit to PF00376 2C MerR family regulatory protein 2C score 1.4e-07 NC_002163.1 RefSeq region 1158824 1158892 . + . ID=id2241;gene=hspR;Name=id2241;Dbxref=GeneID:905521;gbkey=misc_feature;Note=PS00552 Bacterial regulatory proteins 2C merR family signature ### NC_002163.1 RefSeq CDS 1159168 1160793 . + 0 ID=cds1115;Parent=gene1181;gene=kefB;Name=YP_002344622.1;Dbxref=GOA:Q0P925 InterPro:IPR003148 InterPro:IPR006153 InterPro:IPR016040 UniProtKB FTrEMBL:Q0P925 Genbank:YP_002344622.1 GeneID:905522;gbkey=CDS;product=glutathione-regulated potassium-efflux system protein;Note=Original 282000 29 note: Cj1231 2C kefB 2C probable glutathione-regulated potassium-efflux system protein 2Clen: 541 aa 3B similar to e.g. KEFC_ECOLI glutathione-regulated potassium-efflux system protein 28620 aa 29 2C fasta scores 3B opt: 803 z-score: 903.5 E 28 29: 0 2C 30.8 25 identity in 494 aa overlap. 37.7 25 identity to HP0471 7EUpdated 282006 29 note: Pfam domains PF02254 TrkA-N domain and PF00999 Sodium 2Fhydrogen exchanger family were identified within CDS. Also 2C thirteen probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Identity scores for matching Escherichia coli were marginal. kept within product function. Functional classification -Transport 2Fbinding proteins - Cations 7EPMID:2046548 2C PMID:1325937 NC_002163.1 RefSeq gene 1159168 1160793 . + . ID=gene1181;gene=kefB;Name=kefB;locus_tag=Cj1231;Dbxref=GeneID:905522;gbkey=Gene NC_002163.1 RefSeq region 1159177 1159233 . + . ID=id2242;gene=kefB;Name=id2242;Dbxref=GeneID:905522;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1231 by TMHMM2.0 at aa 4-22 2C 29-48 2C 52-71 2C 83-105 2C115-133 2C 146-168 2C 178-200 2C 207-229 2C 233-250 2C 262-281 2C291-313 2C 320-342 and 352-374 NC_002163.1 RefSeq region 1159252 1159311 . + . ID=id2242;gene=kefB;Name=id2242;Dbxref=GeneID:905522;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1231 by TMHMM2.0 at aa 4-22 2C 29-48 2C 52-71 2C 83-105 2C115-133 2C 146-168 2C 178-200 2C 207-229 2C 233-250 2C 262-281 2C291-313 2C 320-342 and 352-374 NC_002163.1 RefSeq region 1159321 1159380 . + . ID=id2242;gene=kefB;Name=id2242;Dbxref=GeneID:905522;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1231 by TMHMM2.0 at aa 4-22 2C 29-48 2C 52-71 2C 83-105 2C115-133 2C 146-168 2C 178-200 2C 207-229 2C 233-250 2C 262-281 2C291-313 2C 320-342 and 352-374 NC_002163.1 RefSeq region 1159414 1159482 . + . ID=id2242;gene=kefB;Name=id2242;Dbxref=GeneID:905522;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1231 by TMHMM2.0 at aa 4-22 2C 29-48 2C 52-71 2C 83-105 2C115-133 2C 146-168 2C 178-200 2C 207-229 2C 233-250 2C 262-281 2C291-313 2C 320-342 and 352-374 NC_002163.1 RefSeq region 1159510 1159566 . + . ID=id2242;gene=kefB;Name=id2242;Dbxref=GeneID:905522;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1231 by TMHMM2.0 at aa 4-22 2C 29-48 2C 52-71 2C 83-105 2C115-133 2C 146-168 2C 178-200 2C 207-229 2C 233-250 2C 262-281 2C291-313 2C 320-342 and 352-374 NC_002163.1 RefSeq region 1159603 1159671 . + . ID=id2242;gene=kefB;Name=id2242;Dbxref=GeneID:905522;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1231 by TMHMM2.0 at aa 4-22 2C 29-48 2C 52-71 2C 83-105 2C115-133 2C 146-168 2C 178-200 2C 207-229 2C 233-250 2C 262-281 2C291-313 2C 320-342 and 352-374 NC_002163.1 RefSeq region 1159699 1159767 . + . ID=id2242;gene=kefB;Name=id2242;Dbxref=GeneID:905522;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1231 by TMHMM2.0 at aa 4-22 2C 29-48 2C 52-71 2C 83-105 2C115-133 2C 146-168 2C 178-200 2C 207-229 2C 233-250 2C 262-281 2C291-313 2C 320-342 and 352-374 NC_002163.1 RefSeq region 1159786 1159854 . + . ID=id2242;gene=kefB;Name=id2242;Dbxref=GeneID:905522;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1231 by TMHMM2.0 at aa 4-22 2C 29-48 2C 52-71 2C 83-105 2C115-133 2C 146-168 2C 178-200 2C 207-229 2C 233-250 2C 262-281 2C291-313 2C 320-342 and 352-374 NC_002163.1 RefSeq region 1159864 1159917 . + . ID=id2242;gene=kefB;Name=id2242;Dbxref=GeneID:905522;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1231 by TMHMM2.0 at aa 4-22 2C 29-48 2C 52-71 2C 83-105 2C115-133 2C 146-168 2C 178-200 2C 207-229 2C 233-250 2C 262-281 2C291-313 2C 320-342 and 352-374 NC_002163.1 RefSeq region 1159951 1160010 . + . ID=id2242;gene=kefB;Name=id2242;Dbxref=GeneID:905522;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1231 by TMHMM2.0 at aa 4-22 2C 29-48 2C 52-71 2C 83-105 2C115-133 2C 146-168 2C 178-200 2C 207-229 2C 233-250 2C 262-281 2C291-313 2C 320-342 and 352-374 NC_002163.1 RefSeq region 1160038 1160106 . + . ID=id2242;gene=kefB;Name=id2242;Dbxref=GeneID:905522;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1231 by TMHMM2.0 at aa 4-22 2C 29-48 2C 52-71 2C 83-105 2C115-133 2C 146-168 2C 178-200 2C 207-229 2C 233-250 2C 262-281 2C291-313 2C 320-342 and 352-374 NC_002163.1 RefSeq region 1160125 1160193 . + . ID=id2242;gene=kefB;Name=id2242;Dbxref=GeneID:905522;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1231 by TMHMM2.0 at aa 4-22 2C 29-48 2C 52-71 2C 83-105 2C115-133 2C 146-168 2C 178-200 2C 207-229 2C 233-250 2C 262-281 2C291-313 2C 320-342 and 352-374 NC_002163.1 RefSeq region 1160221 1160289 . + . ID=id2242;gene=kefB;Name=id2242;Dbxref=GeneID:905522;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1231 by TMHMM2.0 at aa 4-22 2C 29-48 2C 52-71 2C 83-105 2C115-133 2C 146-168 2C 178-200 2C 207-229 2C 233-250 2C 262-281 2C291-313 2C 320-342 and 352-374 NC_002163.1 RefSeq region 1160374 1160697 . + . ID=id2243;gene=kefB;Name=id2243;Dbxref=GeneID:905522;gbkey=misc_feature;Note=HMMPfam hit to PF02254 2C TrkA-N domain 2C score 5.9e-08 ### NC_002163.1 RefSeq CDS 1160803 1161135 . + 0 ID=cds1116;Parent=gene1182;Name=YP_002344623.1;Dbxref=UniProtKB FTrEMBL:Q0P924 Genbank:YP_002344623.1 GeneID:905523;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1232 2C unknown 2C len: 110 aa 3B no Hp match. Lys-rich. Functional classification -Unknown NC_002163.1 RefSeq gene 1160803 1161135 . + . ID=gene1182;Name=Cj1232;locus_tag=Cj1232;Dbxref=GeneID:905523;gbkey=Gene NC_002163.1 RefSeq region 1161132 1161680 . + . ID=id2244;Name=id2244;Dbxref=GeneID:905524;gbkey=misc_feature;Note=HMMPfam hit to PF00702 2C haloacid dehalogenase-like hydrolase 2C score 4.5e-18 NC_002163.1 RefSeq gene 1161132 1161752 . + . ID=gene1183;Name=Cj1233;locus_tag=Cj1233;Dbxref=GeneID:905524;gbkey=Gene NC_002163.1 RefSeq CDS 1161132 1161752 . + 0 ID=cds1117;Parent=gene1183;Name=YP_002344624.1;Dbxref=GOA:Q0P923 InterPro:IPR005834 InterPro:IPR006439 UniProtKB FTrEMBL:Q0P923 Genbank:YP_002344624.1 GeneID:905524;gbkey=CDS;product=HAD-superfamily hydrolase;Note=Original 282000 29 note: Cj1233 2C probable hydrolase 2Clen: 206 aa 3B similar to e.g. GPH_ECOLI phosphoglycolate phosphatase 28252 aa 29 2C fasta scores 3B opt: 177 z-score: 216.3 E 28 29: 9.5e-05 2C 27.6 25 identity in 199 aa overlap. No Hp match. Contains Pfam match to entry PF00702 Hydrolase 2Chaloacid dehalogenase-like hydrolase. Also similar to Cj1477c 2827.3 25 identity in 205 aa overlap 29 7EUpdated 282006 29 note: Characterisation work within Escherichia coli 2C however 2C identity scores were marginal. Product modified to more specific family member based on motif matches. kept within product function. Functional classification - Misc 7EPMID:13129953 2C PMID:10572959 ### NC_002163.1 UTR_Extractor 5'-UTR 1161785 1161807 . + . ID=utr447;locus_tag=Cj1234;product=glycyl-tRNA synthetase subunit beta NC_002163.1 RefSeq CDS 1161808 1163802 . + 0 ID=cds1118;Parent=gene1184;gene=glyS;Name=YP_002344625.1;Dbxref=GOA:Q0P922 InterPro:IPR002311 InterPro:IPR006194 InterPro:IPR015944 UniProtKB FTrEMBL:Q0P922 Genbank:YP_002344625.1 GeneID:905525;gbkey=CDS;product=glycyl-tRNA synthetase subunit beta;Note=glycine--tRNA ligase beta chain 3B glyS 3B class II aminoacyl tRNA synthetase 3B tetramer of alpha 282 29beta 282 29 3B catalyzes a two-step reaction 3B first charging a glycine molecule by linking the carboxyl group to the alpha-phosphate of ATP 3B second by transfer of the aminoacyl-adenylate to its tRNA NC_002163.1 RefSeq gene 1161808 1163802 . + . ID=gene1184;gene=glyS;Name=glyS;locus_tag=Cj1234;Dbxref=GeneID:905525;gbkey=Gene NC_002163.1 RefSeq region 1161817 1163430 . + . ID=id2245;gene=glyS;Name=id2245;Dbxref=GeneID:905525;gbkey=misc_feature;Note=HMMPfam hit to PF02092 2C Glycyl-tRNA synthetase beta subunit 2C score 6.5e-195 NC_002163.1 RefSeq gene 1163799 1164620 . + . ID=gene1185;gene=Cj1235;Name=Cj1235;locus_tag=Cj1235;Dbxref=GeneID:905526;gbkey=Gene NC_002163.1 RefSeq CDS 1163799 1164620 . + 0 ID=cds1119;Parent=gene1185;Name=YP_002344626.1;Dbxref=GOA:Q0P921 InterPro:IPR002886 InterPro:IPR016047 UniProtKB FTrEMBL:Q0P921 Genbank:YP_002344626.1 GeneID:905526;gbkey=CDS;product=peptidase M23 family protein;Note=Original 282000 29 note: Cj1235 2C probable periplasmic protein 2C len: 273 aa 3B similar to many e.g. TR:Q57503 28EMBL:U07173 29 Vibrio cholerae ToxR-activated gene 2C tagE 28302 aa 29 2C fasta scores 3B opt: 319 z-score: 373.7 E 28 29: 1.6e-13 2C 37.0 25 identity in 192 aa overlap 2C and YEBA_ECOLI 28419 aa 29 2C fasta scores 3B opt: 299 z-score: 348.5 E 28 29: 4.1e-12 2C 44.3 25 identity in 115 aa overlap. No Hp ortholog. Also similar to Cj0131 2830.2 25 identity in 222 aa overlap 29 2CCj1087c 2840.7 25 identity in 123 aa overlap 29 2C and Cj1215 2829.6 25 identity in 206 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01551 Peptidase family M23 identified within CDS. Further support given to product function. Product modified to more specific family member based on motif results. No specific characterisation has been carried out yet 2C so kept within product function. Functional classification -Degradation of macromolecules - Proteins 2C peptides and glycopeptides NC_002163.1 RefSeq region 1164294 1164581 . + . ID=id2246;Name=id2246;Dbxref=GeneID:905526;gbkey=misc_feature;Note=HMMPfam hit to PF01551 2C Peptidase family M23 2C score 6.7e-45 NC_002163.1 RefSeq gene 1164617 1165567 . + . ID=gene1186;Name=Cj1236;locus_tag=Cj1236;Dbxref=GeneID:905527;gbkey=Gene NC_002163.1 RefSeq CDS 1164617 1165567 . + 0 ID=cds1120;Parent=gene1186;Name=YP_002344627.1;Dbxref=InterPro:IPR003788 UniProtKB FTrEMBL:Q0P920 Genbank:YP_002344627.1 GeneID:905527;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1236 2C unknown 2C len: 316 aa 3B similar to hypothetical proteins e.g. TR:O66873 28EMBL:AE000698 29 Aquifex aeolicus AQ_622 28320 aa 29 2C fasta scores 3B opt: 263 z-score: 318.9 E 28 29: 1.8e-10 2C 23.8 25 identity in 323 aa overlap. 32.4 25 identity to HP0812 7EUpdated 282006 29 note: Pfam domain PF02636 Uncharacterized ACR 2C COG1565 identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq region 1164737 1165459 . + . ID=id2247;Name=id2247;Dbxref=GeneID:905527;gbkey=misc_feature;Note=HMMPfam hit to PF02636 2C Uncharacterized ACR 2CCOG1565 2C score 2.2e-05 NC_002163.1 RefSeq CDS 1165564 1166538 . - 0 ID=cds1121;Parent=gene1187;Name=YP_002344628.1;Dbxref=GOA:Q0P919 InterPro:IPR003695 UniProtKB FTrEMBL:Q0P919 Genbank:YP_002344628.1 GeneID:905528;gbkey=CDS;product=phosphatase;Note=Original 282000 29 note: Cj1237c 2C possible phosphatase 2C len: 324 aa 3B weak similarity to e.g. GPPA_ECOLI guanosine-5 27-triphosphate 2C3 27-diphosphate pyrophosphatase 28494 aa 29 2C fasta scores 3B opt: 174 z-score: 201.9 E 28 29: 0.0006 2C 25.7 25 identity in 323 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02541 Ppx 2FGppA phosphatase family was identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score carried out yet 2C so kept within product function 28previously was posssible 29. Functional classification -Misc NC_002163.1 RefSeq gene 1165564 1166538 . - . ID=gene1187;Name=Cj1237c;locus_tag=Cj1237c;Dbxref=GeneID:905528;gbkey=Gene NC_002163.1 RefSeq region 1165573 1166499 . - . ID=id2248;Name=id2248;Dbxref=GeneID:905528;gbkey=misc_feature;Note=HMMPfam hit to PF02541 2C Ppx 2FGppA phosphatase family 2C score 1.7e-06 ### NC_002163.1 UTR_Extractor 5'-UTR 1166539 1166560 . - . ID=utr448;locus_tag=Cj1237c;product=putative phosphatase NC_002163.1 UTR_Extractor 5'-UTR 1166572 1166593 . + . ID=utr449;locus_tag=Cj1238;product=pyridoxine 5 27-phosphate synthase NC_002163.1 RefSeq region 1166594 1167364 . + . ID=id2249;gene=pdxJ;Name=id2249;Dbxref=GeneID:905529;gbkey=misc_feature;Note=HMMPfam hit to PF03740 2C Pyridoxal phosphate biosynthesis protein Pdx 2C score 7.6e-178 NC_002163.1 RefSeq CDS 1166594 1167367 . + 0 ID=cds1122;Parent=gene1188;gene=pdxJ;Name=YP_002344629.1;Dbxref=GOA:Q9PN59 HSSP:P24223 InterPro:IPR004569 InterPro:IPR013785 UniProtKB FSwiss-Prot:Q9PN59 Genbank:YP_002344629.1 GeneID:905529;gbkey=CDS;product=pyridoxine 5 27-phosphate synthase;Note=involved in the de novo synthesis of pyridoxine 28Vitamin B6 29 NC_002163.1 RefSeq gene 1166594 1167367 . + . ID=gene1188;gene=pdxJ;Name=pdxJ;locus_tag=Cj1238;Dbxref=GeneID:905529;gbkey=Gene NC_002163.1 RefSeq CDS 1167364 1168458 . + 0 ID=cds1123;Parent=gene1189;gene=pdxA;Name=YP_002344630.1;Dbxref=GOA:Q9PN58 InterPro:IPR005255 UniProtKB FSwiss-Prot:Q9PN58 Genbank:YP_002344630.1 GeneID:905530;gbkey=CDS;product=4-hydroxythreonine-4-phosphate dehydrogenase;Note=catalyzes oxidation of 4- 28phosphohydroxy 29-L-threonine into 2-amino-3-oxo-4- 28phosphohydroxy 29butyric acid which decarboxylates to form 1-amino-3- 28phosphohydroxy 29propan-2-one 283-amino-2-oxopropyl phosphate 29 NC_002163.1 RefSeq gene 1167364 1168458 . + . ID=gene1189;gene=pdxA;Name=pdxA;locus_tag=Cj1239;Dbxref=GeneID:905530;gbkey=Gene NC_002163.1 RefSeq region 1167427 1168437 . + . ID=id2250;gene=pdxA;Name=id2250;Dbxref=GeneID:905530;gbkey=misc_feature;Note=HMMPfam hit to PF04166 2C Pyridoxal phosphate biosynthetic protein Pdx 2C score 1.4e-135 NC_002163.1 RefSeq gene 1168448 1169050 . - . ID=gene1190;gene=Cj1240c;Name=Cj1240c;locus_tag=Cj1240c;Dbxref=GeneID:905531;gbkey=Gene NC_002163.1 RefSeq CDS 1168448 1169050 . - 0 ID=cds1124;Parent=gene1190;Name=YP_002344631.1;Dbxref=GOA:Q0P916 UniProtKB FTrEMBL:Q0P916 Genbank:YP_002344631.1 GeneID:905531;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1240c 2C probable periplasmic protein 2C len: 200 aa 3B no Hp match. Functional classification - Miscellaneous periplasmic proteins ### NC_002163.1 UTR_Extractor 5'-UTR 1169051 1169258 . - . ID=utr450;locus_tag=Cj1240c;product=putative periplasmic protein NC_002163.1 UTR_Extractor 5'-UTR 1169137 1169162 . + . ID=utr451;locus_tag=Cj1241;product=putative MFS transport protein NC_002163.1 RefSeq gene 1169163 1170362 . + . ID=gene1191;Name=Cj1241;locus_tag=Cj1241;Dbxref=GeneID:905532;gbkey=Gene NC_002163.1 RefSeq CDS 1169163 1170362 . + 0 ID=cds1125;Parent=gene1191;Name=YP_002344632.1;Dbxref=GOA:Q0P915 InterPro:IPR007114 InterPro:IPR011701 UniProtKB FTrEMBL:Q0P915 Genbank:YP_002344632.1 GeneID:905532;gbkey=CDS;product=MFS transport protein;Note=Original 282000 29 note: Cj1241 2C probable transmembrane transport protein 2C len: 399 aa 3B similar to e.g. ARAJ_ECOLI protein ARAJ precursor 28394 aa 29 2C fasta scores 3B opt: 579 z-score: 680.4 E 28 29: 1.3e-30 2C 28.8 25 identity in 385 aa overlap 2C and CMLR_STRLI chloramphenicol resistance protein 28392 aa 29 2C fasta scores 3B opt: 444 z-score: 523.2 E 28 29: 7.6e-22 2C 25.5 25 identity in 380 aa overlap. 27.4 25 identity to HP1185 7EUpdated 282006 29 note: Pfam domain PF07690 Major Facilitator Superfamily identified within CDS. Also 2Ctwelve probable transmembrane helices predicted by TMHMM2.0. Product modified to more specific family member based on motif match. No specific characterisation with acceptable identity score carried out yet 2C so kept within product function. Literature search identified paper giving further clues to product function. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:16048946 NC_002163.1 RefSeq region 1169181 1169249 . + . ID=id2251;Name=id2251;Dbxref=GeneID:905532;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1241 by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-90 2C 100-122 2C129-151 2C 156-178 2C 203-225 2C 240-259 2C 268-290 2C 295-317 2C338-360 and 364-381 NC_002163.1 RefSeq region 1169193 1170230 . + . ID=id2252;Name=id2252;Dbxref=GeneID:905532;gbkey=misc_feature;Note=HMMPfam hit to PF07690 2C Major Facilitator Superfamily 2C score 2.7e-39 NC_002163.1 RefSeq region 1169292 1169360 . + . ID=id2251;Name=id2251;Dbxref=GeneID:905532;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1241 by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-90 2C 100-122 2C129-151 2C 156-178 2C 203-225 2C 240-259 2C 268-290 2C 295-317 2C338-360 and 364-381 NC_002163.1 RefSeq region 1169379 1169432 . + . ID=id2251;Name=id2251;Dbxref=GeneID:905532;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1241 by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-90 2C 100-122 2C129-151 2C 156-178 2C 203-225 2C 240-259 2C 268-290 2C 295-317 2C338-360 and 364-381 NC_002163.1 RefSeq region 1169460 1169528 . + . ID=id2251;Name=id2251;Dbxref=GeneID:905532;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1241 by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-90 2C 100-122 2C129-151 2C 156-178 2C 203-225 2C 240-259 2C 268-290 2C 295-317 2C338-360 and 364-381 NC_002163.1 RefSeq region 1169547 1169615 . + . ID=id2251;Name=id2251;Dbxref=GeneID:905532;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1241 by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-90 2C 100-122 2C129-151 2C 156-178 2C 203-225 2C 240-259 2C 268-290 2C 295-317 2C338-360 and 364-381 NC_002163.1 RefSeq region 1169628 1169696 . + . ID=id2251;Name=id2251;Dbxref=GeneID:905532;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1241 by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-90 2C 100-122 2C129-151 2C 156-178 2C 203-225 2C 240-259 2C 268-290 2C 295-317 2C338-360 and 364-381 NC_002163.1 RefSeq region 1169769 1169837 . + . ID=id2251;Name=id2251;Dbxref=GeneID:905532;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1241 by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-90 2C 100-122 2C129-151 2C 156-178 2C 203-225 2C 240-259 2C 268-290 2C 295-317 2C338-360 and 364-381 NC_002163.1 RefSeq region 1169880 1169939 . + . ID=id2251;Name=id2251;Dbxref=GeneID:905532;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1241 by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-90 2C 100-122 2C129-151 2C 156-178 2C 203-225 2C 240-259 2C 268-290 2C 295-317 2C338-360 and 364-381 NC_002163.1 RefSeq region 1169964 1170032 . + . ID=id2251;Name=id2251;Dbxref=GeneID:905532;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1241 by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-90 2C 100-122 2C129-151 2C 156-178 2C 203-225 2C 240-259 2C 268-290 2C 295-317 2C338-360 and 364-381 NC_002163.1 RefSeq region 1170045 1170113 . + . ID=id2251;Name=id2251;Dbxref=GeneID:905532;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1241 by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-90 2C 100-122 2C129-151 2C 156-178 2C 203-225 2C 240-259 2C 268-290 2C 295-317 2C338-360 and 364-381 NC_002163.1 RefSeq region 1170174 1170242 . + . ID=id2251;Name=id2251;Dbxref=GeneID:905532;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1241 by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-90 2C 100-122 2C129-151 2C 156-178 2C 203-225 2C 240-259 2C 268-290 2C 295-317 2C338-360 and 364-381 NC_002163.1 RefSeq region 1170252 1170305 . + . ID=id2251;Name=id2251;Dbxref=GeneID:905532;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1241 by TMHMM2.0 at aa 7-29 2C 44-66 2C 73-90 2C 100-122 2C129-151 2C 156-178 2C 203-225 2C 240-259 2C 268-290 2C 295-317 2C338-360 and 364-381 ### NC_002163.1 UTR_Extractor 5'-UTR 1170393 1170417 . + . ID=utr452;locus_tag=Cj1242;product=hypothetical protein NC_002163.1 RefSeq gene 1170418 1170738 . + . ID=gene1192;Name=Cj1242;locus_tag=Cj1242;Dbxref=GeneID:905533;gbkey=Gene NC_002163.1 RefSeq CDS 1170418 1170738 . + 0 ID=cds1126;Parent=gene1192;Name=YP_002344633.1;Dbxref=UniProtKB FTrEMBL:Q0P914 Genbank:YP_002344633.1 GeneID:905533;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1242 2C unknown 2C len: 106 aa 3B no Hp match 7EUpdated 282006 29 note: Literature search identified papers giving potential clues to product function. Functional classification - Unknown 7EPMID:14985343 2C PMID:15812042 NC_002163.1 UTR_Extractor 5'-UTR 1170905 1170921 . + . ID=utr453;locus_tag=Cj1243;product=uroporphyrinogen decarboxylase NC_002163.1 RefSeq CDS 1170922 1171944 . + 0 ID=cds1127;Parent=gene1193;gene=hemE;Name=YP_002344634.1;Dbxref=GOA:Q9PN54 HSSP:P06132 InterPro:IPR000257 InterPro:IPR006361 UniProtKB FSwiss-Prot:Q9PN54 Genbank:YP_002344634.1 GeneID:905534;gbkey=CDS;product=uroporphyrinogen decarboxylase;Note=catalyzes the formation of coproporphyrinogen from uroporphyrinogen III NC_002163.1 RefSeq gene 1170922 1171944 . + . ID=gene1193;gene=hemE;Name=hemE;locus_tag=Cj1243;Dbxref=GeneID:905534;gbkey=Gene NC_002163.1 RefSeq region 1170928 1171932 . + . ID=id2253;gene=hemE;Name=id2253;Dbxref=GeneID:905534;gbkey=misc_feature;Note=HMMPfam hit to PF01208 2C Uroporphyrinogen decarboxylase 28URO-D 29 2C score 2.1e-132 NC_002163.1 RefSeq region 1170967 1170996 . + . ID=id2254;gene=hemE;Name=id2254;Dbxref=GeneID:905534;gbkey=misc_feature;Note=PS00906 Uroporphyrinogen decarboxylase signature 1 NC_002163.1 RefSeq CDS 1171941 1172843 . + 0 ID=cds1128;Parent=gene1194;Name=YP_002344635.1;Dbxref=GOA:Q0P912 InterPro:IPR006638 InterPro:IPR007197 UniProtKB FTrEMBL:Q0P912 Genbank:YP_002344635.1 GeneID:905535;gbkey=CDS;product=radical SAM domain-containing protein;Note=Original 282000 29 note: Cj1244 2C unknown 2C len: 300 aa 3B similar to hypothetical proteins e.g. YD12_METJA Methanococcus jannaschii MJ1312 28321 aa 29 2C fasta scores 3B opt: 436 z-score: 499.9 E 28 29: 1.5e-20 2C 30.7 25 identity in 313 aa overlap. 40.1 25 identity to HP0117 7EUpdated 282006 29 note: Pfam domain PF04055 Radical SAM superfamily identified within CDS. Product modified to more specific family member based on motif match. No specific characterisation carried out yet 2C so kept within product function. Functional classification -Misc NC_002163.1 RefSeq gene 1171941 1172843 . + . ID=gene1194;gene=Cj1244;Name=Cj1244;locus_tag=Cj1244;Dbxref=GeneID:905535;gbkey=Gene NC_002163.1 RefSeq region 1172004 1172516 . + . ID=id2255;Name=id2255;Dbxref=GeneID:905535;gbkey=misc_feature;Note=HMMPfam hit to PF04055 2C Radical SAM superfamily 2Cscore 4.1e-16 NC_002163.1 RefSeq CDS 1172840 1174036 . - 0 ID=cds1129;Parent=gene1195;Name=YP_002344636.1;Dbxref=UniProtKB FTrEMBL:Q0P911 Genbank:YP_002344636.1 GeneID:905536;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1245c 2C possible membrane protein 2C len: 398 aa 3B no Hp match 7EUpdated 282006 29 note: Two probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 1172840 1174036 . - . ID=gene1195;Name=Cj1245c;locus_tag=Cj1245c;Dbxref=GeneID:905536;gbkey=Gene NC_002163.1 RefSeq region 1173884 1173937 . - . ID=id116;Name=id116;Dbxref=GeneID:905536;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1245c by TMHMM2.0 at aa 2-19 and 34-51 NC_002163.1 RefSeq region 1173980 1174033 . - . ID=id116;Name=id116;Dbxref=GeneID:905536;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1245c by TMHMM2.0 at aa 2-19 and 34-51 ### NC_002163.1 UTR_Extractor 5'-UTR 1174037 1174264 . - . ID=utr454;locus_tag=Cj1245c;product=hypothetical protein NC_002163.1 RefSeq CDS 1174038 1175840 . - 0 ID=cds1130;Parent=gene1196;gene=uvrC;Name=YP_002344637.1;Dbxref=GOA:Q9PN51 InterPro:IPR000305 InterPro:IPR001162 InterPro:IPR001943 InterPro:IPR004791 UniProtKB FSwiss-Prot:Q9PN51 Genbank:YP_002344637.1 GeneID:905537;gbkey=CDS;product=excinuclease ABC subunit C;Note=The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5 27 and 3 27 sides of the lesion. The N-terminal half is responsible for the 3 27 incision and the C-terminal half is responsible for the 5 27 incision NC_002163.1 RefSeq gene 1174038 1175840 . - . ID=gene1196;gene=uvrC;Name=uvrC;locus_tag=Cj1246c;Dbxref=GeneID:905537;gbkey=Gene NC_002163.1 RefSeq region 1175127 1175234 . - . ID=id2256;gene=uvrC;Name=id2256;Dbxref=GeneID:905537;gbkey=misc_feature;Note=HMMPfam hit to PF02151 2C UvrB 2FuvrC motif 2C score 2.9e-08 NC_002163.1 RefSeq region 1175526 1175795 . - . ID=id2257;gene=uvrC;Name=id2257;Dbxref=GeneID:905537;gbkey=misc_feature;Note=HMMPfam hit to PF01541 2C GIY-YIG catalytic domain 2Cscore 1.4e-29 NC_002163.1 RefSeq gene 1175833 1176327 . - . ID=gene1197;gene=Cj1247c;Name=Cj1247c;locus_tag=Cj1247c;Dbxref=GeneID:905538;gbkey=Gene NC_002163.1 RefSeq CDS 1175833 1176327 . - 0 ID=cds1131;Parent=gene1197;Name=YP_002344638.1;Dbxref=UniProtKB FTrEMBL:Q0P909 Genbank:YP_002344638.1 GeneID:905538;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1247c 2C unknown 2C len: 164 aa 3B 27.1 25 identity to HP0820. Functional classification -Conserved hypothetical proteins NC_002163.1 UTR_Extractor 5'-UTR 1176327 1176327 . - . ID=utr455;locus_tag=Cj1247c;product=hypothetical protein ### NC_002163.1 RefSeq CDS 1176466 1178001 . + 0 ID=cds1132;Parent=gene1198;gene=guaA;Name=YP_002344639.1;Dbxref=GOA:Q9PN49 HSSP:P04079 InterPro:IPR000991 InterPro:IPR001317 InterPro:IPR001674 InterPro:IPR004506 InterPro:IPR004739 InterPro:IPR006220 InterPro:IPR011702 InterPro:IPR012998 InterPro:IPR014729 UniProtKB FSwiss-Prot:Q9PN49 Genbank:YP_002344639.1 GeneID:905539;gbkey=CDS;product=GMP synthase;Note=contains glutamine-hydrolyzing domain and glutamine amidotransferase 3B GMP-binding domain 3B functions to produce GMP from XMP in the IMP pathway NC_002163.1 RefSeq gene 1176466 1178001 . + . ID=gene1198;gene=guaA;Name=guaA;locus_tag=Cj1248;Dbxref=GeneID:905539;gbkey=Gene NC_002163.1 RefSeq region 1176484 1177032 . + . ID=id2258;gene=guaA;Name=id2258;Dbxref=GeneID:905539;gbkey=misc_feature;Note=HMMPfam hit to PF00117 2C Glutamine amidotransferase class-I 2C score 1.7e-57 NC_002163.1 RefSeq region 1176694 1176729 . + . ID=id2259;gene=guaA;Name=id2259;Dbxref=GeneID:905539;gbkey=misc_feature;Note=PS00442 Glutamine amidotransferases class-I active site NC_002163.1 RefSeq region 1177636 1177995 . + . ID=id2260;gene=guaA;Name=id2260;Dbxref=GeneID:905539;gbkey=misc_feature;Note=HMMPfam hit to PF00958 2C GMP synthase C terminal domain 2C score 1e-65 ### NC_002163.1 UTR_Extractor 5'-UTR 1178066 1178086 . + . ID=utr456;locus_tag=Cj1249;product=hypothetical protein NC_002163.1 RefSeq gene 1178087 1179547 . + . ID=gene1199;Name=Cj1249;locus_tag=Cj1249;Dbxref=GeneID:905540;gbkey=Gene NC_002163.1 RefSeq CDS 1178087 1179547 . + 0 ID=cds1133;Parent=gene1199;Name=YP_002344640.1;Dbxref=UniProtKB FTrEMBL:Q0P907 Genbank:YP_002344640.1 GeneID:905540;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1249 2C unknown 2C len: 486 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 RefSeq gene 1179587 1179772 . + . ID=NC_002163.1:6S_RNA;Name=NC_002163.1:6S_RNA;locus_tag=6S_RNA NC_002163.1 RefSeq sRNA 1179587 1179772 . + . ID=NC_002163.1:6S_RNA:unknown_transcript_1;Parent=NC_002163.1:6S_RNA;Name=NC_002163.1:6S_RNA:unknown_transcript_1;locus_tag=6S_RNA;gbkey=misc_RNA;product=6S_RNA NC_002163.1 RefSeq gene 1179610 1179623 . - . ID=NC_002163.1:pRNA;Name=NC_002163.1:pRNA;locus_tag=pRNA NC_002163.1 RefSeq sRNA 1179610 1179623 . - . ID=NC_002163.1:pRNA:unknown_transcript_1;Parent=NC_002163.1:pRNA;Name=NC_002163.1:pRNA:unknown_transcript_1;locus_tag=pRNA;gbkey=misc_RNA;product=pRNA ### NC_002163.1 RefSeq region 1179787 1180080 . + . ID=id2261;gene=purD;Name=id2261;Dbxref=GeneID:905541;gbkey=misc_feature;Note=HMMPfam hit to PF02844 2C Phosphoribosylglycinamide synthetase 2C N doma 2C score 1.3e-23 NC_002163.1 RefSeq CDS 1179787 1181037 . + 0 ID=cds1134;Parent=gene1200;gene=purD;Name=YP_002344641.1;Dbxref=GOA:Q9PN47 HSSP:P15640 InterPro:IPR000115 InterPro:IPR011761 InterPro:IPR013815 InterPro:IPR013816 InterPro:IPR013817 UniProtKB FSwiss-Prot:Q9PN47 Genbank:YP_002344641.1 GeneID:905541;gbkey=CDS;product=phosphoribosylamine--glycine ligase;Note=catalyzes the formation of N 281 29- 285-phospho-D-ribosyl 29glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis NC_002163.1 RefSeq gene 1179787 1181037 . + . ID=gene1200;gene=purD;Name=purD;locus_tag=Cj1250;Dbxref=GeneID:905541;gbkey=Gene NC_002163.1 RefSeq region 1180084 1180332 . + . ID=id2262;gene=purD;Name=id2262;Dbxref=GeneID:905541;gbkey=misc_feature;Note=HMMPfam hit to PF02842 2C Phosphoribosylglycinamide synthetase 2C B doma 2C score 8.3e-40 NC_002163.1 RefSeq region 1180333 1180746 . + . ID=id2263;gene=purD;Name=id2263;Dbxref=GeneID:905541;gbkey=misc_feature;Note=HMMPfam hit to PF01071 2C Phosphoribosylglycinamide synthetase 2C ATP-gr 2C score 5.4e-67 NC_002163.1 RefSeq region 1180756 1181031 . + . ID=id2264;gene=purD;Name=id2264;Dbxref=GeneID:905541;gbkey=misc_feature;Note=HMMPfam hit to PF02843 2C Phosphoribosylglycinamide synthetase 2C C doma 2C score 4.1e-34 NC_002163.1 RefSeq gene 1181034 1181486 . + . ID=gene1201;gene=Cj1251;Name=Cj1251;locus_tag=Cj1251;Dbxref=GeneID:905542;gbkey=Gene NC_002163.1 RefSeq CDS 1181034 1181486 . + 0 ID=cds1135;Parent=gene1201;Name=YP_002344642.1;Dbxref=GOA:Q0P905 InterPro:IPR010432 UniProtKB FTrEMBL:Q0P905 Genbank:YP_002344642.1 GeneID:905542;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1251 2C unknown 2C len: 150 aa 3B similar to hypothetical proteins e.g. TR:Q56614 28EMBL:U39068 29 Vibrio cholerae orfY 28145 aa 29 2C fasta scores 3B opt: 220 z-score: 291.8 E 28 29: 5.9e-09 2C 28.6 25 identity in 140 aa overlap. 27.9 25 identity to HP1217 7EUpdated 282006 29 note: Pfam domain PF06271 RDD family identified within CDS. Also 2C two probable transmembrane helices predicted by TMHMM2.0. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq region 1181079 1181477 . + . ID=id2265;Name=id2265;Dbxref=GeneID:905542;gbkey=misc_feature;Note=HMMPfam hit to PF06271 2C RDD family 2C score 5.3e-39 NC_002163.1 RefSeq region 1181100 1181159 . + . ID=id2266;Name=id2266;Dbxref=GeneID:905542;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1251 by TMHMM2.0 at aa 23-42 and 62-84 NC_002163.1 RefSeq region 1181217 1181285 . + . ID=id2266;Name=id2266;Dbxref=GeneID:905542;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1251 by TMHMM2.0 at aa 23-42 and 62-84 NC_002163.1 RefSeq gene 1181476 1183524 . + . ID=gene1202;Name=Cj1252;locus_tag=Cj1252;Dbxref=GeneID:905543;gbkey=Gene NC_002163.1 RefSeq CDS 1181476 1183524 . + 0 ID=cds1136;Parent=gene1202;Name=YP_002344643.1;Dbxref=GOA:Q0P904 InterPro:IPR007543 UniProtKB FTrEMBL:Q0P904 Genbank:YP_002344643.1 GeneID:905543;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1252 2C probable periplasmic protein 2C len: 682 aa 3B some similarity to proteins involved in outer membrane permeability e.g. OSTA_ECOLI organic solvent tolerance protein precursor 28784 aa 29 2C fasta scores 3B opt: 223 z-score: 255.4 E 28 29: 6.3e-07 2C 20.3 25 identity in 507 aa overlap. 27.9 25 identity to HP1216. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF04453 Organic solvent tolerance protein identified within CDS. No specific characterisation with acceptable identity score identified yet 2C so kept within product function. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 1182232 1183278 . + . ID=id2267;Name=id2267;Dbxref=GeneID:905543;gbkey=misc_feature;Note=HMMPfam hit to PF04453 2C Organic solvent tolerance protein 2C score 6.9e-85 ### NC_002163.1 RefSeq CDS 1183594 1185753 . + 0 ID=cds1137;Parent=gene1203;gene=pnp;Name=YP_002344644.1;Dbxref=GOA:Q0P903 InterPro:IPR001247 InterPro:IPR003029 InterPro:IPR004087 InterPro:IPR004088 InterPro:IPR012162 InterPro:IPR012340 InterPro:IPR015847 InterPro:IPR015848 UniProtKB FSwiss-Prot:Q0P903 Genbank:YP_002344644.1 GeneID:905544;gbkey=CDS;product=polynucleotide phosphorylase;Note=Original 282000 29 note: Cj1253 2C pnp 2C probable polyribonucleotide nucleotidyltransferase 2C len: 719 aa 3B similar to e.g. PNP_ECOLI polyribonucleotide nucleotidyltransferase 28EC 2.7.7.8 29 28711 aa 29 2C fasta scores 3B opt: 1068 z-score: 1130.9 E 28 29: 0 2C 38.9 25 identity in 730 aa overlap. 49.2 25 identity to HP1213. Contains Pfam match to entry PF00575 S1 2C S1 RNA binding domain 2C Pfam match to entry PF00013 KH-domain 2C KH domain family of RNA binding proteins 2C and Pfam match to entry PF01138 RNase_PH 2C Prokaryotic ribonuclease PH 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score 2C so not added to product function. Functional classification - RNA synthesis 2C RNA modification and DNA transcription 7EPMID:16079137 2C PMID:2432069 2C PMID:10931296 NC_002163.1 RefSeq gene 1183594 1185753 . + . ID=gene1203;gene=pnp;Name=pnp;locus_tag=Cj1253;Dbxref=GeneID:905544;gbkey=Gene NC_002163.1 RefSeq region 1183615 1184010 . + . ID=id2268;gene=pnp;Name=id2268;Dbxref=GeneID:905544;gbkey=misc_feature;Note=HMMPfam hit to PF01138 2C 3 27 exoribonuclease family 2Cdomain 2C score 3.8e-27 NC_002163.1 RefSeq region 1184017 1184292 . + . ID=id2269;gene=pnp;Name=id2269;Dbxref=GeneID:905544;gbkey=misc_feature;Note=HMMPfam hit to PF03725 2C 3 27 exoribonuclease family 2Cdomain 2C score 1.7e-07 NC_002163.1 RefSeq region 1184386 1184616 . + . ID=id2270;gene=pnp;Name=id2270;Dbxref=GeneID:905544;gbkey=misc_feature;Note=HMMPfam hit to PF03726 2C Polyribonucleotide nucleotidyltransferase 2C 2C score 3.1e-25 NC_002163.1 RefSeq region 1184623 1185024 . + . ID=id2271;gene=pnp;Name=id2271;Dbxref=GeneID:905544;gbkey=misc_feature;Note=HMMPfam hit to PF01138 2C 3 27 exoribonuclease family 2Cdomain 2C score 4.7e-47 NC_002163.1 RefSeq region 1185031 1185243 . + . ID=id2272;gene=pnp;Name=id2272;Dbxref=GeneID:905544;gbkey=misc_feature;Note=HMMPfam hit to PF03725 2C 3 27 exoribonuclease family 2Cdomain 2C score 6.1e-20 NC_002163.1 RefSeq region 1185316 1185492 . + . ID=id2273;gene=pnp;Name=id2273;Dbxref=GeneID:905544;gbkey=misc_feature;Note=HMMPfam hit to PF00013 2C KH domain 2C score 1.6e-13 NC_002163.1 RefSeq region 1185553 1185747 . + . ID=id2274;gene=pnp;Name=id2274;Dbxref=GeneID:905544;gbkey=misc_feature;Note=HMMPfam hit to PF00575 2C S1 RNA binding domain 2Cscore 5.7e-06 NC_002163.1 RefSeq gene 1185750 1186232 . + . ID=gene1204;gene=Cj1254;Name=Cj1254;locus_tag=Cj1254;Dbxref=GeneID:905545;gbkey=Gene NC_002163.1 RefSeq CDS 1185750 1186232 . + 0 ID=cds1138;Parent=gene1204;Name=YP_002344645.1;Dbxref=InterPro:IPR005122 UniProtKB FTrEMBL:Q0P902 Genbank:YP_002344645.1 GeneID:905545;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1254 2C unknown 2C len: 160 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins and also to G 2FU mismatch-specific DNA glycosyl from other bacteria. Functional classification - Unknown ### NC_002163.1 RefSeq CDS 1186290 1186499 . + 0 ID=cds1139;Parent=gene1205;Name=YP_002344646.1;Dbxref=GOA:Q0P901 InterPro:IPR004370 UniProtKB FTrEMBL:Q0P901 Genbank:YP_002344646.1 GeneID:905546;gbkey=CDS;product=isomerase;Note=Original 282000 29 note: Cj1255 2C possible isomerase 2Clen: 69 aa 3B highly similar to hypothetical protein from Erwinia chrysanthemi YKDK_ERWCH in KDGK 28pectin degradation 29 5 27region 2873 aa 29 2C fasta scores 3B opt: 259 z-score: 374.4 E 28 29: 1.5e-13 2C 61.2 25 identity in 67 aa overlap. Some similarity to plasmid-borne isomerases involed in toluene degradation e.g. XYLH_PSEPU 4-oxalocrotonate tautomerase 2862 aa 29 2C fasta scores 3B opt: 104 z-score: 164.7 E 28 29: 0.071 2C 30.8 25 identity in 65 aa overlap 2C and to chromosomal hypothetical proteins e.g. YDCE_ECOLI 2877 aa 29 2C fasta scores 3B opt: 84 z-score: 136.1 E 28 29: 2.8 2C 27.8 25 identity in 54 aa overlap. 64.2 25 identity to HP0924. Also similar to Cj0270 2837.7 25 identity in 69 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01361 Tautomerase enzyme identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score identified. kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 1186290 1186499 . + . ID=gene1205;Name=Cj1255;locus_tag=Cj1255;Dbxref=GeneID:905546;gbkey=Gene NC_002163.1 RefSeq region 1186293 1186481 . + . ID=id2275;Name=id2275;Dbxref=GeneID:905546;gbkey=misc_feature;Note=HMMPfam hit to PF01361 2C Tautomerase enzyme 2C score 3.6e-27 NC_002163.1 RefSeq gene 1186496 1187158 . - . ID=gene1206;Name=Cj1256c;locus_tag=Cj1256c;Dbxref=GeneID:905547;gbkey=Gene NC_002163.1 RefSeq CDS 1186496 1187158 . - 0 ID=cds1140;Parent=gene1206;Name=YP_002344647.1;Dbxref=GOA:Q0P900 UniProtKB FTrEMBL:Q0P900 Genbank:YP_002344647.1 GeneID:905547;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1256c 2C possible membrane protein 2C len: 220 aa 3B no Hp match. Contains possible membrane spanning domain at N-terminus. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 1187096 1187149 . - . ID=id2276;Name=id2276;Dbxref=GeneID:905547;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1256c by TMHMM2.0 at aa 4-21 ### NC_002163.1 RefSeq CDS 1187176 1188360 . - 0 ID=cds1141;Parent=gene1207;Name=YP_002344648.1;Dbxref=GOA:Q0P8Z9 InterPro:IPR001958 InterPro:IPR007114 InterPro:IPR011701 UniProtKB FTrEMBL:Q0P8Z9 Genbank:YP_002344648.1 GeneID:905548;gbkey=CDS;product=efflux pump protein;Note=Original 282000 29 note: Cj1257c 2C possible efflux pump 2C len: 394 aa 3B similar to TR:CAA07482 28EMBL:AJ007367 29 Streptococcus pneumoniae multi-drug resistance efflux pump pmrA 28399 aa 29 2C fasta scores 3B opt: 854 z-score: 1007.9 E 28 29: 0 2C 37.6 25 identity in 380 aa overlap. Also similar hypothetical transporters e.g. YCEE_ECOLI 28408 aa 29 2C fasta scores 3B opt: 830 z-score: 965.7 E 28 29: 0 2C 35.8 25 identity in 383 aa overlap 2C and to other members of the major facilitator family 2C e.g. BMR1_BACSU multidrug resistance protein 1 28389 aa 29 2C fasta scores 3B opt: 345 z-score: 405.2 E 28 29: 2.8e-15 2C 24.2 25 identity in 389 aa overlap. No Hp match. Contains Pfam match to entry PF00083 sugar_tr 2CSugar 28and other 29 transporters 7EUpdated 282006 29 note: Pfam domain PF07690 Major Facilitator Superfamily identified within CDS. Also 2Ctwelve probable transmembrane helices predicted by TMHMM2.0. Further support given to function. Some characterisation within Escherichia coli. Literature search identified paper giving further clues to product function 28PMID:16048946 29. Functional classification -Drug 2Fanalogue sensitivity 7EPMID:1537791 2C PMID:11566977 2C PMID:16048946 NC_002163.1 RefSeq gene 1187176 1188360 . - . ID=gene1207;Name=Cj1257c;locus_tag=Cj1257c;Dbxref=GeneID:905548;gbkey=Gene NC_002163.1 RefSeq region 1187212 1187271 . - . ID=id117;Name=id117;Dbxref=GeneID:905548;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1257c by TMHMM2.0 at aa 7-29 2C 44-66 2C 78-100 2C 104-126 2C133-155 2C 165-187 2C 207-229 2C 239-261 2C 273-295 2C 300-322 2C343-360 and 364-383 NC_002163.1 RefSeq region 1187281 1187334 . - . ID=id117;Name=id117;Dbxref=GeneID:905548;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1257c by TMHMM2.0 at aa 7-29 2C 44-66 2C 78-100 2C 104-126 2C133-155 2C 165-187 2C 207-229 2C 239-261 2C 273-295 2C 300-322 2C343-360 and 364-383 NC_002163.1 RefSeq region 1187287 1188330 . - . ID=id2277;Name=id2277;Dbxref=GeneID:905548;gbkey=misc_feature;Note=HMMPfam hit to PF07690 2C Major Facilitator Superfamily 2C score 9.6e-44 NC_002163.1 RefSeq region 1187395 1187463 . - . ID=id117;Name=id117;Dbxref=GeneID:905548;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1257c by TMHMM2.0 at aa 7-29 2C 44-66 2C 78-100 2C 104-126 2C133-155 2C 165-187 2C 207-229 2C 239-261 2C 273-295 2C 300-322 2C343-360 and 364-383 NC_002163.1 RefSeq region 1187476 1187544 . - . ID=id117;Name=id117;Dbxref=GeneID:905548;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1257c by TMHMM2.0 at aa 7-29 2C 44-66 2C 78-100 2C 104-126 2C133-155 2C 165-187 2C 207-229 2C 239-261 2C 273-295 2C 300-322 2C343-360 and 364-383 NC_002163.1 RefSeq region 1187578 1187646 . - . ID=id117;Name=id117;Dbxref=GeneID:905548;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1257c by TMHMM2.0 at aa 7-29 2C 44-66 2C 78-100 2C 104-126 2C133-155 2C 165-187 2C 207-229 2C 239-261 2C 273-295 2C 300-322 2C343-360 and 364-383 NC_002163.1 RefSeq region 1187674 1187742 . - . ID=id117;Name=id117;Dbxref=GeneID:905548;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1257c by TMHMM2.0 at aa 7-29 2C 44-66 2C 78-100 2C 104-126 2C133-155 2C 165-187 2C 207-229 2C 239-261 2C 273-295 2C 300-322 2C343-360 and 364-383 NC_002163.1 RefSeq region 1187800 1187868 . - . ID=id117;Name=id117;Dbxref=GeneID:905548;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1257c by TMHMM2.0 at aa 7-29 2C 44-66 2C 78-100 2C 104-126 2C133-155 2C 165-187 2C 207-229 2C 239-261 2C 273-295 2C 300-322 2C343-360 and 364-383 NC_002163.1 RefSeq region 1187896 1187964 . - . ID=id117;Name=id117;Dbxref=GeneID:905548;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1257c by TMHMM2.0 at aa 7-29 2C 44-66 2C 78-100 2C 104-126 2C133-155 2C 165-187 2C 207-229 2C 239-261 2C 273-295 2C 300-322 2C343-360 and 364-383 NC_002163.1 RefSeq region 1187983 1188051 . - . ID=id117;Name=id117;Dbxref=GeneID:905548;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1257c by TMHMM2.0 at aa 7-29 2C 44-66 2C 78-100 2C 104-126 2C133-155 2C 165-187 2C 207-229 2C 239-261 2C 273-295 2C 300-322 2C343-360 and 364-383 NC_002163.1 RefSeq region 1188061 1188129 . - . ID=id117;Name=id117;Dbxref=GeneID:905548;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1257c by TMHMM2.0 at aa 7-29 2C 44-66 2C 78-100 2C 104-126 2C133-155 2C 165-187 2C 207-229 2C 239-261 2C 273-295 2C 300-322 2C343-360 and 364-383 NC_002163.1 RefSeq region 1188163 1188231 . - . ID=id117;Name=id117;Dbxref=GeneID:905548;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1257c by TMHMM2.0 at aa 7-29 2C 44-66 2C 78-100 2C 104-126 2C133-155 2C 165-187 2C 207-229 2C 239-261 2C 273-295 2C 300-322 2C343-360 and 364-383 NC_002163.1 RefSeq region 1188274 1188342 . - . ID=id117;Name=id117;Dbxref=GeneID:905548;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1257c by TMHMM2.0 at aa 7-29 2C 44-66 2C 78-100 2C 104-126 2C133-155 2C 165-187 2C 207-229 2C 239-261 2C 273-295 2C 300-322 2C343-360 and 364-383 NC_002163.1 UTR_Extractor 5'-UTR 1188360 1188360 . - . ID=utr457;locus_tag=Cj1257c;product=putative efflux pump ### NC_002163.1 UTR_Extractor 5'-UTR 1188384 1188413 . + . ID=utr458;locus_tag=Cj1258;product=putative phosphotyrosine protein phosphatase NC_002163.1 RefSeq gene 1188414 1188869 . + . ID=gene1208;Name=Cj1258;locus_tag=Cj1258;Dbxref=GeneID:905549;gbkey=Gene NC_002163.1 RefSeq CDS 1188414 1188869 . + 0 ID=cds1142;Parent=gene1208;Name=YP_002344649.1;Dbxref=GOA:Q0P8Z8 InterPro:IPR000106 PDB:2GI4 UniProtKB FTrEMBL:Q0P8Z8 Genbank:YP_002344649.1 GeneID:905549;gbkey=CDS;product=phosphotyrosine protein phosphatase;Note=Original 282000 29 note: Cj1258 2C possible phosphotyrosine protein phosphatase 2C len: 151 aa 3B simlar to e.g. PPAL_YEAST low molecular weight phosphotyrosine protein phosphatase 28EC 3.1.3.48 29 28161 aa 29 2C fasta scores 3B opt: 279 z-score: 343.4 E 28 29: 7.9e-12 2C 37.6 25 identity in 149 aa overlap 2C and YWLE_BACSU low molecular weight protein-tyrosine protein phosphatase 28150 aa 29 2Cfasta scores 3B opt: 191 z-score: 240.4 E 28 29: 4.3e-06 2C 27.7 25 identity in 148 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF01451 Low molecular weight phosphotyrosine protein identified within CDS. Further support given to pututive function. Possible changed to . Specific characterisation with acceptable identity score not carried out yet 2C so kept in product function. Functional classification -Protein translation and modification NC_002163.1 RefSeq region 1188417 1188857 . + . ID=id2278;Name=id2278;Dbxref=GeneID:905549;gbkey=misc_feature;Note=HMMPfam hit to PF01451 2C Low molecular weight phosphotyrosine protein 2C score 1.8e-28 ### NC_002163.1 RefSeq gene 1188925 1188997 . + . ID=NC_002163.1:CJnc140;Name=NC_002163.1:CJnc140;locus_tag=CJnc140 NC_002163.1 RefSeq sRNA 1188925 1188997 . + . ID=NC_002163.1:CJnc140:unknown_transcript_1;Parent=NC_002163.1:CJnc140;Name=NC_002163.1:CJnc140:unknown_transcript_1;locus_tag=CJnc140;gbkey=misc_RNA;product=CJnc140 NC_002163.1 UTR_Extractor 5'-UTR 1189090 1189120 . + . ID=utr459;locus_tag=Cj1259;product=major outer membrane protein NC_002163.1 RefSeq region 1189121 1190392 . + . ID=id2279;gene=porA;Name=id2279;Dbxref=GeneID:905550;gbkey=misc_feature;Note=HMMPfam hit to PF05538 2C Campylobacter major outer membrane prote 2C score 0 NC_002163.1 RefSeq gene 1189121 1190395 . + . ID=gene1209;gene=porA;Name=porA;locus_tag=Cj1259;Dbxref=GeneID:905550;gbkey=Gene NC_002163.1 RefSeq CDS 1189121 1190395 . + 0 ID=cds1143;Parent=gene1209;gene=porA;Name=YP_002344650.1;Dbxref=GOA:P80672 InterPro:IPR008439 UniProtKB FSwiss-Prot:P80672 Genbank:YP_002344650.1 GeneID:905550;gbkey=CDS;product=major outer membrane protein;Note=Original 282000 29 note: Cj1259 2C porA 2C major outer membrane protein 28MOMP 29 2C len: 424 aa 3B 94.6 25 identical to TR:AAC82317 28EMBL:U96452 29 C. jejuni major outer membrane porin 28424 aa 29 2C and 98.0 25 identity to MOMP_CAMJE major outer membrane protein 28fragments 29 28399 aa 29. No hp match. Also simlar in part to Cj1021c 2863 aa 2C 34.5 25 identity in 55 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF05538 Campylobacter major outer membrane protein identified within CDS. Further support given to product function. Characterised within Campylobacter jejuni 2C so not added to product function. Functional classification -Membranes 2C lipoproteins and porins 7EPMID:7543469 2C PMID:9163918 ### NC_002163.1 RefSeq CDS 1190510 1191631 . - 0 ID=cds1144;Parent=gene1210;gene=dnaJ;Name=YP_002344651.1;Dbxref=GOA:O85213 HSSP:P08622 InterPro:IPR001305 InterPro:IPR001623 InterPro:IPR002939 InterPro:IPR003095 InterPro:IPR012724 InterPro:IPR015609 UniProtKB FSwiss-Prot:O85213 Genbank:YP_002344651.1 GeneID:905551;gbkey=CDS;product=molecular chaperone DnaJ;Note=chaperone Hsp40 3B co-chaperone with DnaK 3B Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins 2C also in an autonomous 2C dnaK-independent fashion NC_002163.1 RefSeq gene 1190510 1191631 . - . ID=gene1210;gene=dnaJ;Name=dnaJ;locus_tag=Cj1260c;Dbxref=GeneID:905551;gbkey=Gene NC_002163.1 RefSeq region 1190591 1190953 . - . ID=id2280;gene=dnaJ;Name=id2280;Dbxref=GeneID:905551;gbkey=misc_feature;Note=HMMPfam hit to PF01556 2C DnaJ C terminal region 2Cscore 2e-59 NC_002163.1 RefSeq region 1190990 1191229 . - . ID=id2281;gene=dnaJ;Name=id2281;Dbxref=GeneID:905551;gbkey=misc_feature;Note=HMMPfam hit to PF00684 2C DnaJ central domain 284 repeats 29 2C score 1.2e-22 NC_002163.1 RefSeq region 1191119 1191190 . - . ID=id2282;gene=dnaJ;Name=id2282;Dbxref=GeneID:905551;gbkey=misc_feature;Note=PS00637 CXXCXGXG dnaJ domain signature NC_002163.1 RefSeq region 1191425 1191622 . - . ID=id2283;gene=dnaJ;Name=id2283;Dbxref=GeneID:905551;gbkey=misc_feature;Note=HMMPfam hit to PF00226 2C DnaJ domain 2C score 1.4e-39 NC_002163.1 RefSeq region 1191437 1191496 . - . ID=id2284;gene=dnaJ;Name=id2284;Dbxref=GeneID:905551;gbkey=misc_feature;Note=PS00636 Nt-dnaJ domain signature ### NC_002163.1 UTR_Extractor 5'-UTR 1191632 1191691 . - . ID=utr460;locus_tag=Cj1260c;product=chaperone protein DnaJ NC_002163.1 UTR_Extractor 5'-UTR 1191758 1191787 . + . ID=utr461;locus_tag=Cj1261;product=two-component regulator NC_002163.1 RefSeq CDS 1191788 1192459 . + 0 ID=cds1145;Parent=gene1211;gene=racR;Name=YP_002344652.1;Dbxref=GOA:O68795 HSSP:Q9WYN0 InterPro:IPR001789 InterPro:IPR001867 UniProtKB FTrEMBL:O68795 Genbank:YP_002344652.1 GeneID:905552;gbkey=CDS;product=two-component regulator;Note=Original 282000 29 note: Cj1261 2C racR 2C two-component regulator 2C len: 223 aa 3B identical to TR:O68795 28EMBL:AF053960 29 C. jejuni response regulator protein 28223 aa 29 2C and similar to e.g. BAER_ECOLI transcriptional regulatory protein BAER 28240 aa 29 2C fasta scores 3B opt: 485 z-score: 583.5 E 28 29: 3.3e-25 2C 37.4 25 identity in 219 aa overlap. 52.0 25 identity to HP0166. Also simlar to Cj1227c 2850.7 25 identity in 223 aa overlap 29. Contains Pfam match to entry PF00072 response_reg 2C Response regulator receiver domain 2C and Pfam match to entry PF00486 trans_reg_C 2CTranscriptional regulatory protein 2C C terminal 7EUpdated 282006 29 note: Characterisation work carried out in Campylobacter jejuni 2C so not added to product function. Literature search identified paper linking product function to be involved in virulence associated factors 28PMID:16392901 29. Functional classification - Signal transduction 7EPMID:10322038 2C PMID:16392901 NC_002163.1 RefSeq gene 1191788 1192459 . + . ID=gene1211;gene=racR;Name=racR;locus_tag=Cj1261;Dbxref=GeneID:905552;gbkey=Gene NC_002163.1 RefSeq region 1191791 1192144 . + . ID=id2285;gene=racR;Name=id2285;Dbxref=GeneID:905552;gbkey=misc_feature;Note=HMMPfam hit to PF00072 2C Response regulator receiver domain 2C score 1.5e-28 NC_002163.1 RefSeq region 1192220 1192450 . + . ID=id2286;gene=racR;Name=id2286;Dbxref=GeneID:905552;gbkey=misc_feature;Note=HMMPfam hit to PF00486 2C Transcriptional regulatory protein 2C C te 2C score 1.7e-18 NC_002163.1 RefSeq CDS 1192456 1193691 . + 0 ID=cds1146;Parent=gene1212;gene=racS;Name=YP_002344653.1;Dbxref=GOA:Q0P8Z4 InterPro:IPR003594 InterPro:IPR003660 InterPro:IPR003661 InterPro:IPR005467 UniProtKB FTrEMBL:Q0P8Z4 Genbank:YP_002344653.1 GeneID:905553;gbkey=CDS;product=two-component sensor histidine kinase;Note=Original 282000 29 note: Cj1262 2C racS 2C probable two-component sensor 28histidine kinase 29 2C len: 411 aa 3B 99.5 25 identical to TR:O68796 28EMBL:AF053961 29 C. jejuni histidine protein kinase 28fragment 29 28189 aa 29 2C and similar to e.g. ENVZ_ECOLI osmolarity sensor protein ENVZ 28450 aa 29 2C fast scores 3B opt: 188 z-score: 217.1 E 28 29: 8.5e-05 2C 24.4 25 identity in 242 aa overlap. N-term has 28.2 25 identity to HP0165 2C C-term has 37.9 25 identity to HP0164. Also similar to Cj1226c 2831.3 25 identity in 412 aa overlap 29. Contains Pfam match to entry PF00512 signal 2CSignal carboxyl-terminal domain 2C and Pfam match to entry PF00149 STphosphatase 2C Ser 2FThr protein phosphatases 7EUpdated 282006 29 note: Characterisation work carried out in Campylobacter jejuni 2C so not added to product function. Functional classification - Signal transduction 7EPMID:10322038 NC_002163.1 RefSeq gene 1192456 1193691 . + . ID=gene1212;gene=racS;Name=racS;locus_tag=Cj1262;Dbxref=GeneID:905553;gbkey=Gene NC_002163.1 RefSeq region 1192480 1192527 . + . ID=id2287;gene=racS;Name=id2287;Dbxref=GeneID:905553;gbkey=misc_feature;Note=PS00038 Myc-type 2C 27helix-loop-helix 27 dimerization domain signature NC_002163.1 RefSeq region 1192486 1192545 . + . ID=id2288;gene=racS;Name=id2288;Dbxref=GeneID:905553;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1262 by TMHMM2.0 at aa 11-30 and 132-154 NC_002163.1 RefSeq region 1192849 1192917 . + . ID=id2288;gene=racS;Name=id2288;Dbxref=GeneID:905553;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1262 by TMHMM2.0 at aa 11-30 and 132-154 NC_002163.1 RefSeq region 1192858 1193064 . + . ID=id2289;gene=racS;Name=id2289;Dbxref=GeneID:905553;gbkey=misc_feature;Note=HMMPfam hit to PF00672 2C HAMP domain 2C score 9.5e-06 NC_002163.1 RefSeq region 1192900 1192947 . + . ID=id2290;gene=racS;Name=id2290;Dbxref=GeneID:905553;gbkey=misc_feature;Note=PS00146 Beta-lactamase class-A active site NC_002163.1 RefSeq region 1193074 1193241 . + . ID=id2291;gene=racS;Name=id2291;Dbxref=GeneID:905553;gbkey=misc_feature;Note=HMMPfam hit to PF00512 2C His Kinase A 28phosphoacceptor 29 domain 2C score 2.9e-05 NC_002163.1 RefSeq region 1193377 1193682 . + . ID=id2292;gene=racS;Name=id2292;Dbxref=GeneID:905553;gbkey=misc_feature;Note=HMMPfam hit to PF02518 2C Histidine kinase- 2C DNA gyrase B- 2C and HSP90 2C score 3.8e-07 NC_002163.1 RefSeq CDS 1193691 1194263 . + 0 ID=cds1147;Parent=gene1213;gene=recR;Name=YP_002344654.1;Dbxref=GOA:Q9PN35 InterPro:IPR000093 InterPro:IPR015967 UniProtKB FSwiss-Prot:Q9PN35 Genbank:YP_002344654.1 GeneID:905554;gbkey=CDS;product=recombination protein RecR;Note=involved in a recombinational process of DNA repair 2C independent of the recBC complex NC_002163.1 RefSeq gene 1193691 1194263 . + . ID=gene1213;gene=recR;Name=recR;locus_tag=Cj1263;Dbxref=GeneID:905554;gbkey=Gene NC_002163.1 RefSeq region 1193805 1193930 . + . ID=id2293;gene=recR;Name=id2293;Dbxref=GeneID:905554;gbkey=misc_feature;Note=HMMPfam hit to PF02132 2C RecR protein 2C score 1.8e-13 NC_002163.1 RefSeq region 1193862 1193924 . + . ID=id2294;gene=recR;Name=id2294;Dbxref=GeneID:905554;gbkey=misc_feature;Note=PS01300 RecR protein signature NC_002163.1 RefSeq CDS 1194260 1194796 . - 0 ID=cds1148;Parent=gene1214;gene=hydD;Name=YP_002344655.1;Dbxref=GOA:Q0P8Z2 InterPro:IPR000671 UniProtKB FTrEMBL:Q0P8Z2 Genbank:YP_002344655.1 GeneID:905555;gbkey=CDS;product=hydrogenase maturation protease;Note=Original 282000 29 note: Cj1264c 2C hydD 2C probable hydrogenase maturation protease 2C len: 178 aa 3B simlar to e.g. HYDD_WOLSU HYDD protein 28159 aa 29 2C fasta scores 3B opt: 443 z-score: 561.5 E 28 29: 5.6e-24 2C 42.5 25 identity in 160 aa overlap 2C and HYBD_ECOLI hydrogenase 2 maturation protease 28164 aa 29 2C fasta scores 3B opt: 212 z-score: 275.6 E 28 29: 4.7e-08 2C 28.1 25 identity in 128 aa overlap. 42.7 25 identity to HP0634 7EUpdated 282006 29 note: Pfam domain PF01750 Hydrogenase maturation protease identified within CDS. Further support given to product function. Some characterisation work within Wolinella succinogenes and Escherichia coli to different designations. kept within product function. Functional classification -Energy metabolism - Respiration 7EPMID:1587288 2C PMID:2180913 2C PMID:14726233 NC_002163.1 RefSeq gene 1194260 1194796 . - . ID=gene1214;gene=hydD;Name=hydD;locus_tag=Cj1264c;Dbxref=GeneID:905555;gbkey=Gene NC_002163.1 RefSeq region 1194344 1194739 . - . ID=id2295;gene=hydD;Name=id2295;Dbxref=GeneID:905555;gbkey=misc_feature;Note=HMMPfam hit to PF01750 2C Hydrogenase maturation protease 2C score 2.7e-22 NC_002163.1 RefSeq gene 1194793 1195485 . - . ID=gene1215;gene=hydC;Name=hydC;locus_tag=Cj1265c;Dbxref=GeneID:905556;gbkey=Gene NC_002163.1 RefSeq CDS 1194793 1195485 . - 0 ID=cds1149;Parent=gene1215;gene=hydC;Name=YP_002344656.1;Dbxref=GOA:Q0P8Z1 InterPro:IPR000516 InterPro:IPR011577 UniProtKB FTrEMBL:Q0P8Z1 Genbank:YP_002344656.1 GeneID:905556;gbkey=CDS;product=Ni 2FFe-hydrogenase B-type cytochrome subunit;Note=Original 282000 29 note: Cj1265c 2C hydC 2C probable Ni 2FFe-hydrogenase B-type cytochrome subunit 2C len: 230 aa 3B similar to e.g. CYBH_WOLSU quinone-reactive Ni 2FFe-hydrogenase B-type cytochrome subunit 28230 aa 29 2Cfasta scores 3B opt: 771 z-score: 968.2 E 28 29: 0 2C 49.8 25 identity in 225 aa overlap 2C and CYBH_ECOLI probable Ni 2FFe-hydrogenase B-type cytochrome subunit 28235 aa 29 2Cfasta scores 3B opt: 344 z-score: 437.4 E 28 29: 4.6e-17 2C 25.5 25 identity in 231 aa overlap. 41.1 25 identity to HP0633. Contains PS00883 Nickel-dependent hydrogenases b-type cytochrome subunit signature 2 2C and fam match to entry PF01292 Ni_hydr_CYTB 2C Nickel-dependent hydrogenases b-type cytochrome subunit 7EUpdated 282006 29 note: Four probable transmembrane helices predicted by TMHMM2.0. Characterised within Wolinella succinogenes with acceptable identity score 2C so not added to product function. Functional classification - Energy metabolism - Respiration 7EPMID:10525739 2C PMID:1587288 2C PMID:2180913 NC_002163.1 RefSeq region 1194823 1195449 . - . ID=id2296;gene=hydC;Name=id2296;Dbxref=GeneID:905556;gbkey=misc_feature;Note=HMMPfam hit to PF01292 2C Cytochrome b561 family 2Cscore 2.6e-37 NC_002163.1 RefSeq region 1194862 1194930 . - . ID=id118;gene=hydC;Name=id118;Dbxref=GeneID:905556;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1265c by TMHMM2.0 at aa 25-44 2C 64-86 2C 131-153 and 186-208 NC_002163.1 RefSeq region 1194889 1194942 . - . ID=id2297;gene=hydC;Name=id2297;Dbxref=GeneID:905556;gbkey=misc_feature;Note=PS00883 Nickel-dependent hydrogenases b-type cytochrome subunit signature 2 NC_002163.1 RefSeq region 1195027 1195095 . - . ID=id118;gene=hydC;Name=id118;Dbxref=GeneID:905556;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1265c by TMHMM2.0 at aa 25-44 2C 64-86 2C 131-153 and 186-208 NC_002163.1 RefSeq region 1195228 1195296 . - . ID=id118;gene=hydC;Name=id118;Dbxref=GeneID:905556;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1265c by TMHMM2.0 at aa 25-44 2C 64-86 2C 131-153 and 186-208 NC_002163.1 RefSeq region 1195258 1195290 . - . ID=id2298;gene=hydC;Name=id2298;Dbxref=GeneID:905556;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1195354 1195413 . - . ID=id118;gene=hydC;Name=id118;Dbxref=GeneID:905556;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1265c by TMHMM2.0 at aa 25-44 2C 64-86 2C 131-153 and 186-208 ### NC_002163.1 RefSeq CDS 1195496 1197211 . - 0 ID=cds1150;Parent=gene1216;gene=hydB;Name=YP_002344657.1;Dbxref=GOA:Q0P8Z0 InterPro:IPR001501 UniProtKB FTrEMBL:Q0P8Z0 Genbank:YP_002344657.1 GeneID:905557;gbkey=CDS;product=Ni 2FFe-hydrogenase large subunit;Note=Original 282000 29 note: Cj1266c 2C hydB 2C probable Ni 2FFe-hydrogenase large subunit 2C len: 571 aa 3B similar to e.g. MBHL_WOLSU quinone-reactive Ni 2FFe-hydrogenase large chain 28575 aa 29 2C fasta scores 3B opt: 2619 z-score: 3068.8 E 28 29: 0 2C 65.3 25 identity in 567 aa overlap 2C and MBHM_ECOLI hydrogenase-2 large chain 28567 aa 29 2C fasta scores 3B opt: 1355 z-score: 1587.5 E 28 29: 0 2C 42.1 25 identity in 589 aa overlap. 64.7 25 identity to HP0632. Contains PS00507 and PS00508 Nickel-dependent hydrogenases large subunit signatures 1 and 2 2C and Pfam match to entry PF00374 NiFeSe_Hases 2C Nickel-dependent hydrogenases 7EUpdated 282006 29 note: Characterised within Wolinella succinogenes 2C so not added to product function. Functional classification - Energy metabolism -Respiration 7EPMID:10525739 2C PMID:1587288 2C PMID:2180913 NC_002163.1 RefSeq gene 1195496 1197211 . - . ID=gene1216;gene=hydB;Name=hydB;locus_tag=Cj1266c;Dbxref=GeneID:905557;gbkey=Gene NC_002163.1 RefSeq region 1195553 1195582 . - . ID=id2300;gene=hydB;Name=id2300;Dbxref=GeneID:905557;gbkey=misc_feature;Note=PS00508 Nickel-dependent hydrogenases large subunit signature 2 NC_002163.1 RefSeq region 1195553 1197094 . - . ID=id2299;gene=hydB;Name=id2299;Dbxref=GeneID:905557;gbkey=misc_feature;Note=HMMPfam hit to PF00374 2C Nickel-dependent hydrogenase 2C score 5.7e-256 NC_002163.1 RefSeq region 1197017 1197094 . - . ID=id2301;gene=hydB;Name=id2301;Dbxref=GeneID:905557;gbkey=misc_feature;Note=PS00507 Nickel-dependent hydrogenases large subunit signature 1 ### NC_002163.1 RefSeq CDS 1197214 1198353 . - 0 ID=cds1151;Parent=gene1217;gene=hydA;Name=YP_002344658.1;Dbxref=GOA:Q0P8Y9 InterPro:IPR000585 InterPro:IPR001821 InterPro:IPR006137 InterPro:IPR006311 InterPro:IPR013634 UniProtKB FTrEMBL:Q0P8Y9 Genbank:YP_002344658.1 GeneID:905558;gbkey=CDS;product=Ni 2FFe-hydrogenase small subunit;Note=Original 282000 29 note: Cj1267c 2C hydA 2C probable Ni 2FFe-hydrogenase small subunit 2C len: 379 aa 3B similar to e.g. MBHS_WOLSU quinone-reactive Ni 2FFe-hydrogenase small chain precursor 28354 aa 29 2C fasta scores 3B opt: 1968 z-score: 2288.8 E 28 29: 0 2C 78.1 25 identity in 351 aa overlap 2C and MBHS_ECOLI hydrogenase-1 small chain precursor 28372 aa 29 2Cfasta scores 3B opt: 1058 z-score: 1232.4 E 28 29: 0 2C 44.0 25 identity in 361 aa overlap. 68.2 25 identity to HP0631. Also similar to Cj1399c 2850.8 25 identity in 329 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01058 NADH ubiquinone oxidoreductase 2C 20 Kd subunit identified within CDS. Further support given to product function. Characterised within Wolinella succinogenes 2C so not added to product function. Functional classification -Energy metabolism - Respiration 7EPMID:10525739 2C PMID:1587288 2C PMID:2180913 NC_002163.1 RefSeq gene 1197214 1198353 . - . ID=gene1217;gene=hydA;Name=hydA;locus_tag=Cj1267c;Dbxref=GeneID:905558;gbkey=Gene NC_002163.1 RefSeq region 1197664 1197984 . - . ID=id2302;gene=hydA;Name=id2302;Dbxref=GeneID:905558;gbkey=misc_feature;Note=HMMPfam hit to PF01058 2C NADH ubiquinone oxidoreductase 2C 20 Kd sub 2C score 7.5e-05 NC_002163.1 RefSeq region 1197970 1198014 . - . ID=id2303;gene=hydA;Name=id2303;Dbxref=GeneID:905558;gbkey=misc_feature;Note=PS00024 Hemopexin domain signature ### NC_002163.1 UTR_Extractor 5'-UTR 1198354 1198385 . - . ID=utr462;locus_tag=Cj1267c;product=Ni 2FFe-hydrogenase small chain NC_002163.1 RefSeq CDS 1198474 1200315 . - 0 ID=cds1152;Parent=gene1218;gene=mnmC;Name=YP_002344659.1;Dbxref=GOA:Q9PN30 InterPro:IPR006076 InterPro:IPR008471 InterPro:IPR017610 UniProtKB FSwiss-Prot:Q9PN30 Genbank:YP_002344659.1 GeneID:905559;gbkey=CDS;product=5-methylaminomethyl-2-thiouridine methyltransferase;Note=catalyzes the formation of 5-methylaminomethyl-2-thiouridine in position 34 of the anticodon of tRNA molecules NC_002163.1 RefSeq gene 1198474 1200315 . - . ID=gene1218;gene=mnmC;Name=mnmC;locus_tag=Cj1268c;Dbxref=GeneID:905559;gbkey=Gene NC_002163.1 RefSeq region 1198567 1199574 . - . ID=id2304;gene=mnmC;Name=id2304;Dbxref=GeneID:905559;gbkey=misc_feature;Note=HMMPfam hit to PF01266 2C FAD dependent oxidoreductase 2C score 2e-31 NC_002163.1 RefSeq region 1199641 1200309 . - . ID=id2305;gene=mnmC;Name=id2305;Dbxref=GeneID:905559;gbkey=misc_feature;Note=HMMPfam hit to PF05430 2C Protein of unknown function 28DUF752 29 2C score 4.9e-111 NC_002163.1 RefSeq CDS 1200312 1202291 . - 0 ID=cds1153;Parent=gene1219;gene=amiA;Name=YP_002344660.1;Dbxref=GOA:Q0P8Y7 InterPro:IPR002508 UniProtKB FTrEMBL:Q0P8Y7 Genbank:YP_002344660.1 GeneID:905560;gbkey=CDS;product=N-acetylmuramoyl-L-alanine amidase;Note=Original 282000 29 note: Cj1269c 2C amiA 2C probable N-acetylmuramoyl-L-alanine amidase 2C len: 659 aa 3B similar in N-terminus to many e.g. AMIA_ECOLI probable N-acetylmuramoyl-L-alanine amidase AMIA precursor 28EC 3.5.1.28 29 28289 aa 29 2C fasta scores 3B opt: 393 z-score: 409.5 E 28 29: 1.6e-15 2C 32.2 25 identity in 264 aa overlap 2C and CWLB_BACSU N-acetylmuramoyl-L-alanine amidase CWLB precursor 28496 aa 29 2C fasta scores 3B opt: 250 z-score: 260.4 E 28 29: 3.3e-07 2C 24.9 25 identity in 365 aa overlap. Similar in N-term to HP0772 2851.8 25 identity in 253 aa overlap 29. C-term approx 400 aa appear to be unique. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF01520 N-acetylmuramoyl-L-alanine amidase identified within CDS. Further support given to product function. Characterised in Escherchia coli with marginal identity score. Appropriate motifs present. not added to product function. Functional classification - Murein sacculus and peptidoglycan 7EPMID:12787347 2C PMID:6137479 2C PMID:11454209 2CPMID:12787347 NC_002163.1 RefSeq gene 1200312 1202291 . - . ID=gene1219;gene=amiA;Name=amiA;locus_tag=Cj1269c;Dbxref=GeneID:905560;gbkey=Gene NC_002163.1 RefSeq region 1200324 1200803 . - . ID=id2306;gene=amiA;Name=id2306;Dbxref=GeneID:905560;gbkey=misc_feature;Note=HMMPfam hit to PF01520 2C N-acetylmuramoyl-L-alanine amidase 2C score 2.7e-47 NC_002163.1 RefSeq CDS 1202291 1203382 . - 0 ID=cds1154;Parent=gene1220;Name=YP_002344661.1;Dbxref=GOA:Q0P8Y6 InterPro:IPR004136 InterPro:IPR013785 UniProtKB FTrEMBL:Q0P8Y6 Genbank:YP_002344661.1 GeneID:905561;gbkey=CDS;product=2-nitropropane dioxygenase;Note=Original 282000 29 note: Cj1270c 2C unknown 2C len: 363 aa 3B similar to hypothetical proteins e.g. TR:O66549 28EMBL:AE000676 29 Aquifex aeolicus AQ_159 28182 aa 29 2C fasta scores 3B opt: 550 z-score: 647.2 E 28 29: 9.5e-29 2C 52.2 25 identity in 161 aa overlap. 61.1 25 identity to HP0773 7EUpdated 282006 29 note: Pfam domain PF03060 2-nitropropane dioxygenase identified within CDS. Product function modified to more specific family member based on motif match. No specific characterisation has been carried out yet 2C so kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 1202291 1203382 . - . ID=gene1220;gene=Cj1270c;Name=Cj1270c;locus_tag=Cj1270c;Dbxref=GeneID:905561;gbkey=Gene NC_002163.1 RefSeq region 1202297 1203373 . - . ID=id2307;Name=id2307;Dbxref=GeneID:905561;gbkey=misc_feature;Note=HMMPfam hit to PF03060 2C 2-nitropropane dioxygenase 2Cscore 5.8e-95 NC_002163.1 RefSeq gene 1203379 1204584 . - . ID=gene1221;gene=tyrS;Name=tyrS;locus_tag=Cj1271c;Dbxref=GeneID:905562;gbkey=Gene NC_002163.1 RefSeq CDS 1203379 1204584 . - 0 ID=cds1155;Parent=gene1221;gene=tyrS;Name=YP_002344662.1;Dbxref=GOA:Q9PN27 HSSP:P83453 InterPro:IPR001412 InterPro:IPR002305 InterPro:IPR002307 InterPro:IPR002942 InterPro:IPR014729 UniProtKB FSwiss-Prot:Q9PN27 Genbank:YP_002344662.1 GeneID:905562;gbkey=CDS;product=tyrosyl-tRNA synthetase;Note=catalyzes the formation of tyrosyl-tRNA 28Tyr 29 from tyrosine and tRNA 28Tyr 29 NC_002163.1 RefSeq region 1203427 1203570 . - . ID=id2308;gene=tyrS;Name=id2308;Dbxref=GeneID:905562;gbkey=misc_feature;Note=HMMPfam hit to PF01479 2C S4 domain 2C score 0.0012 NC_002163.1 RefSeq region 1203619 1204491 . - . ID=id2309;gene=tyrS;Name=id2309;Dbxref=GeneID:905562;gbkey=misc_feature;Note=HMMPfam hit to PF00579 2C tRNA synthetases class I 28W and Y 29 2C score 8.6e-97 NC_002163.1 RefSeq region 1204420 1204452 . - . ID=id2310;gene=tyrS;Name=id2310;Dbxref=GeneID:905562;gbkey=misc_feature;Note=PS00178 Aminoacyl-transfer RNA synthetases class-I signature ### NC_002163.1 RefSeq CDS 1204596 1206791 . - 0 ID=cds1156;Parent=gene1222;gene=spoT;Name=YP_002344663.1;Dbxref=GOA:Q0P8Y4 InterPro:IPR002912 InterPro:IPR003607 InterPro:IPR004095 InterPro:IPR004811 InterPro:IPR006674 InterPro:IPR007685 UniProtKB FTrEMBL:Q0P8Y4 Genbank:YP_002344663.1 GeneID:905563;gbkey=CDS;product=guanosine-3 27 2C5 27-bis 28diphosphate 29 3 27-pyrophosphohydrolase;Note=Original 282000 29 note: Cj1272c 2C spoT 2C probable guanosine-3 27 2C5 27-bis 28diphosphate 29 3 27-pyrophosphohydrolase 2Clen: 731 aa 3B similar to e.g. SPOT_ECOLI guanosine-3 27 2C5 27-bis 28diphosphate 29 3 27-pyrophosphohydrolase 28EC 3.1.7.2 29 28702 aa 29 2C fasta scores 3B opt: 1208 z-score: 1408.2 E 28 29: 0 2C 32.8 25 identity in 677 aa overlap. 40.7 25 identity to HP0775. Also similar to e.g. RELA_ECOLI GTP pyrophosphokinase 28744 aa 29 2C fasta scores 3B opt: 855 z-score: 995.9 E 28 29: 0 2C 28.3 25 identity in 668 aa overlap. There appears to be no distinct relA homolog in Cj or Hp 7EUpdated 282006 29 note: Pfam domains PF01842 ACT domain 2C PF02824 TGS domain 2C PF04607 Region found in RelA 2F SpoT proteins and PF01966 HD domain were all identified within CDS. Further support given to product function. Still not specifically characterised with acceptable identity score 2C so kept within product function. Literature search identified paper giving further clues to product function. Functional classification - Broad regulatory functions 7EPMID:15773975 2C PMID:2549050 NC_002163.1 RefSeq gene 1204596 1206791 . - . ID=gene1222;gene=spoT;Name=spoT;locus_tag=Cj1272c;Dbxref=GeneID:905563;gbkey=Gene NC_002163.1 RefSeq region 1204620 1204844 . - . ID=id2311;gene=spoT;Name=id2311;Dbxref=GeneID:905563;gbkey=misc_feature;Note=HMMPfam hit to PF01842 2C ACT domain 2C score 1.3e-06 NC_002163.1 RefSeq region 1205364 1205555 . - . ID=id2312;gene=spoT;Name=id2312;Dbxref=GeneID:905563;gbkey=misc_feature;Note=HMMPfam hit to PF02824 2C TGS domain 2C score 6.4e-20 NC_002163.1 RefSeq region 1205676 1206005 . - . ID=id2313;gene=spoT;Name=id2313;Dbxref=GeneID:905563;gbkey=misc_feature;Note=HMMPfam hit to PF04607 2C Region found in RelA 2F SpoT proteins 2C score 2.4e-45 NC_002163.1 RefSeq region 1206285 1206608 . - . ID=id2314;gene=spoT;Name=id2314;Dbxref=GeneID:905563;gbkey=misc_feature;Note=HMMPfam hit to PF01966 2C HD domain 2C score 8.1e-07 NC_002163.1 RefSeq region 1206636 1206653 . - . ID=id2315;gene=spoT;Name=id2315;Dbxref=GeneID:905563;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature NC_002163.1 RefSeq gene 1206775 1206999 . - . ID=gene1223;gene=rpoZ;Name=rpoZ;locus_tag=Cj1273c;Dbxref=GeneID:905564;gbkey=Gene NC_002163.1 RefSeq CDS 1206775 1206999 . - 0 ID=cds1157;Parent=gene1223;gene=rpoZ;Name=YP_002344664.1;Dbxref=GOA:Q9PN25 InterPro:IPR003716 InterPro:IPR006110 UniProtKB FSwiss-Prot:Q9PN25 Genbank:YP_002344664.1 GeneID:905564;gbkey=CDS;product=DNA-directed RNA polymerase subunit omega;Note=Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta 27 subunit thereby facilitating its interaction with the beta and alpha subunits NC_002163.1 RefSeq region 1206790 1206954 . - . ID=id2316;gene=rpoZ;Name=id2316;Dbxref=GeneID:905564;gbkey=misc_feature;Note=HMMPfam hit to PF01192 2C RNA polymerase Rpb6 2C score 2.8e-19 ### NC_002163.1 RefSeq gene 1207010 1207729 . - . ID=gene1224;gene=pyrH;Name=pyrH;locus_tag=Cj1274c;Dbxref=GeneID:905565;gbkey=Gene NC_002163.1 RefSeq CDS 1207010 1207729 . - 0 ID=cds1158;Parent=gene1224;gene=pyrH;Name=YP_002344665.1;Dbxref=GOA:Q9PN24 InterPro:IPR001048 InterPro:IPR011817 InterPro:IPR015963 UniProtKB FSwiss-Prot:Q9PN24 Genbank:YP_002344665.1 GeneID:905565;gbkey=CDS;product=uridylate kinase;Note=Catalyzes the phosphorylation of UMP to UDP NC_002163.1 RefSeq region 1207085 1207717 . - . ID=id2317;gene=pyrH;Name=id2317;Dbxref=GeneID:905565;gbkey=misc_feature;Note=HMMPfam hit to PF00696 2C Amino acid kinase family 2Cscore 7.1e-54 ### NC_002163.1 UTR_Extractor 5'-UTR 1207730 1207747 . - . ID=utr463;locus_tag=Cj1274c;product=uridylate kinase NC_002163.1 RefSeq CDS 1207781 1208974 . - 0 ID=cds1159;Parent=gene1225;Name=YP_002344666.1;Dbxref=GOA:Q0P8Y1 InterPro:IPR002886 InterPro:IPR016047 UniProtKB FTrEMBL:Q0P8Y1 Genbank:YP_002344666.1 GeneID:905566;gbkey=CDS;product=peptidase M23 family protein;Note=Original 282000 29 note: Cj1275c 2C probable periplasmic protein 2C len: 397 aa 3B weak similarity to hypothetical proteins e.g. YIBP_ECOLI 28419 aa 29 2C fasta scores 3B opt: 203 z-score: 198.7 E 28 29: 0.0009 2C 21.5 25 identity in 396 aa overlap. 36.4 25 identity to HP0750. Contains probable N-terminal signal sequence and coiled-coil regions between approx. aa 30-100 and 165-230 7EUpdated 282006 29 note: Pfam domain PF01551 Peptidase family M23 identified within CDS. Also 2C one probable transmembrane helix predicted by TMHMM2.0. Product modified to more specific family member based on motif match. No specific characterisation has been carried out yet 2C so kept within product function. Functional classification - Degradation of macromolecules - Proteins 2Cpeptides and glycopeptides. Functional classification -Degradation of macromolecules - Proteins 2C peptides and glycopeptides NC_002163.1 RefSeq gene 1207781 1208974 . - . ID=gene1225;Name=Cj1275c;locus_tag=Cj1275c;Dbxref=GeneID:905566;gbkey=Gene NC_002163.1 RefSeq region 1207805 1208080 . - . ID=id2318;Name=id2318;Dbxref=GeneID:905566;gbkey=misc_feature;Note=HMMPfam hit to PF01551 2C Peptidase family M23 2C score 1e-18 NC_002163.1 RefSeq region 1208903 1208962 . - . ID=id2319;Name=id2319;Dbxref=GeneID:905566;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1275c by TMHMM2.0 at aa 5-24 NC_002163.1 RefSeq gene 1208971 1209777 . - . ID=gene1226;Name=Cj1276c;locus_tag=Cj1276c;Dbxref=GeneID:905567;gbkey=Gene NC_002163.1 RefSeq CDS 1208971 1209777 . - 0 ID=cds1160;Parent=gene1226;Name=YP_002344667.1;Dbxref=UniProtKB FTrEMBL:Q0P8Y0 Genbank:YP_002344667.1 GeneID:905567;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj1276c 2C probable integral membrane protein 2C len: 268 aa 3B 32.1 25 identity to HP0749 7EUpdated 282006 29 note: Four probable transmembrane helices predicted by TMHMM2.0. No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 1208989 1209057 . - . ID=id119;Name=id119;Dbxref=GeneID:905567;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1276c by TMHMM2.0 at aa 7-29 2C 143-165 2C 199-221 and 241-263 NC_002163.1 RefSeq region 1209115 1209183 . - . ID=id119;Name=id119;Dbxref=GeneID:905567;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1276c by TMHMM2.0 at aa 7-29 2C 143-165 2C 199-221 and 241-263 NC_002163.1 RefSeq region 1209283 1209351 . - . ID=id119;Name=id119;Dbxref=GeneID:905567;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1276c by TMHMM2.0 at aa 7-29 2C 143-165 2C 199-221 and 241-263 NC_002163.1 RefSeq region 1209691 1209759 . - . ID=id119;Name=id119;Dbxref=GeneID:905567;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1276c by TMHMM2.0 at aa 7-29 2C 143-165 2C 199-221 and 241-263 NC_002163.1 RefSeq CDS 1209764 1210429 . - 0 ID=cds1161;Parent=gene1227;Name=YP_002344668.1;Dbxref=GOA:Q0P8X9 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FTrEMBL:Q0P8X9 Genbank:YP_002344668.1 GeneID:905568;gbkey=CDS;product=ABC transporter ATP-binding protein;Note=Original 282000 29 note: Cj1277c 2C probable ABC transporter ATP-binding protein 2C len: 221 aa 3B similar to many e.g. YCFV_ECOLI hypothetical ABC transporter ATP-binding protein 28233 aa 29 2C fast scores 3B opt: 464 z-score: 566.5 E 28 29: 2.9e-24 2C 38.2 25 identity in 220 aa overlap 2C and FTSE_ECOLI cell division ATP-binding protein FTSE 28222 aa 29 2C fasta scores 3B opt: 455 z-score: 556.0 E 28 29: 1.1e-23 2C 38.5 25 identity in 213 aa overlap. 54.8 25 identity to HP0748. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00211 ABC transporters family signature 2C and Pfam match to entry PF00005 ABC_tran 2C ABC transporters 7EUpdated 282006 29 note: Similar to more than one characterised strain 2Fgenus. Literature search added for further information. kept within product function. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:11844772 2C PMID:10783239 2C PMID:12823819 NC_002163.1 RefSeq gene 1209764 1210429 . - . ID=gene1227;Name=Cj1277c;locus_tag=Cj1277c;Dbxref=GeneID:905568;gbkey=Gene NC_002163.1 RefSeq region 1209785 1210345 . - . ID=id2320;Name=id2320;Dbxref=GeneID:905568;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 2.7e-54 NC_002163.1 RefSeq region 1209971 1210015 . - . ID=id2321;Name=id2321;Dbxref=GeneID:905568;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq region 1210301 1210324 . - . ID=id2322;Name=id2322;Dbxref=GeneID:905568;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 UTR_Extractor 5'-UTR 1210430 1210458 . - . ID=utr464;locus_tag=Cj1277c;product=putative ABC transporter ATP-binding protein NC_002163.1 RefSeq CDS 1210499 1211677 . - 0 ID=cds1162;Parent=gene1228;gene=trmB;Name=YP_002344669.1;Dbxref=GOA:Q9PN20 InterPro:IPR003358 InterPro:IPR004395 UniProtKB FSwiss-Prot:Q9PN20 Genbank:YP_002344669.1 GeneID:905569;gbkey=CDS;product=tRNA 28guanine-N 287 29- 29-methyltransferase;Note=tRNA 28guanine-N 287 29- 29-methyltransferase 3B catalyzes the formation of N 287 29-methylguanine at position 46 28m7G46 29 in tRNA by transferring the methyl residue from S-adenosyl-L-methionine NC_002163.1 RefSeq gene 1210499 1211677 . - . ID=gene1228;gene=trmB;Name=trmB;locus_tag=Cj1278c;Dbxref=GeneID:905569;gbkey=Gene NC_002163.1 RefSeq region 1210829 1211401 . - . ID=id2323;gene=trmB;Name=id2323;Dbxref=GeneID:905569;gbkey=misc_feature;Note=HMMPfam hit to PF02390 2C methyltransferase 2Cscore 6.1e-37 NC_002163.1 RefSeq gene 1211677 1212912 . - . ID=gene1229;gene=Cj1279c;Name=Cj1279c;locus_tag=Cj1279c;Dbxref=GeneID:905570;gbkey=Gene NC_002163.1 RefSeq CDS 1211677 1212912 . - 0 ID=cds1163;Parent=gene1229;Name=YP_002344670.1;Dbxref=InterPro:IPR003961 InterPro:IPR008957 UniProtKB FTrEMBL:Q0P8X7 Genbank:YP_002344670.1 GeneID:905570;gbkey=CDS;product=fibronectin domain-containing lipoprotein;Note=Original 282000 29 note: Cj1279c 2C probable fibronectin domain-containing lipoprotein 2C len: 411 aa 3B 31.1 25 identity to HP0746. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Also contains 4x Pfam match to entry PF00041 fn3 2C Fibronectin type III domain 7EUpdated 282006 29 note: Specific characterisation with acceptable identity score has not been carried out yet 2C so kept within product function. Functional classification - Pathogenicity NC_002163.1 UTR_Extractor 5'-UTR 1211678 1211928 . - . ID=utr465;locus_tag=Cj1278c;product=tRNA 28guanine-N 287 29- 29-methyltransferase NC_002163.1 RefSeq region 1211701 1211937 . - . ID=id2324;Name=id2324;Dbxref=GeneID:905570;gbkey=misc_feature;Note=HMMPfam hit to PF00041 2C Fibronectin type III domain 2C score 0.0033 NC_002163.1 RefSeq region 1211980 1212219 . - . ID=id2325;Name=id2325;Dbxref=GeneID:905570;gbkey=misc_feature;Note=HMMPfam hit to PF00041 2C Fibronectin type III domain 2C score 0.0079 NC_002163.1 RefSeq region 1212250 1212507 . - . ID=id2326;Name=id2326;Dbxref=GeneID:905570;gbkey=misc_feature;Note=HMMPfam hit to PF00041 2C Fibronectin type III domain 2C score 0.0037 NC_002163.1 RefSeq region 1212547 1212792 . - . ID=id2327;Name=id2327;Dbxref=GeneID:905570;gbkey=misc_feature;Note=HMMPfam hit to PF00041 2C Fibronectin type III domain 2C score 0.0015 NC_002163.1 RefSeq region 1212850 1212882 . - . ID=id2328;Name=id2328;Dbxref=GeneID:905570;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq CDS 1212857 1213825 . - 0 ID=cds1164;Parent=gene1230;Name=YP_002344671.1;Dbxref=GOA:Q0P8X6 InterPro:IPR002942 InterPro:IPR006145 InterPro:IPR006224 InterPro:IPR006225 UniProtKB FTrEMBL:Q0P8X6 Genbank:YP_002344671.1 GeneID:905571;gbkey=CDS;product=ribosomal pseudouridine synthase;Note=Original 282000 29 note: Cj1280c 2C probable ribosomal pseudouridine synthase 2C len: 322 aa 3B similar to e.g. RLUD_ZYMMO ribosomal large subunit pseudouridine synthase D 28EC 4.2.1.70 29 28317 aa 29 2C fasta scores 3B opt: 508 z-score: 590.1 E 28 29: 1.4e-25 2C 33.5 25 identity in 310 aa overlap. 51.4 25 identity to HP0745. Also similar to Cj0708 2826.9 25 identity in 223 aa overlap 29 2C and Cj0022c 2831.7 25 identity in 246 aa overlap 29. Contains PS01129 Hypothetical yabO 2FyceC 2FsfhB family signature 2C and Pfam match to entry PF00849 YABO 2C Hypothetical yabO 2FyceC 2FsfhB family 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score carried out yet 2C so kept within product function. Functional classification - Ribosomal protein synthesis and modification NC_002163.1 RefSeq gene 1212857 1213825 . - . ID=gene1230;Name=Cj1280c;locus_tag=Cj1280c;Dbxref=GeneID:905571;gbkey=Gene NC_002163.1 RefSeq region 1213097 1213573 . - . ID=id2329;Name=id2329;Dbxref=GeneID:905571;gbkey=misc_feature;Note=HMMPfam hit to PF00849 2C RNA pseudouridylate synthase 2C score 4e-45 NC_002163.1 RefSeq region 1213391 1213435 . - . ID=id2330;Name=id2330;Dbxref=GeneID:905571;gbkey=misc_feature;Note=PS01129 Rlu family of pseudouridine synthase signature NC_002163.1 RefSeq region 1213658 1213798 . - . ID=id2331;Name=id2331;Dbxref=GeneID:905571;gbkey=misc_feature;Note=HMMPfam hit to PF01479 2C S4 domain 2C score 4.3e-11 ### NC_002163.1 UTR_Extractor 5'-UTR 1213826 1213863 . - . ID=utr466;locus_tag=Cj1280c;product=putative ribosomal pseudouridine synthase NC_002163.1 UTR_Extractor 5'-UTR 1213877 1213902 . + . ID=utr467;locus_tag=Cj1282;product=RodA protein NC_002163.1 RefSeq CDS 1213903 1215003 . + 0 ID=cds1165;Parent=gene1231;gene=mrdB;Name=YP_002344672.1;Dbxref=GOA:Q0P8X5 InterPro:IPR001182 InterPro:IPR011923 UniProtKB FTrEMBL:Q0P8X5 Genbank:YP_002344672.1 GeneID:905572;gbkey=CDS;product=rod shape-determining protein RodA;Note=Original 282000 29 note: Cj1282 2C mrdB 2C probable RodA protein homolog 2C len: 366 aa 3B similar to e.g. RODA_ECOLI rod shape-determining protein RODA 28370 aa 29 2C fasta scores 3B opt: 699 z-score: 837.9 E 28 29: 0 2C 35.8 25 identity in 355 aa overlap 2C and SP5E_BACSU stage V sporulation protein E 28366 aa 29 2C fasta scores 3B opt: 526 z-score: 632.0 E 28 29: 6.6e-28 2C30.3 25 identity in 337 aa overlap. 52.8 25 identity to HP0743. Contains Pfam match to entry PF01098 FTSW_RODA_SPOVE 2C Cell cycle protein 7EUpdated 282006 29 note: Nine probable transmembrane helices predicted by TMHMM2.0. Homolog designation kept within product function. Functional classification -Murein sacculus and peptidoglycan 7EPMID:6243629 NC_002163.1 RefSeq gene 1213903 1215003 . + . ID=gene1231;gene=mrdB;Name=mrdB;locus_tag=Cj1282;Dbxref=GeneID:905572;gbkey=Gene NC_002163.1 RefSeq region 1213906 1214979 . + . ID=id2332;gene=mrdB;Name=id2332;Dbxref=GeneID:905572;gbkey=misc_feature;Note=HMMPfam hit to PF01098 2C Cell cycle protein 2C score 1.9e-95 NC_002163.1 RefSeq region 1213945 1214013 . + . ID=id2333;gene=mrdB;Name=id2333;Dbxref=GeneID:905572;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1282 by TMHMM2.0 at aa 15-37 2C 44-61 2C 65-87 2C 138-153 2C158-177 2C 182-201 2C 265-287 2C 300-322 and 332-354 NC_002163.1 RefSeq region 1214032 1214085 . + . ID=id2333;gene=mrdB;Name=id2333;Dbxref=GeneID:905572;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1282 by TMHMM2.0 at aa 15-37 2C 44-61 2C 65-87 2C 138-153 2C158-177 2C 182-201 2C 265-287 2C 300-322 and 332-354 NC_002163.1 RefSeq region 1214095 1214163 . + . ID=id2333;gene=mrdB;Name=id2333;Dbxref=GeneID:905572;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1282 by TMHMM2.0 at aa 15-37 2C 44-61 2C 65-87 2C 138-153 2C158-177 2C 182-201 2C 265-287 2C 300-322 and 332-354 NC_002163.1 RefSeq region 1214314 1214361 . + . ID=id2333;gene=mrdB;Name=id2333;Dbxref=GeneID:905572;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1282 by TMHMM2.0 at aa 15-37 2C 44-61 2C 65-87 2C 138-153 2C158-177 2C 182-201 2C 265-287 2C 300-322 and 332-354 NC_002163.1 RefSeq region 1214374 1214433 . + . ID=id2333;gene=mrdB;Name=id2333;Dbxref=GeneID:905572;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1282 by TMHMM2.0 at aa 15-37 2C 44-61 2C 65-87 2C 138-153 2C158-177 2C 182-201 2C 265-287 2C 300-322 and 332-354 NC_002163.1 RefSeq region 1214446 1214505 . + . ID=id2333;gene=mrdB;Name=id2333;Dbxref=GeneID:905572;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1282 by TMHMM2.0 at aa 15-37 2C 44-61 2C 65-87 2C 138-153 2C158-177 2C 182-201 2C 265-287 2C 300-322 and 332-354 NC_002163.1 RefSeq region 1214695 1214763 . + . ID=id2333;gene=mrdB;Name=id2333;Dbxref=GeneID:905572;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1282 by TMHMM2.0 at aa 15-37 2C 44-61 2C 65-87 2C 138-153 2C158-177 2C 182-201 2C 265-287 2C 300-322 and 332-354 NC_002163.1 RefSeq region 1214800 1214868 . + . ID=id2333;gene=mrdB;Name=id2333;Dbxref=GeneID:905572;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1282 by TMHMM2.0 at aa 15-37 2C 44-61 2C 65-87 2C 138-153 2C158-177 2C 182-201 2C 265-287 2C 300-322 and 332-354 NC_002163.1 RefSeq region 1214896 1214964 . + . ID=id2333;gene=mrdB;Name=id2333;Dbxref=GeneID:905572;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1282 by TMHMM2.0 at aa 15-37 2C 44-61 2C 65-87 2C 138-153 2C158-177 2C 182-201 2C 265-287 2C 300-322 and 332-354 ### NC_002163.1 RefSeq gene 1215057 1215133 . + . ID=gene1232;gene=tRNAMet;Name=tRNAMet;locus_tag=Cjp23;Dbxref=GeneID:905573;gbkey=Gene NC_002163.1 RefSeq tRNA 1215057 1215133 . + . ID=rna38;Parent=gene1232;gene=tRNAMet;Name=rna38;Dbxref=GeneID:905573;gbkey=tRNA;product=tRNA-Met;Note=tRNA Met anticodon CAT 2C Cove score 97.76 NC_002163.1 RefSeq exon 1215057 1215133 . + . ID=id2334;Parent=rna38;gene=tRNAMet;Name=id2334;Dbxref=GeneID:905573;gbkey=tRNA;product=tRNA-Met;Note=tRNA Met anticodon CAT 2C Cove score 97.76 NC_002163.1 RefSeq gene 1215241 1215316 . - . ID=gene1233;gene=tRNAPhe;Name=tRNAPhe;locus_tag=Cjp24;Dbxref=GeneID:905574;gbkey=Gene NC_002163.1 RefSeq tRNA 1215241 1215316 . - . ID=rna39;Parent=gene1233;gene=tRNAPhe;Name=rna39;Dbxref=GeneID:905574;gbkey=tRNA;product=tRNA-Phe;Note=tRNA Phe anticodon GAA 2C Cove score 85.44 NC_002163.1 RefSeq exon 1215241 1215316 . - . ID=id2335;Parent=rna39;gene=tRNAPhe;Name=id2335;Dbxref=GeneID:905574;gbkey=tRNA;product=tRNA-Phe;Note=tRNA Phe anticodon GAA 2C Cove score 85.44 NC_002163.1 UTR_Extractor 5'-UTR 1215429 1215455 . + . ID=utr468;locus_tag=Cj1283;product=putative K 2B uptake protein NC_002163.1 RefSeq CDS 1215456 1216799 . + 0 ID=cds1166;Parent=gene1234;gene=ktrB;Name=YP_002344673.1;Dbxref=GOA:Q0P8X4 InterPro:IPR003445 InterPro:IPR004772 UniProtKB FTrEMBL:Q0P8X4 Genbank:YP_002344673.1 GeneID:905575;gbkey=CDS;product=K 2B uptake protein;Note=Original 282000 29 note: Cj1283 2C ktrB 2C probable K 2B uptake protein 2C len: 447 aa 3B similar to e.g. TR:O87953 28EMBL:D89592 29 Vibrio alginolyticus K 2B-uptake system KTRB protein 28455 aa 29 2C fasta scores 3B opt: 844 z-score: 981.2 E 28 29: 0 2C 33.8 25 identity in 438 aa overlap. Also similar to NTPJ_ENTHR V-type sodium ATP synthase subunit J 28451 aa 29 2Cfasta scores 3B opt: 853 z-score: 991.7 E 28 29: 0 2C 33.3 25 identity in 447 aa overlap 2C and TRKH_ECOLI TRK system potassium uptake protein TRKH 28483 aa 29 2C fasta scores 3B opt: 210 z-score: 247.5 E 28 29: 1.7e-06 2C 26.8 25 identity in 426 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02386 Cation transport protein domain identified within CDS. Also 2Celeven probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity score yet 2C so kept within product function. Functional classification - Transport 2Fbinding proteins - Cations 7EPMID:16210320 2C PMID:12562800 2C PMID:9642210 NC_002163.1 RefSeq gene 1215456 1216799 . + . ID=gene1234;gene=ktrB;Name=ktrB;locus_tag=Cj1283;Dbxref=GeneID:905575;gbkey=Gene NC_002163.1 RefSeq region 1215492 1215551 . + . ID=id2336;gene=ktrB;Name=id2336;Dbxref=GeneID:905575;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1283 by TMHMM2.0 at aa 13-32 2C 42-59 2C 72-94 2C 127-149 2C156-175 2C 190-212 2C 225-247 2C 290-324 2C 345-367 2C 382-404 and 409-430 NC_002163.1 RefSeq region 1215579 1215632 . + . ID=id2336;gene=ktrB;Name=id2336;Dbxref=GeneID:905575;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1283 by TMHMM2.0 at aa 13-32 2C 42-59 2C 72-94 2C 127-149 2C156-175 2C 190-212 2C 225-247 2C 290-324 2C 345-367 2C 382-404 and 409-430 NC_002163.1 RefSeq region 1215669 1215737 . + . ID=id2336;gene=ktrB;Name=id2336;Dbxref=GeneID:905575;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1283 by TMHMM2.0 at aa 13-32 2C 42-59 2C 72-94 2C 127-149 2C156-175 2C 190-212 2C 225-247 2C 290-324 2C 345-367 2C 382-404 and 409-430 NC_002163.1 RefSeq region 1215786 1216757 . + . ID=id2337;gene=ktrB;Name=id2337;Dbxref=GeneID:905575;gbkey=misc_feature;Note=HMMPfam hit to PF02386 2C Cation transport protein 2Cscore 7.5e-81 NC_002163.1 RefSeq region 1215834 1215902 . + . ID=id2336;gene=ktrB;Name=id2336;Dbxref=GeneID:905575;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1283 by TMHMM2.0 at aa 13-32 2C 42-59 2C 72-94 2C 127-149 2C156-175 2C 190-212 2C 225-247 2C 290-324 2C 345-367 2C 382-404 and 409-430 NC_002163.1 RefSeq region 1215921 1215980 . + . ID=id2336;gene=ktrB;Name=id2336;Dbxref=GeneID:905575;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1283 by TMHMM2.0 at aa 13-32 2C 42-59 2C 72-94 2C 127-149 2C156-175 2C 190-212 2C 225-247 2C 290-324 2C 345-367 2C 382-404 and 409-430 NC_002163.1 RefSeq region 1216023 1216091 . + . ID=id2336;gene=ktrB;Name=id2336;Dbxref=GeneID:905575;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1283 by TMHMM2.0 at aa 13-32 2C 42-59 2C 72-94 2C 127-149 2C156-175 2C 190-212 2C 225-247 2C 290-324 2C 345-367 2C 382-404 and 409-430 NC_002163.1 RefSeq region 1216128 1216196 . + . ID=id2336;gene=ktrB;Name=id2336;Dbxref=GeneID:905575;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1283 by TMHMM2.0 at aa 13-32 2C 42-59 2C 72-94 2C 127-149 2C156-175 2C 190-212 2C 225-247 2C 290-324 2C 345-367 2C 382-404 and 409-430 NC_002163.1 RefSeq region 1216323 1216427 . + . ID=id2336;gene=ktrB;Name=id2336;Dbxref=GeneID:905575;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1283 by TMHMM2.0 at aa 13-32 2C 42-59 2C 72-94 2C 127-149 2C156-175 2C 190-212 2C 225-247 2C 290-324 2C 345-367 2C 382-404 and 409-430 NC_002163.1 RefSeq region 1216488 1216556 . + . ID=id2336;gene=ktrB;Name=id2336;Dbxref=GeneID:905575;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1283 by TMHMM2.0 at aa 13-32 2C 42-59 2C 72-94 2C 127-149 2C156-175 2C 190-212 2C 225-247 2C 290-324 2C 345-367 2C 382-404 and 409-430 NC_002163.1 RefSeq region 1216599 1216667 . + . ID=id2336;gene=ktrB;Name=id2336;Dbxref=GeneID:905575;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1283 by TMHMM2.0 at aa 13-32 2C 42-59 2C 72-94 2C 127-149 2C156-175 2C 190-212 2C 225-247 2C 290-324 2C 345-367 2C 382-404 and 409-430 NC_002163.1 RefSeq region 1216680 1216745 . + . ID=id2336;gene=ktrB;Name=id2336;Dbxref=GeneID:905575;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1283 by TMHMM2.0 at aa 13-32 2C 42-59 2C 72-94 2C 127-149 2C156-175 2C 190-212 2C 225-247 2C 290-324 2C 345-367 2C 382-404 and 409-430 ### NC_002163.1 RefSeq CDS 1216810 1217460 . + 0 ID=cds1167;Parent=gene1235;gene=ktrA;Name=YP_002344674.1;Dbxref=GOA:Q0P8X3 InterPro:IPR003148 InterPro:IPR006037 InterPro:IPR016040 UniProtKB FTrEMBL:Q0P8X3 Genbank:YP_002344674.1 GeneID:905576;gbkey=CDS;product=K 2B uptake protein;Note=Original 282000 29 note: Cj1284 2C ktrA 2C probable K 2B uptake protein 2C len: 216 aa 3B similar to e.g. TR:O87952 28EMBL:D89592 29 Vibrio alginolyticus K 2B-uptake system KTRA protein 28220 aa 29 2C fasta scores 3B opt: 316 z-score: 371.1 E 28 29: 2.3e-13 2C 29.2 25 identity in 212 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domains PF02254 TrkA-N domain and PF02080 TrkA-C domain identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score yet 2C so kept within product function. Functional classification - Transport 2Fbinding proteins - Cations 7EPMID:16210320 2C PMID:12562800 2C PMID:9642210 NC_002163.1 RefSeq gene 1216810 1217460 . + . ID=gene1235;gene=ktrA;Name=ktrA;locus_tag=Cj1284;Dbxref=GeneID:905576;gbkey=Gene NC_002163.1 RefSeq region 1216822 1217172 . + . ID=id2338;gene=ktrA;Name=id2338;Dbxref=GeneID:905576;gbkey=misc_feature;Note=HMMPfam hit to PF02254 2C TrkA-N domain 2C score 1.4e-30 NC_002163.1 RefSeq region 1217257 1217457 . + . ID=id2339;gene=ktrA;Name=id2339;Dbxref=GeneID:905576;gbkey=misc_feature;Note=HMMPfam hit to PF02080 2C TrkA-C domain 2C score 3.7e-05 NC_002163.1 RefSeq CDS 1217457 1218128 . - 0 ID=cds1168;Parent=gene1236;Name=YP_002344675.1;Dbxref=InterPro:IPR003773 UniProtKB FTrEMBL:Q0P8X2 Genbank:YP_002344675.1 GeneID:905577;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1285c 2C unknown 2C len: 223 aa 3B similar to hypothetical proteins e.g. TR:O29858 28EMBL:AE001077 29 Archaeoglobus fulgidus AF0389 28249 aa 29 2Cfasta scores 3B opt: 120 z-score: 148.0 E 28 29: 0.61 2C 23.7 25 identity in 257 aa overlap. 46.8 25 identity to HP0778 7EUpdated 282006 29 note: Pfam domains PF02621 Uncharacterized ACR 2C COG1427 identified within CDS. Conserved added to product funtion. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 1217457 1218128 . - . ID=gene1236;gene=Cj1285c;Name=Cj1285c;locus_tag=Cj1285c;Dbxref=GeneID:905577;gbkey=Gene NC_002163.1 RefSeq region 1217463 1218104 . - . ID=id2340;Name=id2340;Dbxref=GeneID:905577;gbkey=misc_feature;Note=HMMPfam hit to PF02621 2C Uncharacterized ACR 2CCOG1427 2C score 3.5e-26 ### NC_002163.1 RefSeq CDS 1218134 1218760 . - 0 ID=cds1169;Parent=gene1237;gene=upp;Name=YP_002344676.1;Dbxref=GOA:Q9PN13 HSSP:P70881 InterPro:IPR000836 InterPro:IPR005765 UniProtKB FSwiss-Prot:Q9PN13 Genbank:YP_002344676.1 GeneID:905578;gbkey=CDS;product=uracil phosphoribosyltransferase;Note=Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate NC_002163.1 RefSeq gene 1218134 1218760 . - . ID=gene1237;gene=upp;Name=upp;locus_tag=Cj1286c;Dbxref=GeneID:905578;gbkey=Gene NC_002163.1 RefSeq region 1218254 1218601 . - . ID=id2341;gene=upp;Name=id2341;Dbxref=GeneID:905578;gbkey=misc_feature;Note=HMMPfam hit to PF00156 2C Phosphoribosyl transferase domain 2C score 6e-05 NC_002163.1 RefSeq CDS 1218757 1219992 . - 0 ID=cds1170;Parent=gene1238;Name=YP_002344677.1;Dbxref=GOA:Q0P8X0 InterPro:IPR012301 InterPro:IPR012302 InterPro:IPR015884 InterPro:IPR016040 UniProtKB FTrEMBL:Q0P8X0 Genbank:YP_002344677.1 GeneID:905579;gbkey=CDS;product=malate oxidoreductase;Note=Original 282000 29 note: Cj1287c 2C probable malate oxidoreductase 2C len: 411 aa 3B highly similar to many e.g. MAOX_BACST malate oxidoreductase 28NAD 29 28EC 1.1.1.38 29 28478 aa 29 2C fasta scores 3B opt: 1193 z-score: 1304.5 E 28 29: 0 2C 49.9 25 identity in 411 aa overlap. No Hp match. Contains Pfam match to entry PF00390 malic 2C Malic enzymes 7EUpdated 282006 29 note: Characterised in more than one genus with acceptable identity scores 2C so not added to product function. Functional classification -Central intermediary metabolism - Gluconeogenesis 7EPMID:1371255 2C PMID:7798145 2C PMID:9535928 2CPMID:36376 NC_002163.1 RefSeq gene 1218757 1219992 . - . ID=gene1238;gene=Cj1287c;Name=Cj1287c;locus_tag=Cj1287c;Dbxref=GeneID:905579;gbkey=Gene NC_002163.1 RefSeq region 1218820 1219524 . - . ID=id2342;Name=id2342;Dbxref=GeneID:905579;gbkey=misc_feature;Note=HMMPfam hit to PF03949 2C Malic enzyme 2C NAD binding domain 2C score 4.5e-126 NC_002163.1 RefSeq region 1219528 1219953 . - . ID=id2343;Name=id2343;Dbxref=GeneID:905579;gbkey=misc_feature;Note=HMMPfam hit to PF00390 2C Malic enzyme 2C N-terminal domain 2C score 1.6e-74 ### NC_002163.1 UTR_Extractor 5'-UTR 1219993 1220223 . - . ID=utr469;locus_tag=Cj1287c;product=malate oxidoreductase NC_002163.1 RefSeq CDS 1219994 1221385 . - 0 ID=cds1171;Parent=gene1239;gene=gltX;Name=YP_002344678.1;Dbxref=GOA:O52914 HSSP:P00962 InterPro:IPR000924 InterPro:IPR001412 InterPro:IPR004527 InterPro:IPR008925 InterPro:IPR014729 UniProtKB FSwiss-Prot:O52914 Genbank:YP_002344678.1 GeneID:905580;gbkey=CDS;product=glutamyl-tRNA synthetase;Note=Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation NC_002163.1 RefSeq gene 1219994 1221385 . - . ID=gene1239;gene=gltX;Name=gltX;locus_tag=Cj1288c;Dbxref=GeneID:905580;gbkey=Gene NC_002163.1 RefSeq region 1220462 1221376 . - . ID=id2344;gene=gltX;Name=id2344;Dbxref=GeneID:905580;gbkey=misc_feature;Note=HMMPfam hit to PF00749 2C tRNA synthetases class I 28E and Q 29 2C cata 2C score 7.3e-141 NC_002163.1 RefSeq region 1221320 1221355 . - . ID=id2345;gene=gltX;Name=id2345;Dbxref=GeneID:905580;gbkey=misc_feature;Note=PS00178 Aminoacyl-transfer RNA synthetases class-I signature ### NC_002163.1 UTR_Extractor 5'-UTR 1221425 1221449 . + . ID=utr470;locus_tag=Cj1289;product=putative periplasmic protein NC_002163.1 RefSeq gene 1221450 1222265 . + . ID=gene1240;Name=Cj1289;locus_tag=Cj1289;Dbxref=GeneID:905581;gbkey=Gene NC_002163.1 RefSeq CDS 1221450 1222265 . + 0 ID=cds1172;Parent=gene1240;Name=YP_002344679.1;Dbxref=InterPro:IPR015391 UniProtKB FTrEMBL:Q0P8W8 Genbank:YP_002344679.1 GeneID:905581;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1289 2C possible periplasmic protein 2C len: 271 aa 3B 25.8 25 identity to C-terminus of HP0659. Contains possible N-terminal signal sequence. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 1221462 1221530 . + . ID=id2346;Name=id2346;Dbxref=GeneID:905581;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1289 by TMHMM2.0 at aa 5-27 ### NC_002163.1 RefSeq CDS 1222303 1223634 . - 0 ID=cds1173;Parent=gene1241;gene=accC;Name=YP_002344680.1;Dbxref=GOA:Q0P8W7 InterPro:IPR004549 InterPro:IPR005479 InterPro:IPR005481 InterPro:IPR005482 InterPro:IPR011761 InterPro:IPR011764 InterPro:IPR013816 InterPro:IPR013817 UniProtKB FTrEMBL:Q0P8W7 Genbank:YP_002344680.1 GeneID:905582;gbkey=CDS;product=biotin carboxylase;Note=biotin carboxylase 3B biotin carboxylase catalyzes the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-CoA 3B catalyzes the formation of malonyl-CoA 2C which in turn controls the rate of fatty acid metabolism NC_002163.1 RefSeq gene 1222303 1223634 . - . ID=gene1241;gene=accC;Name=accC;locus_tag=Cj1290c;Dbxref=GeneID:905582;gbkey=Gene NC_002163.1 RefSeq region 1222312 1222629 . - . ID=id2347;gene=accC;Name=id2347;Dbxref=GeneID:905582;gbkey=misc_feature;Note=HMMPfam hit to PF02785 2C Biotin carboxylase C-terminal domain 2C score 2.5e-57 NC_002163.1 RefSeq region 1222627 1223289 . - . ID=id2348;gene=accC;Name=id2348;Dbxref=GeneID:905582;gbkey=misc_feature;Note=HMMPfam hit to PF02786 2C Carbamoyl-phosphate synthase L chain 2C 2C score 3.4e-108 NC_002163.1 RefSeq region 1222753 1222776 . - . ID=id2349;gene=accC;Name=id2349;Dbxref=GeneID:905582;gbkey=misc_feature;Note=PS00867 Carbamoyl-phosphate synthase subdomain signature 2 NC_002163.1 RefSeq region 1223131 1223175 . - . ID=id2350;gene=accC;Name=id2350;Dbxref=GeneID:905582;gbkey=misc_feature;Note=PS00866 Carbamoyl-phosphate synthase subdomain signature 1 NC_002163.1 RefSeq region 1223293 1223631 . - . ID=id2351;gene=accC;Name=id2351;Dbxref=GeneID:905582;gbkey=misc_feature;Note=HMMPfam hit to PF00289 2C Carbamoyl-phosphate synthase L chain 2C 2C score 1.6e-46 ### NC_002163.1 RefSeq CDS 1223636 1224091 . - 0 ID=cds1174;Parent=gene1242;gene=accB;Name=YP_002344681.1;Dbxref=GOA:Q0P8W6 InterPro:IPR000089 InterPro:IPR001249 InterPro:IPR001638 UniProtKB FTrEMBL:Q0P8W6 Genbank:YP_002344681.1 GeneID:905583;gbkey=CDS;product=biotin carboxyl carrier protein of acetyl-CoA carboxylase;Note=Original 282000 29 note: Cj1291c 2C accB 2C probable biotin carboxyl carrier protein of acetyl-CoA carboxylase 2Clen: 151 aa 3B similar to e.g. BCCP_ECOLI biotin carboxyl carrier protein of acetyl-CoA carboxylase 28EC 6.4.1.2 29 28156 aa 29 2C fasta scores 3B opt: 307 z-score: 329.6 E 28 29: 4.6e-11 2C 38.9 25 identity in 162 aa overlap. 41.4 25 identity to HP0371. Contains Pfam match to entry PF00364 biotin_req_enzy 2C Biotin-requiring enzymes 7EUpdated 282006 29 note: Some characterisation work carried out within Bacillus subtilis. kept within product function. Functional classification - Fatty acid biosynthesis 7EPMID:7592499 2C PMID:1358874 NC_002163.1 RefSeq gene 1223636 1224091 . - . ID=gene1242;gene=accB;Name=accB;locus_tag=Cj1291c;Dbxref=GeneID:905583;gbkey=Gene NC_002163.1 RefSeq region 1223648 1223872 . - . ID=id2352;gene=accB;Name=id2352;Dbxref=GeneID:905583;gbkey=misc_feature;Note=HMMPfam hit to PF00364 2C Biotin-requiring enzyme 2Cscore 9e-27 NC_002163.1 RefSeq region 1223969 1224010 . - . ID=id2353;gene=accB;Name=id2353;Dbxref=GeneID:905583;gbkey=misc_feature;Note=PS01039 Bacterial extracellular solute-binding proteins 2C family 3 signature ### NC_002163.1 UTR_Extractor 5'-UTR 1224092 1224122 . - . ID=utr471;locus_tag=Cj1291c;product=putative biotin carboxyl carrier protein of acetyl-CoA carboxylase NC_002163.1 RefSeq gene 1224239 1224799 . + . ID=gene1243;gene=dcd;Name=dcd;locus_tag=Cj1292;Dbxref=GeneID:905584;gbkey=Gene NC_002163.1 RefSeq CDS 1224239 1224799 . + 0 ID=cds1175;Parent=gene1243;gene=dcd;Name=YP_002344682.1;Dbxref=GOA:Q9PN07 InterPro:IPR011962 UniProtKB FSwiss-Prot:Q9PN07 Genbank:YP_002344682.1 GeneID:905584;gbkey=CDS;product=deoxycytidine triphosphate deaminase;Note=Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis NC_002163.1 RefSeq region 1224311 1224787 . + . ID=id2354;gene=dcd;Name=id2354;Dbxref=GeneID:905584;gbkey=misc_feature;Note=HMMPfam hit to PF00692 2C dUTPase 2C score 0.00019 ### NC_002163.1 UTR_Extractor 5'-UTR 1224823 1224848 . + . ID=utr472;locus_tag=Cj1293;product=UDP-GlcNAc-specific C4 2C6 dehydratase 2FC5 epimerase NC_002163.1 RefSeq region 1224849 1225745 . + . ID=id2355;gene=pseB;Name=id2355;Dbxref=GeneID:905585;gbkey=misc_feature;Note=HMMPfam hit to PF02719 2C Polysaccharide biosynthesis protein 2C score 7e-09 NC_002163.1 RefSeq gene 1224849 1225853 . + . ID=gene1244;gene=pseB;Name=pseB;locus_tag=Cj1293;Dbxref=GeneID:905585;gbkey=Gene NC_002163.1 RefSeq CDS 1224849 1225853 . + 0 ID=cds1176;Parent=gene1244;gene=pseB;Name=YP_002344683.1;Dbxref=GOA:Q0P8W4 InterPro:IPR003869 InterPro:IPR016040 UniProtKB FTrEMBL:Q0P8W4 Genbank:YP_002344683.1 GeneID:905585;gbkey=CDS;product=UDP-GlcNAc-specific C4 2C6 dehydratase 2FC5 epimerase;Note=Original 282000 29 note: Cj1293 2C possible sugar nucleotide epimerase 2Fdehydratase 2C len: 334 aa 3B similar to many e..g TR:Q45984 28EMBL:U27301 29 Caulobacter crescentus FLAA1 protein 28331 aa 29 2C fasta scores 3B opt: 1240 z-score: 1410.9 E 28 29: 0 2C 57.8 25 identity in 329 aa overlap 2CCAPD_STAAU CAPD protein 28599 aa 29 2C fasta scores 3B opt: 529 z-score: 602.6 E 28 29: 2.9e-26 2C 33.9 25 identity in 319 aa overlap 2C and TR:O69130 28EMBL:AF064070 29 Burkholderia pseudomallei epimerase 2Fdehydratase WBII 28637 aa 29 2Cfasta scores 3B opt: 433 z-score: 493.6 E 28 29: 3.4e-20 2C 30.5 25 identity in 282 aa overlap. 64.6 25 identity to HP0840. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 7EUpdated 282006 29 note: Pfam domain PF02719 Polysaccharide biosynthesis protein identified within CDS. Further support given to product function. Characterised within Campylobacter jejuni. Product function modified to more specific family member. Cj1293 is involved in flagellin glycosylation and has USP-GlcNAc C 286 29 dehydratase activity. This enzyme catalyzes the first step in the biosynthesis of bacillosamine 2C a sugar found in Campylobacter jejuni glycosylation motifs 28PMID:14960321 29. Recently 2C Cj1293 enzyme was found to exhibit C6 dehydratase as well as a newly identified C5 epimerase activity that resulted in the production of UDP-2-acetamido-2 2C6-dideoxy-beta-L-arabino-4-hexulose and UDP-2-acetamido-2 2C6-dideoxy-alpha-D-xylo-4-hexulose 28PMID:16286454 29. Plays a direct role in CMP-Pse5NAc7NAc or CMP-Pse5NAc7Am pathyways. Logan 28Susan.Logan@nrc-cnrc.gc.ca 29 personal communication. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Surface structures 7EPMID:16421095 2C PMID:16286454 2C PMID:14960321 2CPMID:14617187 2C PMID:16573682 2C PMID:12781527 NC_002163.1 RefSeq region 1224882 1224905 . + . ID=id2356;gene=pseB;Name=id2356;Dbxref=GeneID:905585;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 RefSeq CDS 1225855 1226985 . + 0 ID=cds1177;Parent=gene1245;gene=pseC;Name=YP_002344684.1;Dbxref=GOA:Q0P8W3 InterPro:IPR000653 InterPro:IPR015421 InterPro:IPR015422 UniProtKB FTrEMBL:Q0P8W3 Genbank:YP_002344684.1 GeneID:905586;gbkey=CDS;product=C4 aminotransferase;Note=Original 282000 29 note: Cj1294 2C probable aminotransferase 2C len: 376 aa 3B similar to many members of the degT family e.g. SPSC_BACSU spore coat polysaccharide biosynthesis protein 28389 aa 29 2C fasta scores 3B opt: 586 z-score: 676.7 E 28 29: 2.1e-30 2C 35.3 25 identity in 385 aa overlap 2C and TR:O88001 28EMBL:AJ007747 29 Bordetella bronchiseptica amino-sugar biosynthesis protein WLBC 28366 aa 29 2C fasta scores 3B opt: 482 z-score: 558.1 E 28 29: 8.7e-24 2C 28.8 25 identity in 330 aa overlap. 44.8 25 identity to HP0366 . Contains Pfam match to entry PF01041 DegT_DnrJ_EryC1 2C DegT 2FDnrJ 2FEryC1 2FStrS family 7EUpdated 282006 29 note: Specific characterisation with acceptable identity scores has been carried out in Campylobacter jejuni 2C Product modified to more specific family. not added to product function. Cj1294 was demonstrated to be a pyridoxal phosphate-dependent aminotransferase specific for UDP-4-keto-6-deoxy-GlcNAc. These results indicate that Cj1294 is involved in the biosynthesis of diacetamidofucosamine 2C a C4 epimer of diacetamidobacillosamine not yet described in C. jejuni proteoglycans 2C suggesting that the composition of C. jejuni proteoglycans is more variable than anticipated 28PMID:15790564 29. Recent work has demonstrated that Cj1294 utilize only UDP-2-acetamido-2 2C6-dideoxy-beta-L-arabino-4-hexulose as substrate producing UDP-4-amino-4 2C6-dideoxy-beta-L-AltNAc 2Ca precursor in the pseudaminic acid biosynthetic pathway 28PMID:16286454 29. Plays a direct role in CMP-Pse5NAc7NAc or CMP-Pse5NAc7Am pathyways. Logan 28Susan.Logan@nrc-cnrc.gc.ca 29 personal communication. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Surface structures 7EPMID:16421095 2C PMID:15790564 2C PMID:16286454 2CPMID:14960321 2C PMID:14617187 2C PMID:12704196 2CPMID:16573682 2C PMID:12781527 NC_002163.1 RefSeq gene 1225855 1226985 . + . ID=gene1245;gene=pseC;Name=pseC;locus_tag=Cj1294;Dbxref=GeneID:905586;gbkey=Gene NC_002163.1 RefSeq region 1225873 1226946 . + . ID=id2357;gene=pseC;Name=id2357;Dbxref=GeneID:905586;gbkey=misc_feature;Note=HMMPfam hit to PF01041 2C DegT 2FDnrJ 2FEryC1 2FStrS aminotransferase 2C score 4.6e-110 NC_002163.1 RefSeq gene 1226978 1228285 . + . ID=gene1246;gene=Cj1295;Name=Cj1295;locus_tag=Cj1295;Dbxref=GeneID:905587;gbkey=Gene NC_002163.1 RefSeq CDS 1226978 1228285 . + 0 ID=cds1178;Parent=gene1246;Name=YP_002344685.1;Dbxref=GOA:Q0P8W2 InterPro:IPR012353 UniProtKB FTrEMBL:Q0P8W2 Genbank:YP_002344685.1 GeneID:905587;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1295 2C unknown 2C len: 435 aa 3B no Hp match 7EUpdated 282006 29 note: PIR 28Protein Information Resource 29 database has a match with IPR012353 Uncharacterised conserved protein 2C PIRSF01524 polysaccharide biosynthesis aminopeptidase-like protein. Members of this group from Streptomyces sp. and Brucella melitensis are encoded by polysaccharide biosynthesis gene clusters 2C and are believed to be involved in polysaccharide biosynthesis 28PMID:12644223 29. Members of this group exhibit distant sequence similarity to aminopeptidases. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Unknown 7EPMID:12644223 2C PMID:16573682 2C PMID:12781527 NC_002163.1 RefSeq repeat_region 1227121 1227129 . + . ID=id2358;Name=id2358;Dbxref=GeneID:905587;gbkey=repeat_region;Note=G 289 29 NC_002163.1 RefSeq pseudogene 1228282 1229075 . + . ID=gene1247;Name=Cj1296;locus_tag=Cj1296;Dbxref=GeneID:905588;gbkey=Gene NC_002163.1 RefSeq repeat_region 1228591 1228599 . + . ID=id2359;Name=id2359;Dbxref=GeneID:905588;gbkey=repeat_region;Note=G 289 29 ### NC_002163.1 RefSeq gene 1229096 1229887 . + . ID=gene1248;Name=Cj1298;locus_tag=Cj1298;Dbxref=GeneID:905590;gbkey=Gene NC_002163.1 RefSeq CDS 1229096 1229887 . + 0 ID=cds1179;Parent=gene1248;Name=YP_002344688.1;Dbxref=GOA:Q0P8V9 UniProtKB FTrEMBL:Q0P8V9 Genbank:YP_002344688.1 GeneID:905590;gbkey=CDS;product=N-acetyltransferase;Note=Original 282000 29 note: Cj1298 2C unknown 2C len: 263 aa 3B weak similarity to aminoglycoside N3 27-acetyltransferases e.g. AAC4_SALSP aminoglycoside N3 27-acetyltransferase IV 28261 aa 29 2C fasta scores 3B opt: 139 z-score: 177.8 E 28 29: 0.014 2C 25.7 25 identity in 175 aa overlap. Similar in N- and C-terminus to upstream ORFs Cj1296 2865.7 25 identity in 105 aa overlap 29 2C and Cj1297 2844.7 25 identity in 141 aa overlap 29. No Hp match. There is a G 289 29 tract that 2C if variable 2C would allow fusion of Cj1296 and Cj1297. There is no equivalent repetitive tract in this CDS 7EUpdated 282006 29 note: Literature search identified paper linking product function of Cj1296 2FCj1297 2FCj1298 to antimicrobial efflux pumps. Some characterisation work within Campylobacter jejuni. Product function modified to more specific family member. kept within product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Surface structures 7EPMID:15790564 2C PMID:16573682 2C PMID:12781527 NC_002163.1 UTR_Extractor 5'-UTR 1229886 1229917 . + . ID=utr473;locus_tag=Cj1299;product=putative acyl carrier protein ### NC_002163.1 RefSeq CDS 1229918 1230148 . + 0 ID=cds1180;Parent=gene1249;gene=acpP2;Name=YP_002344689.1;Dbxref=UniProtKB FTrEMBL:Q0P8V8 Genbank:YP_002344689.1 GeneID:905591;gbkey=CDS;product=acyl carrier protein;Note=Original 282000 29 note: Cj1299 2C acpP2 2C probable acyl carrier protein 2C len: 76 aa 3B similar to many e.g. ACPH_MYCGE acyl carrier protein homolog 2884 aa 29 2C fasta scores 3B opt: 111 z-score: 172.6 E 28 29: 0.026 2C 35.8 25 identity in 81 aa overlap. No Hp match. Also similar to acpP Cj0441 2834.1 25 identity in 41 aa overlap 29 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score carried out yet. kept within product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Fatty acid biosynthesis 7EPMID:16573682 2C PMID:12781527 NC_002163.1 RefSeq gene 1229918 1230148 . + . ID=gene1249;gene=acpP2;Name=acpP2;locus_tag=Cj1299;Dbxref=GeneID:905591;gbkey=Gene NC_002163.1 RefSeq gene 1230145 1231038 . + . ID=gene1250;gene=Cj1300;Name=Cj1300;locus_tag=Cj1300;Dbxref=GeneID:905592;gbkey=Gene NC_002163.1 RefSeq CDS 1230145 1231038 . + 0 ID=cds1181;Parent=gene1250;Name=YP_002344690.1;Dbxref=GOA:Q0P8V7 InterPro:IPR013217 UniProtKB FTrEMBL:Q0P8V7 Genbank:YP_002344690.1 GeneID:905592;gbkey=CDS;product=SAM domain-containing methyltransferase;Note=Original 282000 29 note: Cj1300 2C unknown 2C len: 297 aa 3B no Hp match 7EUpdated 282006 29 note: Prosite domains PS50193 SAM_BIND 2C SAM 28and some other nucleotide 29 binding motif and PS50124 MET_TRANS 2C Generic methyltransferase were both identified within CDS. Product modified to more specific family member based on motif results. Specific characterisation has not been carried out yet. kept within product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Misc 7EPMID:16573682 2C PMID:12781527 NC_002163.1 RefSeq gene 1231031 1231447 . + . ID=gene1251;Name=Cj1301;locus_tag=Cj1301;Dbxref=GeneID:905593;gbkey=Gene NC_002163.1 RefSeq CDS 1231031 1231447 . + 0 ID=cds1182;Parent=gene1251;Name=YP_002344691.1;Dbxref=GOA:Q0P8V6 UniProtKB FTrEMBL:Q0P8V6 Genbank:YP_002344691.1 GeneID:905593;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1301 2C unknown 2C len: 138 aa 3B similar to a hypothetical protein from Pyrococcus horikoshii TR:O58010 28EMBL:AP000001 29 PH0272 28136 aa 29 2Cfasta scores 3B opt: 137 z-score: 188.8 E 28 29: 0.0032 2C 32.8 25 identity in 137 aa overlap. No Hp match 7EUpdated 282006 29 note: Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Conserved hypothetical proteins 7EPMID:16573682 2C PMID:12781527 NC_002163.1 RefSeq region 1231049 1231081 . + . ID=id2360;Name=id2360;Dbxref=GeneID:905593;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq CDS 1231444 1233006 . + 0 ID=cds1183;Parent=gene1252;Name=YP_002344692.1;Dbxref=InterPro:IPR010033 InterPro:IPR010037 UniProtKB FTrEMBL:Q0P8V5 Genbank:YP_002344692.1 GeneID:905594;gbkey=CDS;product=HAD-superfamily hydrolase;Note=Original 282000 29 note: Cj1302 2C unknown 2C len: 520 aa 3B no Hp match 7EUpdated 282006 29 note: TIGRFAM domain TIGR01681 HAD-SF-IIIC 2C HAD-superfamily phosphatase subfamily IIIC identified within CDS. Product modified to more specific family member based on motif match. No specific characterisation with acceptable identity score carried out yet 2C so kept within product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Misc 7EPMID:16573682 2C PMID:12781527 NC_002163.1 RefSeq gene 1231444 1233006 . + . ID=gene1252;Name=Cj1302;locus_tag=Cj1302;Dbxref=GeneID:905594;gbkey=Gene NC_002163.1 RefSeq region 1232701 1232733 . + . ID=id2361;Name=id2361;Dbxref=GeneID:905594;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq CDS 1232996 1234057 . + 0 ID=cds1184;Parent=gene1253;gene=fabH2;Name=YP_002344693.1;Dbxref=GOA:Q9PMZ6 HSSP:P24249 InterPro:IPR013747 InterPro:IPR013751 InterPro:IPR016038 UniProtKB FSwiss-Prot:Q9PMZ6 Genbank:YP_002344693.1 GeneID:905595;gbkey=CDS;product=3-oxoacyl-ACP synthase;Note=FabH 3B beta-ketoacyl-acyl carrier protein synthase III 3B catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation 3B differs from 3-oxoacyl- 28acyl carrier protein 29 synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs 3B paralogs which do not contain the N-X-R ACP-binding site motif NC_002163.1 RefSeq gene 1232996 1234057 . + . ID=gene1253;gene=fabH2;Name=fabH2;locus_tag=Cj1303;Dbxref=GeneID:905595;gbkey=Gene NC_002163.1 RefSeq gene 1234057 1234278 . + . ID=gene1254;gene=acpP3;Name=acpP3;locus_tag=Cj1304;Dbxref=GeneID:905596;gbkey=Gene NC_002163.1 RefSeq CDS 1234057 1234278 . + 0 ID=cds1185;Parent=gene1254;gene=acpP3;Name=YP_002344694.1;Dbxref=UniProtKB FTrEMBL:Q0P8V3 Genbank:YP_002344694.1 GeneID:905596;gbkey=CDS;product=acyl carrier protein;Note=Original 282000 29 note: Cj1304 2C acpP3 2C probable acyl carrier protein 2C len: 73 aa 3B similar to e.g. CP_MYXXA acyl carrier protein 2878 aa 29 2C fasta scores 3B opt: 101 z-score: 157.0 E 28 29: 0.19 2C 28.4 25 identity in 74 aa overlap. No Hp match. Also similar to acpP2 Cj1299 2825.4 25 identity in 63 aa overlap 29 7EUpdated 282006 29 note: No specific charactersiation with acceptable identity score has been carried out yet 2Cso kept within product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Fatty acid biosynthesis 7EPMID:16573682 2C PMID:12781527 ### NC_002163.1 RefSeq gene 1234292 1235509 . - . ID=gene1255;Name=Cj1305c;locus_tag=Cj1305c;Dbxref=GeneID:905597;gbkey=Gene NC_002163.1 RefSeq CDS 1234292 1235509 . - 0 ID=cds1186;Parent=gene1255;Name=YP_002344695.1;Dbxref=UniProtKB FTrEMBL:Q0P8V2 Genbank:YP_002344695.1 GeneID:905597;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1305c 2C unknown 2C len: 405 aa 3B no Hp match. A member of the 617 family of C.j. proteins containing homopolymeric tracts 3B similar to Cj0617 2FCj0618 2838.9 25 identity in 180 aa overlap 2F37.1 25 identity in 221 aa overlap 29 2C Cj1306c 2878.1 25 identity in 407 aa overlap 29 2C Cj1310c 2863.7 25 identity in 402 aa overlap 29 2C Cj1342c 2838.0 25 identity in 426 aa overlap 29. Contains a variable polyG-tract at aa 194 3B G 289 29 28consensus 29 gives this ORF 2C G 2810 29 would cause truncation after 22 aa 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Unknown 7EPMID:16573682 2C PMID:12781527 NC_002163.1 UTR_Extractor 5'-UTR 1235510 1235749 . - . ID=utr474;locus_tag=Cj1305c;product=hypothetical protein NC_002163.1 RefSeq gene 1235522 1236748 . - . ID=gene1256;Name=Cj1306c;locus_tag=Cj1306c;Dbxref=GeneID:905598;gbkey=Gene NC_002163.1 RefSeq CDS 1235522 1236748 . - 0 ID=cds1187;Parent=gene1256;Name=YP_002344696.1;Dbxref=UniProtKB FTrEMBL:Q0P8V1 Genbank:YP_002344696.1 GeneID:905598;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1306c 2C unknown 2C len: 405 aa 3B no Hp match. A member of the 617 family of C.j. proteins containing homopolymeric tracts 3B similar to Cj1310c 2859.8 25 identity in 410 aa overlap 29 2C Cj1305c 2878.1 25 identity in 407 aa overlap 29 2C Cj1342c 2838.5 25 identity in 426 aa overlap 29 and Cj0617 2FCj0618 2839.2 25 identity in 181 aa overlap 2F39.5 25 identity in 220 aa overlap 29. Contains a variable polyG-tract at aa 194 3B G 289 29 28consensus 29 gives this ORF 2C G 288 29 would cause truncation after 5 aa 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Unknown 7EPMID:16573682 2C PMID:12781527 ### NC_002163.1 UTR_Extractor 5'-UTR 1236749 1236773 . - . ID=utr475;locus_tag=Cj1306c;product=hypothetical protein NC_002163.1 RefSeq CDS 1236809 1238317 . + 0 ID=cds1188;Parent=gene1257;Name=YP_002344697.1;Dbxref=GOA:Q0P8V0 InterPro:IPR000873 UniProtKB FTrEMBL:Q0P8V0 Genbank:YP_002344697.1 GeneID:905599;gbkey=CDS;product=amino acid activating protein;Note=Original 282000 29 note: Cj1307 2C possible amino acid activating enzyme 2C len: 502 aa 3B similar to e.g. DLTA_BACSU D-alanine-activating enzyme 28EC 6.3.2.- 29 28503 aa 29 2C fasta scores 3B opt: 726 z-score: 837.7 E 28 29: 0 2C 30.3 25 identity in 495 aa overlap 2C and to parts of ENTF_ECOLI enterobactin synthetase component F 281293 aa 29 2C fasta scores 3B opt: 549 z-score: 627.8 E 28 29: 1.1e-27 2C 27.4 25 identity in 460 aa overlap 2C and GRSB_BACBR gramicidin S synthetase II 284451 aa 29 2C fasta scores 3B opt: 571 z-score: 644.7 E 28 29: 1.3e-28 2C29.9 25 identity in 508 aa overlap. No Hp match. Contains PS00455 AMP-binding domain signature 2C and Pfam match to entry PF00501 AMP-binding 2C AMP-binding enzyme 7EUpdated 282006 29 note: Similar to many different designations 2C however 2C no specific characterisation with acceptable identity score carried out yet. kept within product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Cell envelope 7EPMID:7797557 2C PMID:16573682 2C PMID:12781527 NC_002163.1 RefSeq gene 1236809 1238317 . + . ID=gene1257;Name=Cj1307;locus_tag=Cj1307;Dbxref=GeneID:905599;gbkey=Gene NC_002163.1 RefSeq region 1236908 1238140 . + . ID=id2362;Name=id2362;Dbxref=GeneID:905599;gbkey=misc_feature;Note=HMMPfam hit to PF00501 2C AMP-binding enzyme 2C score 1.4e-85 NC_002163.1 RefSeq region 1237274 1237309 . + . ID=id2363;Name=id2363;Dbxref=GeneID:905599;gbkey=misc_feature;Note=PS00455 AMP-binding domain signature ### NC_002163.1 RefSeq gene 1238357 1238584 . + . ID=gene1258;Name=Cj1308;locus_tag=Cj1308;Dbxref=GeneID:905600;gbkey=Gene NC_002163.1 RefSeq CDS 1238357 1238584 . + 0 ID=cds1189;Parent=gene1258;Name=YP_002344698.1;Dbxref=UniProtKB FTrEMBL:Q0P8U9 Genbank:YP_002344698.1 GeneID:905600;gbkey=CDS;product=acyl carrier protein;Note=Original 282000 29 note: Cj1308 2C acpP4 2C possible acyl carrier protein 2C len: 75 aa 3B some similartiy to e.g. ACP_CYAPA acyl carrier protein 28103 aa 29 2C fasta scores 3B opt: 84 z-score: 126.5 E 28 29: 9.5 2C 31.3 25 identity in 64 aa overlap. No Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score carried out yet. kept within product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Fatty acid biosynthesis 7EPMID:7797557 2C PMID:16573682 2C PMID:12781527 NC_002163.1 RefSeq gene 1238581 1239651 . - . ID=gene1259;Name=Cj1309c;locus_tag=Cj1309c;Dbxref=GeneID:905601;gbkey=Gene NC_002163.1 RefSeq CDS 1238581 1239651 . - 0 ID=cds1190;Parent=gene1259;Name=YP_002344699.1;Dbxref=UniProtKB FTrEMBL:Q0P8U8 Genbank:YP_002344699.1 GeneID:905601;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1309c 2C unknown 2C len 356 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Unknown 7EPMID:16573682 2C PMID:12781527 ### NC_002163.1 RefSeq gene 1239673 1240887 . - . ID=gene1260;Name=Cj1310c;locus_tag=Cj1310c;Dbxref=GeneID:905602;gbkey=Gene NC_002163.1 RefSeq CDS 1239673 1240887 . - 0 ID=cds1191;Parent=gene1260;Name=YP_002344700.1;Dbxref=UniProtKB FTrEMBL:Q0P8U7 Genbank:YP_002344700.1 GeneID:905602;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1310c 2C unknown 2C len: 404 aa 3B no Hp match. A member of the 617 family of C.j. proteins containing homopolymeric tracts 3B similar to Cj1305c 2863.7 25 identity in 402 aa overlap 29 2C Cj1306c 2859.8 25 identity in 410 aa overlap 29 2C Cj1342c 2837.1 25 identity in 426 aa overlap 29 and Cj0617 2FCj0618 2837.4 25 identity in 182 aa overlap 2F34.1 25 identity in 220 aa overlap 29. Contains a variable polyG-tract at aa 194 3B G 289 29 28consensus 29 gives this ORF 2C G 2810 29 would cause truncation after 22 aa 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Unknown 7EPMID:16573682 2C PMID:12781527 NC_002163.1 UTR_Extractor 5'-UTR 1240888 1240911 . - . ID=utr476;locus_tag=Cj1310c;product=hypothetical protein NC_002163.1 UTR_Extractor 5'-UTR 1240947 1240965 . + . ID=utr477;locus_tag=Cj1311;product=putative acylneuraminate cytidylyltransferase NC_002163.1 RefSeq CDS 1240966 1241664 . + 0 ID=cds1192;Parent=gene1261;gene=pseF;Name=YP_002344701.1;Dbxref=GOA:Q0P8U6 InterPro:IPR003329 UniProtKB FTrEMBL:Q0P8U6 Genbank:YP_002344701.1 GeneID:905603;gbkey=CDS;product=acylneuraminate cytidylyltransferase;Note=Original 282000 29 note: Cj1311 2C neuA2 2C probable acylneuraminate cytidylyltransferase 28CMP-N-acetylneuraminic acid synthetase 29 2C len: 232 aa 3B simlar to e.g. NEUA_ECOLI acylneuraminate cytidylyltransferase 28EC 2.7.7.43 29 28CMP-N-acetylneuraminic acid synthetase 29 28419 aa 29 2C fasta scores 3B opt: 316 z-score: 379.1 E 28 29: 8.2e-14 2C 29.0 25 identity in 231 aa overlap. 39.6 25 identity to HP0326. Also similar to Cj1143 2831.6 25 identity in 215 aa overlap 29 2C and Cj1331 2832.9 25 identity in 234 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF02348 Cytidylyltransferase identified within CDS. Further support given to product function. Characterised within Escherichia coli with marginal identity score. kept within product function. Recently designated within Campylobacter jejuni 81176 as pseF. Recent analysis work carried out in Campylobacter shows role in pseudaminic acid synthesis. PseF is thought to allow PseAc to form CMP-PseAc. Plays a direct role in CMP-Pse5NAc7NAc or CMP-Pse5NAc7Am pathyways. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Surface polysaccharides 2C lipopolysaccharides and antigens 7EPMID:2549035 2C PMID:16573682 2C PMID:12781527 NC_002163.1 RefSeq gene 1240966 1241664 . + . ID=gene1261;gene=pseF;Name=pseF;locus_tag=Cj1311;Dbxref=GeneID:905603;gbkey=Gene NC_002163.1 RefSeq region 1240975 1241661 . + . ID=id2364;gene=pseF;Name=id2364;Dbxref=GeneID:905603;gbkey=misc_feature;Note=HMMPfam hit to PF02348 2C Cytidylyltransferase 2C score 2e-25 NC_002163.1 RefSeq gene 1241648 1242472 . + . ID=gene1262;gene=pseG;Name=pseG;locus_tag=Cj1312;Dbxref=GeneID:905604;gbkey=Gene NC_002163.1 RefSeq CDS 1241648 1242472 . + 0 ID=cds1193;Parent=gene1262;gene=pseG;Name=YP_002344702.1;Dbxref=UniProtKB FTrEMBL:Q0P8U5 Genbank:YP_002344702.1 GeneID:905604;gbkey=CDS;product=nucleotidase;Note=Original 282000 29 note: Cj1312 2C possible flagellar protein 2C len: 274 aa 3B similar to e.g. SPSG_BACSU spore coat polysaccharide biosynthesis protein SPSG 28222 aa 29 2Cfasta scores 3B opt: 166 z-score: 208.1 E 28 29: 0.00028 2C 24.8 25 identity in 226 aa overlap 2C and TR:Q45987 28EMBL:U27302 29 Caulobacter crescentus FLAR 28329 aa 29 2C fasta scores 3B opt: 234 z-score: 286.7 E 28 29: 1.2e-08 2C 23.1 25 identity in 277 aa overlap 7EUpdated 282006 29 note: Characterised in Campylobacter jejuni 28PMID:16728396 29. Product function further updated. not added to product function. Plays a direct role in CMP-Pse5NAc7NAc or CMP-Pse5NAc7Am pathyways. Logan 28Susan.Logan@nrc-cnrc.gc.ca 29 personal communication. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Surface structures 7EPMID:16728396 2C PMID:16751642 2C PMID:16573682 2CPMID:12781527 2C PMID:16684771 2C PMID:16728396 NC_002163.1 RefSeq gene 1242469 1242942 . + . ID=gene1263;gene=pseH;Name=pseH;locus_tag=Cj1313;Dbxref=GeneID:905605;gbkey=Gene NC_002163.1 RefSeq CDS 1242469 1242942 . + 0 ID=cds1194;Parent=gene1263;gene=pseH;Name=YP_002344703.1;Dbxref=GOA:Q0P8U4 InterPro:IPR000182 InterPro:IPR016181 UniProtKB FTrEMBL:Q0P8U4 Genbank:YP_002344703.1 GeneID:905605;gbkey=CDS;product=N-acetyltransferase;Note=Original 282000 29 note: Cj1313 2C possible flagellar protein 2C len: 157 aa 3B similar to e.g. TR:Q45990 28EMBL:U28867 29 Caulobacter crescentus FLAG. 31.9 25 identity to HP0327 7EUpdated 282006 29 note: Pfam domain PF00583 Acetyltransferase 28GNAT 29 family identified within CDS. Recent characterisation work in Campylobacter has linked this protein to be part of the biosynthetic pathway for pseudaminic acid and bacillosamine biosynthesis. In particular 2C PseH is thought to operate between UDP-6-deosy-beta-L-AltNAc4NAc to 6-deoxy-beta-L-AltNAc4NAc. Plays a direct role in CMP-Pse5NAc7NAc or CMP-Pse5NAc7Am pathyways. Logan 28Susan.Logan@nrc-cnrc.gc.ca 29 personal communication. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Surface structures 7EPMID:16684771 2C PMID:16751642 2C PMID:9748431 2CPMID:16573682 2C PMID:12781527 NC_002163.1 RefSeq region 1242637 1242870 . + . ID=id2365;gene=pseH;Name=id2365;Dbxref=GeneID:905605;gbkey=misc_feature;Note=HMMPfam hit to PF00583 2C Acetyltransferase 28GNAT 29 family 2C score 1.3e-10 NC_002163.1 RefSeq gene 1242907 1243653 . - . ID=gene1264;gene=hisF;Name=hisF;locus_tag=Cj1314c;Dbxref=GeneID:905606;gbkey=Gene NC_002163.1 RefSeq CDS 1242907 1243653 . - 0 ID=cds1195;Parent=gene1264;gene=hisF;Name=YP_002344704.1;Dbxref=GOA:Q0P8U3 HSSP:P33734 InterPro:IPR006062 InterPro:IPR013785 UniProtKB FSwiss-Prot:Q0P8U3 Genbank:YP_002344704.1 GeneID:905606;gbkey=CDS;product=imidazole glycerol phosphate synthase subunit HisF;Note=catalyzes the conversion of 5- 5B 285-phospho-1-deoxyribulos-1-ylamino 29methylideneamino 5D-1- 285-phosphoribosyl 29imidazole-4-carboxamide and glutamine to imidazole-glycerolphosphate 2C 5-aminoimidazol-4-carboxamideribonucleotide and glutamate 3B the HisF subunit acts as a cyclase NC_002163.1 RefSeq region 1242964 1243641 . - . ID=id2366;gene=hisF;Name=id2366;Dbxref=GeneID:905606;gbkey=misc_feature;Note=HMMPfam hit to PF00977 2C Histidine biosynthesis protein 2C score 1.2e-71 ### NC_002163.1 RefSeq CDS 1243654 1244259 . - 0 ID=cds1196;Parent=gene1265;gene=hisH;Name=YP_002344705.1;Dbxref=GOA:Q0P8U2 HSSP:P33734 InterPro:IPR000991 InterPro:IPR010139 InterPro:IPR011702 InterPro:IPR012998 InterPro:IPR016226 UniProtKB FSwiss-Prot:Q0P8U2 Genbank:YP_002344705.1 GeneID:905607;gbkey=CDS;product=imidazole glycerol phosphate synthase subunit HisH;Note=with HisF IGPS catalyzes the conversion of phosphoribulosyl-formimino-5-aminoimidazole-4-carboxamide ribonucleotide phosphate and glutamine to imidazole-glycerol phosphate 2C 5-aminoimidazol-4-carboxamide ribonucleotide 2C and glutamate in histidine biosynthesis 3B the HisH subunit provides the glutamine amidotransferase activity that produces the ammonia necessary to HisF for the synthesis of imidazole-glycerol phosphate and 5-aminoimidazol-4-carboxamide ribonucleotide NC_002163.1 RefSeq gene 1243654 1244259 . - . ID=gene1265;gene=hisH;Name=hisH;locus_tag=Cj1315c;Dbxref=GeneID:905607;gbkey=Gene NC_002163.1 RefSeq region 1243657 1244253 . - . ID=id2367;gene=hisH;Name=id2367;Dbxref=GeneID:905607;gbkey=misc_feature;Note=HMMPfam hit to PF00117 2C Glutamine amidotransferase class-I 2C score 1.6e-38 NC_002163.1 RefSeq region 1243660 1244238 . - . ID=id2368;gene=hisH;Name=id2368;Dbxref=GeneID:905607;gbkey=misc_feature;Note=HMMPfam hit to PF01174 2C SNO glutamine amidotransferase family 2C score 0.0029 NC_002163.1 RefSeq region 1244002 1244037 . - . ID=id2369;gene=hisH;Name=id2369;Dbxref=GeneID:905607;gbkey=misc_feature;Note=PS00442 Glutamine amidotransferases class-I active site NC_002163.1 RefSeq CDS 1244256 1245392 . - 0 ID=cds1197;Parent=gene1266;gene=pseA;Name=YP_002344706.1;Dbxref=UniProtKB FTrEMBL:Q0P8U1 Genbank:YP_002344706.1 GeneID:905608;gbkey=CDS;product=pseudaminic acid biosynthesis PseA protein;Note=Original 282000 29 note: Cj1316c 2C unknown 2C len: 378 aa 3B similar to e.g. TR:P72140 28EMBL:U50396 29 Pseudomonas aeruginosa WBPG 28lipopolysaccharide gene cluster 29 28376 aa 29 2C fasta scores 3B opt: 257 z-score: 302.0 E 28 29: 1.6e-09 2C23.5 25 identity in 366 aa overlap. No Hp match. Also similar to Cj1324 2833.2 25 identity in 373 aa overlap 29 7EUpdated 282006 29 note: Prosite domain PS00761 SPASE_I_3 2C Peptidase S26A 2C signal peptidase I identified within CDS. Product function modified to more specific family member based on motif match. PseA has been proposed to play a role in the pseudaminic acid biosynthetic pathway by appearing to synthesize pseudaminic acid 28PseAm 29 directly from PseAc by transfer of an acetamidino group 28PMID:11461915 29. Plays a direct role in CMP-Pse5NAc7NAc or CMP-Pse5NAc7Am biosynthesis or transfer. Logan 28Susan.Logan@nrc-cnrc.gc.ca 29 personal communication. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Surface structures 7EPMID:16573682 2C PMID:12781527 2C PMID:16684771 NC_002163.1 RefSeq gene 1244256 1245392 . - . ID=gene1266;gene=pseA;Name=pseA;locus_tag=Cj1316c;Dbxref=GeneID:905608;gbkey=Gene NC_002163.1 RefSeq region 1244259 1244270 . - . ID=id2370;gene=pseA;Name=id2370;Dbxref=GeneID:905608;gbkey=misc_feature;Note=PS00294 Prenyl group binding site 28CAAX box 29 NC_002163.1 RefSeq region 1244961 1245002 . - . ID=id2371;gene=pseA;Name=id2371;Dbxref=GeneID:905608;gbkey=misc_feature;Note=PS00761 Signal peptidases I signature 3 ### NC_002163.1 UTR_Extractor 5'-UTR 1245393 1245413 . - . ID=utr478;locus_tag=Cj1316c;product=pseudaminic acid biosynthesis PseA protein NC_002163.1 UTR_Extractor 5'-UTR 1245612 1245649 . + . ID=utr479;locus_tag=Cj1317;product=Pse synthetase NC_002163.1 RefSeq CDS 1245650 1246681 . + 0 ID=cds1198;Parent=gene1267;gene=pseI;Name=YP_002344707.1;Dbxref=GOA:Q0P8U0 InterPro:IPR006190 InterPro:IPR013132 InterPro:IPR013785 InterPro:IPR013974 UniProtKB FTrEMBL:Q0P8U0 Genbank:YP_002344707.1 GeneID:905609;gbkey=CDS;product=N-acetylneuraminic acid synthetase;Note=Original 282000 29 note: Cj1317 2C neuB3 2CN-acetylneuraminic acid synthetase 2C len: 343 aa 3B 97.6 25 identical to TR:O52907 28EMBL:AJ000855 29 C. jejuni neuB 2C and similar to e.g. TR:Q57265 28EMBL:U40740 29 Neisseria meningitidis N-acetylneuraminic acid synthetase 28EC 4.1.3.- 29 28349 aa 29 2C fasta scores 3B opt: 584 z-score: 664.1 E 28 29: 1.1e-29 2C 35.1 25 identity in 350 aa overlap. 49.5 25 identity to HP0178. Also similar to Cj1327 2836.3 25 identity in 336 aa overlap 29 2C and Cj1141 2834.7 25 identity in 340 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF03102 NeuB family identified within CDS. Further support given to product function. Recent characterisation has shown PseI to be responsible for the conversion of 6-deoxy-beta-L-AltNAc4NAc to Pse5NAc7NAc in the pseudaminic acid biosynthesis pathway. Plays a direct role in CMP-Pse5NAc7NAc or CMP-Pse5NAc7Am pathyways. Logan 28Susan.Logan@nrc-cnrc.gc.ca 29 personal communication. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Surface structures 7EPMID:11461915 2C PMID:16120604 2C PMID:10712693 2CPMID:11832511 2C PMID:16421095 NC_002163.1 RefSeq gene 1245650 1246681 . + . ID=gene1267;gene=pseI;Name=pseI;locus_tag=Cj1317;Dbxref=GeneID:905609;gbkey=Gene NC_002163.1 RefSeq region 1245743 1246465 . + . ID=id2372;gene=pseI;Name=id2372;Dbxref=GeneID:905609;gbkey=misc_feature;Note=HMMPfam hit to PF03102 2C NeuB family 2C score 2.3e-103 NC_002163.1 RefSeq region 1246508 1246678 . + . ID=id2373;gene=pseI;Name=id2373;Dbxref=GeneID:905609;gbkey=misc_feature;Note=HMMPfam hit to PF01354 2C Antifreeze-like domain 2Cscore 5.4e-28 NC_002163.1 RefSeq repeat_region 1246670 1248629 . + . ID=id2374;gene=pseI;Name=id2374;gbkey=repeat_region;Note=repeat 3 3B identical to 1263498..1265455 28approx. positions 29 NC_002163.1 RefSeq CDS 1246678 1248627 . + 0 ID=cds1199;Parent=gene1268;gene=maf1;Name=YP_002344708.1;Dbxref=InterPro:IPR002826 UniProtKB FTrEMBL:Q0P8S3 Genbank:YP_002344708.1 GeneID:905610;gbkey=CDS;product=motility accessory factor;Note=Original 282000 29 note: Cj1318 2C unknown 2C len: 649 aa 3B no Hp ortholog 2C but 33.9 25 identity to HP0114. A member of the 1318 family of proteins. Similar to Cj1335 2FCj1336 28100.0 25 identity in 59 aa overlap 2F100.0 25 identity in 592 aa overlap 29 2C Cj1333 2872.5 25 identity in 658 aa overlap 29 2CCj1334 2841.5 25 identity in 648 aa overlap 29 2C Cj1337 2848.1 25 identity in 643 aa overlap 29 2C Cj1341c 2830.2 25 identity in 640 aa overlap 29 2C Cj1340c 2831.4 25 identity in 641 aa overlap 29. Contains G 2810-11 29 polymorphic tract at aa 57. G 2811 29 28consensus 29 gives this ORF 2C G 2810 29 causes truncation after 1 aa 7EUpdated 282006 29 note: Pfam domain PF01973 Protein of unknown function DUF115 identified within CDS. Characterisation work has been carried out within Campylobacter jejuni 28PMID:11895937 29. Product function modified to more specific family member. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Misc 7EPMID:11895937 2C PMID:16573682 2C PMID:12781527 NC_002163.1 RefSeq gene 1246678 1248627 . + . ID=gene1268;gene=maf1;Name=maf1;locus_tag=Cj1318;Dbxref=GeneID:905610;gbkey=Gene NC_002163.1 RefSeq region 1247329 1247835 . + . ID=id2375;gene=maf1;Name=id2375;Dbxref=GeneID:905610;gbkey=misc_feature;Note=HMMPfam hit to PF01973 2C Protein of unknown function DUF115 2C score 4.6e-79 NC_002163.1 UTR_Extractor 5'-UTR 1248434 1248623 . + . ID=utr480;locus_tag=Cj1319;product=putative nucleotide sugar dehydratase NC_002163.1 RefSeq gene 1248624 1249595 . + . ID=gene1269;Name=Cj1319;locus_tag=Cj1319;Dbxref=GeneID:905611;gbkey=Gene NC_002163.1 RefSeq CDS 1248624 1249595 . + 0 ID=cds1200;Parent=gene1269;Name=YP_002344709.1;Dbxref=GOA:Q0P8T8 InterPro:IPR001509 InterPro:IPR016040 UniProtKB FTrEMBL:Q0P8T8 Genbank:YP_002344709.1 GeneID:905611;gbkey=CDS;product=nucleotide sugar dehydratase;Note=Original 282000 29 note: Cj1319 2C probable nucleotide sugar dehydratase 2C len: 323 aa 3B similar to e.g. TR:Q54116 28EMBL:L37354 29 thymidine diphosphoglucose 4 2C6-dehydratase 28329 aa 29 2C fasta scores 3B opt: 526 z-score: 600.3 E 28 29: 3.9e-26 2C 29.5 25 identity in 315 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00106 adh_short 2CAlcohol 2Fother dehydrogenases 2C short chain type 7EUpdated 282006 29 note: Pfam domain now altered to PF01370 NAD dependent epimerase 2Fdehydratase family. Further support given to product function. No specific characterisation with acceptable identity score carried out yet. kept within product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification -Surface polysaccharides 2C lipopolysaccharides and antigens 7EPMID:16573682 2C PMID:12781527 NC_002163.1 RefSeq region 1248633 1249562 . + . ID=id2376;Name=id2376;Dbxref=GeneID:905611;gbkey=misc_feature;Note=HMMPfam hit to PF01370 2C NAD dependent epimerase 2Fdehydratase family 2C score 5e-63 NC_002163.1 RefSeq CDS 1249588 1250742 . + 0 ID=cds1201;Parent=gene1270;Name=YP_002344710.1;Dbxref=GOA:Q0P8T7 InterPro:IPR000653 InterPro:IPR015421 InterPro:IPR015422 UniProtKB FTrEMBL:Q0P8T7 Genbank:YP_002344710.1 GeneID:905612;gbkey=CDS;product=DegT family aminotransferase;Note=Original 282000 29 note: Cj1320 2C probable aminotransferase 2C len: 384 aa 3B similar to members of the degT family e.g. TR:Q06953 28EMBL:X59554 29 Vibrio cholerae RFBE protein 28367 aa 29 2C fasta scores 3B opt: 315 z-score: 377.4 E 28 29: 1e-13 2C 32.7 25 identity in 361 aa overlap. No Hp ortholog. Contains Pfam match to entry PF01041 DegT_DnrJ_EryC1 2C DegT 2FDnrJ 2FEryC1 2FStrS family 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score has been carried out yet. kept within product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Surface polysaccharides 2C lipopolysaccharides and antigens 7EPMID:16573682 2C PMID:12781527 NC_002163.1 RefSeq gene 1249588 1250742 . + . ID=gene1270;Name=Cj1320;locus_tag=Cj1320;Dbxref=GeneID:905612;gbkey=Gene NC_002163.1 RefSeq region 1249654 1250739 . + . ID=id2377;Name=id2377;Dbxref=GeneID:905612;gbkey=misc_feature;Note=HMMPfam hit to PF01041 2C DegT 2FDnrJ 2FEryC1 2FStrS aminotransferase 2C score 1.3e-71 NC_002163.1 UTR_Extractor 5'-UTR 1250728 1250851 . + . ID=utr481;locus_tag=Cj1321;product=putative transferase ### NC_002163.1 RefSeq pseudogene 1250852 1251394 . + . ID=gene1271;Name=Cj1321;locus_tag=Cj1321;Dbxref=GeneID:905613;gbkey=Gene NC_002163.1 RefSeq pseudogene 1251467 1252161 . + . ID=gene1272;Name=Cj1322;locus_tag=Cj1322;Dbxref=GeneID:905614;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 1252251 1252277 . + . ID=utr482;locus_tag=Cj1324;product=hypothetical protein NC_002163.1 RefSeq gene 1252278 1253399 . + . ID=gene1273;Name=Cj1324;locus_tag=Cj1324;Dbxref=GeneID:905616;gbkey=Gene NC_002163.1 RefSeq CDS 1252278 1253399 . + 0 ID=cds1202;Parent=gene1273;Name=YP_002344714.1;Dbxref=UniProtKB FTrEMBL:Q0P8T3 Genbank:YP_002344714.1 GeneID:905616;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1324 2C unknown 2C len: 373 aa 3B some similarity to TR:P72140 28EMBL:U50396 29 Pseudomonas aeruginosa WBPG 28lipopolysaccharide gene cluster 29 28376 aa 29 2C fasta scores 3B opt: 166 z-score: 199.7 E 28 29: 0.0008 2C20.1 25 identity in 378 aa overlap. No Hp match. Also similar to Cj1316c 7EUpdated 282006 29 note: Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Literature search identified paper linking Cj1321-Cj1326 as being a glycosylation islet 28PMID:16230626 29. Also shows some similarity to Cj1316 pseudaminic acid biosynthesis PseA protein. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:16230626 2C PMID:16573682 2C PMID:12781527 NC_002163.1 RefSeq CDS 1253417 1253671 . + 0 ID=cds1203a;Parent=gene1274;Name=YP_002344715.1;Dbxref=GOA:Q0P8T2 InterPro:IPR013216 UniProtKB FTrEMBL:Q0P8T2 Genbank:YP_002344715.1 GeneID:905617;gbkey=CDS;product=methyltransferase;Note=Original 282000 29 note: Cj1326 2C unknown 2C len: 140 aa 3B no Hp match. Contains polyporphic sequence G 289-10 29 at N-terminus 3B G 289 29 allows translation from the upstream CDS Cj1325 2C G 2810 29 28consensus 29 would only allow this CDS to start at aa 22. Similar to Cj0171 2851.9 25 identity in 135 aa overlap 29 2C which also contains a polymorphic sequence allowing possible translation from Cj0170 7EOriginal 282000 29 note: Cj1325 2C unknown 2C len: 89 aa 3B no Hp match. Contains polyporphic sequence G 289-10 29 at C-terminus 3B G 2810 29 28consensus 29 gives this translation stop 2CG 289 29 allows translation into the downstream CDS Cj1326. Similar to Cj0170 2873.8 25 identity in 61 aa overlap 29 2C which also contains a polymorphic sequence allowing possible translation into Cj0171 7EUpdated 282006 29 note: Pfam domains PF08241 and PPF08242 both Methyltransferase domains were identified within CDS. Product function modified to more specific family member. No specific characterisation has been carried out yet. kept within product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Literature search identified paper linking Cj1321-Cj1326 as being a glycosylation islet 28PMID:16230626 29. Coding sequences have been merged to reflect the complete amino acid sequence for this gene regardless of phase. Previous annotation gave Cj1325 and Cj1326 as seperate CDS. Merging of these CDSs has lead to loss of the downstream CDS. Functional classification - Misc 7EPMID:16230626 2C PMID:14985343 NC_002163.1 RefSeq gene 1253417 1254092 . + . ID=gene1274;Name=Cj1325;locus_tag=Cj1325;Dbxref=GeneID:905617;gbkey=Gene NC_002163.1 RefSeq CDS 1253673 1254092 . + 0 ID=cds1203b;Parent=gene1274;Name=YP_002344715.1;Dbxref=GOA:Q0P8T2 InterPro:IPR013216 UniProtKB FTrEMBL:Q0P8T2 Genbank:YP_002344715.1 GeneID:905617;gbkey=CDS;product=methyltransferase;Note=Original 282000 29 note: Cj1326 2C unknown 2C len: 140 aa 3B no Hp match. Contains polyporphic sequence G 289-10 29 at N-terminus 3B G 289 29 allows translation from the upstream CDS Cj1325 2C G 2810 29 28consensus 29 would only allow this CDS to start at aa 22. Similar to Cj0171 2851.9 25 identity in 135 aa overlap 29 2C which also contains a polymorphic sequence allowing possible translation from Cj0170 7EOriginal 282000 29 note: Cj1325 2C unknown 2C len: 89 aa 3B no Hp match. Contains polyporphic sequence G 289-10 29 at C-terminus 3B G 2810 29 28consensus 29 gives this translation stop 2CG 289 29 allows translation into the downstream CDS Cj1326. Similar to Cj0170 2873.8 25 identity in 61 aa overlap 29 2C which also contains a polymorphic sequence allowing possible translation into Cj0171 7EUpdated 282006 29 note: Pfam domains PF08241 and PPF08242 both Methyltransferase domains were identified within CDS. Product function modified to more specific family member. No specific characterisation has been carried out yet. kept within product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Literature search identified paper linking Cj1321-Cj1326 as being a glycosylation islet 28PMID:16230626 29. Coding sequences have been merged to reflect the complete amino acid sequence for this gene regardless of phase. Previous annotation gave Cj1325 and Cj1326 as seperate CDS. Merging of these CDSs has lead to loss of the downstream CDS. Functional classification - Misc 7EPMID:16230626 2C PMID:14985343 NC_002163.1 RefSeq CDS 1254132 1255136 . + 0 ID=cds1204;Parent=gene1275;gene=neuB2;Name=YP_002344716.1;Dbxref=GOA:Q0P8T1 InterPro:IPR005479 InterPro:IPR006190 InterPro:IPR013132 InterPro:IPR013785 InterPro:IPR013974 UniProtKB FTrEMBL:Q0P8T1 Genbank:YP_002344716.1 GeneID:905619;gbkey=CDS;product=N-acetylneuraminic acid synthetase;Note=Original 282000 29 note: Cj1327 2C neuB2 2CN-acetylneuraminic acid synthetase 2C len: 334 aa 3B similar to e.g. TR:Q46675 28EMBL:U05248 29 E.coli polysialic acid gene cluster region 2 neuB 28346 aa 29 2C fasta scores 3B opt: 1112 z-score: 1285.6 E 28 29: 0 2C 51.5 25 identity in 336 aa overlap 2C and TR:Q57265 28EMBL:U40740 29 Neisseria meningitidis N-acetylneuraminic acid synthetase 28EC 4.1.3.- 29 28349 aa 29 2C fasta scores 3B opt: 624 z-score: 724.6 E 28 29: 4.6e-33 2C 34.5 25 identity in 333 aa overlap 7EUpdated 282006 29 note: Pfam domains PF03102 NeuB family was identified within CDS. Prosite domains PS00141 ASP_PROTEASE 2C Peptidase aspartic 2C active site and PS00867 CPSASE_2 2C Carbamoyl-phosphate synthase L chain 2CATP-binding were both identified within CDS. Further support given to product function. Characterised within Campylobacter jejuni 28PMID:10712693 29. not added to product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:10712693 2C PMID:16573682 2C PMID:12781527 NC_002163.1 RefSeq gene 1254132 1255136 . + . ID=gene1275;gene=neuB2;Name=neuB2;locus_tag=Cj1327;Dbxref=GeneID:905619;gbkey=Gene NC_002163.1 RefSeq region 1254201 1254929 . + . ID=id2378;gene=neuB2;Name=id2378;Dbxref=GeneID:905619;gbkey=misc_feature;Note=HMMPfam hit to PF03102 2C NeuB family 2C score 1.8e-121 NC_002163.1 RefSeq region 1254210 1254245 . + . ID=id2379;gene=neuB2;Name=id2379;Dbxref=GeneID:905619;gbkey=misc_feature;Note=PS00141 Eukaryotic and viral aspartyl proteases active site NC_002163.1 RefSeq region 1254672 1254695 . + . ID=id2380;gene=neuB2;Name=id2380;Dbxref=GeneID:905619;gbkey=misc_feature;Note=PS00867 Carbamoyl-phosphate synthase subdomain signature 2 NC_002163.1 RefSeq region 1254762 1254794 . + . ID=id2381;gene=neuB2;Name=id2381;Dbxref=GeneID:905619;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1254975 1255133 . + . ID=id2382;gene=neuB2;Name=id2382;Dbxref=GeneID:905619;gbkey=misc_feature;Note=HMMPfam hit to PF01354 2C Antifreeze-like domain 2Cscore 3.8e-15 NC_002163.1 RefSeq CDS 1255129 1256283 . + 0 ID=cds1205;Parent=gene1276;gene=neuC2;Name=YP_002344717.1;Dbxref=GOA:Q0P8T0 InterPro:IPR003331 UniProtKB FTrEMBL:Q0P8T0 Genbank:YP_002344717.1 GeneID:905620;gbkey=CDS;product=UDP-N-acetylglucosamine 2-epimerase;Note=Original 282000 29 note: Cj1328 2C neuC2 2C probable N-acetylglucosamine-6-phosphate 2-epimerase 2FN-acetylglucosamine-6-phosphatase 2C len: 371 aa 3B similar to e.g. TR:Q47400 28EMBL:M84026 29 E. coli neuC 28391 aa 29 2C fasta scores 3B opt: 779 z-score: 889.7 E 28 29: 0 2C36.1 25 identity in 388 aa overlap 2C and TR:Q57141 28EMBL:X78068 29 Neisseria meningitidis N-acetylglucosamine-6-phosphate 2-epimerase 28EC 5.1.3.- 29 2F N-acetylglucosamine-6-phosphatase 28EC 3.1.3.- 29 28377 aa 29 2Cfatsta scores 3B opt: 561 z-score: 642.7 E 28 29: 1.7e-28 2C 33.5 25 identity in 391 aa overlap. No Hp match. Also similar to Cj1142 2834.6 25 identity in 384 aa overlap 29 7EUpdated 282006 29 note: Some characterisation work within Campylobacter coli 28PMID:8825781 2C PMID:12406231 29. Product function updated and kept within product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Surface structures 7EPMID:10712693 2C PMID:16573682 2C PMID:12781527 2CPMID:16481326 2C PMID:12406231 2C PMID:8825781 NC_002163.1 RefSeq gene 1255129 1256283 . + . ID=gene1276;gene=neuC2;Name=neuC2;locus_tag=Cj1328;Dbxref=GeneID:905620;gbkey=Gene NC_002163.1 RefSeq region 1255198 1256232 . + . ID=id2383;gene=neuC2;Name=id2383;Dbxref=GeneID:905620;gbkey=misc_feature;Note=HMMPfam hit to PF02350 2C UDP-N-acetylglucosamine 2-epimerase 2C score 2.9e-153 NC_002163.1 UTR_Extractor 5'-UTR 1256261 1256291 . + . ID=utr483;locus_tag=Cj1329;product=putative sugar-phosphate nucleotide transferase ### NC_002163.1 RefSeq region 1256292 1256447 . + . ID=id2384;Name=id2384;Dbxref=GeneID:905621;gbkey=misc_feature;Note=HMMPfam hit to PF00571 2C CBS domain 2C score 0.0046 NC_002163.1 RefSeq CDS 1256292 1257317 . + 0 ID=cds1206;Parent=gene1277;Name=YP_002344718.1;Dbxref=GOA:Q0P8S9 InterPro:IPR000644 InterPro:IPR005835 UniProtKB FTrEMBL:Q0P8S9 Genbank:YP_002344718.1 GeneID:905621;gbkey=CDS;product=sugar-phosphate nucleotide transferase;Note=Original 282000 29 note: Cj1329 2C probable sugar-phosphate nucleotide transferase 2C len: 341 aa 3B similar in C-term 28120 aa - end 29 to many predicted transferases 2C and to MPG1_YEAST mannose-1-phosphate guanyltransferase 28361 aa 29 2C fasta scores 3B opt: 304 z-score: 343.2 E 28 29: 8.1e-12 2C 28.9 25 identity in 225 aa overlap. N-term has some similarity to CBS domains in nucleotide dehydrogenases e.g. IMDH_BACSU inosine-5 27-monophosphate dehydrogenase 28513 aa 29 2C blastp scores 3B E 3D0.00034 2C 30 25 identity in 116 overlap. N-term contains 2x Pfam match to entry PF00571 CBS 2C CBS domain 2CC-term contains Pfam match to entry PF00483 NTP_transferase 2C Nucleotidyl transferase. No Hp match. Also similar in C-terminus to Cj1423c 2835.6 25 identity in 216 aa overlap 29 7EUpdated 282006 29 note: Some characterisation work carried out in Campylobacter coli 28PMID:12406231 29. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:16573682 2C PMID:12781527 2C PMID:12406231 NC_002163.1 RefSeq gene 1256292 1257317 . + . ID=gene1277;Name=Cj1329;locus_tag=Cj1329;Dbxref=GeneID:905621;gbkey=Gene NC_002163.1 RefSeq region 1256478 1256639 . + . ID=id2385;Name=id2385;Dbxref=GeneID:905621;gbkey=misc_feature;Note=HMMPfam hit to PF00571 2C CBS domain 2C score 8.5e-07 NC_002163.1 RefSeq region 1256649 1257308 . + . ID=id2386;Name=id2386;Dbxref=GeneID:905621;gbkey=misc_feature;Note=HMMPfam hit to PF00483 2C Nucleotidyl transferase 2Cscore 4.2e-30 NC_002163.1 RefSeq gene 1257314 1258219 . + . ID=gene1278;Name=Cj1330;locus_tag=Cj1330;Dbxref=GeneID:905622;gbkey=Gene NC_002163.1 RefSeq CDS 1257314 1258219 . + 0 ID=cds1207;Parent=gene1278;Name=YP_002344719.1;Dbxref=GOA:Q0P8S8 UniProtKB FTrEMBL:Q0P8S8 Genbank:YP_002344719.1 GeneID:905622;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1330 2C unknown 2C len: 301 aa 3B some similarity to predicted oxidoreductases e.g. TR:O26961 28EMBL:AE000863 29 Methanobacterium thermoautotrophicum MTH875 28predicted 3-chlorobenzoate-3 2C4-dioxygenase dyhydrogenase related protein 29 28318 aa 29 2C fasta scores 3B opt: 199 z-score: 244.0 E 28 29: 2.7e-06 2C 24.7 25 identity in 267 aa overlap 2C and TR:Q53739 28EMBL:X92429 29 Streptomyces alboniger predicted oxido-reductase 28338 aa 29 2C fasta scores 3B opt: 135 z-score: 167.8 E 28 29: 0.048 2C 27.0 25 identity in 196 aa overlap. No Hp match 7EUpdated 282006 29 note: Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Conserved hypothetical proteins 7EPMID:16573682 2C PMID:12781527 NC_002163.1 UTR_Extractor 5'-UTR 1258037 1258211 . + . ID=utr484;locus_tag=Cj1331;product=acylneuraminate cytidylyltransferase NC_002163.1 RefSeq CDS 1258212 1258919 . + 0 ID=cds1208;Parent=gene1279;gene=ptmB;Name=YP_002344720.1;Dbxref=GOA:Q0P8S7 InterPro:IPR003329 UniProtKB FTrEMBL:Q0P8S7 Genbank:YP_002344720.1 GeneID:905623;gbkey=CDS;product=acylneuraminate cytidylyltransferase;Note=Original 282000 29 note: Cj1331 2C ptmB 2C neuA3 2C probable acylneuraminate cytidylyltransferase 28CMP-N-acetylneuraminic acid synthetase 29 2C len: 235 aa 3B 83.8 25 identical to PTMB_CAMCO posttranslational flagellin modification protein B 28235 aa 29 2C and simlar to e.g. NEUA_NEIME acylneuraminate cytidylyltransferase 28EC 2.7.7.43 29 28228 aa 29 2C fasta scores 3B opt: 357 z-score: 438.8 E 28 29: 3.8e-17 2C 30.1 25 identity in 226 aa overlap. No Hp ortholog. Also similar to e.g. Cj1311 neuA2 2832.9 25 identity in 234 aa overlap 29 and Cj1143 neuA 2834.7 25 identity in 219 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF02348 Cytidylyltransferase identified within CDS. Further support given to product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Surface structures 7EPMID:16573682 2C PMID:12781527 2C PMID:8825781 NC_002163.1 RefSeq gene 1258212 1258919 . + . ID=gene1279;gene=ptmB;Name=ptmB;locus_tag=Cj1331;Dbxref=GeneID:905623;gbkey=Gene NC_002163.1 RefSeq region 1258224 1258841 . + . ID=id2387;gene=ptmB;Name=id2387;Dbxref=GeneID:905623;gbkey=misc_feature;Note=HMMPfam hit to PF02348 2C Cytidylyltransferase 2C score 6.7e-53 NC_002163.1 RefSeq gene 1258919 1259689 . + . ID=gene1280;gene=ptmA;Name=ptmA;locus_tag=Cj1332;Dbxref=GeneID:905624;gbkey=Gene NC_002163.1 RefSeq CDS 1258919 1259689 . + 0 ID=cds1209;Parent=gene1280;gene=ptmA;Name=YP_002344721.1;Dbxref=GOA:Q0P8S6 InterPro:IPR002198 InterPro:IPR002347 InterPro:IPR016040 UniProtKB FTrEMBL:Q0P8S6 Genbank:YP_002344721.1 GeneID:905624;gbkey=CDS;product=flagellin modification protein A;Note=Original 282000 29 note: Cj1332 2C ptmA 2C probable oxidoreductase 2C len: 256 aa 3B 79.3 25 identical to PTMA_CAMCO posttranslational flagellin modification protein A 28256 aa 29 2C and similar to e.g. DHG2_BACME glucose 1-dehydrogenase II 28261 aa 29 2C fasta scores 3B opt: 236 z-score: 281.8 E 28 29: 2.1e-08 2C 24.1 25 identity in 261 aa overlap. No Hp ortholog. Contains fam match to entry PF00106 adh_short 2C Alcohol 2Fother dehydrogenases 2C short chain type 2C and Pfam match to entry PF00678 adh_short_C2 2CShort chain dehydrogenase 2Freductase C-terminus 7EUpdated 282006 29 note: kept within product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Surface structures 7EPMID:16573682 2C PMID:12781527 2C PMID:8825781 NC_002163.1 RefSeq region 1258937 1259680 . + . ID=id2388;gene=ptmA;Name=id2388;Dbxref=GeneID:905624;gbkey=misc_feature;Note=HMMPfam hit to PF00106 2C short chain dehydrogenase 2Cscore 2.9e-15 NC_002163.1 RefSeq gene 1259677 1261638 . + . ID=gene1281;gene=pseD;Name=pseD;locus_tag=Cj1333;Dbxref=GeneID:905625;gbkey=Gene NC_002163.1 RefSeq CDS 1259677 1261638 . + 0 ID=cds1210;Parent=gene1281;gene=pseD;Name=YP_002344722.1;Dbxref=InterPro:IPR002826 UniProtKB FTrEMBL:Q0P8S5 Genbank:YP_002344722.1 GeneID:905625;gbkey=CDS;product=motility accessory factor PseD;Note=Original 282000 29 note: Cj1333 2C unknown 2C len: 653 aa 3B no Hp ortholog 2C but 34.6 25 identity to HP0114. A member of the 1318 family of proteins. Similar to Cj1318 2872.5 25 identity in 658 aa overlap 29 2C Cj1337 2848.6 25 identity in 636 aa overlap 29 2C Cj1334 2841.8 25 identity in 644 aa overlap 29 2CCj1340c 2830.4 25 identity in 615 aa overlap 29 2C Cj1341c 2831.2 25 identity in 616 aa overlap 29 and Cj1335 2FCj1336 2894.2 25 identity in 52 aa overlap 2F71.7 25 identity in 597 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01973 Protein of unknown function DUF115 identified within CDS. Characterised work has been carried out within Campylobacter jejuni 28PMID:16573682 29 and noted to play a role in attachment of pseudaminic acid. Previously designated at Maf2 28motility accessory protein 29. Recently shown to play no part in CMP-Pse5NAc7NAc or CMP-Pse5NAc7Am pathyways. Logan 28Susan.Logan@nrc-cnrc.gc.ca 29 personal communication. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Misc 7EPMID:11832511 2C PMID:11895937 2C PMID:16573682 2CPMID:12781527 2C PMID:11895937 2C PMID:16573682 NC_002163.1 RefSeq region 1260313 1260825 . + . ID=id2389;gene=pseD;Name=id2389;Dbxref=GeneID:905625;gbkey=misc_feature;Note=HMMPfam hit to PF01973 2C Protein of unknown function DUF115 2C score 4.1e-85 NC_002163.1 UTR_Extractor 5'-UTR 1261445 1261634 . + . ID=utr485;locus_tag=Cj1334;product=motility accessory factor NC_002163.1 RefSeq gene 1261635 1263494 . + . ID=gene1282;gene=maf3;Name=maf3;locus_tag=Cj1334;Dbxref=GeneID:905626;gbkey=Gene NC_002163.1 RefSeq CDS 1261635 1263494 . + 0 ID=cds1211;Parent=gene1282;gene=maf3;Name=YP_002344723.1;Dbxref=InterPro:IPR002826 UniProtKB FTrEMBL:Q0P8S4 Genbank:YP_002344723.1 GeneID:905626;gbkey=CDS;product=motility accessory factor;Note=Original 282000 29 note: Cj1334 2C unknown 2C len: 619 aa 3B no Hp ortholog 2C but 34.8 25 identity to HP0114. A member of the 1318 family of proteins. Similar to Cj1333 2841.9 25 identity in 645 aa overlap 29 2C Cj1318 2841.0 25 identity in 647 aa overlap 29 2C Cj1336 2841.9 25 identity in 590 aa overlap 29 2CCj1337 2843.8 25 identity in 628 aa overlap 29 2C Cj1341c 2834.3 25 identity in 621 aa overlap 29 2C and Cj1340c 2834.0 25 identity in 618 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01973 Protein of unknown function DUF115 identified within CDS. Some characterisation work has been carried out within Campylobacter jejuni. Product funciton updated to more specific family member. Recently shown to play no part in CMP-Pse5NAc7NAc or CMP-Pse5NAc7Am pathyways. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Misc 7EPMID:11832511 2C PMID:16573682 2C PMID:12781527 2CPMID:16573682 NC_002163.1 RefSeq region 1262241 1262753 . + . ID=id2390;gene=maf3;Name=id2390;Dbxref=GeneID:905626;gbkey=misc_feature;Note=HMMPfam hit to PF01973 2C Protein of unknown function DUF115 2C score 3.1e-83 ### NC_002163.1 RefSeq repeat_region 1263499 1265456 . + . ID=id2391;Name=id2391;gbkey=repeat_region;Note=repeat 3 3B identical to 1246669..1248628 28approx. positions 29 NC_002163.1 RefSeq CDS 1263507 1263677 . + 0 ID=cds1212a;Parent=gene1283;gene=maf4;Name=YP_002344724.1;Dbxref=InterPro:IPR002826 UniProtKB FTrEMBL:Q0P8S3 Genbank:YP_002344724.1 GeneID:905627;gbkey=CDS;product=motility accessory factor;Note=Original 282000 29 note: Cj1335 2C unknown 2C len: 60 aa 3B no Hp match. A member of the 1318 family of proteins. Identical to the N-terminus of Cj1318 28100.0 25 identity in 59 aa overlap 29 and similar to Cj1333 2894.2 25 identity in 52 aa overlap 29. Contains a G 289-10 29 polymorphic region at aa 57. G 289 29 28consensus 29 gives this ORF 2C G 2810 29 would extend the ORF by 18 aa. G 288 29 or G 2811 29 28not seen in shotgun 29 would allow translation into the downstream ORF Cj1336 2Cgiving a protein similar to other members of the 1318 family 7EOriginal 282000 29 note: Cj1336 2C unknown 2C len: 593 aa 3B no Hp ortholog 2C but 34.0 25 identity to HP0114. A member of the 1318 family of proteins. Identical to Cj1318 28except the C-term 2C 100.0 25 identity in 592 aa overlap 29 2C ands similar to Cj1333 2871.7 25 identity in 597 aa overlap 29 2CCj1334 2842.3 25 identity in 591 aa overlap 29 2C Cj1337 2848.6 25 identity in 586 aa overlap 29 2C Cj1341c 2830.8 25 identity in 578 aa overlap 29 and Cj1340c 2832.0 25 identity in 579 aa overlap 29. Contains a G 289-10 29 polymorphic region at aa 2. G 289 29 28consensus 29 gives this ORF 2C G 2810 29 would allow translation to start at aa 21. G 288 29 or G 2811 29 28not seen in shotgun 29 would allow translation from the upstream ORF Cj1335 2C giving a protein similar to other members of the 1318 family 7EUpdated 282006 29 note: Pfam domain PF01973 Protein of unknown function DUF115 identified within CDS. Some characterisation work has been carried out within Campylobacter jejuni. Product funciton updated to more specific family member. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Coding sequences have been merged to reflect the complete amino acid sequence for this gene regardless of phase. Previous annotation gave Cj1335 and Cj1336 as seperate CDS. Merging of these CDSs has lead to loss of the downstream CDS. Functional classification - Misc 7EPMID:11832511 2C PMID:16573682 2C PMID:12781527 NC_002163.1 RefSeq gene 1263507 1265454 . + . ID=gene1283;gene=maf4;Name=maf4;locus_tag=Cj1335;Dbxref=GeneID:905627;gbkey=Gene NC_002163.1 RefSeq CDS 1263676 1265454 . + 0 ID=cds1212b;Parent=gene1283;gene=maf4;Name=YP_002344724.1;Dbxref=InterPro:IPR002826 UniProtKB FTrEMBL:Q0P8S3 Genbank:YP_002344724.1 GeneID:905627;gbkey=CDS;product=motility accessory factor;Note=Original 282000 29 note: Cj1335 2C unknown 2C len: 60 aa 3B no Hp match. A member of the 1318 family of proteins. Identical to the N-terminus of Cj1318 28100.0 25 identity in 59 aa overlap 29 and similar to Cj1333 2894.2 25 identity in 52 aa overlap 29. Contains a G 289-10 29 polymorphic region at aa 57. G 289 29 28consensus 29 gives this ORF 2C G 2810 29 would extend the ORF by 18 aa. G 288 29 or G 2811 29 28not seen in shotgun 29 would allow translation into the downstream ORF Cj1336 2Cgiving a protein similar to other members of the 1318 family 7EOriginal 282000 29 note: Cj1336 2C unknown 2C len: 593 aa 3B no Hp ortholog 2C but 34.0 25 identity to HP0114. A member of the 1318 family of proteins. Identical to Cj1318 28except the C-term 2C 100.0 25 identity in 592 aa overlap 29 2C ands similar to Cj1333 2871.7 25 identity in 597 aa overlap 29 2CCj1334 2842.3 25 identity in 591 aa overlap 29 2C Cj1337 2848.6 25 identity in 586 aa overlap 29 2C Cj1341c 2830.8 25 identity in 578 aa overlap 29 and Cj1340c 2832.0 25 identity in 579 aa overlap 29. Contains a G 289-10 29 polymorphic region at aa 2. G 289 29 28consensus 29 gives this ORF 2C G 2810 29 would allow translation to start at aa 21. G 288 29 or G 2811 29 28not seen in shotgun 29 would allow translation from the upstream ORF Cj1335 2C giving a protein similar to other members of the 1318 family 7EUpdated 282006 29 note: Pfam domain PF01973 Protein of unknown function DUF115 identified within CDS. Some characterisation work has been carried out within Campylobacter jejuni. Product funciton updated to more specific family member. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Coding sequences have been merged to reflect the complete amino acid sequence for this gene regardless of phase. Previous annotation gave Cj1335 and Cj1336 as seperate CDS. Merging of these CDSs has lead to loss of the downstream CDS. Functional classification - Misc 7EPMID:11832511 2C PMID:16573682 2C PMID:12781527 NC_002163.1 RefSeq region 1264156 1264662 . + . ID=id2392;gene=maf4;Name=id2392;Dbxref=GeneID:905627;gbkey=misc_feature;Note=HMMPfam hit to PF01973 2C Protein of unknown function DUF115 2C score 4.6e-79 NC_002163.1 UTR_Extractor 5'-UTR 1265261 1265450 . + . ID=utr486;locus_tag=Cj1337;product=PseE protein NC_002163.1 RefSeq CDS 1265451 1267337 . + 0 ID=cds1213;Parent=gene1284;gene=pseE;Name=YP_002344725.1;Dbxref=InterPro:IPR002826 UniProtKB FTrEMBL:Q0P8S2 Genbank:YP_002344725.1 GeneID:905629;gbkey=CDS;product=motility accessory factor PseE;Note=Original 282000 29 note: Cj1337 2C unknown 2C len: 628 aa 3B 35.0 25 identity to HP0114. A member of the 1318 family of proteins. Simlar to Cj1333 2848.6 25 identity in 636 aa overlap 29 2C Cj1318 2848.1 25 identity in 643 aa overlap 29 2CCj1336 2848.6 25 identity in 586 aa overlap 29 2C Cj1334 2843.6 25 identity in 628 aa overlap 29 2C Cj1340c 2832.2 25 identity in 624 aa overlap 29 2C Cj1341c 2831.9 25 identity in 627 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01973 Protein of unknown function DUF115 identified within CDS. Some characterisation work carried out within Campylobacter jejuni. Product function modified. Recent research has shown that PseE does not play a role in the pseudaminic acid pathway 2C however 2C may be involved in glycan transfer to flagellin 28PMID:16684771 29. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Misc 7EPMID:16684771 2C PMID:16573682 2C PMID:12781527 2CPMID:11461915 NC_002163.1 RefSeq gene 1265451 1267337 . + . ID=gene1284;gene=pseE;Name=pseE;locus_tag=Cj1337;Dbxref=GeneID:905629;gbkey=Gene NC_002163.1 RefSeq region 1266069 1266581 . + . ID=id2393;gene=pseE;Name=id2393;Dbxref=GeneID:905629;gbkey=misc_feature;Note=HMMPfam hit to PF01973 2C Protein of unknown function DUF115 2C score 9.6e-90 ### NC_002163.1 RefSeq CDS 1267368 1269086 . - 0 ID=cds1214;Parent=gene1285;gene=flaB;Name=YP_002344726.1;Dbxref=GOA:P56964 InterPro:IPR001029 InterPro:IPR001492 InterPro:IPR010810 UniProtKB FSwiss-Prot:P56964 Genbank:YP_002344726.1 GeneID:905630;gbkey=CDS;product=flagellin;Note=FlaB 3B structural flagella protein 3B in Helicobacter the flagella are composed of flagellin A and flagellin B 3B the amounts of each seem to be controlled by environmental conditions NC_002163.1 RefSeq gene 1267368 1269086 . - . ID=gene1285;gene=flaB;Name=flaB;locus_tag=Cj1338c;Dbxref=GeneID:905630;gbkey=Gene NC_002163.1 RefSeq region 1267437 1267652 . - . ID=id2394;gene=flaB;Name=id2394;Dbxref=GeneID:905630;gbkey=misc_feature;Note=HMMPfam hit to PF00700 2C Bacterial flagellin C-terminus 2C score 6.3e-36 NC_002163.1 RefSeq region 1268178 1268333 . - . ID=id2395;gene=flaB;Name=id2395;Dbxref=GeneID:905630;gbkey=misc_feature;Note=HMMPfam hit to PF07196 2C Flagellin hook IN motif 2Cscore 2.2e-10 NC_002163.1 RefSeq region 1268346 1268528 . - . ID=id2396;gene=flaB;Name=id2396;Dbxref=GeneID:905630;gbkey=misc_feature;Note=HMMPfam hit to PF07196 2C Flagellin hook IN motif 2Cscore 5.4e-08 NC_002163.1 RefSeq region 1268577 1269002 . - . ID=id2397;gene=flaB;Name=id2397;Dbxref=GeneID:905630;gbkey=misc_feature;Note=HMMPfam hit to PF00669 2C Bacterial flagellin N-terminus 2C score 6.6e-69 ### NC_002163.1 UTR_Extractor 5'-UTR 1269087 1269112 . - . ID=utr487;locus_tag=Cj1338c;product=flagellin NC_002163.1 RefSeq CDS 1269232 1270950 . - 0 ID=cds1215;Parent=gene1286;gene=flaA;Name=YP_002344727.1;Dbxref=GOA:P56963 InterPro:IPR001029 InterPro:IPR001492 InterPro:IPR010810 UniProtKB FSwiss-Prot:P56963 Genbank:YP_002344727.1 GeneID:905631;gbkey=CDS;product=flagellin;Note=FlaA 3B structural flagella protein 3B in Helicobacter the flagella are composed of flagellin A and flagellin B 3B the amounts of each seem to be controlled by environmental conditions NC_002163.1 RefSeq gene 1269232 1270950 . - . ID=gene1286;gene=flaA;Name=flaA;locus_tag=Cj1339c;Dbxref=GeneID:905631;gbkey=Gene NC_002163.1 RefSeq region 1269301 1269516 . - . ID=id2398;gene=flaA;Name=id2398;Dbxref=GeneID:905631;gbkey=misc_feature;Note=HMMPfam hit to PF00700 2C Bacterial flagellin C-terminus 2C score 1.5e-36 NC_002163.1 RefSeq region 1270042 1270197 . - . ID=id2399;gene=flaA;Name=id2399;Dbxref=GeneID:905631;gbkey=misc_feature;Note=HMMPfam hit to PF07196 2C Flagellin hook IN motif 2Cscore 2.2e-11 NC_002163.1 RefSeq region 1270210 1270392 . - . ID=id2400;gene=flaA;Name=id2400;Dbxref=GeneID:905631;gbkey=misc_feature;Note=HMMPfam hit to PF07196 2C Flagellin hook IN motif 2Cscore 3.2e-09 NC_002163.1 RefSeq region 1270441 1270866 . - . ID=id2401;gene=flaA;Name=id2401;Dbxref=GeneID:905631;gbkey=misc_feature;Note=HMMPfam hit to PF00669 2C Bacterial flagellin N-terminus 2C score 7.1e-69 ### NC_002163.1 UTR_Extractor 5'-UTR 1270951 1270994 . - . ID=utr488;locus_tag=Cj1339c;product=flagellin NC_002163.1 RefSeq CDS 1271047 1272864 . - 0 ID=cds1216;Parent=gene1287;Name=YP_002344728.1;Dbxref=InterPro:IPR002826 UniProtKB FTrEMBL:Q0P8R9 Genbank:YP_002344728.1 GeneID:905632;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1340c 2C unknown 2C len: 605 aa 3B no Hp ortholog 2C but 28.5 25 identity to HP0114. A member of the 1318 family of proteins. Similar to Cj1341c 2883.4 25 identity in 598 aa overlap 29 2C Cj1337 2832.5 25 identity in 625 aa overlap 29 2C Cj1333 2830.4 25 identity in 615 aa overlap 29 2CCj1336 2832.0 25 identity in 579 aa overlap 29 2C Cj1318 2831.4 25 identity in 641 aa overlap 29 2C and Cj1334 2834.1 25 identity in 618 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01973 Protein of unknown function DUF115 identified within CDS. Conserved added to product function. Literature search identified paper giving further clues to product function 28PMID:11895937 29. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Conserved hypothetical proteins 7EPMID:11895937 2C PMID:16573682 2C PMID:12781527 NC_002163.1 RefSeq gene 1271047 1272864 . - . ID=gene1287;Name=Cj1340c;locus_tag=Cj1340c;Dbxref=GeneID:905632;gbkey=Gene NC_002163.1 RefSeq region 1271755 1272255 . - . ID=id2402;Name=id2402;Dbxref=GeneID:905632;gbkey=misc_feature;Note=HMMPfam hit to PF01973 2C Protein of unknown function DUF115 2C score 8.8e-71 NC_002163.1 RefSeq gene 1272861 1274684 . - . ID=gene1288;gene=maf6;Name=maf6;locus_tag=Cj1341c;Dbxref=GeneID:905633;gbkey=Gene NC_002163.1 RefSeq CDS 1272861 1274684 . - 0 ID=cds1217;Parent=gene1288;gene=maf6;Name=YP_002344729.1;Dbxref=InterPro:IPR002826 UniProtKB FTrEMBL:Q0P8R8 Genbank:YP_002344729.1 GeneID:905633;gbkey=CDS;product=motility accessory factor;Note=Original 282000 29 note: Cj1341c 2C unknown 2C len: 607 aa 3B no Hp ortholog 2C but 28.4 25 identity to HP0114. A member of the 1318 family of proteins. Similar to Cj1340c 2883.4 25 identity in 598 aa overlap 29 2C Cj1334 2834.6 25 identity in 622 aa overlap 29 2C Cj1336 2830.8 25 identity in 578 aa overlap 29 2CCj1333 2831.2 25 identity in 616 aa overlap 29 2C Cj1318 2830.2 25 identity in 640 aa overlap 29 2C and Cj1337 2832.0 25 identity in 628 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01973 Protein of unknown function DUF115 identified within CDS. Some characterisation work carried out within Campylobacter jejuni. Product modified to more specific family member. Recently shown to play no part in CMP-Pse5NAc7NAc or CMP-Pse5NAc7Am pathyways. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Misc 7EPMID:11832511 2C PMID:16573682 2C PMID:12781527 2CPMID:16573682 NC_002163.1 RefSeq region 1273584 1274075 . - . ID=id2403;gene=maf6;Name=id2403;Dbxref=GeneID:905633;gbkey=misc_feature;Note=HMMPfam hit to PF01973 2C Protein of unknown function DUF115 2C score 9.8e-73 ### NC_002163.1 RefSeq CDS 1274694 1275935 . - 0 ID=cds1218;Parent=gene1289;gene=maf7;Name=YP_002344730.1;Dbxref=UniProtKB FTrEMBL:Q0P8R7 Genbank:YP_002344730.1 GeneID:905634;gbkey=CDS;product=motility accessory factor;Note=Original 282000 29 note: Cj1342c 2C unknown 2C len: 413 aa 3B no Hp match. A member of the 617 family of C.j. proteins containing homopolymeric tracts 3B similar to Cj1310c 2837.3 25 identity in 424 aa overlap 29 2C Cj1305c 2838.5 25 identity in 423 aa overlap 29 2C Cj0617 2FCj0618 2849.7 25 identity in 191 aa overlap 2F43.4 25 identity in 221 aa overlap 29 2CCj1306c 2838.3 25 identity in 426 aa overlap 29. Contains C 289-10 29 polymorphic region at aa 188. C 289 29 consensus gives this ORF 2C C 2810 29 gives truncation after a further 19 aa 7EUpdated 282006 29 note: Some characterisation work carried out within Campylobacter jejuni. Product modified to more specific family member.Recently shown to play no part in CMP-Pse5NAc7NAc or CMP-Pse5NAc7Am pathyways. Identifed as part of Campylobacter jejuni O-linked glycosylation locus 28Cj1293 - Cj1342 29. Functional classification - Misc 7EPMID:11832511 2C PMID:16573682 2C PMID:12781527 2CPMID:16573682 NC_002163.1 RefSeq gene 1274694 1275935 . - . ID=gene1289;gene=maf7;Name=maf7;locus_tag=Cj1342c;Dbxref=GeneID:905634;gbkey=Gene NC_002163.1 RefSeq CDS 1275935 1276450 . - 0 ID=cds1219;Parent=gene1290;Name=YP_002344731.1;Dbxref=GOA:Q0P8R6 InterPro:IPR000983 InterPro:IPR012902 UniProtKB FTrEMBL:Q0P8R6 Genbank:YP_002344731.1 GeneID:905635;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1343c 2C probable periplasmic protein 2C len: 171 aa 3B no Hp match. Some similarity to N-terminus of secretion proteins e.g. GSPG_ECOLI general secretion pathway protein 28145 aa 29 2C fasta scores 3B opt: 153 z-score: 192.8 E 28 29: 0.0019 2C 35.6 25 identity in 59 aa overlap. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF07963 Prokaryotic N-terminal methylation motif identified within CDS. Further support given to product function. Literature search identified paper giving further clues to product function. Functional classification - Miscellaneous periplasmic proteins 7EPMID:12949093 NC_002163.1 RefSeq gene 1275935 1276450 . - . ID=gene1290;gene=maf7;Name=maf7;locus_tag=Cj1343c;Dbxref=GeneID:905635;gbkey=Gene NC_002163.1 RefSeq region 1276373 1276432 . - . ID=id2405;Name=id2405;Dbxref=GeneID:905635;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1343c by TMHMM2.0 at aa 7-26 NC_002163.1 RefSeq region 1276373 1276444 . - . ID=id2404;Name=id2404;Dbxref=GeneID:905635;gbkey=misc_feature;Note=HMMPfam hit to PF07963 2C Prokaryotic N-terminal methylation motif 2C score 1.5e-06 ### NC_002163.1 RefSeq CDS 1276451 1277458 . - 0 ID=cds1220;Parent=gene1291;Name=YP_002344732.1;Dbxref=GOA:Q0P8R5 InterPro:IPR000905 InterPro:IPR009180 UniProtKB FSwiss-Prot:Q0P8R5 Genbank:YP_002344732.1 GeneID:905636;gbkey=CDS;product=DNA-binding 2Firon metalloprotein 2FAP endonuclease;Note=in most organisms 2C only the N-terminal domain is present in a single polypeptide 3B in some archaea this domain is fused to a kinase domain 3B this gene is essential for growth in Escherichia coli and Bacillus subtilis 3B the secreted glycoprotease from Pasteurella haemolytica showed specificity for O-sialoglycosylated proteins 3B the Pyrococcus structure shows DNA-binding properties 2C iron-binding 2C ATP-binding 2C and AP endonuclease activity NC_002163.1 RefSeq gene 1276451 1277458 . - . ID=gene1291;Name=Cj1344c;locus_tag=Cj1344c;Dbxref=GeneID:905636;gbkey=Gene NC_002163.1 RefSeq region 1277087 1277332 . - . ID=id2406;Name=id2406;Dbxref=GeneID:905636;gbkey=misc_feature;Note=HMMPfam hit to PF00814 2C Glycoprotease family 2C score 2.3e-19 NC_002163.1 RefSeq region 1277114 1277176 . - . ID=id2407;Name=id2407;Dbxref=GeneID:905636;gbkey=misc_feature;Note=PS01016 Glycoprotease family signature NC_002163.1 RefSeq gene 1277455 1278849 . - . ID=gene1292;Name=Cj1345c;locus_tag=Cj1345c;Dbxref=GeneID:905637;gbkey=Gene NC_002163.1 RefSeq CDS 1277455 1278849 . - 0 ID=cds1221;Parent=gene1292;Name=YP_002344733.1;Dbxref=UniProtKB FTrEMBL:Q0P8R4 Genbank:YP_002344733.1 GeneID:905637;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1345c 2C probable periplasmic protein 2C len: 464 aa 3B 41.2 25 identity to HP1075. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Paper identified linking protein to glycoprotein. Functional classification -Miscellaneous periplasmic proteins 7EPMID:12186869 ### NC_002163.1 RefSeq CDS 1278851 1279921 . - 0 ID=cds1222;Parent=gene1293;gene=dxr;Name=YP_002344734.1;Dbxref=GOA:Q9PMV3 HSSP:P45568 InterPro:IPR003821 InterPro:IPR013512 InterPro:IPR013644 UniProtKB FSwiss-Prot:Q9PMV3 Genbank:YP_002344734.1 GeneID:905638;gbkey=CDS;product=1-deoxy-D-xylulose 5-phosphate reductoisomerase;Note=catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate 28DXP 29 to 2-C-methyl-D-erythritol 4-phosphate NC_002163.1 RefSeq gene 1278851 1279921 . - . ID=gene1293;gene=dxr;Name=dxr;locus_tag=Cj1346c;Dbxref=GeneID:905638;gbkey=Gene NC_002163.1 RefSeq region 1278860 1279921 . - . ID=id2408;gene=dxr;Name=id2408;Dbxref=GeneID:905638;gbkey=misc_feature;Note=HMMPfam hit to PF02670 2C 1-deoxy-D-xylulose 5-phosphate reduct 2C score 5.7e-116 NC_002163.1 RefSeq region 1279562 1279921 . - . ID=id2409;gene=dxr;Name=id2409;Dbxref=GeneID:905638;gbkey=misc_feature;Note=PS00430 TonB-dependent receptor proteins signature 1 NC_002163.1 RefSeq gene 1279918 1280643 . - . ID=gene1294;gene=cdsA;Name=cdsA;locus_tag=Cj1347c;Dbxref=GeneID:905639;gbkey=Gene NC_002163.1 RefSeq CDS 1279918 1280643 . - 0 ID=cds1223;Parent=gene1294;gene=cdsA;Name=YP_002344735.1;Dbxref=GOA:Q0P8R2 InterPro:IPR000374 UniProtKB FTrEMBL:Q0P8R2 Genbank:YP_002344735.1 GeneID:905639;gbkey=CDS;product=phosphatidate cytidylyltransferase;Note=Original 282000 29 note: Cj1347c 2C cdsA 2C probable phosphatidate cytidylyltransferase 2C len: 241 aa 3B similar to e.g. CDSA_ECOLI phosphatidate cytidylyltransferase 28EC 2.7.7.41 29 28249 aa 29 2C fasta scores 3B opt: 381 z-score: 465.5 E 28 29: 1.2e-18 2C 40.7 25 identity in 182 aa overlap. 39.3 25 identity to HP0215. Contains PS01315 Phosphatidate cytidylyltransferase signature 2C and Pfam match to entry PF01148 Cytidylyltrans 2C Phosphatidate cytidylyltransferase 7EUpdated 282006 29 note: Characterised in Escherichia coli with acceptable identity score. not added to product function. Seven probable transmembrane helices predicted by TMHMM2.0. Functional classification - Fatty acid biosynthesis 7EPMID:9083091 2C PMID:2995359 NC_002163.1 RefSeq region 1279921 1280634 . - . ID=id2410;gene=cdsA;Name=id2410;Dbxref=GeneID:905639;gbkey=misc_feature;Note=HMMPfam hit to PF01148 2C Cytidylyltransferase family 2C score 7.5e-79 NC_002163.1 RefSeq region 1279960 1280040 . - . ID=id2411;gene=cdsA;Name=id2411;Dbxref=GeneID:905639;gbkey=misc_feature;Note=PS01315 Phosphatidate cytidylyltransferase signature NC_002163.1 RefSeq region 1280032 1280091 . - . ID=id120;gene=cdsA;Name=id120;Dbxref=GeneID:905639;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1347c by TMHMM2.0 at aa 10-41 2C 48-67 2C 71-88 2C 95-114 2C119-138 2C 159-181 and 185-204 NC_002163.1 RefSeq region 1280101 1280169 . - . ID=id120;gene=cdsA;Name=id120;Dbxref=GeneID:905639;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1347c by TMHMM2.0 at aa 10-41 2C 48-67 2C 71-88 2C 95-114 2C119-138 2C 159-181 and 185-204 NC_002163.1 RefSeq region 1280230 1280289 . - . ID=id120;gene=cdsA;Name=id120;Dbxref=GeneID:905639;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1347c by TMHMM2.0 at aa 10-41 2C 48-67 2C 71-88 2C 95-114 2C119-138 2C 159-181 and 185-204 NC_002163.1 RefSeq region 1280251 1280283 . - . ID=id2412;gene=cdsA;Name=id2412;Dbxref=GeneID:905639;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1280302 1280361 . - . ID=id120;gene=cdsA;Name=id120;Dbxref=GeneID:905639;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1347c by TMHMM2.0 at aa 10-41 2C 48-67 2C 71-88 2C 95-114 2C119-138 2C 159-181 and 185-204 NC_002163.1 RefSeq region 1280380 1280433 . - . ID=id120;gene=cdsA;Name=id120;Dbxref=GeneID:905639;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1347c by TMHMM2.0 at aa 10-41 2C 48-67 2C 71-88 2C 95-114 2C119-138 2C 159-181 and 185-204 NC_002163.1 RefSeq region 1280443 1280502 . - . ID=id120;gene=cdsA;Name=id120;Dbxref=GeneID:905639;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1347c by TMHMM2.0 at aa 10-41 2C 48-67 2C 71-88 2C 95-114 2C119-138 2C 159-181 and 185-204 NC_002163.1 RefSeq region 1280521 1280616 . - . ID=id120;gene=cdsA;Name=id120;Dbxref=GeneID:905639;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1347c by TMHMM2.0 at aa 10-41 2C 48-67 2C 71-88 2C 95-114 2C119-138 2C 159-181 and 185-204 ### NC_002163.1 RefSeq gene 1280652 1280990 . - . ID=gene1295;Name=Cj1348c;locus_tag=Cj1348c;Dbxref=GeneID:905640;gbkey=Gene NC_002163.1 RefSeq CDS 1280652 1280990 . - 0 ID=cds1224;Parent=gene1295;Name=YP_002344736.1;Dbxref=UniProtKB FTrEMBL:Q0P8R1 Genbank:YP_002344736.1 GeneID:905640;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1348c 2C probable coiled-coil protein 2C len: 112 aa 3B Lys- 2C Glu-rich 2C highly hydrophilic 2Ccontains probable coiled-coil from approx aa 50-80. No Hp match. Functional classification - Unknown NC_002163.1 UTR_Extractor 5'-UTR 1280991 1281130 . - . ID=utr489;locus_tag=Cj1348c;product=putative coiled-coil protein NC_002163.1 RefSeq CDS 1280992 1282299 . - 0 ID=cds1225;Parent=gene1296;Name=YP_002344737.1;Dbxref=InterPro:IPR008532 UniProtKB FTrEMBL:Q0P8R0 Genbank:YP_002344737.1 GeneID:905641;gbkey=CDS;product=fibronectin 2Ffibrinogen-binding protein;Note=Original 282000 29 note: Cj1349c 2C possible fibronectin 2Ffibrinogen-binding protein 2C len: aa 3B similar to TR:Q54858 28EMBL:L28919 29 Streptococcus pyogenes fibronectin 2Ffibrinogen-binding protein FBP54 28474 aa 29 2Cfasta scores 3B opt: 213 z-score: 230.0 E 28 29: 1.7e-05 2C 23.2 25 identity in 466 aa overlap. 30.6 25 identity to HP1392 7EUpdated 282006 29 note: Pfam domain PF05670 Domain of unknown function 28DUF814 29 identified within CDS. No specific characterisation with acceptable identity score carried out yet 2C so kept within product function. Functional classification - Pathogenicity NC_002163.1 RefSeq gene 1280992 1282299 . - . ID=gene1296;Name=Cj1349c;locus_tag=Cj1349c;Dbxref=GeneID:905641;gbkey=Gene NC_002163.1 RefSeq region 1281052 1281312 . - . ID=id2413;Name=id2413;Dbxref=GeneID:905641;gbkey=misc_feature;Note=HMMPfam hit to PF05670 2C Domain of unknown function 28DUF814 29 2C score 1.5e-35 NC_002163.1 UTR_Extractor 5'-UTR 1282299 1282299 . - . ID=utr490;locus_tag=Cj1349c;product=putative fibronectin 2Ffibrinogen-binding protein ### NC_002163.1 RefSeq CDS 1282361 1282936 . + 0 ID=cds1226;Parent=gene1297;gene=mobA;Name=YP_002344738.1;Dbxref=GOA:Q9PMU9 UniProtKB FSwiss-Prot:Q9PMU9 Genbank:YP_002344738.1 GeneID:905642;gbkey=CDS;product=molybdopterin-guanine dinucleotide biosynthesis protein;Note=Original 282000 29 note: Cj1350 2C mobA 2C probable molybdopterin-guanine dinucleotide biosynthesis protein 2Clen: 191 aa 3B similar to e.g. MOBA_ECOLI molybdopterin-guanine dinucleotide biosynthesis protein A 28194 aa 29 2C fasta scores 3B opt: 194 z-score: 249.0 E 28 29: 1.5e-06 2C 22.9 25 identity in 192 aa overlap. 26.6 25 identity to HP0769 7EUpdated 282006 29 note: Some characterisation in Escherichia coli 2C however 2C identity score was unacceptable. Thus 2C kept within product function. Functional classification - Biosynthesis of cofactors 2Cprosthetic groups and carriers - Molybdopterin 7EPMID:10978347 NC_002163.1 RefSeq gene 1282361 1282936 . + . ID=gene1297;gene=mobA;Name=mobA;locus_tag=Cj1350;Dbxref=GeneID:905642;gbkey=Gene NC_002163.1 RefSeq gene 1282933 1283922 . + . ID=gene1298;gene=pldA;Name=pldA;locus_tag=Cj1351;Dbxref=GeneID:905643;gbkey=Gene NC_002163.1 RefSeq CDS 1282933 1283922 . + 0 ID=cds1227;Parent=gene1298;gene=pldA;Name=YP_002344739.1;Dbxref=GOA:Q0P8Q8 InterPro:IPR003187 UniProtKB FTrEMBL:Q0P8Q8 Genbank:YP_002344739.1 GeneID:905643;gbkey=CDS;product=phospholipase A;Note=Original 282000 29 note: Cj1351 2C pldA 2C probable phospholipase A 2C len: 329 aa 3B highly similar to TR:O32349 28EMBL:Y11031 29 Campylobacter coli phospholipase A 28297 aa 29 2Cfasta scores 3B opt: 1544 z-score: 1835.1 E 28 29: 0 2C 75.2 25 identity in 298 aa overlap 2C and similar to e.g. PA1_ECOLI phospholipase A1 precursor 28EC 3.1.1.32 29 28289 aa 29 2C fasta scores 3B opt: 467 z-score: 560.5 E 28 29: 6.4e-24 2C 34.7 25 identity in 262 aa overlap. 25.5 25 identity to HP0499. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF02253 Phospholipase A1 identified within CDS. Further support given to product function. Characterised within Campylobacter coli 2C so not added to product function 28PMID:9119448 29. Functional classification -Pathogenicity 7EPMID:9119448 2C PMID:8300539 NC_002163.1 RefSeq region 1283128 1283916 . + . ID=id2414;gene=pldA;Name=id2414;Dbxref=GeneID:905643;gbkey=misc_feature;Note=HMMPfam hit to PF02253 2C Phospholipase A1 2C score 4.1e-135 ### NC_002163.1 RefSeq gene 1284008 1284976 . + . ID=gene1299;gene=ceuB;Name=ceuB;locus_tag=Cj1352;Dbxref=GeneID:905644;gbkey=Gene NC_002163.1 RefSeq CDS 1284008 1284976 . + 0 ID=cds1228;Parent=gene1299;gene=ceuB;Name=YP_002344740.1;Dbxref=GOA:Q0P8Q7 InterPro:IPR000522 UniProtKB FTrEMBL:Q0P8Q7 Genbank:YP_002344740.1 GeneID:905644;gbkey=CDS;product=enterochelin uptake permease;Note=Original 282000 29 note: Cj1352 2C ceuB 2C probable enterochelin uptake permease 2C len: 322 aa 3B highly similar to TR:Q46003 28EMBL:X88849 29 Campylobacter coli ceuB 28322 aa 29 2C fasta scores 3B opt: 1839 z-score: 2038.7 E 28 29: 0 2C 89.1 25 identity in 322 aa overlap 2C and similar to e.g. FATD_VIBAN ferric anguibactin transport system permease FATD 28314 aa 29 2C fasta scores 3B opt: 921 z-score: 1026.8 E 28 29: 0 2C43.3 25 identity in 305 aa overlap. Also similar to Cj1615 2831.0 25 identity in 326 aa overlap 29 2C and Cj1353 2827.2 25 identity in 316 aa overlap 29. Contains Pfam match to entry PF01032 FecCD_family 2C FecCD transport family 7EUpdated 282006 29 note: Nine probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Campylobacter coli 2Cso not added to product function. Functional classification - Transport 2Fbinding proteins - Cations 7EPMID:8574410 NC_002163.1 RefSeq region 1284038 1284106 . + . ID=id2415;gene=ceuB;Name=id2415;Dbxref=GeneID:905644;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1352 by TMHMM2.0 at aa 11-33 2C 54-76 2C 96-125 2C 138-160 2C180-202 2C 214-236 2C 241-263 2C 270-292 and 297-316 NC_002163.1 RefSeq region 1284086 1284958 . + . ID=id2416;gene=ceuB;Name=id2416;Dbxref=GeneID:905644;gbkey=misc_feature;Note=HMMPfam hit to PF01032 2C FecCD transport family 2Cscore 1.7e-49 NC_002163.1 RefSeq region 1284167 1284235 . + . ID=id2415;gene=ceuB;Name=id2415;Dbxref=GeneID:905644;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1352 by TMHMM2.0 at aa 11-33 2C 54-76 2C 96-125 2C 138-160 2C180-202 2C 214-236 2C 241-263 2C 270-292 and 297-316 NC_002163.1 RefSeq region 1284293 1284382 . + . ID=id2415;gene=ceuB;Name=id2415;Dbxref=GeneID:905644;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1352 by TMHMM2.0 at aa 11-33 2C 54-76 2C 96-125 2C 138-160 2C180-202 2C 214-236 2C 241-263 2C 270-292 and 297-316 NC_002163.1 RefSeq region 1284419 1284487 . + . ID=id2415;gene=ceuB;Name=id2415;Dbxref=GeneID:905644;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1352 by TMHMM2.0 at aa 11-33 2C 54-76 2C 96-125 2C 138-160 2C180-202 2C 214-236 2C 241-263 2C 270-292 and 297-316 NC_002163.1 RefSeq region 1284545 1284613 . + . ID=id2415;gene=ceuB;Name=id2415;Dbxref=GeneID:905644;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1352 by TMHMM2.0 at aa 11-33 2C 54-76 2C 96-125 2C 138-160 2C180-202 2C 214-236 2C 241-263 2C 270-292 and 297-316 NC_002163.1 RefSeq region 1284647 1284715 . + . ID=id2415;gene=ceuB;Name=id2415;Dbxref=GeneID:905644;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1352 by TMHMM2.0 at aa 11-33 2C 54-76 2C 96-125 2C 138-160 2C180-202 2C 214-236 2C 241-263 2C 270-292 and 297-316 NC_002163.1 UTR_Extractor 5'-UTR 1284682 1284968 . + . ID=utr491;locus_tag=Cj1353;product=enterochelin uptake permease NC_002163.1 RefSeq region 1284728 1284796 . + . ID=id2415;gene=ceuB;Name=id2415;Dbxref=GeneID:905644;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1352 by TMHMM2.0 at aa 11-33 2C 54-76 2C 96-125 2C 138-160 2C180-202 2C 214-236 2C 241-263 2C 270-292 and 297-316 NC_002163.1 RefSeq region 1284815 1284883 . + . ID=id2415;gene=ceuB;Name=id2415;Dbxref=GeneID:905644;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1352 by TMHMM2.0 at aa 11-33 2C 54-76 2C 96-125 2C 138-160 2C180-202 2C 214-236 2C 241-263 2C 270-292 and 297-316 NC_002163.1 RefSeq region 1284896 1284955 . + . ID=id2415;gene=ceuB;Name=id2415;Dbxref=GeneID:905644;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1352 by TMHMM2.0 at aa 11-33 2C 54-76 2C 96-125 2C 138-160 2C180-202 2C 214-236 2C 241-263 2C 270-292 and 297-316 NC_002163.1 RefSeq CDS 1284969 1285907 . + 0 ID=cds1229;Parent=gene1300;gene=ceuC;Name=YP_002344741.1;Dbxref=GOA:Q0P8Q6 InterPro:IPR000522 UniProtKB FTrEMBL:Q0P8Q6 Genbank:YP_002344741.1 GeneID:905645;gbkey=CDS;product=enterochelin uptake permease;Note=Original 282000 29 note: Cj1353 2C ceuC 2C probable enterochelin uptake permease 2C len: 312 aa 3B highly similar to TR:Q46004 28EMBL:X88849 29 Campylobacter coli ceuC 28312 aa 29 2C fasta scores 3B opt: 1784 z-score: 2112.8 E 28 29: 0 2C 88.8 25 identity in 312 aa overlap 2C and similar to e.g. FATC_VIBAN ferric anguibactin transport system permease FATC 28317 aa 29 2C fasta scores 3B opt: 593 z-score: 708.6 E 28 29: 3.6e-32 2C 31.7 25 identity in 306 aa overlap. No Hp ortholog. Also similar to e.g. Cj1352 2827.2 25 identity in 316 aa overlap 29 2C and Cj1615 2827.5 25 identity in 298 aa overlap 29. Contains Pfam match to entry PF01032 FecCD_family 2C FecCD transport family 7EUpdated 282006 29 note: Nine probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Campylobacter coli 2Cso not added to product function. Functional classification - Transport 2Fbinding proteins - Cations 7EPMID:8574410 NC_002163.1 RefSeq gene 1284969 1285907 . + . ID=gene1300;gene=ceuC;Name=ceuC;locus_tag=Cj1353;Dbxref=GeneID:905645;gbkey=Gene NC_002163.1 RefSeq region 1284981 1285049 . + . ID=id2417;gene=ceuC;Name=id2417;Dbxref=GeneID:905645;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1353 by TMHMM2.0 at aa 5-27 2C 37-59 2C 64-86 2C 101-120 2C125-147 2C 170-192 2C 222-244 2C 259-281 and 288-307 NC_002163.1 RefSeq region 1284993 1285892 . + . ID=id2418;gene=ceuC;Name=id2418;Dbxref=GeneID:905645;gbkey=misc_feature;Note=HMMPfam hit to PF01032 2C FecCD transport family 2Cscore 3.3e-17 NC_002163.1 RefSeq region 1285077 1285145 . + . ID=id2417;gene=ceuC;Name=id2417;Dbxref=GeneID:905645;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1353 by TMHMM2.0 at aa 5-27 2C 37-59 2C 64-86 2C 101-120 2C125-147 2C 170-192 2C 222-244 2C 259-281 and 288-307 NC_002163.1 RefSeq region 1285158 1285226 . + . ID=id2417;gene=ceuC;Name=id2417;Dbxref=GeneID:905645;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1353 by TMHMM2.0 at aa 5-27 2C 37-59 2C 64-86 2C 101-120 2C125-147 2C 170-192 2C 222-244 2C 259-281 and 288-307 NC_002163.1 RefSeq region 1285269 1285328 . + . ID=id2417;gene=ceuC;Name=id2417;Dbxref=GeneID:905645;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1353 by TMHMM2.0 at aa 5-27 2C 37-59 2C 64-86 2C 101-120 2C125-147 2C 170-192 2C 222-244 2C 259-281 and 288-307 NC_002163.1 RefSeq region 1285341 1285409 . + . ID=id2417;gene=ceuC;Name=id2417;Dbxref=GeneID:905645;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1353 by TMHMM2.0 at aa 5-27 2C 37-59 2C 64-86 2C 101-120 2C125-147 2C 170-192 2C 222-244 2C 259-281 and 288-307 NC_002163.1 RefSeq region 1285476 1285544 . + . ID=id2417;gene=ceuC;Name=id2417;Dbxref=GeneID:905645;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1353 by TMHMM2.0 at aa 5-27 2C 37-59 2C 64-86 2C 101-120 2C125-147 2C 170-192 2C 222-244 2C 259-281 and 288-307 NC_002163.1 RefSeq region 1285632 1285700 . + . ID=id2417;gene=ceuC;Name=id2417;Dbxref=GeneID:905645;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1353 by TMHMM2.0 at aa 5-27 2C 37-59 2C 64-86 2C 101-120 2C125-147 2C 170-192 2C 222-244 2C 259-281 and 288-307 NC_002163.1 RefSeq region 1285743 1285811 . + . ID=id2417;gene=ceuC;Name=id2417;Dbxref=GeneID:905645;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1353 by TMHMM2.0 at aa 5-27 2C 37-59 2C 64-86 2C 101-120 2C125-147 2C 170-192 2C 222-244 2C 259-281 and 288-307 NC_002163.1 RefSeq region 1285830 1285889 . + . ID=id2417;gene=ceuC;Name=id2417;Dbxref=GeneID:905645;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1353 by TMHMM2.0 at aa 5-27 2C 37-59 2C 64-86 2C 101-120 2C125-147 2C 170-192 2C 222-244 2C 259-281 and 288-307 NC_002163.1 RefSeq gene 1285904 1286659 . + . ID=gene1301;gene=ceuD;Name=ceuD;locus_tag=Cj1354;Dbxref=GeneID:905646;gbkey=Gene NC_002163.1 RefSeq CDS 1285904 1286659 . + 0 ID=cds1230;Parent=gene1301;gene=ceuD;Name=YP_002344742.1;Dbxref=GOA:Q0P8Q5 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FTrEMBL:Q0P8Q5 Genbank:YP_002344742.1 GeneID:905646;gbkey=CDS;product=enterochelin uptake ATP-binding protein;Note=Original 282000 29 note: Cj1354 2C ceuD 2C probable enterochelin uptake ATP-binding protein 2C len: 251 aa 3B highly similar to TR:Q46005 28EMBL:X88849 29 Campylobacter coli ceuD 28251 aa 29 2C fasta scores 3B opt: 1258 z-score: 1347.9 E 28 29: 0 2C 82.5 25 identity in 246 aa overlap 2C and similar to e.g. FHUC_BACSU ferrichrome transport ATP-binding protein 28269 aa 29 2C fasta scores 3B opt: 613 z-score: 663.4 E 28 29: 1.2e-29 2C 38.0 25 identity in 245 aa overlap. No Hp ortholog. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00211 ABC transporters family signature 2C and Pfam match to entry PF00005 ABC_tran 2C ABC transporters 7EUpdated 282006 29 note: Characterised within Campylobacter coli 2C so not added to product function. Functional classification - Transport 2Fbinding proteins - Cations 7EPMID:8574410 NC_002163.1 RefSeq region 1285982 1286539 . + . ID=id2419;gene=ceuD;Name=id2419;Dbxref=GeneID:905646;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 9.3e-49 NC_002163.1 RefSeq region 1286003 1286026 . + . ID=id2420;gene=ceuD;Name=id2420;Dbxref=GeneID:905646;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 1286309 1286353 . + . ID=id2421;gene=ceuD;Name=id2421;Dbxref=GeneID:905646;gbkey=misc_feature;Note=PS00211 ABC transporters family signature ### NC_002163.1 RefSeq CDS 1286672 1287664 . + 0 ID=cds1231;Parent=gene1302;gene=ceuE;Name=YP_002344743.1;Dbxref=GOA:Q0P8Q4 InterPro:IPR002491 PDB:2CHU UniProtKB FTrEMBL:Q0P8Q4 Genbank:YP_002344743.1 GeneID:905647;gbkey=CDS;product=enterochelin uptake substrate-binding protein;Note=Original 282000 29 note: Cj1355 2C ceuE 2C probable enterochelin uptake periplasmic binding protein 2C len: 330 aa 3B highly similar to TR:Q46006 28EMBL:X88849 29 Campylobacter coli ceuE 28328 aa 29 2C fasta scores 3B opt: 1903 z-score: 2111.3 E 28 29: 0 2C 90.6 25 identity in 330 aa overlap 2Cand similar to e.g. FATB_VIBAN ferric anguibactin-binding protein precursor 28322 aa 29 2C fasta scores 3B opt: 540 z-score: 605.4 E 28 29: 2e-26 2C 30.1 25 identity in 279 aa overlap. No Hp match. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site 7EUpdated 282006 29 note: Characterised within Campylobacter coli 2C so not added to product function. Pfam domain PF01497 Periplasmic binding protein identified within CDS. Further support given to product function. Functional classification - Transport 2Fbinding proteins - Cations 7EPMID:8574410 NC_002163.1 RefSeq gene 1286672 1287664 . + . ID=gene1302;gene=ceuE;Name=ceuE;locus_tag=Cj1355;Dbxref=GeneID:905647;gbkey=Gene NC_002163.1 RefSeq region 1286702 1286734 . + . ID=id2422;gene=ceuE;Name=id2422;Dbxref=GeneID:905647;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1286879 1287589 . + . ID=id2423;gene=ceuE;Name=id2423;Dbxref=GeneID:905647;gbkey=misc_feature;Note=HMMPfam hit to PF01497 2C Periplasmic binding protein 2C score 1.2e-72 ### NC_002163.1 RefSeq gene 1287737 1287826 . - . ID=gene1303;gene=tRNASer;Name=tRNASer;locus_tag=Cjp25;Dbxref=GeneID:905648;gbkey=Gene NC_002163.1 RefSeq tRNA 1287737 1287826 . - . ID=rna40;Parent=gene1303;gene=tRNASer;Name=rna40;Dbxref=GeneID:905648;gbkey=tRNA;product=tRNA-Ser;Note=tRNA Ser anticodon GCT 2C Cove score 68.31 NC_002163.1 RefSeq exon 1287737 1287826 . - . ID=id2424;Parent=rna40;gene=tRNASer;Name=id2424;Dbxref=GeneID:905648;gbkey=tRNA;product=tRNA-Ser;Note=tRNA Ser anticodon GCT 2C Cove score 68.31 NC_002163.1 RefSeq CDS 1287890 1288444 . - 0 ID=cds1232;Parent=gene1304;Name=YP_002344744.1;Dbxref=UniProtKB FTrEMBL:Q0P8Q3 Genbank:YP_002344744.1 GeneID:905649;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj1356c 2C probable integral membrane protein 2C len: 184 aa 3B highly similar to TR:Q46007 28EMBL:X88849 29 Campylobacter coli ORF 28210 aa 29 2C fasta scores 3B opt: 545 z-score: 652.8 E 28 29: 4.6e-29 2C 67.1 25 identity in 210 aa overlap. 31.8 25 identity to HP0234 7EUpdated 282006 29 note: Three probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 1287890 1288444 . - . ID=gene1304;Name=Cj1356c;locus_tag=Cj1356c;Dbxref=GeneID:905649;gbkey=Gene NC_002163.1 RefSeq region 1287896 1287949 . - . ID=id121;Name=id121;Dbxref=GeneID:905649;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1356c by TMHMM2.0 at aa 13-35 2C 131-153 and 166-183 NC_002163.1 RefSeq region 1287986 1288054 . - . ID=id121;Name=id121;Dbxref=GeneID:905649;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1356c by TMHMM2.0 at aa 13-35 2C 131-153 and 166-183 NC_002163.1 RefSeq region 1288340 1288408 . - . ID=id121;Name=id121;Dbxref=GeneID:905649;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1356c by TMHMM2.0 at aa 13-35 2C 131-153 and 166-183 ### NC_002163.1 RefSeq CDS 1288580 1290412 . - 0 ID=cds1233;Parent=gene1305;gene=nrfA;Name=YP_002344745.1;Dbxref=GOA:Q0P8Q2 InterPro:IPR003321 InterPro:IPR011031 UniProtKB FTrEMBL:Q0P8Q2 Genbank:YP_002344745.1 GeneID:905650;gbkey=CDS;product=cytochrome C;Note=Original 282000 29 note: Cj1357c 2C probable periplasmic cytochrome C 2C len: 610 aa 3B similar to e.g. NRFA_ECOLI cytochrome C552 precursor 28478 aa 29 2C fasta scores 3B opt: 298 z-score: 333.9 E 28 29: 2.7e-11 2C 31.0 25 identity in 455 aa overlap. No Hp match. Contains probable N-terminal signal sequence and 5x PS00190 Cytochrome c family heme-binding site signature 7EUpdated 282006 29 note: Pfam domain PF02335 Cytochrome c552 was identified within CDS. Further support given to product function. Characterisation work carried out within Wolinella succinogenes 28PMID:10672190 2C PMID:10984487 29. Identity score was marginal. kept within product function. Functional classification - Energy metabolism -Electron transport 7EPMID:10672190 2C PMID:10984487 2C PMID:12095623 2CPMID:12618466 NC_002163.1 RefSeq gene 1288580 1290412 . - . ID=gene1305;gene=nrfA;Name=nrfA;locus_tag=Cj1357c;Dbxref=GeneID:905650;gbkey=Gene NC_002163.1 RefSeq region 1288634 1290307 . - . ID=id2425;gene=nrfA;Name=id2425;Dbxref=GeneID:905650;gbkey=misc_feature;Note=HMMPfam hit to PF02335 2C Cytochrome c552 2C score 1.9e-15 NC_002163.1 RefSeq region 1289153 1289170 . - . ID=id2426;gene=nrfA;Name=id2426;Dbxref=GeneID:905650;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature NC_002163.1 RefSeq region 1289246 1289263 . - . ID=id2427;gene=nrfA;Name=id2427;Dbxref=GeneID:905650;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature NC_002163.1 RefSeq region 1289624 1289641 . - . ID=id2428;gene=nrfA;Name=id2428;Dbxref=GeneID:905650;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature NC_002163.1 RefSeq region 1289765 1289782 . - . ID=id2429;gene=nrfA;Name=id2429;Dbxref=GeneID:905650;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature NC_002163.1 RefSeq region 1289948 1289965 . - . ID=id2430;gene=nrfA;Name=id2430;Dbxref=GeneID:905650;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature NC_002163.1 RefSeq region 1290347 1290400 . - . ID=id2431;gene=nrfA;Name=id2431;Dbxref=GeneID:905650;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1357c by TMHMM2.0 at aa 5-22 ### NC_002163.1 RefSeq CDS 1290427 1290942 . - 0 ID=cds1234;Parent=gene1306;gene=nrfH;Name=YP_002344746.1;Dbxref=InterPro:IPR005126 InterPro:IPR011031 InterPro:IPR017571 UniProtKB FTrEMBL:Q0P8Q1 Genbank:YP_002344746.1 GeneID:905651;gbkey=CDS;product=cytochrome C;Note=Original 282000 29 note: Cj1358c 2C probable periplasmic cytochrome C 2C len: 171 aa 3B similar to e.g. NAPC_ECOLI cytochrome C-type protein NAPC 28200 aa 29 2C fasta scores opt: 201 z-score: 242.9 E 28 29: 3.1e-06 2C 34.5 25 identity in 165 aa overlap. No Hp match. Contains probable N-terminal signal sequence and 3x PS00190 Cytochrome c family heme-binding site signature 7EUpdated 282006 29 note: Pfam domain PF03264 NapC 2FNirT cytochrome c family 2C N-terminal was identified within CDS. Further support given to product function. Characterisation work carried out within Wolinella succinogenes 28PMID:10672190 29. Identity score was marginal. was kept within product function. Functional classification - Energy metabolism - Electron transport 7EPMID:10672190 2C PMID:12095623 2C PMID:12618466 NC_002163.1 RefSeq gene 1290427 1290942 . - . ID=gene1306;gene=nrfH;Name=nrfH;locus_tag=Cj1358c;Dbxref=GeneID:905651;gbkey=Gene NC_002163.1 RefSeq region 1290433 1290909 . - . ID=id2432;gene=nrfH;Name=id2432;Dbxref=GeneID:905651;gbkey=misc_feature;Note=HMMPfam hit to PF03264 2C NapC 2FNirT cytochrome c family 2C N-termin 2C score 8.9e-12 NC_002163.1 RefSeq region 1290454 1290471 . - . ID=id2433;gene=nrfH;Name=id2433;Dbxref=GeneID:905651;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature NC_002163.1 RefSeq region 1290688 1290705 . - . ID=id2434;gene=nrfH;Name=id2434;Dbxref=GeneID:905651;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature NC_002163.1 RefSeq region 1290778 1290795 . - . ID=id2435;gene=nrfH;Name=id2435;Dbxref=GeneID:905651;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature NC_002163.1 RefSeq region 1290838 1290906 . - . ID=id2436;gene=nrfH;Name=id2436;Dbxref=GeneID:905651;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1358c by TMHMM2.0 at aa 13-35 ### NC_002163.1 UTR_Extractor 5'-UTR 1290943 1290996 . - . ID=utr492;locus_tag=Cj1358c;product=putative periplasmic cytochrome C NC_002163.1 RefSeq gene 1291131 1293215 . + . ID=gene1307;gene=ppk;Name=ppk;locus_tag=Cj1359;Dbxref=GeneID:905652;gbkey=Gene NC_002163.1 RefSeq CDS 1291131 1293215 . + 0 ID=cds1235;Parent=gene1307;gene=ppk;Name=YP_002344747.1;Dbxref=GOA:Q9PMU0 InterPro:IPR003414 UniProtKB FSwiss-Prot:Q9PMU0 Genbank:YP_002344747.1 GeneID:905652;gbkey=CDS;product=polyphosphate kinase;Note=catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate NC_002163.1 RefSeq region 1291143 1293137 . + . ID=id2437;gene=ppk;Name=id2437;Dbxref=GeneID:905652;gbkey=misc_feature;Note=HMMPfam hit to PF02503 2C Polyphosphate kinase 2C score 0 ### NC_002163.1 RefSeq gene 1293300 1293658 . - . ID=gene1308;Name=Cjs01;locus_tag=Cjs01;Dbxref=GeneID:3245046;gbkey=Gene NC_002163.1 RefSeq transcript 1293300 1293658 . - . ID=rna41;Parent=gene1308;Name=tmRNA;Dbxref=GeneID:3245046;gbkey=misc_RNA;Note=10Sa RNA 28tmRNA 29 2C Proteolysis Tag: 28A 29ANNVKFAPAYAKAA 7EUpdated 282006 29 note: Rfam domain RF00023 2C tmRNA also identified within CDS. Further support given to product function NC_002163.1 RefSeq exon 1293300 1293658 . - . ID=id2438;Parent=rna41;Name=id2438;Dbxref=GeneID:3245046;gbkey=misc_RNA;Note=10Sa RNA 28tmRNA 29 2C Proteolysis Tag: 28A 29ANNVKFAPAYAKAA 7EUpdated 282006 29 note: Rfam domain RF00023 2C tmRNA also identified within CDS. Further support given to product function NC_002163.1 RefSeq gene 1293659 1294111 . - . ID=gene1309;Name=Cj1361c;locus_tag=Cj1361c;Dbxref=GeneID:905654;gbkey=Gene NC_002163.1 RefSeq CDS 1293659 1294111 . - 0 ID=cds1236;Parent=gene1309;Name=YP_002344749.1;Dbxref=GOA:Q0P8P8 UniProtKB FTrEMBL:Q0P8P8 Genbank:YP_002344749.1 GeneID:905654;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1361c 2C unknown 2C len: 150 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 UTR_Extractor 5'-UTR 1294130 1294159 . + . ID=utr493;locus_tag=Cj1362;product=Holliday junction DNA helicase RuvB NC_002163.1 RefSeq CDS 1294160 1295167 . + 0 ID=cds1237;Parent=gene1310;gene=ruvB;Name=YP_002344750.1;Dbxref=GOA:Q9PMT7 HSSP:Q56313 InterPro:IPR003593 InterPro:IPR003959 InterPro:IPR004605 InterPro:IPR008823 InterPro:IPR008824 InterPro:IPR011991 UniProtKB FSwiss-Prot:Q9PMT7 Genbank:YP_002344750.1 GeneID:905655;gbkey=CDS;product=Holliday junction DNA helicase RuvB;Note=promotes strand exchange during homologous recombination 3B RuvAB complex promotes branch migration 3B RuvABC complex scans the DNA during branch migration and resolves Holliday junctions at consensus sequences 3B forms hexameric rings around opposite DNA arms 3B requires ATP for branch migration and orientation of RuvAB complex determines direction of migration NC_002163.1 RefSeq gene 1294160 1295167 . + . ID=gene1310;gene=ruvB;Name=ruvB;locus_tag=Cj1362;Dbxref=GeneID:905655;gbkey=Gene NC_002163.1 RefSeq region 1294163 1294318 . + . ID=id2439;gene=ruvB;Name=id2439;Dbxref=GeneID:905655;gbkey=misc_feature;Note=HMMPfam hit to PF05496 2C Holliday junction DNA helicase ruvB N-termin 2C score 1.3e-26 NC_002163.1 RefSeq region 1294319 1294858 . + . ID=id2440;gene=ruvB;Name=id2440;Dbxref=GeneID:905655;gbkey=misc_feature;Note=HMMPfam hit to PF00004 2C ATPase family associated with various cellul 2C score 5.5e-28 NC_002163.1 RefSeq region 1294334 1294357 . + . ID=id2441;gene=ruvB;Name=id2441;Dbxref=GeneID:905655;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 1294907 1295140 . + . ID=id2442;gene=ruvB;Name=id2442;Dbxref=GeneID:905655;gbkey=misc_feature;Note=HMMPfam hit to PF05491 2C Holliday junction DNA helicase ruvB C-termin 2C score 4.6e-39 ### NC_002163.1 RefSeq CDS 1295171 1296214 . + 0 ID=cds1238;Parent=gene1311;gene=amaA;Name=YP_002344751.1;Dbxref=GOA:Q0P8P6 InterPro:IPR002549 UniProtKB FTrEMBL:Q0P8P6 Genbank:YP_002344751.1 GeneID:905656;gbkey=CDS;product=acid membrane antigen A;Note=Original 282000 29 note: Cj1363 2C amaA 2C acid membrane antigen A 2C len: 347 aa 3B similar to many hypothetical membrane proteins e.g. TR:O66948 28EMBL:AE000705 29 Aquifex aeolicus AQ_740 28353 aa 29 2C fasta scores 3B opt: 268 z-score: 311.7 E 28 29: 4.6e-10 2C 24.1 25 identity in 352 aa overlap. 32.2 25 identity to HP0567. Identical in part to TR:O69293 28EMBL:Y16882 29 C. jejuni predicted outer membrane protein from rearranged lambda clone 28364 aa 29. 28Phillippa Connerton 28p.connerton@ic.ac.uk 29 pers. comm. 29 7EUpdated 282006 29 note: Seven probable transmembrane helices predicted by TMHMM2.0. Pfam domain PF01594 Domain of unknown function DUF20 also identified within CDS. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 1295171 1296214 . + . ID=gene1311;gene=amaA;Name=amaA;locus_tag=Cj1363;Dbxref=GeneID:905656;gbkey=Gene NC_002163.1 RefSeq region 1295186 1296187 . + . ID=id2443;gene=amaA;Name=id2443;Dbxref=GeneID:905656;gbkey=misc_feature;Note=HMMPfam hit to PF01594 2C Domain of unknown function DUF20 2C score 3.5e-68 NC_002163.1 RefSeq region 1295189 1295293 . + . ID=id2444;gene=amaA;Name=id2444;Dbxref=GeneID:905656;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1363 by TMHMM2.0 at aa 7-41 2C 56-78 2C 157-179 2C 194-216 2C225-247 2C 262-284 and 305-327 NC_002163.1 RefSeq region 1295336 1295404 . + . ID=id2444;gene=amaA;Name=id2444;Dbxref=GeneID:905656;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1363 by TMHMM2.0 at aa 7-41 2C 56-78 2C 157-179 2C 194-216 2C225-247 2C 262-284 and 305-327 NC_002163.1 RefSeq region 1295639 1295707 . + . ID=id2444;gene=amaA;Name=id2444;Dbxref=GeneID:905656;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1363 by TMHMM2.0 at aa 7-41 2C 56-78 2C 157-179 2C 194-216 2C225-247 2C 262-284 and 305-327 NC_002163.1 RefSeq region 1295750 1295818 . + . ID=id2444;gene=amaA;Name=id2444;Dbxref=GeneID:905656;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1363 by TMHMM2.0 at aa 7-41 2C 56-78 2C 157-179 2C 194-216 2C225-247 2C 262-284 and 305-327 NC_002163.1 RefSeq region 1295843 1295911 . + . ID=id2444;gene=amaA;Name=id2444;Dbxref=GeneID:905656;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1363 by TMHMM2.0 at aa 7-41 2C 56-78 2C 157-179 2C 194-216 2C225-247 2C 262-284 and 305-327 NC_002163.1 RefSeq region 1295954 1296022 . + . ID=id2444;gene=amaA;Name=id2444;Dbxref=GeneID:905656;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1363 by TMHMM2.0 at aa 7-41 2C 56-78 2C 157-179 2C 194-216 2C225-247 2C 262-284 and 305-327 NC_002163.1 RefSeq region 1296083 1296151 . + . ID=id2444;gene=amaA;Name=id2444;Dbxref=GeneID:905656;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1363 by TMHMM2.0 at aa 7-41 2C 56-78 2C 157-179 2C 194-216 2C225-247 2C 262-284 and 305-327 ### NC_002163.1 RefSeq CDS 1296244 1297635 . - 0 ID=cds1239;Parent=gene1312;gene=fumC;Name=YP_002344752.1;Dbxref=GOA:O69294 HSSP:P05042 InterPro:IPR000362 InterPro:IPR003031 InterPro:IPR005677 UniProtKB FSwiss-Prot:O69294 Genbank:YP_002344752.1 GeneID:905657;gbkey=CDS;product=fumarate hydratase;Note=class II family 28does not require metal 29 3B tetrameric enzyme 3B fumarase C 3B reversibly converts 28S 29-malate to fumarate and water 3B functions in the TCA cycle NC_002163.1 RefSeq gene 1296244 1297635 . - . ID=gene1312;gene=fumC;Name=fumC;locus_tag=Cj1364c;Dbxref=GeneID:905657;gbkey=Gene NC_002163.1 RefSeq region 1296613 1297605 . - . ID=id2445;gene=fumC;Name=id2445;Dbxref=GeneID:905657;gbkey=misc_feature;Note=HMMPfam hit to PF00206 2C Lyase 2C score 3.2e-163 NC_002163.1 RefSeq region 1296661 1296690 . - . ID=id2446;gene=fumC;Name=id2446;Dbxref=GeneID:905657;gbkey=misc_feature;Note=PS00163 Fumarate lyases signature ### NC_002163.1 RefSeq CDS 1297691 1300816 . - 0 ID=cds1240;Parent=gene1313;Name=YP_002344753.1;Dbxref=GOA:Q0P8P4 InterPro:IPR000209 InterPro:IPR005546 InterPro:IPR013425 InterPro:IPR015500 InterPro:IPR017318 UniProtKB FTrEMBL:Q0P8P4 Genbank:YP_002344753.1 GeneID:905658;gbkey=CDS;product=serine protease;Note=Original 282000 29 note: Cj1365c 2C probable secreted serine protease 2C len: 1041 aa 3B similar to e.g. TR:Q54484 28EMBL:D78380 29 Serratia marcescens serine protease homologue SSP-H2 281034 aa 29 2C fasta scores 3B opt: 245 z-score: 257.1 E 28 29: 5.1e-07 2C 23.5 25 identity in 591 aa overlap 2C and PRTS_SERMA extracellular serine protease precursor 28EC 3.4.21.- 29 281045 aa 29 2C fasta scores 3B opt: 205 z-score: 214.6 E 28 29: 0.00012 2C 23.7 25 identity in 615 aa overlap. No Hp match. Contains PS00137 Serine proteases 2Csubtilase family 2C histidine active site 2C PS00138 Serine proteases 2C subtilase family 2C serine active site 2C Pfam match to entry PF00082 subtilase 2C Subtilase family of serine proteases 2C and probable N-terminal signal sequence 7EUpdated 282006 29 note: Specific characterisation with acceptable identity scores not carried out yet 2C so kept within product function. Functional classification - Degradation of macromolecules - Proteins 2Cpeptides and glycopeptides NC_002163.1 RefSeq gene 1297691 1300816 . - . ID=gene1313;Name=Cj1365c;locus_tag=Cj1365c;Dbxref=GeneID:905658;gbkey=Gene NC_002163.1 RefSeq region 1297718 1298494 . - . ID=id2447;Name=id2447;Dbxref=GeneID:905658;gbkey=misc_feature;Note=HMMPfam hit to PF03797 2C Autotransporter beta-domain 2C score 3.7e-37 NC_002163.1 RefSeq region 1299773 1300762 . - . ID=id2448;Name=id2448;Dbxref=GeneID:905658;gbkey=misc_feature;Note=HMMPfam hit to PF00082 2C Subtilase family 2C score 6.3e-11 NC_002163.1 RefSeq region 1299917 1299949 . - . ID=id2449;Name=id2449;Dbxref=GeneID:905658;gbkey=misc_feature;Note=PS00138 Serine proteases 2C subtilase family 2C serine active site NC_002163.1 RefSeq region 1300547 1300579 . - . ID=id2450;Name=id2450;Dbxref=GeneID:905658;gbkey=misc_feature;Note=PS00137 Serine proteases 2C subtilase family 2Chistidine active site ### NC_002163.1 RefSeq CDS 1300819 1302615 . - 0 ID=cds1241;Parent=gene1314;gene=glmS;Name=YP_002344754.1;Dbxref=GOA:Q9PMT4 HSSP:P17169 InterPro:IPR000583 InterPro:IPR001347 InterPro:IPR005855 UniProtKB FSwiss-Prot:Q9PMT4 Genbank:YP_002344754.1 GeneID:905659;gbkey=CDS;product=glucosamine--fructose-6-phosphate aminotransferase;Note=Catalyzes the first step in hexosamine metabolism 2C converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source NC_002163.1 RefSeq gene 1300819 1302615 . - . ID=gene1314;gene=glmS;Name=glmS;locus_tag=Cj1366c;Dbxref=GeneID:905659;gbkey=Gene NC_002163.1 RefSeq region 1300864 1301265 . - . ID=id2451;gene=glmS;Name=id2451;Dbxref=GeneID:905659;gbkey=misc_feature;Note=HMMPfam hit to PF01380 2C SIS domain 2C score 0.00048 NC_002163.1 RefSeq region 1301365 1301769 . - . ID=id2452;gene=glmS;Name=id2452;Dbxref=GeneID:905659;gbkey=misc_feature;Note=HMMPfam hit to PF01380 2C SIS domain 2C score 3e-39 NC_002163.1 RefSeq region 1302031 1302612 . - . ID=id2453;gene=glmS;Name=id2453;Dbxref=GeneID:905659;gbkey=misc_feature;Note=HMMPfam hit to PF00310 2C Glutamine amidotransferases class-II 2C score 9.2e-23 NC_002163.1 RefSeq region 1302598 1302615 . - . ID=id2454;gene=glmS;Name=id2454;Dbxref=GeneID:905659;gbkey=misc_feature;Note=PS00443 Glutamine amidotransferases class-II active site ### NC_002163.1 UTR_Extractor 5'-UTR 1302616 1302841 . - . ID=utr494;locus_tag=Cj1366c;product=glucosamine--fructose-6-phosphate aminotransferase NC_002163.1 RefSeq gene 1302620 1304968 . - . ID=gene1315;Name=Cj1367c;locus_tag=Cj1367c;Dbxref=GeneID:905660;gbkey=Gene NC_002163.1 RefSeq CDS 1302620 1304968 . - 0 ID=cds1242;Parent=gene1315;Name=YP_002344755.1;Dbxref=GOA:Q0P8P2 UniProtKB FTrEMBL:Q0P8P2 Genbank:YP_002344755.1 GeneID:905660;gbkey=CDS;product=nucleotidyltransferase;Note=Original 282000 29 note: Cj1367c 2C possible nucleotidyltransferase 2C len: 782 aa 3B weak similarity to TR:Q53245 28EMBL:U47030 29 Rhizobium tropici uridylyltransferase 2Furidylyl-removing enzyme 28971 aa 29 2Cfasta scores 3B opt: 202 z-score: 226.1 E 28 29: 2.7e-05 2C 19.7 25 identity in 857 aa overlap 2C and GLND_HAEIN 5Bprotein-PII 5D uridylyltransferase 28863 aa 29 2C fasta scores 3B opt: 119 z-score: 133.2 E 28 29: 4 2C 19.5 25 identity in 822 aa overlap 2C 28blastp score 3B E 3D4.3e-07 29. No Hp match. Contains C 281-2 29 polymorphic region at aa 148 3B C 282 29 28consensus 29 gives this ORF 2C C 281 29 gives truncation after 2B8 aa 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score carried out yet 2C so kept within product funciton. Functional classification - Misc ### NC_002163.1 UTR_Extractor 5'-UTR 1304969 1305000 . - . ID=utr495;locus_tag=Cj1367c;product=putative nucleotidyltransferase NC_002163.1 UTR_Extractor 5'-UTR 1305082 1305111 . + . ID=utr496;locus_tag=Cj1368;product=hypothetical protein NC_002163.1 RefSeq gene 1305112 1306176 . + . ID=gene1316;Name=Cj1368;locus_tag=Cj1368;Dbxref=GeneID:905661;gbkey=Gene NC_002163.1 RefSeq CDS 1305112 1306176 . + 0 ID=cds1243;Parent=gene1316;Name=YP_002344756.1;Dbxref=GOA:Q0P8P1 InterPro:IPR005244 InterPro:IPR006638 InterPro:IPR007197 InterPro:IPR013785 UniProtKB FTrEMBL:Q0P8P1 Genbank:YP_002344756.1 GeneID:905661;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1368 2C unknown 2C len: 354 aa 3B similar to hypothetical proteins e.g. TR:O66888 28EMBL:AE000700 29 Aquifex aeolicus AQ_648 28371 aa 29 2C fasta scores 3B opt: 956 z-score: 1117.5 E 28 29: 0 2C 44.1 25 identity in 349 aa overlap. 57.4 25 identity to HP0654. Also similar to Cj0462 2835.5 25 identity in 349 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF04055 Radical SAM superfamily identified within CDS. Product modified to more specific family member based on motif match. No specific characterisation carried out yet 2C so kept within product function. Functional classification -Misc NC_002163.1 RefSeq region 1305271 1305789 . + . ID=id2455;Name=id2455;Dbxref=GeneID:905661;gbkey=misc_feature;Note=HMMPfam hit to PF04055 2C Radical SAM superfamily 2Cscore 2.2e-16 ### NC_002163.1 RefSeq CDS 1306186 1307505 . + 0 ID=cds1244;Parent=gene1317;Name=YP_002344757.1;Dbxref=GOA:Q0P8P0 InterPro:IPR006043 UniProtKB FTrEMBL:Q0P8P0 Genbank:YP_002344757.1 GeneID:905662;gbkey=CDS;product=permease;Note=Original 282000 29 note: Cj1369 2C probable transmembrane transport protein 2C len: 439 aa 3B similar to many hypothetical membrane proteins e.g. YJCD_ECOLI 28449 aa 29 2C fasta scores 3B opt: 897 z-score: 1039.1 E 28 29: 0 2C 34.7 25 identity in 429 aa overlap. 50.7 25 identity to HP1175. Contains Pfam match to entry PF00860 xan_ur_permease 2CXanthine 2Furacil permeases family 7EUpdated 282006 29 note: Pfam domain PF00860 Permease family protein identified within CDS. Also 2C thirteen probable transmembrane helices predicted by TMHMM2.0. Product modified to more specific family member based on motif search. No specific characterisation has been been carried out yet 2C so kept within product function. Functional classification - Transport 2Fbinding proteins -Other NC_002163.1 RefSeq gene 1306186 1307505 . + . ID=gene1317;Name=Cj1369;locus_tag=Cj1369;Dbxref=GeneID:905662;gbkey=Gene NC_002163.1 RefSeq region 1306225 1307385 . + . ID=id2456;Name=id2456;Dbxref=GeneID:905662;gbkey=misc_feature;Note=HMMPfam hit to PF00860 2C Permease family 2C score 4e-21 NC_002163.1 RefSeq region 1306234 1306302 . + . ID=id2457;Name=id2457;Dbxref=GeneID:905662;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1369 by TMHMM2.0 at aa 17-39 2C 44-66 2C 73-95 2C 100-122 2C131-153 2C 168-186 2C 191-208 2C 246-268 2C 289-311 2C 321-343 2C350-367 2C 377-408 and 420-438 NC_002163.1 RefSeq region 1306315 1306383 . + . ID=id2457;Name=id2457;Dbxref=GeneID:905662;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1369 by TMHMM2.0 at aa 17-39 2C 44-66 2C 73-95 2C 100-122 2C131-153 2C 168-186 2C 191-208 2C 246-268 2C 289-311 2C 321-343 2C350-367 2C 377-408 and 420-438 NC_002163.1 RefSeq region 1306402 1306470 . + . ID=id2457;Name=id2457;Dbxref=GeneID:905662;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1369 by TMHMM2.0 at aa 17-39 2C 44-66 2C 73-95 2C 100-122 2C131-153 2C 168-186 2C 191-208 2C 246-268 2C 289-311 2C 321-343 2C350-367 2C 377-408 and 420-438 NC_002163.1 RefSeq region 1306483 1306551 . + . ID=id2457;Name=id2457;Dbxref=GeneID:905662;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1369 by TMHMM2.0 at aa 17-39 2C 44-66 2C 73-95 2C 100-122 2C131-153 2C 168-186 2C 191-208 2C 246-268 2C 289-311 2C 321-343 2C350-367 2C 377-408 and 420-438 NC_002163.1 RefSeq region 1306576 1306644 . + . ID=id2457;Name=id2457;Dbxref=GeneID:905662;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1369 by TMHMM2.0 at aa 17-39 2C 44-66 2C 73-95 2C 100-122 2C131-153 2C 168-186 2C 191-208 2C 246-268 2C 289-311 2C 321-343 2C350-367 2C 377-408 and 420-438 NC_002163.1 RefSeq region 1306687 1306743 . + . ID=id2457;Name=id2457;Dbxref=GeneID:905662;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1369 by TMHMM2.0 at aa 17-39 2C 44-66 2C 73-95 2C 100-122 2C131-153 2C 168-186 2C 191-208 2C 246-268 2C 289-311 2C 321-343 2C350-367 2C 377-408 and 420-438 NC_002163.1 RefSeq region 1306756 1306809 . + . ID=id2457;Name=id2457;Dbxref=GeneID:905662;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1369 by TMHMM2.0 at aa 17-39 2C 44-66 2C 73-95 2C 100-122 2C131-153 2C 168-186 2C 191-208 2C 246-268 2C 289-311 2C 321-343 2C350-367 2C 377-408 and 420-438 NC_002163.1 RefSeq region 1306921 1306989 . + . ID=id2457;Name=id2457;Dbxref=GeneID:905662;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1369 by TMHMM2.0 at aa 17-39 2C 44-66 2C 73-95 2C 100-122 2C131-153 2C 168-186 2C 191-208 2C 246-268 2C 289-311 2C 321-343 2C350-367 2C 377-408 and 420-438 NC_002163.1 RefSeq region 1307050 1307118 . + . ID=id2457;Name=id2457;Dbxref=GeneID:905662;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1369 by TMHMM2.0 at aa 17-39 2C 44-66 2C 73-95 2C 100-122 2C131-153 2C 168-186 2C 191-208 2C 246-268 2C 289-311 2C 321-343 2C350-367 2C 377-408 and 420-438 NC_002163.1 RefSeq region 1307146 1307214 . + . ID=id2457;Name=id2457;Dbxref=GeneID:905662;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1369 by TMHMM2.0 at aa 17-39 2C 44-66 2C 73-95 2C 100-122 2C131-153 2C 168-186 2C 191-208 2C 246-268 2C 289-311 2C 321-343 2C350-367 2C 377-408 and 420-438 NC_002163.1 RefSeq region 1307233 1307286 . + . ID=id2457;Name=id2457;Dbxref=GeneID:905662;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1369 by TMHMM2.0 at aa 17-39 2C 44-66 2C 73-95 2C 100-122 2C131-153 2C 168-186 2C 191-208 2C 246-268 2C 289-311 2C 321-343 2C350-367 2C 377-408 and 420-438 NC_002163.1 RefSeq region 1307314 1307409 . + . ID=id2457;Name=id2457;Dbxref=GeneID:905662;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1369 by TMHMM2.0 at aa 17-39 2C 44-66 2C 73-95 2C 100-122 2C131-153 2C 168-186 2C 191-208 2C 246-268 2C 289-311 2C 321-343 2C350-367 2C 377-408 and 420-438 NC_002163.1 RefSeq region 1307443 1307499 . + . ID=id2457;Name=id2457;Dbxref=GeneID:905662;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1369 by TMHMM2.0 at aa 17-39 2C 44-66 2C 73-95 2C 100-122 2C131-153 2C 168-186 2C 191-208 2C 246-268 2C 289-311 2C 321-343 2C350-367 2C 377-408 and 420-438 ### NC_002163.1 RefSeq region 1307519 1307914 . + . ID=id2458;Name=id2458;Dbxref=GeneID:905663;gbkey=misc_feature;Note=HMMPfam hit to PF00156 2C Phosphoribosyl transferase domain 2C score 1.2e-06 NC_002163.1 RefSeq gene 1307519 1307962 . + . ID=gene1318;Name=Cj1370;locus_tag=Cj1370;Dbxref=GeneID:905663;gbkey=Gene NC_002163.1 RefSeq CDS 1307519 1307962 . + 0 ID=cds1245;Parent=gene1318;Name=YP_002344758.1;Dbxref=GOA:Q0P8N9 InterPro:IPR000836 InterPro:IPR002375 UniProtKB FTrEMBL:Q0P8N9 Genbank:YP_002344758.1 GeneID:905663;gbkey=CDS;product=nucleotide phosphoribosyltransferase;Note=Original 282000 29 note: Cj1370 2C possible nucleotide phosphoribosyltransferase 2C len: 147 aa 3B similar to e.g. TR:O50284 28EMBL:AF035967 29 hypoxanthine ribosyl transferase 28176 aa 29 2C fasta scores 3B opt: 158 z-score: 205.5 E 28 29: 0.00038 2C 26.2 25 identity in 145 aa overlap 2C and XGPT_ECOLI xanthine-guanine phosphoribosyltransferase 28152 aa 29 2C fasta scores 3B opt: 128 z-score: 170.3 E 28 29: 0.035 2C 24.6 25 identity in 142 aa overlap. 39.5 25 identity to HP0735. Contains PS00103 Purine 2Fpyrimidine phosphoribosyl transferases signature 7EUpdated 282006 29 note: Pfam domain PF00156 Phosphoribosyl transferase domain identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score carried out yet 2C so kept within product function. Functional classification - Salvage of nucleosides and nucleotides NC_002163.1 RefSeq region 1307765 1307803 . + . ID=id2459;Name=id2459;Dbxref=GeneID:905663;gbkey=misc_feature;Note=PS00103 Purine 2Fpyrimidine phosphoribosyl transferases signature ### NC_002163.1 UTR_Extractor 5'-UTR 1307982 1308006 . + . ID=utr497;locus_tag=Cj1371;product=putative periplasmic protein NC_002163.1 RefSeq gene 1308007 1308705 . + . ID=gene1319;Name=Cj1371;locus_tag=Cj1371;Dbxref=GeneID:905664;gbkey=Gene NC_002163.1 RefSeq CDS 1308007 1308705 . + 0 ID=cds1246;Parent=gene1319;Name=YP_002344759.1;Dbxref=GOA:Q0P8N8 InterPro:IPR007428 UniProtKB FTrEMBL:Q0P8N8 Genbank:YP_002344759.1 GeneID:905664;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1371 2C probable periplasmic protein 28vacJ homolog 29 2C len: 232 aa 3B similar to e.g. VACJ_SHIFL VACJ lipoprotein precursor 28required for intercellular spreading of Shigella flexneri 29 28251 aa 29 2Cfasta scores 3B opt: 310 z-score: 377.2 E 28 29: 1e-13 2C 32.5 25 identity in 197 aa overlap. No Hp match. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF04333 VacJ like lipoprotein identitied within CDS. Further support given to product function. kept within product function. Functional classification - Pathogenicity 7EPMID:8145644 NC_002163.1 RefSeq region 1308100 1308702 . + . ID=id2460;Name=id2460;Dbxref=GeneID:905664;gbkey=misc_feature;Note=HMMPfam hit to PF04333 2C VacJ like lipoprotein 2Cscore 1.9e-116 ### NC_002163.1 RefSeq CDS 1308715 1309284 . + 0 ID=cds1247;Parent=gene1320;Name=YP_002344760.1;Dbxref=InterPro:IPR008869 UniProtKB FTrEMBL:Q0P8N7 Genbank:YP_002344760.1 GeneID:905665;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1372 2C probable periplasmic protein 2C len: 189 aa 3B similar to e.g. YRBC_ECOLI 28211 aa 29 2Cfasta scores 3B opt: 189 z-score: 222.3 E 28 29: 4.4e-05 2C 22.5 25 identity in 200 aa overlap. No Hp match. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF05494 Toluene tolerance 2C Ttg2 identified within CDS. This family is a transporter which shows similarity to ABC transporters. No specific characterisation with acceptable identity score carried out yet 2C so kept within product function. Functional classification - Miscellaneous periplasmic proteins 7EPMID:9658016 NC_002163.1 RefSeq gene 1308715 1309284 . + . ID=gene1320;Name=Cj1372;locus_tag=Cj1372;Dbxref=GeneID:905665;gbkey=Gene NC_002163.1 RefSeq region 1308754 1309275 . + . ID=id2461;Name=id2461;Dbxref=GeneID:905665;gbkey=misc_feature;Note=HMMPfam hit to PF05494 2C Toluene tolerance 2C Ttg2 2Cscore 3.8e-69 NC_002163.1 RefSeq gene 1309284 1311755 . + . ID=gene1321;Name=Cj1373;locus_tag=Cj1373;Dbxref=GeneID:905666;gbkey=Gene NC_002163.1 RefSeq CDS 1309284 1311755 . + 0 ID=cds1248;Parent=gene1321;Name=YP_002344761.1;Dbxref=GOA:Q0P8N6 InterPro:IPR000731 UniProtKB FTrEMBL:Q0P8N6 Genbank:YP_002344761.1 GeneID:905666;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj1373 2C probable integral membrane protein 2C len: 823 aa 3B similar to hypothetical membrane proteins e.g. TR:O51268 28EMBL:AE001135 29 Borrelia burgdorferi conserved hypothetical integral membrane protein 28767 aa 29 2C fasta scores 3B opt: 331 z-score: 348.2 E 28 29: 4.2e-12 2C 24.8 25 identity in 840 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02460 Patched family protein identified within CDS. Prosite domain PS50156 SSD x2 2C Sterol-sensing 5TM box was also identified within CDS. Also 2C thirteen probable transmembrane helices predicted by TMHMM2.0. No specific characterisation carried out yet 2C so kept within product function. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 1309326 1309379 . + . ID=id2462;Name=id2462;Dbxref=GeneID:905666;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1373 by TMHMM2.0 at aa 15-32 2C 228-245 2C 249-268 2C 273-295 2C299-321 2C 353-375 2C 379-401 2C 433-450 2C 651-673 2C 680-702 2C706-728 2C 748-770 and 780-802 NC_002163.1 RefSeq region 1309965 1310018 . + . ID=id2462;Name=id2462;Dbxref=GeneID:905666;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1373 by TMHMM2.0 at aa 15-32 2C 228-245 2C 249-268 2C 273-295 2C299-321 2C 353-375 2C 379-401 2C 433-450 2C 651-673 2C 680-702 2C706-728 2C 748-770 and 780-802 NC_002163.1 RefSeq region 1310028 1310087 . + . ID=id2462;Name=id2462;Dbxref=GeneID:905666;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1373 by TMHMM2.0 at aa 15-32 2C 228-245 2C 249-268 2C 273-295 2C299-321 2C 353-375 2C 379-401 2C 433-450 2C 651-673 2C 680-702 2C706-728 2C 748-770 and 780-802 NC_002163.1 RefSeq region 1310100 1310168 . + . ID=id2462;Name=id2462;Dbxref=GeneID:905666;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1373 by TMHMM2.0 at aa 15-32 2C 228-245 2C 249-268 2C 273-295 2C299-321 2C 353-375 2C 379-401 2C 433-450 2C 651-673 2C 680-702 2C706-728 2C 748-770 and 780-802 NC_002163.1 RefSeq region 1310178 1310246 . + . ID=id2462;Name=id2462;Dbxref=GeneID:905666;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1373 by TMHMM2.0 at aa 15-32 2C 228-245 2C 249-268 2C 273-295 2C299-321 2C 353-375 2C 379-401 2C 433-450 2C 651-673 2C 680-702 2C706-728 2C 748-770 and 780-802 NC_002163.1 RefSeq region 1310340 1310408 . + . ID=id2462;Name=id2462;Dbxref=GeneID:905666;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1373 by TMHMM2.0 at aa 15-32 2C 228-245 2C 249-268 2C 273-295 2C299-321 2C 353-375 2C 379-401 2C 433-450 2C 651-673 2C 680-702 2C706-728 2C 748-770 and 780-802 NC_002163.1 RefSeq region 1310418 1310486 . + . ID=id2462;Name=id2462;Dbxref=GeneID:905666;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1373 by TMHMM2.0 at aa 15-32 2C 228-245 2C 249-268 2C 273-295 2C299-321 2C 353-375 2C 379-401 2C 433-450 2C 651-673 2C 680-702 2C706-728 2C 748-770 and 780-802 NC_002163.1 RefSeq region 1310580 1310633 . + . ID=id2462;Name=id2462;Dbxref=GeneID:905666;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1373 by TMHMM2.0 at aa 15-32 2C 228-245 2C 249-268 2C 273-295 2C299-321 2C 353-375 2C 379-401 2C 433-450 2C 651-673 2C 680-702 2C706-728 2C 748-770 and 780-802 NC_002163.1 RefSeq region 1311234 1311302 . + . ID=id2462;Name=id2462;Dbxref=GeneID:905666;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1373 by TMHMM2.0 at aa 15-32 2C 228-245 2C 249-268 2C 273-295 2C299-321 2C 353-375 2C 379-401 2C 433-450 2C 651-673 2C 680-702 2C706-728 2C 748-770 and 780-802 NC_002163.1 RefSeq region 1311321 1311389 . + . ID=id2462;Name=id2462;Dbxref=GeneID:905666;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1373 by TMHMM2.0 at aa 15-32 2C 228-245 2C 249-268 2C 273-295 2C299-321 2C 353-375 2C 379-401 2C 433-450 2C 651-673 2C 680-702 2C706-728 2C 748-770 and 780-802 NC_002163.1 RefSeq region 1311399 1311467 . + . ID=id2462;Name=id2462;Dbxref=GeneID:905666;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1373 by TMHMM2.0 at aa 15-32 2C 228-245 2C 249-268 2C 273-295 2C299-321 2C 353-375 2C 379-401 2C 433-450 2C 651-673 2C 680-702 2C706-728 2C 748-770 and 780-802 NC_002163.1 RefSeq region 1311525 1311593 . + . ID=id2462;Name=id2462;Dbxref=GeneID:905666;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1373 by TMHMM2.0 at aa 15-32 2C 228-245 2C 249-268 2C 273-295 2C299-321 2C 353-375 2C 379-401 2C 433-450 2C 651-673 2C 680-702 2C706-728 2C 748-770 and 780-802 NC_002163.1 RefSeq region 1311621 1311689 . + . ID=id2462;Name=id2462;Dbxref=GeneID:905666;gbkey=misc_feature;Note=13 probable transmembrane helices predicted for Cj1373 by TMHMM2.0 at aa 15-32 2C 228-245 2C 249-268 2C 273-295 2C299-321 2C 353-375 2C 379-401 2C 433-450 2C 651-673 2C 680-702 2C706-728 2C 748-770 and 780-802 ### NC_002163.1 RefSeq gene 1311786 1312388 . - . ID=gene1322;Name=Cj1374c;locus_tag=Cj1374c;Dbxref=GeneID:905667;gbkey=Gene NC_002163.1 RefSeq CDS 1311786 1312388 . - 0 ID=cds1249;Parent=gene1322;Name=YP_002344762.1;Dbxref=GOA:Q9PMS6 HSSP:Q57679 InterPro:IPR002637 UniProtKB FSwiss-Prot:Q9PMS6 Genbank:YP_002344762.1 GeneID:905667;gbkey=CDS;product=deoxyribonucleotide triphosphate pyrophosphatase;Note=HAM1-like protein 3B Rec-dependent growth 3B RgdB 3B yggV 3B it is suspected that this protein functions to remove misincorporated bases such as xanthine or hypoxanthine NC_002163.1 RefSeq region 1311807 1312382 . - . ID=id2463;Name=id2463;Dbxref=GeneID:905667;gbkey=misc_feature;Note=HMMPfam hit to PF01725 2C Ham1 family 2C score 1.5e-52 ### NC_002163.1 UTR_Extractor 5'-UTR 1312389 1312424 . - . ID=utr498;locus_tag=Cj1374c;product=putative deoxyribonucleotide triphosphate pyrophosphatase NC_002163.1 UTR_Extractor 5'-UTR 1312522 1312554 . + . ID=utr499;locus_tag=Cj1375;product=putative multidrug efflux transporter NC_002163.1 RefSeq CDS 1312555 1313850 . + 0 ID=cds1250;Parent=gene1323;Name=YP_002344763.1;Dbxref=GOA:Q0P8N4 InterPro:IPR001958 InterPro:IPR007114 InterPro:IPR011701 UniProtKB FTrEMBL:Q0P8N4 Genbank:YP_002344763.1 GeneID:905668;gbkey=CDS;product=multidrug efflux transporter;Note=Original 282000 29 note: Cj1375 2C probable efflux protein 2C len: 431 aa 3B similar to members of the major facilitator family e.g. BMR1_BACSU multidrug resistance protein 1 28multidrug-efflux transporter 1 29 28389 aa 29 2C fasta scores 3B opt: 364 z-score: 415.1 E 28 29: 8e-16 2C 27.1 25 identity in 384 aa overlap 2C and NORA_STAAU quinolone resistance NORA protein 28388 aa 29 2C fasta scores 3B opt: 353 z-score: 402.8 E 28 29: 3.9e-15 2C 26.7 25 identity in 375 aa overlap. 41.9 25 identity to HP1181. Also similar to Cj0035c 2824.7 25 identity in 372 aa overlap 29. Contains Pfam match to entry PF00083 sugar_tr 2C Sugar 28and other 29 transporters 7EUpdated 282006 29 note: Pfam domain PF07690 Major Facilitator Superfamily identified within CDS. Prints motif also identified TCRTETA domain 2C Tetracycline resistance protein signature IPR001958. Also 2C eleven probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Product function further modified. No specific characterisation with acceptable identity score carried out yet 2C so kept within product function. Functional classification - Drug 2Fanalogue sensitivity 7EPMID:7961792 NC_002163.1 RefSeq gene 1312555 1313850 . + . ID=gene1323;Name=Cj1375;locus_tag=Cj1375;Dbxref=GeneID:905668;gbkey=Gene NC_002163.1 RefSeq region 1312576 1313604 . + . ID=id2465;Name=id2465;Dbxref=GeneID:905668;gbkey=misc_feature;Note=HMMPfam hit to PF07690 2C Major Facilitator Superfamily 2C score 1.6e-61 NC_002163.1 RefSeq region 1312576 1313697 . + . ID=id2464;Name=id2464;Dbxref=GeneID:905668;gbkey=misc_feature;Note=HMMPfam hit to PF00083 2C Sugar 28and other 29 transporter 2C score 8.1e-05 NC_002163.1 RefSeq region 1312582 1312650 . + . ID=id2466;Name=id2466;Dbxref=GeneID:905668;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1375 by TMHMM2.0 at aa 10-32 2C 39-61 2C 71-93 2C 129-151 2C155-177 2C 205-227 2C 237-259 2C 268-285 2C 289-306 2C 327-349 and 353-375 NC_002163.1 RefSeq region 1312669 1312737 . + . ID=id2466;Name=id2466;Dbxref=GeneID:905668;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1375 by TMHMM2.0 at aa 10-32 2C 39-61 2C 71-93 2C 129-151 2C155-177 2C 205-227 2C 237-259 2C 268-285 2C 289-306 2C 327-349 and 353-375 NC_002163.1 RefSeq region 1312765 1312833 . + . ID=id2466;Name=id2466;Dbxref=GeneID:905668;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1375 by TMHMM2.0 at aa 10-32 2C 39-61 2C 71-93 2C 129-151 2C155-177 2C 205-227 2C 237-259 2C 268-285 2C 289-306 2C 327-349 and 353-375 NC_002163.1 RefSeq region 1312939 1313007 . + . ID=id2466;Name=id2466;Dbxref=GeneID:905668;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1375 by TMHMM2.0 at aa 10-32 2C 39-61 2C 71-93 2C 129-151 2C155-177 2C 205-227 2C 237-259 2C 268-285 2C 289-306 2C 327-349 and 353-375 NC_002163.1 RefSeq region 1313017 1313085 . + . ID=id2466;Name=id2466;Dbxref=GeneID:905668;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1375 by TMHMM2.0 at aa 10-32 2C 39-61 2C 71-93 2C 129-151 2C155-177 2C 205-227 2C 237-259 2C 268-285 2C 289-306 2C 327-349 and 353-375 NC_002163.1 RefSeq region 1313167 1313235 . + . ID=id2466;Name=id2466;Dbxref=GeneID:905668;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1375 by TMHMM2.0 at aa 10-32 2C 39-61 2C 71-93 2C 129-151 2C155-177 2C 205-227 2C 237-259 2C 268-285 2C 289-306 2C 327-349 and 353-375 NC_002163.1 RefSeq region 1313263 1313331 . + . ID=id2466;Name=id2466;Dbxref=GeneID:905668;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1375 by TMHMM2.0 at aa 10-32 2C 39-61 2C 71-93 2C 129-151 2C155-177 2C 205-227 2C 237-259 2C 268-285 2C 289-306 2C 327-349 and 353-375 NC_002163.1 RefSeq region 1313356 1313409 . + . ID=id2466;Name=id2466;Dbxref=GeneID:905668;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1375 by TMHMM2.0 at aa 10-32 2C 39-61 2C 71-93 2C 129-151 2C155-177 2C 205-227 2C 237-259 2C 268-285 2C 289-306 2C 327-349 and 353-375 NC_002163.1 RefSeq region 1313419 1313472 . + . ID=id2466;Name=id2466;Dbxref=GeneID:905668;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1375 by TMHMM2.0 at aa 10-32 2C 39-61 2C 71-93 2C 129-151 2C155-177 2C 205-227 2C 237-259 2C 268-285 2C 289-306 2C 327-349 and 353-375 NC_002163.1 RefSeq region 1313533 1313601 . + . ID=id2466;Name=id2466;Dbxref=GeneID:905668;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1375 by TMHMM2.0 at aa 10-32 2C 39-61 2C 71-93 2C 129-151 2C155-177 2C 205-227 2C 237-259 2C 268-285 2C 289-306 2C 327-349 and 353-375 NC_002163.1 RefSeq region 1313611 1313679 . + . ID=id2466;Name=id2466;Dbxref=GeneID:905668;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1375 by TMHMM2.0 at aa 10-32 2C 39-61 2C 71-93 2C 129-151 2C155-177 2C 205-227 2C 237-259 2C 268-285 2C 289-306 2C 327-349 and 353-375 NC_002163.1 RefSeq gene 1313847 1314656 . + . ID=gene1324;Name=Cj1376;locus_tag=Cj1376;Dbxref=GeneID:905669;gbkey=Gene NC_002163.1 RefSeq CDS 1313847 1314656 . + 0 ID=cds1251;Parent=gene1324;Name=YP_002344764.1;Dbxref=UniProtKB FTrEMBL:Q0P8N3 Genbank:YP_002344764.1 GeneID:905669;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1376 2C probable periplasmic protein 2C len: 269 aa 3B similar to TR:O32102 28EMBL:Z99120 29 B. subtilis YUII protein 28314 aa 29 2C fasta scores 3B opt: 209 z-score: 257.4 E 28 29: 4.9e-07 2C 30.6 25 identity in 242 aa overlap 2C and TR:O54506 28EMBL:U97227 29 Salmonella enterica IROE 28305 aa 29 2C fasta scores 3B opt: 195 z-score: 240.9 E 28 29: 4.1e-06 2C 26.4 25 identity in 277 aa overlap. No Hp match. Contains probable N-terminal signal sequence. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq CDS 1314649 1316310 . - 0 ID=cds1252;Parent=gene1325;Name=YP_002344765.1;Dbxref=GOA:Q0P8N2 InterPro:IPR001450 UniProtKB FTrEMBL:Q0P8N2 Genbank:YP_002344765.1 GeneID:905670;gbkey=CDS;product=ferredoxin;Note=Original 282000 29 note: Cj1377c 2C probable ferredoxin 2Clen: 553 aa 3B limited similarity to e.g. HYCF_ECOLI formate hydrogenlyase subunit 6 28180 aa 29 2C fasta scores 3B opt: 212 z-score: 241.0 E 28 29: 4e-06 2C 30.6 25 identity in 134 aa overlap. No Hp match. Contains PS00198 4Fe-4S ferredoxins 2Ciron-sulfur binding region signature 2C and 2x Pfam match to entry PF00037 fer4 2C 4Fe-4S ferredoxins and related iron-sulfur cluster binding domains 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score carried out yet 2C so kept within product function. Functional classification - Energy metabolism - Electron transport NC_002163.1 RefSeq gene 1314649 1316310 . - . ID=gene1325;Name=Cj1377c;locus_tag=Cj1377c;Dbxref=GeneID:905670;gbkey=Gene NC_002163.1 RefSeq region 1314979 1315050 . - . ID=id2467;Name=id2467;Dbxref=GeneID:905670;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 7.5e-05 NC_002163.1 RefSeq region 1315537 1315608 . - . ID=id2468;Name=id2468;Dbxref=GeneID:905670;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 0.00013 NC_002163.1 RefSeq region 1315552 1315587 . - . ID=id2469;Name=id2469;Dbxref=GeneID:905670;gbkey=misc_feature;Note=PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature ### NC_002163.1 UTR_Extractor 5'-UTR 1316311 1316344 . - . ID=utr500;locus_tag=Cj1377c;product=putative ferredoxin NC_002163.1 UTR_Extractor 5'-UTR 1316368 1316387 . + . ID=utr501;locus_tag=Cj1378;product=selenocysteine synthase NC_002163.1 RefSeq CDS 1316388 1317710 . + 0 ID=cds1253;Parent=gene1326;gene=selA;Name=YP_002344766.1;Dbxref=GOA:Q9PMS2 InterPro:IPR004534 UniProtKB FSwiss-Prot:Q9PMS2 Genbank:YP_002344766.1 GeneID:905671;gbkey=CDS;product=selenocysteine synthase;Note=catalyzes the formation of selenocysteinyl-tRNA 28Sec 29 from seryl-tRNA 28Sec 29 and L-selenophosphate in selenoprotein biosynthesis NC_002163.1 RefSeq gene 1316388 1317710 . + . ID=gene1326;gene=selA;Name=selA;locus_tag=Cj1378;Dbxref=GeneID:905671;gbkey=Gene NC_002163.1 RefSeq region 1316598 1317656 . + . ID=id2470;gene=selA;Name=id2470;Dbxref=GeneID:905671;gbkey=misc_feature;Note=HMMPfam hit to PF03841 2C L-seryl-tRNA selenium transferase 2C score 4.4e-220 NC_002163.1 RefSeq region 1317707 1318210 . + . ID=id2471;gene=selB;Name=id2471;Dbxref=GeneID:905672;gbkey=misc_feature;Note=HMMPfam hit to PF00009 2C Elongation factor Tu GTP binding domain 2C score 1.3e-28 NC_002163.1 RefSeq CDS 1317707 1319512 . + 0 ID=cds1254;Parent=gene1327;gene=selB;Name=YP_002344767.1;Dbxref=GOA:Q0P8N0 InterPro:IPR000795 InterPro:IPR004161 InterPro:IPR004535 InterPro:IPR005225 InterPro:IPR011991 InterPro:IPR015191 UniProtKB FTrEMBL:Q0P8N0 Genbank:YP_002344767.1 GeneID:905672;gbkey=CDS;product=selenocysteine-specific elongation factor;Note=Original 282000 29 note: Cj1379 2C selB 2C probable selenocysteine-specific elongation factor 2C len: 601 aa 3B similar to e.g. SELB_ECOLI selenocysteine-specific elongation factor 28614 aa 29 2C fasta scores 3B opt: 479 z-score: 491.6 E 28 29: 4.4e-20 2C 26.2 25 identity in 362 aa overlap. No Hp ortholog. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C and Pfam match to entry PF00009 GTP_EFTU 2C Elongation factor Tu family 7EUpdated 282006 29 note: kept within product function as no characterisation with acceptable identity score has been carried out yet. Functional classification - Protein translation and modification 7EPMID:2140572 2C PMID:16511023 NC_002163.1 RefSeq gene 1317707 1319512 . + . ID=gene1327;gene=selB;Name=selB;locus_tag=Cj1379;Dbxref=GeneID:905672;gbkey=Gene NC_002163.1 RefSeq region 1317734 1317757 . + . ID=id2472;gene=selB;Name=id2472;Dbxref=GeneID:905672;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 UTR_Extractor 5'-UTR 1319534 1319560 . + . ID=utr502;locus_tag=Cj1380;product=putative periplasmic protein NC_002163.1 RefSeq gene 1319561 1320271 . + . ID=gene1328;Name=Cj1380;locus_tag=Cj1380;Dbxref=GeneID:905673;gbkey=Gene NC_002163.1 RefSeq CDS 1319561 1320271 . + 0 ID=cds1255;Parent=gene1328;Name=YP_002344768.1;Dbxref=GOA:Q0P8M9 InterPro:IPR012335 UniProtKB FTrEMBL:Q0P8M9 Genbank:YP_002344768.1 GeneID:905673;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1380 2C probable periplasmic protein 2C len: 236 aa 3B some similarity to e.g. DSBG_ECOLI thiol:disulfide interchange protein DSBG precursor 28248 aa 29 2C fasta scores 3B opt: 138 z-score: 165.8 E 28 29: 0.062 2C26.8 25 identity in 164 aa overlap 28the active site is conserved 29. 34.1 25 identity to HP0231. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Paper identified linking protein to glycoprotein. Functional classification -Miscellaneous periplasmic proteins 7EPMID:12186869 NC_002163.1 RefSeq CDS 1320277 1320807 . + 0 ID=cds1256;Parent=gene1329;Name=YP_002344769.1;Dbxref=GOA:Q0P8M8 UniProtKB FTrEMBL:Q0P8M8 Genbank:YP_002344769.1 GeneID:905674;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj1381 2C probable lipoprotein 2Clen: 176 aa 3B no Hp match. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 1320277 1320807 . + . ID=gene1329;Name=Cj1381;locus_tag=Cj1381;Dbxref=GeneID:905674;gbkey=Gene NC_002163.1 RefSeq region 1320295 1320363 . + . ID=id2473;Name=id2473;Dbxref=GeneID:905674;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1381 by TMHMM2.0 at aa 7-29 NC_002163.1 RefSeq region 1320301 1320333 . + . ID=id2474;Name=id2474;Dbxref=GeneID:905674;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq CDS 1320852 1321343 . - 0 ID=cds1257;Parent=gene1330;gene=fldA;Name=YP_002344770.1;Dbxref=GOA:Q0P8M7 InterPro:IPR001094 InterPro:IPR001226 InterPro:IPR008254 InterPro:IPR010086 UniProtKB FTrEMBL:Q0P8M7 Genbank:YP_002344770.1 GeneID:905675;gbkey=CDS;product=flavodoxin FldA;Note=An electron-transfer protein 3B flavodoxin binds one FMN molecule 2C which serves as a redox-active prosthetic group NC_002163.1 RefSeq gene 1320852 1321343 . - . ID=gene1330;gene=fldA;Name=fldA;locus_tag=Cj1382c;Dbxref=GeneID:905675;gbkey=Gene NC_002163.1 RefSeq region 1320882 1321331 . - . ID=id2475;gene=fldA;Name=id2475;Dbxref=GeneID:905675;gbkey=misc_feature;Note=HMMPfam hit to PF00258 2C Flavodoxin 2C score 6.8e-43 NC_002163.1 RefSeq region 1321113 1321136 . - . ID=id2476;gene=fldA;Name=id2476;Dbxref=GeneID:905675;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 1321281 1321331 . - . ID=id2477;gene=fldA;Name=id2477;Dbxref=GeneID:905675;gbkey=misc_feature;Note=PS00201 Flavodoxin signature NC_002163.1 RefSeq gene 1321343 1322038 . - . ID=gene1331;gene=Cj1383c;Name=Cj1383c;locus_tag=Cj1383c;Dbxref=GeneID:905676;gbkey=Gene NC_002163.1 RefSeq CDS 1321343 1322038 . - 0 ID=cds1258;Parent=gene1331;Name=YP_002344771.1;Dbxref=UniProtKB FTrEMBL:Q0P8M6 Genbank:YP_002344771.1 GeneID:905676;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1383c 2C unknown 2C len: 231 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Literature search identified paper giving further clues to product function. Functional classification - Unknown 7EPMID:15231804 ### NC_002163.1 RefSeq gene 1322041 1322355 . - . ID=gene1332;Name=Cj1384c;locus_tag=Cj1384c;Dbxref=GeneID:905677;gbkey=Gene NC_002163.1 RefSeq CDS 1322041 1322355 . - 0 ID=cds1259;Parent=gene1332;Name=YP_002344772.1;Dbxref=InterPro:IPR016772 UniProtKB FTrEMBL:Q0P8M5 Genbank:YP_002344772.1 GeneID:905677;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1384c 2C unknown 2C len: 104 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Literature search identified paper giving further clues to product function. Functional classification - Unknown 7EPMID:15231804 NC_002163.1 RefSeq CDS 1322526 1323950 . + 0 ID=cds1260;Parent=gene1333;gene=katA;Name=YP_002344773.1;Dbxref=GOA:Q59296 HSSP:P42321 InterPro:IPR002226 InterPro:IPR011614 UniProtKB FSwiss-Prot:Q59296 Genbank:YP_002344773.1 GeneID:905678;gbkey=CDS;product=catalase;Note=Original 282000 29 note: Cj1385 2C katA 2C catalase 2C len: 474 aa 3B 98.5 25 identical to TR:Q59296 28EMBL:X85130 29 C. jejuni catalase 28EC 1.11.1.6 29 28507 aa 29 2C and similar to e.g. CATA_BRUAB catalase 28498 aa 29 2C fasta scores 3B opt: 2093 z-score: 2432.5 E 28 29: 0 2C 65.6 25 identity in 474 aa overlap. 56.1 25 identity to HP0875. Contains PS00437 Catalase proximal heme-ligand signature 2C and Pfam match to entry PF00199 catalase 7EUpdated 282006 29 note: Characterised within Campylobacter jejuni 2C so not added to product function. Functional classification - Detoxification 7EPMID:7670638 NC_002163.1 RefSeq gene 1322526 1323950 . + . ID=gene1333;gene=katA;Name=katA;locus_tag=Cj1385;Dbxref=GeneID:905678;gbkey=Gene NC_002163.1 RefSeq region 1322538 1323689 . + . ID=id2478;gene=katA;Name=id2478;Dbxref=GeneID:905678;gbkey=misc_feature;Note=HMMPfam hit to PF00199 2C Catalase 2C score 4.1e-259 NC_002163.1 RefSeq region 1323513 1323539 . + . ID=id2479;gene=katA;Name=id2479;Dbxref=GeneID:905678;gbkey=misc_feature;Note=PS00437 Catalase proximal heme-ligand signature ### NC_002163.1 RefSeq CDS 1324007 1324477 . + 0 ID=cds1261;Parent=gene1334;Name=YP_002344774.1;Dbxref=InterPro:IPR002110 UniProtKB FTrEMBL:Q0P8M3 Genbank:YP_002344774.1 GeneID:905679;gbkey=CDS;product=ankyrin repeat-containing protein;Note=Original 282000 29 note: Cj1386 2C ankyrin-repeat containing protein 2C len: 412 aa 3B similar to proteins downstream of catalase in Pseudomonads e.g. TR:P95546 28EMBL:U16026 29 Pseudomonas syringae ANKF precursor 28183 aa 29 2C fasta scores 3B opt: 217 z-score: 286.8 E 28 29: 1.2e-08 2C31.3 25 identity in 134 aa overlap 2C and to eukaryotic ankyrin proteins e.g. ANK1_MOUSE ankyrin 281862 aa 29 2C fasta scores 3B opt: 181 z-score: 226.3 E 28 29: 2.8e-05 2C 29.1 25 identity in 117 aa overlap. No Hp match. Also similar to Cj0834c 2829.3 25 identity in 99 aa overlap 29. Contains 2x Pfam match to entry PF00023 ank 2C Ank repeat 7EUpdated 282006 29 note: Literature search identified paper giving further clues to product function. Functional classification - Misc 7EPMID:15632442 NC_002163.1 RefSeq gene 1324007 1324477 . + . ID=gene1334;Name=Cj1386;locus_tag=Cj1386;Dbxref=GeneID:905679;gbkey=Gene NC_002163.1 RefSeq region 1324145 1324243 . + . ID=id2480;Name=id2480;Dbxref=GeneID:905679;gbkey=misc_feature;Note=HMMPfam hit to PF00023 2C Ankyrin repeat 2C score 6.5e-07 NC_002163.1 RefSeq region 1324244 1324342 . + . ID=id2481;Name=id2481;Dbxref=GeneID:905679;gbkey=misc_feature;Note=HMMPfam hit to PF00023 2C Ankyrin repeat 2C score 0.0047 NC_002163.1 RefSeq region 1324343 1324441 . + . ID=id2482;Name=id2482;Dbxref=GeneID:905679;gbkey=misc_feature;Note=HMMPfam hit to PF00023 2C Ankyrin repeat 2C score 7.4 ### NC_002163.1 RefSeq gene 1324478 1325134 . - . ID=gene1335;Name=Cj1387c;locus_tag=Cj1387c;Dbxref=GeneID:905680;gbkey=Gene NC_002163.1 RefSeq CDS 1324478 1325134 . - 0 ID=cds1262;Parent=gene1335;Name=YP_002344775.1;Dbxref=InterPro:IPR013559 UniProtKB FTrEMBL:Q0P8M2 Genbank:YP_002344775.1 GeneID:905680;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1387c 2C unknown 2C len: 218 aa 3B similar to hypothetical proteins e.g. YHEO_ECOLI 28240 aa 29 2C fasta scores 3B opt: 164 z-score: 202.0 E 28 29: 0.00063 2C29.4 25 identity in 204 aa overlap. No Hp match. Contains probable helix-turn-helix motif at aa 194-215 28Score 1100 2C 2B2.93 SD 29. Functional classification - Broad regulatory functions NC_002163.1 UTR_Extractor 5'-UTR 1325135 1325165 . - . ID=utr503;locus_tag=Cj1387c;product=helix-turn-helix containing protein NC_002163.1 UTR_Extractor 5'-UTR 1325272 1325301 . + . ID=utr504;locus_tag=Cj1388;product=putative endoribonuclease L-PSP NC_002163.1 RefSeq region 1325302 1325658 . + . ID=id2483;Name=id2483;Dbxref=GeneID:905681;gbkey=misc_feature;Note=HMMPfam hit to PF01042 2C Endoribonuclease L-PSP 2Cscore 1.6e-56 NC_002163.1 RefSeq gene 1325302 1325664 . + . ID=gene1336;Name=Cj1388;locus_tag=Cj1388;Dbxref=GeneID:905681;gbkey=Gene NC_002163.1 RefSeq CDS 1325302 1325664 . + 0 ID=cds1263;Parent=gene1336;Name=YP_002344776.1;Dbxref=InterPro:IPR006056 InterPro:IPR006175 InterPro:IPR013813 UniProtKB FTrEMBL:Q0P8M1 Genbank:YP_002344776.1 GeneID:905681;gbkey=CDS;product=endoribonuclease L-PSP;Note=Original 282000 29 note: Cj1388 2C unknown 2C len: 120 aa 3B similar to prokaryotic hypothetical proteins e.g. YA28_PYRHO Pyrococcus horikoshii PHAL028 28137 aa 29 2C fasta scores 3B opt: 399 z-score: 503.4 E 28 29: 1e-20 2C 53.8 25 identity in 117 aa overlap 2C and to e.g. UK14_HUMAN 14.5 KD translational inhibitor protein 28137 aa 29 2C fasta scores 3B opt: 384 z-score: 485.1 E 28 29: 1.1e-19 2C 48.3 25 identity in 116 aa overlap. 53.0 25 identity to HP0944. Also similar to Cj0327 2834.4 25 identity in 96 aa overlap 29. Contains Pfam match to entry PF01042 DUF10 2C Domain of unknown function 7EUpdated 282006 29 note: Pfam domain PF01042 Endoribonuclease L-PSP identified within CDS. This domain is found in endoribonucleases 2C which are active on single-stranded mRNA and inhibit protein synthesis by cleavage of mRNA. Product modified to more specific family member based on motif results. No specific characterisation has been carried out yet 2C so kept within product function. Functional classification -DNA replication 2C restriction 2Fmodification 2C recombination and repair NC_002163.1 RefSeq region 1325584 1325646 . + . ID=id2484;Name=id2484;Dbxref=GeneID:905681;gbkey=misc_feature;Note=PS01094 Uncharacterized protein family UPF0076 signature ### NC_002163.1 RefSeq region 1325668 1326117 . + . ID=id2485;Name=id2485;Dbxref=PSEUDO:CAL35501.1 GeneID:905682;gbkey=misc_feature;Note=Original 282000 29 note: Cj1389 2C probable transmembrane transport protein pseudogene 2C len: 1437 bp 3B similar to e.g. YHCL_ECOLI hypothetical transport protein 28455 aa 29 28approx 45 25 identity 29 2C and DCUC_ECOLI C4-dicarboxylate anaerobic carrier 28461 aa 29 28approx 31 25 identity 29. No Hp match 7EUpdated 282006 29 note: Pfam domain PF03606 C4-dicarboxylate anaerobic carrier identified within CDS. Also 2C twelve probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Some characterisation work has been carried out within Escherichia coli with acceptable identity score 2C however 2Coriginal designation was . Thus 2C kept within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification -Transport 2Fbinding proteins - Carbohydrates 2C organic acids and alcohols 7EPMID:10525738 NC_002163.1 RefSeq pseudogene 1325668 1327107 . + . ID=gene1337;Name=Cj1389;locus_tag=Cj1389;Dbxref=GeneID:905682;gbkey=Gene NC_002163.1 RefSeq region 1325671 1326117 . + . ID=id2486;Name=id2486;Dbxref=GeneID:905682;gbkey=misc_feature;Note=HMMPfam hit to PF03606 2C C4-dicarboxylate anaerobic carrier 2C score 2.1e-56 NC_002163.1 RefSeq region 1325677 1325724 . + . ID=id2487;Name=id2487;Dbxref=GeneID:905682;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1389 by TMHMM2.0 at aa 4-19 2C 26-48 2C 68-90 2C 110-132 2C137-159 2C 191-213 2C 254-276 2C 297-317 2C 337-359 2C 372-394 2C427-449 and 456-478 NC_002163.1 RefSeq region 1325743 1325811 . + . ID=id2487;Name=id2487;Dbxref=GeneID:905682;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1389 by TMHMM2.0 at aa 4-19 2C 26-48 2C 68-90 2C 110-132 2C137-159 2C 191-213 2C 254-276 2C 297-317 2C 337-359 2C 372-394 2C427-449 and 456-478 NC_002163.1 RefSeq region 1325869 1325937 . + . ID=id2487;Name=id2487;Dbxref=GeneID:905682;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1389 by TMHMM2.0 at aa 4-19 2C 26-48 2C 68-90 2C 110-132 2C137-159 2C 191-213 2C 254-276 2C 297-317 2C 337-359 2C 372-394 2C427-449 and 456-478 NC_002163.1 RefSeq region 1325995 1326063 . + . ID=id2487;Name=id2487;Dbxref=GeneID:905682;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1389 by TMHMM2.0 at aa 4-19 2C 26-48 2C 68-90 2C 110-132 2C137-159 2C 191-213 2C 254-276 2C 297-317 2C 337-359 2C 372-394 2C427-449 and 456-478 NC_002163.1 RefSeq region 1326076 1326117 . + . ID=id2487;Name=id2487;Dbxref=GeneID:905682;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1389 by TMHMM2.0 at aa 4-19 2C 26-48 2C 68-90 2C 110-132 2C137-159 2C 191-213 2C 254-276 2C 297-317 2C 337-359 2C 372-394 2C427-449 and 456-478 NC_002163.1 RefSeq region 1326120 1326146 . + . ID=id2487;Name=id2487;Dbxref=GeneID:905682;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1389 by TMHMM2.0 at aa 4-19 2C 26-48 2C 68-90 2C 110-132 2C137-159 2C 191-213 2C 254-276 2C 297-317 2C 337-359 2C 372-394 2C427-449 and 456-478 NC_002163.1 RefSeq region 1326120 1326567 . + . ID=id2485;Name=id2485;Dbxref=PSEUDO:CAL35501.1 GeneID:905682;gbkey=misc_feature;Note=Original 282000 29 note: Cj1389 2C probable transmembrane transport protein pseudogene 2C len: 1437 bp 3B similar to e.g. YHCL_ECOLI hypothetical transport protein 28455 aa 29 28approx 45 25 identity 29 2C and DCUC_ECOLI C4-dicarboxylate anaerobic carrier 28461 aa 29 28approx 31 25 identity 29. No Hp match 7EUpdated 282006 29 note: Pfam domain PF03606 C4-dicarboxylate anaerobic carrier identified within CDS. Also 2C twelve probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Some characterisation work has been carried out within Escherichia coli with acceptable identity score 2C however 2Coriginal designation was . Thus 2C kept within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification -Transport 2Fbinding proteins - Carbohydrates 2C organic acids and alcohols 7EPMID:10525738 NC_002163.1 RefSeq region 1326120 1327104 . + . ID=id2486;Name=id2486;Dbxref=GeneID:905682;gbkey=misc_feature;Note=HMMPfam hit to PF03606 2C C4-dicarboxylate anaerobic carrier 2C score 2.1e-56 NC_002163.1 RefSeq region 1326240 1326308 . + . ID=id2487;Name=id2487;Dbxref=GeneID:905682;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1389 by TMHMM2.0 at aa 4-19 2C 26-48 2C 68-90 2C 110-132 2C137-159 2C 191-213 2C 254-276 2C 297-317 2C 337-359 2C 372-394 2C427-449 and 456-478 NC_002163.1 RefSeq region 1326429 1326497 . + . ID=id2487;Name=id2487;Dbxref=GeneID:905682;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1389 by TMHMM2.0 at aa 4-19 2C 26-48 2C 68-90 2C 110-132 2C137-159 2C 191-213 2C 254-276 2C 297-317 2C 337-359 2C 372-394 2C427-449 and 456-478 NC_002163.1 RefSeq region 1326558 1326618 . + . ID=id2487;Name=id2487;Dbxref=GeneID:905682;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1389 by TMHMM2.0 at aa 4-19 2C 26-48 2C 68-90 2C 110-132 2C137-159 2C 191-213 2C 254-276 2C 297-317 2C 337-359 2C 372-394 2C427-449 and 456-478 NC_002163.1 RefSeq region 1326566 1327107 . + . ID=id2485;Name=id2485;Dbxref=PSEUDO:CAL35501.1 GeneID:905682;gbkey=misc_feature;Note=Original 282000 29 note: Cj1389 2C probable transmembrane transport protein pseudogene 2C len: 1437 bp 3B similar to e.g. YHCL_ECOLI hypothetical transport protein 28455 aa 29 28approx 45 25 identity 29 2C and DCUC_ECOLI C4-dicarboxylate anaerobic carrier 28461 aa 29 28approx 31 25 identity 29. No Hp match 7EUpdated 282006 29 note: Pfam domain PF03606 C4-dicarboxylate anaerobic carrier identified within CDS. Also 2C twelve probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Some characterisation work has been carried out within Escherichia coli with acceptable identity score 2C however 2Coriginal designation was . Thus 2C kept within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification -Transport 2Fbinding proteins - Carbohydrates 2C organic acids and alcohols 7EPMID:10525738 NC_002163.1 RefSeq region 1326676 1326744 . + . ID=id2487;Name=id2487;Dbxref=GeneID:905682;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1389 by TMHMM2.0 at aa 4-19 2C 26-48 2C 68-90 2C 110-132 2C137-159 2C 191-213 2C 254-276 2C 297-317 2C 337-359 2C 372-394 2C427-449 and 456-478 NC_002163.1 RefSeq region 1326781 1326849 . + . ID=id2487;Name=id2487;Dbxref=GeneID:905682;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1389 by TMHMM2.0 at aa 4-19 2C 26-48 2C 68-90 2C 110-132 2C137-159 2C 191-213 2C 254-276 2C 297-317 2C 337-359 2C 372-394 2C427-449 and 456-478 NC_002163.1 RefSeq region 1326946 1327014 . + . ID=id2487;Name=id2487;Dbxref=GeneID:905682;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1389 by TMHMM2.0 at aa 4-19 2C 26-48 2C 68-90 2C 110-132 2C137-159 2C 191-213 2C 254-276 2C 297-317 2C 337-359 2C 372-394 2C427-449 and 456-478 NC_002163.1 RefSeq region 1327033 1327101 . + . ID=id2487;Name=id2487;Dbxref=GeneID:905682;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1389 by TMHMM2.0 at aa 4-19 2C 26-48 2C 68-90 2C 110-132 2C137-159 2C 191-213 2C 254-276 2C 297-317 2C 337-359 2C 372-394 2C427-449 and 456-478 ### NC_002163.1 RefSeq CDS 1327120 1327257 . + 0 ID=cds1264;Parent=gene1338;gene=metC';Name=YP_002344777.1;Dbxref=GOA:Q0P8M0 UniProtKB FTrEMBL:Q0P8M0 Genbank:YP_002344777.1 GeneID:5066043;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1392 2C metC 27 2C probable cystathionine beta-lyase 2C N-terminus 2C len: 348 aa 3B similar to many e.g. METC_HAEIN cystathionine beta-lyase 28EC 4.4.1.8 29 28396 aa 29 2C fasta scores 3B opt: 88 z-score: 151.7 E 28 29: 0.4 2C 45.2 25 identity in 42 aa overlap. No Hp match. Note that the rest of metC is in the downstream ORF Cj1393. This may represent a pseudogene fragment 2C or possibly programmed ribosomal frameshifting 7EUpdated 282006 29 note: Gene names for Cj1392 and Cj1393 are identical with a 27 denoting two separate terminals for the same CDS. May well be a pseudogene. kept within product function. Functional classification - Amino acid biosynthesis - Aspartate family 7EPMID:8831789 NC_002163.1 RefSeq gene 1327120 1327257 . + . ID=gene1338;gene=metC';Name=metC';locus_tag=Cj1392;Dbxref=GeneID:5066043;gbkey=Gene NC_002163.1 RefSeq CDS 1327236 1328282 . + 0 ID=cds1265;Parent=gene1339;gene=metC';Name=YP_002344778.1;Dbxref=GOA:Q0P8L9 InterPro:IPR000277 InterPro:IPR015421 InterPro:IPR015422 UniProtKB FTrEMBL:Q0P8L9 Genbank:YP_002344778.1 GeneID:905683;gbkey=CDS;product=cystathionine beta-lyase;Note=Original 282000 29 note: Cj1393 2C metC 27 2C probable cystathionine beta-lyase 2C len: 348 aa 3B similar to many e.g. METC_ECOLI cystathionine beta-lyase 28EC 4.4.1.8 29 28395 aa 29 2C fasta scores 3B opt: 802 z-score: 979.2 E 28 29: 0 2C 35.6 25 identity in 354 aa overlap. 36.2 25 identity to HP0106. Also similar to Cj1727c 2C 30.0 25 identity in 363 aa overlap. Contains PS00868 Cys 2FMet metabolism enzymes pyridoxal-phosphate attachment site 2C and Pfam match to entry PF01053 Cys_Met_Meta_PP 2C Gamma-family of PLP-dependent enzymes. Note that the N-terminal 50 aa of the protein appear to be in the upstream ORF Cj1392. This may represent a pseudogene fragment 2C or possibly programmed ribosomal frameshifting 7EUpdated 282006 29 note: Gene names for Cj1392 and Cj1393 are identical with a 27 denoting two separate terminals for the same CDS. May well be a pseudogene. kept in product function. Functional classification - Amino acid biosynthesis - Aspartate family 7EPMID:8831789 NC_002163.1 RefSeq gene 1327236 1328282 . + . ID=gene1339;gene=metC';Name=metC';locus_tag=Cj1393;Dbxref=GeneID:905683;gbkey=Gene NC_002163.1 RefSeq region 1327248 1328267 . + . ID=id2488;gene=metC';Name=id2488;Dbxref=GeneID:905683;gbkey=misc_feature;Note=HMMPfam hit to PF01053 2C Cys 2FMet metabolism PLP-dependent enzy 2C score 5.3e-97 NC_002163.1 RefSeq region 1327710 1327754 . + . ID=id2489;gene=metC';Name=id2489;Dbxref=GeneID:905683;gbkey=misc_feature;Note=PS00868 Cys 2FMet metabolism enzymes pyridoxal-phosphate attachment site ### NC_002163.1 RefSeq CDS 1328292 1329659 . + 0 ID=cds1266;Parent=gene1340;Name=YP_002344779.1;Dbxref=GOA:Q0P8L8 InterPro:IPR000362 InterPro:IPR001865 UniProtKB FTrEMBL:Q0P8L8 Genbank:YP_002344779.1 GeneID:905684;gbkey=CDS;product=adenylosuccinate lyase;Note=Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide NC_002163.1 RefSeq gene 1328292 1329659 . + . ID=gene1340;Name=Cj1394;locus_tag=Cj1394;Dbxref=GeneID:905684;gbkey=Gene NC_002163.1 RefSeq region 1328331 1329206 . + . ID=id2490;Name=id2490;Dbxref=GeneID:905684;gbkey=misc_feature;Note=HMMPfam hit to PF00206 2C Lyase 2C score 2.2e-28 NC_002163.1 RefSeq region 1329123 1329152 . + . ID=id2491;Name=id2491;Dbxref=GeneID:905684;gbkey=misc_feature;Note=PS00163 Fumarate lyases signature NC_002163.1 RefSeq region 1329561 1329596 . + . ID=id2492;Name=id2492;Dbxref=GeneID:905684;gbkey=misc_feature;Note=PS00962 Ribosomal protein S2 signature 1 ### NC_002163.1 RefSeq region 1329668 1330993 . + . ID=id2494;Name=id2494;Dbxref=GeneID:905685;gbkey=misc_feature;Note=HMMPfam hit to PF03972 2C MmgE 2FPrpD family 2C score 6.2e-57 NC_002163.1 RefSeq pseudogene 1329668 1331008 . + . ID=gene1341;Name=Cj1395;locus_tag=Cj1395;Dbxref=GeneID:905685;gbkey=Gene NC_002163.1 RefSeq region 1329668 1331008 . + . ID=id2493;Name=id2493;Dbxref=GeneID:905685;gbkey=misc_feature;Note=Original 282000 29 note: Cj1395 2C possible pseudogene 2Clen: 1338 bp 3B similar to hypothetical proteins e.g. YXEQ_BACSU 28445 aa 29 28approx 25 25 identity 29 2C and IRG1_MOUSE immune-responsive protein 1 28fragment 29 28646 aa 29 28approx 30 25 identity 29. No Hp match 7EUpdated 282006 29 note: Pfam domain PF03972 MmgE 2FPrpD family identified within CDS. Further support given to product function. No specific characterisation has been carried out with acceptable identity scores yet. Thus 2C kept within product function. Functional classification - Misc ### NC_002163.1 UTR_Extractor 5'-UTR 1331069 1331089 . + . ID=utr505;locus_tag=Cj1397;product=putative ferrous iron transport protein NC_002163.1 RefSeq region 1331090 1331308 . + . ID=id2495;Name=id2495;Dbxref=GeneID:905686;gbkey=misc_feature;Note=HMMPfam hit to PF04023 2C FeoA domain 2C score 1.4e-18 NC_002163.1 RefSeq gene 1331090 1331314 . + . ID=gene1342;Name=Cj1397;locus_tag=Cj1397;Dbxref=GeneID:905686;gbkey=Gene NC_002163.1 RefSeq CDS 1331090 1331314 . + 0 ID=cds1267;Parent=gene1342;Name=YP_002344780.1;Dbxref=GOA:Q9PMR0 InterPro:IPR007167 UniProtKB FSwiss-Prot:Q9PMR0 Genbank:YP_002344780.1 GeneID:905686;gbkey=CDS;product=ferrous iron transport protein;Note=Original 282000 29 note: Cj1397 2C unknown 2C len: 74 aa 3B similar to hypothetical proteins e.g. TR:AAD06110 28EMBL:AE001486 29 H. pylori J99 JHP0533 2878 aa 29 2C fasta scores 3B opt: 143 z-score: 219.1 E 28 29: 6.9e-05 2C 41.2 25 identity in 68 aa overlap 2C and TR:P73181 28EMBL:D90904 29 Synechocystis sp. ssr2333 2879 aa 29 2C fasta scores 3B opt: 94 z-score: 151.5 E 28 29: 0.41 2C 28.6 25 identity in 77 aa overlap. Not predicted in TIGR Hp 2C but 38.8 25 identity to c 28615977..616192 29 7EUpdated 282006 29 note: Pfam domain PF04023 FeoA domain identified within CDS. This family of protein is thought to be involved in Fe2 2B transport. Product modified to more specific family member based on motif search result. No characterisation has been carried out yet 2C so kept in product function. Functional classification - Transport 2Fbinding proteins - Cations 7EPMID:8407793 NC_002163.1 RefSeq gene 1331311 1333152 . + . ID=gene1343;gene=feoB;Name=feoB;locus_tag=Cj1398;Dbxref=GeneID:905687;gbkey=Gene NC_002163.1 RefSeq CDS 1331311 1333152 . + 0 ID=cds1268;Parent=gene1343;gene=feoB;Name=YP_002344781.1;Dbxref=GOA:Q9PMQ9 HSSP:Q9X1F8 InterPro:IPR001806 InterPro:IPR002917 InterPro:IPR003373 InterPro:IPR005225 InterPro:IPR005289 InterPro:IPR011619 InterPro:IPR011640 InterPro:IPR011642 UniProtKB FSwiss-Prot:Q9PMQ9 Genbank:YP_002344781.1 GeneID:905687;gbkey=CDS;product=ferrous iron transport protein;Note=Original 282000 29 note: Cj1398 2C feoB 2C probable ferrous iron transport protein 2C len: 613 aa 3B similar to many e.g. FEOB_ECOLI ferrous iron transport protein B 28773 aa 29 2C fasta scores 3B opt: 726 z-score: 805.2 E 28 29: 0 2C 29.3 25 identity in 726 aa overlap. 50.5 25 identity to HP0687. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 7EUpdated 282006 29 note: Pfam domains PF01926 GTPase of unknown function 2C PF02421 Ferrous iron transport protein B 2C PF07670 Nucleoside recognition 2C PF07664 Ferrous iron transport protein B C terminus and PF07670 Nucleoside recognition were all identified within CDS. Also 2C ten probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Some characterisation work within Campylobacter jejuni and Escherichia coli with acceptable identity scores. not added to product function. Functional classification -Transport 2Fbinding proteins - Cations 7EPMID:14735223 2C PMID:12446835 NC_002163.1 RefSeq region 1331320 1331667 . + . ID=id2496;gene=feoB;Name=id2496;Dbxref=GeneID:905687;gbkey=misc_feature;Note=HMMPfam hit to PF01926 2C GTPase of unknown function 2Cscore 1.4e-33 NC_002163.1 RefSeq region 1331338 1331361 . + . ID=id2497;gene=feoB;Name=id2497;Dbxref=GeneID:905687;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 1331764 1332147 . + . ID=id2498;gene=feoB;Name=id2498;Dbxref=GeneID:905687;gbkey=misc_feature;Note=HMMPfam hit to PF02421 2C Ferrous iron transport protein B 2C score 1.9e-46 NC_002163.1 RefSeq region 1331956 1332024 . + . ID=id2499;gene=feoB;Name=id2499;Dbxref=GeneID:905687;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1398 by TMHMM2.0 at aa 216-238 2C 266-288 2C 290-312 2C327-344 2C 357-379 2C 389-407 2C 449-466 2C 510-532 2C 553-575 and 585-607 NC_002163.1 RefSeq region 1332106 1332174 . + . ID=id2499;gene=feoB;Name=id2499;Dbxref=GeneID:905687;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1398 by TMHMM2.0 at aa 216-238 2C 266-288 2C 290-312 2C327-344 2C 357-379 2C 389-407 2C 449-466 2C 510-532 2C 553-575 and 585-607 NC_002163.1 RefSeq region 1332157 1332450 . + . ID=id2500;gene=feoB;Name=id2500;Dbxref=GeneID:905687;gbkey=misc_feature;Note=HMMPfam hit to PF07670 2C Nucleoside recognition 2Cscore 2.1e-12 NC_002163.1 RefSeq region 1332178 1332246 . + . ID=id2499;gene=feoB;Name=id2499;Dbxref=GeneID:905687;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1398 by TMHMM2.0 at aa 216-238 2C 266-288 2C 290-312 2C327-344 2C 357-379 2C 389-407 2C 449-466 2C 510-532 2C 553-575 and 585-607 NC_002163.1 RefSeq region 1332286 1332318 . + . ID=id2501;gene=feoB;Name=id2501;Dbxref=GeneID:905687;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1332289 1332342 . + . ID=id2499;gene=feoB;Name=id2499;Dbxref=GeneID:905687;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1398 by TMHMM2.0 at aa 216-238 2C 266-288 2C 290-312 2C327-344 2C 357-379 2C 389-407 2C 449-466 2C 510-532 2C 553-575 and 585-607 NC_002163.1 RefSeq region 1332379 1332447 . + . ID=id2499;gene=feoB;Name=id2499;Dbxref=GeneID:905687;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1398 by TMHMM2.0 at aa 216-238 2C 266-288 2C 290-312 2C327-344 2C 357-379 2C 389-407 2C 449-466 2C 510-532 2C 553-575 and 585-607 NC_002163.1 RefSeq region 1332472 1332633 . + . ID=id2502;gene=feoB;Name=id2502;Dbxref=GeneID:905687;gbkey=misc_feature;Note=HMMPfam hit to PF07664 2C Ferrous iron transport protein B C terminus 2C score 4.8e-21 NC_002163.1 RefSeq region 1332475 1332531 . + . ID=id2499;gene=feoB;Name=id2499;Dbxref=GeneID:905687;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1398 by TMHMM2.0 at aa 216-238 2C 266-288 2C 290-312 2C327-344 2C 357-379 2C 389-407 2C 449-466 2C 510-532 2C 553-575 and 585-607 NC_002163.1 RefSeq region 1332646 1333062 . + . ID=id2503;gene=feoB;Name=id2503;Dbxref=GeneID:905687;gbkey=misc_feature;Note=HMMPfam hit to PF07670 2C Nucleoside recognition 2Cscore 4.1e-19 NC_002163.1 RefSeq region 1332655 1332708 . + . ID=id2499;gene=feoB;Name=id2499;Dbxref=GeneID:905687;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1398 by TMHMM2.0 at aa 216-238 2C 266-288 2C 290-312 2C327-344 2C 357-379 2C 389-407 2C 449-466 2C 510-532 2C 553-575 and 585-607 NC_002163.1 RefSeq region 1332838 1332906 . + . ID=id2499;gene=feoB;Name=id2499;Dbxref=GeneID:905687;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1398 by TMHMM2.0 at aa 216-238 2C 266-288 2C 290-312 2C327-344 2C 357-379 2C 389-407 2C 449-466 2C 510-532 2C 553-575 and 585-607 NC_002163.1 RefSeq region 1332967 1333035 . + . ID=id2499;gene=feoB;Name=id2499;Dbxref=GeneID:905687;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1398 by TMHMM2.0 at aa 216-238 2C 266-288 2C 290-312 2C327-344 2C 357-379 2C 389-407 2C 449-466 2C 510-532 2C 553-575 and 585-607 NC_002163.1 RefSeq region 1333063 1333131 . + . ID=id2499;gene=feoB;Name=id2499;Dbxref=GeneID:905687;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1398 by TMHMM2.0 at aa 216-238 2C 266-288 2C 290-312 2C327-344 2C 357-379 2C 389-407 2C 449-466 2C 510-532 2C 553-575 and 585-607 NC_002163.1 RefSeq gene 1333149 1334642 . - . ID=gene1344;gene=hydA2;Name=hydA2;locus_tag=Cj1399c;Dbxref=GeneID:905688;gbkey=Gene NC_002163.1 RefSeq CDS 1333149 1334642 . - 0 ID=cds1269;Parent=gene1344;gene=hydA2;Name=YP_002344782.1;Dbxref=GOA:Q0P8L5 InterPro:IPR001821 InterPro:IPR006137 InterPro:IPR013634 UniProtKB FTrEMBL:Q0P8L5 Genbank:YP_002344782.1 GeneID:905688;gbkey=CDS;product=Ni 2FFe-hydrogenase small subunit;Note=Original 282000 29 note: Cj1399c 2C hydA2 2C probable Ni 2FFe-hydrogenase small subunit 2C len: 497 aa 3B similar to e.g. MBHS_WOLSU quinone-reactive Ni 2FFe-hydrogenase small chain 28354 aa 29 2C fasta scores 3B opt: 1122 z-score: 1317.8 E 28 29: 0 2C 52.6 25 identity in 285 aa overlap. No Hp ortholog. Also similar to Cj1267c 2851.5 25 identity in 330 aa overlap 29. Contains C-terminal extension not present in other hydrogenase small subunits 7EUpdated 282006 29 note: Pfam domain PF01058 NADH ubiquinone oxidoreductase 2C 20 Kd subunit identified within CDS. Further support given to product function. Characterised within Wolinella succinogenes 2C however 2Csequence alignment was only partial. Thus 2C kept within product function. Functional classification -Energy metabolism - Respiration 7EPMID:1587288 NC_002163.1 RefSeq region 1333992 1334306 . - . ID=id2504;gene=hydA2;Name=id2504;Dbxref=GeneID:905688;gbkey=misc_feature;Note=HMMPfam hit to PF01058 2C NADH ubiquinone oxidoreductase 2C 20 Kd sub 2C score 6e-06 ### NC_002163.1 RefSeq gene 1334646 1335470 . - . ID=gene1345;gene=fabI;Name=fabI;locus_tag=Cj1400c;Dbxref=GeneID:905689;gbkey=Gene NC_002163.1 RefSeq CDS 1334646 1335470 . - 0 ID=cds1270;Parent=gene1345;gene=fabI;Name=YP_002344783.1;Dbxref=GOA:Q0P8L4 InterPro:IPR002198 InterPro:IPR002347 InterPro:IPR014358 InterPro:IPR016040 UniProtKB FTrEMBL:Q0P8L4 Genbank:YP_002344783.1 GeneID:905689;gbkey=CDS;product=enoyl-ACP reductase;Note=Catalyzes a key regulatory step in fatty acid biosynthesis NC_002163.1 RefSeq region 1334724 1335446 . - . ID=id2505;gene=fabI;Name=id2505;Dbxref=GeneID:905689;gbkey=misc_feature;Note=HMMPfam hit to PF00106 2C short chain dehydrogenase 2Cscore 4.6e-20 ### NC_002163.1 RefSeq CDS 1335474 1336145 . - 0 ID=cds1271;Parent=gene1346;gene=tpiA;Name=YP_002344784.1;Dbxref=GOA:Q9PMQ6 HSSP:P36204 InterPro:IPR000652 InterPro:IPR013785 UniProtKB FSwiss-Prot:Q9PMQ6 Genbank:YP_002344784.1 GeneID:905690;gbkey=CDS;product=triosephosphate isomerase;Note=Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate NC_002163.1 RefSeq gene 1335474 1336145 . - . ID=gene1346;gene=tpiA;Name=tpiA;locus_tag=Cj1401c;Dbxref=GeneID:905690;gbkey=Gene NC_002163.1 RefSeq region 1335480 1336142 . - . ID=id2506;gene=tpiA;Name=id2506;Dbxref=GeneID:905690;gbkey=misc_feature;Note=HMMPfam hit to PF00121 2C Triosephosphate isomerase 2Cscore 1.3e-29 NC_002163.1 RefSeq CDS 1336142 1337344 . - 0 ID=cds1272;Parent=gene1347;gene=pgk;Name=YP_002344785.1;Dbxref=GOA:Q9PMQ5 HSSP:P36204 InterPro:IPR001576 InterPro:IPR015824 InterPro:IPR015901 InterPro:IPR015911 UniProtKB FSwiss-Prot:Q9PMQ5 Genbank:YP_002344785.1 GeneID:905691;gbkey=CDS;product=phosphoglycerate kinase;Note=Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway NC_002163.1 RefSeq gene 1336142 1337344 . - . ID=gene1347;gene=pgk;Name=pgk;locus_tag=Cj1402c;Dbxref=GeneID:905691;gbkey=Gene NC_002163.1 RefSeq region 1336151 1337341 . - . ID=id2507;gene=pgk;Name=id2507;Dbxref=GeneID:905691;gbkey=misc_feature;Note=HMMPfam hit to PF00162 2C Phosphoglycerate kinase 2Cscore 1.6e-207 NC_002163.1 RefSeq region 1337267 1337299 . - . ID=id2508;gene=pgk;Name=id2508;Dbxref=GeneID:905691;gbkey=misc_feature;Note=PS00111 Phosphoglycerate kinase signature ### NC_002163.1 RefSeq CDS 1337347 1338345 . - 0 ID=cds1273;Parent=gene1348;gene=gapA;Name=YP_002344786.1;Dbxref=GOA:Q0P8L1 InterPro:IPR000173 InterPro:IPR006424 UniProtKB FTrEMBL:Q0P8L1 Genbank:YP_002344786.1 GeneID:905692;gbkey=CDS;product=glyceraldehyde 3-phosphate dehydrogenase;Note=Original 282000 29 note: Cj1403c 2C gapA 2C glyceraldehyde 3-phosphate dehydrogenase 2C len: 332 aa 3B similar to e.g. G3P1_BACSU glyceraldehyde 3-phosphate dehydrogenase 1 28334 aa 29 2C fasta scores 3B opt: 1070 z-score: 1216.4 E 28 29: 0 2C 50.3 25 identity in 332 aa overlap. 45.6 25 identity to HP1346 and 46.7 25 identity to HP0921. Contains Pfam match to entry PF00044 gpdh 2C glyceraldehyde 3-phosphate dehydrogenases 2Cand PS00071 Glyceraldehyde 3-phosphate dehydrogenase active site 7EUpdated 282006 29 note: Pfam domains PF02800 and PF00044 Glyceraldehyde 3-phosphate dehydrogenase 2CC-terminal and N-terminal were both identified within CDS. Further support given to product function. Characterised within Bacillus subtilis with acceptable identity score. not added to product function. Functional classification - Energy metabolism - Glycolysis 7EPMID:10799476 NC_002163.1 RefSeq gene 1337347 1338345 . - . ID=gene1348;gene=gapA;Name=gapA;locus_tag=Cj1403c;Dbxref=GeneID:905692;gbkey=Gene NC_002163.1 RefSeq region 1337413 1337895 . - . ID=id2509;gene=gapA;Name=id2509;Dbxref=GeneID:905692;gbkey=misc_feature;Note=HMMPfam hit to PF02800 2C Glyceraldehyde 3-phosphate dehydrogenase 2C C- 2C score 7.5e-92 NC_002163.1 RefSeq region 1337881 1337904 . - . ID=id2510;gene=gapA;Name=id2510;Dbxref=GeneID:905692;gbkey=misc_feature;Note=PS00071 Glyceraldehyde 3-phosphate dehydrogenase active site NC_002163.1 RefSeq region 1337896 1338339 . - . ID=id2511;gene=gapA;Name=id2511;Dbxref=GeneID:905692;gbkey=misc_feature;Note=HMMPfam hit to PF00044 2C Glyceraldehyde 3-phosphate dehydrogenase 2C NA 2C score 1.2e-77 ### NC_002163.1 UTR_Extractor 5'-UTR 1338346 1338370 . - . ID=utr506;locus_tag=Cj1403c;product=glyceraldehyde 3-phosphate dehydrogenase NC_002163.1 UTR_Extractor 5'-UTR 1338377 1338403 . + . ID=utr507;locus_tag=Cj1404;product=putative nicotinate-nucleotide adenylyltransferase NC_002163.1 RefSeq gene 1338404 1338949 . + . ID=gene1349;gene=nadD;Name=nadD;locus_tag=Cj1404;Dbxref=GeneID:905693;gbkey=Gene NC_002163.1 RefSeq CDS 1338404 1338949 . + 0 ID=cds1274;Parent=gene1349;gene=nadD;Name=YP_002344787.1;Dbxref=GOA:Q9PMQ3 HSSP:P54455 InterPro:IPR004820 InterPro:IPR004821 InterPro:IPR005248 InterPro:IPR014729 UniProtKB FSwiss-Prot:Q9PMQ3 Genbank:YP_002344787.1 GeneID:905693;gbkey=CDS;product=nicotinate-nucleotide adenylyltransferase;Note=Original 282000 29 note: Cj1404 2C unknown 2C len: 181 aa 3B similar to hypothetical proteins e.g. YQEJ_BACSU 28189 aa 29 2Cfasta scores 3B opt: 305 z-score: 391.3 E 28 29: 1.8e-14 2C 30.2 25 identity in 182 aa overlap. 40.4 25 identity to HP1337 7EUpdated 282006 29 note: Pfam domain PF01467 Cytidylyltransferase identified within CDS. Product modified to more specific family member based on motif match. Characterised within Bacillus subtilis 2C however 2Cidentity scores were marginal. Thus 2C kept within product function. Functional classification - Misc 7EPMID:11704676 2C PMID:16153292 NC_002163.1 RefSeq region 1338416 1338874 . + . ID=id2512;gene=nadD;Name=id2512;Dbxref=GeneID:905693;gbkey=misc_feature;Note=HMMPfam hit to PF01467 2C Cytidylyltransferase 2C score 2.2e-24 ### NC_002163.1 UTR_Extractor 5'-UTR 1338959 1338976 . + . ID=utr508;locus_tag=Cj1405;product=hypothetical protein NC_002163.1 RefSeq gene 1338977 1339303 . + . ID=gene1350;Name=Cj1405;locus_tag=Cj1405;Dbxref=GeneID:905694;gbkey=Gene NC_002163.1 RefSeq CDS 1338977 1339303 . + 0 ID=cds1275;Parent=gene1350;Name=YP_002344788.1;Dbxref=InterPro:IPR004394 UniProtKB FTrEMBL:Q0P8K9 Genbank:YP_002344788.1 GeneID:905694;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1405 2C unknown 2C len: 108 aa 3B similar to hypothetical proteins e.g. YBEB_ECOLI 28105 aa 29 2Cfasta scores 3B opt: 185 z-score: 245.5 E 28 29: 2.4e-06 2C 28.1 25 identity in 96 aa overlap. 51.4 25 identity to HP1414 7EUpdated 282006 29 note: Pfam domain PF02410 Domain of unknown function DUF143 identified within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq region 1338980 1339279 . + . ID=id2513;Name=id2513;Dbxref=GeneID:905694;gbkey=misc_feature;Note=HMMPfam hit to PF02410 2C Domain of unknown function DUF143 2C score 6.4e-28 ### NC_002163.1 RefSeq gene 1339362 1339712 . - . ID=gene1351;Name=Cj1406c;locus_tag=Cj1406c;Dbxref=GeneID:905695;gbkey=Gene NC_002163.1 RefSeq CDS 1339362 1339712 . - 0 ID=cds1276;Parent=gene1351;Name=YP_002344789.1;Dbxref=InterPro:IPR009468 UniProtKB FTrEMBL:Q0P8K8 Genbank:YP_002344789.1 GeneID:905695;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1406c 2C probable periplasmic protein 2C len: 116 aa 3B similar to YQJC_ECOLI 28predicted periplasmic protein 29 28127 aa 29 2C fasta scores 3B opt: 160 z-score: 185.2 E 28 29: 0.0054 32.4 25 identity in 111 aa overlap. No Hp match. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF06476 Protein of unknown function 28DUF1090 29 identified within CDS. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 1339365 1339700 . - . ID=id2514;Name=id2514;Dbxref=GeneID:905695;gbkey=misc_feature;Note=HMMPfam hit to PF06476 2C Protein of unknown function 28DUF1090 29 2C score 4.6e-49 ### NC_002163.1 UTR_Extractor 5'-UTR 1339713 1339742 . - . ID=utr509;locus_tag=Cj1406c;product=putative periplasmic protein NC_002163.1 RefSeq CDS 1339759 1341147 . - 0 ID=cds1277;Parent=gene1352;Name=YP_002344790.1;Dbxref=GOA:Q0P8K7 InterPro:IPR005841 InterPro:IPR005843 InterPro:IPR005844 InterPro:IPR005845 InterPro:IPR005846 InterPro:IPR016055 UniProtKB FTrEMBL:Q0P8K7 Genbank:YP_002344790.1 GeneID:905696;gbkey=CDS;product=phospho-sugar mutase;Note=Original 282000 29 note: Cj1407c 2C probable phospho-sugar mutase 2C len: 462 aa 3B simial to e.g. ALGC_PSEAE phosphomannomutase 28462 aa 29 2C fasta scores 3B opt: 1037 z-score: 1216.2 E 28 29: 0 2C 40.7 25 identity in 457 aa overlap 2C and PGMU_NEIGO phosphoglucomutase 28460 aa 29 2C fasta scores 3B opt: 884 z-score: 1037.2 E 28 29: 0 2C 35.4 25 identity in 435 aa overlap. 44.7 25 identity to HP1275. Contains Pfam match to entry PF00408 PGM_PMM 2C Phosphoglucomutase and phosphomannomutase 2C and PS00017 ATP 2FGTP-binding site motif A 28P-loop 29. Also similar to Cj0360 2828.8 25 identity in 386 aa overlap 29 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score identified. kept within product function. Functional classification -Central intermediary metabolism - General 7EPMID:11839312 2C PMID:8050998 NC_002163.1 RefSeq gene 1339759 1341147 . - . ID=gene1352;Name=Cj1407c;locus_tag=Cj1407c;Dbxref=GeneID:905696;gbkey=Gene NC_002163.1 RefSeq region 1339774 1340034 . - . ID=id2515;Name=id2515;Dbxref=GeneID:905696;gbkey=misc_feature;Note=HMMPfam hit to PF00408 2CPhosphoglucomutase 2Fphosphomannomutase 2C C- 2C score 3.7e-09 NC_002163.1 RefSeq region 1340044 1340364 . - . ID=id2516;Name=id2516;Dbxref=GeneID:905696;gbkey=misc_feature;Note=HMMPfam hit to PF02880 2CPhosphoglucomutase 2Fphosphomannomutase 2C al 2C score 2e-16 NC_002163.1 RefSeq region 1340236 1340259 . - . ID=id2517;Name=id2517;Dbxref=GeneID:905696;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 1340365 1340676 . - . ID=id2518;Name=id2518;Dbxref=GeneID:905696;gbkey=misc_feature;Note=HMMPfam hit to PF02879 2CPhosphoglucomutase 2Fphosphomannomutase 2C al 2C score 4.9e-23 NC_002163.1 RefSeq region 1340704 1341123 . - . ID=id2519;Name=id2519;Dbxref=GeneID:905696;gbkey=misc_feature;Note=HMMPfam hit to PF02878 2CPhosphoglucomutase 2Fphosphomannomutase 2C al 2C score 1.3e-42 ### NC_002163.1 UTR_Extractor 5'-UTR 1341148 1341211 . - . ID=utr510;locus_tag=Cj1407c;product=putative phospho-sugar mutase NC_002163.1 UTR_Extractor 5'-UTR 1341222 1341249 . + . ID=utr511;locus_tag=Cj1408;product=flagellar basal body-associated protein FliL NC_002163.1 RefSeq CDS 1341250 1341786 . + 0 ID=cds1278;Parent=gene1353;gene=fliL;Name=YP_002344791.1;Dbxref=GOA:Q0P8K6 InterPro:IPR005503 UniProtKB FTrEMBL:Q0P8K6 Genbank:YP_002344791.1 GeneID:905697;gbkey=CDS;product=flagellar basal body-associated protein FliL;Note=interacts with the cytoplasmic MS ring of the basal body and may act to stabilize the MotAB complexes which surround the MS ring NC_002163.1 RefSeq gene 1341250 1341786 . + . ID=gene1353;gene=fliL;Name=fliL;locus_tag=Cj1408;Dbxref=GeneID:905697;gbkey=Gene NC_002163.1 RefSeq region 1341295 1341783 . + . ID=id2520;gene=fliL;Name=id2520;Dbxref=GeneID:905697;gbkey=misc_feature;Note=HMMPfam hit to PF03748 2C Flagellar basal body-associated protein FliL 2C score 6.8e-64 NC_002163.1 RefSeq region 1341304 1341372 . + . ID=id2521;gene=fliL;Name=id2521;Dbxref=GeneID:905697;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1408 by TMHMM2.0 at aa 19-41 NC_002163.1 UTR_Extractor 5'-UTR 1341643 1341785 . + . ID=utr512;locus_tag=Cj1409;product=4 27-phosphopantetheinyl transferase NC_002163.1 RefSeq gene 1341786 1342133 . + . ID=gene1354;gene=acpS;Name=acpS;locus_tag=Cj1409;Dbxref=GeneID:905698;gbkey=Gene NC_002163.1 RefSeq CDS 1341786 1342133 . + 0 ID=cds1279;Parent=gene1354;gene=acpS;Name=YP_002344792.1;Dbxref=GOA:Q9PMP8 HSSP:Q9F7T5 InterPro:IPR002582 InterPro:IPR004568 InterPro:IPR008278 UniProtKB FSwiss-Prot:Q9PMP8 Genbank:YP_002344792.1 GeneID:905698;gbkey=CDS;product=4 27-phosphopantetheinyl transferase;Note=Catalyzes the formation of holo-ACP 2C which mediates the essential transfer of acyl fatty acid intermediates during the biosynthesis of fatty acids and lipids NC_002163.1 RefSeq region 1341792 1341983 . + . ID=id2522;gene=acpS;Name=id2522;Dbxref=GeneID:905698;gbkey=misc_feature;Note=HMMPfam hit to PF01648 2C 4 27-phosphopantetheinyl transferase superfami 2C score 1.4e-14 ### NC_002163.1 RefSeq CDS 1342134 1342553 . - 0 ID=cds1280;Parent=gene1355;Name=YP_002344793.1;Dbxref=UniProtKB FTrEMBL:Q0P8K4 Genbank:YP_002344793.1 GeneID:905699;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1410c 2C possible membrane protein 2C len: 139 aa 3B no Hp match. Contains hydrophobic domain and PS00041 Bacterial regulatory proteins 2C araC family signature. Functional classification - Membranes 2Clipoproteins and porins NC_002163.1 RefSeq gene 1342134 1342553 . - . ID=gene1355;Name=Cj1410c;locus_tag=Cj1410c;Dbxref=GeneID:905699;gbkey=Gene NC_002163.1 RefSeq region 1342377 1342511 . - . ID=id2523;Name=id2523;Dbxref=GeneID:905699;gbkey=misc_feature;Note=PS00041 Bacterial regulatory proteins 2C araC family signature NC_002163.1 RefSeq region 1342389 1342457 . - . ID=id2524;Name=id2524;Dbxref=GeneID:905699;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1410c by TMHMM2.0 at aa 33-55 NC_002163.1 RefSeq gene 1342550 1343911 . - . ID=gene1356;Name=Cj1411c;locus_tag=Cj1411c;Dbxref=GeneID:905700;gbkey=Gene NC_002163.1 RefSeq CDS 1342550 1343911 . - 0 ID=cds1281;Parent=gene1356;Name=YP_002344794.1;Dbxref=GOA:Q0P8K3 InterPro:IPR001128 InterPro:IPR002401 UniProtKB FTrEMBL:Q0P8K3 Genbank:YP_002344794.1 GeneID:905700;gbkey=CDS;product=cytochrome P450;Note=Original 282000 29 note: Cj1411c 2C probable cytochrome P450 2C len: 453 aa 3B similar to many e.g. cytochrome P450 domain of CPXB_BACME cytochrome P450 2FNADPH-cytochrome P450 reductase 281048 aa 29 2C fasta scores 3B opt: 505 z-score: 578.8 E 28 29: 6.4e-25 2C 28.3 25 identity in 407 aa overlap. No Hp match. Contains PS00086 Cytochrome P450 cysteine heme-iron ligand signature 2C and Pfam match to entry PF00067 p450 2CCytochrome P450 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification -Energy metabolism - Electron transport 7EPMID:9308178 NC_002163.1 RefSeq region 1342568 1343890 . - . ID=id2525;Name=id2525;Dbxref=GeneID:905700;gbkey=misc_feature;Note=HMMPfam hit to PF00067 2C Cytochrome P450 2C score 4.3e-68 NC_002163.1 RefSeq region 1342709 1342738 . - . ID=id2526;Name=id2526;Dbxref=GeneID:905700;gbkey=misc_feature;Note=PS00086 Cytochrome P450 cysteine heme-iron ligand signature NC_002163.1 RefSeq gene 1343908 1345029 . - . ID=gene1357;Name=Cj1412c;locus_tag=Cj1412c;Dbxref=GeneID:905701;gbkey=Gene NC_002163.1 RefSeq CDS 1343908 1345029 . - 0 ID=cds1282;Parent=gene1357;Name=YP_002344795.1;Dbxref=GOA:Q0P8K2 UniProtKB FTrEMBL:Q0P8K2 Genbank:YP_002344795.1 GeneID:905701;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj1412c 2C probable integral membrane protein 2C len: 373 aa 3B no Hp match 7EUpdated 282006 29 note: Three probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 UTR_Extractor 5'-UTR 1343912 1344160 . - . ID=utr513;locus_tag=Cj1411c;product=putative cytochrome P450 NC_002163.1 RefSeq region 1343941 1344009 . - . ID=id122;Name=id122;Dbxref=GeneID:905701;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1412c by TMHMM2.0 at aa 115-137 2C 142-164 and 341-363 NC_002163.1 RefSeq region 1344538 1344606 . - . ID=id122;Name=id122;Dbxref=GeneID:905701;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1412c by TMHMM2.0 at aa 115-137 2C 142-164 and 341-363 NC_002163.1 RefSeq region 1344571 1344603 . - . ID=id2527;Name=id2527;Dbxref=GeneID:905701;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1344619 1344687 . - . ID=id122;Name=id122;Dbxref=GeneID:905701;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1412c by TMHMM2.0 at aa 115-137 2C 142-164 and 341-363 ### NC_002163.1 UTR_Extractor 5'-UTR 1345030 1345047 . - . ID=utr514;locus_tag=Cj1412c;product=putative integral membrane protein NC_002163.1 RefSeq CDS 1345102 1346286 . - 0 ID=cds1283;Parent=gene1358;gene=kpsS;Name=YP_002344796.1;Dbxref=GOA:Q0P8K1 InterPro:IPR007833 UniProtKB FTrEMBL:Q0P8K1 Genbank:YP_002344796.1 GeneID:905702;gbkey=CDS;product=capsule polysaccharide modification protein;Note=Original 282000 29 note: Cj1413c 2C possible polysaccharide modification protein 2C len: 394 aa 3B similar to e.g. LIPB_NEIME capsule polysaccharide modification protein 28419 aa 29 2C fasta scores 3B opt: 744 z-score: 897.9 E 28 29: 0 2C 38.5 25 identity in 395 aa overlap 2C and KSS5_ECOLI capsule polysaccharide export protein KPSS 28389 aa 29 2C fasta scores 3B opt: 919 z-score: 1108.7 E 28 29: 0 2C 40.2 25 identity in 383 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF05159 Capsule polysaccharide biosynthesis protein identified within CDS. Further support given to product function. Possible removed from product function as characterised within more than one genus with acceptable identity scores. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c -Cj1448c 29. Functional classification - Surface polysaccharides 2C lipopolysaccharides and antigens 7EPMID:8326861 2C PMID:8397187 2C PMID:10672176 NC_002163.1 RefSeq gene 1345102 1346286 . - . ID=gene1358;gene=kpsS;Name=kpsS;locus_tag=Cj1413c;Dbxref=GeneID:905702;gbkey=Gene NC_002163.1 RefSeq region 1345126 1346046 . - . ID=id2528;gene=kpsS;Name=id2528;Dbxref=GeneID:905702;gbkey=misc_feature;Note=HMMPfam hit to PF05159 2C Capsule polysaccharide biosynthesis pro 2C score 4.1e-137 NC_002163.1 RefSeq region 1345750 1345818 . - . ID=id2529;gene=kpsS;Name=id2529;Dbxref=GeneID:905702;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1413c by TMHMM2.0 at aa 157-179 NC_002163.1 RefSeq gene 1346283 1348352 . - . ID=gene1359;gene=kpsC;Name=kpsC;locus_tag=Cj1414c;Dbxref=GeneID:905703;gbkey=Gene NC_002163.1 RefSeq CDS 1346283 1348352 . - 0 ID=cds1284;Parent=gene1359;gene=kpsC;Name=YP_002344797.1;Dbxref=GOA:Q0P8K0 InterPro:IPR007833 UniProtKB FTrEMBL:Q0P8K0 Genbank:YP_002344797.1 GeneID:905703;gbkey=CDS;product=capsule polysaccharide modification protein;Note=Original 282000 29 note: Cj1414c 2C possible polysaccharide modification protein 2C len: 689 aa 3B similar to e.g. LIPA_NEIME capsule polysaccharide modification protein 28400 aa 29 2C fasta scores 3B opt: 927 z-score: 1062.5 E 28 29: 0 2C 39.6 25 identity in 394 aa overlap 2C and KSC5_ECOLI capsule polysaccharide export protein KPSC 28675 aa 29 2C fasta scores 3B opt: 724 z-score: 827.0 E 28 29: 0 2C 38.5 25 identity in 655 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF05159 Capsule polysaccharide biosynthesis protein identified within CDS. Further support given to product function. Possible removed from product function due to characterisation within more than one genus with acceptable identity scores. Literature search identified papers giving further clues to product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:8326861 2C PMID:8397187 2C PMID:15612919 2CPMID:10672176 NC_002163.1 UTR_Extractor 5'-UTR 1346287 1346390 . - . ID=utr515;locus_tag=Cj1413c;product=capsule polysaccharide modification protein NC_002163.1 RefSeq region 1346451 1347257 . - . ID=id2530;gene=kpsC;Name=id2530;Dbxref=GeneID:905703;gbkey=misc_feature;Note=HMMPfam hit to PF05159 2C Capsule polysaccharide biosynthesis pro 2C score 2.5e-118 NC_002163.1 RefSeq region 1347477 1348256 . - . ID=id2531;gene=kpsC;Name=id2531;Dbxref=GeneID:905703;gbkey=misc_feature;Note=HMMPfam hit to PF05159 2C Capsule polysaccharide biosynthesis pro 2C score 2.5e-81 NC_002163.1 RefSeq gene 1348349 1348861 . - . ID=gene1360;gene=cysC;Name=cysC;locus_tag=Cj1415c;Dbxref=GeneID:905704;gbkey=Gene NC_002163.1 RefSeq CDS 1348349 1348861 . - 0 ID=cds1285;Parent=gene1360;gene=cysC;Name=YP_002344798.1;Dbxref=GOA:Q0P8J9 InterPro:IPR000623 InterPro:IPR002891 UniProtKB FTrEMBL:Q0P8J9 Genbank:YP_002344798.1 GeneID:905704;gbkey=CDS;product=adenylylsulfate kinase;Note=converts ATP and adenylyl sulfate to ADP and 3 27-phosphoadenylyl sulfate 3B in Escherichia coli this enzyme functions in cysteine biosynthesis NC_002163.1 RefSeq region 1348397 1348852 . - . ID=id2532;gene=cysC;Name=id2532;Dbxref=GeneID:905704;gbkey=misc_feature;Note=HMMPfam hit to PF01583 2C Adenylylsulphate kinase 2Cscore 2.7e-17 NC_002163.1 RefSeq region 1348805 1348828 . - . ID=id2533;gene=cysC;Name=id2533;Dbxref=GeneID:905704;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 1348851 1349612 . - 0 ID=cds1286;Parent=gene1361;Name=YP_002344799.1;Dbxref=GOA:Q0P8J8 InterPro:IPR005835 UniProtKB FTrEMBL:Q0P8J8 Genbank:YP_002344799.1 GeneID:905705;gbkey=CDS;product=sugar nucleotidyltransferase;Note=Original 282000 29 note: Cj1416c 2C probable sugar nucleotidyltransferase 2C len: 253 aa 3B similar to predicted nucleotidyltransferases e.g. TR:O29123 28EMBL:AE001025 29 Archaeoglobus fulgidus predicted glucose-1-phosphate cytidylyltransferase AF1142 28241 aa 29 2C fasta scores 3B opt: 252 z-score: 309.2 E 28 29: 6.7e-10 2C 26.7 25 identity in 251 aa overlap. Also similar in part to LICC_HAEIN LICC protein 28involved in LPS synthesis 29 28198 aa 29 2C fasta scores 3B opt: 209 z-score: 259.6 E 28 29: 3.9e-07 2C 32.7 25 identity in 107 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00483 NTP_transferase 2C Nucleotidyl transferase 7EUpdated 282006 29 note: Specific characterisation still required 2C so kept within product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2C lipopolysaccharides and antigens 7EPMID:15612919 2C PMID:10672176 NC_002163.1 RefSeq gene 1348851 1349612 . - . ID=gene1361;gene=Cj1416c;Name=Cj1416c;locus_tag=Cj1416c;Dbxref=GeneID:905705;gbkey=Gene NC_002163.1 RefSeq region 1348863 1349609 . - . ID=id2534;Name=id2534;Dbxref=GeneID:905705;gbkey=misc_feature;Note=HMMPfam hit to PF00483 2C Nucleotidyl transferase 2Cscore 0.00053 ### NC_002163.1 UTR_Extractor 5'-UTR 1349613 1349684 . - . ID=utr516;locus_tag=Cj1416c;product=putative sugar nucleotidyltransferase NC_002163.1 RefSeq gene 1349614 1350216 . - . ID=gene1362;Name=Cj1417c;locus_tag=Cj1417c;Dbxref=GeneID:905706;gbkey=Gene NC_002163.1 RefSeq CDS 1349614 1350216 . - 0 ID=cds1287;Parent=gene1362;Name=YP_002344800.1;Dbxref=GOA:Q0P8J7 UniProtKB FTrEMBL:Q0P8J7 Genbank:YP_002344800.1 GeneID:905706;gbkey=CDS;product=amidotransferase;Note=Original 282000 29 note: Cj1417c 2C unknown 2C len: 200 aa 3B some similarity to the C-terminus of carbamoyl-phosphate synthase small subunitss e.g. CARX_BACSU carbamoyl-phosphate synthase 2Carginine-specific 2C small chain 28353 aa 29 2C fasta scores 3B opt: 134 z-score: 174.1 E 28 29: 0.022 2C 27.3 25 identity in 99 aa overlap. No Hp ortholog 7EUpdated 282006 29 note: Pfam domain PF00117 2C Glutamine amidotransferase class-I identified within CDS. Product function modified to more specific family member based on motif match. kept within product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Misc 7EPMID:15612919 2C PMID:10672176 NC_002163.1 RefSeq gene 1350207 1352546 . - . ID=gene1363;Name=Cj1418c;locus_tag=Cj1418c;Dbxref=GeneID:905707;gbkey=Gene NC_002163.1 RefSeq CDS 1350207 1352546 . - 0 ID=cds1288;Parent=gene1363;Name=YP_002344801.1;Dbxref=GOA:Q0P8J6 InterPro:IPR008279 UniProtKB FTrEMBL:Q0P8J6 Genbank:YP_002344801.1 GeneID:905707;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1418c 2C unknown 2C len: 779 aa 3B weak similarity in part to several phosphoenolpyruvate synthases e.g. PPSA_STAMA probable phosphoenolpyruvate synthase 28834 aa 29 2C fasta scores 3B opt: 166 z-score: 182.8 E 28 29: 0.0074 2C 23.9 25 identity in 226 aa overlap. No Hp ortholog 7EUpdated 282006 29 note: Interpro IPR008279 2CPEP-utilising enzyme 2C mobile region identified within CDS. Product modified to more specific family member. Similar to phosphoenolpyruvate synthase and pyruvate kinase in other bacteria with unnacceptable identity scores. kept within product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Misc 7EPMID:15612919 2C PMID:10672176 2C PMID:2176881 ### NC_002163.1 UTR_Extractor 5'-UTR 1352547 1352761 . - . ID=utr517;locus_tag=Cj1418c;product=hypothetical protein NC_002163.1 RefSeq gene 1352561 1353322 . - . ID=gene1364;Name=Cj1419c;locus_tag=Cj1419c;Dbxref=GeneID:905708;gbkey=Gene NC_002163.1 RefSeq CDS 1352561 1353322 . - 0 ID=cds1289;Parent=gene1364;Name=YP_002344802.1;Dbxref=GOA:Q0P8J5 InterPro:IPR013216 UniProtKB FTrEMBL:Q0P8J5 Genbank:YP_002344802.1 GeneID:905708;gbkey=CDS;product=methyltransferase;Note=Original 282000 29 note: Cj1419c 2C possible methyltransferase 2C len: 253 aa 3B similar to hypothetical proteins e.g. TR:O53392 28EMBL:AL021841 29 Mycobacterium tuberculosis Rv3342 28MTV016.42 29 28243 aa 29 2C fasta scores 3B opt: 210 z-score: 250.1 E 28 29: 1.3e-06 2C 32.0 25 identity in 122 aa overlap. Also contains weak similarity in part to several methyltransferases e.g. UBIE_ECOLI ubiquinone 2Fmenaquinone biosynthesis methyltransferase 28251 aa 29 2C fasta scores 3B opt: 141 z-score: 171.3 E 28 29: 0.032 2C24.2 25 identity in 132 aa overlap. No Hp match. Also similar to Cj1420c 2833.7 25 identity in 255 aa overlap 29 7EUpdated 282006 29 note: Running individual Pfam search identified PF08241 and PF08242 Methyltransferase domains. Further support given to product function. No specific characterisation carried out yet. Literature search identified papers giving further clues to product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Misc 7EPMID:15612919 2C PMID:10672176 ### NC_002163.1 RefSeq CDS 1353375 1354148 . - 0 ID=cds1290;Parent=gene1365;Name=YP_002344803.1;Dbxref=GOA:Q0P8J4 InterPro:IPR002345 InterPro:IPR013216 UniProtKB FTrEMBL:Q0P8J4 Genbank:YP_002344803.1 GeneID:905709;gbkey=CDS;product=methyltransferase;Note=Original 282000 29 note: Cj1420c 2C unknown 2C len: 258 aa 3B similar to hypothetical proteins e.g. TR:O53392 28EMBL:AL021841 29 Mycobacterium tuberculosis Rv3342 28MTV016.42 29 28243 aa 29 2C fasta scores 3B opt: 219 z-score: 263.3 E 28 29: 2.4e-07 2C 30.7 25 identity in 137 aa overlap. Also similar to Cj1419c 2834.1 25 identity in 255 aa overlap 29. Contains C 289-10 29 polymorphic region at aa 132. C9 28consensus 29 gives this ORF 2C C10 would give truncation after a further 19 aa 7EUpdated 282006 29 note: Prostie domain PS00213 LIPOCALIN 2C Lipocalin signature identified within CDS. Conserved added to product function. Running individual Pfam search identified PF08241 and PF08242 Methyltransferase domains. Product modified to more specific family member based on motif search results. No specific characterisation has been carried out yet 2C so kept within product function. Literature search identified paper giving further clues to product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Misc 7EPMID:15612919 2C PMID:10672176 NC_002163.1 RefSeq gene 1353375 1354148 . - . ID=gene1365;Name=Cj1420c;locus_tag=Cj1420c;Dbxref=GeneID:905709;gbkey=Gene NC_002163.1 RefSeq region 1353507 1353542 . - . ID=id2535;Name=id2535;Dbxref=GeneID:905709;gbkey=misc_feature;Note=PS00213 Lipocalin signature NC_002163.1 RefSeq region 1354133 1382483 . + . ID=id2536;Name=id2536;gbkey=misc_feature;Note=region with low G 2BC: 26.5 25 NC_002163.1 UTR_Extractor 5'-UTR 1354149 1354173 . - . ID=utr518;locus_tag=Cj1420c;product=putative methyltransferase NC_002163.1 RefSeq CDS 1354215 1356053 . - 0 ID=cds1291;Parent=gene1366;Name=YP_002344804.1;Dbxref=GOA:Q0P8J3 UniProtKB FTrEMBL:Q0P8J3 Genbank:YP_002344804.1 GeneID:905710;gbkey=CDS;product=sugar transferase;Note=Original 282000 29 note: Cj1421c 2C possible sugar transferase 2C len: 612 aa 3B no Hp match. Similar to polymorphic tract-containing genes Cj1422c 28overall 58.2 25 identity in 636 aa overlap 2C but N- and C-terminal 250 and 40 aa are identical 29 2C Cj0685c 2828.0 25 identity in 404 aa overlap 29. N-terminus is simlar to parts of Cj1431c 2838.6 25 identity in 114 aa overlap 29 2C and sugar transferases Cj1434c 2839.6 25 identity in 111 aa overlap 29 2Cand Cj1438c 2834.6 25 identity in 127 aa overlap 29. Contains C 288-10 29 polymorphic tract at aa 30. C9 28consensus 29 gives this ORF 2C C8 gives truncation after 2B1 aa 2C C10 gives truncation after 2B5 aa. functional assignment is based on family clustering 28BLASTP 29 with other C. jejuni predicted sugar transferases e.g. Cj1434c 2C and Cj1438c 7EUpdated 282006 29 note: Identified within the Campylobacter jejuni Capsule locus 28Cj1413c - Cj1448c 29. No specific characterisation has been carried out yet. kept within product function. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:15612919 2C PMID:10672176 NC_002163.1 RefSeq gene 1354215 1356053 . - . ID=gene1366;Name=Cj1421c;locus_tag=Cj1421c;Dbxref=GeneID:905710;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 1356054 1356090 . - . ID=utr519;locus_tag=Cj1421c;product=putative sugar transferase NC_002163.1 RefSeq CDS 1356108 1357985 . - 0 ID=cds1292;Parent=gene1367;Name=YP_002344805.1;Dbxref=GOA:Q0P8J2 InterPro:IPR000425 UniProtKB FTrEMBL:Q0P8J2 Genbank:YP_002344805.1 GeneID:905711;gbkey=CDS;product=sugar transferase;Note=Original 282000 29 note: Cj1422c 2C possible sugar transferase 2C len: 625 aa 3B no Hp match. Similar to polymorphic tract-containing genes Cj1421c 28overall 58.2 25 identity in 636 aa overlap 2C but N- and C-terminal 250 and 40 aa are identical 29 2C Cj0685c 2825.6 25 identity in 442 aa overlap 29. N-terminus is simlar to parts of Cj1431c 2838.6 25 identity in 114 aa overlap 29 2C and sugar transferases Cj1434c 2839.6 25 identity in 111 aa overlap 29 2Cand Cj1438c 2823.5 25 identity in 452 aa overlap 29. Contains C 289-10 29 polymorphic tract at aa 30. C9 28consensus 29 gives this ORF 2C C10 gives truncation after 2B5 aa. functional assignment is based on family clustering 28BLASTP 29 with other C. jejuni predicted sugar transferases e.g. Cj1434c 2C and Cj1438c 7EUpdated 282006 29 note: Prosite PS00221 MIP family signature identified within CDS. No specific characterisation has been carried out yet. kept within product function. Identified within the Campylobacter jejuni Capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:15612919 2C PMID:10672176 NC_002163.1 RefSeq gene 1356108 1357985 . - . ID=gene1367;Name=Cj1422c;locus_tag=Cj1422c;Dbxref=GeneID:905711;gbkey=Gene NC_002163.1 RefSeq region 1356117 1356143 . - . ID=id2537;Name=id2537;Dbxref=GeneID:905711;gbkey=misc_feature;Note=PS00221 MIP family signature NC_002163.1 UTR_Extractor 5'-UTR 1357986 1358022 . - . ID=utr520;locus_tag=Cj1422c;product=putative sugar transferase NC_002163.1 RefSeq CDS 1358036 1358701 . - 0 ID=cds1293;Parent=gene1368;gene=hddC;Name=YP_002344806.1;Dbxref=GOA:Q0P8J1 InterPro:IPR005835 UniProtKB FTrEMBL:Q0P8J1 Genbank:YP_002344806.1 GeneID:905712;gbkey=CDS;product=D-glycero-D-manno-heptose 1-phosphate guanosyltransferase;Note=Original 282000 29 note: Cj1423c 2C possible sugar-phosphate nucleotidyltransferase 2C len: 221 aa 3B similar to many predicted nucleotidyltransferases 2C e.g. TR:O58775 28EMBL:AP000004 29 Pyrococcus horikoshii hypothetical sugar-phosphate nucleotydyl transferase PH1022 28416 aa 29 2C fasta scores 3B opt: 413 z-score: 496.0 E 28 29: 2.6e-20 2C 34.3 25 identity in 230 aa overlap 2C and MPG1_YEAST mannose-1-phosphate guanyltransferase 28361 aa 29 2Cfasta scores 3B opt: 258 z-score: 313.4 E 28 29: 3.9e-10 2C 28.9 25 identity in 232 aa overlap. Contains Pfam match to entry PF00483 NTP_transferase 2C Nucleotidyl transferase. No Hp ortholog. Also similar to Cj1329 2835.6 25 identity in 216 aa overlap 29 7EUpdated 282006 29 note: Some characterisation work carried out within Campylobacter jejuni. Product function modified to more specific family member. kept within product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:15612919 2C PMID:10672176 NC_002163.1 RefSeq gene 1358036 1358701 . - . ID=gene1368;gene=hddC;Name=hddC;locus_tag=Cj1423c;Dbxref=GeneID:905712;gbkey=Gene NC_002163.1 RefSeq region 1358039 1358698 . - . ID=id2538;gene=hddC;Name=id2538;Dbxref=GeneID:905712;gbkey=misc_feature;Note=HMMPfam hit to PF00483 2C Nucleotidyl transferase 2Cscore 1.9e-13 NC_002163.1 RefSeq gene 1358689 1359294 . - . ID=gene1369;gene=gmhA2;Name=gmhA2;locus_tag=Cj1424c;Dbxref=GeneID:905713;gbkey=Gene NC_002163.1 RefSeq CDS 1358689 1359294 . - 0 ID=cds1294;Parent=gene1369;gene=gmhA2;Name=YP_002344807.1;Dbxref=GOA:Q9PMN3 InterPro:IPR001347 InterPro:IPR004515 UniProtKB FSwiss-Prot:Q9PMN3 Genbank:YP_002344807.1 GeneID:905713;gbkey=CDS;product=phosphoheptose isomerase;Note=Original 282000 29 note: Cj1424c 2C gmhA2 2C probable phosphoheptose isomerase 2C len: 201 aa 3B similar to many e.g. LPCA_ECOLI phosphoheptose isomerase 28EC 5.-.-.- 29 28192 aa 29 2C fasta scores 3B opt: 453 z-score: 548.7 E 28 29: 3.1e-23 2C39.2 25 identity in 186 aa overlap. No Hp ortholog. Also similar to Cj1149c gmhA 2857.8 25 identity in 147 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01380 SIS domain identified within CDS. Further support given to product function. Characterisation work carried out within Campylobacter jejuni and Escherichia coli 2C so removed from product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:15612919 2C PMID:10672176 2C PMID:12101286 NC_002163.1 RefSeq region 1358710 1359177 . - . ID=id2539;gene=gmhA2;Name=id2539;Dbxref=GeneID:905713;gbkey=misc_feature;Note=HMMPfam hit to PF01380 2C SIS domain 2C score 1.4e-11 NC_002163.1 RefSeq CDS 1359282 1360301 . - 0 ID=cds1295;Parent=gene1370;gene=hddA;Name=YP_002344808.1;Dbxref=GOA:Q0P8I9 InterPro:IPR001174 InterPro:IPR006162 InterPro:IPR006204 InterPro:IPR013750 InterPro:IPR014606 InterPro:IPR014721 UniProtKB FTrEMBL:Q0P8I9 Genbank:YP_002344808.1 GeneID:905714;gbkey=CDS;product=D-glycero-D-manno-heptose 7-phosphate kinase;Note=Original 282000 29 note: Cj1425c 2C possible sugar kinase 2C len: 339 aa 3B similar to e.g. GAL1_LACHE galactokinase 28388 aa 29 2C fasta scores 3B opt: 186 z-score: 227.6 E 28 29: 2.4e-05 2C 24.3 25 identity in 371 aa overlap. Contains PS00012 Phosphopantetheine attachment site. No Hp match 7EUpdated 282006 29 note: Pfam domain PF00288 GHMP kinases ATP-binding protein identified within CDS. Further support given to product function. Literature search identified work carried out within Campylobacter jejuni. Not yet fully characterised 2C so kept within product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:15612919 2C PMID:10672176 NC_002163.1 RefSeq gene 1359282 1360301 . - . ID=gene1370;gene=hddA;Name=hddA;locus_tag=Cj1425c;Dbxref=GeneID:905714;gbkey=Gene NC_002163.1 RefSeq region 1359381 1360010 . - . ID=id2540;gene=hddA;Name=id2540;Dbxref=GeneID:905714;gbkey=misc_feature;Note=HMMPfam hit to PF00288 2C GHMP kinases ATP-binding protei 2C score 5.8e-42 NC_002163.1 RefSeq region 1359921 1359968 . - . ID=id2541;gene=hddA;Name=id2541;Dbxref=GeneID:905714;gbkey=misc_feature;Note=PS00012 Phosphopantetheine attachment site NC_002163.1 UTR_Extractor 5'-UTR 1360302 1360313 . - . ID=utr521;locus_tag=Cj1425c;product=putative D-glycero-D-manno-heptose 7-phosphate kinase NC_002163.1 RefSeq CDS 1360321 1361172 . - 0 ID=cds1296;Parent=gene1371;Name=YP_002344809.1;Dbxref=GOA:Q0P8I8 InterPro:IPR006342 UniProtKB FTrEMBL:Q0P8I8 Genbank:YP_002344809.1 GeneID:905715;gbkey=CDS;product=methyltransferase family protein;Note=Original 282000 29 note: Cj1426c 2C unknown 2C len: 283 aa 3B no Hp match. Contains C 2810-11 29 polymorphic region at aa 99. C10 28consensus 29 gives this ORF 2C C11 gives truncation after 2B8 aa 7EUpdated 282006 29 note: TIGRFAM motif TIGR01444 Methyltransferase FkbM 2C identified within CDS. Product modified to more specific family member based on motif match. No specific characterisation has been carried out yet 2C so kept within product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c -Cj1448c 29. Functional classification - Misc 7EPMID:15612919 2C PMID:10672176 NC_002163.1 RefSeq gene 1360321 1361172 . - . ID=gene1371;Name=Cj1426c;locus_tag=Cj1426c;Dbxref=GeneID:905715;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 1361173 1361450 . - . ID=utr522;locus_tag=Cj1426c;product=putative methyltransferase family protein NC_002163.1 RefSeq CDS 1361191 1362132 . - 0 ID=cds1297;Parent=gene1372;Name=YP_002344810.1;Dbxref=GOA:Q0P8I7 InterPro:IPR001509 InterPro:IPR016040 UniProtKB FTrEMBL:Q0P8I7 Genbank:YP_002344810.1 GeneID:905716;gbkey=CDS;product=sugar-nucleotide epimerase 2Fdehydratease;Note=Original 282000 29 note: Cj1427c 2C probable sugar-nucleotide epimerase 2Fdehydratease 2C len: 313 aa 3B similar to many predicted epimerases 2Fdehydrateases e.g. TR:Q25130 28EMBL:D25537 29 HALOCYNTHIA RORETZI 28SEA SQUIRT 29 gene with similarity to UDPglucose4-epimerases and 3beta-hydroxysteroid dehydrogenase 2Fisomerases HREPIB 28241 aa 29 2C fasta scores 3B opt: 585 z-score: 691.2 E 28 29: 3.5e-31 2C44.2 25 identity in 208 aa overlap 2C and TR:O73960 28EMBL:AP000002 29 Pyrococcus horikoshii hypothetical UDP-glucose 4-epimerase 28318 aa 29 2C fasta scores 3B opt: 304 z-score: 361.7 E 28 29: 7.9e-13 2C 26.4 25 identity in 326 aa overlap. No Hp ortholog 7EUpdated 282006 29 note: Pfam domain PF01370 NAD dependent epimerase 2Fdehydratase family identified within CDS. Further support given to product function. Literature search identified papers giving further information on product function. kept within product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2C lipopolysaccharides and antigens 7EPMID:15612919 2C PMID:10672176 2C PMID:9708982 NC_002163.1 RefSeq gene 1361191 1362132 . - . ID=gene1372;Name=Cj1427c;locus_tag=Cj1427c;Dbxref=GeneID:905716;gbkey=Gene NC_002163.1 RefSeq gene 1362156 1363196 . - . ID=gene1373;gene=fcl;Name=fcl;locus_tag=Cj1428c;Dbxref=GeneID:905717;gbkey=Gene NC_002163.1 RefSeq CDS 1362156 1363196 . - 0 ID=cds1298;Parent=gene1373;gene=fcl;Name=YP_002344811.1;Dbxref=GOA:Q0P8I6 InterPro:IPR001509 InterPro:IPR016040 UniProtKB FTrEMBL:Q0P8I6 Genbank:YP_002344811.1 GeneID:905717;gbkey=CDS;product=GDP-L-fucose synthetase;Note=Original 282000 29 note: Cj1428c 2C fcl 2C probable fucose synthetase 2C len: 346 aa 3B similar to e.g. FCL_ECOLI fucose synthetase 28321 aa 29 2C fasta scores 3B opt: 562 z-score: 690.0 E 28 29: 4.1e-31 2C 39.0 25 identity in 341 aa overlap. 29.6 25 identity to HP0045. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 7EUpdated 282006 29 note: Pfam domain PF01370 NAD dependent epimerase 2Fdehydratase family identified within CDS. Further support given to product function. Literature search identified papers giving further information on product function. Characterised within Escherichia coli with acceptable identity score. not added to product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:15612919 2C PMID:10672176 2C PMID:11021971 2CPMID:9862812 NC_002163.1 RefSeq region 1362663 1362686 . - . ID=id2542;gene=fcl;Name=id2542;Dbxref=GeneID:905717;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq gene 1363196 1364122 . - . ID=gene1374;Name=Cj1429c;locus_tag=Cj1429c;Dbxref=GeneID:905718;gbkey=Gene NC_002163.1 RefSeq CDS 1363196 1364122 . - 0 ID=cds1299;Parent=gene1374;Name=YP_002344812.1;Dbxref=UniProtKB FTrEMBL:Q0P8I5 Genbank:YP_002344812.1 GeneID:905718;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1429c 2C unknown 2C len: 308 aa 3B no Hp match. Contains C 289-10 29 polymorphic region at aa 98. C10 28consensus 29 gives this ORF 2C C9 would give truncation after 2B1 aa 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Unknown 7EPMID:15612919 2C PMID:10672176 NC_002163.1 UTR_Extractor 5'-UTR 1363197 1363281 . - . ID=utr523;locus_tag=Cj1428c;product=GDP-L-fucose synthetase NC_002163.1 RefSeq gene 1364126 1364671 . - . ID=gene1375;gene=rfbC;Name=rfbC;locus_tag=Cj1430c;Dbxref=GeneID:905719;gbkey=Gene NC_002163.1 RefSeq CDS 1364126 1364671 . - 0 ID=cds1300;Parent=gene1375;gene=rfbC;Name=YP_002344813.1;Dbxref=GOA:Q0P8I4 InterPro:IPR000888 InterPro:IPR014710 UniProtKB FTrEMBL:Q0P8I4 Genbank:YP_002344813.1 GeneID:905719;gbkey=CDS;product=dTDP-4-dehydrorhamnose 3 2C5-epimerase;Note=Original 282000 29 note: Cj1430c 2C probable nucleotide-sugar epimerase 2Fdehydratase 2C len: 181 aa 3B similar to e.g. RFBC_ECOLI DTDP-4-dehydrorhamnose 3 2C5-epimerase 28185 aa 29 2C fasta scores 3B opt: 303 z-score: 386.2 E 28 29: 3.4e-14 2C 33.9 25 identity in 165 aa overlap 2C and TR:Q46770 28EMBL:U23775 29 E. coli rmlC DTDP-6-deoxy-l-lyxo-4-hexulose reductase 28183 aa 29 2C fasta scores 3B opt: 306 z-score: 390.0 E 28 29: 2.1e-14 2C 33.5 25 identity in 164 aa overlap. No Hp match. Contains Pfam match to entry PF00908 dTDP_sugar_isom 2CdTDP-4-dehydrorhamnose 3 2C5-epimerase 7EUpdated 282006 29 note: Pfam domain PF00908 dTDP-4-dehydrorhamnose 3 2C5-epimerase identified within CDS. Further support given to product function. Literature search identified papers giving further information on product function. Product function modified based on literature search information. Characterised within Escherichia coli with marginal identity score. kept within product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:15612919 2C PMID:10672176 2C PMID:7517390 NC_002163.1 RefSeq region 1364138 1364668 . - . ID=id2543;gene=rfbC;Name=id2543;Dbxref=GeneID:905719;gbkey=misc_feature;Note=HMMPfam hit to PF00908 2C dTDP-4-dehydrorhamnose 3 2C5-epimerase 2C score 9.4e-17 NC_002163.1 RefSeq CDS 1364671 1366419 . - 0 ID=cds1301;Parent=gene1376;gene=hddC;Name=YP_002344814.1;Dbxref=GOA:Q0P8I3 InterPro:IPR000873 UniProtKB FTrEMBL:Q0P8I3 Genbank:YP_002344814.1 GeneID:905720;gbkey=CDS;product=capsular polysaccharide heptosyltransferase;Note=Original 282000 29 note: Cj1431c 2C unknown 2C len: 582 aa 3B no Hp match. Similar in part to N-termini of Cj1421c 2838.6 25 identity in 114 aa overlap 29 2C and Cj1422c 2838.6 25 identity in 114 aa overlap 29. Contains PS00455 AMP-binding domain signature 7EUpdated 282006 29 note: Characterised within Campylobacter jejuni. Product modified to more specific family member based on literature search results. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2C lipopolysaccharides and antigens 7EPMID:15612919 NC_002163.1 RefSeq gene 1364671 1366419 . - . ID=gene1376;gene=hddC;Name=hddC;locus_tag=Cj1431c;Dbxref=GeneID:905720;gbkey=Gene NC_002163.1 RefSeq region 1365574 1365609 . - . ID=id2544;gene=hddC;Name=id2544;Dbxref=GeneID:905720;gbkey=misc_feature;Note=PS00455 AMP-binding domain signature NC_002163.1 RefSeq gene 1366422 1369517 . - . ID=gene1377;Name=Cj1432c;locus_tag=Cj1432c;Dbxref=GeneID:905721;gbkey=Gene NC_002163.1 RefSeq CDS 1366422 1369517 . - 0 ID=cds1302;Parent=gene1377;Name=YP_002344815.1;Dbxref=GOA:Q0P8I2 InterPro:IPR001296 InterPro:IPR006439 UniProtKB FTrEMBL:Q0P8I2 Genbank:YP_002344815.1 GeneID:905721;gbkey=CDS;product=sugar transferase;Note=Original 282000 29 note: Cj1432c 2C possible sugar transferase 2C len: 1031 aa 3B weakly similar to e.g. TR:Q48232 28EMBL:X78559 29 Haemophilus influenzae orf3 in DNA for serotypE B capsulation locus 281215 aa 29 2C fasta scores 3B opt: 361 z-score: 398.4 E 28 29: 7.2e-15 2C 22.8 25 identity in 1029 aa overlap 2C and TR:O84910 28EMBL:AF010183 29 glycosyltransferase WBPZ 28381 aa 29 2C fasta scores 3B opt: 161 z-score: 182.7 E 28 29: 0.0074 2C 23.1 25 identity in 251 aa overlap. Contains Pfam match to entry PF00534 Glycos_transf_1 2C Glycosyl transferases group 1. Also similar to Cj1434c 2823.1 25 identity in 424 aa overlap 29 7EUpdated 282006 29 note: Literature search identified papers giving further clues about product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2C lipopolysaccharides and antigens 7EPMID:15612919 2C PMID:10672176 NC_002163.1 RefSeq region 1368522 1369040 . - . ID=id2545;Name=id2545;Dbxref=GeneID:905721;gbkey=misc_feature;Note=HMMPfam hit to PF00534 2C Glycosyl transferases group 2C score 3.7e-23 NC_002163.1 RefSeq gene 1369527 1370633 . - . ID=gene1378;Name=Cj1433c;locus_tag=Cj1433c;Dbxref=GeneID:905722;gbkey=Gene NC_002163.1 RefSeq CDS 1369527 1370633 . - 0 ID=cds1303;Parent=gene1378;Name=YP_002344816.1;Dbxref=GOA:Q0P8I1 InterPro:IPR007197 UniProtKB FTrEMBL:Q0P8I1 Genbank:YP_002344816.1 GeneID:905722;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1433c 2C unknown 2C len: 368 aa 3B no Hp match. Contains 9 repeats of the aa sequence KIDLNNT near the N-terminus 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Unknown 7EPMID:15612919 2C PMID:10672176 NC_002163.1 RefSeq repeat_region 1370374 1370562 . - . ID=id2546;Name=id2546;Dbxref=GeneID:905722;gbkey=repeat_region;Note=9 copies of 21bp repeat NC_002163.1 UTR_Extractor 5'-UTR 1370634 1370660 . - . ID=utr524;locus_tag=Cj1433c;product=hypothetical protein NC_002163.1 RefSeq CDS 1370667 1372004 . - 0 ID=cds1304;Parent=gene1379;Name=YP_002344817.1;Dbxref=GOA:Q0P8I0 InterPro:IPR001173 UniProtKB FTrEMBL:Q0P8I0 Genbank:YP_002344817.1 GeneID:905723;gbkey=CDS;product=sugar transferase;Note=Original 282000 29 note: Cj1434c 2C probable sugar transferase 2C len: 445 aa 3B similar in N-terminus to e.g. TR:O07340 28EMBL:O07340 29 Streptococcus pneumoniae SS-1 2C4-galactosyltransferase 28318 aa 29 2C fasta scores 3B opt: 344 z-score: 405.7 E 28 29: 2.8e-15 2C 27.3 25 identity in 326 aa overlap. No Hp ortholog. Highly similar to Cj1438c 2872.4 25 identity in 456 aa overlap 29. Contains Pfam match to entry PF00535 Glycos_transf_2 2C Glycosyl transferases 7EUpdated 282006 29 note: No specific characterisation has been carried out yet 2C so kept within product function. Literature search identified papers giving further clues to product funciton. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:15612919 2C PMID:10672176 NC_002163.1 RefSeq gene 1370667 1372004 . - . ID=gene1379;Name=Cj1434c;locus_tag=Cj1434c;Dbxref=GeneID:905723;gbkey=Gene NC_002163.1 RefSeq region 1371477 1371977 . - . ID=id2547;Name=id2547;Dbxref=GeneID:905723;gbkey=misc_feature;Note=HMMPfam hit to PF00535 2C Glycosyl transferase 2C score 7.9e-35 NC_002163.1 RefSeq stem_loop 1371481 1371516 . + . ID=id2548;Name=id2548;gbkey=stem_loop NC_002163.1 RefSeq CDS 1372056 1372691 . - 0 ID=cds1305;Parent=gene1380;Name=YP_002344818.1;Dbxref=GOA:Q0P8H9 InterPro:IPR006383 InterPro:IPR006385 UniProtKB FTrEMBL:Q0P8H9 Genbank:YP_002344818.1 GeneID:905724;gbkey=CDS;product=phosphatase;Note=Original 282000 29 note: Cj1435c 2C unknown 2C len: 211 aa 3B similar to TR:Q58989 28EMBL:U67599 29 Methanococcus jannaschii hypothetical protein MJ1594 28211 aa 29 2C fasta scores 3B opt: 177 z-score: 228.6 E 28 29: 2.1e-05 2C 23.5 25 identity in 196 aa overlap. No Hp match 7EUpdated 282006 29 note: TIGRFAM motifs identified HAD-superfamily proteins within CDS. Literature search identified paper giving further information to product function. Product function modified to more specific family member due to motif identification and literature search. Specific characterisation still required 2C so kept within product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Misc 7EPMID:15612919 2C PMID:10672176 NC_002163.1 RefSeq gene 1372056 1372691 . - . ID=gene1380;Name=Cj1435c;locus_tag=Cj1435c;Dbxref=GeneID:905724;gbkey=Gene NC_002163.1 RefSeq CDS 1372695 1373867 . - 0 ID=cds1306;Parent=gene1381;Name=YP_002344819.1;Dbxref=GOA:Q0P8H8 InterPro:IPR004838 InterPro:IPR004839 InterPro:IPR015421 InterPro:IPR015422 UniProtKB FTrEMBL:Q0P8H8 Genbank:YP_002344819.1 GeneID:905725;gbkey=CDS;product=aminotransferase;Note=Original 282000 29 note: Cj1436c 2C probable aminotransferase 2C len: 390 aa 3B weakly similar to e.g. HIS8_BACSU histidinol-phosphate aminotransferase 28360 aa 29 2Cfasta scores 3B opt: 304 z-score: 351.9 E 28 29: 2.8e-12 2C 25.5 25 identity in 318 aa overlap. No Hp match. Also similar to Cj0317 28hisC 29 2825.7 25 identity in 304 aa overlap 29 2C and Cj1437c 2823.1 25 identity in 347 aa overlap 29. Contains PS00105 Aminotransferases class-I pyridoxal-phosphate attachment site 7EUpdated 282006 29 note: Pfam domain PF00155 Aminotransferase class I and II identified within CDS. Further support given to product function. Characterised within Bacillus subtilis with marginal identity score. removed from product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Misc 7EPMID:15612919 2C PMID:10672176 NC_002163.1 RefSeq gene 1372695 1373867 . - . ID=gene1381;Name=Cj1436c;locus_tag=Cj1436c;Dbxref=GeneID:905725;gbkey=Gene NC_002163.1 RefSeq region 1372704 1373594 . - . ID=id2549;Name=id2549;Dbxref=GeneID:905725;gbkey=misc_feature;Note=HMMPfam hit to PF00155 2C Aminotransferase class I and II 2C score 2.2e-07 NC_002163.1 RefSeq region 1373109 1373150 . - . ID=id2550;Name=id2550;Dbxref=GeneID:905725;gbkey=misc_feature;Note=PS00105 Aminotransferases class-I pyridoxal-phosphate attachment site NC_002163.1 RefSeq gene 1373917 1375020 . - . ID=gene1382;Name=Cj1437c;locus_tag=Cj1437c;Dbxref=GeneID:905726;gbkey=Gene NC_002163.1 RefSeq CDS 1373917 1375020 . - 0 ID=cds1307;Parent=gene1382;Name=YP_002344820.1;Dbxref=GOA:Q0P8H7 InterPro:IPR001917 InterPro:IPR004839 InterPro:IPR015421 UniProtKB FTrEMBL:Q0P8H7 Genbank:YP_002344820.1 GeneID:905726;gbkey=CDS;product=aminotransferase;Note=Original 282000 29 note: Cj1437c 2C probable aminotransferase 2C len: 367 aa 3B similar to e.g. HIS8_BACSU histidinol-phosphate aminotransferase 28360 aa 29 2C fasta scores 3B opt: 408 z-score: 478.1 E 28 29: 2.6e-19 2C 28.6 25 identity in 360 aa overlap. No Hp match. Also similar to Cj0317 28hisC 29 2829.9 25 identity in 344 aa overlap 29 2C and Cj1436c 2823.3 25 identity in 347 aa overlap 29. Contains Pfam match to entry PF00222 aminotran_2 2C Aminotransferases class-II 2C and PS00599 Aminotransferases class-II pyridoxal-phosphate attachment site 7EUpdated 282006 29 note: Pfam domain PF00155 Aminotransferase class I and II identified within CDS. Further support given to product function. Characterised within Bacillus subtilis with marginal identity score. Appropriate motifs present. removed from product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Misc 7EPMID:15612919 2C PMID:10672176 NC_002163.1 RefSeq region 1373947 1374810 . - . ID=id2551;Name=id2551;Dbxref=GeneID:905726;gbkey=misc_feature;Note=HMMPfam hit to PF00155 2C Aminotransferase class I and II 2C score 9.2e-15 NC_002163.1 RefSeq repeat_region 1374136 1374144 . + . ID=id2552;Name=id2552;gbkey=repeat_region;Note=C 289 29 NC_002163.1 RefSeq region 1374346 1374375 . - . ID=id2553;Name=id2553;Dbxref=GeneID:905726;gbkey=misc_feature;Note=PS00599 Aminotransferases class-II pyridoxal-phosphate attachment site NC_002163.1 RefSeq gene 1375007 1377337 . - . ID=gene1383;Name=Cj1438c;locus_tag=Cj1438c;Dbxref=GeneID:905727;gbkey=Gene NC_002163.1 RefSeq CDS 1375007 1377337 . - 0 ID=cds1308;Parent=gene1383;Name=YP_002344821.1;Dbxref=GOA:Q0P8H6 InterPro:IPR001173 UniProtKB FTrEMBL:Q0P8H6 Genbank:YP_002344821.1 GeneID:905727;gbkey=CDS;product=sugar transferase;Note=Original 282000 29 note: Cj1438c 2C probable sugar transferase 2C len: 776 aa 3B similar in N-terminus to e.g. TR:O07340 28EMBL:O07340 29 Streptococcus pneumoniae SS-1 2C4-galactosyltransferase 28318 aa 29 2C fasta scores 3B opt: 325 z-score: 375.2 E 28 29: 1.4e-13 2C 26.9 25 identity in 316 aa overlap. Similar in C-terminus to TR:O31348 28EMBL:Y11138 29 Bacillus cereus hypothetical protein 28ORF2 29 28300 aa 29 2Cfasta scores 3B opt: 355 z-score: 409.9 E 28 29: 1.7e-15 2C 31.2 25 identity in 340 aa overlap. 27.7 25 identity in 260 aa overlap to HP0102. Also highly similar to Cj1434c 2872.9 25 identity in 457 aa overlap 29 in N-term 2C and similar to Cj1421c 2834.6 25 identity in 127 aa overlap 29 and Cj1422c 2823.5 25 identity in 452 aa overlap 29 in C-term. Contains Pfam match to entry PF00535 Glycos_transf_2 2C Glycosyl transferases 7EUpdated 282006 29 note: Literature search identified paper giving further information on product function. Specific characterisation still required 2C so kept within product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:15612919 2C PMID:10672176 NC_002163.1 RefSeq region 1375103 1375150 . - . ID=id2554;Name=id2554;Dbxref=GeneID:905727;gbkey=misc_feature;Note=PS00225 Crystallins beta and gamma 27Greek key 27 motif signature NC_002163.1 RefSeq region 1376843 1377310 . - . ID=id2555;Name=id2555;Dbxref=GeneID:905727;gbkey=misc_feature;Note=HMMPfam hit to PF00535 2C Glycosyl transferase 2C score 2.8e-36 NC_002163.1 RefSeq CDS 1377339 1378445 . - 0 ID=cds1309;Parent=gene1384;gene=glf;Name=YP_002344822.1;Dbxref=GOA:Q0P8H5 InterPro:IPR004379 InterPro:IPR006076 InterPro:IPR015899 InterPro:IPR016040 UniProtKB FTrEMBL:Q0P8H5 Genbank:YP_002344822.1 GeneID:905728;gbkey=CDS;product=UDP-galactopyranose mutase;Note=Original 282000 29 note: Cj1439c 2C glf 2C probable UDP-galactopyranose mutase 2C len: aa 3B highly simiar to e.g. TR:O86897 28EMBL:AJ006986 29 Streptococcus pneumoniae polysaccharide capsule bisynthesis cluster UDP-galactopyranose mutase 28EC 5.4.99.9 29 28369 aa 29 2C fasta scores 3B opt: 1546 z-score: 1775.3 E 28 29: 0 2C 59.9 25 identity in 364 aa overlap 2C and GLF_ECOLI UDP-galactopyranose mutase 28EC 5.4.99.9 29 28367 aa 29 2C fasta scores 3B opt: 1545 z-score: 1774.2 E 28 29: 0 2C 60.8 25 identity in 362 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF03275 UDP-galactopyranose mutase identified within CDS. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. not added to product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:8576037 2C PMID:15947206 2C PMID:10672176 NC_002163.1 RefSeq gene 1377339 1378445 . - . ID=gene1384;gene=glf;Name=glf;locus_tag=Cj1439c;Dbxref=GeneID:905728;gbkey=Gene NC_002163.1 RefSeq region 1377411 1378013 . - . ID=id2556;gene=glf;Name=id2556;Dbxref=GeneID:905728;gbkey=misc_feature;Note=HMMPfam hit to PF03275 2C UDP-galactopyranose mutase 2Cscore 2e-114 NC_002163.1 UTR_Extractor 5'-UTR 1378446 1378466 . - . ID=utr525;locus_tag=Cj1439c;product=UDP-galactopyranose mutase NC_002163.1 RefSeq CDS 1378483 1379706 . - 0 ID=cds1310;Parent=gene1385;Name=YP_002344823.1;Dbxref=GOA:Q0P8H4 InterPro:IPR001173 UniProtKB FTrEMBL:Q0P8H4 Genbank:YP_002344823.1 GeneID:905729;gbkey=CDS;product=sugar transferase;Note=Original 282000 29 note: Cj1440c 2C probable sugar transferase 2C len: 407 aa 3B similar in N-terminus to e.g. TR:O07340 28EMBL:O07340 29 Streptococcus pneumoniae SS-1 2C4-galactosyltransferase 28318 aa 29 2C fasta scores 3B opt: 280 z-score: 326.2 E 28 29: 7.5e-11 2C 26.7 25 identity in 374 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00535 Glycos_transf_2 2C Glycosyl transferases 7EUpdated 282006 29 note: Literature search identified papers giving further information towards product function. Specific characterisation still required 2C so kept within product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:15612919 2C PMID:10672176 2C PMID:11422559 NC_002163.1 RefSeq gene 1378483 1379706 . - . ID=gene1385;Name=Cj1440c;locus_tag=Cj1440c;Dbxref=GeneID:905729;gbkey=Gene NC_002163.1 RefSeq region 1378516 1378584 . - . ID=id2557;Name=id2557;Dbxref=GeneID:905729;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1440c by TMHMM2.0 at aa 375-397 NC_002163.1 RefSeq region 1379044 1379694 . - . ID=id2558;Name=id2558;Dbxref=GeneID:905729;gbkey=misc_feature;Note=HMMPfam hit to PF00535 2C Glycosyl transferase 2C score 2.1e-23 NC_002163.1 UTR_Extractor 5'-UTR 1379707 1379890 . - . ID=utr526;locus_tag=Cj1440c;product=putative sugar transferase NC_002163.1 RefSeq CDS 1379716 1380897 . - 0 ID=cds1311;Parent=gene1386;gene=kfiD;Name=YP_002344824.1;Dbxref=GOA:Q0P8H3 InterPro:IPR001732 InterPro:IPR014026 InterPro:IPR014027 InterPro:IPR014028 InterPro:IPR016040 InterPro:IPR017476 UniProtKB FTrEMBL:Q0P8H3 Genbank:YP_002344824.1 GeneID:905730;gbkey=CDS;product=UDP-glucose 6-dehydrogenase;Note=Original 282000 29 note: Cj1441c 2C kfiD 2C probable UDP-glucose 6-dehydrogenase 2C len: 393 aa 3B similar to many e.g. UDG5_ECOLI UDP-glucose 6-dehydrogenase 28EC 1.1.1.22 29 28392 aa 29 2C fasta scores 3B opt: 1386 z-score: 1511.4 E 28 29: 0 2C52.3 25 identity in 392 aa overlap. No Hp match. Contains Pfam match to entry PF00984 UDPG_MGDP_dh 2CUDP-glucose 2FGDP-mannose dehydrogenase family 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. removed from product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Central intermediary metabolism - Sugar nucleotides 7EPMID:12851388 2C PMID:9383197 2C PMID:7635844 2CPMID:12392544 NC_002163.1 RefSeq gene 1379716 1380897 . - . ID=gene1386;gene=kfiD;Name=kfiD;locus_tag=Cj1441c;Dbxref=GeneID:905730;gbkey=Gene NC_002163.1 RefSeq region 1379725 1379994 . - . ID=id2559;gene=kfiD;Name=id2559;Dbxref=GeneID:905730;gbkey=misc_feature;Note=HMMPfam hit to PF03720 2C UDP-glucose 2FGDP-mannose dehydrogenase 2C score 5.2e-06 NC_002163.1 RefSeq region 1380043 1380324 . - . ID=id2560;gene=kfiD;Name=id2560;Dbxref=GeneID:905730;gbkey=misc_feature;Note=HMMPfam hit to PF00984 2C UDP-glucose 2FGDP-mannose dehydrogenase 2C score 3.7e-29 NC_002163.1 RefSeq region 1380352 1380897 . - . ID=id2561;gene=kfiD;Name=id2561;Dbxref=GeneID:905730;gbkey=misc_feature;Note=HMMPfam hit to PF03721 2C UDP-glucose 2FGDP-mannose dehydrogenase 2C score 3.8e-33 NC_002163.1 RefSeq CDS 1380894 1382528 . - 0 ID=cds1312;Parent=gene1387;Name=YP_002344825.1;Dbxref=GOA:Q0P8H2 UniProtKB FTrEMBL:Q0P8H2 Genbank:YP_002344825.1 GeneID:905731;gbkey=CDS;product=sugar transferase;Note=Original 282000 29 note: Cj1442c 2C unknown 2C len: 544 aa 3B no Hp match 7EUpdated 282006 29 note: Literature search identified papers giving further information about product function. Specific characterisation still required 2C so kept within product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:15612919 2C PMID:10672176 2C PMID:11422559 NC_002163.1 RefSeq gene 1380894 1382528 . - . ID=gene1387;Name=Cj1442c;locus_tag=Cj1442c;Dbxref=GeneID:905731;gbkey=Gene NC_002163.1 RefSeq CDS 1382528 1383475 . - 0 ID=cds1313;Parent=gene1388;gene=kpsF;Name=YP_002344826.1;Dbxref=GOA:Q0P8H1 InterPro:IPR000644 InterPro:IPR001347 InterPro:IPR004800 UniProtKB FTrEMBL:Q0P8H1 Genbank:YP_002344826.1 GeneID:905732;gbkey=CDS;product=D-arabinose 5-phosphate isomerase;Note=Original 282000 29 note: Cj1443c 2C kpsF 2C unknown 2C len: 315 aa 3B similar to hypothetical proteins belonging to the kpsF 2FgutQ family e.g. KSF1_ECOLI KPSF protein 28317 aa 29 2Cfasta scores 3B opt: 849 z-score: 979.3 E 28 29: 0 2C 46.5 25 identity in 297 aa overlap. 38.7 25 identity to HP1429. Contains 2x Pfam match to entry PF00571 CBS 2C CBS domain 7EUpdated 282006 29 note: Pfam domain PF01380 SIS domain identified within CDS. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. Product function modified to more specific family member. not added to product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:16390329 2C PMID:11956197 2C PMID:10672176 NC_002163.1 RefSeq gene 1382528 1383475 . - . ID=gene1388;gene=kpsF;Name=kpsF;locus_tag=Cj1443c;Dbxref=GeneID:905732;gbkey=Gene NC_002163.1 RefSeq region 1382537 1382683 . - . ID=id2562;gene=kpsF;Name=id2562;Dbxref=GeneID:905732;gbkey=misc_feature;Note=HMMPfam hit to PF00571 2C CBS domain 2C score 0.0016 NC_002163.1 RefSeq region 1382720 1382878 . - . ID=id2563;gene=kpsF;Name=id2563;Dbxref=GeneID:905732;gbkey=misc_feature;Note=HMMPfam hit to PF00571 2C CBS domain 2C score 8.1e-10 NC_002163.1 RefSeq region 1382969 1383376 . - . ID=id2564;gene=kpsF;Name=id2564;Dbxref=GeneID:905732;gbkey=misc_feature;Note=HMMPfam hit to PF01380 2C SIS domain 2C score 1.1e-30 ### NC_002163.1 RefSeq gene 1383486 1385144 . - . ID=gene1389;gene=kpsD;Name=kpsD;locus_tag=Cj1444c;Dbxref=GeneID:905733;gbkey=Gene NC_002163.1 RefSeq CDS 1383486 1385144 . - 0 ID=cds1314;Parent=gene1389;gene=kpsD;Name=YP_002344827.1;Dbxref=GOA:Q0P8H0 InterPro:IPR003715 UniProtKB FTrEMBL:Q0P8H0 Genbank:YP_002344827.1 GeneID:905733;gbkey=CDS;product=capsule polysaccharide export system substrate-binding protein;Note=Original 282000 29 note: Cj1444c 2C kpsD 2C probable capsule polysaccharide export system periplasmic protein 2Clen: aa 3B similar to e.g. KSD1_ECOLI polysialic acid transport protein KPSD PREC 28558 aa 29 2C fasta scores 3B opt: 1187 z-score: 1306.9 E 28 29: 0 2C 36.1 25 identity in 560 aa overlap. Contains probable N-terminal signal sequence. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02563 Polysaccharide biosynthesis 2Fexport protein identified within CDS. Paper identified linking protein to glycoprotein 28PMID:Cj12186869 29. Characterised within Escherichia coli with acceptable identity score. removed from product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:12186869 2C PMID:8021185 2C PMID:16420360 2CPMID:10672176 NC_002163.1 RefSeq region 1384569 1384931 . - . ID=id2565;gene=kpsD;Name=id2565;Dbxref=GeneID:905733;gbkey=misc_feature;Note=HMMPfam hit to PF02563 2C Polysaccharide biosynthesis 2Fexport protei 2C score 2.1e-48 ### NC_002163.1 UTR_Extractor 5'-UTR 1385145 1385199 . - . ID=utr527;locus_tag=Cj1444c;product=capsule polysaccharide export system periplasmic protein NC_002163.1 RefSeq CDS 1385146 1386264 . - 0 ID=cds1315;Parent=gene1390;gene=kpsE;Name=YP_002344828.1;Dbxref=GOA:Q0P8G9 InterPro:IPR003856 UniProtKB FTrEMBL:Q0P8G9 Genbank:YP_002344828.1 GeneID:905734;gbkey=CDS;product=capsule polysaccharide export system inner membrane protein;Note=Original 282000 29 note: Cj1445c 2C kpsE 2C probable capsule polysaccharide export system inner membrane protein 2C len: 372 aa 3B similar to e.g. KSE1_ECOLI capsule polysaccharide export inner-membrane protein 28382 aa 29 2Cfasta scores 3B opt: 752 z-score: 755.4 E 28 29: 0 2C 34.2 25 identity in 351 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02706 Chain length determinant protein identified within CDS. Further support given to product function. Two probable transmembrane helices predicted by TMHMM2.0. Characterised within Escherichia coli with acceptable identity score. removed from product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:8253690 2C PMID:7868584 2C PMID:11467848 2CPMID:10672176 NC_002163.1 RefSeq gene 1385146 1386264 . - . ID=gene1390;gene=kpsE;Name=kpsE;locus_tag=Cj1445c;Dbxref=GeneID:905734;gbkey=Gene NC_002163.1 RefSeq region 1385161 1385229 . - . ID=id123;gene=kpsE;Name=id123;Dbxref=GeneID:905734;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1445c by TMHMM2.0 at aa 22-44 and 346-368 NC_002163.1 RefSeq region 1385773 1386240 . - . ID=id2566;gene=kpsE;Name=id2566;Dbxref=GeneID:905734;gbkey=misc_feature;Note=HMMPfam hit to PF02706 2C Chain length determinant protein 2C score 0.013 NC_002163.1 RefSeq region 1386133 1386201 . - . ID=id123;gene=kpsE;Name=id123;Dbxref=GeneID:905734;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1445c by TMHMM2.0 at aa 22-44 and 346-368 NC_002163.1 RefSeq CDS 1386264 1386926 . - 0 ID=cds1316;Parent=gene1391;gene=kpsT;Name=YP_002344829.1;Dbxref=GOA:O69286 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FTrEMBL:O69286 Genbank:YP_002344829.1 GeneID:905735;gbkey=CDS;product=capsule polysaccharide export ATP-binding protein;Note=Original 282000 29 note: Cj1447c 2C kpsT 2C probable capsule polysaccharide export ATP-binding protein 2C len: 220 aa 3B identical to TR:O69286 28EMBL:AJ000856 29 C. jejuni ABC transporter protein 28220 aa 29 2C and highly similar to e.g. KST1_ECOLI polysialic acid transport ATP-binding protein 28219 aa 29 2C fasta scores 3B opt: 810 z-score: 945.3 E 28 29: 0 2C 58.7 25 identity in 218 aa overlap. No Hp ortholog. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2CPS00211 ABC transporters family signature 2C and Pfam match to entry PF00005 ABC_tran 2C ABC transporters 7EUpdated 282006 29 note: Characterised within Campylobacter jejuni. removed from product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2Clipopolysaccharides and antigens 7EPMID:12855177 2C PMID:9802032 2C PMID:10672176 2CPMID:11359581 NC_002163.1 RefSeq gene 1386264 1386926 . - . ID=gene1391;gene=kpsT;Name=kpsT;locus_tag=Cj1447c;Dbxref=GeneID:905735;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 1386265 1386337 . - . ID=utr528;locus_tag=Cj1445c;product=capsule polysaccharide export system inner membrane protein NC_002163.1 RefSeq region 1386324 1386833 . - . ID=id2567;gene=kpsT;Name=id2567;Dbxref=GeneID:905735;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 8.2e-21 NC_002163.1 RefSeq region 1386504 1386548 . - . ID=id2568;gene=kpsT;Name=id2568;Dbxref=GeneID:905735;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq region 1386789 1386812 . - . ID=id2569;gene=kpsT;Name=id2569;Dbxref=GeneID:905735;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 1386923 1387705 . - 0 ID=cds1317;Parent=gene1392;gene=kpsM;Name=YP_002344830.1;Dbxref=GOA:O69285 InterPro:IPR000412 InterPro:IPR013525 InterPro:IPR013526 UniProtKB FTrEMBL:O69285 Genbank:YP_002344830.1 GeneID:905736;gbkey=CDS;product=capsule polysaccharide export system inner membrane protein;Note=Original 282000 29 note: Cj1448c 2C kpsM 2C probable capsule polysaccharide export system inner membrane protein 2C len: 260 aa 3B identical to TR:O69285 28EMBL:AJ000856 29 C. jejuni ABC transporter protein 28260 aa 29 2C and highly similar to e.g. KPM1_ECOLI polysialic acid transport protein KPSM 28258 aa 29 2C fasta scores 3B opt: 488 z-score: 558.3 E 28 29: 8.9e-24 2C 34.3 25 identity in 254 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF01061 ABC-2 type transporter identified within CDS. Further support given to product function. Also 2C six probable transmembrane helices predicted by TMHMM2.0. Characterised within Escherichia coli and Campylobacter jejuni with acceptable identity scores. not added to product function. Identifed as part of Campylobacter jejuni capsule locus 28Cj1413c - Cj1448c 29. Functional classification - Surface polysaccharides 2C lipopolysaccharides and antigens 7EPMID:7715449 2C PMID:12855177 2C PMID:11500474 2CPMID:11359581 2C PMID:10672176 2C PMID:16436427 NC_002163.1 RefSeq gene 1386923 1387705 . - . ID=gene1392;gene=kpsM;Name=kpsM;locus_tag=Cj1448c;Dbxref=GeneID:905736;gbkey=Gene NC_002163.1 RefSeq region 1386959 1387027 . - . ID=id124;gene=kpsM;Name=id124;Dbxref=GeneID:905736;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1448c by TMHMM2.0 at aa 24-46 2C 56-78 2C 107-129 2C 144-166 2C171-193 and 227-249 NC_002163.1 RefSeq region 1387052 1387699 . - . ID=id2570;gene=kpsM;Name=id2570;Dbxref=GeneID:905736;gbkey=misc_feature;Note=HMMPfam hit to PF01061 2C ABC-2 type transporter 2Cscore 5.2e-10 NC_002163.1 RefSeq region 1387127 1387195 . - . ID=id124;gene=kpsM;Name=id124;Dbxref=GeneID:905736;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1448c by TMHMM2.0 at aa 24-46 2C 56-78 2C 107-129 2C 144-166 2C171-193 and 227-249 NC_002163.1 RefSeq region 1387208 1387276 . - . ID=id124;gene=kpsM;Name=id124;Dbxref=GeneID:905736;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1448c by TMHMM2.0 at aa 24-46 2C 56-78 2C 107-129 2C 144-166 2C171-193 and 227-249 NC_002163.1 RefSeq region 1387319 1387387 . - . ID=id124;gene=kpsM;Name=id124;Dbxref=GeneID:905736;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1448c by TMHMM2.0 at aa 24-46 2C 56-78 2C 107-129 2C 144-166 2C171-193 and 227-249 NC_002163.1 RefSeq region 1387472 1387540 . - . ID=id124;gene=kpsM;Name=id124;Dbxref=GeneID:905736;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1448c by TMHMM2.0 at aa 24-46 2C 56-78 2C 107-129 2C 144-166 2C171-193 and 227-249 NC_002163.1 RefSeq region 1387568 1387636 . - . ID=id124;gene=kpsM;Name=id124;Dbxref=GeneID:905736;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1448c by TMHMM2.0 at aa 24-46 2C 56-78 2C 107-129 2C 144-166 2C171-193 and 227-249 ### NC_002163.1 UTR_Extractor 5'-UTR 1387706 1387736 . - . ID=utr529;locus_tag=Cj1448c;product=capsule polysaccharide export system inner membrane protein NC_002163.1 RefSeq gene 1387777 1388184 . - . ID=gene1393;Name=Cj1449c;locus_tag=Cj1449c;Dbxref=GeneID:905737;gbkey=Gene NC_002163.1 RefSeq CDS 1387777 1388184 . - 0 ID=cds1318;Parent=gene1393;Name=YP_002344831.1;Dbxref=InterPro:IPR011194 UniProtKB FSwiss-Prot:Q9PML1 Genbank:YP_002344831.1 GeneID:905737;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1449c 2C unknown 2C len: 135 aa 3B similar to YHBP_ECOLI hypothetical protein 28147 aa 29 2Cfasta scores 3B opt: 236 z-score: 315.0 E 28 29: 3.2e-10 2C 30.5 25 identity in 131 aa overlap. No Hp match. Functional classification - Conserved hypothetical proteins NC_002163.1 UTR_Extractor 5'-UTR 1388185 1388187 . - . ID=utr530;locus_tag=Cj1449c;product=hypothetical protein NC_002163.1 UTR_Extractor 5'-UTR 1388235 1388258 . + . ID=utr531;locus_tag=Cj1450;product=putative ATP 2FGTP-binding protein NC_002163.1 RefSeq gene 1388259 1388822 . + . ID=gene1394;Name=Cj1450;locus_tag=Cj1450;Dbxref=GeneID:905738;gbkey=Gene NC_002163.1 RefSeq CDS 1388259 1388822 . + 0 ID=cds1319;Parent=gene1394;Name=YP_002344832.1;Dbxref=UniProtKB FTrEMBL:Q0P8G5 Genbank:YP_002344832.1 GeneID:905738;gbkey=CDS;product=ATP 2FGTP-binding protein;Note=Original 282000 29 note: Cj1450 2C probable ATP 2FGTP-binding protein 2C len: 187 aa 3B no Hp match. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2Cand probable coiled-coil domain at C-terminus 28aa 150-175 29 7EUpdated 282006 29 note: Literature search identified paper giving further clues to product function. Functional classification - Unknown 7EPMID:16740937 NC_002163.1 RefSeq region 1388364 1388387 . + . ID=id2571;Name=id2571;Dbxref=GeneID:905738;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 RefSeq gene 1388859 1389548 . + . ID=gene1395;gene=dut;Name=dut;locus_tag=Cj1451;Dbxref=GeneID:905739;gbkey=Gene NC_002163.1 RefSeq CDS 1388859 1389548 . + 0 ID=cds1320;Parent=gene1395;gene=dut;Name=YP_002344833.1;Dbxref=GOA:Q0P8G4 InterPro:IPR014871 UniProtKB FTrEMBL:Q0P8G4 Genbank:YP_002344833.1 GeneID:905739;gbkey=CDS;product=dUTPase;Note=Original 282000 29 note: Cj1451 2C dut 2C possible dUTPase 2C len: 229 aa 3B similar to two enzymes of eukaryotic origin e.g. TR:O15826 28EMBL:L76742 29 Leishmania major characterised dUTPase 28EC 3.6.1.23 29 28dUTP pyrophosphatase 29 28268 aa 29 2C fasta scores 3B opt: 311 z-score: 382.3 E 28 29: 5.7e-14 2C 33.6 25 identity in 226 aa overlap 2C and TR:O15923 28EMBL:U93211 29 Trypanosoma cruzi deoxyuridine triphosphatase 28283 aa 29 2C fasta scores 3B opt: 198 z-score: 246.6 E 28 29: 2.1e-06 2C 32.9 25 identity in 228 aa overlap. No Hp match. C.j. does not have a homolog of the E. coli dut gene. H.p. has an E. coli-like dut gene 7EUpdated 282006 29 note: Characterisation work carried out within Campylobacter jejuni. removed from product function. Functional classification -2 27-deoxyribonucleotide biosynthesis 7EPMID:15364583 NC_002163.1 RefSeq CDS 1389550 1390263 . + 0 ID=cds1321;Parent=gene1396;Name=YP_002344834.1;Dbxref=GOA:Q0P8G3 InterPro:IPR007496 UniProtKB FTrEMBL:Q0P8G3 Genbank:YP_002344834.1 GeneID:905740;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj1452 2C possible integral membrane protein 2C len: 237 aa 3B 29.7 25 identity to HP0174. Contains four large hydrophobic domains 7EUpdated 282006 29 note: Pfam domain PF04401 Protein of unknown function 28DUF540 29 identified within CDS. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 1389550 1390263 . + . ID=gene1396;Name=Cj1452;locus_tag=Cj1452;Dbxref=GeneID:905740;gbkey=Gene NC_002163.1 RefSeq region 1389607 1389675 . + . ID=id2572;Name=id2572;Dbxref=GeneID:905740;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1452 by TMHMM2.0 at aa 20-42 2C 57-79 2C 81-103 2C 136-158 and 201-223 NC_002163.1 RefSeq region 1389658 1390242 . + . ID=id2573;Name=id2573;Dbxref=GeneID:905740;gbkey=misc_feature;Note=HMMPfam hit to PF04401 2C Protein of unknown function 28DUF540 29 2C score 3e-75 NC_002163.1 RefSeq region 1389718 1389786 . + . ID=id2572;Name=id2572;Dbxref=GeneID:905740;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1452 by TMHMM2.0 at aa 20-42 2C 57-79 2C 81-103 2C 136-158 and 201-223 NC_002163.1 RefSeq region 1389790 1389858 . + . ID=id2572;Name=id2572;Dbxref=GeneID:905740;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1452 by TMHMM2.0 at aa 20-42 2C 57-79 2C 81-103 2C 136-158 and 201-223 NC_002163.1 RefSeq region 1389955 1390023 . + . ID=id2572;Name=id2572;Dbxref=GeneID:905740;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1452 by TMHMM2.0 at aa 20-42 2C 57-79 2C 81-103 2C 136-158 and 201-223 NC_002163.1 RefSeq region 1390150 1390218 . + . ID=id2572;Name=id2572;Dbxref=GeneID:905740;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1452 by TMHMM2.0 at aa 20-42 2C 57-79 2C 81-103 2C 136-158 and 201-223 NC_002163.1 RefSeq CDS 1390246 1391211 . - 0 ID=cds1322;Parent=gene1397;gene=tilS;Name=YP_002344835.1;Dbxref=GOA:Q9PMK7 InterPro:IPR011063 InterPro:IPR012094 InterPro:IPR012795 InterPro:IPR014729 UniProtKB FSwiss-Prot:Q9PMK7 Genbank:YP_002344835.1 GeneID:905741;gbkey=CDS;product=tRNA 28Ile 29-lysidine synthase;Note=Original 282000 29 note: Cj1453c 2C unknown 2C len: 321 aa 3B similar to hypothetical proteins e.g. YACA_BACSU 28486 aa 29 2C fasta scores 3B opt: 290 z-score: 342.2 E 28 29: 9.7e-12 2C26.8 25 identity in 257 aa overlap. 40.7 25 identity to HP0728 7EUpdated 282006 29 note: Pfam domain PF01171 PP-loop family identified within CDS. Characterisation work has been carried out within Escherichia coli and Bacillus subtilis and has been designated as tRNA 28Ile 29-lysidine synthase. Product modified to more specific famlily member. Identity scores were marginal 2C so kept within product function. Functional classification -Aminoacyl tRNA synthetases and their modification 7EPMID:14527414 2C PMID:15894617 2C PMID:16039592 NC_002163.1 RefSeq gene 1390246 1391211 . - . ID=gene1397;gene=tilS;Name=tilS;locus_tag=Cj1453c;Dbxref=GeneID:905741;gbkey=Gene NC_002163.1 RefSeq region 1390588 1391169 . - . ID=id2574;gene=tilS;Name=id2574;Dbxref=GeneID:905741;gbkey=misc_feature;Note=HMMPfam hit to PF01171 2C PP-loop family 2C score 6.8e-90 NC_002163.1 RefSeq CDS 1391201 1392520 . - 0 ID=cds1323;Parent=gene1398;Name=YP_002344836.1;Dbxref=GOA:Q0P8G1 InterPro:IPR005839 InterPro:IPR005840 InterPro:IPR006638 InterPro:IPR007197 InterPro:IPR013848 UniProtKB FTrEMBL:Q0P8G1 Genbank:YP_002344836.1 GeneID:905742;gbkey=CDS;product=radical SAM protein;Note=Original 282000 29 note: Cj1454c 2C unknown 2C len: 439 aa 3B similar to hypothetical proteins e.g. YLIG_ECOLI 28441 aa 29 2C fasta scores 3B opt: 671 z-score: 748.3 E 28 29: 0 2C 34.2 25 identity in 433 aa overlap. 52.1 25 identity to HP0734. Also similar to Cj1006c 2828.6 25 identity in 419 aa overlap 29 2C and Cj0458c 2826.7 25 identity in 371 aa overlap 29. Contains PS01278 Uncharacterized protein family UPF0004 signature 2Cand Pfam match to entry PF00919 UPF0004 2C Uncharacterized protein family UPF0004 7EUpdated 282006 29 note: Pfam domain PF04055 Radical SAM superfamily identified within CDS. Product function modified to modified to more specific family member. No specific characterisation identified yet 2C so kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 1391201 1392520 . - . ID=gene1398;gene=Cj1454c;Name=Cj1454c;locus_tag=Cj1454c;Dbxref=GeneID:905742;gbkey=Gene NC_002163.1 RefSeq region 1391588 1392103 . - . ID=id2575;Name=id2575;Dbxref=GeneID:905742;gbkey=misc_feature;Note=HMMPfam hit to PF04055 2C Radical SAM superfamily 2Cscore 4.3e-21 NC_002163.1 RefSeq region 1392041 1392103 . - . ID=id2576;Name=id2576;Dbxref=GeneID:905742;gbkey=misc_feature;Note=PS01278 Uncharacterized protein family UPF0004 signature NC_002163.1 RefSeq region 1392227 1392514 . - . ID=id2577;Name=id2577;Dbxref=GeneID:905742;gbkey=misc_feature;Note=HMMPfam hit to PF00919 2C Uncharacterized protein family UPF0004 2C score 9e-37 ### NC_002163.1 UTR_Extractor 5'-UTR 1392521 1392572 . - . ID=utr532;locus_tag=Cj1454c;product=putative radical SAM domain family protein NC_002163.1 UTR_Extractor 5'-UTR 1392561 1392593 . + . ID=utr533;locus_tag=Cj1455;product=peptide chain release factor 2 ### NC_002163.1 RefSeq CDS 1392594 1393691 . + 0 ID=cds1324;Parent=gene1399;gene=prfB;Name=YP_002344837.1;Dbxref=GOA:Q9PMK5 HSSP:P07012 InterPro:IPR000352 InterPro:IPR004374 InterPro:IPR005139 UniProtKB FSwiss-Prot:Q9PMK5 Genbank:YP_002344837.1 GeneID:905743;gbkey=CDS;product=peptide chain release factor 2;Note=recognizes the termination signals UGA and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF2 3B in some organisms control of PrfB protein levels is maintained through a 2B1 ribosomal frameshifting mechanism 3B this protein is similar to release factor 1 NC_002163.1 RefSeq gene 1392594 1393691 . + . ID=gene1399;gene=prfB;Name=prfB;locus_tag=Cj1455;Dbxref=GeneID:905743;gbkey=Gene NC_002163.1 RefSeq region 1392843 1393175 . + . ID=id2578;gene=prfB;Name=id2578;Dbxref=GeneID:905743;gbkey=misc_feature;Note=HMMPfam hit to PF03462 2C PCRF domain 2C score 2.7e-50 NC_002163.1 RefSeq region 1393269 1393598 . + . ID=id2579;gene=prfB;Name=id2579;Dbxref=GeneID:905743;gbkey=misc_feature;Note=HMMPfam hit to PF00472 2C Peptidyl-tRNA hydrolase domain 2C score 2e-67 NC_002163.1 RefSeq region 1393323 1393373 . + . ID=id2580;gene=prfB;Name=id2580;Dbxref=GeneID:905743;gbkey=misc_feature;Note=PS00745 Prokaryotic-type class I peptide chain release factors signature ### NC_002163.1 RefSeq gene 1393745 1393825 . - . ID=NC_002163.1:CJnc150;Name=NC_002163.1:CJnc150;locus_tag=CJnc150 NC_002163.1 RefSeq sRNA 1393745 1393825 . - . ID=NC_002163.1:CJnc150:unknown_transcript_1;Parent=NC_002163.1:CJnc150;Name=NC_002163.1:CJnc150:unknown_transcript_1;locus_tag=CJnc150;gbkey=misc_RNA;product=CJnc150 NC_002163.1 RefSeq gene 1393849 1394163 . - . ID=gene1400;Name=Cj1456c;locus_tag=Cj1456c;Dbxref=GeneID:905744;gbkey=Gene NC_002163.1 RefSeq CDS 1393849 1394163 . - 0 ID=cds1325;Parent=gene1400;Name=YP_002344838.1;Dbxref=GOA:Q0P8F9 UniProtKB FTrEMBL:Q0P8F9 Genbank:YP_002344838.1 GeneID:905744;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1456c 2C probable periplasmic protein 2C len: 104 aa 3B no Hp match. Contains possible N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 UTR_Extractor 5'-UTR 1394164 1394193 . - . ID=utr534;locus_tag=Cj1456c;product=putative periplasmic protein NC_002163.1 RefSeq CDS 1394285 1395403 . - 0 ID=cds1326;Parent=gene1401;gene=truD;Name=YP_002344839.1;Dbxref=GOA:Q9PMK3 InterPro:IPR001656 InterPro:IPR011760 UniProtKB FSwiss-Prot:Q9PMK3 Genbank:YP_002344839.1 GeneID:905745;gbkey=CDS;product=tRNA pseudouridine synthase D;Note=catalyzes the modification of U13 in tRNA 28Glu 29 NC_002163.1 RefSeq gene 1394285 1395403 . - . ID=gene1401;gene=truD;Name=truD;locus_tag=Cj1457c;Dbxref=GeneID:905745;gbkey=Gene NC_002163.1 RefSeq region 1394294 1395376 . - . ID=id2581;gene=truD;Name=id2581;Dbxref=GeneID:905745;gbkey=misc_feature;Note=HMMPfam hit to PF01142 2C tRNA pseudouridine synthase D 28TruD 29 2C score 7.8e-165 NC_002163.1 RefSeq gene 1395372 1396193 . - . ID=gene1402;gene=thiL;Name=thiL;locus_tag=Cj1458c;Dbxref=GeneID:905746;gbkey=Gene NC_002163.1 RefSeq CDS 1395372 1396193 . - 0 ID=cds1327;Parent=gene1402;gene=thiL;Name=YP_002344840.1;Dbxref=GOA:Q0P8F7 InterPro:IPR010918 UniProtKB FTrEMBL:Q0P8F7 Genbank:YP_002344840.1 GeneID:905746;gbkey=CDS;product=thiamine monophosphate kinase;Note=catalyzes the formation of thiamine diphosphate from thiamine phosphate ant ATP NC_002163.1 RefSeq region 1395384 1395788 . - . ID=id2582;gene=thiL;Name=id2582;Dbxref=GeneID:905746;gbkey=misc_feature;Note=HMMPfam hit to PF02769 2C AIR synthase related protein 2C C-terminal dom 2C score 0.0019 ### NC_002163.1 UTR_Extractor 5'-UTR 1396194 1396196 . - . ID=utr535;locus_tag=Cj1458c;product=thiamine monophosphate kinase NC_002163.1 UTR_Extractor 5'-UTR 1396262 1396279 . + . ID=utr536;locus_tag=Cj1459;product=hypothetical protein NC_002163.1 RefSeq CDS 1396280 1397353 . + 0 ID=cds1328;Parent=gene1403;Name=YP_002344841.1;Dbxref=GOA:Q0P8F6 UniProtKB FTrEMBL:Q0P8F6 Genbank:YP_002344841.1 GeneID:905747;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1459 2C unknown 2C len: 357 aa 3B 24.8 25 identity to HP0468. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 1396280 1397353 . + . ID=gene1403;Name=Cj1459;locus_tag=Cj1459;Dbxref=GeneID:905747;gbkey=Gene NC_002163.1 RefSeq CDS 1397350 1397733 . + 0 ID=cds1329;Parent=gene1404;Name=YP_002344842.1;Dbxref=GOA:Q0P8F5 UniProtKB FTrEMBL:Q0P8F5 Genbank:YP_002344842.1 GeneID:905748;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1460 2C unknown 2C len: 127 aa 3B 41.0 25 identity to HP0811. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 1397350 1397733 . + . ID=gene1404;Name=Cj1460;locus_tag=Cj1460;Dbxref=GeneID:905748;gbkey=Gene NC_002163.1 RefSeq gene 1397726 1398409 . + . ID=gene1405;Name=Cj1461;locus_tag=Cj1461;Dbxref=GeneID:905749;gbkey=Gene NC_002163.1 RefSeq CDS 1397726 1398409 . + 0 ID=cds1330;Parent=gene1405;Name=YP_002344843.1;Dbxref=GOA:Q0P8F4 InterPro:IPR002052 InterPro:IPR004398 InterPro:IPR016065 UniProtKB FTrEMBL:Q0P8F4 Genbank:YP_002344843.1 GeneID:905749;gbkey=CDS;product=DNA methylase;Note=Original 282000 29 note: Cj1461 2C possible DNA methylase 2C len: 227 aa 3B similar to hypothetical proteins e.g. YHHF_ECOLI 28198 aa 29 2C fasta scores 3B opt: 186 z-score: 224.4 E 28 29: 3.5e-05 2C 27.1 25 identity in 181 aa overlap. 37.2 25 identity to HP0810. Contains PS00092 N-6 Adenine-specific DNA methylases signature 7EUpdated 282006 29 note: Pfam domain PF03602 Conserved hypothetical protein identified within CDS. Specific characterisation with acceptable identity score has not been carried out yet 2C so kept within product function. Functional classification - DNA replication 2Crestriction 2Fmodification 2C recombination and repair NC_002163.1 RefSeq region 1397855 1398403 . + . ID=id2583;Name=id2583;Dbxref=GeneID:905749;gbkey=misc_feature;Note=HMMPfam hit to PF03602 2C Conserved hypothetical protein 2C score 5.6e-69 NC_002163.1 RefSeq region 1398197 1398217 . + . ID=id2584;Name=id2584;Dbxref=GeneID:905749;gbkey=misc_feature;Note=PS00092 N-6 Adenine-specific DNA methylases signature ### NC_002163.1 UTR_Extractor 5'-UTR 1398444 1398467 . + . ID=utr537;locus_tag=Cj1462;product=flagellar basal body P-ring protein NC_002163.1 RefSeq CDS 1398468 1399514 . + 0 ID=cds1331;Parent=gene1406;gene=flgI;Name=YP_002344844.1;Dbxref=GOA:Q9PMJ8 InterPro:IPR001782 UniProtKB FSwiss-Prot:Q9PMJ8 Genbank:YP_002344844.1 GeneID:905750;gbkey=CDS;product=flagellar basal body P-ring protein;Note=part of the basal body which consists of four rings L 2C P 2C S 2C and M mounted on a central rod 3B Vibrio parahaemolyticus 2C Yersinia 2C Bradyrhizobium and other bacteria have two copies of this and other flagellar genes 3B the V. parahaemolyticus protein is associated with the polar flagella and the Bradyrhizobium protein is associated with the thick flagellum NC_002163.1 RefSeq gene 1398468 1399514 . + . ID=gene1406;gene=flgI;Name=flgI;locus_tag=Cj1462;Dbxref=GeneID:905750;gbkey=Gene NC_002163.1 RefSeq region 1398519 1399511 . + . ID=id2585;gene=flgI;Name=id2585;Dbxref=GeneID:905750;gbkey=misc_feature;Note=HMMPfam hit to PF02119 2C Flagellar P-ring protein 2Cscore 1.4e-130 NC_002163.1 RefSeq gene 1399514 1399855 . + . ID=gene1407;gene=flgJ;Name=flgJ;locus_tag=Cj1463;Dbxref=GeneID:905751;gbkey=Gene NC_002163.1 RefSeq CDS 1399514 1399855 . + 0 ID=cds1332;Parent=gene1407;gene=flgJ;Name=YP_002344845.1;Dbxref=InterPro:IPR016511 UniProtKB FSwiss-Prot:Q9PMJ7 Genbank:YP_002344845.1 GeneID:905751;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1463 2C unknown 2C len: 113 aa 3B 46.0 25 identity to HP0245 7EUpdated 282006 29 note: Literature search identified papers giving clues to product function. C.Penn unpublished observation has predicted to be FlgJ. Functional classification - Conserved hypothetical proteins 7EPMID:14617189 2C PMID:14960570 2C PMID:15812042 ### NC_002163.1 RefSeq gene 1399918 1400115 . + . ID=gene1408;gene=flgM;Name=flgM;locus_tag=Cj1464;Dbxref=GeneID:905752;gbkey=Gene NC_002163.1 RefSeq CDS 1399918 1400115 . + 0 ID=cds1333;Parent=gene1408;gene=flgM;Name=YP_002344846.1;Dbxref=GOA:Q0P8F1 UniProtKB FTrEMBL:Q0P8F1 Genbank:YP_002344846.1 GeneID:905752;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1464 2C unknown 2C len: 65 aa 3B no Hp match 7EUpdated 282006 29 note: Literature search identified papers giving further clues to product function. Has been linked to flagellar anti FliA 28sigma 28 29 factor FlgM protein. Functional classification - Unknown 7EPMID:14617189 2C PMID:14702320 2C PMID:14985343 NC_002163.1 RefSeq gene 1400158 1400592 . + . ID=gene1409;Name=Cj1465;locus_tag=Cj1465;Dbxref=GeneID:905753;gbkey=Gene NC_002163.1 RefSeq CDS 1400158 1400592 . + 0 ID=cds1334;Parent=gene1409;Name=YP_002344847.1;Dbxref=GOA:Q0P8F0 UniProtKB FTrEMBL:Q0P8F0 Genbank:YP_002344847.1 GeneID:905753;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1465 2C unknown 2C len: 144 aa 3B 31.9 25 identity to HP1120 7EUpdated 282006 29 note: Literature search identified paper giving clues to product function. Product function linked to possible flagellar gene. Similar story for uncharacterised upstream genes Cj1463 and Cj1464. Functional classification - Conserved hypothetical proteins 7EPMID:14702320 NC_002163.1 RefSeq CDS 1400602 1402428 . + 0 ID=cds1335;Parent=gene1410;gene=flgK;Name=YP_002344848.1;Dbxref=GOA:Q0P8E9 InterPro:IPR001444 InterPro:IPR002371 InterPro:IPR010930 UniProtKB FTrEMBL:Q0P8E9 Genbank:YP_002344848.1 GeneID:905754;gbkey=CDS;product=flagellar hook-associated protein FlgK;Note=with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook NC_002163.1 RefSeq gene 1400602 1402428 . + . ID=gene1410;gene=flgK;Name=flgK;locus_tag=Cj1466;Dbxref=GeneID:905754;gbkey=Gene NC_002163.1 RefSeq region 1400620 1400712 . + . ID=id2586;gene=flgK;Name=id2586;Dbxref=GeneID:905754;gbkey=misc_feature;Note=HMMPfam hit to PF00460 2C Flagella basal body rod protein 2C score 2.1e-05 NC_002163.1 RefSeq region 1402303 1402419 . + . ID=id2587;gene=flgK;Name=id2587;Dbxref=GeneID:905754;gbkey=misc_feature;Note=HMMPfam hit to PF06429 2C Domain of unknown function 28DUF1078 29 2C score 6.6e-18 ### NC_002163.1 RefSeq gene 1402445 1403209 . + . ID=gene1411;Name=Cj1467;locus_tag=Cj1467;Dbxref=GeneID:905755;gbkey=Gene NC_002163.1 RefSeq CDS 1402445 1403209 . + 0 ID=cds1336;Parent=gene1411;Name=YP_002344849.1;Dbxref=InterPro:IPR014127 UniProtKB FTrEMBL:Q0P8E8 Genbank:YP_002344849.1 GeneID:905755;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1467 2C unknown 2C len: 254 aa 3B some similarity to TR:O51480 28EMBL:AE001154 29 Borrelia burgdorferi BB0530 28217 aa 29 2C fasta scores 3B opt: 331 z-score: 404.6 E 28 29: 3.2e-15 2C 32.8 25 identity in 189 aa overlap. No Hp match. Functional classification -Conserved hypothetical proteins NC_002163.1 UTR_Extractor 5'-UTR 1403085 1403212 . + . ID=utr538;locus_tag=Cj1468;product=putative integral membrane protein ### NC_002163.1 RefSeq gene 1403213 1403977 . + . ID=gene1412;Name=Cj1468;locus_tag=Cj1468;Dbxref=GeneID:905756;gbkey=Gene NC_002163.1 RefSeq CDS 1403213 1403977 . + 0 ID=cds1337;Parent=gene1412;Name=YP_002344850.1;Dbxref=GOA:Q0P8E7 InterPro:IPR002781 UniProtKB FTrEMBL:Q0P8E7 Genbank:YP_002344850.1 GeneID:905756;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj1468 2C probable integral membrane protein 2C len: 254 aa 3B similar to hypothetical membrane proteins e.g. YFCA_ECOLI 28269 aa 29 2C fasta scores 3B opt: 612 z-score: 731.5 E 28 29: 0 2C 43.4 25 identity in 242 aa overlap. No Hp ortholog 7EUpdated 282006 29 note: Pfam domain PF01925 Domain of unknown function DUF81 identified within CDS. Also 2C seven probable transmembrane helices predicted by TMHMM2.0. Furhter support given to product function. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq region 1403231 1403299 . + . ID=id2588;Name=id2588;Dbxref=GeneID:905756;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1468 by TMHMM2.0 at aa 7-29 2C 76-98 2C 105-122 2C 149-171 2C183-200 2C 204-226 and 233-250 NC_002163.1 RefSeq region 1403246 1403959 . + . ID=id2589;Name=id2589;Dbxref=GeneID:905756;gbkey=misc_feature;Note=HMMPfam hit to PF01925 2C Domain of unknown function DUF81 2C score 5.8e-34 NC_002163.1 RefSeq region 1403306 1403338 . + . ID=id2590;Name=id2590;Dbxref=GeneID:905756;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1403438 1403506 . + . ID=id2588;Name=id2588;Dbxref=GeneID:905756;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1468 by TMHMM2.0 at aa 7-29 2C 76-98 2C 105-122 2C 149-171 2C183-200 2C 204-226 and 233-250 NC_002163.1 RefSeq region 1403525 1403578 . + . ID=id2588;Name=id2588;Dbxref=GeneID:905756;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1468 by TMHMM2.0 at aa 7-29 2C 76-98 2C 105-122 2C 149-171 2C183-200 2C 204-226 and 233-250 NC_002163.1 RefSeq region 1403657 1403725 . + . ID=id2588;Name=id2588;Dbxref=GeneID:905756;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1468 by TMHMM2.0 at aa 7-29 2C 76-98 2C 105-122 2C 149-171 2C183-200 2C 204-226 and 233-250 NC_002163.1 RefSeq region 1403678 1403710 . + . ID=id2591;Name=id2591;Dbxref=GeneID:905756;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1403759 1403812 . + . ID=id2588;Name=id2588;Dbxref=GeneID:905756;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1468 by TMHMM2.0 at aa 7-29 2C 76-98 2C 105-122 2C 149-171 2C183-200 2C 204-226 and 233-250 NC_002163.1 RefSeq region 1403822 1403890 . + . ID=id2588;Name=id2588;Dbxref=GeneID:905756;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1468 by TMHMM2.0 at aa 7-29 2C 76-98 2C 105-122 2C 149-171 2C183-200 2C 204-226 and 233-250 NC_002163.1 RefSeq region 1403909 1403962 . + . ID=id2588;Name=id2588;Dbxref=GeneID:905756;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1468 by TMHMM2.0 at aa 7-29 2C 76-98 2C 105-122 2C 149-171 2C183-200 2C 204-226 and 233-250 NC_002163.1 RefSeq region 1403970 1404347 . - . ID=id2592;Name=id2592;Dbxref=PSEUDO:CAL35577.1 GeneID:905757;gbkey=misc_feature;Note=Original 282000 29 note: Cj1470c 2C probable type II protein secretion system F protein pseudogene 2C len: 1178 bp 3B similar to e.g. HOFC_ECOLI protein transport protein HOFC 28400 aa 29 2822.7 25 identity 29and GSPF_PSEAE general secretion pathway protein F 28405 aa 29 2823.0 25 identity 29. Contains Pfam match to entry PF00482 GSPII_F 2C Bacterial type II secretion system protein F domain. No Hp match 7EUpdated 282006 29 note: Pfam domain PF00482 Bacterial type II secretion system protein F domain identified within CDS. Also 2C four probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterisation paper within Campylobacter attached. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Protein and peptide secretion 7EPMID:12949093 NC_002163.1 RefSeq pseudogene 1403970 1405150 . - . ID=gene1413;Name=Cj1470c;locus_tag=Cj1470c;Dbxref=GeneID:905757;gbkey=Gene NC_002163.1 RefSeq region 1404006 1404347 . - . ID=id2593;Name=id2593;Dbxref=GeneID:905757;gbkey=misc_feature;Note=HMMPfam hit to PF00482 2C Bacterial type II secretion system protein F 2C score 2.4e-15 NC_002163.1 RefSeq region 1404015 1404083 . - . ID=id125;Name=id125;Dbxref=GeneID:905757;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1470c by TMHMM2.0 at aa 156-178 2C 209-231 2C 246-268 and 357-379 NC_002163.1 RefSeq region 1404347 1404347 . - . ID=id125;Name=id125;Dbxref=GeneID:905757;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1470c by TMHMM2.0 at aa 156-178 2C 209-231 2C 246-268 and 357-379 NC_002163.1 RefSeq region 1404347 1404373 . - . ID=id2593;Name=id2593;Dbxref=GeneID:905757;gbkey=misc_feature;Note=HMMPfam hit to PF00482 2C Bacterial type II secretion system protein F 2C score 2.4e-15 NC_002163.1 RefSeq region 1404347 1404415 . - . ID=id125;Name=id125;Dbxref=GeneID:905757;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1470c by TMHMM2.0 at aa 156-178 2C 209-231 2C 246-268 and 357-379 NC_002163.1 RefSeq region 1404347 1405150 . - . ID=id2592;Name=id2592;Dbxref=PSEUDO:CAL35577.1 GeneID:905757;gbkey=misc_feature;Note=Original 282000 29 note: Cj1470c 2C probable type II protein secretion system F protein pseudogene 2C len: 1178 bp 3B similar to e.g. HOFC_ECOLI protein transport protein HOFC 28400 aa 29 2822.7 25 identity 29and GSPF_PSEAE general secretion pathway protein F 28405 aa 29 2823.0 25 identity 29. Contains Pfam match to entry PF00482 GSPII_F 2C Bacterial type II secretion system protein F domain. No Hp match 7EUpdated 282006 29 note: Pfam domain PF00482 Bacterial type II secretion system protein F domain identified within CDS. Also 2C four probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterisation paper within Campylobacter attached. Thus 2C not added to product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Protein and peptide secretion 7EPMID:12949093 NC_002163.1 RefSeq region 1404458 1404526 . - . ID=id125;Name=id125;Dbxref=GeneID:905757;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1470c by TMHMM2.0 at aa 156-178 2C 209-231 2C 246-268 and 357-379 NC_002163.1 RefSeq region 1404614 1404973 . - . ID=id2594;Name=id2594;Dbxref=GeneID:905757;gbkey=misc_feature;Note=HMMPfam hit to PF00482 2C Bacterial type II secretion system protein F 2C score 5.9e-21 NC_002163.1 RefSeq region 1404617 1404685 . - . ID=id125;Name=id125;Dbxref=GeneID:905757;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1470c by TMHMM2.0 at aa 156-178 2C 209-231 2C 246-268 and 357-379 NC_002163.1 RefSeq gene 1405147 1406706 . - . ID=gene1414;gene=ctsE;Name=ctsE;locus_tag=Cj1471c;Dbxref=GeneID:905758;gbkey=Gene NC_002163.1 RefSeq CDS 1405147 1406706 . - 0 ID=cds1338;Parent=gene1414;gene=ctsE;Name=YP_002344851.1;Dbxref=GOA:Q0P8E6 InterPro:IPR001482 InterPro:IPR003593 UniProtKB FTrEMBL:Q0P8E6 Genbank:YP_002344851.1 GeneID:905758;gbkey=CDS;product=type II protein secretion system E protein;Note=Original 282000 29 note: Cj1471c 2C probable type II protein secretion system E protein 2C len: 519 aa 3B similar to e.g. GSPE_ERWCA general secretion pathway protein E 28498 aa 29 2C fasta scores 3B opt: 993 z-score: 1102.0 E 28 29: 0 2C38.2 25 identity in 487 aa overlap 2C and HOFB_ECOLI protein transport protein HOFB 28461 aa 29 2C fasta scores 3B opt: 925 z-score: 1027.3 E 28 29: 0 2C 37.7 25 identity in 453 aa overlap. No Hp match. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00662 Bacterial type II secretion system protein E signature 2C and Pfam match to entry PF00437 GSPII_E 2C Bacterial type II secretion system protein 7EUpdated 282006 29 note: Some characterisation in Campylobacter jejuni. New gene name designated. Similar to more than one genus with acceptable similarty scores. kept within product function. Functional classification - Protein and peptide secretion 7EPMID:12949093 2C PMID:1971619 NC_002163.1 RefSeq region 1405441 1406277 . - . ID=id2595;gene=ctsE;Name=id2595;Dbxref=GeneID:905758;gbkey=misc_feature;Note=HMMPfam hit to PF00437 2C Type II 2FIV secretion system protein 2C score 5.9e-102 NC_002163.1 RefSeq region 1405618 1405662 . - . ID=id2596;gene=ctsE;Name=id2596;Dbxref=GeneID:905758;gbkey=misc_feature;Note=PS00662 Bacterial type II secretion system protein E signature NC_002163.1 RefSeq region 1405816 1405839 . - . ID=id2597;gene=ctsE;Name=id2597;Dbxref=GeneID:905758;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 1406696 1407283 . - 0 ID=cds1339;Parent=gene1415;Name=YP_002344852.1;Dbxref=UniProtKB FTrEMBL:Q0P8E5 Genbank:YP_002344852.1 GeneID:905759;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1472c 2C probable membrane protein 2C len: 195 aa 3B no Hp match 7EUpdated 282006 29 note: One probable transmembrane helix predicted by TMHMM2.0. Literature search identified paper giving further clues to product function. Functional classification - Membranes 2C lipoproteins and porins 7EPMID:12949093 NC_002163.1 RefSeq gene 1406696 1407283 . - . ID=gene1415;gene=Cj1472c;Name=Cj1472c;locus_tag=Cj1472c;Dbxref=GeneID:905759;gbkey=Gene NC_002163.1 RefSeq region 1407158 1407226 . - . ID=id2598;Name=id2598;Dbxref=GeneID:905759;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1472c by TMHMM2.0 at aa 20-42 ### NC_002163.1 RefSeq CDS 1407287 1407895 . - 0 ID=cds1340;Parent=gene1416;gene=ctsP;Name=YP_002344853.1;Dbxref=GOA:Q0P8E4 InterPro:IPR003593 UniProtKB FTrEMBL:Q0P8E4 Genbank:YP_002344853.1 GeneID:905760;gbkey=CDS;product=ATP 2FGTP-binding protein;Note=Original 282000 29 note: Cj1473c 2C probable ATP 2FGTP-binding protein 2C len: 202 aa 3B no Hp match. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 7EUpdated 282006 29 note: Literature search identified paper giving further clues to product function. Functional classification - Unknown 7EPMID:12949093 NC_002163.1 RefSeq gene 1407287 1407895 . - . ID=gene1416;gene=ctsP;Name=ctsP;locus_tag=Cj1473c;Dbxref=GeneID:905760;gbkey=Gene NC_002163.1 RefSeq region 1407785 1407808 . - . ID=id2599;gene=ctsP;Name=id2599;Dbxref=GeneID:905760;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq gene 1407888 1409306 . - . ID=gene1417;gene=ctsD;Name=ctsD;locus_tag=Cj1474c;Dbxref=GeneID:905761;gbkey=Gene NC_002163.1 RefSeq CDS 1407888 1409306 . - 0 ID=cds1341;Parent=gene1417;gene=ctsD;Name=YP_002344854.1;Dbxref=GOA:Q0P8E3 InterPro:IPR001775 InterPro:IPR004846 InterPro:IPR011514 InterPro:IPR011662 InterPro:IPR013358 UniProtKB FTrEMBL:Q0P8E3 Genbank:YP_002344854.1 GeneID:905761;gbkey=CDS;product=type II protein secretion system D protein;Note=Original 282000 29 note: Cj1474c 2C probable type II protein secretion system D protein 2C len: 472 aa 3B similar to e.g. GSPD_PSEAE general secretion pathway protein D precursor 28658 aa 29 2C fasta scores 3B opt: 305 z-score: 332.5 E 28 29: 3.4e-11 2C 26.5 25 identity in 268 aa overlap. No Hp match. Contains Pfam match to entry PF00263 Bac_GSPproteins 2C Bacterial type II secretion system protein 2C and probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domains PF07655 Secretin N-terminal domain and PF07660 Secretin and TonB N terminus short domain were both identified within CDS. Literature search identified paper giving further clues to product function. kept within product function. Functional classification - Protein and peptide secretion 7EPMID:12949093 NC_002163.1 RefSeq region 1407939 1408655 . - . ID=id2600;gene=ctsD;Name=id2600;Dbxref=GeneID:905761;gbkey=misc_feature;Note=HMMPfam hit to PF00263 2C Bacterial type II and III secretion syst 2C score 1e-73 NC_002163.1 RefSeq region 1408764 1408991 . - . ID=id2601;gene=ctsD;Name=id2601;Dbxref=GeneID:905761;gbkey=misc_feature;Note=HMMPfam hit to PF07655 2C Secretin N-terminal domain 2Cscore 1.3e-38 NC_002163.1 RefSeq region 1408995 1409159 . - . ID=id2602;gene=ctsD;Name=id2602;Dbxref=GeneID:905761;gbkey=misc_feature;Note=HMMPfam hit to PF07660 2C Secretin and TonB N terminus short domai 2C score 2.6e-08 NC_002163.1 RefSeq CDS 1409278 1409595 . - 0 ID=cds1342;Parent=gene1418;gene=ctsR;Name=YP_002344855.1;Dbxref=UniProtKB FTrEMBL:Q0P8E2 Genbank:YP_002344855.1 GeneID:905762;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1475c 2C unknown 2C len: 105 aa 3B no Hp match 7EUpdated 282006 29 note: Literature search identified paper giving further clues to product function. Functional classification - Unknown 7EPMID:12949093 NC_002163.1 RefSeq gene 1409278 1409595 . - . ID=gene1418;gene=ctsR;Name=ctsR;locus_tag=Cj1475c;Dbxref=GeneID:905762;gbkey=Gene ### NC_002163.1 RefSeq CDS 1409619 1413179 . - 0 ID=cds1343;Parent=gene1419;Name=YP_002344856.1;Dbxref=GOA:Q0P8E1 InterPro:IPR001450 InterPro:IPR002869 InterPro:IPR002880 InterPro:IPR011766 InterPro:IPR011895 InterPro:IPR015941 UniProtKB FTrEMBL:Q0P8E1 Genbank:YP_002344856.1 GeneID:905763;gbkey=CDS;product=pyruvate-flavodoxin oxidoreductase;Note=Original 282000 29 note: Cj1476c 2C probable pyruvate-flavodoxin oxidoreductase 2C len: 1186 aa 3B highly similar to many e.g. NIFJ_ECOLI probable pyruvate-flavodoxin oxidoreductase 281174 aa 29 2C fasta scores 3B opt: 3586 z-score: 3799.5 E 28 29: 0 2C 47.2 25 identity in 1193 aa overlap. N-term has 28.6 25 identity to HP1110 2CC-term has 29.7 25 identity to HP1111. Contains 2x PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature 2Cand Pfam match to entry PF00037 fer4 2C 4Fe-4S ferredoxins and related iron-sulfur cluster binding domains 7EUpdated 282006 29 note: Pfam domains PF02775 Thiamine pyrophosphate enzyme 2C C-terminal 2C PF01558 Pyruvate ferredoxin 2Fflavodoxin oxidoreductase and PF01855 Pyruvate flavodoxin 2Fferredoxin oxidoreductase were all identified within CDS. Further support given to product function. Characterised in Escherichia coli with acceptable identity score. not added to product function. Functional classification - Energy metabolism - Electron transport NC_002163.1 RefSeq gene 1409619 1413179 . - . ID=gene1419;Name=Cj1476c;locus_tag=Cj1476c;Dbxref=GeneID:905763;gbkey=Gene NC_002163.1 RefSeq region 1409934 1410731 . - . ID=id2603;Name=id2603;Dbxref=GeneID:905763;gbkey=misc_feature;Note=HMMPfam hit to PF02775 2C Thiamine pyrophosphate enzyme 2C C-termina 2C score 5.1e-104 NC_002163.1 RefSeq region 1410882 1410953 . - . ID=id2604;Name=id2604;Dbxref=GeneID:905763;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 0.00046 NC_002163.1 RefSeq region 1410897 1410932 . - . ID=id2605;Name=id2605;Dbxref=GeneID:905763;gbkey=misc_feature;Note=PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature NC_002163.1 RefSeq region 1411056 1411127 . - . ID=id2606;Name=id2606;Dbxref=GeneID:905763;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 7.6e-06 NC_002163.1 RefSeq region 1411071 1411106 . - . ID=id2607;Name=id2607;Dbxref=GeneID:905763;gbkey=misc_feature;Note=PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature NC_002163.1 RefSeq region 1411353 1411907 . - . ID=id2608;Name=id2608;Dbxref=GeneID:905763;gbkey=misc_feature;Note=HMMPfam hit to PF01558 2C Pyruvate ferredoxin 2Fflavodoxin oxidoredu 2C score 1.7e-68 NC_002163.1 RefSeq region 1412436 1413134 . - . ID=id2609;Name=id2609;Dbxref=GeneID:905763;gbkey=misc_feature;Note=HMMPfam hit to PF01855 2C Pyruvate flavodoxin 2Fferredoxin oxidoredu 2C score 2.4e-108 ### NC_002163.1 UTR_Extractor 5'-UTR 1413180 1413219 . - . ID=utr539;locus_tag=Cj1476c;product=pyruvate-flavodoxin oxidoreductase NC_002163.1 RefSeq CDS 1413272 1413913 . - 0 ID=cds1344;Parent=gene1420;Name=YP_002344857.1;Dbxref=GOA:Q0P8E0 InterPro:IPR005834 InterPro:IPR006439 UniProtKB FTrEMBL:Q0P8E0 Genbank:YP_002344857.1 GeneID:905764;gbkey=CDS;product=hydrolase;Note=Original 282000 29 note: Cj1477c 2C probable hydrolase 2Clen: 206 aa 3B similar to e.g. GPH_ECOLI phosphoglycolate phosphatase 28252 aa 29 2C fasta scores 3B opt: 209 z-score: 257.5 E 28 29: 5.1e-07 2C 27.5 25 identity in 222 aa overlap. Contains Pfam match to entry PF00702 Hydrolase 2C haloacid dehalogenase-like hydrolase. Also similar to Cj1233 2827.3 25 identity in 205 aa overlap 29. No Hp match 7EUpdated 282006 29 note: Similar to different types of hydrolases. kept within product function. Functional classification - Misc 7EPMID:12576589 NC_002163.1 RefSeq gene 1413272 1413913 . - . ID=gene1420;Name=Cj1477c;locus_tag=Cj1477c;Dbxref=GeneID:905764;gbkey=Gene NC_002163.1 RefSeq region 1413359 1413910 . - . ID=id2610;Name=id2610;Dbxref=GeneID:905764;gbkey=misc_feature;Note=HMMPfam hit to PF00702 2C haloacid dehalogenase-like hydrolase 2C score 2e-19 NC_002163.1 RefSeq gene 1413913 1414872 . - . ID=gene1421;gene=cadF;Name=cadF;locus_tag=Cj1478c;Dbxref=GeneID:905765;gbkey=Gene NC_002163.1 RefSeq CDS 1413913 1414872 . - 0 ID=cds1345;Parent=gene1421;gene=cadF;Name=YP_002344858.1;Dbxref=GOA:Q0P8D9 InterPro:IPR000498 InterPro:IPR006664 InterPro:IPR006665 InterPro:IPR006690 InterPro:IPR011250 UniProtKB FTrEMBL:Q0P8D9 Genbank:YP_002344858.1 GeneID:905765;gbkey=CDS;product=outer membrane fibronectin-binding protein;Note=Original 282000 29 note: Cj1478c 2C cadF 2C outer membrane fibronectin-binding protein 2C len: 319 aa 3B 82.8 25 identical to TR:O06895 28EMBL:U87559 29 C. jejuni CADF precursor 28fibronectin-binding protein 29 28326 aa 29 2C and similar to many oprF proteins e.g. PORF_PSEFL outer membrane porin F precursor 28root adhesin 29 28326 aa 29 2C fasta scores 3B opt: 401 z-score: 458.6 E 28 29: 3.2e-18 2C 29.1 25 identity in 316 aa overlap. No Hp match. Contains PS01068 OmpA-like domain 2Cand Pfam match to entry PF00691 OmpA 2C OmpA family 7EUpdated 282006 29 note: Characterised within Campylobacter jejuni 2C so not added to product function. Functional classification - Pathogenicity 7EPMID:9220003 2C PMID:9435102 2C PMID:16091041 NC_002163.1 RefSeq region 1413943 1414230 . - . ID=id2611;gene=cadF;Name=id2611;Dbxref=GeneID:905765;gbkey=misc_feature;Note=HMMPfam hit to PF00691 2C OmpA family 2C score 2.6e-37 NC_002163.1 RefSeq region 1413997 1414131 . - . ID=id2612;gene=cadF;Name=id2612;Dbxref=GeneID:905765;gbkey=misc_feature;Note=PS01068 OmpA-like domain NC_002163.1 RefSeq region 1414354 1414872 . - . ID=id2613;gene=cadF;Name=id2613;Dbxref=GeneID:905765;gbkey=misc_feature;Note=HMMPfam hit to PF01389 2C OmpA-like transmembrane domain 2C score 0.00072 ### NC_002163.1 UTR_Extractor 5'-UTR 1414873 1414914 . - . ID=utr540;locus_tag=Cj1478c;product=outer membrane fibronectin-binding protein NC_002163.1 RefSeq CDS 1414997 1415386 . - 0 ID=cds1346;Parent=gene1422;gene=rpsI;Name=YP_002344859.1;Dbxref=GOA:Q9PMI3 HSSP:P80374 InterPro:IPR000754 InterPro:IPR014721 UniProtKB FSwiss-Prot:Q9PMI3 Genbank:YP_002344859.1 GeneID:905766;gbkey=CDS;product=30S ribosomal protein S9;Note=forms a direct contact with the tRNA during translation NC_002163.1 RefSeq gene 1414997 1415386 . - . ID=gene1422;gene=rpsI;Name=rpsI;locus_tag=Cj1479c;Dbxref=GeneID:905766;gbkey=Gene NC_002163.1 RefSeq region 1415000 1415365 . - . ID=id2614;gene=rpsI;Name=id2614;Dbxref=GeneID:905766;gbkey=misc_feature;Note=HMMPfam hit to PF00380 2C Ribosomal protein S9 2FS16 2Cscore 2.5e-47 NC_002163.1 RefSeq region 1415129 1415185 . - . ID=id2615;gene=rpsI;Name=id2615;Dbxref=GeneID:905766;gbkey=misc_feature;Note=PS00360 Ribosomal protein S9 signature ### NC_002163.1 RefSeq CDS 1415389 1415814 . - 0 ID=cds1347;Parent=gene1423;gene=rplM;Name=YP_002344860.1;Dbxref=GOA:Q0P8D7 InterPro:IPR005822 InterPro:IPR005823 UniProtKB FTrEMBL:Q0P8D7 Genbank:YP_002344860.1 GeneID:905767;gbkey=CDS;product=50S ribosomal protein L13;Note=in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit NC_002163.1 RefSeq gene 1415389 1415814 . - . ID=gene1423;gene=rplM;Name=rplM;locus_tag=Cj1480c;Dbxref=GeneID:905767;gbkey=Gene NC_002163.1 RefSeq region 1415398 1415775 . - . ID=id2616;gene=rplM;Name=id2616;Dbxref=GeneID:905767;gbkey=misc_feature;Note=HMMPfam hit to PF00572 2C Ribosomal protein L13 2Cscore 7.7e-54 NC_002163.1 RefSeq region 1415434 1415502 . - . ID=id2617;gene=rplM;Name=id2617;Dbxref=GeneID:905767;gbkey=misc_feature;Note=PS00783 Ribosomal protein L13 signature ### NC_002163.1 UTR_Extractor 5'-UTR 1415815 1415843 . - . ID=utr541;locus_tag=Cj1480c;product=50S ribosomal protein L13 NC_002163.1 RefSeq CDS 1415898 1418663 . - 0 ID=cds1348;Parent=gene1424;Name=YP_002344861.1;Dbxref=GOA:Q0P8D6 InterPro:IPR000212 InterPro:IPR014016 InterPro:IPR014017 UniProtKB FTrEMBL:Q0P8D6 Genbank:YP_002344861.1 GeneID:905768;gbkey=CDS;product=recombination protein RecB;Note=Original 282000 29 note: Cj1481c 2C possible helicase 2Clen: 921 aa 3B weak similarity to several predicted helicases e.g. UVRD_MYCGE DNA helicase II homolog 28703 aa 29 2C fasta scores 3B opt: 220 z-score: 237.1 E 28 29: 7e-06 2C 24.5 25 identity in 715 aa overlap 2C and to e.g. ADDA_BACSU ATP-dependent nuclease subunit A 28contains helicase activity 29 281232 aa 29 2C fasta scores 3B opt: 204 z-score: 216.2 E 28 29: 0.0001 2C 23.0 25 identity in 868 aa overlap. 30.5 25 identity to HP1553. Also similar to predicted helicases Cj1101 2823.9 25 identity in 532 aa overlap 29 2C and Cj0777 2824.1 25 identity in 673 aa overlap 29. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 7EUpdated 282006 29 note: Pfam domain PF00580 UvrD 2FREP helicase identified within CDS. Further support given to product function. Not yet specifically characterised within related bacteria with acceptable identity score. Thus 2C kept within product function. Functional classification - DNA replication 2Crestriction 2Fmodification 2C recombination and repair NC_002163.1 RefSeq gene 1415898 1418663 . - . ID=gene1424;Name=Cj1481c;locus_tag=Cj1481c;Dbxref=GeneID:905768;gbkey=Gene NC_002163.1 RefSeq region 1416843 1418660 . - . ID=id2618;Name=id2618;Dbxref=GeneID:905768;gbkey=misc_feature;Note=HMMPfam hit to PF00580 2C UvrD 2FREP helicase 2C score 3.9e-28 NC_002163.1 RefSeq region 1418607 1418630 . - . ID=id2619;Name=id2619;Dbxref=GeneID:905768;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 1418660 1421026 . - 0 ID=cds1349;Parent=gene1425;Name=YP_002344862.1;Dbxref=UniProtKB FTrEMBL:Q0P8D5 Genbank:YP_002344862.1 GeneID:905769;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1482c 2C unknown 2C len: 788 aa 3B 29.5 25 identity to HP1089. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 1418660 1421026 . - . ID=gene1425;Name=Cj1482c;locus_tag=Cj1482c;Dbxref=GeneID:905769;gbkey=Gene NC_002163.1 RefSeq gene 1421023 1421544 . - . ID=gene1426;Name=Cj1483c;locus_tag=Cj1483c;Dbxref=GeneID:905770;gbkey=Gene NC_002163.1 RefSeq CDS 1421023 1421544 . - 0 ID=cds1350;Parent=gene1426;Name=YP_002344863.1;Dbxref=GOA:Q0P8D4 UniProtKB FTrEMBL:Q0P8D4 Genbank:YP_002344863.1 GeneID:905770;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj1483c 2C probable lipoprotein 2C len: 173 aa 3B 30.8 25 identity 28in N-term 29 to HP0150. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 UTR_Extractor 5'-UTR 1421027 1421310 . - . ID=utr542;locus_tag=Cj1482c;product=hypothetical protein NC_002163.1 RefSeq region 1421458 1421526 . - . ID=id2620;Name=id2620;Dbxref=GeneID:905770;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1483c by TMHMM2.0 at aa 7-29 NC_002163.1 RefSeq region 1421473 1421505 . - . ID=id2621;Name=id2621;Dbxref=GeneID:905770;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq gene 1421531 1422133 . - . ID=gene1427;Name=Cj1484c;locus_tag=Cj1484c;Dbxref=GeneID:905771;gbkey=Gene NC_002163.1 RefSeq CDS 1421531 1422133 . - 0 ID=cds1351;Parent=gene1427;Name=YP_002344864.1;Dbxref=UniProtKB FTrEMBL:Q0P8D3 Genbank:YP_002344864.1 GeneID:905771;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1484c 2C probable membrane protein 2C len: 200 aa 3B no Hp match. Contains probable N-terminal signal sequence and probable C-terminal transmembrane domain. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 UTR_Extractor 5'-UTR 1421545 1421570 . - . ID=utr543;locus_tag=Cj1483c;product=putative lipoprotein NC_002163.1 RefSeq region 1421570 1421629 . - . ID=id126;Name=id126;Dbxref=GeneID:905771;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1484c by TMHMM2.0 at aa 9-31 and 169-188 NC_002163.1 RefSeq region 1422041 1422109 . - . ID=id126;Name=id126;Dbxref=GeneID:905771;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1484c by TMHMM2.0 at aa 9-31 and 169-188 NC_002163.1 RefSeq CDS 1422130 1422231 . - 0 ID=cds1352;Parent=gene1428;Name=YP_002344865.1;Dbxref=UniProtKB FTrEMBL:Q0P8D2 Genbank:YP_002344865.1 GeneID:905772;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1485c 2C probable periplasmic protein 2C len: 33 aa 3B no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 1422130 1422231 . - . ID=gene1428;Name=Cj1485c;locus_tag=Cj1485c;Dbxref=GeneID:905772;gbkey=Gene NC_002163.1 RefSeq region 1422154 1422213 . - . ID=id2622;Name=id2622;Dbxref=GeneID:905772;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1485c by TMHMM2.0 at aa 7-26 NC_002163.1 RefSeq gene 1422228 1422449 . - . ID=gene1429;Name=Cj1486c;locus_tag=Cj1486c;Dbxref=GeneID:905773;gbkey=Gene NC_002163.1 RefSeq CDS 1422228 1422449 . - 0 ID=cds1353;Parent=gene1429;Name=YP_002344866.1;Dbxref=UniProtKB FTrEMBL:Q0P8D1 Genbank:YP_002344866.1 GeneID:905773;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1486c 2C probable periplasmic protein 2C len: 73 aa 3B no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 1422339 1422407 . - . ID=id2623;Name=id2623;Dbxref=GeneID:905773;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1486c by TMHMM2.0 at aa 15-37 NC_002163.1 RefSeq gene 1422446 1423309 . - . ID=gene1430;gene=ccoP;Name=ccoP;locus_tag=Cj1487c;Dbxref=GeneID:905774;gbkey=Gene NC_002163.1 RefSeq CDS 1422446 1423309 . - 0 ID=cds1354;Parent=gene1430;gene=ccoP;Name=YP_002344867.1;Dbxref=GOA:Q0P8D0 InterPro:IPR003088 InterPro:IPR004678 InterPro:IPR009056 UniProtKB FTrEMBL:Q0P8D0 Genbank:YP_002344867.1 GeneID:905774;gbkey=CDS;product=cb-type cytochrome C oxidase subunit III;Note=Original 282000 29 note: Cj1487c 2C ccoP 2C cb-type cytochrome C oxidase subunit III 2C len: 287 aa 3B simlar to TR:O87196 28EMBL:AB018105 29 H. pylori characterised cb-type cytochrome C oxidase subunit III 28EC 1.9.3.1 29 28292 aa 29 2Cfasta scores 3B opt: 952 z-score: 1043.8 E 28 29: 0 2C 51.0 25 identity in 292 aa overlap 28 3DHP0147 2C 51.2 25 identity 29. Contains 2x Pfam match to entry PF00034 cytochrome_c 2C and 2x PS00190 Cytochrome c family heme-binding site signature 7EUpdated 282006 29 note: Characterised in Helicobacter pylori with acceptable identity score. not added to product function. Functional classification - Energy metabolism - Electron transport 7EPMID:9880817 NC_002163.1 RefSeq region 1422458 1422679 . - . ID=id2624;gene=ccoP;Name=id2624;Dbxref=GeneID:905774;gbkey=misc_feature;Note=HMMPfam hit to PF00034 2C Cytochrome c 2C score 4.4e-07 NC_002163.1 RefSeq region 1422635 1422652 . - . ID=id2625;gene=ccoP;Name=id2625;Dbxref=GeneID:905774;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature NC_002163.1 RefSeq region 1422716 1422955 . - . ID=id2626;gene=ccoP;Name=id2626;Dbxref=GeneID:905774;gbkey=misc_feature;Note=HMMPfam hit to PF00034 2C Cytochrome c 2C score 0.0077 NC_002163.1 RefSeq region 1422908 1422925 . - . ID=id2627;gene=ccoP;Name=id2627;Dbxref=GeneID:905774;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature NC_002163.1 RefSeq region 1423055 1423123 . - . ID=id127;gene=ccoP;Name=id127;Dbxref=GeneID:905774;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1487c by TMHMM2.0 at aa 10-30 and 63-85 NC_002163.1 RefSeq region 1423220 1423282 . - . ID=id127;gene=ccoP;Name=id127;Dbxref=GeneID:905774;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1487c by TMHMM2.0 at aa 10-30 and 63-85 NC_002163.1 RefSeq CDS 1423309 1423572 . - 0 ID=cds1355;Parent=gene1431;gene=ccoQ;Name=YP_002344868.1;Dbxref=GOA:Q0P8C9 InterPro:IPR014107 UniProtKB FTrEMBL:Q0P8C9 Genbank:YP_002344868.1 GeneID:905775;gbkey=CDS;product=cb-type cytochrome C oxidase subunit IV;Note=Original 282000 29 note: Cj1488c 2C ccoQ 2C cb-type cytochrome C oxidase subunit IV 2C len: 87 aa 3B similar to TR:O87195 28EMBL:AB018105 29 H. pylori characterised cb-type cytochrome C oxidase subunit IV 28EC 1.9.3.1 29 2872 aa 29 2Cfasta scores 3B opt: 143 z-score: 226.7 E 28 29: 2.6e-05 2C 35.1 25 identity in 57 aa overlap 28 3DHP0146 29 7EUpdated 282006 29 note: Characterised in Helicobacter pylori with acceptable identity score. not added to product function. Functional classification - Energy metabolism - Electron transport 7EPMID:9880817 NC_002163.1 RefSeq gene 1423309 1423572 . - . ID=gene1431;gene=ccoQ;Name=ccoQ;locus_tag=Cj1488c;Dbxref=GeneID:905775;gbkey=Gene NC_002163.1 RefSeq region 1423420 1423488 . - . ID=id2628;gene=ccoQ;Name=id2628;Dbxref=GeneID:905775;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1488c by TMHMM2.0 at aa 29-51 ### NC_002163.1 RefSeq CDS 1423577 1424242 . - 0 ID=cds1356;Parent=gene1432;gene=ccoO;Name=YP_002344869.1;Dbxref=GOA:Q0P8C8 InterPro:IPR003468 InterPro:IPR009056 UniProtKB FTrEMBL:Q0P8C8 Genbank:YP_002344869.1 GeneID:905776;gbkey=CDS;product=cbb3-type cytochrome c oxidase subunit II;Note=CcoO 3B FixO NC_002163.1 RefSeq gene 1423577 1424242 . - . ID=gene1432;gene=ccoO;Name=ccoO;locus_tag=Cj1489c;Dbxref=GeneID:905776;gbkey=Gene NC_002163.1 RefSeq region 1423580 1424239 . - . ID=id2629;gene=ccoO;Name=id2629;Dbxref=GeneID:905776;gbkey=misc_feature;Note=HMMPfam hit to PF02433 2C Cytochrome C oxidase 2Cmono-heme subunit 2FFixO 2C score 2.2e-99 NC_002163.1 RefSeq region 1424045 1424062 . - . ID=id2630;gene=ccoO;Name=id2630;Dbxref=GeneID:905776;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature NC_002163.1 RefSeq region 1424147 1424215 . - . ID=id2631;gene=ccoO;Name=id2631;Dbxref=GeneID:905776;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1489c by TMHMM2.0 at aa 10-32 ### NC_002163.1 RefSeq CDS 1424255 1425721 . - 0 ID=cds1357;Parent=gene1433;gene=ccoN;Name=YP_002344870.1;Dbxref=GOA:Q0P8C7 InterPro:IPR000883 InterPro:IPR004677 UniProtKB FTrEMBL:Q0P8C7 Genbank:YP_002344870.1 GeneID:905777;gbkey=CDS;product=cbb3-type cytochrome c oxidase subunit I;Note=CcoN 3B FixN NC_002163.1 RefSeq gene 1424255 1425721 . - . ID=gene1433;gene=ccoN;Name=ccoN;locus_tag=Cj1490c;Dbxref=GeneID:905777;gbkey=Gene NC_002163.1 RefSeq region 1424342 1424410 . - . ID=id128;gene=ccoN;Name=id128;Dbxref=GeneID:905777;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1490c by TMHMM2.0 at aa 13-35 2C 60-82 2C 102-124 2C 134-156 2C163-182 2C 216-238 2C 251-273 2C 283-305 2C 317-339 2C 354-376 2C396-418 and 438-460 NC_002163.1 RefSeq region 1424393 1425721 . - . ID=id2632;gene=ccoN;Name=id2632;Dbxref=GeneID:905777;gbkey=misc_feature;Note=HMMPfam hit to PF00115 2C Cytochrome C and Quinol oxidase polypeptide 2C score 3.1e-12 NC_002163.1 RefSeq region 1424468 1424536 . - . ID=id128;gene=ccoN;Name=id128;Dbxref=GeneID:905777;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1490c by TMHMM2.0 at aa 13-35 2C 60-82 2C 102-124 2C 134-156 2C163-182 2C 216-238 2C 251-273 2C 283-305 2C 317-339 2C 354-376 2C396-418 and 438-460 NC_002163.1 RefSeq region 1424594 1424662 . - . ID=id128;gene=ccoN;Name=id128;Dbxref=GeneID:905777;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1490c by TMHMM2.0 at aa 13-35 2C 60-82 2C 102-124 2C 134-156 2C163-182 2C 216-238 2C 251-273 2C 283-305 2C 317-339 2C 354-376 2C396-418 and 438-460 NC_002163.1 RefSeq region 1424705 1424773 . - . ID=id128;gene=ccoN;Name=id128;Dbxref=GeneID:905777;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1490c by TMHMM2.0 at aa 13-35 2C 60-82 2C 102-124 2C 134-156 2C163-182 2C 216-238 2C 251-273 2C 283-305 2C 317-339 2C 354-376 2C396-418 and 438-460 NC_002163.1 RefSeq region 1424807 1424875 . - . ID=id128;gene=ccoN;Name=id128;Dbxref=GeneID:905777;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1490c by TMHMM2.0 at aa 13-35 2C 60-82 2C 102-124 2C 134-156 2C163-182 2C 216-238 2C 251-273 2C 283-305 2C 317-339 2C 354-376 2C396-418 and 438-460 NC_002163.1 RefSeq region 1424903 1424971 . - . ID=id128;gene=ccoN;Name=id128;Dbxref=GeneID:905777;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1490c by TMHMM2.0 at aa 13-35 2C 60-82 2C 102-124 2C 134-156 2C163-182 2C 216-238 2C 251-273 2C 283-305 2C 317-339 2C 354-376 2C396-418 and 438-460 NC_002163.1 RefSeq region 1424912 1425079 . - . ID=id2633;gene=ccoN;Name=id2633;Dbxref=GeneID:905777;gbkey=misc_feature;Note=PS00077 Heme-copper oxidase catalytic subunit 2Ccopper B binding region signature NC_002163.1 RefSeq region 1425008 1425076 . - . ID=id128;gene=ccoN;Name=id128;Dbxref=GeneID:905777;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1490c by TMHMM2.0 at aa 13-35 2C 60-82 2C 102-124 2C 134-156 2C163-182 2C 216-238 2C 251-273 2C 283-305 2C 317-339 2C 354-376 2C396-418 and 438-460 NC_002163.1 RefSeq region 1425176 1425235 . - . ID=id128;gene=ccoN;Name=id128;Dbxref=GeneID:905777;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1490c by TMHMM2.0 at aa 13-35 2C 60-82 2C 102-124 2C 134-156 2C163-182 2C 216-238 2C 251-273 2C 283-305 2C 317-339 2C 354-376 2C396-418 and 438-460 NC_002163.1 RefSeq region 1425254 1425322 . - . ID=id128;gene=ccoN;Name=id128;Dbxref=GeneID:905777;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1490c by TMHMM2.0 at aa 13-35 2C 60-82 2C 102-124 2C 134-156 2C163-182 2C 216-238 2C 251-273 2C 283-305 2C 317-339 2C 354-376 2C396-418 and 438-460 NC_002163.1 RefSeq region 1425350 1425418 . - . ID=id128;gene=ccoN;Name=id128;Dbxref=GeneID:905777;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1490c by TMHMM2.0 at aa 13-35 2C 60-82 2C 102-124 2C 134-156 2C163-182 2C 216-238 2C 251-273 2C 283-305 2C 317-339 2C 354-376 2C396-418 and 438-460 NC_002163.1 RefSeq region 1425476 1425544 . - . ID=id128;gene=ccoN;Name=id128;Dbxref=GeneID:905777;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1490c by TMHMM2.0 at aa 13-35 2C 60-82 2C 102-124 2C 134-156 2C163-182 2C 216-238 2C 251-273 2C 283-305 2C 317-339 2C 354-376 2C396-418 and 438-460 NC_002163.1 RefSeq region 1425617 1425685 . - . ID=id128;gene=ccoN;Name=id128;Dbxref=GeneID:905777;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1490c by TMHMM2.0 at aa 13-35 2C 60-82 2C 102-124 2C 134-156 2C163-182 2C 216-238 2C 251-273 2C 283-305 2C 317-339 2C 354-376 2C396-418 and 438-460 ### NC_002163.1 UTR_Extractor 5'-UTR 1425722 1425751 . - . ID=utr544;locus_tag=Cj1490c;product=cbb3-type cytochrome c oxidase subunit I NC_002163.1 RefSeq CDS 1425847 1426527 . - 0 ID=cds1358;Parent=gene1434;Name=YP_002344871.1;Dbxref=GOA:Q0P8C6 InterPro:IPR001789 InterPro:IPR001867 UniProtKB FTrEMBL:Q0P8C6 Genbank:YP_002344871.1 GeneID:905778;gbkey=CDS;product=two-component regulator;Note=Original 282000 29 note: Cj1491c 2C probable two-component regulator 2C len: 226 aa 3B similar to many e.g. VANR_ENTFA regulatory protein VANRB 28220 aa 29 2C fasta scores 3B opt: 322 z-score: 369.3 E 28 29: 3e-13 2C 29.9 25 identity in 214 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00072 response_reg 2C Response regulator receiver domain 7EUpdated 282006 29 note: Pfam domain PF00486 Transcriptional regulatory protein 2C C terminal identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score has been carried out yet 2C so kept within product function. Functional classification - Signal transduction NC_002163.1 RefSeq gene 1425847 1426527 . - . ID=gene1434;Name=Cj1491c;locus_tag=Cj1491c;Dbxref=GeneID:905778;gbkey=Gene NC_002163.1 RefSeq region 1425862 1426074 . - . ID=id2634;Name=id2634;Dbxref=GeneID:905778;gbkey=misc_feature;Note=HMMPfam hit to PF00486 2C Transcriptional regulatory protein 2C C te 2C score 3.9e-18 NC_002163.1 RefSeq region 1426147 1426506 . - . ID=id2635;Name=id2635;Dbxref=GeneID:905778;gbkey=misc_feature;Note=HMMPfam hit to PF00072 2C Response regulator receiver domain 2C score 4.4e-32 ### NC_002163.1 UTR_Extractor 5'-UTR 1426528 1426690 . - . ID=utr545;locus_tag=Cj1491c;product=putative two-component regulator NC_002163.1 RefSeq CDS 1426530 1427741 . - 0 ID=cds1359;Parent=gene1435;Name=YP_002344872.1;Dbxref=GOA:Q0P8C5 InterPro:IPR000014 InterPro:IPR000700 InterPro:IPR001610 InterPro:IPR003594 InterPro:IPR004358 InterPro:IPR005467 InterPro:IPR013655 UniProtKB FTrEMBL:Q0P8C5 Genbank:YP_002344872.1 GeneID:905779;gbkey=CDS;product=two-component sensor;Note=Original 282000 29 note: Cj1492c 2C probable two-component sensor 2C len: 403 aa 3B similar to many e.g. KINC_BACSU sporulation kinase C 28428 aa 29 2C fasta scores 3B opt: 281 z-score: 301.1 E 28 29: 1.9e-09 2C 29.3 25 identity in 242 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00512 signal 2C Signal carboxyl-terminal domain 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score has been carried out yet 2Cso kept within product function. Functional classification - Signal transduction NC_002163.1 RefSeq gene 1426530 1427741 . - . ID=gene1435;Name=Cj1492c;locus_tag=Cj1492c;Dbxref=GeneID:905779;gbkey=Gene NC_002163.1 RefSeq region 1426545 1426874 . - . ID=id2636;Name=id2636;Dbxref=GeneID:905779;gbkey=misc_feature;Note=HMMPfam hit to PF02518 2C Histidine kinase- 2C DNA gyrase B- 2C and HSP90 2C score 1.3e-26 NC_002163.1 RefSeq CDS 1427738 1428397 . - 0 ID=cds1360;Parent=gene1436;Name=YP_002344873.1;Dbxref=UniProtKB FTrEMBL:Q0P8C4 Genbank:YP_002344873.1 GeneID:905783;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj1493c 2C probable integral membrane protein 2C len: 219 aa 3B 33.9 25 identity to HP0861 7EUpdated 282006 29 note: Six probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 1427738 1428397 . - . ID=gene1436;Name=Cj1493c;locus_tag=Cj1493c;Dbxref=GeneID:905783;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 1427742 1427781 . - . ID=utr546;locus_tag=Cj1492c;product=putative two-component sensor NC_002163.1 RefSeq region 1427744 1427812 . - . ID=id129;Name=id129;Dbxref=GeneID:905783;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1493c by TMHMM2.0 at aa 13-35 2C 50-72 2C 79-101 2C 130-152 2C159-181 and 196-218 NC_002163.1 RefSeq region 1427855 1427923 . - . ID=id129;Name=id129;Dbxref=GeneID:905783;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1493c by TMHMM2.0 at aa 13-35 2C 50-72 2C 79-101 2C 130-152 2C159-181 and 196-218 NC_002163.1 RefSeq region 1427942 1428010 . - . ID=id129;Name=id129;Dbxref=GeneID:905783;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1493c by TMHMM2.0 at aa 13-35 2C 50-72 2C 79-101 2C 130-152 2C159-181 and 196-218 NC_002163.1 RefSeq region 1428095 1428163 . - . ID=id129;Name=id129;Dbxref=GeneID:905783;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1493c by TMHMM2.0 at aa 13-35 2C 50-72 2C 79-101 2C 130-152 2C159-181 and 196-218 NC_002163.1 RefSeq region 1428182 1428250 . - . ID=id129;Name=id129;Dbxref=GeneID:905783;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1493c by TMHMM2.0 at aa 13-35 2C 50-72 2C 79-101 2C 130-152 2C159-181 and 196-218 NC_002163.1 RefSeq region 1428293 1428361 . - . ID=id129;Name=id129;Dbxref=GeneID:905783;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1493c by TMHMM2.0 at aa 13-35 2C 50-72 2C 79-101 2C 130-152 2C159-181 and 196-218 NC_002163.1 RefSeq gene 1428394 1429512 . - . ID=gene1437;gene=carA;Name=carA;locus_tag=Cj1494c;Dbxref=GeneID:905785;gbkey=Gene NC_002163.1 RefSeq CDS 1428394 1429512 . - 0 ID=cds1361;Parent=gene1437;gene=carA;Name=YP_002344874.1;Dbxref=GOA:Q9PMG8 HSSP:P00907 InterPro:IPR000991 InterPro:IPR001317 InterPro:IPR002474 InterPro:IPR006220 InterPro:IPR006274 InterPro:IPR011702 InterPro:IPR012998 UniProtKB FSwiss-Prot:Q9PMG8 Genbank:YP_002344874.1 GeneID:905785;gbkey=CDS;product=carbamoyl phosphate synthase small subunit;Note=catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways 3B forms an octamer composed of four CarAB dimers NC_002163.1 RefSeq region 1428400 1428945 . - . ID=id2637;gene=carA;Name=id2637;Dbxref=GeneID:905785;gbkey=misc_feature;Note=HMMPfam hit to PF00117 2C Glutamine amidotransferase class-I 2C score 1.5e-57 NC_002163.1 RefSeq region 1428691 1428726 . - . ID=id2638;gene=carA;Name=id2638;Dbxref=GeneID:905785;gbkey=misc_feature;Note=PS00442 Glutamine amidotransferases class-I active site NC_002163.1 RefSeq region 1429075 1429509 . - . ID=id2639;gene=carA;Name=id2639;Dbxref=GeneID:905785;gbkey=misc_feature;Note=HMMPfam hit to PF00988 2C Carbamoyl-phosphate synthase small ch 2C score 5.6e-55 NC_002163.1 RefSeq gene 1429512 1430063 . - . ID=gene1438;gene=Cj1495c;Name=Cj1495c;locus_tag=Cj1495c;Dbxref=GeneID:905784;gbkey=Gene NC_002163.1 RefSeq CDS 1429512 1430063 . - 0 ID=cds1362;Parent=gene1438;Name=YP_002344875.1;Dbxref=InterPro:IPR007463 UniProtKB FTrEMBL:Q0P8C2 Genbank:YP_002344875.1 GeneID:905784;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1495c 2C unknown 2C len: 183 aa 3B similar to hypothetical proteins e.g. TR:O67633 28EMBL:AE000754 29 Aquifex aeolicus AQ_1752 28183 aa 29 2C fasta scores 3B opt: 268 z-score: 310.8 E 28 29: 5.4e-10 2C 24.6 25 identity in 183 aa overlap. 45.4 25 identity to HP1236 7EUpdated 282006 29 note: Pfam domain PF04368 Protein of unknown function 28DUF507 29 identified within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq region 1429515 1430063 . - . ID=id2640;Name=id2640;Dbxref=GeneID:905784;gbkey=misc_feature;Note=HMMPfam hit to PF04368 2C Protein of unknown function 28DUF507 29 2C score 1.5e-129 ### NC_002163.1 UTR_Extractor 5'-UTR 1430064 1430087 . - . ID=utr547;locus_tag=Cj1495c;product=hypothetical protein NC_002163.1 RefSeq CDS 1430156 1430674 . - 0 ID=cds1363;Parent=gene1439;Name=YP_002344876.1;Dbxref=GOA:Q0P8C1 UniProtKB FTrEMBL:Q0P8C1 Genbank:YP_002344876.1 GeneID:906007;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1496c 2C probable periplasmic protein 2C len: 172 aa 3B similar to TR:O30719 28EMBL:AF016039 29 H. pylori PDP protein 28HP0257 29 28223 aa 29 2C fasta scores 3B opt: 232 z-score: 243.0 E 28 29: 3.3e-06 2C 33.3 25 identity in 177 aa overlap. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Paper identified linking protein to glycoprotein. Functional classification -Miscellaneous periplasmic proteins 7EPMID:12186869 NC_002163.1 RefSeq gene 1430156 1430674 . - . ID=gene1439;Name=Cj1496c;locus_tag=Cj1496c;Dbxref=GeneID:906007;gbkey=Gene NC_002163.1 RefSeq CDS 1430667 1431095 . - 0 ID=cds1364;Parent=gene1440;Name=YP_002344877.1;Dbxref=UniProtKB FTrEMBL:Q0P8C0 Genbank:YP_002344877.1 GeneID:905781;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1497c 2C unknown 2C len: 142 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 RefSeq gene 1430667 1431095 . - . ID=gene1440;Name=Cj1497c;locus_tag=Cj1497c;Dbxref=GeneID:905781;gbkey=Gene NC_002163.1 RefSeq gene 1431092 1432342 . - . ID=gene1441;gene=purA;Name=purA;locus_tag=Cj1498c;Dbxref=GeneID:905786;gbkey=Gene NC_002163.1 RefSeq CDS 1431092 1432342 . - 0 ID=cds1365;Parent=gene1441;gene=purA;Name=YP_002344878.1;Dbxref=GOA:Q9PMG4 HSSP:P12283 InterPro:IPR001114 UniProtKB FSwiss-Prot:Q9PMG4 Genbank:YP_002344878.1 GeneID:905786;gbkey=CDS;product=adenylosuccinate synthetase;Note=catalyzes the formation of N6- 281 2C2 2C-dicarboxyethyl 29-AMP from L-aspartate 2C inosine monophosphate and GTP in AMP biosynthesis NC_002163.1 UTR_Extractor 5'-UTR 1431096 1431173 . - . ID=utr548;locus_tag=Cj1497c;product=hypothetical protein NC_002163.1 RefSeq region 1431098 1432333 . - . ID=id2641;gene=purA;Name=id2641;Dbxref=GeneID:905786;gbkey=misc_feature;Note=HMMPfam hit to PF00709 2C Adenylosuccinate synthetase 2C score 1.6e-193 NC_002163.1 RefSeq region 1431923 1431958 . - . ID=id2642;gene=purA;Name=id2642;Dbxref=GeneID:905786;gbkey=misc_feature;Note=PS00513 Adenylosuccinate synthetase active site NC_002163.1 RefSeq region 1432289 1432312 . - . ID=id2643;gene=purA;Name=id2643;Dbxref=GeneID:905786;gbkey=misc_feature;Note=PS01266 Adenylosuccinate synthetase GTP-binding site ### NC_002163.1 RefSeq gene 1432370 1432467 . - . ID=gene1442;gene=tRNASeC;Name=tRNASeC;locus_tag=Cjp26;Dbxref=GeneID:905782;gbkey=Gene NC_002163.1 RefSeq tRNA 1432370 1432467 . - . ID=rna42;Parent=gene1442;gene=tRNASeC;Name=rna42;Dbxref=GeneID:905782;gbkey=tRNA;product=tRNA-Sec;Note=tRNA SeC anticodon TCA 2C Cove score 35.94 NC_002163.1 RefSeq exon 1432370 1432467 . - . ID=id2644;Parent=rna42;gene=tRNASeC;Name=id2644;Dbxref=GeneID:905782;gbkey=tRNA;product=tRNA-Sec;Note=tRNA SeC anticodon TCA 2C Cove score 35.94 NC_002163.1 UTR_Extractor 5'-UTR 1432561 1432606 . + . ID=utr549;locus_tag=Cj1500;product=putative inner membrane protein NC_002163.1 RefSeq CDS 1432607 1433815 . + 0 ID=cds1366;Parent=gene1443;Name=YP_002344879.1;Dbxref=InterPro:IPR007272 UniProtKB FTrEMBL:Q0P8B8 Genbank:YP_002344879.1 GeneID:905787;gbkey=CDS;product=inner membrane protein;Note=Original 282000 29 note: Cj1500 2C probable integral membrane protein 2C len: 402 aa 3B similar to hypothetical membrane protens e.g. YEDE_ECOLI 28401 aa 29 2C fasta scores 3B opt: 722 z-score: 819.1 E 28 29: 0 2C 44.3 25 identity in 395 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain x2 PF04143 YeeE 2FYedE family 28DUF395 29 identified within CDS. Also 2C ten probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 1432607 1433815 . + . ID=gene1443;Name=Cj1500;locus_tag=Cj1500;Dbxref=GeneID:905787;gbkey=Gene NC_002163.1 RefSeq region 1432661 1432729 . + . ID=id2645;Name=id2645;Dbxref=GeneID:905787;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1500 by TMHMM2.0 at aa 19-41 2C 80-97 2C 110-129 2C 139-161 2C194-216 2C 226-244 2C 265-287 2C 297-319 2C 331-353 and 368-390 NC_002163.1 RefSeq region 1432841 1432873 . + . ID=id2646;Name=id2646;Dbxref=GeneID:905787;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1432844 1432897 . + . ID=id2645;Name=id2645;Dbxref=GeneID:905787;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1500 by TMHMM2.0 at aa 19-41 2C 80-97 2C 110-129 2C 139-161 2C194-216 2C 226-244 2C 265-287 2C 297-319 2C 331-353 and 368-390 NC_002163.1 RefSeq region 1432916 1433110 . + . ID=id2647;Name=id2647;Dbxref=GeneID:905787;gbkey=misc_feature;Note=HMMPfam hit to PF04143 2C YeeE 2FYedE family 28DUF395 29 2Cscore 1.3e-20 NC_002163.1 RefSeq region 1432934 1432993 . + . ID=id2645;Name=id2645;Dbxref=GeneID:905787;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1500 by TMHMM2.0 at aa 19-41 2C 80-97 2C 110-129 2C 139-161 2C194-216 2C 226-244 2C 265-287 2C 297-319 2C 331-353 and 368-390 NC_002163.1 RefSeq region 1433021 1433089 . + . ID=id2645;Name=id2645;Dbxref=GeneID:905787;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1500 by TMHMM2.0 at aa 19-41 2C 80-97 2C 110-129 2C 139-161 2C194-216 2C 226-244 2C 265-287 2C 297-319 2C 331-353 and 368-390 NC_002163.1 RefSeq region 1433186 1433254 . + . ID=id2645;Name=id2645;Dbxref=GeneID:905787;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1500 by TMHMM2.0 at aa 19-41 2C 80-97 2C 110-129 2C 139-161 2C194-216 2C 226-244 2C 265-287 2C 297-319 2C 331-353 and 368-390 NC_002163.1 RefSeq region 1433282 1433338 . + . ID=id2645;Name=id2645;Dbxref=GeneID:905787;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1500 by TMHMM2.0 at aa 19-41 2C 80-97 2C 110-129 2C 139-161 2C194-216 2C 226-244 2C 265-287 2C 297-319 2C 331-353 and 368-390 NC_002163.1 RefSeq region 1433399 1433467 . + . ID=id2645;Name=id2645;Dbxref=GeneID:905787;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1500 by TMHMM2.0 at aa 19-41 2C 80-97 2C 110-129 2C 139-161 2C194-216 2C 226-244 2C 265-287 2C 297-319 2C 331-353 and 368-390 NC_002163.1 RefSeq region 1433474 1433665 . + . ID=id2648;Name=id2648;Dbxref=GeneID:905787;gbkey=misc_feature;Note=HMMPfam hit to PF04143 2C YeeE 2FYedE family 28DUF395 29 2Cscore 6.5e-17 NC_002163.1 RefSeq region 1433495 1433563 . + . ID=id2645;Name=id2645;Dbxref=GeneID:905787;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1500 by TMHMM2.0 at aa 19-41 2C 80-97 2C 110-129 2C 139-161 2C194-216 2C 226-244 2C 265-287 2C 297-319 2C 331-353 and 368-390 NC_002163.1 RefSeq region 1433522 1433554 . + . ID=id2649;Name=id2649;Dbxref=GeneID:905787;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1433597 1433665 . + . ID=id2645;Name=id2645;Dbxref=GeneID:905787;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1500 by TMHMM2.0 at aa 19-41 2C 80-97 2C 110-129 2C 139-161 2C194-216 2C 226-244 2C 265-287 2C 297-319 2C 331-353 and 368-390 NC_002163.1 RefSeq region 1433708 1433776 . + . ID=id2645;Name=id2645;Dbxref=GeneID:905787;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1500 by TMHMM2.0 at aa 19-41 2C 80-97 2C 110-129 2C 139-161 2C194-216 2C 226-244 2C 265-287 2C 297-319 2C 331-353 and 368-390 ### NC_002163.1 RefSeq CDS 1433819 1434046 . + 0 ID=cds1367;Parent=gene1444;Name=YP_002344880.1;Dbxref=GOA:Q0P8B7 InterPro:IPR001455 UniProtKB FTrEMBL:Q0P8B7 Genbank:YP_002344880.1 GeneID:905791;gbkey=CDS;product=hypothetical protein;Note=Updated 282006 29 note: Conserved added to product function due to present motif within CDS 7EOriginal 282000 29 note: Cj1501 2C unknown 2C len: 85 aa 3B similar to hypothetical proteins e.g. YEDF_ECOLI 2877 aa 29 2Cfasta scores 3B opt: 341 z-score: 453.8 E 28 29: 5.9e-18 2C 65.7 25 identity in 70 aa overlap. No Hp match. Contains PS01148 Uncharacterized protein family UPF0033 signature 2C and Pfam match to entry PF01206 UPF0033 2C Uncharacterized protein family UPF0033 NC_002163.1 RefSeq gene 1433819 1434046 . + . ID=gene1444;Name=Cj1501;locus_tag=Cj1501;Dbxref=GeneID:905791;gbkey=Gene NC_002163.1 RefSeq region 1433825 1434040 . + . ID=id2650;Name=id2650;Dbxref=GeneID:905791;gbkey=misc_feature;Note=HMMPfam hit to PF01206 2C SirA-like protein 2C score 1.6e-27 NC_002163.1 RefSeq region 1433837 1433875 . + . ID=id2651;Name=id2651;Dbxref=GeneID:905791;gbkey=misc_feature;Note=PS01148 Uncharacterized protein family UPF0033 signature ### NC_002163.1 RefSeq CDS 1434062 1435549 . - 0 ID=cds1368;Parent=gene1445;gene=putP;Name=YP_002344881.1;Dbxref=GOA:Q0P8B6 InterPro:IPR001734 InterPro:IPR011851 UniProtKB FTrEMBL:Q0P8B6 Genbank:YP_002344881.1 GeneID:905789;gbkey=CDS;product=sodium 2Fproline symporter;Note=Original 282000 29 note: Cj1502c 2C putP 2C probable sodium 2Fproline symporter 2C len: 495 aa 3B similar to many e.g. PUTP_ECOLI sodium 2Fproline symporter 28proline permease 29 28502 aa 29 2C fatsa scores 3B opt: 1695 z-score: 1986.4 E 28 29: 0 2C 51.7 25 identity in 487 aa overlap. 74.9 25 identity to HP0055. Contains Pfam match to entry PF00474 SSF 2C Sodium:solute symporter family 7EUpdated 282006 29 note: Twelve probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli with acceptable identity scores. kept within product function. Functional classification -Transport 2Fbinding proteins - Amino acids and amines 7EPMID:1567896 2C PMID:3302614 NC_002163.1 RefSeq gene 1434062 1435549 . - . ID=gene1445;gene=putP;Name=putP;locus_tag=Cj1502c;Dbxref=GeneID:905789;gbkey=Gene NC_002163.1 RefSeq region 1434110 1434178 . - . ID=id130;gene=putP;Name=id130;Dbxref=GeneID:905789;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1502c by TMHMM2.0 at aa 13-35 2C 80-102 2C 133-155 2C 165-187 2C200-222 2C 237-259 2C 280-302 2C 330-352 2C 373-395 2C 405-427 2C434-453 and 458-480 NC_002163.1 RefSeq region 1434191 1434250 . - . ID=id130;gene=putP;Name=id130;Dbxref=GeneID:905789;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1502c by TMHMM2.0 at aa 13-35 2C 80-102 2C 133-155 2C 165-187 2C200-222 2C 237-259 2C 280-302 2C 330-352 2C 373-395 2C 405-427 2C434-453 and 458-480 NC_002163.1 RefSeq region 1434224 1435420 . - . ID=id2652;gene=putP;Name=id2652;Dbxref=GeneID:905789;gbkey=misc_feature;Note=HMMPfam hit to PF00474 2C Sodium:solute symporter family 2C score 2e-120 NC_002163.1 RefSeq region 1434269 1434337 . - . ID=id130;gene=putP;Name=id130;Dbxref=GeneID:905789;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1502c by TMHMM2.0 at aa 13-35 2C 80-102 2C 133-155 2C 165-187 2C200-222 2C 237-259 2C 280-302 2C 330-352 2C 373-395 2C 405-427 2C434-453 and 458-480 NC_002163.1 RefSeq region 1434365 1434433 . - . ID=id130;gene=putP;Name=id130;Dbxref=GeneID:905789;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1502c by TMHMM2.0 at aa 13-35 2C 80-102 2C 133-155 2C 165-187 2C200-222 2C 237-259 2C 280-302 2C 330-352 2C 373-395 2C 405-427 2C434-453 and 458-480 NC_002163.1 RefSeq region 1434494 1434562 . - . ID=id130;gene=putP;Name=id130;Dbxref=GeneID:905789;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1502c by TMHMM2.0 at aa 13-35 2C 80-102 2C 133-155 2C 165-187 2C200-222 2C 237-259 2C 280-302 2C 330-352 2C 373-395 2C 405-427 2C434-453 and 458-480 NC_002163.1 RefSeq region 1434644 1434712 . - . ID=id130;gene=putP;Name=id130;Dbxref=GeneID:905789;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1502c by TMHMM2.0 at aa 13-35 2C 80-102 2C 133-155 2C 165-187 2C200-222 2C 237-259 2C 280-302 2C 330-352 2C 373-395 2C 405-427 2C434-453 and 458-480 NC_002163.1 RefSeq region 1434665 1434697 . - . ID=id2653;gene=putP;Name=id2653;Dbxref=GeneID:905789;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1434773 1434841 . - . ID=id130;gene=putP;Name=id130;Dbxref=GeneID:905789;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1502c by TMHMM2.0 at aa 13-35 2C 80-102 2C 133-155 2C 165-187 2C200-222 2C 237-259 2C 280-302 2C 330-352 2C 373-395 2C 405-427 2C434-453 and 458-480 NC_002163.1 RefSeq region 1434884 1434952 . - . ID=id130;gene=putP;Name=id130;Dbxref=GeneID:905789;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1502c by TMHMM2.0 at aa 13-35 2C 80-102 2C 133-155 2C 165-187 2C200-222 2C 237-259 2C 280-302 2C 330-352 2C 373-395 2C 405-427 2C434-453 and 458-480 NC_002163.1 RefSeq region 1434989 1435057 . - . ID=id130;gene=putP;Name=id130;Dbxref=GeneID:905789;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1502c by TMHMM2.0 at aa 13-35 2C 80-102 2C 133-155 2C 165-187 2C200-222 2C 237-259 2C 280-302 2C 330-352 2C 373-395 2C 405-427 2C434-453 and 458-480 NC_002163.1 RefSeq region 1435085 1435153 . - . ID=id130;gene=putP;Name=id130;Dbxref=GeneID:905789;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1502c by TMHMM2.0 at aa 13-35 2C 80-102 2C 133-155 2C 165-187 2C200-222 2C 237-259 2C 280-302 2C 330-352 2C 373-395 2C 405-427 2C434-453 and 458-480 NC_002163.1 RefSeq region 1435244 1435312 . - . ID=id130;gene=putP;Name=id130;Dbxref=GeneID:905789;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1502c by TMHMM2.0 at aa 13-35 2C 80-102 2C 133-155 2C 165-187 2C200-222 2C 237-259 2C 280-302 2C 330-352 2C 373-395 2C 405-427 2C434-453 and 458-480 NC_002163.1 RefSeq region 1435445 1435513 . - . ID=id130;gene=putP;Name=id130;Dbxref=GeneID:905789;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1502c by TMHMM2.0 at aa 13-35 2C 80-102 2C 133-155 2C 165-187 2C200-222 2C 237-259 2C 280-302 2C 330-352 2C 373-395 2C 405-427 2C434-453 and 458-480 NC_002163.1 RefSeq CDS 1435549 1439037 . - 0 ID=cds1369;Parent=gene1446;gene=putA;Name=YP_002344882.1;Dbxref=GOA:Q0P8B5 InterPro:IPR002872 InterPro:IPR015590 InterPro:IPR016160 InterPro:IPR016162 UniProtKB FTrEMBL:Q0P8B5 Genbank:YP_002344882.1 GeneID:905792;gbkey=CDS;product=proline dehydrogenase 2Fdelta-1-pyrroline-5-carboxylate dehydrogenase;Note=Original 282000 29 note: Cj1503c 2C putA 2C possible proline dehydrogenase 2Fdelta-1-pyrroline-5-carboxylate dehydrogenase 2C len: 1162 aa 3B similar to e.g. PUTA_ECOLI bifunctional PUTA protein 5Bincludes: proline dehydrogenase 28EC 1.5.99.8 29 3B delta-1-pyrroline-5-carboxylate dehydrogenase 28EC 1.5.1.12 29 281320 aa 29 2C fasta scores 3B opt: 611 z-score: 639.8 E 28 29: 2.6e-28 2C 26.9 25 identity in 892 aa overlap. 65.0 25 identity to HP0056. Contains Pfam match to entry PF00171 aldedh 2C Aldehyde dehydrogenase 2C PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00687 Aldehyde dehydrogenases glutamic acid active site 2C and PS00070 Aldehyde dehydrogenases cysteine active site 7EUpdated 282006 29 note: Pfam domain PF01619 Proline dehydrogenase also identified within CDS. Further support given to product function. Characterised within Escherichia coli 2C however 2C identity score was not acceptable. kept within product function. Functional classification - Degradation - Amino acids 7EPMID:15449943 2C PMID:7966312 2C PMID:12009917 NC_002163.1 RefSeq gene 1435549 1439037 . - . ID=gene1446;gene=putA;Name=putA;locus_tag=Cj1503c;Dbxref=GeneID:905792;gbkey=Gene NC_002163.1 RefSeq region 1436146 1437504 . - . ID=id2654;gene=putA;Name=id2654;Dbxref=GeneID:905792;gbkey=misc_feature;Note=HMMPfam hit to PF00171 2C Aldehyde dehydrogenase family 2C score 1.3e-29 NC_002163.1 RefSeq region 1436722 1436757 . - . ID=id2655;gene=putA;Name=id2655;Dbxref=GeneID:905792;gbkey=misc_feature;Note=PS00070 Aldehyde dehydrogenases cysteine active site NC_002163.1 RefSeq region 1436818 1436841 . - . ID=id2656;gene=putA;Name=id2656;Dbxref=GeneID:905792;gbkey=misc_feature;Note=PS00687 Aldehyde dehydrogenases glutamic acid active site NC_002163.1 RefSeq region 1437265 1437288 . - . ID=id2657;gene=putA;Name=id2657;Dbxref=GeneID:905792;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 1437769 1438788 . - . ID=id2658;gene=putA;Name=id2658;Dbxref=GeneID:905792;gbkey=misc_feature;Note=HMMPfam hit to PF01619 2C Proline dehydrogenase 2Cscore 5.2e-98 ### NC_002163.1 UTR_Extractor 5'-UTR 1439038 1439054 . - . ID=utr550;locus_tag=Cj1503c;product=putative proline dehydrogenase 2Fdelta-1-pyrroline-5-carboxylate dehydrogenase NC_002163.1 RefSeq gene 1439168 1440094 . - . ID=gene1447;gene=selD;Name=selD;locus_tag=Cj1504c;Dbxref=GeneID:905797;gbkey=Gene NC_002163.1 RefSeq CDS 1439168 1440094 . - 0 ID=cds1370;Parent=gene1447;gene=selD;Name=YP_002344883.1;Dbxref=GOA:Q9PMF9 InterPro:IPR004536 InterPro:IPR010918 UniProtKB FSwiss-Prot:Q9PMF9 Genbank:YP_002344883.1 GeneID:905797;gbkey=CDS;product=selenide 2Cwater dikinase;Note=Original 282000 29 note: Cj1504c 2C selD 2C probable selenide 2Cwater dikinase 2C len: 308 aa 3B similar to e.g. SELD_ECOLI selenide 2Cwater dikinase 28selenophosphate synthetase 29 28EC 2.7.9.3 29 28347 aa 29 2C fasta scores 3B opt: 638 z-score: 720.3 E 28 29: 8.4e-33 2C 37.2 25 identity in 298 aa overlap. No Hp match. Contains Pfam match to entry PF00586 AIRS 2C AIR synthase related proteins 7EUpdated 282006 29 note: Characterised wihtin Escherichia coli with acceptable identity score. kept within product function. Functional classification -Aminoacyl tRNA synthetases and their modification 7EPMID:2405383 2C PMID:1527085 NC_002163.1 RefSeq region 1439171 1439695 . - . ID=id2659;gene=selD;Name=id2659;Dbxref=GeneID:905797;gbkey=misc_feature;Note=HMMPfam hit to PF02769 2C AIR synthase related protein 2C C-terminal dom 2C score 2.9e-21 ### NC_002163.1 UTR_Extractor 5'-UTR 1440095 1440150 . - . ID=utr551;locus_tag=Cj1504c;product=putative selenide 2Cwater dikinase NC_002163.1 RefSeq gene 1440200 1440772 . - . ID=gene1448;Name=Cj1505c;locus_tag=Cj1505c;Dbxref=GeneID:905793;gbkey=Gene NC_002163.1 RefSeq CDS 1440200 1440772 . - 0 ID=cds1371;Parent=gene1448;Name=YP_002344884.1;Dbxref=GOA:Q0P8B3 InterPro:IPR001455 UniProtKB FTrEMBL:Q0P8B3 Genbank:YP_002344884.1 GeneID:905793;gbkey=CDS;product=two-component response regulator;Note=Original 282000 29 note: Cj1505c 2C unknown 2C len: 190 aa 3B similar in N-term to hypothetical proteins e.g. Y990_METJA 2875 aa 29 2C fasta scores 3B opt: 121 z-score: 164.1 E 28 29: 0.081 2C 33.3 25 identity in 69 aa overlap. No Hp match. Some simlarity to Cj1492c 2821.1 25 identity in 190 aa overlap 29. Contains Pfam match to entry PF01206 UPF0033 2CUncharacterized protein family UPF0033 7EUpdated 282006 29 note: Pfam domain PF01206 SirA-like protein identified within CDS. Product modified to more specific family member based on motif match. No specific characterisation with acceptable identity score carried out yet 2C so kept within product function. Functional classification - Signal transduction 7EPMID:14645287 NC_002163.1 RefSeq region 1440566 1440772 . - . ID=id2660;Name=id2660;Dbxref=GeneID:905793;gbkey=misc_feature;Note=HMMPfam hit to PF01206 2C SirA-like protein 2C score 5.6e-06 ### NC_002163.1 RefSeq CDS 1440883 1442985 . - 0 ID=cds1372;Parent=gene1449;Name=YP_002344885.1;Dbxref=GOA:Q0P8B2 InterPro:IPR003660 InterPro:IPR004089 UniProtKB FTrEMBL:Q0P8B2 Genbank:YP_002344885.1 GeneID:905796;gbkey=CDS;product=MCP-type signal transduction protein;Note=Original 282000 29 note: Cj1506c 2C probable MCP-type signal transduction protein 2C len: 700 aa 3B similar to many e.g. TR:CAB38318 28EMBL:AJ132321 29 Halobacterium salinarium arginine chemotaxis CAR protein 28452 aa 29 2C fasta scores 3B opt: 382 z-score: 382.7 E 28 29: 5.4e-14 2C 29.9 25 identity in 281 aa overlap. Contains two possible transmembrane domains and Pfam match to entry PF00015 MCPsignal 2CMethyl-accepting chemotaxis protein 28MCP 29 signaling domain. 35.3 25 identity to HP0099 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score carried out yet. kept in product function. Functional classification -Signal transduction 7EPMID:9750306 NC_002163.1 RefSeq gene 1440883 1442985 . - . ID=gene1449;Name=Cj1506c;locus_tag=Cj1506c;Dbxref=GeneID:905796;gbkey=Gene NC_002163.1 RefSeq region 1440895 1441458 . - . ID=id2661;Name=id2661;Dbxref=GeneID:905796;gbkey=misc_feature;Note=HMMPfam hit to PF00015 2C Methyl-accepting chemotaxis protein 28MCP 29 s 2C score 1.7e-18 NC_002163.1 RefSeq region 1441936 1442004 . - . ID=id131;Name=id131;Dbxref=GeneID:905796;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1506c by TMHMM2.0 at aa 7-29 and 328-350 NC_002163.1 RefSeq region 1442899 1442967 . - . ID=id131;Name=id131;Dbxref=GeneID:905796;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1506c by TMHMM2.0 at aa 7-29 and 328-350 ### NC_002163.1 UTR_Extractor 5'-UTR 1442986 1443012 . - . ID=utr552;locus_tag=Cj1506c;product=putative MCP-type signal transduction protein NC_002163.1 RefSeq CDS 1443095 1443832 . - 0 ID=cds1373;Parent=gene1450;Name=YP_002344886.1;Dbxref=InterPro:IPR011991 UniProtKB FTrEMBL:Q0P8B1 Genbank:YP_002344886.1 GeneID:905800;gbkey=CDS;product=regulatory protein;Note=Original 282000 29 note: Cj1507c 2C unknown 2C len: 245 aa 3B no Hp match 7EUpdated 282006 29 note: Pfam domain PF00126 Bacterial regulatory helix-turn-helix protein 2C lysR family identified within CDS. Product modified to more specific family based on motif match. No specific characterisation has been carried out yet 2C so kept within product function. Literature search identified paper giving further clues to product function. Functional classification - Broad regulatory functions 7EPMID:14641908 NC_002163.1 RefSeq gene 1443095 1443832 . - . ID=gene1450;Name=Cj1507c;locus_tag=Cj1507c;Dbxref=GeneID:905800;gbkey=Gene NC_002163.1 RefSeq region 1443188 1443367 . - . ID=id2662;Name=id2662;Dbxref=GeneID:905800;gbkey=misc_feature;Note=HMMPfam hit to PF00126 2C Bacterial regulatory helix-turn-helix protei 2C score 4.4e-13 NC_002163.1 RefSeq gene 1443825 1444607 . - . ID=gene1451;gene=fdhD;Name=fdhD;locus_tag=Cj1508c;Dbxref=GeneID:905799;gbkey=Gene NC_002163.1 RefSeq CDS 1443825 1444607 . - 0 ID=cds1374;Parent=gene1451;gene=fdhD;Name=YP_002344887.1;Dbxref=GOA:Q0P8B0 InterPro:IPR003786 UniProtKB FTrEMBL:Q0P8B0 Genbank:YP_002344887.1 GeneID:905799;gbkey=CDS;product=formate dehydrogenase accessory protein;Note=involved in the production or activity of formate dehydrogenase-H which is active when nitrate is not present during anaerobic growth NC_002163.1 RefSeq region 1443840 1444565 . - . ID=id2663;gene=fdhD;Name=id2663;Dbxref=GeneID:905799;gbkey=misc_feature;Note=HMMPfam hit to PF02634 2C FdhD 2FNarQ family 2C score 9.6e-48 ### NC_002163.1 UTR_Extractor 5'-UTR 1444608 1444630 . - . ID=utr553;locus_tag=Cj1508c;product=formate dehydrogenase accessory protein NC_002163.1 RefSeq CDS 1444774 1445706 . - 0 ID=cds1375;Parent=gene1452;gene=fdhC;Name=YP_002344888.1;Dbxref=GOA:Q0P8A9 InterPro:IPR006471 UniProtKB FTrEMBL:Q0P8A9 Genbank:YP_002344888.1 GeneID:905794;gbkey=CDS;product=formate dehydrogenase cytochrome B subunit;Note=Original 282000 29 note: Cj1509c 2C fdhC 2C probable formate dehydrogenase 2C cytochrome B subunit 2C len: 310 aa 3B similar to e.g. TR:P28180 28EMBL:X54057 29 Wolinella succinogenes formate dehydrogenase C precursor 28306 aa 29 2Cfasta scores 3B opt: 634 z-score: 759.3 E 28 29: 0 2C 42.8 25 identity in 318 aa overlap 2C and FDNI_ECOLI formate dehydrogenase 2C nitrate-inducible 2C cytochrome B556 28fdn 29 subunit 28217 aa 29 2C fasta scores 3B opt: 189 z-score: 234.3 E 28 29: 9.9e-06 2C 25.5 25 identity in 212 aa overlap. No Hp ortholog 7EUpdated 282006 29 note: Six probable transmembrane helices predicted by TMHMM2.0. Some characterisation in Wolinella succinogenes with acceptable identity score. kept in product function. Functional classification - Energy metabolism - Respiration -Anaerobic 7EPMID:9006048 2C PMID:1781728 NC_002163.1 RefSeq gene 1444774 1445706 . - . ID=gene1452;gene=fdhC;Name=fdhC;locus_tag=Cj1509c;Dbxref=GeneID:905794;gbkey=Gene NC_002163.1 RefSeq region 1444921 1444989 . - . ID=id132;gene=fdhC;Name=id132;Dbxref=GeneID:905794;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1509c by TMHMM2.0 at aa 5-24 2C 56-78 2C 99-121 2C 136-156 2C194-216 and 240-262 NC_002163.1 RefSeq region 1445059 1445127 . - . ID=id132;gene=fdhC;Name=id132;Dbxref=GeneID:905794;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1509c by TMHMM2.0 at aa 5-24 2C 56-78 2C 99-121 2C 136-156 2C194-216 and 240-262 NC_002163.1 RefSeq region 1445239 1445301 . - . ID=id132;gene=fdhC;Name=id132;Dbxref=GeneID:905794;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1509c by TMHMM2.0 at aa 5-24 2C 56-78 2C 99-121 2C 136-156 2C194-216 and 240-262 NC_002163.1 RefSeq region 1445344 1445412 . - . ID=id132;gene=fdhC;Name=id132;Dbxref=GeneID:905794;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1509c by TMHMM2.0 at aa 5-24 2C 56-78 2C 99-121 2C 136-156 2C194-216 and 240-262 NC_002163.1 RefSeq region 1445473 1445541 . - . ID=id132;gene=fdhC;Name=id132;Dbxref=GeneID:905794;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1509c by TMHMM2.0 at aa 5-24 2C 56-78 2C 99-121 2C 136-156 2C194-216 and 240-262 NC_002163.1 RefSeq region 1445635 1445694 . - . ID=id132;gene=fdhC;Name=id132;Dbxref=GeneID:905794;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1509c by TMHMM2.0 at aa 5-24 2C 56-78 2C 99-121 2C 136-156 2C194-216 and 240-262 NC_002163.1 RefSeq gene 1445703 1446344 . - . ID=gene1453;gene=fdhB;Name=fdhB;locus_tag=Cj1510c;Dbxref=GeneID:905790;gbkey=Gene NC_002163.1 RefSeq CDS 1445703 1446344 . - 0 ID=cds1376;Parent=gene1453;gene=fdhB;Name=YP_002344889.1;Dbxref=GOA:Q0P8A8 InterPro:IPR001450 UniProtKB FTrEMBL:Q0P8A8 Genbank:YP_002344889.1 GeneID:905790;gbkey=CDS;product=formate dehydrogenase iron-sulfur subunit;Note=Original 282000 29 note: Cj1510c 2C fdhB 2C probable formate dehydrogenase iron-sulfur subunit 2C len: 213 aa 3B similar to e.g. FDHB_WOLSU formate dehydrogenase iron-sulfur subunit 28EC 1.2.1.2 29 28200 aa 29 2C fasta scores 3B opt: 1025 z-score: 1153.1 E 28 29: 0 2C 69.5 25 identity in 197 aa overlap. No Hp ortholog. Contains PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature 2C and Pfam match to entry PF00037 fer4 2C 4Fe-4S ferredoxins and related iron-sulfur cluster binding domains 7EUpdated 282006 29 note: Some characterisation in Wolinella succinogenes with acceptable identity score. kept within product function. Functional classification - Energy metabolism - Respiration -Anaerobic 7EPMID:1781728 2C PMID:9006048 NC_002163.1 RefSeq region 1446003 1446074 . - . ID=id2664;gene=fdhB;Name=id2664;Dbxref=GeneID:905790;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 5e-07 NC_002163.1 RefSeq region 1446018 1446053 . - . ID=id2665;gene=fdhB;Name=id2665;Dbxref=GeneID:905790;gbkey=misc_feature;Note=PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature NC_002163.1 RefSeq gene 1446341 1449145 . - . ID=gene1454;gene=fdhA;Name=fdhA;locus_tag=Cj1511c;Dbxref=GeneID:905795;gbkey=Gene NC_002163.1 RefSeq CDS 1446341 1449145 . - 0 ID=cds1377;Parent=gene1454;gene=fdhA;Name=YP_002344890.1;Dbxref=GOA:Q0P8A7 InterPro:IPR006311 InterPro:IPR009010 UniProtKB FTrEMBL:Q0P8A7 Genbank:YP_002344890.1 GeneID:905795;gbkey=CDS;product=formate dehydrogenase large subunit;Note=Original 282000 29 note: Cj1511c 2C fdhA 2C probable formate dehydrogenase large subunit 2C len: 934 aa 3B similar to e.g. TR:P28179 28EMBL:X54057 29 Wolinella succinogenes formate dehydrogenase large subunit precursor 28EC 1.2.1.2 29 28939 aa 29 2C fasta scores 3B opt: 3368 z-score: 3913.9 E 28 29: 7.3e-211 2C 52.8 25 identity in 930 aa overlap 2C and FDHF_ECOLI formate dehydrogenase H 28EC 1.2.1.2 29 28formate-hydrogen-lyase-linked 2C selenocysteine-containing polypeptide 29 28715 aa 29 2C fasta scores 3B opt: 813 z-score: 943.1 E 28 29: 2.2e-45 2C 30.9 25 identity in 696 aa overlap. No Hp match. Contains Pfam match to entry PF00384 molybdopterin 2C Prokaryotic molybdopterin oxidoreductases 2Cand PS00551 Prokaryotic molybdopterin oxidoreductases signature 1. Note that TGA codes for Selenocysteine at codon 181 complement 281448602..1448604 29 7EUpdated 282006 29 note: Different characterisation in Escherichia coli and Wolinella succinogenes with acceptable identity scores to both. kept within product function. Functional classification - Energy metabolism - Respiration - Anaerobic 7EPMID:2941757 2C PMID:9036855 2C PMID:9006048 NC_002163.1 UTR_Extractor 5'-UTR 1446345 1446398 . - . ID=utr554;locus_tag=Cj1510c;product=putative formate dehydrogenase iron-sulfur subunit NC_002163.1 RefSeq region 1446422 1446757 . - . ID=id2666;gene=fdhA;Name=id2666;Dbxref=GeneID:905795;gbkey=misc_feature;Note=HMMPfam hit to PF01568 2C Molydopterin dinucleotide binding dom 2C score 1.3e-17 NC_002163.1 RefSeq region 1447484 1448827 . - . ID=id2667;gene=fdhA;Name=id2667;Dbxref=GeneID:905795;gbkey=misc_feature;Note=HMMPfam hit to PF00384 2C Molybdopterin oxidoreductase 2C score 1e-61 NC_002163.1 RefSeq region 1448603 1448605 . - . ID=id2668;gene=fdhA;Name=id2668;Dbxref=GeneID:905795;gbkey=misc_feature;Note=TGA codes for Selenocysteine in Cj1511c NC_002163.1 RefSeq region 1448834 1448998 . - . ID=id2669;gene=fdhA;Name=id2669;Dbxref=GeneID:905795;gbkey=misc_feature;Note=HMMPfam hit to PF04879 2C Molybdopterin oxidoreductase Fe4S4 do 2C score 1.9e-19 NC_002163.1 RefSeq region 1448930 1448983 . - . ID=id2670;gene=fdhA;Name=id2670;Dbxref=GeneID:905795;gbkey=misc_feature;Note=PS00551 Prokaryotic molybdopterin oxidoreductases signature 1 NC_002163.1 RefSeq gene 1449145 1449336 . - . ID=gene1455;gene=Cj1513c;Name=Cj1513c;locus_tag=Cj1513c;Dbxref=GeneID:905788;gbkey=Gene NC_002163.1 RefSeq CDS 1449145 1449336 . - 0 ID=cds1378;Parent=gene1455;Name=YP_002344891.1;Dbxref=InterPro:IPR006311 UniProtKB FTrEMBL:Q0P8A6 Genbank:YP_002344891.1 GeneID:905788;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1513c 2C possible periplasmic protein 2C len: 63 aa 3B no Hp match. Contains possible N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 1449311 1450024 . - . ID=gene1456;Name=Cj1514c;locus_tag=Cj1514c;Dbxref=GeneID:905802;gbkey=Gene NC_002163.1 RefSeq CDS 1449311 1450024 . - 0 ID=cds1379;Parent=gene1456;Name=YP_002344892.1;Dbxref=UniProtKB FTrEMBL:Q0P8A5 Genbank:YP_002344892.1 GeneID:905802;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1514c 2C unknown 2C len: 237 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown ### NC_002163.1 UTR_Extractor 5'-UTR 1450025 1450118 . - . ID=utr555;locus_tag=Cj1514c;product=hypothetical protein NC_002163.1 RefSeq gene 1450328 1451476 . - . ID=gene1457;Name=Cj1515c;locus_tag=Cj1515c;Dbxref=GeneID:905798;gbkey=Gene NC_002163.1 RefSeq CDS 1450328 1451476 . - 0 ID=cds1380;Parent=gene1457;Name=YP_002344893.1;Dbxref=GOA:Q0P8A4 InterPro:IPR000183 InterPro:IPR005730 UniProtKB FTrEMBL:Q0P8A4 Genbank:YP_002344893.1 GeneID:905798;gbkey=CDS;product=decarboxylase;Note=Original 282000 29 note: Cj1515c 2C probable decarboxylase 2C len: 382 aa 3B similar to TR:Q56575 28EMBL:D31783 29 Vibrio alginolyticus carboxynorspermidine decarboxylase 28377 aa 29 2C fasta scores 3B opt: 667 z-score: 807.5 E 28 29: 0 2C 36.6 25 identity in 380 aa overlap. 45.8 25 identity to HP0020 7EUpdated 282006 29 note: Pfam domain PF00278 Pyridoxal-dependent decarboxylase 2C C-terminal identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score carried out yet 2C so kept within product function. Functional classification - Misc NC_002163.1 RefSeq region 1450391 1450747 . - . ID=id2671;Name=id2671;Dbxref=GeneID:905798;gbkey=misc_feature;Note=HMMPfam hit to PF00278 2C Pyridoxal-dependent decarboxylase 2C C- 2C score 0.0031 ### NC_002163.1 UTR_Extractor 5'-UTR 1451477 1451496 . - . ID=utr556;locus_tag=Cj1515c;product=putative decarboxylase NC_002163.1 RefSeq CDS 1451600 1453141 . + 0 ID=cds1381;Parent=gene1458;Name=YP_002344894.1;Dbxref=GOA:Q0P8A3 InterPro:IPR001117 InterPro:IPR002355 InterPro:IPR006311 InterPro:IPR008972 InterPro:IPR011706 InterPro:IPR011707 UniProtKB FTrEMBL:Q0P8A3 Genbank:YP_002344894.1 GeneID:905803;gbkey=CDS;product=oxidoreductase;Note=Original 282000 29 note: Cj1516 2C probable periplasmic oxidoreductase 2C len: 1539 aa 3B similar to members of the multicoper oxidase family e.g. YACK_ECOLI probable blue-copper protein yack precursor 28516 aa 29 2C fasta scores 3B opt: 376 z-score: 429.0 E 28 29: 1.4e-16 2C 28.7 25 identity in 460 aa overlap 2C and BLRO_MYRVE bilirubin oxidase precursor 28572 aa 29 2C fasta scores 3B opt: 309 z-score: 352.2 E 28 29: 2.7e-12 2C 24.8 25 identity in 499 aa overlap. No Hp match. Contains possible N-terminal signal sequence 2C Pfam match to entry PF00394 Cu-oxidase 2C Multicopper oxidase 2C and PS00080 Multicopper oxidases signature 2 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score carried out yet 2C so kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 1451600 1453141 . + . ID=gene1458;Name=Cj1516;locus_tag=Cj1516;Dbxref=GeneID:905803;gbkey=Gene NC_002163.1 RefSeq region 1451861 1452217 . + . ID=id2672;Name=id2672;Dbxref=GeneID:905803;gbkey=misc_feature;Note=HMMPfam hit to PF07732 2C Multicopper oxidase 2C score 3.7e-48 NC_002163.1 RefSeq region 1452233 1452652 . + . ID=id2673;Name=id2673;Dbxref=GeneID:905803;gbkey=misc_feature;Note=HMMPfam hit to PF00394 2C Multicopper oxidase 2C score 9.1e-05 NC_002163.1 RefSeq region 1452779 1453135 . + . ID=id2674;Name=id2674;Dbxref=GeneID:905803;gbkey=misc_feature;Note=HMMPfam hit to PF07731 2C Multicopper oxidase 2C score 1.5e-18 NC_002163.1 RefSeq region 1453079 1453114 . + . ID=id2675;Name=id2675;Dbxref=GeneID:905803;gbkey=misc_feature;Note=PS00080 Multicopper oxidases signature 2 ### NC_002163.1 RefSeq CDS 1453143 1453364 . + 0 ID=cds1382;Parent=gene1459;gene=moaD;Name=YP_002344895.1;Dbxref=GOA:Q0P8A2 InterPro:IPR003749 InterPro:IPR012675 UniProtKB FTrEMBL:Q0P8A2 Genbank:YP_002344895.1 GeneID:905801;gbkey=CDS;product=molybdopterin converting factor subunit 1;Note=Original 282000 29 note: Cj1517 2C moaD 2C possible molybdopterin converting factor 2C subunit 1 2C len: 73 aa 3B similar to many predicted moaD genes 2C e.g. TR:O31706 28EMBL:AF012285 29 Bacillus subtilis molybdopterin converting factor 28subunit 1 29 2877 aa 29 2C fasta scores 3B opt: 111 z-score: 167.7 E 28 29: 0.051 2C 30.5 25 identity in 59 aa overlap 2C and weakly similar to MOAD_ECOLI molybdopterin 5Bmpt 5D converting factor 2C subunit 1 2881 aa 29 2C fasta scores 3B opt: 81 z-score: 127.5 E 28 29: 8.8 2C 38.5 25 identity in 26 aa overlap. 61.6 25 identity to HP0801 7EUpdated 282006 29 note: Pfam domain PF02597 ThiS family identified within CDS. Further support given to product function. Specific characterisation with an acceptable similairty score has not been carried out yet 2Cso kept within product function. Functional classification - Biosynthesis of cofactors 2C prosthetic groups and carriers - Molybdopterin NC_002163.1 RefSeq gene 1453143 1453364 . + . ID=gene1459;gene=moaD;Name=moaD;locus_tag=Cj1517;Dbxref=GeneID:905801;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 1453151 1453364 . + . ID=utr557;locus_tag=Cj1518;product=putative molybdopterin converting factor subunit 2 NC_002163.1 RefSeq region 1453152 1453361 . + . ID=id2676;gene=moaD;Name=id2676;Dbxref=GeneID:905801;gbkey=misc_feature;Note=HMMPfam hit to PF02597 2C ThiS family 2C score 3.1e-13 ### NC_002163.1 RefSeq gene 1453365 1453811 . + . ID=gene1460;gene=moaE;Name=moaE;locus_tag=Cj1518;Dbxref=GeneID:905805;gbkey=Gene NC_002163.1 RefSeq CDS 1453365 1453811 . + 0 ID=cds1383;Parent=gene1460;gene=moaE;Name=YP_002344896.1;Dbxref=GOA:Q0P8A1 InterPro:IPR003448 UniProtKB FTrEMBL:Q0P8A1 Genbank:YP_002344896.1 GeneID:905805;gbkey=CDS;product=molybdopterin converting factor subunit 2;Note=Original 282000 29 note: Cj1518 2C moaE 2C possible molybdopterin converting factor 2C subunit 2 2C len: 148 aa 3B similar to many predicted moaE genes 2C e.g. TR:O31705 28EMBL:AF012285 29 Bacillus subtilis molybdopterin converting factor 28subunit 2 29 28157 aa 29 2C fasta scores 3B opt: 134 z-score: 182.4 E 28 29: 0.0078 2C 25.2 25 identity in 131 aa overlap 2C and to MOAE_ECOLI molybdopterin 5Bmpt 5D converting factor 2C subunit 2 28149 aa 29 2C fasta scores opt: 133 z-score: 181.4 E 28 29: 0.0087 2C 26.0 25 identity in 123 aa overlap. 50.4 25 identity to HP0800 7EUpdated 282006 29 note: Pfam domain PF02391 MoaE protein identified within CDS. Further support given to product function. Specific characterisation with acceptable similairty score has not been carried out yet 2Cso kept within product function. Functional classification - Biosynthesis of cofactors 2C prosthetic groups and carriers - Molybdopterin NC_002163.1 RefSeq region 1453371 1453718 . + . ID=id2677;gene=moaE;Name=id2677;Dbxref=GeneID:905805;gbkey=misc_feature;Note=HMMPfam hit to PF02391 2C MoaE protein 2C score 0.00028 ### NC_002163.1 RefSeq CDS 1453815 1455005 . + 0 ID=cds1384;Parent=gene1461;gene=moeA2;Name=YP_002344897.1;Dbxref=GOA:Q0P8A0 InterPro:IPR001453 InterPro:IPR005110 InterPro:IPR005111 UniProtKB FTrEMBL:Q0P8A0 Genbank:YP_002344897.1 GeneID:905804;gbkey=CDS;product=molybdopterin biosynthesis protein;Note=Original 282000 29 note: Cj1519 2C moeA2 2C probable molybdopterin biosynthesis protein 2C len: 396 aa 3B similar to e.g. MOEA_ECOLI molybdopterin biosynthesis MOEA protein 28411 aa 29 2C fasta scores 3B opt: 541 z-score: 624.0 E 28 29: 1.9e-27 2C 29.2 25 identity in 366 aa overlap. No Hp ortholog 2Cbut 37.3 25 identity to HP0172. Also similar to Cj0857c moeA 2833.3 25 identity in 378 aa overlap 29. Contains Pfam match to entry PF00994 MoCF_biosynth 2C Molybdenum cofactor biosynthesis protein 7EUpdated 282006 29 note: Pfam domains PF03453 MoeA N-terminal region 28domain I and II 29 2C PF00994 Probable molybdopterin binding domain and PF03454 MoeA C-terminal region 28domain IV 29 were all identified within CDS. Further support given to product function. Specific characterisation with acceptable similairty score has not been carried out yet 2C so kept within product function. Functional classification - Biosynthesis of cofactors 2C prosthetic groups and carriers - Molybdopterin NC_002163.1 RefSeq gene 1453815 1455005 . + . ID=gene1461;gene=moeA2;Name=moeA2;locus_tag=Cj1519;Dbxref=GeneID:905804;gbkey=Gene NC_002163.1 RefSeq region 1453818 1454297 . + . ID=id2678;gene=moeA2;Name=id2678;Dbxref=GeneID:905804;gbkey=misc_feature;Note=HMMPfam hit to PF03453 2C MoeA N-terminal region 28domain I and II 2C score 1.3e-69 NC_002163.1 RefSeq region 1454325 1454726 . + . ID=id2679;gene=moeA2;Name=id2679;Dbxref=GeneID:905804;gbkey=misc_feature;Note=HMMPfam hit to PF00994 2C Probable molybdopterin binding domain 2C score 1.6e-30 NC_002163.1 RefSeq region 1454778 1455002 . + . ID=id2680;gene=moeA2;Name=id2680;Dbxref=GeneID:905804;gbkey=misc_feature;Note=HMMPfam hit to PF03454 2C MoeA C-terminal region 28domain IV 29 2C score 4.1e-16 ### NC_002163.1 RefSeq repeat_region 1455126 1455160 . + . ID=id2682;Name=id2682;gbkey=repeat_region;Note=CRISPR repeat NC_002163.1 RefSeq repeat_region 1455126 1455424 . + . ID=id2681;Name=id2681;gbkey=repeat_region;Note=CRISPR 7EUpdated 282006 29 note: Cj1520 has now been removed due to identification of CRISPR repeat region 7EPMID:11952905 2C PMID:16612537 2C PMID:16545108 NC_002163.1 RefSeq gene 1455167 1455204 . + . ID=NC_002163.1:CRISPR_11168_1;Name=NC_002163.1:CRISPR_11168_1;locus_tag=CRISPR_11168_1 NC_002163.1 RefSeq sRNA 1455167 1455204 . + . ID=NC_002163.1:CRISPR_11168_1:unknown_transcript_1;Parent=NC_002163.1:CRISPR_11168_1;Name=NC_002163.1:CRISPR_11168_1:unknown_transcript_1;locus_tag=CRISPR_11168_1;gbkey=misc_RNA;product=CRISPR_11168_1 NC_002163.1 RefSeq repeat_region 1455192 1455226 . + . ID=id2683;Name=id2683;gbkey=repeat_region;Note=CRISPR repeat NC_002163.1 RefSeq gene 1455232 1455269 . + . ID=NC_002163.1:CRISPR_11168_2;Name=NC_002163.1:CRISPR_11168_2;locus_tag=CRISPR_11168_2 NC_002163.1 RefSeq sRNA 1455232 1455269 . + . ID=NC_002163.1:CRISPR_11168_2:unknown_transcript_1;Parent=NC_002163.1:CRISPR_11168_2;Name=NC_002163.1:CRISPR_11168_2:unknown_transcript_1;locus_tag=CRISPR_11168_2;gbkey=misc_RNA;product=CRISPR_11168_2 NC_002163.1 RefSeq region 1455235 1455288 . + . ID=id2684;Name=id2684;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1520 by TMHMM2.0 at aa 46-63 NC_002163.1 RefSeq repeat_region 1455258 1455292 . + . ID=id2685;Name=id2685;gbkey=repeat_region;Note=CRISPR repeat NC_002163.1 RefSeq gene 1455299 1455336 . + . ID=NC_002163.1:CRISPR_11168_3;Name=NC_002163.1:CRISPR_11168_3;locus_tag=CRISPR_11168_3 NC_002163.1 RefSeq sRNA 1455299 1455336 . + . ID=NC_002163.1:CRISPR_11168_3:unknown_transcript_1;Parent=NC_002163.1:CRISPR_11168_3;Name=NC_002163.1:CRISPR_11168_3:unknown_transcript_1;locus_tag=CRISPR_11168_3;gbkey=misc_RNA;product=CRISPR_11168_3 NC_002163.1 RefSeq repeat_region 1455324 1455358 . + . ID=id2686;Name=id2686;gbkey=repeat_region;Note=CRISPR repeat NC_002163.1 RefSeq sRNA 1455363 1455400 . + . ID=NC_002163.1:CRISPR_11168_4:unknown_transcript_1;Parent=NC_002163.1:CRISPR_11168_4;Name=NC_002163.1:CRISPR_11168_4:unknown_transcript_1;locus_tag=CRISPR_11168_4;gbkey=misc_RNA;product=CRISPR_11168_4 NC_002163.1 RefSeq gene 1455363 1455400 . + . ID=NC_002163.1:CRISPR_11168_4;Name=NC_002163.1:CRISPR_11168_4;locus_tag=CRISPR_11168_4 NC_002163.1 RefSeq repeat_region 1455390 1455424 . + . ID=id2687;Name=id2687;gbkey=repeat_region;Note=CRISPR repeat ### NC_002163.1 RefSeq sRNA 1455497 1455570 . + . ID=NC_002163.1:TracrRNA:unknown_transcript_1;Parent=NC_002163.1:TracrRNA;Name=NC_002163.1:TracrRNA:unknown_transcript_1;locus_tag=TracrRNA;gbkey=misc_RNA;product=TracrRNA NC_002163.1 RefSeq gene 1455497 1455570 . + . ID=NC_002163.1:TracrRNA;Name=NC_002163.1:TracrRNA;locus_tag=TracrRNA NC_002163.1 RefSeq CDS 1455569 1456000 . - 0 ID=cds1385;Parent=gene1462;Name=YP_002344898.1;Dbxref=InterPro:IPR003799 UniProtKB FTrEMBL:Q0P899 Genbank:YP_002344898.1 GeneID:905810;gbkey=CDS;product=CRISPR-associated protein;Note=Original 282000 29 note: Cj1521c 2C unknown 2C len: 143 aa 3B no Hp match 7EUpdated 282006 29 note: Cj1521c 2CCJ1522c and Cj1523c are believed to be CRISPR-associated proteins that contribute to the CRISPR repeat region formation. Functional classification - Misc 7EPMID:11952905 2C PMID:16612537 2C PMID:16545108 NC_002163.1 RefSeq gene 1455569 1456000 . - . ID=gene1462;Name=Cj1521c;locus_tag=Cj1521c;Dbxref=GeneID:905810;gbkey=Gene NC_002163.1 RefSeq gene 1455993 1456883 . - . ID=gene1463;Name=Cj1522c;locus_tag=Cj1522c;Dbxref=GeneID:905808;gbkey=Gene NC_002163.1 RefSeq CDS 1455993 1456883 . - 0 ID=cds1386;Parent=gene1463;Name=YP_002344899.1;Dbxref=GOA:Q0P898 InterPro:IPR002729 UniProtKB FTrEMBL:Q0P898 Genbank:YP_002344899.1 GeneID:905808;gbkey=CDS;product=CRISPR-associated protein;Note=Original 282000 29 note: Cj1522c 2C unknown 2C len: 296 aa 3B very weak simlarity to TR:O28401 28EMBL:AE000973 29 Archaeoglobus fulgidus AF1878 28345 aa 29 2C fasta scores 3B opt: 156 z-score: 198.5 E 28 29: 0.00099 2C 25.3 25 identity in 281 aa overlap. No Hp match 7EUpdated 282006 29 note: Cj1521c 2CCJ1522c and Cj1523c are believed to be CRISPR-associated proteins that contribute to the CRISPR repeat region formation. Functional classification - Misc 7EPMID:11952905 2C PMID:16612537 2C PMID:16545108 NC_002163.1 RefSeq gene 1456880 1459834 . - . ID=gene1464;Name=Cj1523c;locus_tag=Cj1523c;Dbxref=GeneID:905809;gbkey=Gene NC_002163.1 RefSeq CDS 1456880 1459834 . - 0 ID=cds1387;Parent=gene1464;Name=YP_002344900.1;Dbxref=InterPro:IPR010145 UniProtKB FTrEMBL:Q0P897 Genbank:YP_002344900.1 GeneID:905809;gbkey=CDS;product=CRISPR-associated protein;Note=Original 282000 29 note: Cj1523c 2C unknown 2C len: 984 aa 3B no Hp match 7EUpdated 282006 29 note: Cj1521c 2CCJ1522c and Cj1523c are believed to be CRISPR-associated proteins that contribute to the CRISPR repeat region formation. Functional classification - Misc 7EPMID:11952905 2C PMID:16612537 2C PMID:16545108 ### NC_002163.1 UTR_Extractor 5'-UTR 1459835 1459864 . - . ID=utr558;locus_tag=Cj1523c;product=putative CRISPR-associated protein NC_002163.1 UTR_Extractor 5'-UTR 1460014 1460036 . + . ID=utr559;locus_tag=Cj1528;product=pseudo NC_002163.1 RefSeq region 1460037 1460126 . + . ID=id2688;Name=id2688;Dbxref=GeneID:905811;gbkey=misc_feature;Note=Original 282000 29 note: Cj1528 2C probable transmembrane transport protein pseudogene 2C len: 1191 bp 3B similar to DCUC_ECOLI C4-dicarboxylate anaerobic carrier 28461 aa 29 2C approx. 31.6 25 identity 2C and YHCL_ECOLI 28455 aa 29 approx. 28.0 25 identity. No Hp match. Some similarity to Cj1389 28probable transmembrane transport protein pseudogene 29 2C approx. 36.7 25 identity. May extend further upstream 7EUpdated 282006 29 note: Pfam domain PF03606 C4-dicarboxylate anaerobic carrier identified within CDS. Also 2C ten probable transmembrane helices predicted for Cj1528 by TMHMM2.0. Further support given to product function. Product is a pseudogene 2C however 2C was modified to more specific family member based on motif match. Identity scores were marginal 2C so was kept within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Carbohydrates 2C organic acids and alcohols 7EPMID:10525738 NC_002163.1 RefSeq pseudogene 1460037 1461474 . + . ID=gene1465;Name=Cj1528;locus_tag=Cj1528;Dbxref=GeneID:905811;gbkey=Gene NC_002163.1 RefSeq region 1460046 1460099 . + . ID=id2690;Name=id2690;Dbxref=GeneID:905811;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1528 by TMHMM2.0 at aa 4-21 2C 26-48 2C 68-90 2C 119-153 2C200-222 2C 248-270 2C 274-291 2C 304-326 2C 352-374 and 444-461 NC_002163.1 RefSeq region 1460046 1460126 . + . ID=id2689;Name=id2689;Dbxref=GeneID:905811;gbkey=misc_feature;Note=HMMPfam hit to PF03606 2C C4-dicarboxylate anaerobic carrier 2C score 5.5e-08 NC_002163.1 RefSeq region 1460112 1460126 . + . ID=id2690;Name=id2690;Dbxref=GeneID:905811;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1528 by TMHMM2.0 at aa 4-21 2C 26-48 2C 68-90 2C 119-153 2C200-222 2C 248-270 2C 274-291 2C 304-326 2C 352-374 and 444-461 NC_002163.1 RefSeq region 1460126 1460179 . + . ID=id2690;Name=id2690;Dbxref=GeneID:905811;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1528 by TMHMM2.0 at aa 4-21 2C 26-48 2C 68-90 2C 119-153 2C200-222 2C 248-270 2C 274-291 2C 304-326 2C 352-374 and 444-461 NC_002163.1 RefSeq region 1460126 1460236 . + . ID=id2689;Name=id2689;Dbxref=GeneID:905811;gbkey=misc_feature;Note=HMMPfam hit to PF03606 2C C4-dicarboxylate anaerobic carrier 2C score 5.5e-08 NC_002163.1 RefSeq region 1460126 1460236 . + . ID=id2688;Name=id2688;Dbxref=GeneID:905811;gbkey=misc_feature;Note=Original 282000 29 note: Cj1528 2C probable transmembrane transport protein pseudogene 2C len: 1191 bp 3B similar to DCUC_ECOLI C4-dicarboxylate anaerobic carrier 28461 aa 29 2C approx. 31.6 25 identity 2C and YHCL_ECOLI 28455 aa 29 approx. 28.0 25 identity. No Hp match. Some similarity to Cj1389 28probable transmembrane transport protein pseudogene 29 2C approx. 36.7 25 identity. May extend further upstream 7EUpdated 282006 29 note: Pfam domain PF03606 C4-dicarboxylate anaerobic carrier identified within CDS. Also 2C ten probable transmembrane helices predicted for Cj1528 by TMHMM2.0. Further support given to product function. Product is a pseudogene 2C however 2C was modified to more specific family member based on motif match. Identity scores were marginal 2C so was kept within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Carbohydrates 2C organic acids and alcohols 7EPMID:10525738 NC_002163.1 RefSeq region 1460236 1460236 . + . ID=id2690;Name=id2690;Dbxref=GeneID:905811;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1528 by TMHMM2.0 at aa 4-21 2C 26-48 2C 68-90 2C 119-153 2C200-222 2C 248-270 2C 274-291 2C 304-326 2C 352-374 and 444-461 NC_002163.1 RefSeq region 1460236 1460304 . + . ID=id2690;Name=id2690;Dbxref=GeneID:905811;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1528 by TMHMM2.0 at aa 4-21 2C 26-48 2C 68-90 2C 119-153 2C200-222 2C 248-270 2C 274-291 2C 304-326 2C 352-374 and 444-461 NC_002163.1 RefSeq region 1460236 1460382 . + . ID=id2688;Name=id2688;Dbxref=GeneID:905811;gbkey=misc_feature;Note=Original 282000 29 note: Cj1528 2C probable transmembrane transport protein pseudogene 2C len: 1191 bp 3B similar to DCUC_ECOLI C4-dicarboxylate anaerobic carrier 28461 aa 29 2C approx. 31.6 25 identity 2C and YHCL_ECOLI 28455 aa 29 approx. 28.0 25 identity. No Hp match. Some similarity to Cj1389 28probable transmembrane transport protein pseudogene 29 2C approx. 36.7 25 identity. May extend further upstream 7EUpdated 282006 29 note: Pfam domain PF03606 C4-dicarboxylate anaerobic carrier identified within CDS. Also 2C ten probable transmembrane helices predicted for Cj1528 by TMHMM2.0. Further support given to product function. Product is a pseudogene 2C however 2C was modified to more specific family member based on motif match. Identity scores were marginal 2C so was kept within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Carbohydrates 2C organic acids and alcohols 7EPMID:10525738 NC_002163.1 RefSeq region 1460236 1460382 . + . ID=id2689;Name=id2689;Dbxref=GeneID:905811;gbkey=misc_feature;Note=HMMPfam hit to PF03606 2C C4-dicarboxylate anaerobic carrier 2C score 5.5e-08 NC_002163.1 RefSeq region 1460384 1460668 . + . ID=id2688;Name=id2688;Dbxref=GeneID:905811;gbkey=misc_feature;Note=Original 282000 29 note: Cj1528 2C probable transmembrane transport protein pseudogene 2C len: 1191 bp 3B similar to DCUC_ECOLI C4-dicarboxylate anaerobic carrier 28461 aa 29 2C approx. 31.6 25 identity 2C and YHCL_ECOLI 28455 aa 29 approx. 28.0 25 identity. No Hp match. Some similarity to Cj1389 28probable transmembrane transport protein pseudogene 29 2C approx. 36.7 25 identity. May extend further upstream 7EUpdated 282006 29 note: Pfam domain PF03606 C4-dicarboxylate anaerobic carrier identified within CDS. Also 2C ten probable transmembrane helices predicted for Cj1528 by TMHMM2.0. Further support given to product function. Product is a pseudogene 2C however 2C was modified to more specific family member based on motif match. Identity scores were marginal 2C so was kept within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Carbohydrates 2C organic acids and alcohols 7EPMID:10525738 NC_002163.1 RefSeq region 1460384 1460668 . + . ID=id2689;Name=id2689;Dbxref=GeneID:905811;gbkey=misc_feature;Note=HMMPfam hit to PF03606 2C C4-dicarboxylate anaerobic carrier 2C score 5.5e-08 NC_002163.1 RefSeq region 1460390 1460494 . + . ID=id2690;Name=id2690;Dbxref=GeneID:905811;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1528 by TMHMM2.0 at aa 4-21 2C 26-48 2C 68-90 2C 119-153 2C200-222 2C 248-270 2C 274-291 2C 304-326 2C 352-374 and 444-461 NC_002163.1 RefSeq region 1460633 1460668 . + . ID=id2690;Name=id2690;Dbxref=GeneID:905811;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1528 by TMHMM2.0 at aa 4-21 2C 26-48 2C 68-90 2C 119-153 2C200-222 2C 248-270 2C 274-291 2C 304-326 2C 352-374 and 444-461 NC_002163.1 RefSeq region 1460670 1460702 . + . ID=id2690;Name=id2690;Dbxref=GeneID:905811;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1528 by TMHMM2.0 at aa 4-21 2C 26-48 2C 68-90 2C 119-153 2C200-222 2C 248-270 2C 274-291 2C 304-326 2C 352-374 and 444-461 NC_002163.1 RefSeq region 1460670 1460786 . + . ID=id2689;Name=id2689;Dbxref=GeneID:905811;gbkey=misc_feature;Note=HMMPfam hit to PF03606 2C C4-dicarboxylate anaerobic carrier 2C score 5.5e-08 NC_002163.1 RefSeq region 1460670 1460786 . + . ID=id2688;Name=id2688;Dbxref=GeneID:905811;gbkey=misc_feature;Note=Original 282000 29 note: Cj1528 2C probable transmembrane transport protein pseudogene 2C len: 1191 bp 3B similar to DCUC_ECOLI C4-dicarboxylate anaerobic carrier 28461 aa 29 2C approx. 31.6 25 identity 2C and YHCL_ECOLI 28455 aa 29 approx. 28.0 25 identity. No Hp match. Some similarity to Cj1389 28probable transmembrane transport protein pseudogene 29 2C approx. 36.7 25 identity. May extend further upstream 7EUpdated 282006 29 note: Pfam domain PF03606 C4-dicarboxylate anaerobic carrier identified within CDS. Also 2C ten probable transmembrane helices predicted for Cj1528 by TMHMM2.0. Further support given to product function. Product is a pseudogene 2C however 2C was modified to more specific family member based on motif match. Identity scores were marginal 2C so was kept within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Carbohydrates 2C organic acids and alcohols 7EPMID:10525738 NC_002163.1 RefSeq region 1460778 1460786 . + . ID=id2690;Name=id2690;Dbxref=GeneID:905811;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1528 by TMHMM2.0 at aa 4-21 2C 26-48 2C 68-90 2C 119-153 2C200-222 2C 248-270 2C 274-291 2C 304-326 2C 352-374 and 444-461 NC_002163.1 RefSeq region 1460788 1460847 . + . ID=id2690;Name=id2690;Dbxref=GeneID:905811;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1528 by TMHMM2.0 at aa 4-21 2C 26-48 2C 68-90 2C 119-153 2C200-222 2C 248-270 2C 274-291 2C 304-326 2C 352-374 and 444-461 NC_002163.1 RefSeq region 1460788 1461423 . + . ID=id2689;Name=id2689;Dbxref=GeneID:905811;gbkey=misc_feature;Note=HMMPfam hit to PF03606 2C C4-dicarboxylate anaerobic carrier 2C score 5.5e-08 NC_002163.1 RefSeq region 1460788 1461474 . + . ID=id2688;Name=id2688;Dbxref=GeneID:905811;gbkey=misc_feature;Note=Original 282000 29 note: Cj1528 2C probable transmembrane transport protein pseudogene 2C len: 1191 bp 3B similar to DCUC_ECOLI C4-dicarboxylate anaerobic carrier 28461 aa 29 2C approx. 31.6 25 identity 2C and YHCL_ECOLI 28455 aa 29 approx. 28.0 25 identity. No Hp match. Some similarity to Cj1389 28probable transmembrane transport protein pseudogene 29 2C approx. 36.7 25 identity. May extend further upstream 7EUpdated 282006 29 note: Pfam domain PF03606 C4-dicarboxylate anaerobic carrier identified within CDS. Also 2C ten probable transmembrane helices predicted for Cj1528 by TMHMM2.0. Further support given to product function. Product is a pseudogene 2C however 2C was modified to more specific family member based on motif match. Identity scores were marginal 2C so was kept within product function. Coding sequence has been updated to reflect the complete amino acid sequence for the encoded protein regardless of its expression. This will cause differences from the amino acid sequence of the previous annotation. Functional classification - Transport 2Fbinding proteins - Carbohydrates 2C organic acids and alcohols 7EPMID:10525738 NC_002163.1 RefSeq region 1460857 1460910 . + . ID=id2690;Name=id2690;Dbxref=GeneID:905811;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1528 by TMHMM2.0 at aa 4-21 2C 26-48 2C 68-90 2C 119-153 2C200-222 2C 248-270 2C 274-291 2C 304-326 2C 352-374 and 444-461 NC_002163.1 RefSeq region 1460947 1461015 . + . ID=id2690;Name=id2690;Dbxref=GeneID:905811;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1528 by TMHMM2.0 at aa 4-21 2C 26-48 2C 68-90 2C 119-153 2C200-222 2C 248-270 2C 274-291 2C 304-326 2C 352-374 and 444-461 NC_002163.1 RefSeq region 1461091 1461159 . + . ID=id2690;Name=id2690;Dbxref=GeneID:905811;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1528 by TMHMM2.0 at aa 4-21 2C 26-48 2C 68-90 2C 119-153 2C200-222 2C 248-270 2C 274-291 2C 304-326 2C 352-374 and 444-461 NC_002163.1 RefSeq region 1461367 1461420 . + . ID=id2690;Name=id2690;Dbxref=GeneID:905811;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1528 by TMHMM2.0 at aa 4-21 2C 26-48 2C 68-90 2C 119-153 2C200-222 2C 248-270 2C 274-291 2C 304-326 2C 352-374 and 444-461 ### NC_002163.1 RefSeq CDS 1461504 1462493 . - 0 ID=cds1388;Parent=gene1466;gene=purM;Name=YP_002344901.1;Dbxref=GOA:Q0P896 InterPro:IPR000728 InterPro:IPR004733 InterPro:IPR010918 UniProtKB FTrEMBL:Q0P896 Genbank:YP_002344901.1 GeneID:905806;gbkey=CDS;product=phosphoribosylaminoimidazole synthetase;Note=catalyzes the formation of 1- 285-phosphoribosyl 29-5-aminoimidazole from 2- 28formamido 29-N1- 285-phosphoribosyl 29acetamidine and ATP in purine biosynthesis NC_002163.1 RefSeq gene 1461504 1462493 . - . ID=gene1466;gene=purM;Name=purM;locus_tag=Cj1529c;Dbxref=GeneID:905806;gbkey=Gene NC_002163.1 RefSeq region 1461507 1461980 . - . ID=id2691;gene=purM;Name=id2691;Dbxref=GeneID:905806;gbkey=misc_feature;Note=HMMPfam hit to PF02769 2C AIR synthase related protein 2C C-terminal dom 2C score 7.4e-38 NC_002163.1 RefSeq region 1461519 1461554 . - . ID=id2692;gene=purM;Name=id2692;Dbxref=GeneID:905806;gbkey=misc_feature;Note=PS00070 Aldehyde dehydrogenases cysteine active site NC_002163.1 RefSeq region 1462011 1462493 . - . ID=id2693;gene=purM;Name=id2693;Dbxref=GeneID:905806;gbkey=misc_feature;Note=HMMPfam hit to PF00586 2C AIR synthase related protein 2C N-terminal dom 2C score 3.6e-58 ### NC_002163.1 UTR_Extractor 5'-UTR 1462494 1462517 . - . ID=utr560;locus_tag=Cj1529c;product=phosphoribosylaminoimidazole synthetase NC_002163.1 RefSeq CDS 1462554 1463159 . + 0 ID=cds1389;Parent=gene1467;gene=coaE;Name=YP_002344902.1;Dbxref=GOA:Q9PMD9 InterPro:IPR001977 UniProtKB FSwiss-Prot:Q9PMD9 Genbank:YP_002344902.1 GeneID:905813;gbkey=CDS;product=dephospho-CoA kinase;Note=catalyzes the phosphorylation of the 3 27-hydroxyl group of dephosphocoenzyme A to form coenzyme A 3B involved in coenzyme A biosynthesis NC_002163.1 RefSeq gene 1462554 1463159 . + . ID=gene1467;gene=coaE;Name=coaE;locus_tag=Cj1530;Dbxref=GeneID:905813;gbkey=Gene NC_002163.1 RefSeq region 1462560 1462592 . + . ID=id2694;gene=coaE;Name=id2694;Dbxref=GeneID:905813;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1462578 1462601 . + . ID=id2695;gene=coaE;Name=id2695;Dbxref=GeneID:905813;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 1462584 1463105 . + . ID=id2696;gene=coaE;Name=id2696;Dbxref=GeneID:905813;gbkey=misc_feature;Note=HMMPfam hit to PF01121 2C Dephospho-CoA kinase 2C score 1.6e-29 NC_002163.1 UTR_Extractor 5'-UTR 1463134 1463155 . + . ID=utr561;locus_tag=Cj1531;product=diaminopimelate epimerase NC_002163.1 RefSeq CDS 1463156 1463905 . + 0 ID=cds1390;Parent=gene1468;gene=dapF;Name=YP_002344903.1;Dbxref=GOA:Q9PMD8 InterPro:IPR001653 UniProtKB FSwiss-Prot:Q9PMD8 Genbank:YP_002344903.1 GeneID:905812;gbkey=CDS;product=diaminopimelate epimerase;Note=involved in lysine biosynthesis 3B DAP epimerase 3B produces DL-diaminopimelate from LL-diaminopimelate NC_002163.1 RefSeq gene 1463156 1463905 . + . ID=gene1468;gene=dapF;Name=dapF;locus_tag=Cj1531;Dbxref=GeneID:905812;gbkey=Gene NC_002163.1 RefSeq region 1463162 1463509 . + . ID=id2697;gene=dapF;Name=id2697;Dbxref=GeneID:905812;gbkey=misc_feature;Note=HMMPfam hit to PF01678 2C Diaminopimelate epimerase 2Cscore 1.7e-20 NC_002163.1 RefSeq region 1463333 1463377 . + . ID=id2698;gene=dapF;Name=id2698;Dbxref=GeneID:905812;gbkey=misc_feature;Note=PS01326 Diaminopimelate epimerase signature NC_002163.1 RefSeq region 1463543 1463878 . + . ID=id2699;gene=dapF;Name=id2699;Dbxref=GeneID:905812;gbkey=misc_feature;Note=HMMPfam hit to PF01678 2C Diaminopimelate epimerase 2Cscore 1e-07 NC_002163.1 UTR_Extractor 5'-UTR 1463616 1463879 . + . ID=utr562;locus_tag=Cj1532;product=putative periplasmic protein NC_002163.1 RefSeq region 1463720 1463752 . + . ID=id2700;gene=dapF;Name=id2700;Dbxref=GeneID:905812;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq CDS 1463880 1464611 . + 0 ID=cds1391;Parent=gene1469;Name=YP_002344904.1;Dbxref=GOA:Q0P893 UniProtKB FTrEMBL:Q0P893 Genbank:YP_002344904.1 GeneID:905246;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1532 2C possible periplasmic protein 2C len: 243 aa 3B some similarity to N-terminus of BAX_ECOLI BAX protein 28274 aa 29 2C fasta scores 3B opt: 240 z-score: 286.1 E 28 29: 1.3e-08 2C 38.3 25 identity in 120 aa overlap. No Hp match. Contains possible N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF01832 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase 28Glucosaminidase 29 identified within CDS. No specific characterisation carried out yet 2C so kept within product function. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 1463880 1464611 . + . ID=gene1469;gene=Cj1532;Name=Cj1532;locus_tag=Cj1532;Dbxref=GeneID:905246;gbkey=Gene NC_002163.1 RefSeq region 1464168 1464578 . + . ID=id2701;Name=id2701;Dbxref=GeneID:905246;gbkey=misc_feature;Note=HMMPfam hit to PF01832 2C Mannosyl-glycoprotein endo-beta-N-ace 2C score 0.0034 NC_002163.1 RefSeq gene 1464608 1465645 . - . ID=gene1470;Name=Cj1533c;locus_tag=Cj1533c;Dbxref=GeneID:905815;gbkey=Gene NC_002163.1 RefSeq CDS 1464608 1465645 . - 0 ID=cds1392;Parent=gene1470;Name=YP_002344905.1;Dbxref=UniProtKB FTrEMBL:Q0P892 Genbank:YP_002344905.1 GeneID:905815;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1533c 2C unknown 2C len: 345 aa 3B 27.9 25 identity to HP1321. Contains possible helix-turn-helix motif at aa 191-212 28Score 1065 2C 2B2.81 SD 29. Functional classification - Broad regulatory functions ### NC_002163.1 UTR_Extractor 5'-UTR 1465646 1465665 . - . ID=utr563;locus_tag=Cj1533c;product=putative helix-turn-helix containing protein NC_002163.1 RefSeq gene 1465710 1466159 . - . ID=gene1471;Name=Cj1534c;locus_tag=Cj1534c;Dbxref=GeneID:905816;gbkey=Gene NC_002163.1 RefSeq CDS 1465710 1466159 . - 0 ID=cds1393;Parent=gene1471;Name=YP_002344906.1;Dbxref=GOA:Q0P891 HSSP:P43313 InterPro:IPR002177 InterPro:IPR008331 InterPro:IPR012347 UniProtKB FSwiss-Prot:Q0P891 Genbank:YP_002344906.1 GeneID:905816;gbkey=CDS;product=bacterioferritin;Note=Original 282000 29 note: Cj1534c 2C possible bacterioferritin 2C len: 149 aa 3B similar to many members of the DPS family e.g. NAPA_HELPY neutrophil-activating protein A 28 3DHP0243 29 28bacterioferritin 29 28144 aa 29 2C fasta scores 3B opt: 397 z-score: 495.1 E 28 29: 3e-20 2C 41.3 25 identity in 143 aa overlap 2C TPF1_TREPA antigen TPF1 28176 aa 29 2C fasta scores 3B opt: 296 z-score: 372.0 E 28 29: 2.1e-13 2C 33.3 25 identity in 144 aa overlap 2C MRGA_BACSU metalloregulation DNA-binding stress protein 28153 aa 29 2C fasta scores 3B opt: 234 z-score: 298.1 E 28 29: 2.8e-09 2C 33.1 25 identity in 127 aa overlap 2C and FRI_LISIN non-heme iron-containing ferritin 28156 aa 29 2C fasta scores 3B opt: 226 z-score: 288.3 E 28 29: 9.8e-09 2C 31.8 25 identity in 148 aa overlap 7EUpdated 282006 29 note: Pfam domain PF00210 Ferritin-like domain identified within CDS. Further support given to product function. kept within product function. Paper identified linking protein to glycoprotein 28PMID:12186869 29. Functional classification -Transport 2Fbinding proteins - Cations 7EPMID:7883175 2C PMID:8709848 2C PMID:12186869 NC_002163.1 RefSeq region 1465713 1466159 . - . ID=id2702;Name=id2702;Dbxref=GeneID:905816;gbkey=misc_feature;Note=HMMPfam hit to PF00210 2C Ferritin-like domain 2C score 2.5e-39 ### NC_002163.1 RefSeq CDS 1466289 1467509 . - 0 ID=cds1394;Parent=gene1472;gene=pgi;Name=YP_002344907.1;Dbxref=GOA:Q9PMD4 InterPro:IPR001672 UniProtKB FSwiss-Prot:Q9PMD4 Genbank:YP_002344907.1 GeneID:905817;gbkey=CDS;product=glucose-6-phosphate isomerase;Note=catalyzes the formation of D-fructose 6-phosphate from D-glucose 6-phosphate NC_002163.1 RefSeq gene 1466289 1467509 . - . ID=gene1472;gene=pgi;Name=pgi;locus_tag=Cj1535c;Dbxref=GeneID:905817;gbkey=Gene NC_002163.1 RefSeq region 1466292 1467503 . - . ID=id2703;gene=pgi;Name=id2703;Dbxref=GeneID:905817;gbkey=misc_feature;Note=HMMPfam hit to PF00342 2C Phosphoglucose isomerase 2Cscore 1.9e-14 NC_002163.1 RefSeq region 1466319 1466372 . - . ID=id2704;gene=pgi;Name=id2704;Dbxref=GeneID:905817;gbkey=misc_feature;Note=PS00174 Phosphoglucose isomerase signature 2 NC_002163.1 RefSeq region 1467297 1467329 . - . ID=id2705;gene=pgi;Name=id2705;Dbxref=GeneID:905817;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq gene 1467503 1468327 . - . ID=gene1473;gene=galU;Name=galU;locus_tag=Cj1536c;Dbxref=GeneID:905818;gbkey=Gene NC_002163.1 RefSeq CDS 1467503 1468327 . - 0 ID=cds1395;Parent=gene1473;gene=galU;Name=YP_002344908.1;Dbxref=GOA:Q0P889 InterPro:IPR005771 InterPro:IPR005835 UniProtKB FTrEMBL:Q0P889 Genbank:YP_002344908.1 GeneID:905818;gbkey=CDS;product=UTP-glucose-1-phosphate uridylyltransferase;Note=Original 282000 29 note: Cj1536c 2C galU 2C probable UTP--glucose-1-phosphate uridylyltransferase 2C len: 274 aa 3B highly similar to many e.g. GALU_PSEAE UTP--glucose-1-phosphate uridylyltransferase 28EC 2.7.7.9 29 28279 aa 29 2C fasta scores 3B opt: 1245 z-score: 1547.3 E 28 29: 0 2C65.9 25 identity in 270 aa overlap. 61.3 25 identity to HP0646. Contains Pfam match to entry PF00483 NTP_transferase 2C Nucleotidyl transferase 7EUpdated 282006 29 note: Characterised in Pseudomonas aeruginosa with acceptable identity score. Thus 2C was not added to product function. Functional classification - Degradation - Carbon compounds 7EPMID:8169209 NC_002163.1 RefSeq region 1467512 1468303 . - . ID=id2706;gene=galU;Name=id2706;Dbxref=GeneID:905818;gbkey=misc_feature;Note=HMMPfam hit to PF00483 2C Nucleotidyl transferase 2Cscore 3.3e-12 ### NC_002163.1 RefSeq CDS 1468409 1470382 . - 0 ID=cds1396;Parent=gene1474;gene=acs;Name=YP_002344909.1;Dbxref=GOA:Q9PMD2 HSSP:Q8ZKF6 InterPro:IPR000873 InterPro:IPR011904 UniProtKB FSwiss-Prot:Q9PMD2 Genbank:YP_002344909.1 GeneID:905819;gbkey=CDS;product=acetyl-CoA synthetase;Note=Acs 3B catalyzes the conversion of acetate and CoA to acetyl-CoA NC_002163.1 RefSeq gene 1468409 1470382 . - . ID=gene1474;gene=acs;Name=acs;locus_tag=Cj1537c;Dbxref=GeneID:905819;gbkey=Gene NC_002163.1 RefSeq region 1468730 1470055 . - . ID=id2707;gene=acs;Name=id2707;Dbxref=GeneID:905819;gbkey=misc_feature;Note=HMMPfam hit to PF00501 2C AMP-binding enzyme 2C score 7.8e-133 NC_002163.1 RefSeq region 1469567 1469602 . - . ID=id2708;gene=acs;Name=id2708;Dbxref=GeneID:905819;gbkey=misc_feature;Note=PS00455 AMP-binding domain signature ### NC_002163.1 UTR_Extractor 5'-UTR 1470383 1470407 . - . ID=utr564;locus_tag=Cj1537c;product=acetyl-CoA synthetase NC_002163.1 RefSeq CDS 1470520 1471515 . - 0 ID=cds1397;Parent=gene1475;Name=YP_002344910.1;Dbxref=GOA:Q0P887 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FTrEMBL:Q0P887 Genbank:YP_002344910.1 GeneID:905820;gbkey=CDS;product=anion-uptake ABC-transporter ATP-binding protein;Note=Original 282000 29 note: Cj1538c 2C possible anion-uptake ABC-transport system ATP-binding protein 2Clen: 331 aa 3B similar to many e.g. LACK_AGRRD lactose transport ATP-binding protein LACK 28363 aa 29 2C fasta scores 3B opt: 319 z-score: 386.4 E 28 29: 3.3e-14 2C 28.8 25 identity in 208 aa overlap 2C and UGPC_ECOLI SN-glycerol-3-phosphate transport ATP-binding protein 28356 aa 29 2C fasta scores 3B opt: 298 z-score: 361.6 E 28 29: 8.1e-13 2C 32.1 25 identity in 196 aa overlap. No Hp ortholog. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00211 ABC transporters family signature 2C and Pfam match to entry PF00005 ABC_tran 2C ABC transporters. identification as anion-uptake is due to similarities of associated permease Cj1539c 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score carried out yet. kept in product function. Functional classification -Transport 2Fbinding proteins - Anions NC_002163.1 RefSeq gene 1470520 1471515 . - . ID=gene1475;Name=Cj1538c;locus_tag=Cj1538c;Dbxref=GeneID:905820;gbkey=Gene NC_002163.1 RefSeq region 1470523 1470534 . - . ID=id2709;Name=id2709;Dbxref=GeneID:905820;gbkey=misc_feature;Note=PS00294 Prenyl group binding site 28CAAX box 29 NC_002163.1 RefSeq region 1470898 1471437 . - . ID=id2710;Name=id2710;Dbxref=GeneID:905820;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 5.1e-23 NC_002163.1 RefSeq region 1471084 1471128 . - . ID=id2711;Name=id2711;Dbxref=GeneID:905820;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq region 1471393 1471416 . - . ID=id2712;Name=id2712;Dbxref=GeneID:905820;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 RefSeq CDS 1471517 1472236 . - 0 ID=cds1398;Parent=gene1476;Name=YP_002344911.1;Dbxref=GOA:Q0P886 InterPro:IPR000515 UniProtKB FTrEMBL:Q0P886 Genbank:YP_002344911.1 GeneID:905821;gbkey=CDS;product=anion-uptake ABC-transporter permease;Note=Original 282000 29 note: Cj1539c 2C possible anion-uptake ABC-transport system permease 2C len: 239 aa 3B similar to many involved in anion uptake e.g. CYST_ECOLI sulfate transport system permease 28277 aa 29 2C fasta scores 3B opt: 235 z-score: 293.7 E 28 29: 4.9e-09 2C23.6 25 identity in 220 aa overlap 2C and MODB_ECOLI molybdenum transport system permease proteim 28229 aa 29 2Cfasta scores 3B opt: 201 z-score: 253.9 E 28 29: 8.1e-07 2C 25.2 25 identity in 214 aa overlap. No Hp otholog 7EUpdated 282006 29 note: Pfam domain PF00528 Binding-protein-dependent transport system inner membrane component identified within CDS. Also 2C five probable transmembrane helices predicted by TMHMM2.0. No specific characterisation with acceptable identity score 2C so kept within product function. Functional classification - Transport 2Fbinding proteins - Anions NC_002163.1 RefSeq gene 1471517 1472236 . - . ID=gene1476;Name=Cj1539c;locus_tag=Cj1539c;Dbxref=GeneID:905821;gbkey=Gene NC_002163.1 RefSeq region 1471520 1472128 . - . ID=id2713;Name=id2713;Dbxref=GeneID:905821;gbkey=misc_feature;Note=HMMPfam hit to PF00528 2C Binding-protein-dependent transport syst 2C score 7.8e-07 NC_002163.1 RefSeq region 1471535 1471603 . - . ID=id133;Name=id133;Dbxref=GeneID:905821;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1539c by TMHMM2.0 at aa 43-65 2C 72-94 2C 109-131 2C 165-187 and 212-234 NC_002163.1 RefSeq region 1471676 1471744 . - . ID=id133;Name=id133;Dbxref=GeneID:905821;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1539c by TMHMM2.0 at aa 43-65 2C 72-94 2C 109-131 2C 165-187 and 212-234 NC_002163.1 RefSeq region 1471844 1471912 . - . ID=id133;Name=id133;Dbxref=GeneID:905821;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1539c by TMHMM2.0 at aa 43-65 2C 72-94 2C 109-131 2C 165-187 and 212-234 NC_002163.1 RefSeq region 1471955 1472023 . - . ID=id133;Name=id133;Dbxref=GeneID:905821;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1539c by TMHMM2.0 at aa 43-65 2C 72-94 2C 109-131 2C 165-187 and 212-234 NC_002163.1 RefSeq region 1472042 1472110 . - . ID=id133;Name=id133;Dbxref=GeneID:905821;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1539c by TMHMM2.0 at aa 43-65 2C 72-94 2C 109-131 2C 165-187 and 212-234 ### NC_002163.1 UTR_Extractor 5'-UTR 1472255 1472281 . + . ID=utr565;locus_tag=Cj1540;product=putative periplasmic protein NC_002163.1 RefSeq gene 1472282 1473091 . + . ID=gene1477;Name=Cj1540;locus_tag=Cj1540;Dbxref=GeneID:905822;gbkey=Gene NC_002163.1 RefSeq CDS 1472282 1473091 . + 0 ID=cds1399;Parent=gene1477;Name=YP_002344912.1;Dbxref=UniProtKB FTrEMBL:Q0P885 Genbank:YP_002344912.1 GeneID:905822;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1540 2C probable periplasmic protein 2C len: 269 aa 3B similar to TR:O26579 28EMBL:AE000832 29 Methanobacterium thermoautotrophicum MTH479 28293 aa 29 2Cfasta scores 3B opt: 416 z-score: 475.8 E 28 29: 3.5e-19 2C 37.0 25 identity in 273 aa overlap. No Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 UTR_Extractor 5'-UTR 1473207 1473232 . + . ID=utr566;locus_tag=Cj1541;product=LamB 2FYcsF family protein NC_002163.1 RefSeq CDS 1473233 1474000 . + 0 ID=cds1400;Parent=gene1478;Name=YP_002344913.1;Dbxref=InterPro:IPR005501 UniProtKB FSwiss-Prot:Q9PMC8 Genbank:YP_002344913.1 GeneID:905823;gbkey=CDS;product=LamB 2FYcsF family protein;Note=Original 282000 29 note: Cj1541 2C unknown 2C len: 255 aa 3B similar to hypothetical proteins e.g. YCSF_BACSU 28211 aa 29 2Cfasta scores 3B opt: 736 z-score: 875.7 E 28 29: 0 2C 59.9 25 identity in 177 aa overlap 2C and to LAMB_EMENI Aspergillus nidulans lactam utilization protein LAMB 28262 aa 29 2C fasta scores 3B opt: 405 z-score: 485.4 E 28 29: 1e-19 2C 44.9 25 identity in 127 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF03746 LamB 2FYcsF family identified within CDS. No specific characterisation has been carried out yet 2C so kept within product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 1473233 1474000 . + . ID=gene1478;Name=Cj1541;locus_tag=Cj1541;Dbxref=GeneID:905823;gbkey=Gene NC_002163.1 RefSeq region 1473239 1473964 . + . ID=id2714;Name=id2714;Dbxref=GeneID:905823;gbkey=misc_feature;Note=HMMPfam hit to PF03746 2C LamB 2FYcsF family 2C score 8.3e-172 NC_002163.1 UTR_Extractor 5'-UTR 1473899 1474009 . + . ID=utr567;locus_tag=Cj1542;product=putative allophanate hydrolase subunit 1 ### NC_002163.1 RefSeq CDS 1474010 1474750 . + 0 ID=cds1401;Parent=gene1479;Name=YP_002344914.1;Dbxref=GOA:Q0P883 InterPro:IPR003833 InterPro:IPR010016 UniProtKB FTrEMBL:Q0P883 Genbank:YP_002344914.1 GeneID:905826;gbkey=CDS;product=allophanate hydrolase subunit 1;Note=Original 282000 29 note: Cj1542 2C unknown 2C len: 246 aa 3B similar to hypothetical proteins e.g. YCSJ_BACSU 28578 aa 29 2Cfasta scores 3B opt: 569 z-score: 690.1 E 28 29: 4.1e-31 2C 41.8 25 identity in 237 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02682 Allophanate hydrolase subunit 1 identified within CDS. Product modified to more specific family member based on motif match. No specific characterisation has been carried out yet 2C so kept within product function. Also 2Csimilarity to Bacillus subtilis kinase a inhibitor 28sporulation inhibitor kipi 29 28PMID:9334321 29. Functional classification - Degradation - Carbon compounds 7EPMID:9334321 NC_002163.1 RefSeq gene 1474010 1474750 . + . ID=gene1479;Name=Cj1542;locus_tag=Cj1542;Dbxref=GeneID:905826;gbkey=Gene NC_002163.1 RefSeq region 1474013 1474633 . + . ID=id2715;Name=id2715;Dbxref=GeneID:905826;gbkey=misc_feature;Note=HMMPfam hit to PF02682 2C Allophanate hydrolase subunit 2C score 3e-62 NC_002163.1 RefSeq gene 1474731 1475696 . + . ID=gene1480;Name=Cj1543;locus_tag=Cj1543;Dbxref=GeneID:905824;gbkey=Gene NC_002163.1 RefSeq CDS 1474731 1475696 . + 0 ID=cds1402;Parent=gene1480;Name=YP_002344915.1;Dbxref=GOA:Q0P882 InterPro:IPR003778 UniProtKB FTrEMBL:Q0P882 Genbank:YP_002344915.1 GeneID:905824;gbkey=CDS;product=allophanate hydrolase subunit 2;Note=Original 282000 29 note: Cj1543 2C unknown 2C len: 321 aa 3B similar to hypothetical proteins e.g. YBGK_ECOLI 28310 aa 29 2Cfasta scores 3B opt: 553 z-score: 652.4 E 28 29: 5.1e-29 2C 32.7 25 identity in 312 aa overlap. Also similar to part of DUR1_YEAST urea amidolyase 5Bincludes: urea carboxylase 3B allophanate hydrolase 5D 281835 aa 29 2C fasta scores 3B opt: 307 z-score: 353.8 E 28 29: 2.2e-12 2C 28.5 25 identity in 333 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF02626 Allophanate hydrolase subunit 2 identified within CDS. Product modified to more specific family member based on motif match. No specific characterisation has been carried out yet 2C so kept within product function. Functional classification - Degradation - Carbon compounds NC_002163.1 RefSeq region 1474800 1475645 . + . ID=id2716;Name=id2716;Dbxref=GeneID:905824;gbkey=misc_feature;Note=HMMPfam hit to PF02626 2C Allophanate hydrolase subunit 2C score 9.7e-72 NC_002163.1 RefSeq CDS 1475693 1476589 . - 0 ID=cds1403;Parent=gene1481;Name=YP_002344916.1;Dbxref=GOA:Q0P881 InterPro:IPR000620 UniProtKB FTrEMBL:Q0P881 Genbank:YP_002344916.1 GeneID:905162;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj1544c 2C probable integral membrane protein 2C len: 298 aa 3B simlar to hypothetical membrane proteins e.g. YYAM_BACSU 28305 aa 29 2C fasta scores 3B opt: 244 z-score: 300.4 E 28 29: 2.1e-09 2C 22.3 25 identity in 300 aa overlap. No Hp match. Contains Pfam match to entry PF00892 DUF6 2C Integral membrane protein 7EUpdated 282006 29 note: Ten probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 1475693 1476589 . - . ID=gene1481;Name=Cj1544c;locus_tag=Cj1544c;Dbxref=GeneID:905162;gbkey=Gene NC_002163.1 RefSeq region 1475705 1475773 . - . ID=id134;Name=id134;Dbxref=GeneID:905162;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1544c by TMHMM2.0 at aa 7-24 2C 34-56 2C 69-88 2C 98-120 2C133-150 2C 155-177 2C 186-205 2C 220-242 2C 247-269 and 273-295 NC_002163.1 RefSeq region 1475711 1476088 . - . ID=id2717;Name=id2717;Dbxref=GeneID:905162;gbkey=misc_feature;Note=HMMPfam hit to PF00892 2C Integral membrane protein DUF6 2C score 4.2e-19 NC_002163.1 RefSeq region 1475783 1475851 . - . ID=id134;Name=id134;Dbxref=GeneID:905162;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1544c by TMHMM2.0 at aa 7-24 2C 34-56 2C 69-88 2C 98-120 2C133-150 2C 155-177 2C 186-205 2C 220-242 2C 247-269 and 273-295 NC_002163.1 RefSeq region 1475864 1475932 . - . ID=id134;Name=id134;Dbxref=GeneID:905162;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1544c by TMHMM2.0 at aa 7-24 2C 34-56 2C 69-88 2C 98-120 2C133-150 2C 155-177 2C 186-205 2C 220-242 2C 247-269 and 273-295 NC_002163.1 RefSeq region 1475975 1476034 . - . ID=id134;Name=id134;Dbxref=GeneID:905162;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1544c by TMHMM2.0 at aa 7-24 2C 34-56 2C 69-88 2C 98-120 2C133-150 2C 155-177 2C 186-205 2C 220-242 2C 247-269 and 273-295 NC_002163.1 RefSeq region 1476059 1476127 . - . ID=id134;Name=id134;Dbxref=GeneID:905162;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1544c by TMHMM2.0 at aa 7-24 2C 34-56 2C 69-88 2C 98-120 2C133-150 2C 155-177 2C 186-205 2C 220-242 2C 247-269 and 273-295 NC_002163.1 RefSeq region 1476140 1476193 . - . ID=id134;Name=id134;Dbxref=GeneID:905162;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1544c by TMHMM2.0 at aa 7-24 2C 34-56 2C 69-88 2C 98-120 2C133-150 2C 155-177 2C 186-205 2C 220-242 2C 247-269 and 273-295 NC_002163.1 RefSeq region 1476230 1476298 . - . ID=id134;Name=id134;Dbxref=GeneID:905162;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1544c by TMHMM2.0 at aa 7-24 2C 34-56 2C 69-88 2C 98-120 2C133-150 2C 155-177 2C 186-205 2C 220-242 2C 247-269 and 273-295 NC_002163.1 RefSeq region 1476326 1476385 . - . ID=id134;Name=id134;Dbxref=GeneID:905162;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1544c by TMHMM2.0 at aa 7-24 2C 34-56 2C 69-88 2C 98-120 2C133-150 2C 155-177 2C 186-205 2C 220-242 2C 247-269 and 273-295 NC_002163.1 RefSeq region 1476422 1476490 . - . ID=id134;Name=id134;Dbxref=GeneID:905162;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1544c by TMHMM2.0 at aa 7-24 2C 34-56 2C 69-88 2C 98-120 2C133-150 2C 155-177 2C 186-205 2C 220-242 2C 247-269 and 273-295 NC_002163.1 RefSeq region 1476518 1476571 . - . ID=id134;Name=id134;Dbxref=GeneID:905162;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1544c by TMHMM2.0 at aa 7-24 2C 34-56 2C 69-88 2C 98-120 2C133-150 2C 155-177 2C 186-205 2C 220-242 2C 247-269 and 273-295 ### NC_002163.1 RefSeq gene 1476622 1477200 . - . ID=gene1482;Name=Cj1545c;locus_tag=Cj1545c;Dbxref=GeneID:904498;gbkey=Gene NC_002163.1 RefSeq CDS 1476622 1477200 . - 0 ID=cds1404;Parent=gene1482;Name=YP_002344917.1;Dbxref=GOA:Q0P880 InterPro:IPR003680 UniProtKB FTrEMBL:Q0P880 Genbank:YP_002344917.1 GeneID:904498;gbkey=CDS;product=MdaB protein;Note=Original 282000 29 note: Cj1545c 2C unknown 2C len: 192 aa 3B similar to e.g. MDAB_ECOLI modulator of drug activity B 28193 aa 29 2C fasta scores 3B opt: 777 z-score: 934.0 E 28 29: 0 2C57.8 25 identity in 192 aa overlap. Also weak simlarity to many boxidoreductases e.g. YCAK_ECOLI NAD 28P 29H oxidoreductase YCAK 28196 aa 29 2C fasta scores 3B opt: 124 z-score: 159.3 E 28 29: 0.15 2C 24.7 25 identity in 174 aa overlap. 65.1 25 identity to HP0630 7EUpdated 282006 29 note: Pfam domain PF02525 Flavodoxin-like fold identified within CDS. Further support given to product function. Homolog designation kept within product function. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq region 1476625 1477197 . - . ID=id2718;Name=id2718;Dbxref=GeneID:904498;gbkey=misc_feature;Note=HMMPfam hit to PF02525 2C Flavodoxin-like fold 2C score 2.6e-66 ### NC_002163.1 UTR_Extractor 5'-UTR 1477201 1477223 . - . ID=utr568;locus_tag=Cj1545c;product=MdaB protein NC_002163.1 UTR_Extractor 5'-UTR 1477238 1477299 . + . ID=utr569;locus_tag=Cj1546;product=putative transcriptional regulator NC_002163.1 RefSeq CDS 1477300 1477647 . + 0 ID=cds1405;Parent=gene1483;Name=YP_002344918.1;Dbxref=InterPro:IPR002577 UniProtKB FTrEMBL:Q0P879 Genbank:YP_002344918.1 GeneID:905827;gbkey=CDS;product=transcriptional regulator;Note=Original 282000 29 note: Cj1546 2C unknown 2C len: 115 aa 3B similar to hypothetical proteins e.g. YYBR_BACSU 28125 aa 29 2Cfasta scores 3B opt: 278 z-score: 389.5 E 28 29: 2.3e-14 2C 42.5 25 identity in 106 aa overlap. No Hp match. Also similar to Cj1556 2843.6 25 identity in 101 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01638 Transcriptional regulator identified within CDS. Product modified to more specific family member based on motif match. kept within product function. Functional classification - Broad regulatory functions NC_002163.1 RefSeq gene 1477300 1477647 . + . ID=gene1483;Name=Cj1546;locus_tag=Cj1546;Dbxref=GeneID:905827;gbkey=Gene NC_002163.1 RefSeq region 1477360 1477635 . + . ID=id2719;Name=id2719;Dbxref=GeneID:905827;gbkey=misc_feature;Note=HMMPfam hit to PF01638 2C Transcriptional regulator 2Cscore 5.1e-29 NC_002163.1 RefSeq gene 1477635 1478084 . + . ID=gene1484;Name=Cj1547;locus_tag=Cj1547;Dbxref=GeneID:904541;gbkey=Gene NC_002163.1 RefSeq CDS 1477635 1478084 . + 0 ID=cds1406;Parent=gene1484;Name=YP_002344919.1;Dbxref=GOA:Q0P878 InterPro:IPR002345 InterPro:IPR002446 InterPro:IPR012674 InterPro:IPR013208 UniProtKB FTrEMBL:Q0P878 Genbank:YP_002344919.1 GeneID:904541;gbkey=CDS;product=lipocalin family protein;Note=Original 282000 29 note: Cj1547 2C unknown 2C len: 149 aa 3B similar to e.g. BLC_ECOLI outer membrane lipoprotein BLC precursor 28177 aa 29 2C fasta scores 3B opt: 230 z-score: 307.6 E 28 29: 8.2e-10 2C 27.6 25 identity in 145 aa overlap 2C and APD_MOUSE apolipoprotein D precursor 28189 aa 29 2C fasta scores 3B opt: 151 z-score: 206.3 E 28 29: 0.00036 2C 30.3 25 identity in 145 aa overlap. No Hp match. Contains PS00213 Lipocalin signature 2C but no N-terminal signal sequence. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq region 1477653 1477694 . + . ID=id2720;Name=id2720;Dbxref=GeneID:904541;gbkey=misc_feature;Note=PS00213 Lipocalin signature ### NC_002163.1 RefSeq CDS 1478086 1479162 . - 0 ID=cds1407;Parent=gene1485;Name=YP_002344920.1;Dbxref=GOA:Q0P877 InterPro:IPR002085 InterPro:IPR002328 InterPro:IPR013149 InterPro:IPR013154 UniProtKB FTrEMBL:Q0P877 Genbank:YP_002344920.1 GeneID:904495;gbkey=CDS;product=NADP-dependent alcohol dehydrogenase;Note=Original 282000 29 note: Cj1548c 2C probable NADP-dependent alcohol dehydrogenase 2C len: 358 aa 3B similar to e.g. ADH_MYCTU NADP-dependent alcohol dehydrogenase 28EC 1.1.1.2 29 28346 aa 29 2C fasta scores 3B opt: 997 z-score: 1095.7 E 28 29: 0 2C 43.9 25 identity in 344 aa overlap. Also similar to plant lignin production alcohol dehydrogenases e.g. CAD3_ARATH cinnamyl-alcohol dehydrogenase ELI3-2 28359 aa 29 2Cfasta scores 3B opt: 949 z-score: 1043.1 E 28 29: 0 2C 40.9 25 identity in 352 aa overlap. 65.8 25 identity to HP1104. Contains PS00059 Zinc-containing alcohol dehydrogenases signature 2C and Pfam match to entry PF00107 adh_zinc 2CZinc-binding dehydrogenases 7EUpdated 282006 29 note: kept within product function as acceptable identity score to more than one characterised bacteria. Functional classification - Misc 7EPMID:1427101 NC_002163.1 RefSeq gene 1478086 1479162 . - . ID=gene1485;Name=Cj1548c;locus_tag=Cj1548c;Dbxref=GeneID:904495;gbkey=Gene NC_002163.1 RefSeq region 1478098 1479105 . - . ID=id2721;Name=id2721;Dbxref=GeneID:904495;gbkey=misc_feature;Note=HMMPfam hit to PF00107 2C Zinc-binding dehydrogenase 2Cscore 9e-94 NC_002163.1 RefSeq region 1478908 1478952 . - . ID=id2722;Name=id2722;Dbxref=GeneID:904495;gbkey=misc_feature;Note=PS00059 Zinc-containing alcohol dehydrogenases signature ### NC_002163.1 RefSeq CDS 1479390 1482485 . - 0 ID=cds1408;Parent=gene1486;gene=hsdR;Name=YP_002344921.1;Dbxref=GOA:Q7B7T7 InterPro:IPR001650 InterPro:IPR004473 InterPro:IPR006935 InterPro:IPR007409 InterPro:IPR014001 InterPro:IPR014021 UniProtKB FTrEMBL:Q7B7T7 Genbank:YP_002344921.1 GeneID:905828;gbkey=CDS;product=type I restriction enzyme R protein;Note=Original 282000 29 note: Cj1549c 2C probable type I restriction enzyme R protein 2C len: 1031 aa 3B similar to many e.g. T1R1_ECOLI type I restriction enzyme EcoR124II R protein 28EC 3.1.21.3 29 281033 aa 29 2C fasta scores 3B opt: 353 z-score: 372.8 E 28 29: 1.9e-13 2C 23.5 25 identity in 1047 aa overlap. 26.4 25 identity to HP1402 7EUpdated 282006 29 note: Pfam domains PF04851 Type III restriction enzyme 2C res subunit and PF04313 Type I restriction enzyme R protein N terminal were both identified within CDS. Literature search identified work carried out in Campylobacter jejuni. This CDS is the start of a type I locus 28genes Cj1549-Cj1553 29. Some characterisation work within Escherichia coli 2C however 2C kept within product function as identity score was unnacceptable. Functional classification - DNA replication 2C restriction 2Fmodification 2C recombination and repair 7EPMID:15699185 2C PMID:9016588 NC_002163.1 RefSeq gene 1479390 1482485 . - . ID=gene1486;gene=hsdR;Name=hsdR;locus_tag=Cj1549c;Dbxref=GeneID:905828;gbkey=Gene NC_002163.1 RefSeq region 1481118 1481681 . - . ID=id2723;gene=hsdR;Name=id2723;Dbxref=GeneID:905828;gbkey=misc_feature;Note=HMMPfam hit to PF04851 2C Type III restriction enzyme 2C res subunit 2C score 7.8e-10 NC_002163.1 RefSeq region 1481880 1482473 . - . ID=id2724;gene=hsdR;Name=id2724;Dbxref=GeneID:905828;gbkey=misc_feature;Note=HMMPfam hit to PF04313 2C Type I restriction enzyme R protein N termin 2C score 6.1e-73 ### NC_002163.1 UTR_Extractor 5'-UTR 1482486 1482755 . - . ID=utr570;locus_tag=Cj1549c;product=putative type I restriction enzyme R protein NC_002163.1 RefSeq gene 1482488 1484254 . - . ID=gene1487;gene=rloH;Name=rloH;locus_tag=Cj1550c;Dbxref=GeneID:905829;gbkey=Gene NC_002163.1 RefSeq CDS 1482488 1484254 . - 0 ID=cds1409;Parent=gene1487;gene=rloH;Name=YP_002344922.1;Dbxref=GOA:Q0P875 InterPro:IPR003439 UniProtKB FTrEMBL:Q0P875 Genbank:YP_002344922.1 GeneID:905829;gbkey=CDS;product=ATP 2FGTP-binding protein;Note=Original 282000 29 note: Cj1550c 2C probable ATP 2FGTP-binding protein 2C len: 588 aa 3B some similarity to hypothetical proteins e.g. TR:O50349 Lactobacillus helveticus plasmid plh1 hypothetical protein 28495 aa 29 2Cfasta scores 3B opt: 209 z-score: 231.6 E 28 29: 1.4e-05 2C 22.6 25 identity in 412 aa overlap. No Hp match. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 7EUpdated 282006 29 note: Prosite domain PS50893 ABC_TRANSPORTER_2 2C ATP-binding cassette 2C ABC transporter-type domain profile identified within CDS. Literature search identified work carried out within Helicobacter pylori and Campylobacter jejuni. This CDS is within a type I locus 28genes Cj1549-Cj1553 29. kept within product function. Functional classification - Conserved hypothetical proteins 7EPMID:15699185 NC_002163.1 RefSeq region 1484132 1484155 . - . ID=id2725;gene=rloH;Name=id2725;Dbxref=GeneID:905829;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 RefSeq CDS 1484265 1485407 . - 0 ID=cds1410;Parent=gene1488;gene=hsdS;Name=YP_002344923.1;Dbxref=GOA:Q7B7V7 InterPro:IPR000055 UniProtKB FTrEMBL:Q7B7V7 Genbank:YP_002344923.1 GeneID:905830;gbkey=CDS;product=type I restriction enzyme S protein;Note=Original 282000 29 note: Cj1551c 2C probable type I restriction enzyme S protein 2C len: 588 aa 3B simlar to many e.g. T1S_SALTY type I restriction enzymE StySJI specificity protein 28S protein 29 28469 aa 29 2C fasta scores 3B opt: 173 z-score: 199.9 E 28 29: 0.00082 2C 25.6 25 identity in 301 aa overlap. 24.1 25 identity to HP0462 7EUpdated 282006 29 note: Literature search identified work carried out within Helicobacter pylori and Campylobacter jejuni. This CDS is within a type I locus 28genes Cj1549-Cj1553 29. Some characterisation work within Escherichia coli 2C however 2C kept within product function as identity scores were unnacceptable. Functional classification - DNA replication 2Crestriction 2Fmodification 2C recombination and repair 7EPMID:15699185 2C PMID:3025838 2C PMID:1453962 NC_002163.1 RefSeq gene 1484265 1485407 . - . ID=gene1488;gene=hsdS;Name=hsdS;locus_tag=Cj1551c;Dbxref=GeneID:905830;gbkey=Gene NC_002163.1 RefSeq region 1484373 1484861 . - . ID=id2726;gene=hsdS;Name=id2726;Dbxref=GeneID:905830;gbkey=misc_feature;Note=HMMPfam hit to PF01420 2C Type I restriction modification DNA speci 2C score 2.5e-06 NC_002163.1 RefSeq region 1484943 1485398 . - . ID=id2727;gene=hsdS;Name=id2727;Dbxref=GeneID:905830;gbkey=misc_feature;Note=HMMPfam hit to PF01420 2C Type I restriction modification DNA speci 2C score 1.3e-31 ### NC_002163.1 RefSeq CDS 1485626 1487092 . - 0 ID=cds1411;Parent=gene1489;gene=mloB;Name=YP_002344924.1;Dbxref=InterPro:IPR007421 UniProtKB FTrEMBL:Q7B7V6 Genbank:YP_002344924.1 GeneID:905831;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1552c 2C unknown 2C len: 488 aa 3B no Hp match 7EUpdated 282006 29 note: Pfam domain PF04326 Divergent AAA domain identified within CDS. Conserved added to product function. Literature search identified work carried out within Helicobacter pylori and Campylobacter jejuni. This CDS is within a type I locus 28genes Cj1549-Cj1553 29. Functional classification - Unknown 7EPMID:15699185 NC_002163.1 RefSeq gene 1485626 1487092 . - . ID=gene1489;gene=mloB;Name=mloB;locus_tag=Cj1552c;Dbxref=GeneID:905831;gbkey=Gene NC_002163.1 RefSeq region 1486658 1486963 . - . ID=id2728;gene=mloB;Name=id2728;Dbxref=GeneID:905831;gbkey=misc_feature;Note=HMMPfam hit to PF04326 2C Divergent AAA domain 2C score 2.9e-18 NC_002163.1 RefSeq gene 1487089 1488591 . - . ID=gene1490;gene=hsdM;Name=hsdM;locus_tag=Cj1553c;Dbxref=GeneID:905832;gbkey=Gene NC_002163.1 RefSeq CDS 1487089 1488591 . - 0 ID=cds1412;Parent=gene1490;gene=hsdM;Name=YP_002344925.1;Dbxref=GOA:Q7B7V5 InterPro:IPR002052 InterPro:IPR002296 InterPro:IPR003356 UniProtKB FTrEMBL:Q7B7V5 Genbank:YP_002344925.1 GeneID:905832;gbkey=CDS;product=type I restriction enzyme M protein;Note=Original 282000 29 note: Cj1553c 2C probable type I restriction enzyme M protein 2C len: 500 aa 3B simlar to many e.g. T1M1_ECOLI type I restriction enzyme EcoR124II M protein 28EC 2.1.1.72 29 28520 aa 29 2C fasta scores 3B opt: 447 z-score: 527.4 E 28 29: 4.7e-22 2C 25.9 25 identity in 521 aa overlap. 30.2 25 identity to HP0850. Contains PS00092 N-6 Adenine-specific DNA methylases signature 7EUpdated 282006 29 note: Pfam domains PF02384 N-6 DNA Methylase and PF02506 Type I restriction modification system were identified within CDS. Further support given to product function. Literature search identified work carried out within Helicobacter pylori and Campylobacter jejuni. This CDS is within a type I locus 28genes Cj1549-Cj1553 29. Some characterisation work within Escherichia coli 2C however 2C kept within product function as identity scores were unnacceptable. Functional classification - DNA replication 2Crestriction 2Fmodification 2C recombination and repair 7EPMID:15699185 2C PMID:8145241 2C PMID:9016588 NC_002163.1 RefSeq region 1487245 1487748 . - . ID=id2729;gene=hsdM;Name=id2729;Dbxref=GeneID:905832;gbkey=misc_feature;Note=HMMPfam hit to PF02384 2C N-6 DNA Methylase 2C score 5e-66 NC_002163.1 RefSeq region 1487755 1487775 . - . ID=id2730;gene=hsdM;Name=id2730;Dbxref=GeneID:905832;gbkey=misc_feature;Note=PS00092 N-6 Adenine-specific DNA methylases signature NC_002163.1 RefSeq region 1487899 1488585 . - . ID=id2731;gene=hsdM;Name=id2731;Dbxref=GeneID:905832;gbkey=misc_feature;Note=HMMPfam hit to PF02506 2C Type I restriction modification system 2C M 2C score 4.6e-94 ### NC_002163.1 RefSeq gene 1488961 1489596 . - . ID=gene1491;Name=Cj1555c;locus_tag=Cj1555c;Dbxref=GeneID:905833;gbkey=Gene NC_002163.1 RefSeq CDS 1488961 1489596 . - 0 ID=cds1413;Parent=gene1491;Name=YP_002344926.1;Dbxref=GOA:Q0P871 InterPro:IPR016040 UniProtKB FTrEMBL:Q0P871 Genbank:YP_002344926.1 GeneID:905833;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1555c 2C unknown 2C len: 211 aa 3B similar to TR:P71037 Bacillus subtilis YWNB 28213 aa 29 2Cfasta scores 3B opt: 519 z-score: 635.5 E 28 29: 4.5e-28 2C 42.9 25 identity in 212 aa overlap. No Hp match. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq CDS 1489789 1490121 . + 0 ID=cds1414;Parent=gene1492;Name=YP_002344927.1;Dbxref=InterPro:IPR002577 UniProtKB FTrEMBL:Q0P870 Genbank:YP_002344927.1 GeneID:905834;gbkey=CDS;product=transcriptional regulator;Note=Original 282000 29 note: Cj1556 2C unknown 2C len: 110 aa 3B similar to hypothetical proteins e.g. YYBR_BACSU 28125 aa 29 2Cfasta scores 3B opt: 307 z-score: 402.3 E 28 29: 4.3e-15 2C 43.7 25 identity in 103 aa overlap. No Hp match. Also similar to Cj1546 2843.6 25 identity in 101 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01638 Transcriptional regulator identified within CDS. Product modified to more specific family member based on motif match. No specific characterisation has been carried out yet 2C so kept within product function. Functional classification - Broad regulatory functions NC_002163.1 RefSeq gene 1489789 1490121 . + . ID=gene1492;Name=Cj1556;locus_tag=Cj1556;Dbxref=GeneID:905834;gbkey=Gene NC_002163.1 RefSeq region 1489834 1490118 . + . ID=id2732;Name=id2732;Dbxref=GeneID:905834;gbkey=misc_feature;Note=HMMPfam hit to PF01638 2C Transcriptional regulator 2Cscore 1.2e-34 NC_002163.1 RefSeq stem_loop 1490120 1490161 . + . ID=id2733;Name=id2733;gbkey=stem_loop ### NC_002163.1 UTR_Extractor 5'-UTR 1490183 1490205 . + . ID=utr571;locus_tag=Cj1558;product=hypothetical protein NC_002163.1 RefSeq pseudogene 1490206 1491152 . + . ID=gene1493;Name=Cj1560;locus_tag=Cj1560;Dbxref=GeneID:905836;gbkey=Gene NC_002163.1 RefSeq region 1490233 1490301 . + . ID=id2734;Name=id2734;Dbxref=GeneID:905836;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1558 by TMHMM2.0 at aa 10-32 NC_002163.1 RefSeq region 1490328 1491146 . + . ID=id2735;Name=id2735;Dbxref=GeneID:905836;gbkey=misc_feature;Note=HMMPfam hit to PF03773 2C Predicted permease 2C score 1.8e-21 NC_002163.1 RefSeq region 1490370 1490438 . + . ID=id2736;Name=id2736;Dbxref=GeneID:905836;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1560 by TMHMM2.0 at aa 15-37 2C 44-66 2C 71-90 2C 157-179 2C189-206 2C 213-235 and 250-272 NC_002163.1 RefSeq region 1490457 1490525 . + . ID=id2736;Name=id2736;Dbxref=GeneID:905836;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1560 by TMHMM2.0 at aa 15-37 2C 44-66 2C 71-90 2C 157-179 2C189-206 2C 213-235 and 250-272 NC_002163.1 RefSeq region 1490538 1490597 . + . ID=id2736;Name=id2736;Dbxref=GeneID:905836;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1560 by TMHMM2.0 at aa 15-37 2C 44-66 2C 71-90 2C 157-179 2C189-206 2C 213-235 and 250-272 NC_002163.1 RefSeq region 1490796 1490864 . + . ID=id2736;Name=id2736;Dbxref=GeneID:905836;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1560 by TMHMM2.0 at aa 15-37 2C 44-66 2C 71-90 2C 157-179 2C189-206 2C 213-235 and 250-272 NC_002163.1 RefSeq region 1490892 1490945 . + . ID=id2736;Name=id2736;Dbxref=GeneID:905836;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1560 by TMHMM2.0 at aa 15-37 2C 44-66 2C 71-90 2C 157-179 2C189-206 2C 213-235 and 250-272 NC_002163.1 RefSeq region 1490964 1491032 . + . ID=id2736;Name=id2736;Dbxref=GeneID:905836;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1560 by TMHMM2.0 at aa 15-37 2C 44-66 2C 71-90 2C 157-179 2C189-206 2C 213-235 and 250-272 NC_002163.1 RefSeq region 1491075 1491143 . + . ID=id2736;Name=id2736;Dbxref=GeneID:905836;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1560 by TMHMM2.0 at aa 15-37 2C 44-66 2C 71-90 2C 157-179 2C189-206 2C 213-235 and 250-272 NC_002163.1 UTR_Extractor 5'-UTR 1491110 1491161 . + . ID=utr572;locus_tag=Cj1561;product=putative transcriptional regulator ### NC_002163.1 RefSeq pseudogene 1491162 1491605 . + . ID=gene1494;Name=Cj1561;locus_tag=Cj1561;Dbxref=GeneID:905837;gbkey=Gene NC_002163.1 RefSeq gene 1491492 1491923 . - . ID=gene1495;Name=Cj1563c;locus_tag=Cj1563c;Dbxref=GeneID:904355;gbkey=Gene NC_002163.1 RefSeq CDS 1491492 1491923 . - 0 ID=cds1415;Parent=gene1495;Name=YP_002344932.1;Dbxref=GOA:Q0P865 InterPro:IPR000551 UniProtKB FTrEMBL:Q0P865 Genbank:YP_002344932.1 GeneID:904355;gbkey=CDS;product=transcriptional regulator;Note=Original 282000 29 note: Cj1563c 2C probable transcriptional regulator 2C len: 143 aa 3B similar to members of the MerR family e.g. Y186_HAEIN hypothetical transcriptional regulator HI0186 28135 aa 29 2C fasta scores 3B opt: 241 z-score: 290.6 E 28 29: 7.3e-09 2C 31.9 25 identity in 119 aa overlap 2C and BLTR_BACSU multidrug-efflux transporter 2 regulator 28273 aa 29 2C fasta scores 3B opt: 149 z-score: 182.1 E 28 29: 0.008 2C 24.4 25 identity in 127 aa overlap. No Hp match. Contains helix-turn-helix motif at aa 4-25 28Score 1172 2C 2B3.18 SD 29 7EUpdated 282006 29 note: Pfam domain PF00376 MerR family regulatory protein identified within CDS. Further support given to product function. No specific characterisation has been carried out with acceptable identity score 2C so kept within product function. Functional classification - Broad regulatory functions NC_002163.1 RefSeq region 1491801 1491914 . - . ID=id2737;Name=id2737;Dbxref=GeneID:904355;gbkey=misc_feature;Note=HMMPfam hit to PF00376 2C MerR family regulatory protein 2C score 1.4e-08 ### NC_002163.1 UTR_Extractor 5'-UTR 1491988 1492002 . + . ID=utr573;locus_tag=Cj1564;product=putative methyl-accepting chemotaxis signal transduction protein NC_002163.1 RefSeq CDS 1492003 1493991 . + 0 ID=cds1416;Parent=gene1496;Name=YP_002344933.1;Dbxref=GOA:Q0P864 InterPro:IPR004010 InterPro:IPR004089 UniProtKB FTrEMBL:Q0P864 Genbank:YP_002344933.1 GeneID:904333;gbkey=CDS;product=methyl-accepting chemotaxis signal transduction protein;Note=Original 282000 29 note: Cj1564 2C probable methyl-accepting chemotaxis signal transduction protein 2Clen: 662 aa 3B similar to many e.g. TLPC_BACSU methyl-accepting chemotaxis protein TLPC 28573 aa 29 2C fasta scores 3B opt: 351 z-score: 363.6 E 28 29: 6.2e-13 2C 26.2 25 identity in 553 aa overlap. No Hp ortholog. C-terminus contains repeat1 2C and is identical to the other repeat 1-containing genes Cj0262c and Cj0144. Contains N-terminal signal sequence and transmembrane anchor around aa 300. Also contains Pfam match to entry PF00015 MCPsignal 2CMethyl-accepting chemotaxis protein 28MCP 29 signaling domain 7EUpdated 282006 29 note: Two probable transmembrane helices predicted by TMHMM2.0. Characterisation work carried out within Bacillus subtilis 2C however 2C identity scores were marginal. kept within product function. Functional classification - Chemotaxis and mobility 7EPMID:6213619 2C PMID:7921238 NC_002163.1 RefSeq gene 1492003 1493991 . + . ID=gene1496;Name=Cj1564;locus_tag=Cj1564;Dbxref=GeneID:904333;gbkey=Gene NC_002163.1 RefSeq region 1492060 1492128 . + . ID=id2738;Name=id2738;Dbxref=GeneID:904333;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1564 by TMHMM2.0 at aa 20-42 and 291-313 NC_002163.1 RefSeq region 1492489 1492716 . + . ID=id2739;Name=id2739;Dbxref=GeneID:904333;gbkey=misc_feature;Note=HMMPfam hit to PF02743 2C Cache domain 2C score 7e-06 NC_002163.1 RefSeq region 1492873 1492941 . + . ID=id2738;Name=id2738;Dbxref=GeneID:904333;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1564 by TMHMM2.0 at aa 20-42 and 291-313 NC_002163.1 RefSeq repeat_region 1492914 1493991 . + . ID=id2740;Name=id2740;Dbxref=GeneID:904333;gbkey=repeat_region;Note=repeat 1: identical to 147606..148684 and complement 28238817..239964 29 28approximate numbers 29 NC_002163.1 RefSeq region 1493491 1493985 . + . ID=id2741;Name=id2741;Dbxref=GeneID:904333;gbkey=misc_feature;Note=HMMPfam hit to PF00015 2C Methyl-accepting chemotaxis protein 28MCP 29 s 2C score 6.4e-21 ### NC_002163.1 RefSeq CDS 1494034 1496400 . - 0 ID=cds1417;Parent=gene1497;gene=pflA;Name=YP_002344934.1;Dbxref=GOA:Q46092 InterPro:IPR011990 UniProtKB FTrEMBL:Q46092 Genbank:YP_002344934.1 GeneID:905864;gbkey=CDS;product=paralysed flagellum protein;Note=Original 282000 29 note: Cj1565c 2C pflA 2C required for flagellar function 2C len: 788 aa 3B identical to TR:Q46092 28EMBL:U09019 29 C. jejuni pflA 28788 aa 29. 22.7 25 identity to HP1274. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF07719 Tetratricopeptide repeat identified within CDS. Similar to previously characterised PflA protein in Campylobacter jejuni. Paper identified linking protein to glycoprotein. Functional classification - Surface structures 7EPMID:7715450 2C PMID:12186869 NC_002163.1 RefSeq gene 1494034 1496400 . - . ID=gene1497;gene=pflA;Name=pflA;locus_tag=Cj1565c;Dbxref=GeneID:905864;gbkey=Gene NC_002163.1 RefSeq region 1495318 1495419 . - . ID=id2742;gene=pflA;Name=id2742;Dbxref=GeneID:905864;gbkey=misc_feature;Note=HMMPfam hit to PF07719 2C Tetratricopeptide repeat 2Cscore 0.012 NC_002163.1 UTR_Extractor 5'-UTR 1496400 1496400 . - . ID=utr574;locus_tag=Cj1565c;product=paralysed flagellum protein ### NC_002163.1 RefSeq gene 1496422 1497810 . - . ID=gene1498;gene=nuoN;Name=nuoN;locus_tag=Cj1566c;Dbxref=GeneID:905839;gbkey=Gene NC_002163.1 RefSeq CDS 1496422 1497810 . - 0 ID=cds1418;Parent=gene1498;gene=nuoN;Name=YP_002344935.1;Dbxref=GOA:Q0P862 InterPro:IPR001750 UniProtKB FTrEMBL:Q0P862 Genbank:YP_002344935.1 GeneID:905839;gbkey=CDS;product=NADH dehydrogenase I subunit N;Note=Original 282000 29 note: Cj1566c 2C nuoN 2C probable NADH dehydrogenase I chain N 2C len: 462 aa 3B similar to many e.g. NUON_ECOLI NADH dehydrogenase I chain N 28EC 1.6.5.3 29 28425 aa 29 2C fasta scores 3B opt: 592 z-score: 716.4 E 28 29: 1.4e-32 2C32.3 25 identity in 402 aa overlap. 35.3 25 identity to HP1273. Contains Pfam match to entry PF00361 oxidored_q1 2CNADH-Ubiquinone 2Fplastoquinone 28complex I 29 2C various chains 7EUpdated 282006 29 note: Characterised operon within Escherichia coli. Appropriate motifs also present. Identity score was acceptable 2C so not added to product function. Twelve probable transmembrane helices predicted by TMHMM2.0. Functional classification - Energy metabolism - Respiration - Aerobic 7EPMID:7565112 2C PMID:7730262 2C PMID:15368583 2CPMID:12718520 NC_002163.1 RefSeq region 1496428 1496496 . - . ID=id135;gene=nuoN;Name=id135;Dbxref=GeneID:905839;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1566c by TMHMM2.0 at aa 13-35 2C 42-64 2C 79-98 2C 111-133 2C162-184 2C 205-227 2C 237-259 2C 266-288 2C 323-345 2C 365-387 2C397-419 and 439-461 NC_002163.1 RefSeq region 1496554 1496622 . - . ID=id135;gene=nuoN;Name=id135;Dbxref=GeneID:905839;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1566c by TMHMM2.0 at aa 13-35 2C 42-64 2C 79-98 2C 111-133 2C162-184 2C 205-227 2C 237-259 2C 266-288 2C 323-345 2C 365-387 2C397-419 and 439-461 NC_002163.1 RefSeq region 1496578 1497438 . - . ID=id2743;gene=nuoN;Name=id2743;Dbxref=GeneID:905839;gbkey=misc_feature;Note=HMMPfam hit to PF00361 2CNADH-Ubiquinone 2Fplastoquinone 28complex I 29 2C score 2e-50 NC_002163.1 RefSeq region 1496650 1496718 . - . ID=id135;gene=nuoN;Name=id135;Dbxref=GeneID:905839;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1566c by TMHMM2.0 at aa 13-35 2C 42-64 2C 79-98 2C 111-133 2C162-184 2C 205-227 2C 237-259 2C 266-288 2C 323-345 2C 365-387 2C397-419 and 439-461 NC_002163.1 RefSeq region 1496776 1496844 . - . ID=id135;gene=nuoN;Name=id135;Dbxref=GeneID:905839;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1566c by TMHMM2.0 at aa 13-35 2C 42-64 2C 79-98 2C 111-133 2C162-184 2C 205-227 2C 237-259 2C 266-288 2C 323-345 2C 365-387 2C397-419 and 439-461 NC_002163.1 RefSeq region 1496878 1496910 . - . ID=id2744;gene=nuoN;Name=id2744;Dbxref=GeneID:905839;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1496947 1497015 . - . ID=id135;gene=nuoN;Name=id135;Dbxref=GeneID:905839;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1566c by TMHMM2.0 at aa 13-35 2C 42-64 2C 79-98 2C 111-133 2C162-184 2C 205-227 2C 237-259 2C 266-288 2C 323-345 2C 365-387 2C397-419 and 439-461 NC_002163.1 RefSeq region 1497034 1497102 . - . ID=id135;gene=nuoN;Name=id135;Dbxref=GeneID:905839;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1566c by TMHMM2.0 at aa 13-35 2C 42-64 2C 79-98 2C 111-133 2C162-184 2C 205-227 2C 237-259 2C 266-288 2C 323-345 2C 365-387 2C397-419 and 439-461 NC_002163.1 RefSeq region 1497130 1497198 . - . ID=id135;gene=nuoN;Name=id135;Dbxref=GeneID:905839;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1566c by TMHMM2.0 at aa 13-35 2C 42-64 2C 79-98 2C 111-133 2C162-184 2C 205-227 2C 237-259 2C 266-288 2C 323-345 2C 365-387 2C397-419 and 439-461 NC_002163.1 RefSeq region 1497259 1497327 . - . ID=id135;gene=nuoN;Name=id135;Dbxref=GeneID:905839;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1566c by TMHMM2.0 at aa 13-35 2C 42-64 2C 79-98 2C 111-133 2C162-184 2C 205-227 2C 237-259 2C 266-288 2C 323-345 2C 365-387 2C397-419 and 439-461 NC_002163.1 RefSeq region 1497412 1497480 . - . ID=id135;gene=nuoN;Name=id135;Dbxref=GeneID:905839;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1566c by TMHMM2.0 at aa 13-35 2C 42-64 2C 79-98 2C 111-133 2C162-184 2C 205-227 2C 237-259 2C 266-288 2C 323-345 2C 365-387 2C397-419 and 439-461 NC_002163.1 RefSeq region 1497517 1497576 . - . ID=id135;gene=nuoN;Name=id135;Dbxref=GeneID:905839;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1566c by TMHMM2.0 at aa 13-35 2C 42-64 2C 79-98 2C 111-133 2C162-184 2C 205-227 2C 237-259 2C 266-288 2C 323-345 2C 365-387 2C397-419 and 439-461 NC_002163.1 RefSeq region 1497619 1497687 . - . ID=id135;gene=nuoN;Name=id135;Dbxref=GeneID:905839;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1566c by TMHMM2.0 at aa 13-35 2C 42-64 2C 79-98 2C 111-133 2C162-184 2C 205-227 2C 237-259 2C 266-288 2C 323-345 2C 365-387 2C397-419 and 439-461 NC_002163.1 RefSeq region 1497706 1497774 . - . ID=id135;gene=nuoN;Name=id135;Dbxref=GeneID:905839;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1566c by TMHMM2.0 at aa 13-35 2C 42-64 2C 79-98 2C 111-133 2C162-184 2C 205-227 2C 237-259 2C 266-288 2C 323-345 2C 365-387 2C397-419 and 439-461 NC_002163.1 RefSeq CDS 1497800 1499287 . - 0 ID=cds1419;Parent=gene1499;gene=nuoM;Name=YP_002344936.1;Dbxref=GOA:Q0P861 InterPro:IPR001750 InterPro:IPR003918 InterPro:IPR010227 UniProtKB FTrEMBL:Q0P861 Genbank:YP_002344936.1 GeneID:905840;gbkey=CDS;product=NADH dehydrogenase I subunit M;Note=Original 282000 29 note: Cj1567c 2C nuoM 2C probable NADH dehydrogenase I chain M 2C len: 495 aa 3B similar to many e.g. NU4M_CHOCR NADH-ubiquinone oxidoreductase chain 4 28EC 1.6.5.3 29 28492 aa 29 2C fasta scores 3B opt: 1055 z-score: 1213.7 E 28 29: 0 2C 36.4 25 identity in 495 aa overlap 2C and NUOM_ECOLI NADH dehydrogenase I chain M 28EC 1.6.5.3 29 28509 aa 29 2C blastp scores 3B E 3D 1.5e-58 2C 32 25 identity in 419 aa overlap. 40.1 25 identity to HP1272. Contains Pfam match to entry PF00361 oxidored_q1 2C NADH-Ubiquinone 2Fplastoquinone 28complex I 29 2Cvarious chains 7EUpdated 282006 29 note: Characterised operon within Escherichia coli. Appropriate motifs present. Identity score was acceptable 2C so not added to product function. Fourteen probable transmembrane helices predicted by TMHMM2.0. Functional classification - Energy metabolism - Respiration - Aerobic 7EPMID:7565112 2C PMID:7730262 2C PMID:15368583 2CPMID:12923180 NC_002163.1 RefSeq gene 1497800 1499287 . - . ID=gene1499;gene=nuoM;Name=nuoM;locus_tag=Cj1567c;Dbxref=GeneID:905840;gbkey=Gene NC_002163.1 RefSeq region 1497911 1497979 . - . ID=id136;gene=nuoM;Name=id136;Dbxref=GeneID:905840;gbkey=misc_feature;Note=14 probable transmembrane helices predicted for Cj1567c by TMHMM2.0 at aa 4-20 2C 27-49 2C 69-91 2C 98-115 2C119-141 2C 148-170 2C 200-222 2C 229-251 2C 261-283 2C 290-312 2C317-339 2C 359-381 2C 394-416 and 437-459 NC_002163.1 RefSeq region 1498040 1498108 . - . ID=id136;gene=nuoM;Name=id136;Dbxref=GeneID:905840;gbkey=misc_feature;Note=14 probable transmembrane helices predicted for Cj1567c by TMHMM2.0 at aa 4-20 2C 27-49 2C 69-91 2C 98-115 2C119-141 2C 148-170 2C 200-222 2C 229-251 2C 261-283 2C 290-312 2C317-339 2C 359-381 2C 394-416 and 437-459 NC_002163.1 RefSeq region 1498076 1498942 . - . ID=id2745;gene=nuoM;Name=id2745;Dbxref=GeneID:905840;gbkey=misc_feature;Note=HMMPfam hit to PF00361 2CNADH-Ubiquinone 2Fplastoquinone 28complex I 29 2C score 5.3e-59 NC_002163.1 RefSeq region 1498145 1498213 . - . ID=id136;gene=nuoM;Name=id136;Dbxref=GeneID:905840;gbkey=misc_feature;Note=14 probable transmembrane helices predicted for Cj1567c by TMHMM2.0 at aa 4-20 2C 27-49 2C 69-91 2C 98-115 2C119-141 2C 148-170 2C 200-222 2C 229-251 2C 261-283 2C 290-312 2C317-339 2C 359-381 2C 394-416 and 437-459 NC_002163.1 RefSeq region 1498271 1498339 . - . ID=id136;gene=nuoM;Name=id136;Dbxref=GeneID:905840;gbkey=misc_feature;Note=14 probable transmembrane helices predicted for Cj1567c by TMHMM2.0 at aa 4-20 2C 27-49 2C 69-91 2C 98-115 2C119-141 2C 148-170 2C 200-222 2C 229-251 2C 261-283 2C 290-312 2C317-339 2C 359-381 2C 394-416 and 437-459 NC_002163.1 RefSeq region 1498352 1498420 . - . ID=id136;gene=nuoM;Name=id136;Dbxref=GeneID:905840;gbkey=misc_feature;Note=14 probable transmembrane helices predicted for Cj1567c by TMHMM2.0 at aa 4-20 2C 27-49 2C 69-91 2C 98-115 2C119-141 2C 148-170 2C 200-222 2C 229-251 2C 261-283 2C 290-312 2C317-339 2C 359-381 2C 394-416 and 437-459 NC_002163.1 RefSeq region 1498439 1498507 . - . ID=id136;gene=nuoM;Name=id136;Dbxref=GeneID:905840;gbkey=misc_feature;Note=14 probable transmembrane helices predicted for Cj1567c by TMHMM2.0 at aa 4-20 2C 27-49 2C 69-91 2C 98-115 2C119-141 2C 148-170 2C 200-222 2C 229-251 2C 261-283 2C 290-312 2C317-339 2C 359-381 2C 394-416 and 437-459 NC_002163.1 RefSeq region 1498535 1498603 . - . ID=id136;gene=nuoM;Name=id136;Dbxref=GeneID:905840;gbkey=misc_feature;Note=14 probable transmembrane helices predicted for Cj1567c by TMHMM2.0 at aa 4-20 2C 27-49 2C 69-91 2C 98-115 2C119-141 2C 148-170 2C 200-222 2C 229-251 2C 261-283 2C 290-312 2C317-339 2C 359-381 2C 394-416 and 437-459 NC_002163.1 RefSeq region 1498622 1498690 . - . ID=id136;gene=nuoM;Name=id136;Dbxref=GeneID:905840;gbkey=misc_feature;Note=14 probable transmembrane helices predicted for Cj1567c by TMHMM2.0 at aa 4-20 2C 27-49 2C 69-91 2C 98-115 2C119-141 2C 148-170 2C 200-222 2C 229-251 2C 261-283 2C 290-312 2C317-339 2C 359-381 2C 394-416 and 437-459 NC_002163.1 RefSeq region 1498778 1498846 . - . ID=id136;gene=nuoM;Name=id136;Dbxref=GeneID:905840;gbkey=misc_feature;Note=14 probable transmembrane helices predicted for Cj1567c by TMHMM2.0 at aa 4-20 2C 27-49 2C 69-91 2C 98-115 2C119-141 2C 148-170 2C 200-222 2C 229-251 2C 261-283 2C 290-312 2C317-339 2C 359-381 2C 394-416 and 437-459 NC_002163.1 RefSeq region 1498865 1498933 . - . ID=id136;gene=nuoM;Name=id136;Dbxref=GeneID:905840;gbkey=misc_feature;Note=14 probable transmembrane helices predicted for Cj1567c by TMHMM2.0 at aa 4-20 2C 27-49 2C 69-91 2C 98-115 2C119-141 2C 148-170 2C 200-222 2C 229-251 2C 261-283 2C 290-312 2C317-339 2C 359-381 2C 394-416 and 437-459 NC_002163.1 RefSeq region 1498943 1498996 . - . ID=id136;gene=nuoM;Name=id136;Dbxref=GeneID:905840;gbkey=misc_feature;Note=14 probable transmembrane helices predicted for Cj1567c by TMHMM2.0 at aa 4-20 2C 27-49 2C 69-91 2C 98-115 2C119-141 2C 148-170 2C 200-222 2C 229-251 2C 261-283 2C 290-312 2C317-339 2C 359-381 2C 394-416 and 437-459 NC_002163.1 RefSeq region 1499015 1499083 . - . ID=id136;gene=nuoM;Name=id136;Dbxref=GeneID:905840;gbkey=misc_feature;Note=14 probable transmembrane helices predicted for Cj1567c by TMHMM2.0 at aa 4-20 2C 27-49 2C 69-91 2C 98-115 2C119-141 2C 148-170 2C 200-222 2C 229-251 2C 261-283 2C 290-312 2C317-339 2C 359-381 2C 394-416 and 437-459 NC_002163.1 RefSeq region 1499141 1499209 . - . ID=id136;gene=nuoM;Name=id136;Dbxref=GeneID:905840;gbkey=misc_feature;Note=14 probable transmembrane helices predicted for Cj1567c by TMHMM2.0 at aa 4-20 2C 27-49 2C 69-91 2C 98-115 2C119-141 2C 148-170 2C 200-222 2C 229-251 2C 261-283 2C 290-312 2C317-339 2C 359-381 2C 394-416 and 437-459 NC_002163.1 RefSeq region 1499228 1499278 . - . ID=id136;gene=nuoM;Name=id136;Dbxref=GeneID:905840;gbkey=misc_feature;Note=14 probable transmembrane helices predicted for Cj1567c by TMHMM2.0 at aa 4-20 2C 27-49 2C 69-91 2C 98-115 2C119-141 2C 148-170 2C 200-222 2C 229-251 2C 261-283 2C 290-312 2C317-339 2C 359-381 2C 394-416 and 437-459 ### NC_002163.1 RefSeq CDS 1499289 1501079 . - 0 ID=cds1420;Parent=gene1500;gene=nuoL;Name=YP_002344937.1;Dbxref=GOA:Q9PMA7 InterPro:IPR001516 InterPro:IPR001750 InterPro:IPR003916 InterPro:IPR003945 InterPro:IPR010934 UniProtKB FSwiss-Prot:Q9PMA7 Genbank:YP_002344937.1 GeneID:905250;gbkey=CDS;product=NADH dehydrogenase subunit L;Note=Catalyzes the transfer of electrons from NADH to ubiquinone NC_002163.1 RefSeq gene 1499289 1501079 . - . ID=gene1500;gene=nuoL;Name=nuoL;locus_tag=Cj1568c;Dbxref=GeneID:905250;gbkey=Gene NC_002163.1 RefSeq region 1499295 1499363 . - . ID=id137;gene=nuoL;Name=id137;Dbxref=GeneID:905250;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj1568c by TMHMM2.0 at aa 4-23 2C 30-52 2C 76-98 2C 105-124 2C128-150 2C 163-182 2C 202-224 2C 236-258 2C 268-290 2C 297-319 2C323-342 2C 363-385 2C 398-420 2C 441-463 2C 478-500 and 573-595 NC_002163.1 RefSeq region 1499295 1499834 . - . ID=id2746;gene=nuoL;Name=id2746;Dbxref=GeneID:905250;gbkey=misc_feature;Note=HMMPfam hit to PF06455 2C NADH dehydrogenase subunit 5 C-terminus 2C score 0.00052 NC_002163.1 RefSeq region 1499580 1499648 . - . ID=id137;gene=nuoL;Name=id137;Dbxref=GeneID:905250;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj1568c by TMHMM2.0 at aa 4-23 2C 30-52 2C 76-98 2C 105-124 2C128-150 2C 163-182 2C 202-224 2C 236-258 2C 268-290 2C 297-319 2C323-342 2C 363-385 2C 398-420 2C 441-463 2C 478-500 and 573-595 NC_002163.1 RefSeq region 1499691 1499759 . - . ID=id137;gene=nuoL;Name=id137;Dbxref=GeneID:905250;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj1568c by TMHMM2.0 at aa 4-23 2C 30-52 2C 76-98 2C 105-124 2C128-150 2C 163-182 2C 202-224 2C 236-258 2C 268-290 2C 297-319 2C323-342 2C 363-385 2C 398-420 2C 441-463 2C 478-500 and 573-595 NC_002163.1 RefSeq region 1499820 1499888 . - . ID=id137;gene=nuoL;Name=id137;Dbxref=GeneID:905250;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj1568c by TMHMM2.0 at aa 4-23 2C 30-52 2C 76-98 2C 105-124 2C128-150 2C 163-182 2C 202-224 2C 236-258 2C 268-290 2C 297-319 2C323-342 2C 363-385 2C 398-420 2C 441-463 2C 478-500 and 573-595 NC_002163.1 RefSeq region 1499844 1500707 . - . ID=id2747;gene=nuoL;Name=id2747;Dbxref=GeneID:905250;gbkey=misc_feature;Note=HMMPfam hit to PF00361 2CNADH-Ubiquinone 2Fplastoquinone 28complex 2C score 1e-89 NC_002163.1 RefSeq region 1499925 1499993 . - . ID=id137;gene=nuoL;Name=id137;Dbxref=GeneID:905250;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj1568c by TMHMM2.0 at aa 4-23 2C 30-52 2C 76-98 2C 105-124 2C128-150 2C 163-182 2C 202-224 2C 236-258 2C 268-290 2C 297-319 2C323-342 2C 363-385 2C 398-420 2C 441-463 2C 478-500 and 573-595 NC_002163.1 RefSeq region 1500054 1500113 . - . ID=id137;gene=nuoL;Name=id137;Dbxref=GeneID:905250;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj1568c by TMHMM2.0 at aa 4-23 2C 30-52 2C 76-98 2C 105-124 2C128-150 2C 163-182 2C 202-224 2C 236-258 2C 268-290 2C 297-319 2C323-342 2C 363-385 2C 398-420 2C 441-463 2C 478-500 and 573-595 NC_002163.1 RefSeq region 1500123 1500191 . - . ID=id137;gene=nuoL;Name=id137;Dbxref=GeneID:905250;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj1568c by TMHMM2.0 at aa 4-23 2C 30-52 2C 76-98 2C 105-124 2C128-150 2C 163-182 2C 202-224 2C 236-258 2C 268-290 2C 297-319 2C323-342 2C 363-385 2C 398-420 2C 441-463 2C 478-500 and 573-595 NC_002163.1 RefSeq region 1500210 1500278 . - . ID=id137;gene=nuoL;Name=id137;Dbxref=GeneID:905250;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj1568c by TMHMM2.0 at aa 4-23 2C 30-52 2C 76-98 2C 105-124 2C128-150 2C 163-182 2C 202-224 2C 236-258 2C 268-290 2C 297-319 2C323-342 2C 363-385 2C 398-420 2C 441-463 2C 478-500 and 573-595 NC_002163.1 RefSeq region 1500306 1500374 . - . ID=id137;gene=nuoL;Name=id137;Dbxref=GeneID:905250;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj1568c by TMHMM2.0 at aa 4-23 2C 30-52 2C 76-98 2C 105-124 2C128-150 2C 163-182 2C 202-224 2C 236-258 2C 268-290 2C 297-319 2C323-342 2C 363-385 2C 398-420 2C 441-463 2C 478-500 and 573-595 NC_002163.1 RefSeq region 1500408 1500476 . - . ID=id137;gene=nuoL;Name=id137;Dbxref=GeneID:905250;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj1568c by TMHMM2.0 at aa 4-23 2C 30-52 2C 76-98 2C 105-124 2C128-150 2C 163-182 2C 202-224 2C 236-258 2C 268-290 2C 297-319 2C323-342 2C 363-385 2C 398-420 2C 441-463 2C 478-500 and 573-595 NC_002163.1 RefSeq region 1500534 1500593 . - . ID=id137;gene=nuoL;Name=id137;Dbxref=GeneID:905250;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj1568c by TMHMM2.0 at aa 4-23 2C 30-52 2C 76-98 2C 105-124 2C128-150 2C 163-182 2C 202-224 2C 236-258 2C 268-290 2C 297-319 2C323-342 2C 363-385 2C 398-420 2C 441-463 2C 478-500 and 573-595 NC_002163.1 RefSeq region 1500630 1500698 . - . ID=id137;gene=nuoL;Name=id137;Dbxref=GeneID:905250;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj1568c by TMHMM2.0 at aa 4-23 2C 30-52 2C 76-98 2C 105-124 2C128-150 2C 163-182 2C 202-224 2C 236-258 2C 268-290 2C 297-319 2C323-342 2C 363-385 2C 398-420 2C 441-463 2C 478-500 and 573-595 NC_002163.1 RefSeq region 1500708 1500767 . - . ID=id137;gene=nuoL;Name=id137;Dbxref=GeneID:905250;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj1568c by TMHMM2.0 at aa 4-23 2C 30-52 2C 76-98 2C 105-124 2C128-150 2C 163-182 2C 202-224 2C 236-258 2C 268-290 2C 297-319 2C323-342 2C 363-385 2C 398-420 2C 441-463 2C 478-500 and 573-595 NC_002163.1 RefSeq region 1500738 1500911 . - . ID=id2748;gene=nuoL;Name=id2748;Dbxref=GeneID:905250;gbkey=misc_feature;Note=HMMPfam hit to PF00662 2C NADH-Ubiquinone oxidoreductase 28complex 2C score 1.4e-18 NC_002163.1 RefSeq region 1500786 1500854 . - . ID=id137;gene=nuoL;Name=id137;Dbxref=GeneID:905250;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj1568c by TMHMM2.0 at aa 4-23 2C 30-52 2C 76-98 2C 105-124 2C128-150 2C 163-182 2C 202-224 2C 236-258 2C 268-290 2C 297-319 2C323-342 2C 363-385 2C 398-420 2C 441-463 2C 478-500 and 573-595 NC_002163.1 RefSeq region 1500924 1500992 . - . ID=id137;gene=nuoL;Name=id137;Dbxref=GeneID:905250;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj1568c by TMHMM2.0 at aa 4-23 2C 30-52 2C 76-98 2C 105-124 2C128-150 2C 163-182 2C 202-224 2C 236-258 2C 268-290 2C 297-319 2C323-342 2C 363-385 2C 398-420 2C 441-463 2C 478-500 and 573-595 NC_002163.1 RefSeq region 1501011 1501070 . - . ID=id137;gene=nuoL;Name=id137;Dbxref=GeneID:905250;gbkey=misc_feature;Note=16 probable transmembrane helices predicted for Cj1568c by TMHMM2.0 at aa 4-23 2C 30-52 2C 76-98 2C 105-124 2C128-150 2C 163-182 2C 202-224 2C 236-258 2C 268-290 2C 297-319 2C323-342 2C 363-385 2C 398-420 2C 441-463 2C 478-500 and 573-595 NC_002163.1 RefSeq region 1501017 1501049 . - . ID=id2749;gene=nuoL;Name=id2749;Dbxref=GeneID:905250;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq CDS 1501081 1501377 . - 0 ID=cds1421;Parent=gene1501;gene=nuoK;Name=YP_002344938.1;Dbxref=GOA:Q0P859 InterPro:IPR001133 UniProtKB FTrEMBL:Q0P859 Genbank:YP_002344938.1 GeneID:904491;gbkey=CDS;product=NADH dehydrogenase I subunit K;Note=Original 282000 29 note: Cj1569c 2C nuoK 2C probable NADH dehydrogenase I chain K 2C len: 98 aa 3B similar to many e.g. NUOK_ECOLI NADH dehydrogenase I chain K 28EC 1.6.5.3 29 28100 aa 29 2C fasta scores 3B opt: 212 z-score: 302.0 E 28 29: 1.7e-09 2C32.6 25 identity in 95 aa overlap. 45.8 25 identity to HP1270. Contains Pfam match to entry PF00420 oxidored_q2 2CNADH-ubiquinone 2Fplastoquinone oxidoreductase chain 4L 7EUpdated 282006 29 note: Characterised operon within Escherichia coli. Appropriate motifs present. Identity score was acceptable 2C so not added to product function. Three probable transmembrane helices predicted by TMHMM2.0. Functional classification - Energy metabolism - Respiration - Aerobic 7EPMID:7565112 2C PMID:7730262 2C PMID:15368583 2CPMID:15996109 NC_002163.1 RefSeq gene 1501081 1501377 . - . ID=gene1501;gene=nuoK;Name=nuoK;locus_tag=Cj1569c;Dbxref=GeneID:904491;gbkey=Gene NC_002163.1 RefSeq region 1501093 1501368 . - . ID=id2750;gene=nuoK;Name=id2750;Dbxref=GeneID:904491;gbkey=misc_feature;Note=HMMPfam hit to PF00420 2CNADH-ubiquinone 2Fplastoquinone oxidoreduct 2C score 1.5e-33 NC_002163.1 RefSeq region 1501138 1501206 . - . ID=id138;gene=nuoK;Name=id138;Dbxref=GeneID:904491;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1569c by TMHMM2.0 at aa 5-21 2C 26-48 and 58-80 NC_002163.1 RefSeq region 1501171 1501203 . - . ID=id2751;gene=nuoK;Name=id2751;Dbxref=GeneID:904491;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1501234 1501302 . - . ID=id138;gene=nuoK;Name=id138;Dbxref=GeneID:904491;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1569c by TMHMM2.0 at aa 5-21 2C 26-48 and 58-80 NC_002163.1 RefSeq region 1501315 1501365 . - . ID=id138;gene=nuoK;Name=id138;Dbxref=GeneID:904491;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1569c by TMHMM2.0 at aa 5-21 2C 26-48 and 58-80 NC_002163.1 RefSeq gene 1501374 1501892 . - . ID=gene1502;gene=nuoJ;Name=nuoJ;locus_tag=Cj1570c;Dbxref=GeneID:905841;gbkey=Gene NC_002163.1 RefSeq CDS 1501374 1501892 . - 0 ID=cds1422;Parent=gene1502;gene=nuoJ;Name=YP_002344939.1;Dbxref=GOA:Q0P858 InterPro:IPR001457 UniProtKB FTrEMBL:Q0P858 Genbank:YP_002344939.1 GeneID:905841;gbkey=CDS;product=NADH dehydrogenase subunit J;Note=Catalyzes the transfer of electrons from NADH to quinone NC_002163.1 RefSeq region 1501401 1501889 . - . ID=id2752;gene=nuoJ;Name=id2752;Dbxref=GeneID:905841;gbkey=misc_feature;Note=HMMPfam hit to PF00499 2CNADH-ubiquinone 2Fplastoquinone oxidoreduct 2C score 2.8e-07 NC_002163.1 RefSeq region 1501404 1501472 . - . ID=id139;gene=nuoJ;Name=id139;Dbxref=GeneID:905841;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1570c by TMHMM2.0 at aa 5-24 2C 28-47 2C 54-76 2C 91-110 and 141-163 NC_002163.1 RefSeq region 1501563 1501622 . - . ID=id139;gene=nuoJ;Name=id139;Dbxref=GeneID:905841;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1570c by TMHMM2.0 at aa 5-24 2C 28-47 2C 54-76 2C 91-110 and 141-163 NC_002163.1 RefSeq region 1501665 1501733 . - . ID=id139;gene=nuoJ;Name=id139;Dbxref=GeneID:905841;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1570c by TMHMM2.0 at aa 5-24 2C 28-47 2C 54-76 2C 91-110 and 141-163 NC_002163.1 RefSeq region 1501752 1501811 . - . ID=id139;gene=nuoJ;Name=id139;Dbxref=GeneID:905841;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1570c by TMHMM2.0 at aa 5-24 2C 28-47 2C 54-76 2C 91-110 and 141-163 NC_002163.1 RefSeq region 1501821 1501880 . - . ID=id139;gene=nuoJ;Name=id139;Dbxref=GeneID:905841;gbkey=misc_feature;Note=5 probable transmembrane helices predicted for Cj1570c by TMHMM2.0 at aa 5-24 2C 28-47 2C 54-76 2C 91-110 and 141-163 NC_002163.1 RefSeq CDS 1501889 1502530 . - 0 ID=cds1423;Parent=gene1503;gene=nuoI;Name=YP_002344940.1;Dbxref=GOA:Q0P857 HSSP:P00198 InterPro:IPR001450 InterPro:IPR010226 UniProtKB FSwiss-Prot:Q0P857 Genbank:YP_002344940.1 GeneID:905842;gbkey=CDS;product=NADH dehydrogenase subunit I;Note=Catalyzes the transfer of electrons from NADH to quinone NC_002163.1 RefSeq gene 1501889 1502530 . - . ID=gene1503;gene=nuoI;Name=nuoI;locus_tag=Cj1571c;Dbxref=GeneID:905842;gbkey=Gene NC_002163.1 RefSeq region 1502117 1502188 . - . ID=id2753;gene=nuoI;Name=id2753;Dbxref=GeneID:905842;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 2.9e-07 NC_002163.1 RefSeq region 1502132 1502167 . - . ID=id2754;gene=nuoI;Name=id2754;Dbxref=GeneID:905842;gbkey=misc_feature;Note=PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature NC_002163.1 RefSeq region 1502234 1502305 . - . ID=id2755;gene=nuoI;Name=id2755;Dbxref=GeneID:905842;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 0.00011 ### NC_002163.1 RefSeq CDS 1502540 1503538 . - 0 ID=cds1424;Parent=gene1504;gene=nuoH;Name=YP_002344941.1;Dbxref=GOA:Q9PMA3 InterPro:IPR001694 UniProtKB FSwiss-Prot:Q9PMA3 Genbank:YP_002344941.1 GeneID:905843;gbkey=CDS;product=NADH dehydrogenase subunit H;Note=Catalyzes the transfer of electrons from NADH to quinone NC_002163.1 RefSeq gene 1502540 1503538 . - . ID=gene1504;gene=nuoH;Name=nuoH;locus_tag=Cj1572c;Dbxref=GeneID:905843;gbkey=Gene NC_002163.1 RefSeq region 1502546 1503511 . - . ID=id2756;gene=nuoH;Name=id2756;Dbxref=GeneID:905843;gbkey=misc_feature;Note=HMMPfam hit to PF00146 2C NADH dehydrogenase 2C score 8.9e-82 NC_002163.1 RefSeq region 1502549 1502608 . - . ID=id140;gene=nuoH;Name=id140;Dbxref=GeneID:905843;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1572c by TMHMM2.0 at aa 10-32 2C 78-100 2C 120-142 2C 155-177 2C192-214 2C 246-268 2C 272-294 and 311-330 NC_002163.1 RefSeq region 1502657 1502725 . - . ID=id140;gene=nuoH;Name=id140;Dbxref=GeneID:905843;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1572c by TMHMM2.0 at aa 10-32 2C 78-100 2C 120-142 2C 155-177 2C192-214 2C 246-268 2C 272-294 and 311-330 NC_002163.1 RefSeq region 1502735 1502803 . - . ID=id140;gene=nuoH;Name=id140;Dbxref=GeneID:905843;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1572c by TMHMM2.0 at aa 10-32 2C 78-100 2C 120-142 2C 155-177 2C192-214 2C 246-268 2C 272-294 and 311-330 NC_002163.1 RefSeq region 1502897 1502965 . - . ID=id140;gene=nuoH;Name=id140;Dbxref=GeneID:905843;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1572c by TMHMM2.0 at aa 10-32 2C 78-100 2C 120-142 2C 155-177 2C192-214 2C 246-268 2C 272-294 and 311-330 NC_002163.1 RefSeq region 1503008 1503076 . - . ID=id140;gene=nuoH;Name=id140;Dbxref=GeneID:905843;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1572c by TMHMM2.0 at aa 10-32 2C 78-100 2C 120-142 2C 155-177 2C192-214 2C 246-268 2C 272-294 and 311-330 NC_002163.1 RefSeq region 1503113 1503181 . - . ID=id140;gene=nuoH;Name=id140;Dbxref=GeneID:905843;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1572c by TMHMM2.0 at aa 10-32 2C 78-100 2C 120-142 2C 155-177 2C192-214 2C 246-268 2C 272-294 and 311-330 NC_002163.1 RefSeq region 1503239 1503307 . - . ID=id140;gene=nuoH;Name=id140;Dbxref=GeneID:905843;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1572c by TMHMM2.0 at aa 10-32 2C 78-100 2C 120-142 2C 155-177 2C192-214 2C 246-268 2C 272-294 and 311-330 NC_002163.1 RefSeq region 1503335 1503382 . - . ID=id2757;gene=nuoH;Name=id2757;Dbxref=GeneID:905843;gbkey=misc_feature;Note=PS00667 Respiratory-chain NADH dehydrogenase subunit 1 signature 1 NC_002163.1 RefSeq region 1503443 1503511 . - . ID=id140;gene=nuoH;Name=id140;Dbxref=GeneID:905843;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1572c by TMHMM2.0 at aa 10-32 2C 78-100 2C 120-142 2C 155-177 2C192-214 2C 246-268 2C 272-294 and 311-330 NC_002163.1 RefSeq CDS 1503531 1505993 . - 0 ID=cds1425;Parent=gene1505;gene=nuoG;Name=YP_002344942.1;Dbxref=GOA:Q0P855 InterPro:IPR001041 InterPro:IPR001450 UniProtKB FTrEMBL:Q0P855 Genbank:YP_002344942.1 GeneID:905177;gbkey=CDS;product=NADH dehydrogenase subunit G;Note=Catalyzes the transfer of electrons from NADH to ubiquinone NC_002163.1 RefSeq gene 1503531 1505993 . - . ID=gene1505;gene=nuoG;Name=nuoG;locus_tag=Cj1573c;Dbxref=GeneID:905177;gbkey=Gene NC_002163.1 RefSeq region 1505331 1505402 . - . ID=id2758;gene=nuoG;Name=id2758;Dbxref=GeneID:905177;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 2.2e-05 NC_002163.1 RefSeq region 1505346 1505381 . - . ID=id2759;gene=nuoG;Name=id2759;Dbxref=GeneID:905177;gbkey=misc_feature;Note=PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature NC_002163.1 RefSeq region 1505520 1505591 . - . ID=id2760;gene=nuoG;Name=id2760;Dbxref=GeneID:905177;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 0.014 NC_002163.1 RefSeq region 1505799 1505987 . - . ID=id2761;gene=nuoG;Name=id2761;Dbxref=GeneID:905177;gbkey=misc_feature;Note=HMMPfam hit to PF00111 2C 2Fe-2S iron-sulfur cluster binding domain 2C score 2e-07 NC_002163.1 RefSeq gene 1505990 1506682 . - . ID=gene1506;gene=Cj1574c;Name=Cj1574c;locus_tag=Cj1574c;Dbxref=GeneID:905844;gbkey=Gene NC_002163.1 RefSeq CDS 1505990 1506682 . - 0 ID=cds1426;Parent=gene1506;Name=YP_002344943.1;Dbxref=GOA:Q0P854 UniProtKB FTrEMBL:Q0P854 Genbank:YP_002344943.1 GeneID:905844;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1574c 2C unknown 2C len: 230 aa 3B 26.5 25 identity to HP1265. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq CDS 1506679 1506906 . - 0 ID=cds1427;Parent=gene1507;Name=YP_002344944.1;Dbxref=UniProtKB FTrEMBL:Q0P853 Genbank:YP_002344944.1 GeneID:905845;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1575c 2C unknown 2C len: 75 aa 3B 52.0 25 identity to HP1264. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 1506679 1506906 . - . ID=gene1507;Name=Cj1575c;locus_tag=Cj1575c;Dbxref=GeneID:905845;gbkey=Gene NC_002163.1 RefSeq CDS 1506903 1508129 . - 0 ID=cds1428;Parent=gene1508;gene=nuoD;Name=YP_002344945.1;Dbxref=GOA:Q9PM99 InterPro:IPR001135 InterPro:IPR010219 InterPro:IPR014029 UniProtKB FSwiss-Prot:Q9PM99 Genbank:YP_002344945.1 GeneID:905846;gbkey=CDS;product=NADH dehydrogenase subunit D;Note=Catalyzes the transfer of electrons from NADH to quinone NC_002163.1 RefSeq gene 1506903 1508129 . - . ID=gene1508;gene=nuoD;Name=nuoD;locus_tag=Cj1576c;Dbxref=GeneID:905846;gbkey=Gene NC_002163.1 RefSeq region 1506906 1507724 . - . ID=id2762;gene=nuoD;Name=id2762;Dbxref=GeneID:905846;gbkey=misc_feature;Note=HMMPfam hit to PF00346 2C Respiratory-chain NADH dehydrogenase 2C 2C score 6.6e-104 ### NC_002163.1 RefSeq CDS 1508131 1508925 . - 0 ID=cds1429;Parent=gene1509;gene=nuoC;Name=YP_002344946.1;Dbxref=GOA:Q0P851 InterPro:IPR001268 InterPro:IPR010218 UniProtKB FTrEMBL:Q0P851 Genbank:YP_002344946.1 GeneID:905847;gbkey=CDS;product=NADH dehydrogenase subunit C;Note=Catalyzes the transfer of electrons from NADH to ubiquinone NC_002163.1 RefSeq gene 1508131 1508925 . - . ID=gene1509;gene=nuoC;Name=nuoC;locus_tag=Cj1577c;Dbxref=GeneID:905847;gbkey=Gene NC_002163.1 RefSeq region 1508377 1508580 . - . ID=id2763;gene=nuoC;Name=id2763;Dbxref=GeneID:905847;gbkey=misc_feature;Note=HMMPfam hit to PF00329 2C Respiratory-chain NADH dehydrogenase 2C 2C score 1.7e-36 NC_002163.1 RefSeq region 1508443 1508508 . - . ID=id2764;gene=nuoC;Name=id2764;Dbxref=GeneID:905847;gbkey=misc_feature;Note=PS00542 Respiratory chain NADH dehydrogenase 30 Kd subunit signature NC_002163.1 RefSeq CDS 1508922 1509425 . - 0 ID=cds1430;Parent=gene1510;gene=nuoB;Name=YP_002344947.1;Dbxref=GOA:Q0P850 InterPro:IPR006137 InterPro:IPR006138 InterPro:IPR014406 UniProtKB FTrEMBL:Q0P850 Genbank:YP_002344947.1 GeneID:905848;gbkey=CDS;product=NADH dehydrogenase subunit B;Note=The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen NC_002163.1 RefSeq gene 1508922 1509425 . - . ID=gene1510;gene=nuoB;Name=nuoB;locus_tag=Cj1578c;Dbxref=GeneID:905848;gbkey=Gene NC_002163.1 RefSeq region 1508979 1509299 . - . ID=id2765;gene=nuoB;Name=id2765;Dbxref=GeneID:905848;gbkey=misc_feature;Note=HMMPfam hit to PF01058 2C NADH ubiquinone oxidoreductase 2C 20 Kd sub 2C score 1.1e-56 NC_002163.1 RefSeq gene 1509407 1509796 . - . ID=gene1511;gene=nuoA;Name=nuoA;locus_tag=Cj1579c;Dbxref=GeneID:905849;gbkey=Gene NC_002163.1 RefSeq CDS 1509407 1509796 . - 0 ID=cds1431;Parent=gene1511;gene=nuoA;Name=YP_002344948.1;Dbxref=GOA:Q0P849 InterPro:IPR000440 UniProtKB FTrEMBL:Q0P849 Genbank:YP_002344948.1 GeneID:905849;gbkey=CDS;product=NADH dehydrogenase subunit A;Note=Catalyzes the transfer of electrons from NADH to ubiquinone NC_002163.1 RefSeq region 1509422 1509646 . - . ID=id2766;gene=nuoA;Name=id2766;Dbxref=GeneID:905849;gbkey=misc_feature;Note=HMMPfam hit to PF00507 2CNADH-ubiquinone 2Fplastoquinone oxidoreduct 2C score 6.6e-17 NC_002163.1 RefSeq region 1509443 1509511 . - . ID=id141;gene=nuoA;Name=id141;Dbxref=GeneID:905849;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1579c by TMHMM2.0 at aa 10-32 2C 69-91 and 96-118 NC_002163.1 RefSeq region 1509524 1509592 . - . ID=id141;gene=nuoA;Name=id141;Dbxref=GeneID:905849;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1579c by TMHMM2.0 at aa 10-32 2C 69-91 and 96-118 NC_002163.1 RefSeq region 1509701 1509769 . - . ID=id141;gene=nuoA;Name=id141;Dbxref=GeneID:905849;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1579c by TMHMM2.0 at aa 10-32 2C 69-91 and 96-118 ### NC_002163.1 UTR_Extractor 5'-UTR 1509797 1509860 . - . ID=utr575;locus_tag=Cj1579c;product=NADH dehydrogenase subunit A NC_002163.1 RefSeq CDS 1509909 1510574 . - 0 ID=cds1432;Parent=gene1512;Name=YP_002344949.1;Dbxref=GOA:Q0P848 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FTrEMBL:Q0P848 Genbank:YP_002344949.1 GeneID:905850;gbkey=CDS;product=peptide ABC transporter ATP-binding protein;Note=Original 282000 29 note: Cj1580c 2C probable peptide ABC-transport system ATP-binding protein 2C len: 221 aa 3B similar to e.g. DPPF_ECOLI dipeptide transport ATP-binding protein 28334 aa 29 2C fasta scores 3B opt: 436 z-score: 498.1 E 28 29: 2e-20 2C 34.8 25 identity in 210 aa overlap 2C and APPF_BACSU oligopeptide transport ATP-binding protein 28329 aa 29 2C fasta scores 3B opt: 419 z-score: 479.2 E 28 29: 2.3e-19 2C30.8 25 identity in 211 aa overlap. 30.6 25 identity to HP0302. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00211 ABC transporters family signature 2C and Pfam match to entry PF00005 ABC_tran 2C ABC transporters 7EUpdated 282006 29 note: Similar to different transport systems with acceptable identity scores. kept within product function. Functional classification -Transport 2Fbinding proteins - Other NC_002163.1 RefSeq gene 1509909 1510574 . - . ID=gene1512;Name=Cj1580c;locus_tag=Cj1580c;Dbxref=GeneID:905850;gbkey=Gene NC_002163.1 RefSeq region 1509912 1510466 . - . ID=id2767;Name=id2767;Dbxref=GeneID:905850;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 1.6e-35 NC_002163.1 RefSeq region 1510089 1510133 . - . ID=id2768;Name=id2768;Dbxref=GeneID:905850;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq region 1510422 1510445 . - . ID=id2769;Name=id2769;Dbxref=GeneID:905850;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 1510567 1511277 . - 0 ID=cds1433;Parent=gene1513;Name=YP_002344950.1;Dbxref=GOA:Q0P847 InterPro:IPR002078 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FTrEMBL:Q0P847 Genbank:YP_002344950.1 GeneID:905851;gbkey=CDS;product=peptide ABC transporter ATP-binding protein;Note=Original 282000 29 note: Cj1581c 2C probable peptide ABC-transport system ATP-binding protein 2C len: 236 aa 3B similar to e.g. OPPD_ECOLI oligopeptide transport ATP-binding protein 28337 aa 29 2C fasta scores opt: 385 z-score: 442.8 E 28 29: 2.4e-17 2C 31.5 25 identity in 232 aa overlap. 29.8 25 identity to HP0301. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00211 ABC transporters family signature 2C and Pfam match to entry PF00005 ABC_tran 2C ABC transporters 7EUpdated 282006 29 note: Similar to different transport systems with acceptable identity scores. kept within product function. Functional classification -Transport 2Fbinding proteins - Other NC_002163.1 RefSeq gene 1510567 1511277 . - . ID=gene1513;Name=Cj1581c;locus_tag=Cj1581c;Dbxref=GeneID:905851;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 1510575 1510848 . - . ID=utr576;locus_tag=Cj1580c;product=putative peptide ABC transporter ATP-binding protein NC_002163.1 RefSeq region 1510618 1511202 . - . ID=id2770;Name=id2770;Dbxref=GeneID:905851;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 1.5e-29 NC_002163.1 RefSeq region 1510798 1510842 . - . ID=id2771;Name=id2771;Dbxref=GeneID:905851;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq region 1511152 1511193 . - . ID=id2772;Name=id2772;Dbxref=GeneID:905851;gbkey=misc_feature;Note=PS00675 Sigma-54 interaction domain ATP-binding region A signature NC_002163.1 RefSeq region 1511158 1511181 . - . ID=id2773;Name=id2773;Dbxref=GeneID:905851;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 1511274 1512068 . - 0 ID=cds1434;Parent=gene1514;Name=YP_002344951.1;Dbxref=GOA:Q0P846 InterPro:IPR000515 UniProtKB FTrEMBL:Q0P846 Genbank:YP_002344951.1 GeneID:905852;gbkey=CDS;product=peptide ABC transporter permease;Note=Original 282000 29 note: Cj1582c 2C probable peptide ABC-transport system permease 2C len: 264 aa 3B similar to e.g. PPC_BACSU oligopeptide transport permease 28303 aa 29 2C fasta scores 3B opt: 397 z-score: 467.3 E 28 29: 1e-18 2C 29.1 25 identity in 261 aa overlap. 26.3 25 identity to HP0300. Contains Pfam match to entry PF00528 BPD_transp 2C Binding-protein-dependent transport systems inner membrane component 7EUpdated 282006 29 note: Six probable transmembrane helices predicted by TMHMM2.0. Similar to different transport systems with acceptable identity scores. kept within product function. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:16045618 NC_002163.1 RefSeq gene 1511274 1512068 . - . ID=gene1514;Name=Cj1582c;locus_tag=Cj1582c;Dbxref=GeneID:905852;gbkey=Gene NC_002163.1 RefSeq region 1511277 1511873 . - . ID=id2774;Name=id2774;Dbxref=GeneID:905852;gbkey=misc_feature;Note=HMMPfam hit to PF00528 2C Binding-protein-dependent transport syst 2C score 3.9e-14 NC_002163.1 RefSeq region 1511310 1511378 . - . ID=id142;Name=id142;Dbxref=GeneID:905852;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1582c by TMHMM2.0 at aa 7-29 2C 69-91 2C 103-122 2C 126-145 2C176-198 and 231-253 NC_002163.1 RefSeq region 1511475 1511543 . - . ID=id142;Name=id142;Dbxref=GeneID:905852;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1582c by TMHMM2.0 at aa 7-29 2C 69-91 2C 103-122 2C 126-145 2C176-198 and 231-253 NC_002163.1 RefSeq region 1511634 1511693 . - . ID=id142;Name=id142;Dbxref=GeneID:905852;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1582c by TMHMM2.0 at aa 7-29 2C 69-91 2C 103-122 2C 126-145 2C176-198 and 231-253 NC_002163.1 RefSeq region 1511703 1511762 . - . ID=id142;Name=id142;Dbxref=GeneID:905852;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1582c by TMHMM2.0 at aa 7-29 2C 69-91 2C 103-122 2C 126-145 2C176-198 and 231-253 NC_002163.1 RefSeq region 1511796 1511864 . - . ID=id142;Name=id142;Dbxref=GeneID:905852;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1582c by TMHMM2.0 at aa 7-29 2C 69-91 2C 103-122 2C 126-145 2C176-198 and 231-253 NC_002163.1 RefSeq region 1511982 1512050 . - . ID=id142;Name=id142;Dbxref=GeneID:905852;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1582c by TMHMM2.0 at aa 7-29 2C 69-91 2C 103-122 2C 126-145 2C176-198 and 231-253 NC_002163.1 RefSeq CDS 1512055 1512999 . - 0 ID=cds1435;Parent=gene1515;Name=YP_002344952.1;Dbxref=GOA:Q0P845 InterPro:IPR000515 UniProtKB FTrEMBL:Q0P845 Genbank:YP_002344952.1 GeneID:905853;gbkey=CDS;product=peptide ABC transporter permease;Note=Original 282000 29 note: Cj1583c 2C probable peptide ABC-transport system permease 2C len: 314 aa 3B similar to e.g. OPPB_LACLC oligopeptide transport system permease 28319 aa 29 2C fasta scores 3B opt: 476 z-score: 540.7 E 28 29: 8.5e-23 2C 28.4 25 identity in 317 aa overlap. 24.1 25 identity to HP0299 7EUpdated 282006 29 note: Six probable transmembrane helices predicted by TMHMM2.0. Pfam domain PF00528 Binding-protein-dependent transport system inner membrane component identified within CDS. Similar to different transport systems with acceptable identity scores. kept within product function. Functional classification - Transport 2Fbinding proteins - Other NC_002163.1 RefSeq gene 1512055 1512999 . - . ID=gene1515;Name=Cj1583c;locus_tag=Cj1583c;Dbxref=GeneID:905853;gbkey=Gene NC_002163.1 RefSeq region 1512070 1512729 . - . ID=id2775;Name=id2775;Dbxref=GeneID:905853;gbkey=misc_feature;Note=HMMPfam hit to PF00528 2C Binding-protein-dependent transport syst 2C score 2.8e-47 NC_002163.1 RefSeq region 1512100 1512168 . - . ID=id143;Name=id143;Dbxref=GeneID:905853;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1583c by TMHMM2.0 at aa 5-24 2C 96-118 2C 131-153 2C 179-198 2C236-258 and 278-300 NC_002163.1 RefSeq region 1512226 1512294 . - . ID=id143;Name=id143;Dbxref=GeneID:905853;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1583c by TMHMM2.0 at aa 5-24 2C 96-118 2C 131-153 2C 179-198 2C236-258 and 278-300 NC_002163.1 RefSeq region 1512406 1512465 . - . ID=id143;Name=id143;Dbxref=GeneID:905853;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1583c by TMHMM2.0 at aa 5-24 2C 96-118 2C 131-153 2C 179-198 2C236-258 and 278-300 NC_002163.1 RefSeq region 1512541 1512609 . - . ID=id143;Name=id143;Dbxref=GeneID:905853;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1583c by TMHMM2.0 at aa 5-24 2C 96-118 2C 131-153 2C 179-198 2C236-258 and 278-300 NC_002163.1 RefSeq region 1512646 1512714 . - . ID=id143;Name=id143;Dbxref=GeneID:905853;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1583c by TMHMM2.0 at aa 5-24 2C 96-118 2C 131-153 2C 179-198 2C236-258 and 278-300 NC_002163.1 RefSeq region 1512928 1512987 . - . ID=id143;Name=id143;Dbxref=GeneID:905853;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1583c by TMHMM2.0 at aa 5-24 2C 96-118 2C 131-153 2C 179-198 2C236-258 and 278-300 NC_002163.1 RefSeq CDS 1512999 1514534 . - 0 ID=cds1436;Parent=gene1516;Name=YP_002344953.1;Dbxref=GOA:Q0P844 InterPro:IPR000914 InterPro:IPR002052 UniProtKB FTrEMBL:Q0P844 Genbank:YP_002344953.1 GeneID:905854;gbkey=CDS;product=peptide ABC transporter substrate-binding protein;Note=Original 282000 29 note: Cj1584c 2C probable peptide ABC-transport system periplasmic peptide-binding protein 2Clen: 511 aa 3B similar to e.g. APPA_BACSU oligopeptide-binding protein APPA precursor 28543 aa 29 2Cfasta scores 3B opt: 700 z-score: 791.8 E 28 29: 0 2C 30.5 25 identity in 509 aa overlap. 26.7 25 identity to HP0298. Contains probable N-terminal signal sequence and Pfam match to entry PF00496 SBP_bac_5 2C Bacterial extracellular solute-binding proteins 2C family 5 7EUpdated 282006 29 note: Prosite domain PS00092 N6_MTASE 2C N-6 Adenine-specific DNA methylases signature identified within CDS. Similar to different transport systems with acceptable identity scores. kept within product function. Functional classification -Transport 2Fbinding proteins - Other NC_002163.1 RefSeq gene 1512999 1514534 . - . ID=gene1516;Name=Cj1584c;locus_tag=Cj1584c;Dbxref=GeneID:905854;gbkey=Gene NC_002163.1 RefSeq region 1513122 1513142 . - . ID=id2776;Name=id2776;Dbxref=GeneID:905854;gbkey=misc_feature;Note=PS00092 N-6 Adenine-specific DNA methylases signature NC_002163.1 RefSeq region 1513269 1514351 . - . ID=id2777;Name=id2777;Dbxref=GeneID:905854;gbkey=misc_feature;Note=HMMPfam hit to PF00496 2C Bacterial extracellular solute-binding prot 2C score 7.9e-72 ### NC_002163.1 RefSeq CDS 1514644 1517415 . - 0 ID=cds1437;Parent=gene1517;Name=YP_002344954.1;Dbxref=GOA:Q0P843 InterPro:IPR001450 InterPro:IPR004113 InterPro:IPR006094 InterPro:IPR006655 InterPro:IPR012285 InterPro:IPR016167 UniProtKB FTrEMBL:Q0P843 Genbank:YP_002344954.1 GeneID:905855;gbkey=CDS;product=oxidoreductase;Note=Original 282000 29 note: Cj1585c 2C probable oxidoreductase 2C len: 923 aa 3B similar to e.g. YDIJ_ECOLI 281018 aa 29 2C fasta scores 3B opt: 299 z-score: 326.0 E 28 29: 7.7e-11 2C 24.0 25 identity in 668 aa overlap 2C and GLCD_ECOLI glycolate oxidase subunit GLCD 28499 aa 29 2C fasta scores 3B opt: 258 z-score: 285.3 E 28 29: 1.4e-08 2C 23.4 25 identity in 483 aa overlap. 49.2 25 identity to HP1222 28misannotated as D-lactate dehydrogenase 29. Contains PS00551 Prokaryotic molybdopterin oxidoreductases signature 1 2C ands 2x PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature 7EUpdated 282006 29 note: Pfam domains PF02913 FAD linked oxidases 2C C-terminal domain and PF01565 FAD binding domain were identified within CDS. Not specifically characterised with acceptable identity score. Thus 2C kept within product function. Literature search identified paper giving further support to product function. Functional classification - Misc 7EPMID:15292134 NC_002163.1 RefSeq gene 1514644 1517415 . - . ID=gene1517;Name=Cj1585c;locus_tag=Cj1585c;Dbxref=GeneID:905855;gbkey=Gene NC_002163.1 RefSeq region 1515574 1515627 . - . ID=id2778;Name=id2778;Dbxref=GeneID:905855;gbkey=misc_feature;Note=PS00551 Prokaryotic molybdopterin oxidoreductases signature 1 NC_002163.1 RefSeq region 1515595 1515630 . - . ID=id2779;Name=id2779;Dbxref=GeneID:905855;gbkey=misc_feature;Note=PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature NC_002163.1 RefSeq region 1515757 1515828 . - . ID=id2780;Name=id2780;Dbxref=GeneID:905855;gbkey=misc_feature;Note=HMMPfam hit to PF00037 2C 4Fe-4S binding domain 2Cscore 0.0085 NC_002163.1 RefSeq region 1515772 1515807 . - . ID=id2781;Name=id2781;Dbxref=GeneID:905855;gbkey=misc_feature;Note=PS00198 4Fe-4S ferredoxins 2C iron-sulfur binding region signature NC_002163.1 RefSeq region 1515880 1516626 . - . ID=id2782;Name=id2782;Dbxref=GeneID:905855;gbkey=misc_feature;Note=HMMPfam hit to PF02913 2C FAD linked oxidases 2CC-terminal domain 2C score 1.6e-70 NC_002163.1 RefSeq region 1516666 1517298 . - . ID=id2783;Name=id2783;Dbxref=GeneID:905855;gbkey=misc_feature;Note=HMMPfam hit to PF01565 2C FAD binding domain 2C score 3.3e-39 ### NC_002163.1 UTR_Extractor 5'-UTR 1517416 1517436 . - . ID=utr577;locus_tag=Cj1585c;product=putative oxidoreductase NC_002163.1 UTR_Extractor 5'-UTR 1517542 1517566 . + . ID=utr578;locus_tag=Cj1586;product=single domain haemoglobin NC_002163.1 RefSeq gene 1517567 1517989 . + . ID=gene1518;gene=cgb;Name=cgb;locus_tag=Cj1586;Dbxref=GeneID:905856;gbkey=Gene NC_002163.1 RefSeq CDS 1517567 1517989 . + 0 ID=cds1438;Parent=gene1518;gene=cgb;Name=YP_002344955.1;Dbxref=GOA:Q0P842 InterPro:IPR000971 InterPro:IPR012292 UniProtKB FTrEMBL:Q0P842 Genbank:YP_002344955.1 GeneID:905856;gbkey=CDS;product=single domain hemoglobin;Note=Original 282000 29 note: Cj1586 2C probable bacterial haemoglobin 2C len: 140 aa 3B similar to e.g. BAHG_VITST bacterial hemoglobin 28soluble cytochrome O 29 28146 aa 29 2Cfasta scores 3B opt: 417 z-score: 527.0 E 28 29: 4.9e-22 2C 49.6 25 identity in 141 aa overlap. No Hp match. Contains Pfam match to entry PF00042 globin 7EUpdated 282006 29 note: Characterised within Campylobacter jejuni. Cgb protein plays a role in detoxification of NO and related compounds. NssR 28Nitrosative stress sensing Regulator - Cj0466 29 controls the expression of a nitrosative stress-responsive regulon in Campylobacter jejuni which includes ctb 28Cj0465c 29 and cgb 28Cj1586 29. not added to product function. Functional classification - Energy metabolism - Electron transport 7EPMID:16045618 2C PMID:15292134 2C PMID:16339953 2CPMID:16681372 NC_002163.1 RefSeq region 1517579 1517956 . + . ID=id2784;gene=cgb;Name=id2784;Dbxref=GeneID:905856;gbkey=misc_feature;Note=HMMPfam hit to PF00042 2C Globin 2C score 3.3e-12 ### NC_002163.1 RefSeq CDS 1518009 1519640 . - 0 ID=cds1439;Parent=gene1519;Name=YP_002344956.1;Dbxref=GOA:Q0P841 InterPro:IPR003439 InterPro:IPR003593 InterPro:IPR005898 InterPro:IPR011527 UniProtKB FTrEMBL:Q0P841 Genbank:YP_002344956.1 GeneID:905857;gbkey=CDS;product=multidrug transporter membrane protein 2FATP-binding protein;Note=efflux pump for the antibacterial peptide microcin J25 NC_002163.1 RefSeq gene 1518009 1519640 . - . ID=gene1519;Name=Cj1587c;locus_tag=Cj1587c;Dbxref=GeneID:905857;gbkey=Gene NC_002163.1 RefSeq region 1518078 1518605 . - . ID=id2785;Name=id2785;Dbxref=GeneID:905857;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 6.3e-33 NC_002163.1 RefSeq region 1518561 1518584 . - . ID=id2786;Name=id2786;Dbxref=GeneID:905857;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 1518810 1519619 . - . ID=id2787;Name=id2787;Dbxref=GeneID:905857;gbkey=misc_feature;Note=HMMPfam hit to PF00664 2C ABC transporter transmembrane region 2C score 0.00019 NC_002163.1 RefSeq region 1519161 1519229 . - . ID=id144;Name=id144;Dbxref=GeneID:905857;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1587c by TMHMM2.0 at aa 13-35 2C 50-72 and 138-160 NC_002163.1 RefSeq region 1519425 1519493 . - . ID=id144;Name=id144;Dbxref=GeneID:905857;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1587c by TMHMM2.0 at aa 13-35 2C 50-72 and 138-160 NC_002163.1 RefSeq region 1519536 1519604 . - . ID=id144;Name=id144;Dbxref=GeneID:905857;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1587c by TMHMM2.0 at aa 13-35 2C 50-72 and 138-160 ### NC_002163.1 UTR_Extractor 5'-UTR 1519641 1519661 . - . ID=utr579;locus_tag=Cj1587c;product=multidrug transporter membrane component 2FATP-binding component NC_002163.1 RefSeq CDS 1519690 1520985 . - 0 ID=cds1440;Parent=gene1520;Name=YP_002344957.1;Dbxref=GOA:Q0P840 InterPro:IPR005829 InterPro:IPR007114 InterPro:IPR011701 UniProtKB FTrEMBL:Q0P840 Genbank:YP_002344957.1 GeneID:905858;gbkey=CDS;product=MFS transport protein;Note=Original 282000 29 note: Cj1588c 2C probable transmembrane transport protein 2C len: 431 aa 3B similar to e.g. YHJE_ECOLI hypothetical metabolite transport protein 28440 aa 29 2C fasta scores 3B opt: 682 z-score: 771.4 E 28 29: 0 2C28.9 25 identity in 422 aa overlap 2C and PROP_ECOLI proline 2Fbetaine transporter 28proline porter II 29 28500 aa 29 2Cfasta scores 3B opt: 655 z-score: 740.4 E 28 29: 0 2C 30.1 25 identity in 415 aa overlap. No Hp ortholog. Contains PS00217 Sugar transport proteins signature 2 2C and Pfam match to entry PF00083 sugar_tr 2C Sugar 28and other 29 transporters 7EUpdated 282006 29 note: Pfam domain PF07690 Major Facilitator Superfamily identified within CDS. Also 2Ctwelve probable transmembrane helices predicted by TMHMM2.0. Not specifically characterised yet with acceptable identity score. Product function modified based on motif match. kept within product function. Functional classification - Transport 2Fbinding proteins -Other NC_002163.1 RefSeq gene 1519690 1520985 . - . ID=gene1520;Name=Cj1588c;locus_tag=Cj1588c;Dbxref=GeneID:905858;gbkey=Gene NC_002163.1 RefSeq region 1519696 1520949 . - . ID=id2788;Name=id2788;Dbxref=GeneID:905858;gbkey=misc_feature;Note=HMMPfam hit to PF00083 2C Sugar 28and other 29 transporter 2C score 2e-19 NC_002163.1 RefSeq region 1519708 1519776 . - . ID=id145;Name=id145;Dbxref=GeneID:905858;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1588c by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-107 2C 117-139 2C151-173 2C 183-205 2C 241-263 2C 278-300 2C 305-327 2C 332-354 2C367-389 and 404-426 NC_002163.1 RefSeq region 1519804 1520913 . - . ID=id2789;Name=id2789;Dbxref=GeneID:905858;gbkey=misc_feature;Note=HMMPfam hit to PF07690 2C Major Facilitator Superfamily 2C score 4.4e-21 NC_002163.1 RefSeq region 1519819 1519887 . - . ID=id145;Name=id145;Dbxref=GeneID:905858;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1588c by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-107 2C 117-139 2C151-173 2C 183-205 2C 241-263 2C 278-300 2C 305-327 2C 332-354 2C367-389 and 404-426 NC_002163.1 RefSeq region 1519924 1519992 . - . ID=id145;Name=id145;Dbxref=GeneID:905858;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1588c by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-107 2C 117-139 2C151-173 2C 183-205 2C 241-263 2C 278-300 2C 305-327 2C 332-354 2C367-389 and 404-426 NC_002163.1 RefSeq region 1520005 1520073 . - . ID=id145;Name=id145;Dbxref=GeneID:905858;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1588c by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-107 2C 117-139 2C151-173 2C 183-205 2C 241-263 2C 278-300 2C 305-327 2C 332-354 2C367-389 and 404-426 NC_002163.1 RefSeq region 1520086 1520154 . - . ID=id145;Name=id145;Dbxref=GeneID:905858;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1588c by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-107 2C 117-139 2C151-173 2C 183-205 2C 241-263 2C 278-300 2C 305-327 2C 332-354 2C367-389 and 404-426 NC_002163.1 RefSeq region 1520197 1520265 . - . ID=id145;Name=id145;Dbxref=GeneID:905858;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1588c by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-107 2C 117-139 2C151-173 2C 183-205 2C 241-263 2C 278-300 2C 305-327 2C 332-354 2C367-389 and 404-426 NC_002163.1 RefSeq region 1520221 1520253 . - . ID=id2790;Name=id2790;Dbxref=GeneID:905858;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1520371 1520439 . - . ID=id145;Name=id145;Dbxref=GeneID:905858;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1588c by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-107 2C 117-139 2C151-173 2C 183-205 2C 241-263 2C 278-300 2C 305-327 2C 332-354 2C367-389 and 404-426 NC_002163.1 RefSeq region 1520467 1520535 . - . ID=id145;Name=id145;Dbxref=GeneID:905858;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1588c by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-107 2C 117-139 2C151-173 2C 183-205 2C 241-263 2C 278-300 2C 305-327 2C 332-354 2C367-389 and 404-426 NC_002163.1 RefSeq region 1520539 1520616 . - . ID=id2791;Name=id2791;Dbxref=GeneID:905858;gbkey=misc_feature;Note=PS00217 Sugar transport proteins signature 2 NC_002163.1 RefSeq region 1520569 1520637 . - . ID=id145;Name=id145;Dbxref=GeneID:905858;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1588c by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-107 2C 117-139 2C151-173 2C 183-205 2C 241-263 2C 278-300 2C 305-327 2C 332-354 2C367-389 and 404-426 NC_002163.1 RefSeq region 1520665 1520733 . - . ID=id145;Name=id145;Dbxref=GeneID:905858;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1588c by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-107 2C 117-139 2C151-173 2C 183-205 2C 241-263 2C 278-300 2C 305-327 2C 332-354 2C367-389 and 404-426 NC_002163.1 RefSeq region 1520770 1520838 . - . ID=id145;Name=id145;Dbxref=GeneID:905858;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1588c by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-107 2C 117-139 2C151-173 2C 183-205 2C 241-263 2C 278-300 2C 305-327 2C 332-354 2C367-389 and 404-426 NC_002163.1 RefSeq region 1520881 1520949 . - . ID=id145;Name=id145;Dbxref=GeneID:905858;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1588c by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-107 2C 117-139 2C151-173 2C 183-205 2C 241-263 2C 278-300 2C 305-327 2C 332-354 2C367-389 and 404-426 ### NC_002163.1 UTR_Extractor 5'-UTR 1520986 1521015 . - . ID=utr580;locus_tag=Cj1588c;product=putative MFS transport protein NC_002163.1 RefSeq gene 1521072 1521869 . + . ID=gene1521;Name=Cj1589;locus_tag=Cj1589;Dbxref=GeneID:905859;gbkey=Gene NC_002163.1 RefSeq CDS 1521072 1521869 . + 0 ID=cds1441;Parent=gene1521;Name=YP_002344958.1;Dbxref=GOA:Q0P839 InterPro:IPR001279 UniProtKB FTrEMBL:Q0P839 Genbank:YP_002344958.1 GeneID:905859;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1589 2C unknown 2C len: 265 aa 3B some similarity to TR:O34910 28EMBL:AF027868 29 Bacillus subtilis YOBT 28233 aa 29 2C fasta scores 3B opt: 178 z-score: 211.5 E 28 29: 0.00019 2C 27.6 25 identity in 203 aa overlap. No Hp match. Contains Pfam match to entry PF00753 lactamase_B 2C Metallo-beta-lactamase superfamily. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq region 1521279 1521836 . + . ID=id2792;Name=id2792;Dbxref=GeneID:905859;gbkey=misc_feature;Note=HMMPfam hit to PF00753 2C Metallo-beta-lactamase superfamily 2C score 1.1e-20 ### NC_002163.1 UTR_Extractor 5'-UTR 1521930 1521956 . + . ID=utr581;locus_tag=Cj1590;product=translation initiation factor IF-1 NC_002163.1 RefSeq gene 1521957 1522175 . + . ID=gene1522;gene=infA;Name=infA;locus_tag=Cj1590;Dbxref=GeneID:905860;gbkey=Gene NC_002163.1 RefSeq CDS 1521957 1522175 . + 0 ID=cds1442;Parent=gene1522;gene=infA;Name=YP_002344959.1;Dbxref=GOA:Q9PM85 HSSP:P02998 InterPro:IPR003029 InterPro:IPR004368 InterPro:IPR006196 InterPro:IPR012340 UniProtKB FSwiss-Prot:Q9PM85 Genbank:YP_002344959.1 GeneID:905860;gbkey=CDS;product=translation initiation factor IF-1;Note=stimulates the activities of the other two initiation factors 2C IF-2 and IF-3 NC_002163.1 RefSeq region 1521960 1522172 . + . ID=id2793;gene=infA;Name=id2793;Dbxref=GeneID:905860;gbkey=misc_feature;Note=HMMPfam hit to PF00575 2C S1 RNA binding domain 2Cscore 1.1e-10 ### NC_002163.1 UTR_Extractor 5'-UTR 1522215 1522346 . + . ID=utr582;locus_tag=Cj1591;product=50S ribosomal protein L36 NC_002163.1 RefSeq region 1522347 1522457 . + . ID=id2794;gene=rpmJ;Name=id2794;Dbxref=GeneID:905861;gbkey=misc_feature;Note=HMMPfam hit to PF00444 2C Ribosomal protein L36 2Cscore 7.5e-17 NC_002163.1 RefSeq gene 1522347 1522460 . + . ID=gene1523;gene=rpmJ;Name=rpmJ;locus_tag=Cj1591;Dbxref=GeneID:905861;gbkey=Gene NC_002163.1 RefSeq CDS 1522347 1522460 . + 0 ID=cds1443;Parent=gene1523;gene=rpmJ;Name=YP_002344960.1;Dbxref=GOA:Q9PM84 HSSP:P80256 InterPro:IPR000473 UniProtKB FSwiss-Prot:Q9PM84 Genbank:YP_002344960.1 GeneID:905861;gbkey=CDS;product=50S ribosomal protein L36;Note=smallest protein in the large subunit 3B similar to what is found with protein L31 and L33 several bacterial genomes contain paralogs which may be regulated by zinc 3B the protein from Thermus thermophilus has a zinc-binding motif and contains a bound zinc ion 3B the proteins in this group have the motif NC_002163.1 RefSeq region 1522377 1522454 . + . ID=id2795;gene=rpmJ;Name=id2795;Dbxref=GeneID:905861;gbkey=misc_feature;Note=PS00828 Ribosomal protein L36 signature ### NC_002163.1 RefSeq CDS 1522463 1522828 . + 0 ID=cds1444;Parent=gene1524;gene=rpsM;Name=YP_002344961.1;Dbxref=GOA:Q9PM83 InterPro:IPR001892 UniProtKB FSwiss-Prot:Q9PM83 Genbank:YP_002344961.1 GeneID:905825;gbkey=CDS;product=30S ribosomal protein S13;Note=located at the top of the head of the 30S subunit 2C it contacts several helices of the 16S rRNA 3B makes contact with the large subunit via RNA-protein interactions and via protein-protein interactions with L5 3B contacts P-site tRNA NC_002163.1 RefSeq gene 1522463 1522828 . + . ID=gene1524;gene=rpsM;Name=rpsM;locus_tag=Cj1592;Dbxref=GeneID:905825;gbkey=Gene NC_002163.1 RefSeq region 1522469 1522789 . + . ID=id2796;gene=rpsM;Name=id2796;Dbxref=GeneID:905825;gbkey=misc_feature;Note=HMMPfam hit to PF00416 2C Ribosomal protein S13 2FS18 2Cscore 1.5e-50 NC_002163.1 RefSeq region 1522724 1522765 . + . ID=id2797;gene=rpsM;Name=id2797;Dbxref=GeneID:905825;gbkey=misc_feature;Note=PS00646 Ribosomal protein S13 signature ### NC_002163.1 RefSeq CDS 1522838 1523230 . + 0 ID=cds1445;Parent=gene1525;gene=rpsK;Name=YP_002344962.1;Dbxref=GOA:Q9PM82 InterPro:IPR001971 UniProtKB FSwiss-Prot:Q9PM82 Genbank:YP_002344962.1 GeneID:905862;gbkey=CDS;product=30S ribosomal protein S11;Note=located on the platform of the 30S subunit 2C it bridges several disparate RNA helices of the 16S rRNA 3B forms part of the Shine-Dalgarno cleft in the 70S ribosome 3B interacts with S7 and S18 and IF-3 NC_002163.1 RefSeq gene 1522838 1523230 . + . ID=gene1525;gene=rpsK;Name=rpsK;locus_tag=Cj1593;Dbxref=GeneID:905862;gbkey=Gene NC_002163.1 RefSeq region 1522892 1523224 . + . ID=id2798;gene=rpsK;Name=id2798;Dbxref=GeneID:905862;gbkey=misc_feature;Note=HMMPfam hit to PF00411 2C Ribosomal protein S11 2Cscore 6.2e-56 NC_002163.1 UTR_Extractor 5'-UTR 1523208 1523257 . + . ID=utr583;locus_tag=Cj1594;product=30S ribosomal protein S4 ### NC_002163.1 RefSeq CDS 1523258 1523884 . + 0 ID=cds1446;Parent=gene1526;gene=rpsD;Name=YP_002344963.1;Dbxref=GOA:Q9PM81 HSSP:P81288 InterPro:IPR001912 InterPro:IPR002942 InterPro:IPR005709 UniProtKB FSwiss-Prot:Q9PM81 Genbank:YP_002344963.1 GeneID:905863;gbkey=CDS;product=30S ribosomal protein S4;Note=primary rRNA binding protein 3B nucleates 30S assembly 3B involved in translational accuracy with proteins S5 and S12 3B interacts with protein S5 3B involved in autogeneously regulating ribosomal proteins by binding to pseudoknot structures in the polycistronic mRNA 3B interacts with transcription complex and functions similar to protein NusA in antitermination NC_002163.1 RefSeq gene 1523258 1523884 . + . ID=gene1526;gene=rpsD;Name=rpsD;locus_tag=Cj1594;Dbxref=GeneID:905863;gbkey=Gene NC_002163.1 RefSeq region 1523261 1523548 . + . ID=id2799;gene=rpsD;Name=id2799;Dbxref=GeneID:905863;gbkey=misc_feature;Note=HMMPfam hit to PF00163 2C Ribosomal protein S4 2FS9 N-terminal domai 2C score 5.4e-25 NC_002163.1 RefSeq region 1523543 1523617 . + . ID=id2800;gene=rpsD;Name=id2800;Dbxref=GeneID:905863;gbkey=misc_feature;Note=PS00632 Ribosomal protein S4 signature NC_002163.1 RefSeq region 1523549 1523692 . + . ID=id2801;gene=rpsD;Name=id2801;Dbxref=GeneID:905863;gbkey=misc_feature;Note=HMMPfam hit to PF01479 2C S4 domain 2C score 1.3e-23 ### NC_002163.1 RefSeq CDS 1523897 1524910 . + 0 ID=cds1447;Parent=gene1527;gene=rpoA;Name=YP_002344964.1;Dbxref=GOA:Q9PM80 HSSP:P00574 InterPro:IPR011260 InterPro:IPR011261 InterPro:IPR011262 InterPro:IPR011263 InterPro:IPR011773 UniProtKB FSwiss-Prot:Q9PM80 Genbank:YP_002344964.1 GeneID:905865;gbkey=CDS;product=DNA-directed RNA polymerase subunit alpha;Note=catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Dimerization of the alpha subunit is the first step in the sequential assembly of subunits to form the holoenzyme NC_002163.1 RefSeq gene 1523897 1524910 . + . ID=gene1527;gene=rpoA;Name=rpoA;locus_tag=Cj1595;Dbxref=GeneID:905865;gbkey=Gene NC_002163.1 RefSeq region 1523957 1524583 . + . ID=id2802;gene=rpoA;Name=id2802;Dbxref=GeneID:905865;gbkey=misc_feature;Note=HMMPfam hit to PF01193 2C RNA polymerase Rpb3 2FRpb11 dimerisation 2C score 3.8e-15 NC_002163.1 RefSeq region 1524071 1524418 . + . ID=id2803;gene=rpoA;Name=id2803;Dbxref=GeneID:905865;gbkey=misc_feature;Note=HMMPfam hit to PF01000 2C RNA polymerase Rpb3 2FRpoA insert domain 2C score 4.9e-43 NC_002163.1 RefSeq region 1524614 1524817 . + . ID=id2804;gene=rpoA;Name=id2804;Dbxref=GeneID:905865;gbkey=misc_feature;Note=HMMPfam hit to PF03118 2C Bacterial RNA polymerase 2Calpha chain C 2C score 1.2e-22 NC_002163.1 UTR_Extractor 5'-UTR 1524701 1524913 . + . ID=utr584;locus_tag=Cj1596;product=50S ribosomal protein L17 ### NC_002163.1 RefSeq CDS 1524914 1525267 . + 0 ID=cds1448;Parent=gene1528;gene=rplQ;Name=YP_002344965.1;Dbxref=GOA:Q0P832 InterPro:IPR000456 UniProtKB FSwiss-Prot:Q0P832 Genbank:YP_002344965.1 GeneID:905866;gbkey=CDS;product=50S ribosomal protein L17;Note=is a component of the macrolide binding site in the peptidyl transferase center NC_002163.1 RefSeq gene 1524914 1525267 . + . ID=gene1528;gene=rplQ;Name=rplQ;locus_tag=Cj1596;Dbxref=GeneID:905866;gbkey=Gene NC_002163.1 RefSeq region 1524971 1525261 . + . ID=id2805;gene=rplQ;Name=id2805;Dbxref=GeneID:905866;gbkey=misc_feature;Note=HMMPfam hit to PF01196 2C Ribosomal protein L17 2Cscore 1.3e-53 NC_002163.1 RefSeq region 1525013 1525081 . + . ID=id2806;gene=rplQ;Name=id2806;Dbxref=GeneID:905866;gbkey=misc_feature;Note=PS01167 Ribosomal protein L17 signature ### NC_002163.1 UTR_Extractor 5'-UTR 1525411 1525439 . + . ID=utr585;locus_tag=Cj1597;product=ATP phosphoribosyltransferase NC_002163.1 RefSeq gene 1525440 1526339 . + . ID=gene1529;gene=hisG;Name=hisG;locus_tag=Cj1597;Dbxref=GeneID:905867;gbkey=Gene NC_002163.1 RefSeq CDS 1525440 1526339 . + 0 ID=cds1449;Parent=gene1529;gene=hisG;Name=YP_002344966.1;Dbxref=GOA:Q9PM78 HSSP:O33256 InterPro:IPR001348 InterPro:IPR013115 InterPro:IPR013820 InterPro:IPR015867 UniProtKB FSwiss-Prot:Q9PM78 Genbank:YP_002344966.1 GeneID:905867;gbkey=CDS;product=ATP phosphoribosyltransferase;Note=long form of enzyme 3B catalyzes the formation of N 27-5 27-phosphoribosyl-ATP from phosphoribosyl pyrophosphate 3B crucial role in histidine biosynthesis 3B forms active dimers and inactive hexamers which is dependent on concentration of substrates and inhibitors NC_002163.1 RefSeq region 1525596 1526102 . + . ID=id2807;gene=hisG;Name=id2807;Dbxref=GeneID:905867;gbkey=misc_feature;Note=HMMPfam hit to PF01634 2C ATP phosphoribosyltransferase 2C score 4.3e-67 ### NC_002163.1 RefSeq CDS 1526347 1527633 . + 0 ID=cds1450;Parent=gene1530;gene=hisD;Name=YP_002344967.1;Dbxref=GOA:Q9PM77 HSSP:P06988 InterPro:IPR001692 InterPro:IPR012131 UniProtKB FSwiss-Prot:Q9PM77 Genbank:YP_002344967.1 GeneID:905868;gbkey=CDS;product=histidinol dehydrogenase;Note=catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis 3B functions as a dimer NC_002163.1 RefSeq gene 1526347 1527633 . + . ID=gene1530;gene=hisD;Name=hisD;locus_tag=Cj1598;Dbxref=GeneID:905868;gbkey=Gene NC_002163.1 RefSeq region 1526386 1527621 . + . ID=id2808;gene=hisD;Name=id2808;Dbxref=GeneID:905868;gbkey=misc_feature;Note=HMMPfam hit to PF00815 2C Histidinol dehydrogenase 2Cscore 1.1e-233 NC_002163.1 RefSeq region 1527025 1527123 . + . ID=id2809;gene=hisD;Name=id2809;Dbxref=GeneID:905868;gbkey=misc_feature;Note=PS00611 Histidinol dehydrogenase signature NC_002163.1 RefSeq region 1527532 1527555 . + . ID=id2810;gene=hisD;Name=id2810;Dbxref=GeneID:905868;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq CDS 1527630 1528688 . + 0 ID=cds1451;Parent=gene1531;gene=hisB;Name=YP_002344968.1;Dbxref=GOA:Q9PM76 InterPro:IPR000807 InterPro:IPR005954 InterPro:IPR006543 InterPro:IPR006549 InterPro:IPR013954 UniProtKB FSwiss-Prot:Q9PM76 Genbank:YP_002344968.1 GeneID:905869;gbkey=CDS;product=imidazole glycerol-phosphate dehydratase 2Fhistidinol phosphatase;Note=catalyzes the formation of 3- 28imidazol-4-yl 29-2-oxopropyl phosphate from D-ethythro-1- 28imidazol-4-yl 29glycerol 3-phosphate and histidinol from histidinol phosphate NC_002163.1 RefSeq gene 1527630 1528688 . + . ID=gene1531;gene=hisB;Name=hisB;locus_tag=Cj1599;Dbxref=GeneID:905869;gbkey=Gene NC_002163.1 RefSeq region 1528206 1528634 . + . ID=id2811;gene=hisB;Name=id2811;Dbxref=GeneID:905869;gbkey=misc_feature;Note=HMMPfam hit to PF00475 2C Imidazoleglycerol-phosphate dehydratase 2C score 7e-88 NC_002163.1 RefSeq region 1528296 1528337 . + . ID=id2812;gene=hisB;Name=id2812;Dbxref=GeneID:905869;gbkey=misc_feature;Note=PS00954 Imidazoleglycerol-phosphate dehydratase signature 1 NC_002163.1 RefSeq region 1528575 1528613 . + . ID=id2813;gene=hisB;Name=id2813;Dbxref=GeneID:905869;gbkey=misc_feature;Note=PS00955 Imidazoleglycerol-phosphate dehydratase signature 2 NC_002163.1 RefSeq CDS 1528685 1529272 . + 0 ID=cds1452;Parent=gene1532;gene=hisH;Name=YP_002344969.1;Dbxref=GOA:Q9PM75 HSSP:P33734 InterPro:IPR000991 InterPro:IPR006220 InterPro:IPR010139 InterPro:IPR011702 InterPro:IPR012998 InterPro:IPR016226 UniProtKB FSwiss-Prot:Q9PM75 Genbank:YP_002344969.1 GeneID:904385;gbkey=CDS;product=imidazole glycerol phosphate synthase subunit HisH;Note=with HisF IGPS catalyzes the conversion of phosphoribulosyl-formimino-5-aminoimidazole-4-carboxamide ribonucleotide phosphate and glutamine to imidazole-glycerol phosphate 2C 5-aminoimidazol-4-carboxamide ribonucleotide 2C and glutamate in histidine biosynthesis 3B the HisH subunit provides the glutamine amidotransferase activity that produces the ammonia necessary to HisF for the synthesis of imidazole-glycerol phosphate and 5-aminoimidazol-4-carboxamide ribonucleotide NC_002163.1 RefSeq gene 1528685 1529272 . + . ID=gene1532;gene=hisH;Name=hisH;locus_tag=Cj1600;Dbxref=GeneID:904385;gbkey=Gene NC_002163.1 RefSeq region 1528694 1529266 . + . ID=id2814;gene=hisH;Name=id2814;Dbxref=GeneID:904385;gbkey=misc_feature;Note=HMMPfam hit to PF00117 2C Glutamine amidotransferase class-I 2C score 4.8e-34 NC_002163.1 RefSeq region 1528898 1528933 . + . ID=id2815;gene=hisH;Name=id2815;Dbxref=GeneID:904385;gbkey=misc_feature;Note=PS00442 Glutamine amidotransferases class-I active site NC_002163.1 RefSeq CDS 1529269 1530000 . + 0 ID=cds1453;Parent=gene1533;gene=hisA;Name=YP_002344970.1;Dbxref=GOA:Q9PM74 HSSP:Q9X0C7 InterPro:IPR006062 InterPro:IPR006063 InterPro:IPR013785 UniProtKB FSwiss-Prot:Q9PM74 Genbank:YP_002344970.1 GeneID:904505;gbkey=CDS;product=1- 285-phosphoribosyl 29-5- 5B 285-phosphoribosylamino 29methylideneamino 5D imidazole-4-carboxamide isomerase;Note=catalyzes the formation of 5- 285-phospho-1-deoxyribulos-1-ylamino 29methylideneamino-l- 285-phosphoribosyl 29imidazole-4-carboxamide from 1- 285-phosphoribosyl 29-5- 5B 285-phosphoribosylamino 29methylideneamino 5D imidazole-4-carboxamide NC_002163.1 RefSeq gene 1529269 1530000 . + . ID=gene1533;gene=hisA;Name=hisA;locus_tag=Cj1601;Dbxref=GeneID:904505;gbkey=Gene NC_002163.1 RefSeq region 1529275 1529967 . + . ID=id2816;gene=hisA;Name=id2816;Dbxref=GeneID:904505;gbkey=misc_feature;Note=HMMPfam hit to PF00977 2C Histidine biosynthesis protein 2C score 2.9e-103 NC_002163.1 RefSeq region 1529985 1530899 . + . ID=id2817;Name=id2817;Dbxref=GeneID:905870;gbkey=misc_feature;Note=HMMPfam hit to PF04373 2C Protein of unknown function 28DUF511 29 2C score 2.8e-201 NC_002163.1 RefSeq gene 1529985 1530941 . + . ID=gene1534;gene=Cj1602;Name=Cj1602;locus_tag=Cj1602;Dbxref=GeneID:905870;gbkey=Gene NC_002163.1 RefSeq CDS 1529985 1530941 . + 0 ID=cds1454;Parent=gene1534;Name=YP_002344971.1;Dbxref=InterPro:IPR007468 UniProtKB FTrEMBL:Q0P826 Genbank:YP_002344971.1 GeneID:905870;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1602 2C unknown 2C len: 318 aa 3B 35.8 25 identity to HP0852 7EUpdated 282006 29 note: Pfam domain PF04373 Protein of unknown function 28DUF511 29 identified within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins 7EPMID:11956101 2C PMID:15901688 ### NC_002163.1 RefSeq gene 1530942 1531709 . + . ID=gene1535;gene=hisF;Name=hisF;locus_tag=Cj1603;Dbxref=GeneID:905871;gbkey=Gene NC_002163.1 RefSeq CDS 1530942 1531709 . + 0 ID=cds1455;Parent=gene1535;gene=hisF;Name=YP_002344972.1;Dbxref=GOA:Q9PM72 HSSP:Q9X0C6 InterPro:IPR004651 InterPro:IPR006062 InterPro:IPR013785 UniProtKB FSwiss-Prot:Q9PM72 Genbank:YP_002344972.1 GeneID:905871;gbkey=CDS;product=imidazole glycerol phosphate synthase subunit HisF;Note=catalyzes the conversion of 5- 5B 285-phospho-1-deoxyribulos-1-ylamino 29methylideneamino 5D-1- 285-phosphoribosyl 29imidazole-4-carboxamideand glutamine to imidazole-glycerol phosphate 2C 5-aminoimidazol-4-carboxamideribonucleotide and glutamate 3B the HisF subunit acts as a cyclase NC_002163.1 RefSeq region 1530954 1531655 . + . ID=id2818;gene=hisF;Name=id2818;Dbxref=GeneID:905871;gbkey=misc_feature;Note=HMMPfam hit to PF00977 2C Histidine biosynthesis protein 2C score 2.6e-115 ### NC_002163.1 RefSeq CDS 1531711 1532334 . + 0 ID=cds1456;Parent=gene1536;gene=hisI;Name=YP_002344973.1;Dbxref=GOA:Q9PM71 InterPro:IPR002496 InterPro:IPR008179 UniProtKB FSwiss-Prot:Q9PM71 Genbank:YP_002344973.1 GeneID:905159;gbkey=CDS;product=bifunctional phosphoribosyl-AMP cyclohydrolase 2Fphosphoribosyl-ATP pyrophosphatase;Note=catalyzes the formation of 1- 285-phosphoribosyl 29-AMP from 1- 285-phosphoribosyl 29-ATP and the subsequent formation of 1- 285-phosphoribosyl 29-5- 28 285-phosphoribosylamino 29methylideneamino 29imidazole-4-carboxamide from 1- 285-phosphoribosyl 29-AMP in histidine biosynthesis NC_002163.1 RefSeq gene 1531711 1532334 . + . ID=gene1536;gene=hisI;Name=hisI;locus_tag=Cj1604;Dbxref=GeneID:905159;gbkey=Gene NC_002163.1 RefSeq region 1531810 1532034 . + . ID=id2819;gene=hisI;Name=id2819;Dbxref=GeneID:905159;gbkey=misc_feature;Note=HMMPfam hit to PF01502 2C Phosphoribosyl-AMP cyclohydrolase 2C score 5.5e-43 NC_002163.1 RefSeq region 1532062 1532328 . + . ID=id2820;gene=hisI;Name=id2820;Dbxref=GeneID:905159;gbkey=misc_feature;Note=HMMPfam hit to PF01503 2C Phosphoribosyl-ATP pyrophosphohydrolase 2C score 2.6e-44 ### NC_002163.1 RefSeq gene 1532359 1533519 . - . ID=gene1537;gene=dapD;Name=dapD;locus_tag=Cj1605c;Dbxref=GeneID:905872;gbkey=Gene NC_002163.1 RefSeq CDS 1532359 1533519 . - 0 ID=cds1457;Parent=gene1537;gene=dapD;Name=YP_002344974.1;Dbxref=GOA:Q0P823 UniProtKB FTrEMBL:Q0P823 Genbank:YP_002344974.1 GeneID:905872;gbkey=CDS;product=2 2C3 2C4 2C5-tetrahydropyridine-2 2C6-carboxylate N-succinyltransferase;Note=Updated 282006 29 note: Identity score with Escherichia coli was marginal. kept within product function as sequence alignment was partial 7EOriginal 282000 29 note: Cj1605c 2C dapD 2C possible 2 2C3 2C4 2C5-tetrahydropyridine-2-carboxylate N-succinyltransferase 2C len: 386 aa 3B simlar in N-terminus to e.g. TR:O69283 28EMBL:AJ004934 29 Corynebacterium glutamicum tetrahydrodipicolinate succinylase 28EC 2.3.1.117 29 28230 aa 29 2C fasta scores 3B opt: 587 z-score: 643.6 E 28 29: 1.6e-28 2C 47.3 25 identity in 245 aa overlap 2C and weakly similar to DAPD_ECOLI 2 2C3 2C4 2C5-tetrahydropyridine-2-carboxylate N-succinyltransferase 28EC 2.3.1.117 29 28274 aa 29 2C fasta scores 3B opt: 190 z-score: 214.3 E 28 29: 0.00013 2C 27.3 25 identity in 143 aa overlap. 48.5 25 identity to HP0626. Functional classification - Amino acid biosynthesis -Aspartate family NC_002163.1 RefSeq region 1532758 1532790 . - . ID=id2821;gene=dapD;Name=id2821;Dbxref=GeneID:905872;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq CDS 1533545 1534651 . - 0 ID=cds1458;Parent=gene1538;gene=mrp;Name=YP_002344975.1;Dbxref=GOA:Q0P822 InterPro:IPR002744 UniProtKB FTrEMBL:Q0P822 Genbank:YP_002344975.1 GeneID:905873;gbkey=CDS;product=ATP 2FGTP-binding protein;Note=Original 282000 29 note: Cj1606c 2C mrp 2C probable ATP 2FGTP-binding protein 28mrp protein homolog 29 2C len: 368 aa 3B similar to many members of the MRP family e.g. MRP_ECOLI MRP protein 28379 aa 29 2C fasta scores 3B opt: 839 z-score: 921.1 E 28 29: 0 2C 37.1 25 identity in 340 aa overlap. 50.1 25 identity to HP0207. Also similar to Cj0063c 2831.4 25 identity in 159 aa overlap 29. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 7EUpdated 282006 29 note: Pfam domain PF01883 Domain of unknown function DUF59 identified within CDS. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 1533545 1534651 . - . ID=gene1538;gene=mrp;Name=mrp;locus_tag=Cj1606c;Dbxref=GeneID:905873;gbkey=Gene NC_002163.1 RefSeq region 1534316 1534339 . - . ID=id2822;gene=mrp;Name=id2822;Dbxref=GeneID:905873;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 1534430 1534651 . - . ID=id2823;gene=mrp;Name=id2823;Dbxref=GeneID:905873;gbkey=misc_feature;Note=HMMPfam hit to PF01883 2C Domain of unknown function DUF59 2C score 2.9e-05 ### NC_002163.1 UTR_Extractor 5'-UTR 1534652 1534676 . - . ID=utr586;locus_tag=Cj1606c;product=putative ATP 2FGTP-binding protein NC_002163.1 UTR_Extractor 5'-UTR 1534740 1534773 . + . ID=utr587;locus_tag=Cj1607;product=bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2F2-C-methyl-D-erythritol 2 2C4-cyclodiphosphate synthase protein NC_002163.1 RefSeq CDS 1534774 1535889 . + 0 ID=cds1459;Parent=gene1539;gene=ispDF;Name=YP_002344976.1;Dbxref=GOA:Q9PM68 InterPro:IPR001228 InterPro:IPR003526 PDB:1W55 PDB:1W57 UniProtKB FSwiss-Prot:Q9PM68 Genbank:YP_002344976.1 GeneID:905874;gbkey=CDS;product=bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 2F2-C-methyl-D-erythritol 2 2C4-cyclodiphosphate synthase;Note=bifunctional enzyme involved in formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate and 2-C-methyl-D-erythritol 2 2C4-cyclodiphosphate and CMP from 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate 3B involved in isoprenoid and isopentenyl-PP biosynthesis 3B binds divalent cations NC_002163.1 RefSeq gene 1534774 1535889 . + . ID=gene1539;gene=ispDF;Name=ispDF;locus_tag=Cj1607;Dbxref=GeneID:905874;gbkey=Gene NC_002163.1 RefSeq region 1534783 1535373 . + . ID=id2824;gene=ispDF;Name=id2824;Dbxref=GeneID:905874;gbkey=misc_feature;Note=HMMPfam hit to PF01128 2C Uncharacterized protein family UPF0007 2C score 1.3e-11 NC_002163.1 RefSeq region 1535401 1535871 . + . ID=id2825;gene=ispDF;Name=id2825;Dbxref=GeneID:905874;gbkey=misc_feature;Note=HMMPfam hit to PF02542 2C YgbB family 2C score 1.9e-73 NC_002163.1 RefSeq region 1535886 1536218 . + . ID=id2826;Name=id2826;Dbxref=GeneID:905875;gbkey=misc_feature;Note=HMMPfam hit to PF00072 2C Response regulator receiver domain 2C score 8.9e-05 NC_002163.1 RefSeq CDS 1535886 1536773 . + 0 ID=cds1460;Parent=gene1540;Name=YP_002344977.1;Dbxref=GOA:Q0P820 InterPro:IPR001789 InterPro:IPR014483 UniProtKB FTrEMBL:Q0P820 Genbank:YP_002344977.1 GeneID:905875;gbkey=CDS;product=two-component regulator;Note=Original 282000 29 note: Cj1608 2C possible two-component regulator 2C len: 295 aa 2C some similarity to regulatory components of tw-component systems e.g. TR:O87527 28EMBL:AF082668 29 Streptococcus pyogenes capsule synthesis regulator CSRR 28228 aa 29 2C fasta scores 3B opt: 170 z-score: 203.9 E 28 29: 0.00049 2C 35.0 25 identity in 123 aa overlap 2C and BASR_ECOLI transcriptional regulatory protein 28222 aa 29 2C blastp scores 3B E 3D 1.6e-06 29 25 identity in 113 aa overlap. 33.8 25 identity to HP1021. Contains helix-turn-helix motif at aa 271-292 28Score 997 2C 2B2.58 SD 29. Also some similarity to Cj1024c 2822.0 25 identity in 341 aa overlap 29 7EUpdated 282006 29 note: PMID:15901688 7EUpdated 282006 29 note: Pfam domain PF00072 Response regulator receiver domain identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score carried out yet. kept within product function. Literature search identified paper giving further information on product function. Functional classification - Signal transduction 7EPMID:15901688 NC_002163.1 RefSeq gene 1535886 1536773 . + . ID=gene1540;gene=Cj1608;Name=Cj1608;locus_tag=Cj1608;Dbxref=GeneID:905875;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 1536670 1536750 . + . ID=utr588;locus_tag=Cj1609;product=putative sulfate adenylyltransferase NC_002163.1 RefSeq CDS 1536751 1537911 . + 0 ID=cds1461;Parent=gene1541;Name=YP_002344978.1;Dbxref=GOA:Q0P819 InterPro:IPR014729 UniProtKB FTrEMBL:Q0P819 Genbank:YP_002344978.1 GeneID:905876;gbkey=CDS;product=sulfate adenylyltransferase;Note=Original 282000 29 note: Cj1609 2C possible sulfate adenylyltransferase 2C len: 386 aa 3B similar to e.g. TR:O34764 28EMBL: 29 BAcillus subtilis sulfate adenylyltransferase 28382 aa 29 2C fasta scores 3B opt: 360 z-score: 414.1 E 28 29: 9.6e-16 2C 23.4 25 identity in 351 aa overlap 2C and TR:O66036 28EMBL:U84759 29 Chromatium vinosum sulfate adenylyltransferase 28EC 2.7.7.4 29 28397 aa 29 2C fasta scores 3B opt: 273 z-score: 315.2 E 28 29: 3.1e-10 2C 21.8 25 identity in 357 aa overlap. No Hp match 7EUpdated 282006 29 note: No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification -Central intermediary metabolism - Sulphur metabolism NC_002163.1 RefSeq gene 1536751 1537911 . + . ID=gene1541;Name=Cj1609;locus_tag=Cj1609;Dbxref=GeneID:905876;gbkey=Gene ### NC_002163.1 RefSeq region 1537916 1538359 . + . ID=id2827;gene=pgpA;Name=id2827;Dbxref=GeneID:905877;gbkey=misc_feature;Note=HMMPfam hit to PF04608 2CPhosphatidylglycerophosphatase A 2C score 2.9e-86 NC_002163.1 RefSeq CDS 1537916 1538416 . + 0 ID=cds1462;Parent=gene1542;gene=pgpA;Name=YP_002344979.1;Dbxref=GOA:Q0P818 InterPro:IPR007686 UniProtKB FTrEMBL:Q0P818 Genbank:YP_002344979.1 GeneID:905877;gbkey=CDS;product=phosphatidylglycerophosphatase;Note=Original 282000 29 note: Cj1610 2C pgpA 2C probable phosphatidylglycerophosphatase 2C len: 166 aa 3B simlar to e.g. PGPA_ECOLI phosphatidylglycerophosphatase A 28EC 3.1.3.27 29 28172 aa 29 2C fasta scores 3B opt: 238 z-score: 319.5 E 28 29: 1.8e-10 2C 33.3 25 identity in 135 aa overlap. 47.1 25 identity to HP0737 7EUpdated 282006 29 note: Three probable transmembrane helices predicted by TMHMM2.0. Some characterisation work carried out within Escherichia coli 2C however 2C identity score was marginal. Sequence alignment was only partial. kept within product function. Functional classification - Synthesis and modification of macromolecules - Phospholipids 7EPMID:2846510 2C PMID:1309518 NC_002163.1 RefSeq gene 1537916 1538416 . + . ID=gene1542;gene=pgpA;Name=pgpA;locus_tag=Cj1610;Dbxref=GeneID:905877;gbkey=Gene NC_002163.1 RefSeq region 1537973 1538077 . + . ID=id2828;gene=pgpA;Name=id2828;Dbxref=GeneID:905877;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1610 by TMHMM2.0 at aa 20-54 2C 80-102 and 136-158 NC_002163.1 RefSeq region 1538153 1538221 . + . ID=id2828;gene=pgpA;Name=id2828;Dbxref=GeneID:905877;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1610 by TMHMM2.0 at aa 20-54 2C 80-102 and 136-158 NC_002163.1 RefSeq region 1538321 1538389 . + . ID=id2828;gene=pgpA;Name=id2828;Dbxref=GeneID:905877;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1610 by TMHMM2.0 at aa 20-54 2C 80-102 and 136-158 ### NC_002163.1 UTR_Extractor 5'-UTR 1538468 1538494 . + . ID=utr589;locus_tag=Cj1611;product=30S ribosomal protein S20 NC_002163.1 RefSeq gene 1538495 1538758 . + . ID=gene1543;gene=rpsT;Name=rpsT;locus_tag=Cj1611;Dbxref=GeneID:905878;gbkey=Gene NC_002163.1 RefSeq CDS 1538495 1538758 . + 0 ID=cds1463;Parent=gene1543;gene=rpsT;Name=YP_002344980.1;Dbxref=GOA:Q9PM64 InterPro:IPR002583 UniProtKB FSwiss-Prot:Q9PM64 Genbank:YP_002344980.1 GeneID:905878;gbkey=CDS;product=30S ribosomal protein S20;Note=binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase NC_002163.1 RefSeq region 1538498 1538749 . + . ID=id2829;gene=rpsT;Name=id2829;Dbxref=GeneID:905878;gbkey=misc_feature;Note=HMMPfam hit to PF01649 2C Ribosomal protein S20 2Cscore 1.5e-27 ### NC_002163.1 RefSeq CDS 1538777 1539844 . + 0 ID=cds1464;Parent=gene1544;gene=prfA;Name=YP_002344981.1;Dbxref=GOA:Q9PM63 HSSP:P07012 InterPro:IPR000352 InterPro:IPR004373 InterPro:IPR005139 UniProtKB FSwiss-Prot:Q9PM63 Genbank:YP_002344981.1 GeneID:905879;gbkey=CDS;product=peptide chain release factor 1;Note=recognizes the termination signals UAG and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF1 3B this protein is similar to release factor 2 NC_002163.1 RefSeq gene 1538777 1539844 . + . ID=gene1544;gene=prfA;Name=prfA;locus_tag=Cj1612;Dbxref=GeneID:905879;gbkey=Gene NC_002163.1 RefSeq region 1538954 1539301 . + . ID=id2830;gene=prfA;Name=id2830;Dbxref=GeneID:905879;gbkey=misc_feature;Note=HMMPfam hit to PF03462 2C PCRF domain 2C score 3.3e-64 NC_002163.1 RefSeq region 1539392 1539727 . + . ID=id2831;gene=prfA;Name=id2831;Dbxref=GeneID:905879;gbkey=misc_feature;Note=HMMPfam hit to PF00472 2C Peptidyl-tRNA hydrolase domain 2C score 3.8e-74 NC_002163.1 RefSeq region 1539446 1539496 . + . ID=id2832;gene=prfA;Name=id2832;Dbxref=GeneID:905879;gbkey=misc_feature;Note=PS00745 Prokaryotic-type class I peptide chain release factors signature ### NC_002163.1 RefSeq gene 1539858 1540613 . - . ID=gene1545;Name=Cj1613c;locus_tag=Cj1613c;Dbxref=GeneID:905880;gbkey=Gene NC_002163.1 RefSeq CDS 1539858 1540613 . - 0 ID=cds1465;Parent=gene1545;Name=YP_002344982.1;Dbxref=GOA:Q0P815 InterPro:IPR011576 InterPro:IPR012349 InterPro:IPR014419 UniProtKB FTrEMBL:Q0P815 Genbank:YP_002344982.1 GeneID:905880;gbkey=CDS;product=pyridoxamine 5 27-phosphate oxidase;Note=Original 282000 29 note: Cj1613c 2C unknown 2C len: 251 aa 3B similar to hypothetical proteins e.g. Y854_HAEIN hypothetical protein HI0854 28253 aa 29 2C fasta scores 3B opt: 827 z-score: 991.6 E 28 29: 0 2C 48.4 25 identity in 248 aa overlap. 56.1 25 identity to HP0318 7EUpdated 282006 29 note: Pfam domain PF01243 Pyridoxamine 5 27-phosphate oxidase identified within CDS. Product modified to more specific family member based on motif match. No specific characterisation with acceptable identity score has been carried out yet. kept within product function. Literature search identified paper 28PMID:15632442 29 giving further clues to product function. Functional classification - Biosynthesis of cofactors 2C prosthetic groups and carriers - Pyridoxine 7EPMID:15632442 2C PMID:12686112 NC_002163.1 RefSeq region 1540074 1540355 . - . ID=id2833;Name=id2833;Dbxref=GeneID:905880;gbkey=misc_feature;Note=HMMPfam hit to PF01243 2C Pyridoxamine 5 27-phosphate oxidase 2C score 1.5e-17 ### NC_002163.1 UTR_Extractor 5'-UTR 1540614 1540646 . - . ID=utr590;locus_tag=Cj1613c;product=putative pyridoxamine 5 27-phosphate oxidase NC_002163.1 RefSeq gene 1540807 1542936 . + . ID=gene1546;gene=chuA;Name=chuA;locus_tag=Cj1614;Dbxref=GeneID:905881;gbkey=Gene NC_002163.1 RefSeq CDS 1540807 1542936 . + 0 ID=cds1466;Parent=gene1546;gene=chuA;Name=YP_002344983.1;Dbxref=GOA:Q0P814 InterPro:IPR000531 InterPro:IPR012910 UniProtKB FTrEMBL:Q0P814 Genbank:YP_002344983.1 GeneID:905881;gbkey=CDS;product=hemin uptake system outer membrane receptor;Note=Original 282000 29 note: Cj1614 2C chuA 2C haemin uptake system outer membrane receptor 2C len: 709 aa 3B mutants are unable to grow on haemin - see van Vliet et al 2C J. Bact 180 2C 5921-5298 281998 29. Similar to TR:O85161 28EMBL:AF047484 29 Vibrio vulnificus heme receptor 28712 aa 29 2Cfasta scores 3B opt: 270 z-score: 302.6 E 28 29: 1.6e-09 2C 22.9 25 identity in 750 aa overlap 2C and TR:Q56644 28EMBL:L27149 29 Vibrio cholerae heme receptor 28693 aa 29 2C fast scores 3B opt: 242 z-score: 271.3 E 28 29: 8.6e-08 2C 23.0 25 identity in 744 aa overlap. 21.6 25 identity to HP0807. Also similar to Cj0755 2823.6 25 identity in 770 aa overlap 29 2C and Cj0444 2832.1 25 identity in 190 aa overlap 29. Contains Pfam match to entry PF00593 TonB_boxC 2C TonB dependant receptor C-terminal region 7EUpdated 282006 29 note: Characterisation work within Campylobacter jejuni. not added to product function. Functional classification - Transport 2Fbinding proteins - Cations 7EPMID:9157252 2C PMID:9765558 NC_002163.1 RefSeq region 1540939 1541268 . + . ID=id2834;gene=chuA;Name=id2834;Dbxref=GeneID:905881;gbkey=misc_feature;Note=HMMPfam hit to PF07715 2C TonB-dependent Receptor Plug Domain 2C score 2e-14 NC_002163.1 RefSeq region 1542166 1542933 . + . ID=id2835;gene=chuA;Name=id2835;Dbxref=GeneID:905881;gbkey=misc_feature;Note=HMMPfam hit to PF00593 2C TonB dependent receptor 2Cscore 3.8e-21 NC_002163.1 RefSeq gene 1542911 1543897 . + . ID=gene1547;gene=chuB;Name=chuB;locus_tag=Cj1615;Dbxref=GeneID:905882;gbkey=Gene NC_002163.1 RefSeq CDS 1542911 1543897 . + 0 ID=cds1467;Parent=gene1547;gene=chuB;Name=YP_002344984.1;Dbxref=GOA:Q0P813 InterPro:IPR000522 UniProtKB FTrEMBL:Q0P813 Genbank:YP_002344984.1 GeneID:905882;gbkey=CDS;product=hemin uptake system permease;Note=Original 282000 29 note: Cj1615 2C chuB 2C probable haemin uptake system permease 2C len: 328 aa 3B similar to e.g. FHUB_BACSU ferrichrome transport permease FHUB 28384 aa 29 2C fasta scores 3B opt: 505 z-score: 606.7 E 28 29: 1.8e-26 2C 29.5 25 identity in 336 aa overlap. 31.2 25 identity to HP0889. Contains Pfam match to entry PF01032 FecCD_family 2C FecCD transport family. Predicted function is based on apparent co-transcription with Cj1614 chuA 7EUpdated 282006 29 note: Nine probable transmembrane helices predicted by TMHMM2.0. Yet to be specifically characterised with acceptable identity score. kept within product function. Functional classification -Transport 2Fbinding proteins - Cations 7EPMID:9765558 NC_002163.1 RefSeq region 1542944 1543003 . + . ID=id2836;gene=chuB;Name=id2836;Dbxref=GeneID:905882;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1615 by TMHMM2.0 at aa 12-31 2C 63-85 2C 92-110 2C 115-137 2C144-166 2C 186-205 2C 236-258 2C 273-290 and 297-319 NC_002163.1 RefSeq region 1543001 1543879 . + . ID=id2837;gene=chuB;Name=id2837;Dbxref=GeneID:905882;gbkey=misc_feature;Note=HMMPfam hit to PF01032 2C FecCD transport family 2Cscore 7.2e-77 NC_002163.1 RefSeq region 1543097 1543165 . + . ID=id2836;gene=chuB;Name=id2836;Dbxref=GeneID:905882;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1615 by TMHMM2.0 at aa 12-31 2C 63-85 2C 92-110 2C 115-137 2C144-166 2C 186-205 2C 236-258 2C 273-290 and 297-319 NC_002163.1 RefSeq region 1543184 1543240 . + . ID=id2836;gene=chuB;Name=id2836;Dbxref=GeneID:905882;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1615 by TMHMM2.0 at aa 12-31 2C 63-85 2C 92-110 2C 115-137 2C144-166 2C 186-205 2C 236-258 2C 273-290 and 297-319 NC_002163.1 RefSeq region 1543253 1543321 . + . ID=id2836;gene=chuB;Name=id2836;Dbxref=GeneID:905882;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1615 by TMHMM2.0 at aa 12-31 2C 63-85 2C 92-110 2C 115-137 2C144-166 2C 186-205 2C 236-258 2C 273-290 and 297-319 NC_002163.1 RefSeq region 1543340 1543408 . + . ID=id2836;gene=chuB;Name=id2836;Dbxref=GeneID:905882;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1615 by TMHMM2.0 at aa 12-31 2C 63-85 2C 92-110 2C 115-137 2C144-166 2C 186-205 2C 236-258 2C 273-290 and 297-319 NC_002163.1 RefSeq region 1543466 1543525 . + . ID=id2836;gene=chuB;Name=id2836;Dbxref=GeneID:905882;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1615 by TMHMM2.0 at aa 12-31 2C 63-85 2C 92-110 2C 115-137 2C144-166 2C 186-205 2C 236-258 2C 273-290 and 297-319 NC_002163.1 RefSeq region 1543616 1543684 . + . ID=id2836;gene=chuB;Name=id2836;Dbxref=GeneID:905882;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1615 by TMHMM2.0 at aa 12-31 2C 63-85 2C 92-110 2C 115-137 2C144-166 2C 186-205 2C 236-258 2C 273-290 and 297-319 NC_002163.1 RefSeq region 1543727 1543780 . + . ID=id2836;gene=chuB;Name=id2836;Dbxref=GeneID:905882;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1615 by TMHMM2.0 at aa 12-31 2C 63-85 2C 92-110 2C 115-137 2C144-166 2C 186-205 2C 236-258 2C 273-290 and 297-319 NC_002163.1 RefSeq region 1543799 1543867 . + . ID=id2836;gene=chuB;Name=id2836;Dbxref=GeneID:905882;gbkey=misc_feature;Note=9 probable transmembrane helices predicted for Cj1615 by TMHMM2.0 at aa 12-31 2C 63-85 2C 92-110 2C 115-137 2C144-166 2C 186-205 2C 236-258 2C 273-290 and 297-319 NC_002163.1 RefSeq CDS 1543897 1544673 . + 0 ID=cds1468;Parent=gene1548;gene=chuC;Name=YP_002344985.1;Dbxref=GOA:Q0P812 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FTrEMBL:Q0P812 Genbank:YP_002344985.1 GeneID:905883;gbkey=CDS;product=hemin uptake system ATP-binding protein;Note=Original 282000 29 note: Cj1616 2C chuC 2C probable haemin uptake system ATP-binding protein 2C len: 258 aa 3B similar to e.g. FEPC_ECOLI ferric enterobactin transport ATP-binding protein 28271 aa 29 2C fasta scores 3B opt: 477 z-score: 544.5 E 28 29: 5.2e-23 2C 32.6 25 identity in 242 aa overlap. 32.9 25 identity to HP0888. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00211 ABC transporters family signature 2C and Pfam match to entry PF00005 ABC_tran 2C ABC transporters. Predicted function is based on apparent co-transcription with Cj1614 chuA 7EUpdated 282006 29 note: Yet to be specifically characterised with acceptable identity score. kept within product function. Functional classification -Transport 2Fbinding proteins - Cations 7EPMID:9765558 NC_002163.1 RefSeq gene 1543897 1544673 . + . ID=gene1548;gene=chuC;Name=chuC;locus_tag=Cj1616;Dbxref=GeneID:905883;gbkey=Gene NC_002163.1 RefSeq region 1543975 1544541 . + . ID=id2838;gene=chuC;Name=id2838;Dbxref=GeneID:905883;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 2e-47 NC_002163.1 RefSeq region 1543996 1544019 . + . ID=id2839;gene=chuC;Name=id2839;Dbxref=GeneID:905883;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 1544311 1544355 . + . ID=id2840;gene=chuC;Name=id2840;Dbxref=GeneID:905883;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq gene 1544670 1545476 . + . ID=gene1549;gene=chuD;Name=chuD;locus_tag=Cj1617;Dbxref=GeneID:905884;gbkey=Gene NC_002163.1 RefSeq CDS 1544670 1545476 . + 0 ID=cds1469;Parent=gene1549;gene=chuD;Name=YP_002344986.1;Dbxref=GOA:Q0P811 InterPro:IPR002491 UniProtKB FTrEMBL:Q0P811 Genbank:YP_002344986.1 GeneID:905884;gbkey=CDS;product=hemin uptake system substrate-binding protein;Note=Original 282000 29 note: Cj1617 2C chuD 2C probable haemin uptake system periplasmic haemin-binding protein 2C len: 268 aa 3B similar to e.g. HMUT_YERPE hemin-binding periplasmic protein HMUT precursor 28278 aa 29 2C fasta scores 3B opt: 189 z-score: 223.7 E 28 29: 3.9e-05 2C 23.9 25 identity in 230 aa overlap. No Hp match. Contains probable N-terminal signal sequence. Predicted function is based on apparent co-transcription with Cj1614 chuA 7EUpdated 282006 29 note: Pfam domain PF01497 Periplasmic binding protein identified within CDS. Further support given to product function. Yet to be specifically characterised with acceptable identity score. kept within product function. Functional classification -Transport 2Fbinding proteins - Cations 7EPMID:9765558 NC_002163.1 RefSeq region 1544715 1545398 . + . ID=id2841;gene=chuD;Name=id2841;Dbxref=GeneID:905884;gbkey=misc_feature;Note=HMMPfam hit to PF01497 2C Periplasmic binding protein 2C score 2e-31 NC_002163.1 RefSeq CDS 1545473 1546390 . - 0 ID=cds1470;Parent=gene1550;Name=YP_002344987.1;Dbxref=GOA:Q0P810 InterPro:IPR007197 UniProtKB FTrEMBL:Q0P810 Genbank:YP_002344987.1 GeneID:905885;gbkey=CDS;product=radical SAM domain-containing protein;Note=Original 282000 29 note: Cj1618c 2C unknown 2C len: 305 aa 3B weak similarity to hypothetical proteins e.g. TR:Q59026 28EMBL:U67603 29 Methanococcus jannaschii hypothetical protein MJ1632 28255 aa 29 2C fasta scores 3B opt: 138 z-score: 169.9 E 28 29: 0.038 2C 25.8 25 identity in 256 aa overlap 28contains predicted iron-sulfur cluster which is conserved in Cj1618c 29. 34.5 25 identity to HP0568 7EUpdated 282006 29 note: Pfam domain PF04055 Radical SAM superfamily identified within CDS. Product modified to more specific family member based on motif match. No specific characterisation has been carried out yet. kept within product function. Functional classification - Misc NC_002163.1 RefSeq gene 1545473 1546390 . - . ID=gene1550;gene=Cj1618c;Name=Cj1618c;locus_tag=Cj1618c;Dbxref=GeneID:905885;gbkey=Gene NC_002163.1 RefSeq region 1545821 1546309 . - . ID=id2842;Name=id2842;Dbxref=GeneID:905885;gbkey=misc_feature;Note=HMMPfam hit to PF04055 2C Radical SAM superfamily 2Cscore 1.7e-06 ### NC_002163.1 RefSeq CDS 1546496 1547755 . + 0 ID=cds1471;Parent=gene1551;gene=kgtP;Name=YP_002344988.1;Dbxref=GOA:Q0P809 InterPro:IPR005829 InterPro:IPR007114 InterPro:IPR011701 UniProtKB FTrEMBL:Q0P809 Genbank:YP_002344988.1 GeneID:905886;gbkey=CDS;product=alpha-ketoglutarate permease;Note=Original 282000 29 note: Cj1619 2C kgtP 2C probable alpha-ketoglutarate permease 2C len: 419 aa 3B similar to KGTP_ECOLI alpha-ketoglutarate permease 28432 aa 29 2C fasta scores 3B opt: 1348 z-score: 1575.2 E 28 29: 0 2C 49.0 25 identity in 414 aa overlap. 49.9 25 identity to HP1091. Contains PS00217 Sugar transport proteins signature 2 2C and Pfam match to entry PF00083 sugar_tr 2C Sugar 28and other 29 transporters 7EUpdated 282006 29 note: PMID:2053984 7EUpdated 282006 29 note: Twelve probable transmembrane helices predicted by TMHMM2.0. Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Transport 2Fbinding proteins - Carbohydrates 2C organic acids and alcohols 7EPMID:2053984 NC_002163.1 RefSeq gene 1546496 1547755 . + . ID=gene1551;gene=kgtP;Name=kgtP;locus_tag=Cj1619;Dbxref=GeneID:905886;gbkey=Gene NC_002163.1 RefSeq region 1546526 1547728 . + . ID=id2843;gene=kgtP;Name=id2843;Dbxref=GeneID:905886;gbkey=misc_feature;Note=HMMPfam hit to PF00083 2C Sugar 28and other 29 transporter 2C score 4e-45 NC_002163.1 RefSeq region 1546532 1546600 . + . ID=id2844;gene=kgtP;Name=id2844;Dbxref=GeneID:905886;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1619 by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-102 2C 112-134 2C155-174 2C 184-203 2C 230-252 2C 267-289 2C 298-317 2C 327-349 2C361-383 and 393-412 NC_002163.1 RefSeq region 1546541 1547644 . + . ID=id2845;gene=kgtP;Name=id2845;Dbxref=GeneID:905886;gbkey=misc_feature;Note=HMMPfam hit to PF07690 2C Major Facilitator Superfamily 2C score 7.3e-21 NC_002163.1 RefSeq region 1546643 1546711 . + . ID=id2844;gene=kgtP;Name=id2844;Dbxref=GeneID:905886;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1619 by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-102 2C 112-134 2C155-174 2C 184-203 2C 230-252 2C 267-289 2C 298-317 2C 327-349 2C361-383 and 393-412 NC_002163.1 RefSeq region 1546748 1546801 . + . ID=id2844;gene=kgtP;Name=id2844;Dbxref=GeneID:905886;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1619 by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-102 2C 112-134 2C155-174 2C 184-203 2C 230-252 2C 267-289 2C 298-317 2C 327-349 2C361-383 and 393-412 NC_002163.1 RefSeq region 1546829 1546897 . + . ID=id2844;gene=kgtP;Name=id2844;Dbxref=GeneID:905886;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1619 by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-102 2C 112-134 2C155-174 2C 184-203 2C 230-252 2C 267-289 2C 298-317 2C 327-349 2C361-383 and 393-412 NC_002163.1 RefSeq region 1546859 1546936 . + . ID=id2846;gene=kgtP;Name=id2846;Dbxref=GeneID:905886;gbkey=misc_feature;Note=PS00217 Sugar transport proteins signature 2 NC_002163.1 RefSeq region 1546958 1547017 . + . ID=id2844;gene=kgtP;Name=id2844;Dbxref=GeneID:905886;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1619 by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-102 2C 112-134 2C155-174 2C 184-203 2C 230-252 2C 267-289 2C 298-317 2C 327-349 2C361-383 and 393-412 NC_002163.1 RefSeq region 1547045 1547104 . + . ID=id2844;gene=kgtP;Name=id2844;Dbxref=GeneID:905886;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1619 by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-102 2C 112-134 2C155-174 2C 184-203 2C 230-252 2C 267-289 2C 298-317 2C 327-349 2C361-383 and 393-412 NC_002163.1 RefSeq region 1547183 1547251 . + . ID=id2844;gene=kgtP;Name=id2844;Dbxref=GeneID:905886;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1619 by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-102 2C 112-134 2C155-174 2C 184-203 2C 230-252 2C 267-289 2C 298-317 2C 327-349 2C361-383 and 393-412 NC_002163.1 RefSeq region 1547294 1547362 . + . ID=id2844;gene=kgtP;Name=id2844;Dbxref=GeneID:905886;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1619 by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-102 2C 112-134 2C155-174 2C 184-203 2C 230-252 2C 267-289 2C 298-317 2C 327-349 2C361-383 and 393-412 NC_002163.1 RefSeq region 1547387 1547446 . + . ID=id2844;gene=kgtP;Name=id2844;Dbxref=GeneID:905886;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1619 by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-102 2C 112-134 2C155-174 2C 184-203 2C 230-252 2C 267-289 2C 298-317 2C 327-349 2C361-383 and 393-412 NC_002163.1 RefSeq region 1547474 1547542 . + . ID=id2844;gene=kgtP;Name=id2844;Dbxref=GeneID:905886;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1619 by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-102 2C 112-134 2C155-174 2C 184-203 2C 230-252 2C 267-289 2C 298-317 2C 327-349 2C361-383 and 393-412 NC_002163.1 RefSeq region 1547576 1547644 . + . ID=id2844;gene=kgtP;Name=id2844;Dbxref=GeneID:905886;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1619 by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-102 2C 112-134 2C155-174 2C 184-203 2C 230-252 2C 267-289 2C 298-317 2C 327-349 2C361-383 and 393-412 NC_002163.1 RefSeq region 1547672 1547731 . + . ID=id2844;gene=kgtP;Name=id2844;Dbxref=GeneID:905886;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1619 by TMHMM2.0 at aa 13-35 2C 50-72 2C 85-102 2C 112-134 2C155-174 2C 184-203 2C 230-252 2C 267-289 2C 298-317 2C 327-349 2C361-383 and 393-412 NC_002163.1 RefSeq gene 1547741 1548760 . - . ID=gene1552;gene=mutY;Name=mutY;locus_tag=Cj1620c;Dbxref=GeneID:905887;gbkey=Gene NC_002163.1 RefSeq CDS 1547741 1548760 . - 0 ID=cds1472;Parent=gene1552;gene=mutY;Name=YP_002344989.1;Dbxref=GOA:Q0P808 InterPro:IPR000445 InterPro:IPR003265 InterPro:IPR003583 InterPro:IPR003651 InterPro:IPR004036 InterPro:IPR005760 UniProtKB FTrEMBL:Q0P808 Genbank:YP_002344989.1 GeneID:905887;gbkey=CDS;product=A 2FG-specific adenine glycosylase;Note=Original 282000 29 note: Cj1620c 2C mutY 2C probable A 2FG-specific adenine glycosylase 2C len: 339 aa 3B similar to e.g. MUTY_ECOLI A 2FG-specific adenine glycosylase 28EC 3.2.2.- 29 28350 aa 29 2C blastp scores 3B E 3D 1.0e-41 2C 39 25 identity in 271 aa overlap. 47.6 25 identity to HP0142. Contains Pfam match to entry PF00730 Endonuclease_3 2C Endonuclease III 7EUpdated 282006 29 note: Pfam domain PF00730 HhH-GPD superfamily base excision DNA repair and PF00633 Helix-hairpin-helix motif were both identified within CDS. Further support given to product function. Characterisation work has been carried out within Escherichia coli with acceptable identity score. not added to product function. Functional classification -DNA replication 2C restriction 2Fmodification 2C recombination and repair 7EPMID:2197596 2C PMID:9846876 2C PMID:15456766 NC_002163.1 RefSeq region 1548206 1548613 . - . ID=id2847;gene=mutY;Name=id2847;Dbxref=GeneID:905887;gbkey=misc_feature;Note=HMMPfam hit to PF00730 2C HhH-GPD superfamily base excision DNA repair 2C score 2.5e-23 NC_002163.1 RefSeq region 1548329 1548418 . - . ID=id2848;gene=mutY;Name=id2848;Dbxref=GeneID:905887;gbkey=misc_feature;Note=HMMPfam hit to PF00633 2C Helix-hairpin-helix motif 2Cscore 9.8e-07 NC_002163.1 RefSeq region 1548332 1548364 . - . ID=id2849;gene=mutY;Name=id2849;Dbxref=GeneID:905887;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 UTR_Extractor 5'-UTR 1548760 1548760 . - . ID=utr591;locus_tag=Cj1620c;product=A 2FG-specific adenine glycosylase ### NC_002163.1 UTR_Extractor 5'-UTR 1548810 1548832 . + . ID=utr592;locus_tag=Cj1621;product=putative periplasmic protein NC_002163.1 RefSeq gene 1548833 1549585 . + . ID=gene1553;Name=Cj1621;locus_tag=Cj1621;Dbxref=GeneID:905888;gbkey=Gene NC_002163.1 RefSeq CDS 1548833 1549585 . + 0 ID=cds1473;Parent=gene1553;Name=YP_002344990.1;Dbxref=UniProtKB FTrEMBL:Q0P807 Genbank:YP_002344990.1 GeneID:905888;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1621 2C possible periplasmic protein 2C len: 250 aa 3B no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 1548851 1548919 . + . ID=id2850;Name=id2850;Dbxref=GeneID:905888;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1621 by TMHMM2.0 at aa 7-29 ### NC_002163.1 RefSeq gene 1549657 1549731 . + . ID=gene1554;gene=tRNAGly;Name=tRNAGly;locus_tag=Cjp27;Dbxref=GeneID:905889;gbkey=Gene NC_002163.1 RefSeq tRNA 1549657 1549731 . + . ID=rna43;Parent=gene1554;gene=tRNAGly;Name=rna43;Dbxref=GeneID:905889;gbkey=tRNA;product=tRNA-Gly;Note=tRNA Gly anticodon GCC 2C Cove score 88.10 NC_002163.1 RefSeq exon 1549657 1549731 . + . ID=id2851;Parent=rna43;gene=tRNAGly;Name=id2851;Dbxref=GeneID:905889;gbkey=tRNA;product=tRNA-Gly;Note=tRNA Gly anticodon GCC 2C Cove score 88.10 NC_002163.1 RefSeq gene 1549741 1549829 . + . ID=gene1555;gene=tRNALeu;Name=tRNALeu;locus_tag=Cjp28;Dbxref=GeneID:905890;gbkey=Gene NC_002163.1 RefSeq tRNA 1549741 1549829 . + . ID=rna44;Parent=gene1555;gene=tRNALeu;Name=rna44;Dbxref=GeneID:905890;gbkey=tRNA;product=tRNA-Leu;Note=tRNA Leu anticodon TAA 2C Cove score 69.07 NC_002163.1 RefSeq exon 1549741 1549829 . + . ID=id2852;Parent=rna44;gene=tRNALeu;Name=id2852;Dbxref=GeneID:905890;gbkey=tRNA;product=tRNA-Leu;Note=tRNA Leu anticodon TAA 2C Cove score 69.07 NC_002163.1 RefSeq gene 1549848 1549921 . + . ID=gene1556;gene=tRNACys;Name=tRNACys;locus_tag=Cjp29;Dbxref=GeneID:905892;gbkey=Gene NC_002163.1 RefSeq tRNA 1549848 1549921 . + . ID=rna45;Parent=gene1556;gene=tRNACys;Name=rna45;Dbxref=GeneID:905892;gbkey=tRNA;product=tRNA-Cys;Note=tRNA Cys anticodon GCA 2C Cove score 72.19 NC_002163.1 RefSeq exon 1549848 1549921 . + . ID=id2853;Parent=rna45;gene=tRNACys;Name=id2853;Dbxref=GeneID:905892;gbkey=tRNA;product=tRNA-Cys;Note=tRNA Cys anticodon GCA 2C Cove score 72.19 NC_002163.1 RefSeq gene 1549943 1550030 . + . ID=gene1557;gene=tRNASer;Name=tRNASer;locus_tag=Cjp30;Dbxref=GeneID:905893;gbkey=Gene NC_002163.1 RefSeq tRNA 1549943 1550030 . + . ID=rna46;Parent=gene1557;gene=tRNASer;Name=rna46;Dbxref=GeneID:905893;gbkey=tRNA;product=tRNA-Ser;Note=tRNA Ser anticodon TGA 2C Cove score 68.51 NC_002163.1 RefSeq exon 1549943 1550030 . + . ID=id2854;Parent=rna46;gene=tRNASer;Name=id2854;Dbxref=GeneID:905893;gbkey=tRNA;product=tRNA-Ser;Note=tRNA Ser anticodon TGA 2C Cove score 68.51 NC_002163.1 RefSeq CDS 1550235 1551245 . + 0 ID=cds1474;Parent=gene1558;gene=ribD;Name=YP_002344991.1;Dbxref=GOA:Q0P806 InterPro:IPR002125 InterPro:IPR004794 UniProtKB FTrEMBL:Q0P806 Genbank:YP_002344991.1 GeneID:905894;gbkey=CDS;product=riboflavin-specific deaminase 2Freductase;Note=Original 282000 29 note: Cj1622 2C ribD 2C probable riboflavin-specific deaminase 2C len: 336 aa 3B similar to e.g. RIBD_ACTPL riboflavin-specific deaminase 28EC 3.5.4.- 29 28410 aa 29 2C fasta scores 3B opt: 320 z-score: 381.1 E 28 29: 6.6e-14 2C 35.7 25 identity in 235 aa overlap 2C and RIBD_ECOLI riboflavin-specific deaminase 28EC 3.5.4.- 29. 28367 aa 29 2C opt: 249 z-score: 298.4 E 28 29: 2.7e-09 2C 28.4 25 identity in 282 aa overlap. 37.9 25 identity to 3B HP1505. Contains Pfam match to entry PF00383 dCMP_cyt_deam 2C Cytidine and deoxycytidylate deaminases zinc-binding region 7EUpdated 282006 29 note: Characterisation has been carried out within Helicobacter pylori and Escherichia coli and identity scores were acceptable. Product function modified to more specific function. Functional classification - Biosynthesis of cofactors 2C prosthetic groups and carriers - Riboflavin 7EPMID:11024263 2C PMID:9068650 NC_002163.1 RefSeq gene 1550235 1551245 . + . ID=gene1558;gene=ribD;Name=ribD;locus_tag=Cj1622;Dbxref=GeneID:905894;gbkey=Gene NC_002163.1 RefSeq region 1550262 1550639 . + . ID=id2855;gene=ribD;Name=id2855;Dbxref=GeneID:905894;gbkey=misc_feature;Note=HMMPfam hit to PF00383 2C Cytidine and deoxycytidylate deaminase 2C score 4.9e-27 NC_002163.1 UTR_Extractor 5'-UTR 1551182 1551225 . + . ID=utr593;locus_tag=Cj1623;product=hypothetical protein NC_002163.1 RefSeq CDS 1551226 1551747 . + 0 ID=cds1475;Parent=gene1559;Name=YP_002344992.1;Dbxref=UniProtKB FTrEMBL:Q0P805 Genbank:YP_002344992.1 GeneID:905895;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1623 2C probable membrane protein 2C len: 173 aa 3B no Hp match 7EUpdated 282006 29 note: Two probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 1551226 1551747 . + . ID=gene1559;gene=Cj1623;Name=Cj1623;locus_tag=Cj1623;Dbxref=GeneID:905895;gbkey=Gene NC_002163.1 RefSeq region 1551514 1551573 . + . ID=id2856;Name=id2856;Dbxref=GeneID:905895;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1623 by TMHMM2.0 at aa 97-116 and 121-143 NC_002163.1 RefSeq region 1551586 1551654 . + . ID=id2856;Name=id2856;Dbxref=GeneID:905895;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1623 by TMHMM2.0 at aa 97-116 and 121-143 ### NC_002163.1 RefSeq CDS 1551755 1553119 . - 0 ID=cds1476;Parent=gene1560;gene=sdaA;Name=YP_002344993.1;Dbxref=GOA:Q0P804 InterPro:IPR004644 InterPro:IPR005130 InterPro:IPR005131 UniProtKB FTrEMBL:Q0P804 Genbank:YP_002344993.1 GeneID:905896;gbkey=CDS;product=L-serine dehydratase;Note=Original 282000 29 note: Cj1624c 2C sdaA 2C probable L-serine dehydratase 2C len: 454 aa 3B similar to many e.g. SDHL_ECOLI L-serine dehydratase 1 28EC 4.2.1.13 29 28454 aa 29 2Cfasta scores 3B opt: 1316 z-score: 1553.3 E 28 29: 0 2C 46.0 25 identity in 465 aa overlap. 53.4 25 identity to HP0132 7EUpdated 282006 29 note: Pfam domains PF03313 Serine dehydratase alpha chain and PF03315 Serine dehydratase beta chain were identified within CDS. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Degradation - Amino acids 7EPMID:8436113 2C PMID:14688104 NC_002163.1 RefSeq gene 1551755 1553119 . - . ID=gene1560;gene=sdaA;Name=sdaA;locus_tag=Cj1624c;Dbxref=GeneID:905896;gbkey=Gene NC_002163.1 RefSeq region 1551773 1552600 . - . ID=id2857;gene=sdaA;Name=id2857;Dbxref=GeneID:905896;gbkey=misc_feature;Note=HMMPfam hit to PF03313 2C Serine dehydratase alpha chain 2C score 8.3e-143 NC_002163.1 RefSeq region 1552643 1553116 . - . ID=id2858;gene=sdaA;Name=id2858;Dbxref=GeneID:905896;gbkey=misc_feature;Note=HMMPfam hit to PF03315 2C Serine dehydratase beta chain 2C score 8.4e-47 ### NC_002163.1 RefSeq CDS 1553134 1554384 . - 0 ID=cds1477;Parent=gene1561;gene=sdaC;Name=YP_002344994.1;Dbxref=GOA:Q0P803 InterPro:IPR004761 UniProtKB FTrEMBL:Q0P803 Genbank:YP_002344994.1 GeneID:905897;gbkey=CDS;product=amino acid transporter;Note=Original 282000 29 note: Cj1625c 2C sdaC 2C probable serine transporter 2C len: 416 aa 3B similar to e.g. SDAC_ECOLI serine transporter 28429 aa 29 2C fasta scores 3B opt: 1392 z-score: 1574.7 E 28 29: 0 2C 50.1 25 identity in 417 aa overlap 2C and TDCC_ECOLI threonine 2Fserine transporter 28443 aa 29 2C fasta scores 3B opt: 848 z-score: 961.6 E 28 29: 0 2C 43.8 25 identity in 432 aa overlap. 42.0 25 identity to HP0133 7EUpdated 282006 29 note: Prosite domains PS50286 AROMATIC_AA_PERM_2 2C Amino acid 2Fpolyamine transporter II and PS50285 AMINO_ACID_PERMEASE_2 2C Amino acid 2Fpolyamine transporter I were identified within CDS. Further support given to product function. Eleven probable transmembrane helices predicted by TMHMM2.0. Characterised within Escherichia coli with acceptable identity scores. Product function updated. not added to product function. Functional classification - Transport 2Fbinding proteins -Amino acids and amines 7EPMID:8026499 2C PMID:15743941 2C PMID:14688104 NC_002163.1 RefSeq gene 1553134 1554384 . - . ID=gene1561;gene=sdaC;Name=sdaC;locus_tag=Cj1625c;Dbxref=GeneID:905897;gbkey=Gene NC_002163.1 RefSeq region 1553149 1553202 . - . ID=id146;gene=sdaC;Name=id146;Dbxref=GeneID:905897;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1625c by TMHMM2.0 at aa 13-35 2C 39-56 2C 84-106 2C 130-152 2C159-181 2C 201-223 2C 243-265 2C 291-313 2C 334-351 2C 361-383 and 395-412 NC_002163.1 RefSeq region 1553236 1553304 . - . ID=id146;gene=sdaC;Name=id146;Dbxref=GeneID:905897;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1625c by TMHMM2.0 at aa 13-35 2C 39-56 2C 84-106 2C 130-152 2C159-181 2C 201-223 2C 243-265 2C 291-313 2C 334-351 2C 361-383 and 395-412 NC_002163.1 RefSeq region 1553332 1553385 . - . ID=id146;gene=sdaC;Name=id146;Dbxref=GeneID:905897;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1625c by TMHMM2.0 at aa 13-35 2C 39-56 2C 84-106 2C 130-152 2C159-181 2C 201-223 2C 243-265 2C 291-313 2C 334-351 2C 361-383 and 395-412 NC_002163.1 RefSeq region 1553446 1553514 . - . ID=id146;gene=sdaC;Name=id146;Dbxref=GeneID:905897;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1625c by TMHMM2.0 at aa 13-35 2C 39-56 2C 84-106 2C 130-152 2C159-181 2C 201-223 2C 243-265 2C 291-313 2C 334-351 2C 361-383 and 395-412 NC_002163.1 RefSeq region 1553590 1553658 . - . ID=id146;gene=sdaC;Name=id146;Dbxref=GeneID:905897;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1625c by TMHMM2.0 at aa 13-35 2C 39-56 2C 84-106 2C 130-152 2C159-181 2C 201-223 2C 243-265 2C 291-313 2C 334-351 2C 361-383 and 395-412 NC_002163.1 RefSeq region 1553608 1553640 . - . ID=id2859;gene=sdaC;Name=id2859;Dbxref=GeneID:905897;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1553716 1553748 . - . ID=id2860;gene=sdaC;Name=id2860;Dbxref=GeneID:905897;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1553716 1553784 . - . ID=id146;gene=sdaC;Name=id146;Dbxref=GeneID:905897;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1625c by TMHMM2.0 at aa 13-35 2C 39-56 2C 84-106 2C 130-152 2C159-181 2C 201-223 2C 243-265 2C 291-313 2C 334-351 2C 361-383 and 395-412 NC_002163.1 RefSeq region 1553842 1553910 . - . ID=id146;gene=sdaC;Name=id146;Dbxref=GeneID:905897;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1625c by TMHMM2.0 at aa 13-35 2C 39-56 2C 84-106 2C 130-152 2C159-181 2C 201-223 2C 243-265 2C 291-313 2C 334-351 2C 361-383 and 395-412 NC_002163.1 RefSeq region 1553929 1553997 . - . ID=id146;gene=sdaC;Name=id146;Dbxref=GeneID:905897;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1625c by TMHMM2.0 at aa 13-35 2C 39-56 2C 84-106 2C 130-152 2C159-181 2C 201-223 2C 243-265 2C 291-313 2C 334-351 2C 361-383 and 395-412 NC_002163.1 RefSeq region 1554067 1554135 . - . ID=id146;gene=sdaC;Name=id146;Dbxref=GeneID:905897;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1625c by TMHMM2.0 at aa 13-35 2C 39-56 2C 84-106 2C 130-152 2C159-181 2C 201-223 2C 243-265 2C 291-313 2C 334-351 2C 361-383 and 395-412 NC_002163.1 RefSeq region 1554217 1554270 . - . ID=id146;gene=sdaC;Name=id146;Dbxref=GeneID:905897;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1625c by TMHMM2.0 at aa 13-35 2C 39-56 2C 84-106 2C 130-152 2C159-181 2C 201-223 2C 243-265 2C 291-313 2C 334-351 2C 361-383 and 395-412 NC_002163.1 RefSeq region 1554280 1554348 . - . ID=id146;gene=sdaC;Name=id146;Dbxref=GeneID:905897;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1625c by TMHMM2.0 at aa 13-35 2C 39-56 2C 84-106 2C 130-152 2C159-181 2C 201-223 2C 243-265 2C 291-313 2C 334-351 2C 361-383 and 395-412 ### NC_002163.1 UTR_Extractor 5'-UTR 1554385 1554412 . - . ID=utr594;locus_tag=Cj1625c;product=amino acid transporter NC_002163.1 RefSeq gene 1554542 1554568 . + . ID=NC_002163.1:CJnc160;Name=NC_002163.1:CJnc160;locus_tag=CJnc160 NC_002163.1 RefSeq sRNA 1554542 1554568 . + . ID=NC_002163.1:CJnc160:unknown_transcript_1;Parent=NC_002163.1:CJnc160;Name=NC_002163.1:CJnc160:unknown_transcript_1;locus_tag=CJnc160;gbkey=misc_RNA;product=CJnc160 NC_002163.1 RefSeq gene 1554644 1555060 . - . ID=gene1562;Name=Cj1626c;locus_tag=Cj1626c;Dbxref=GeneID:905898;gbkey=Gene NC_002163.1 RefSeq CDS 1554644 1555060 . - 0 ID=cds1478;Parent=gene1562;Name=YP_002344995.1;Dbxref=GOA:Q0P802 UniProtKB FTrEMBL:Q0P802 Genbank:YP_002344995.1 GeneID:905898;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1626c 2C probable periplasmic protein 2C len: 138 aa 3B no Hp match. Also similar to Cj1004 2838.6 25 identity in 140 aa overlap 29 2C and in N-terminus to Cj1722c 2853.1 25 identity in 32 aa overlap 29 7EUpdated 282006 29 note: Literature search identified paper giving further clues to product function. Functional classification - Miscellaneous periplasmic proteins 7EPMID:15554967 NC_002163.1 UTR_Extractor 5'-UTR 1555061 1555083 . - . ID=utr595;locus_tag=Cj1626c;product=putative periplasmic protein NC_002163.1 RefSeq gene 1555124 1555867 . - . ID=gene1563;Name=Cj1627c;locus_tag=Cj1627c;Dbxref=GeneID:905899;gbkey=Gene NC_002163.1 RefSeq CDS 1555124 1555867 . - 0 ID=cds1479;Parent=gene1563;Name=YP_002344996.1;Dbxref=UniProtKB FTrEMBL:Q0P801 Genbank:YP_002344996.1 GeneID:905899;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1627c 2C unknown 2C len: 247 aa 3B no Hp match 7EUpdated 282006 29 note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown NC_002163.1 UTR_Extractor 5'-UTR 1555868 1555890 . - . ID=utr596;locus_tag=Cj1627c;product=hypothetical protein NC_002163.1 RefSeq CDS 1556025 1556450 . + 0 ID=cds1480;Parent=gene1564;gene=exbB2;Name=YP_002344997.1;Dbxref=GOA:Q0P800 InterPro:IPR002898 InterPro:IPR014172 UniProtKB FTrEMBL:Q0P800 Genbank:YP_002344997.1 GeneID:905901;gbkey=CDS;product=ExbB 2FTolQ family transport protein;Note=Original 282000 29 note: Cj1628 2C exbB2 2C probable exbB 2FtolQ family transport protein 2C len: 141 aa 3B similar to many e.g. EXBB_HAEDU biopolymer transport EXBB protein 28150 aa 29 2C fasta scores 3B opt: 426 z-score: 531.7 E 28 29: 2.7e-22 2C 51.2 25 identity in 129 aa overlap. 54.4 25 identity to HP1339. Also similar to Cj0179 exbB 2831.3 25 identity in 150 aa overlap 29 2C and Cj0109 exbB2 2844.4 25 identity in 81 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF01618 MotA 2FTolQ 2FExbB proton channel family identified within CDS. Further support given to product function. Three probable transmembrane helices predicted by TMHMM2.0. No specific characterisation has been carried out yet 2C so kept within product function. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:9781885 NC_002163.1 RefSeq gene 1556025 1556450 . + . ID=gene1564;gene=exbB2;Name=exbB2;locus_tag=Cj1628;Dbxref=GeneID:905901;gbkey=Gene NC_002163.1 RefSeq region 1556034 1556444 . + . ID=id2861;gene=exbB2;Name=id2861;Dbxref=GeneID:905901;gbkey=misc_feature;Note=HMMPfam hit to PF01618 2C MotA 2FTolQ 2FExbB proton channel family 2C score 9.2e-42 NC_002163.1 RefSeq region 1556052 1556108 . + . ID=id2862;gene=exbB2;Name=id2862;Dbxref=GeneID:905901;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1628 by TMHMM2.0 at aa 10-28 2C 61-83 and 103-125 NC_002163.1 RefSeq region 1556205 1556273 . + . ID=id2862;gene=exbB2;Name=id2862;Dbxref=GeneID:905901;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1628 by TMHMM2.0 at aa 10-28 2C 61-83 and 103-125 NC_002163.1 RefSeq region 1556331 1556399 . + . ID=id2862;gene=exbB2;Name=id2862;Dbxref=GeneID:905901;gbkey=misc_feature;Note=3 probable transmembrane helices predicted for Cj1628 by TMHMM2.0 at aa 10-28 2C 61-83 and 103-125 NC_002163.1 RefSeq CDS 1556443 1556832 . + 0 ID=cds1481;Parent=gene1565;gene=exbD2;Name=YP_002344998.1;Dbxref=GOA:Q0P7Z9 InterPro:IPR003400 InterPro:IPR014171 UniProtKB FTrEMBL:Q0P7Z9 Genbank:YP_002344998.1 GeneID:905902;gbkey=CDS;product=ExbD 2FTolR family transport protein;Note=Original 282000 29 note: Cj1629 2C exbD2 2C probable exbD 2FtolR family transport protein 2C len: 129 aa 3B similar to many e.g. EXBD_HAEDU biopolymer transport EXBD protein 28129 aa 29 2C fasta scores 3B opt: 337 z-score: 414.6 E 28 29: 9e-16 2C 44.8 25 identity in 125 aa overlap. 49.6 25 identity to HP1340. Also similar to Cj0180 exbD 2831.1 25 identity in 122 aa overlap 29 and Cj0110 exbD2 2826.4 25 identity in 121 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF02472 Biopolymer transport protein ExbD 2FTolR identified within CDS. Further support given to product function. One probable transmembrane helices predicted by TMHMM2.0. No specific characterisation with acceptable identity score carried out yet 2C so kept within product function. Functional classification - Transport 2Fbinding proteins -Other 7EPMID:9781885 NC_002163.1 RefSeq gene 1556443 1556832 . + . ID=gene1565;gene=exbD2;Name=exbD2;locus_tag=Cj1629;Dbxref=GeneID:905902;gbkey=Gene NC_002163.1 RefSeq region 1556452 1556826 . + . ID=id2863;gene=exbD2;Name=id2863;Dbxref=GeneID:905902;gbkey=misc_feature;Note=HMMPfam hit to PF02472 2C Biopolymer transport protein ExbD 2FTolR 2C score 6.5e-41 NC_002163.1 RefSeq region 1556476 1556544 . + . ID=id2864;gene=exbD2;Name=id2864;Dbxref=GeneID:905902;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1629 by TMHMM2.0 at aa 12-34 NC_002163.1 RefSeq CDS 1556829 1557512 . + 0 ID=cds1482;Parent=gene1566;gene=tonB2;Name=YP_002344999.1;Dbxref=GOA:Q0P7Z8 InterPro:IPR003538 InterPro:IPR006260 UniProtKB FTrEMBL:Q0P7Z8 Genbank:YP_002344999.1 GeneID:905903;gbkey=CDS;product=TonB transport protein;Note=Original 282000 29 note: Cj1630 2C tonB2 2C probable tonB transport protein 2C len: 227 aa 3B similar to many e.g. TONB_CAMCO TONB protein 28232 aa 29 2C fasta scores 3B opt: 412 z-score: 428.1 E 28 29: 1.6e-16 2C 41.9 25 identity in 236 aa overlap. 25.9 25 identity to HP0582. Also similar to Cj0753c tonB 2841.7 25 identity in 230 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF03544 Gram-negative bacterial tonB protein identified within CDS. Further support given to product function. Also 2C one probable transmembrane helix predicted by TMHMM2.0. Some characterisation work carried out within Campylobacter coli with acceptable identity score. Characterisation work also carried out within Vibrio cholerae 2C however 2C identity score was unnacceptable. kept within product function. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:9190817 2C PMID:10689178 2C PMID:15557661 NC_002163.1 RefSeq gene 1556829 1557512 . + . ID=gene1566;gene=tonB2;Name=tonB2;locus_tag=Cj1630;Dbxref=GeneID:905903;gbkey=Gene NC_002163.1 RefSeq region 1556862 1556915 . + . ID=id2865;gene=tonB2;Name=id2865;Dbxref=GeneID:905903;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1630 by TMHMM2.0 at aa 12-29 NC_002163.1 RefSeq region 1557270 1557374 . + . ID=id2866;gene=tonB2;Name=id2866;Dbxref=GeneID:905903;gbkey=misc_feature;Note=HMMPfam hit to PF03544 2C Gram-negative bacterial tonB protein 2C score 3e-13 ### NC_002163.1 RefSeq gene 1557525 1558394 . - . ID=gene1567;Name=Cj1631c;locus_tag=Cj1631c;Dbxref=GeneID:905904;gbkey=Gene NC_002163.1 RefSeq CDS 1557525 1558394 . - 0 ID=cds1483;Parent=gene1567;Name=YP_002345000.1;Dbxref=GOA:Q0P7Z7 InterPro:IPR002048 UniProtKB FTrEMBL:Q0P7Z7 Genbank:YP_002345000.1 GeneID:905904;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1631c 2C unknown 2C len: 289 aa 3B no Hp match. Contains PS00018 EF-hand calcium-binding domain. Functional classification - Unknown NC_002163.1 RefSeq region 1557864 1557902 . - . ID=id2867;Name=id2867;Dbxref=GeneID:905904;gbkey=misc_feature;Note=PS00018 EF-hand calcium-binding domain ### NC_002163.1 RefSeq gene 1558398 1558559 . - . ID=gene1568;Name=Cj1632c;locus_tag=Cj1632c;Dbxref=GeneID:905905;gbkey=Gene NC_002163.1 RefSeq CDS 1558398 1558559 . - 0 ID=cds1484;Parent=gene1568;Name=YP_002345001.1;Dbxref=GOA:Q0P7Z6 UniProtKB FTrEMBL:Q0P7Z6 Genbank:YP_002345001.1 GeneID:905905;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1632c 2C possible periplasmic protein 2C len: 53 aa 3B no Hp match. Contains possible N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 UTR_Extractor 5'-UTR 1558560 1558601 . - . ID=utr597;locus_tag=Cj1632c;product=putative periplasmic protein NC_002163.1 UTR_Extractor 5'-UTR 1558603 1558653 . + . ID=utr598;locus_tag=Cj1633;product=putative ATP-binding protein NC_002163.1 RefSeq gene 1558654 1559637 . + . ID=gene1569;Name=Cj1633;locus_tag=Cj1633;Dbxref=GeneID:905906;gbkey=Gene NC_002163.1 RefSeq CDS 1558654 1559637 . + 0 ID=cds1485;Parent=gene1569;Name=YP_002345002.1;Dbxref=GOA:Q0P7Z5 InterPro:IPR002761 InterPro:IPR014729 UniProtKB FTrEMBL:Q0P7Z5 Genbank:YP_002345002.1 GeneID:905906;gbkey=CDS;product=ATP-binding protein;Note=Original 282000 29 note: Cj1633 2C unknown 2C len: 327 aa 3B similar to hypothetical proteins e.g. TR:O67046 28EMBL:AE000713 29 Aquifex aeolicus AQ_898 28251 aa 29 2C fasta scores 3B opt: 544 z-score: 648.2 E 28 29: 8.8e-29 2C 50.2 25 identity in 221 aa overlap. 44.7 25 identity to HP0013. Contains HP0013 7EUpdated 282006 29 note: Pfam domain PF01902 ATP-binding region identified within CDS. Product function modified to more specific family member based on motif match. kept within product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq region 1558906 1558923 . + . ID=id2868;Name=id2868;Dbxref=GeneID:905906;gbkey=misc_feature;Note=PS00190 Cytochrome c family heme-binding site signature ### NC_002163.1 RefSeq gene 1559676 1559722 . + . ID=NC_002163.1:CJnc170;Name=NC_002163.1:CJnc170;locus_tag=CJnc170 NC_002163.1 RefSeq sRNA 1559676 1559722 . + . ID=NC_002163.1:CJnc170:unknown_transcript_1;Parent=NC_002163.1:CJnc170;Name=NC_002163.1:CJnc170:unknown_transcript_1;locus_tag=CJnc170;gbkey=misc_RNA;product=CJnc170 NC_002163.1 RefSeq CDS 1559723 1560811 . - 0 ID=cds1486;Parent=gene1570;gene=aroC;Name=YP_002345003.1;Dbxref=GOA:Q9PM41 InterPro:IPR000453 PDB:1SQ1 UniProtKB FSwiss-Prot:Q9PM41 Genbank:YP_002345003.1 GeneID:905907;gbkey=CDS;product=chorismate synthase;Note=catalyzes the formation of chorismate from 5-O- 281-carboxyvinyl 29-3-phosphoshikimate in aromatic amino acid biosynthesis NC_002163.1 RefSeq gene 1559723 1560811 . - . ID=gene1570;gene=aroC;Name=aroC;locus_tag=Cj1634c;Dbxref=GeneID:905907;gbkey=Gene NC_002163.1 RefSeq region 1559768 1560790 . - . ID=id2869;gene=aroC;Name=id2869;Dbxref=GeneID:905907;gbkey=misc_feature;Note=HMMPfam hit to PF01264 2C Chorismate synthase 2C score 6.3e-158 NC_002163.1 RefSeq region 1560407 1560451 . - . ID=id2870;gene=aroC;Name=id2870;Dbxref=GeneID:905907;gbkey=misc_feature;Note=PS00788 Chorismate synthase signature 2 NC_002163.1 RefSeq region 1560725 1560772 . - . ID=id2871;gene=aroC;Name=id2871;Dbxref=GeneID:905907;gbkey=misc_feature;Note=PS00787 Chorismate synthase signature 1 NC_002163.1 RefSeq CDS 1560811 1561485 . - 0 ID=cds1487;Parent=gene1571;gene=rnc;Name=YP_002345004.1;Dbxref=GOA:Q9PM40 HSSP:O67082 InterPro:IPR000999 InterPro:IPR001159 InterPro:IPR011907 InterPro:IPR014720 UniProtKB FSwiss-Prot:Q9PM40 Genbank:YP_002345004.1 GeneID:905908;gbkey=CDS;product=ribonuclease III;Note=cytoplasmic enzyme involved in processing rRNA and some mRNAs 3B substrates typically have dsRNA regions 3B forms a homodimer 3B have N-terminal nuclease and C-terminal RNA-binding domains 3B requires magnesium as preferred ion for activity NC_002163.1 RefSeq gene 1560811 1561485 . - . ID=gene1571;gene=rnc;Name=rnc;locus_tag=Cj1635c;Dbxref=GeneID:905908;gbkey=Gene NC_002163.1 RefSeq region 1560823 1561023 . - . ID=id2872;gene=rnc;Name=id2872;Dbxref=GeneID:905908;gbkey=misc_feature;Note=HMMPfam hit to PF00035 2C Double-stranded RNA binding motif 2C score 2.1e-19 NC_002163.1 RefSeq region 1561105 1561377 . - . ID=id2873;gene=rnc;Name=id2873;Dbxref=GeneID:905908;gbkey=misc_feature;Note=HMMPfam hit to PF00636 2C RNase3 domain 2C score 1.2e-41 NC_002163.1 RefSeq region 1561351 1561377 . - . ID=id2874;gene=rnc;Name=id2874;Dbxref=GeneID:905908;gbkey=misc_feature;Note=PS00517 Ribonuclease III family signature NC_002163.1 RefSeq gene 1561472 1561912 . - . ID=gene1572;gene=rnhA;Name=rnhA;locus_tag=Cj1636c;Dbxref=GeneID:905909;gbkey=Gene NC_002163.1 RefSeq CDS 1561472 1561912 . - 0 ID=cds1488;Parent=gene1572;gene=rnhA;Name=YP_002345005.1;Dbxref=GOA:Q9PM39 HSSP:P00647 InterPro:IPR002156 UniProtKB FSwiss-Prot:Q9PM39 Genbank:YP_002345005.1 GeneID:905909;gbkey=CDS;product=ribonuclease H;Note=An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids NC_002163.1 RefSeq region 1561505 1561912 . - . ID=id2875;gene=rnhA;Name=id2875;Dbxref=GeneID:905909;gbkey=misc_feature;Note=HMMPfam hit to PF00075 2C RNase H 2C score 3.7e-46 NC_002163.1 RefSeq CDS 1561899 1562885 . - 0 ID=cds1489;Parent=gene1573;Name=YP_002345006.1;Dbxref=GOA:Q0P7Z1 InterPro:IPR011990 InterPro:IPR013026 InterPro:IPR013105 UniProtKB FTrEMBL:Q0P7Z1 Genbank:YP_002345006.1 GeneID:905910;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1637c 2C probable periplasmic protein 2C len: 328 aa 3B 26.1 25 identity to HP0660. Contains possible N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF07719 Tetratricopeptide repeat identified within CDS. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 1561899 1562885 . - . ID=gene1573;gene=Cj1637c;Name=Cj1637c;locus_tag=Cj1637c;Dbxref=GeneID:905910;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 1561913 1562112 . - . ID=utr599;locus_tag=Cj1636c;product=ribonuclease H NC_002163.1 RefSeq region 1562472 1562573 . - . ID=id2876;Name=id2876;Dbxref=GeneID:905910;gbkey=misc_feature;Note=HMMPfam hit to PF07719 2C Tetratricopeptide repeat 2Cscore 0.0026 NC_002163.1 RefSeq region 1562784 1562852 . - . ID=id2877;Name=id2877;Dbxref=GeneID:905910;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1637c by TMHMM2.0 at aa 12-34 ### NC_002163.1 UTR_Extractor 5'-UTR 1562886 1562907 . - . ID=utr600;locus_tag=Cj1637c;product=putative periplasmic protein NC_002163.1 UTR_Extractor 5'-UTR 1562943 1562954 . + . ID=utr601;locus_tag=Cj1638;product=DNA primase NC_002163.1 RefSeq CDS 1562955 1564772 . + 0 ID=cds1490;Parent=gene1574;gene=dnaG;Name=YP_002345007.1;Dbxref=GOA:Q9PM37 HSSP:P02923 InterPro:IPR002694 InterPro:IPR006154 InterPro:IPR006171 InterPro:IPR006295 InterPro:IPR013264 UniProtKB FSwiss-Prot:Q9PM37 Genbank:YP_002345007.1 GeneID:905911;gbkey=CDS;product=DNA primase;Note=synthesizes RNA primers at the replication forks NC_002163.1 RefSeq gene 1562955 1564772 . + . ID=gene1574;gene=dnaG;Name=dnaG;locus_tag=Cj1638;Dbxref=GeneID:905911;gbkey=Gene NC_002163.1 RefSeq region 1562958 1563251 . + . ID=id2878;gene=dnaG;Name=id2878;Dbxref=GeneID:905911;gbkey=misc_feature;Note=HMMPfam hit to PF01807 2C CHC2 zinc finger 2C score 4.2e-50 NC_002163.1 RefSeq region 1563696 1563935 . + . ID=id2879;gene=dnaG;Name=id2879;Dbxref=GeneID:905911;gbkey=misc_feature;Note=HMMPfam hit to PF01751 2C Toprim domain 2C score 3.7e-18 ### NC_002163.1 RefSeq CDS 1564854 1565126 . + 0 ID=cds1491;Parent=gene1575;Name=YP_002345008.1;Dbxref=GOA:O69292 InterPro:IPR001075 UniProtKB FTrEMBL:O69292 Genbank:YP_002345008.1 GeneID:905912;gbkey=CDS;product=NifU protein;Note=Original 282000 29 note: Cj1639 2C unknown 2C len: 90 aa 3B similar to members of the NIFU family of hypothetical poteins e.g. NIU1_RHOCA NIFU protein 1 28135 aa 29 2C fasta scores 3B opt: 158 z-score: 219.3 E 28 29: 6.8e-05 36.5 25 identity in 63 aa overlap. Identical to TR:O69292 28EMBL:Y16882 29 C. jejuni NIFU-like protein. 52.2 25 identity to HP1492. Contains Pfam match to entry PF01106 NifU-like 2CNifU-like domain. Also similar to N-terminus of Cj0239c 2838.2 25 identity in 76 aa overlap 29. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 1564854 1565126 . + . ID=gene1575;Name=Cj1639;locus_tag=Cj1639;Dbxref=GeneID:905912;gbkey=Gene NC_002163.1 RefSeq region 1564890 1565093 . + . ID=id2880;Name=id2880;Dbxref=GeneID:905912;gbkey=misc_feature;Note=HMMPfam hit to PF01106 2C NifU-like domain 2C score 2.7e-20 NC_002163.1 RefSeq region 1564968 1565000 . + . ID=id2881;Name=id2881;Dbxref=GeneID:905912;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq CDS 1565113 1565664 . + 0 ID=cds1492;Parent=gene1576;Name=YP_002345009.1;Dbxref=UniProtKB FTrEMBL:Q0P7Y8 Genbank:YP_002345009.1 GeneID:905913;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1640 2C unknown 2C len: 183 aa 3B 27.7 25 identity to HP1493. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 1565113 1565664 . + . ID=gene1576;Name=Cj1640;locus_tag=Cj1640;Dbxref=GeneID:905913;gbkey=Gene NC_002163.1 RefSeq region 1565648 1566454 . + . ID=id2882;gene=murE;Name=id2882;Dbxref=GeneID:905914;gbkey=misc_feature;Note=HMMPfam hit to PF01225 2C Mur ligase family 2Ccatalytic domain 2C score 6.2e-36 NC_002163.1 RefSeq CDS 1565648 1566931 . + 0 ID=cds1493;Parent=gene1577;gene=murE;Name=YP_002345010.1;Dbxref=GOA:O69290 HSSP:P22188 InterPro:IPR004101 InterPro:IPR005761 InterPro:IPR013221 UniProtKB FSwiss-Prot:O69290 Genbank:YP_002345010.1 GeneID:905914;gbkey=CDS;product=UDP-N-acetylmuramoylalanyl-D-glutamate--2 2C6-diaminopimelate ligase;Note=involved in cell wall formation 3B peptidoglycan synthesis 3B cytoplasmic enzyme 3B catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-aceylmuramoyl-l-alanyl-d-glutamate NC_002163.1 RefSeq gene 1565648 1566931 . + . ID=gene1577;gene=murE;Name=murE;locus_tag=Cj1641;Dbxref=GeneID:905914;gbkey=Gene NC_002163.1 RefSeq region 1565831 1565902 . + . ID=id2883;gene=murE;Name=id2883;Dbxref=GeneID:905914;gbkey=misc_feature;Note=PS01011 Folylpolyglutamate synthase signature 1 NC_002163.1 RefSeq region 1566383 1566415 . + . ID=id2884;gene=murE;Name=id2884;Dbxref=GeneID:905914;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1566479 1566724 . + . ID=id2885;gene=murE;Name=id2885;Dbxref=GeneID:905914;gbkey=misc_feature;Note=HMMPfam hit to PF02875 2C Mur ligase family 2Cglutamate ligase doma 2C score 9.8e-27 NC_002163.1 UTR_Extractor 5'-UTR 1566830 1566934 . + . ID=utr602;locus_tag=Cj1642;product=hypothetical protein ### NC_002163.1 RefSeq CDS 1566935 1567246 . + 0 ID=cds1494;Parent=gene1578;Name=YP_002345011.1;Dbxref=GOA:Q9PM34 HSSP:P17577 InterPro:IPR004401 UniProtKB FSwiss-Prot:Q9PM34 Genbank:YP_002345011.1 GeneID:905915;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1642 2C unknown 2C len: 309 aa 3B similar to hypothetical proteins e.g. TR:O34247 28EMBL:AJ003049 29 Wolinella succinogenes ORF102 28102 aa 29 2Cfasta scores 3B opt: 351 z-score: 446.1 E 28 29: 1.6e-17 2C 62.5 25 identity in 96 aa overlap 2C and YBAB_ECOLI 28109 aa 29 2C fast scores 3B opt: 182 z-score: 240.6 E 28 29: 4.4e-06 2C 36.7 25 identity in 98 aa overlap. 45.4 25 identity to HP0035 7EUpdated 282006 29 note: Pfam domain PF02575 Uncharacterised BCR 2C YbaB family COG0718 identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq gene 1566935 1567246 . + . ID=gene1578;Name=Cj1642;locus_tag=Cj1642;Dbxref=GeneID:905915;gbkey=Gene NC_002163.1 RefSeq region 1566965 1567237 . + . ID=id2886;Name=id2886;Dbxref=GeneID:905915;gbkey=misc_feature;Note=HMMPfam hit to PF02575 2C Uncharacterised BCR 2C YbaB family COG0718 2C score 9.9e-35 NC_002163.1 RefSeq gene 1567243 1568337 . + . ID=gene1579;Name=Cj1643;locus_tag=Cj1643;Dbxref=GeneID:905916;gbkey=Gene NC_002163.1 RefSeq CDS 1567243 1568337 . + 0 ID=cds1495;Parent=gene1579;Name=YP_002345012.1;Dbxref=GOA:Q0P7Y5 InterPro:IPR001478 UniProtKB FTrEMBL:Q0P7Y5 Genbank:YP_002345012.1 GeneID:905916;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1643 2C probable periplasmic protein 2C len: 364 aa 3B similar to hypothetical proteins e.g. TR:O34248 28EMBL:AJ003049 29 Wolinella succinogenes ORF341 protein 28341 aa 29 2C fasta scores 3B opt: 238 z-score: 283.8 E 28 29: 1.7e-08 2C 23.6 25 identity in 314 aa overlap. 25.5 25 identity to HP0036. Contains probable N-terminal signal sequence 2C and Pfam match to entry PF00595 PDZ 2C PDZ domain 28Also known as DHR or GLGF 29 7EUpdated 282006 29 note: Paper identified linking protein to glycoprotein. Functional classification -Miscellaneous periplasmic proteins 7EPMID:12186869 NC_002163.1 RefSeq CDS 1568334 1569179 . + 0 ID=cds1496;Parent=gene1580;gene=ispA;Name=YP_002345013.1;Dbxref=GOA:Q0P7Y4 InterPro:IPR000092 InterPro:IPR008949 InterPro:IPR017446 UniProtKB FTrEMBL:Q0P7Y4 Genbank:YP_002345013.1 GeneID:905917;gbkey=CDS;product=geranyltranstransferase;Note=Original 282000 29 note: Cj1644 2C ispA 2C probable geranyltranstransferase 2C len: 281 aa 3B similar to many e.g. ISPA_ECOLI geranyltranstransferase 28EC 2.5.1.10 29 28FARN 28299 aa 29 2C fast scores 3B opt: 520 z-score: 633.4 E 28 29: 5.8e-28 2C 37.5 25 identity in 275 aa overlap. 48.0 25 identity to HP0929. Alos similar to Cj0541 2827.6 25 identity in 268 aa overlap 29. Contains PS00723 and PS00444 Polyprenyl synthetases signatures 1 and 2 2C and Pfam match to entry PF00348 polyprenyl_synt 2C Polyprenyl synthetases 7EUpdated 282006 29 note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Biosynthesis of cofactors 2C prosthetic groups and carriers - Menaquinone and ubiquinine 7EPMID:2089044 NC_002163.1 RefSeq gene 1568334 1569179 . + . ID=gene1580;gene=ispA;Name=ispA;locus_tag=Cj1644;Dbxref=GeneID:905917;gbkey=Gene NC_002163.1 RefSeq region 1568403 1569167 . + . ID=id2887;gene=ispA;Name=id2887;Dbxref=GeneID:905917;gbkey=misc_feature;Note=HMMPfam hit to PF00348 2C Polyprenyl synthetase 2Cscore 8.6e-63 NC_002163.1 RefSeq region 1568556 1568606 . + . ID=id2888;gene=ispA;Name=id2888;Dbxref=GeneID:905917;gbkey=misc_feature;Note=PS00723 Polyprenyl synthetases signature 1 NC_002163.1 RefSeq region 1568946 1568984 . + . ID=id2889;gene=ispA;Name=id2889;Dbxref=GeneID:905917;gbkey=misc_feature;Note=PS00444 Polyprenyl synthetases signature 2 ### NC_002163.1 RefSeq CDS 1569190 1571088 . + 0 ID=cds1497;Parent=gene1581;gene=tkt;Name=YP_002345014.1;Dbxref=GOA:Q0P7Y3 InterPro:IPR005474 InterPro:IPR005475 InterPro:IPR005476 InterPro:IPR005478 InterPro:IPR015941 UniProtKB FTrEMBL:Q0P7Y3 Genbank:YP_002345014.1 GeneID:905918;gbkey=CDS;product=transketolase;Note=catalyzes the formation of ribose 5-phosphate and xylulose 5-phosphate from sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate 3B can transfer ketol groups between several groups 3B in Escherichia coli there are two tkt genes 2C tktA expressed during exponential growth and the tktB during stationary phase NC_002163.1 RefSeq gene 1569190 1571088 . + . ID=gene1581;gene=tkt;Name=tkt;locus_tag=Cj1645;Dbxref=GeneID:905918;gbkey=Gene NC_002163.1 RefSeq region 1569202 1570182 . + . ID=id2890;gene=tkt;Name=id2890;Dbxref=GeneID:905918;gbkey=misc_feature;Note=HMMPfam hit to PF00456 2C Transketolase 2C thiamine diphosphate b 2C score 1.1e-148 NC_002163.1 RefSeq region 1569229 1569291 . + . ID=id2891;gene=tkt;Name=id2891;Dbxref=GeneID:905918;gbkey=misc_feature;Note=PS00801 Transketolase signature 1 NC_002163.1 RefSeq region 1570201 1570704 . + . ID=id2892;gene=tkt;Name=id2892;Dbxref=GeneID:905918;gbkey=misc_feature;Note=HMMPfam hit to PF02779 2C Transketolase 2C pyridine binding domai 2C score 3.3e-50 NC_002163.1 RefSeq region 1570528 1570578 . + . ID=id2893;gene=tkt;Name=id2893;Dbxref=GeneID:905918;gbkey=misc_feature;Note=PS00802 Transketolase signature 2 NC_002163.1 RefSeq region 1570738 1571064 . + . ID=id2894;gene=tkt;Name=id2894;Dbxref=GeneID:905918;gbkey=misc_feature;Note=HMMPfam hit to PF02780 2C Transketolase 2C C-terminal domain 2C score 0.00035 ### NC_002163.1 RefSeq CDS 1571090 1572199 . + 0 ID=cds1498;Parent=gene1582;gene=iamB;Name=YP_002345015.1;Dbxref=InterPro:IPR003453 UniProtKB FTrEMBL:Q0P7Y2 Genbank:YP_002345015.1 GeneID:905919;gbkey=CDS;product=ABC transporter permease;Note=Original 282000 29 note: Cj1646 2C iamB 2C possible ABC transport system permease 2C len: 369 aa 3B 91.6 25 identity to TR:O68254 28EMBL:AF023133 29 C. jejuni iamB gene fragment 28133 aa 29. Similar to hypothetical proteins e.g. YRBE_ECOLI 28260 aa 29 2C fast scores 3B opt: 363 z-score: 423.9 E 28 29: 2.7e-16 2C 28.1 25 identity in 256 aa overlap 2C and to TR:AAD17958 28EMBL:AF106002 29 Pseudomonas putida toluene tolerance protein TTG2B 28265 aa 29 2C fast scores 3B opt: 381 z-score: 444.3 E 28 29: 2e-17 2C 30.0 25 identity in 203 aa overlap. 41.1 25 identity to HP1466 7EUpdated 282006 29 note: Pfam domain PF02405 Domain of unknown function DUF140 identified within CDS. Six probable transmembrane helices predicted by TMHMM2.0. Specific characterisation with acceptable identity score has not been carried out yet. kept within product function. Some work carried out within Campylobacter spp. Functional classification - Transport 2Fbinding proteins -Other 7EPMID:11283056 2C PMID:12694614 NC_002163.1 RefSeq gene 1571090 1572199 . + . ID=gene1582;gene=iamB;Name=iamB;locus_tag=Cj1646;Dbxref=GeneID:905919;gbkey=Gene NC_002163.1 RefSeq region 1571453 1571512 . + . ID=id2895;gene=iamB;Name=id2895;Dbxref=GeneID:905919;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1646 by TMHMM2.0 at aa 122-141 2C 161-183 2C 193-215 2C259-281 2C 306-325 and 346-368 NC_002163.1 RefSeq region 1571456 1572184 . + . ID=id2896;gene=iamB;Name=id2896;Dbxref=GeneID:905919;gbkey=misc_feature;Note=HMMPfam hit to PF02405 2C Domain of unknown function DUF140 2C score 1.4e-80 NC_002163.1 RefSeq region 1571570 1571638 . + . ID=id2895;gene=iamB;Name=id2895;Dbxref=GeneID:905919;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1646 by TMHMM2.0 at aa 122-141 2C 161-183 2C 193-215 2C259-281 2C 306-325 and 346-368 NC_002163.1 RefSeq region 1571666 1571734 . + . ID=id2895;gene=iamB;Name=id2895;Dbxref=GeneID:905919;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1646 by TMHMM2.0 at aa 122-141 2C 161-183 2C 193-215 2C259-281 2C 306-325 and 346-368 NC_002163.1 RefSeq region 1571864 1571932 . + . ID=id2895;gene=iamB;Name=id2895;Dbxref=GeneID:905919;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1646 by TMHMM2.0 at aa 122-141 2C 161-183 2C 193-215 2C259-281 2C 306-325 and 346-368 NC_002163.1 RefSeq region 1572005 1572064 . + . ID=id2895;gene=iamB;Name=id2895;Dbxref=GeneID:905919;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1646 by TMHMM2.0 at aa 122-141 2C 161-183 2C 193-215 2C259-281 2C 306-325 and 346-368 NC_002163.1 RefSeq region 1572032 1572064 . + . ID=id2897;gene=iamB;Name=id2897;Dbxref=GeneID:905919;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1572125 1572193 . + . ID=id2895;gene=iamB;Name=id2895;Dbxref=GeneID:905919;gbkey=misc_feature;Note=6 probable transmembrane helices predicted for Cj1646 by TMHMM2.0 at aa 122-141 2C 161-183 2C 193-215 2C259-281 2C 306-325 and 346-368 ### NC_002163.1 RefSeq CDS 1572200 1572922 . + 0 ID=cds1499;Parent=gene1583;gene=iamA;Name=YP_002345016.1;Dbxref=GOA:Q0P7Y1 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FTrEMBL:Q0P7Y1 Genbank:YP_002345016.1 GeneID:905920;gbkey=CDS;product=ABC transporter ATP-binding protein;Note=Original 282000 29 note: Cj1647 2C iamA 2C probable ABC transport system ATP-binding protein 2C len: 240 aa 3B 89.5 25 identity to TR:O68255 28EMBL:AF023133 29 C. jejuni iamA ABC-transporter. Similar to hypothetical proteins e.g. YRBF_ECOLI HYPOTHETICAL ABC transporter ATP-binding protein 28269 aa 29 2C fasta scores 3B opt: 453 z-score: 533.0 E 28 29: 2.3e-22 2C 31.8 25 identity in 239 aa overlap 2C and to TR:AAD17957 28EMBL:AF106002 29 Pseudomonas putida toluene tolerance protein TTG2A 28269 aa 29 2C fasta scores 3B opt: 491 z-score: 576.9 E 28 29: 8.2e-25 2C 34.5 25 identity in 238 aa overlap. 40.5 25 identity to HP1465. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00211 ABC transporters family signature 2C and fam match to entry PF00005 ABC_tran 2C ABC transporters 7EUpdated 282006 29 note: Specific characterisation with acceptable identity score has not been carried out yet. Thus 2C kept within product function. Some work carried out within Campylobacter spp. Functional classification - Transport 2Fbinding proteins - Other 7EPMID:11283056 2C PMID:16300911 NC_002163.1 RefSeq gene 1572200 1572922 . + . ID=gene1583;gene=iamA;Name=iamA;locus_tag=Cj1647;Dbxref=GeneID:905920;gbkey=Gene NC_002163.1 RefSeq region 1572281 1572847 . + . ID=id2898;gene=iamA;Name=id2898;Dbxref=GeneID:905920;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 4e-51 NC_002163.1 RefSeq region 1572302 1572325 . + . ID=id2899;gene=iamA;Name=id2899;Dbxref=GeneID:905920;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 1572617 1572661 . + . ID=id2900;gene=iamA;Name=id2900;Dbxref=GeneID:905920;gbkey=misc_feature;Note=PS00211 ABC transporters family signature ### NC_002163.1 RefSeq CDS 1572925 1573815 . + 0 ID=cds1500;Parent=gene1584;Name=YP_002345017.1;Dbxref=GOA:Q0P7Y0 InterPro:IPR003399 UniProtKB FTrEMBL:Q0P7Y0 Genbank:YP_002345017.1 GeneID:905921;gbkey=CDS;product=ABC transporter substrate-binding protein;Note=Original 282000 29 note: Cj1648 2C possible ABC transport system periplasmic substrate-binding protein 2Clen: 296 aa 3B similar to hypothetical proteins e.g. TR:O67491 28EMBL:AE000744 29 Aquifex aeolicus AQ_1533 28300 aa 29 2C fasta scores 3B opt: 362 z-score: 406.8 E 28 29: 2.4e-15 2C29.7 25 identity in 303 aa overlap 2C and 2C weakly 2C to TR:AAD17959 28EMBL:AF106002 29 Pseudomonas putida toluene tolerance protein TTG2C 28161 aa 29 2C fasta scores 3B opt: 161 z-score: 190.8 E 28 29: 0.0026 2C 28.7 25 identity in 122 aa overlap. 24.0 25 identity to HP1464. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF02470 mce related protein identified within CDS. Specific characterisation with acceptable identity score has not been carried out yet. kept within product function. Functional classification - Transport 2Fbinding proteins - Other NC_002163.1 RefSeq gene 1572925 1573815 . + . ID=gene1584;Name=Cj1648;locus_tag=Cj1648;Dbxref=GeneID:905921;gbkey=Gene NC_002163.1 RefSeq region 1572943 1573011 . + . ID=id2901;Name=id2901;Dbxref=GeneID:905921;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1648 by TMHMM2.0 at aa 7-29 NC_002163.1 RefSeq region 1572952 1573362 . + . ID=id2902;Name=id2902;Dbxref=GeneID:905921;gbkey=misc_feature;Note=HMMPfam hit to PF02470 2C mce related protein 2C score 0.00095 NC_002163.1 RefSeq CDS 1573815 1574414 . + 0 ID=cds1501;Parent=gene1585;Name=YP_002345018.1;Dbxref=GOA:Q0P7X9 UniProtKB FTrEMBL:Q0P7X9 Genbank:YP_002345018.1 GeneID:905922;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj1649 2C probable lipoprotein 2Clen: 199 aa 3B some similarity to YFXK_BRAJA hypothetical protein in 28fragment 29 28180 aa 29 2C fast scores 3B opt: 184 z-score: 235.4 E 28 29: 8.6e-06 2C 24.5 25 identity in 143 aa overlap. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. No Hp match. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 1573815 1574414 . + . ID=gene1585;Name=Cj1649;locus_tag=Cj1649;Dbxref=GeneID:905922;gbkey=Gene NC_002163.1 RefSeq region 1573836 1573868 . + . ID=id2903;Name=id2903;Dbxref=GeneID:905922;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 UTR_Extractor 5'-UTR 1574446 1574469 . + . ID=utr603;locus_tag=Cj1650;product=hypothetical protein NC_002163.1 RefSeq gene 1574470 1574970 . + . ID=gene1586;Name=Cj1650;locus_tag=Cj1650;Dbxref=GeneID:905923;gbkey=Gene NC_002163.1 RefSeq CDS 1574470 1574970 . + 0 ID=cds1502;Parent=gene1586;Name=YP_002345019.1;Dbxref=UniProtKB FTrEMBL:Q0P7X8 Genbank:YP_002345019.1 GeneID:905923;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1650 2C unknown 2C len: 166 aa 3B 30.7 25 identity to HP1076. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq gene 1575014 1575112 . + . ID=NC_002163.1:CJnc180;Name=NC_002163.1:CJnc180;locus_tag=CJnc180 NC_002163.1 RefSeq sRNA 1575014 1575112 . + . ID=NC_002163.1:CJnc180:unknown_transcript_1;Parent=NC_002163.1:CJnc180;Name=NC_002163.1:CJnc180:unknown_transcript_1;locus_tag=CJnc180;gbkey=misc_RNA;product=CJnc180 NC_002163.1 RefSeq gene 1575042 1575257 . - . ID=NC_002163.1:CJnc190;Name=NC_002163.1:CJnc190;locus_tag=CJnc190 NC_002163.1 RefSeq sRNA 1575042 1575257 . - . ID=NC_002163.1:CJnc190:unknown_transcript_1;Parent=NC_002163.1:CJnc190;Name=NC_002163.1:CJnc190:unknown_transcript_1;locus_tag=CJnc190;gbkey=misc_RNA;product=CJnc190 ### NC_002163.1 RefSeq CDS 1575339 1576097 . - 0 ID=cds1503;Parent=gene1587;gene=map;Name=YP_002345020.1;Dbxref=GOA:Q0P7X7 InterPro:IPR000994 InterPro:IPR001714 InterPro:IPR002467 UniProtKB FTrEMBL:Q0P7X7 Genbank:YP_002345020.1 GeneID:905924;gbkey=CDS;product=methionine aminopeptidase;Note=catalyzes the removal of N-terminal amino acids from peptides and arylamides 3B generally Co 28II 29 however activity has been shown for some methionine aminopeptidases with Zn 2C Fe 2C or Mn NC_002163.1 RefSeq gene 1575339 1576097 . - . ID=gene1587;gene=map;Name=map;locus_tag=Cj1651c;Dbxref=GeneID:905924;gbkey=Gene NC_002163.1 RefSeq region 1575345 1576067 . - . ID=id2904;gene=map;Name=id2904;Dbxref=GeneID:905924;gbkey=misc_feature;Note=HMMPfam hit to PF00557 2C metallopeptidase family M24 2C score 1.5e-59 NC_002163.1 RefSeq region 1575549 1575605 . - . ID=id2905;gene=map;Name=id2905;Dbxref=GeneID:905924;gbkey=misc_feature;Note=PS00680 Methionine aminopeptidase subfamily 1 signature ### NC_002163.1 RefSeq CDS 1576099 1576851 . - 0 ID=cds1504;Parent=gene1588;gene=murI;Name=YP_002345021.1;Dbxref=GOA:Q9PM24 HSSP:P56868 InterPro:IPR001920 InterPro:IPR004391 InterPro:IPR015942 UniProtKB FSwiss-Prot:Q9PM24 Genbank:YP_002345021.1 GeneID:905925;gbkey=CDS;product=glutamate racemase;Note=converts L-glutamate to D-glutamate 2C a component of peptidoglycan NC_002163.1 RefSeq gene 1576099 1576851 . - . ID=gene1588;gene=murI;Name=murI;locus_tag=Cj1652c;Dbxref=GeneID:905925;gbkey=Gene NC_002163.1 RefSeq region 1576204 1576848 . - . ID=id2906;gene=murI;Name=id2906;Dbxref=GeneID:905925;gbkey=misc_feature;Note=HMMPfam hit to PF01177 2C Asp 2FGlu 2FHydantoin racemase 2Cscore 2e-90 NC_002163.1 RefSeq region 1576294 1576326 . - . ID=id2907;gene=murI;Name=id2907;Dbxref=GeneID:905925;gbkey=misc_feature;Note=PS00924 Aspartate and glutamate racemases signature 2 NC_002163.1 RefSeq region 1576627 1576653 . - . ID=id2908;gene=murI;Name=id2908;Dbxref=GeneID:905925;gbkey=misc_feature;Note=PS00923 Aspartate and glutamate racemases signature 1 NC_002163.1 RefSeq region 1576741 1576788 . - . ID=id2909;gene=murI;Name=id2909;Dbxref=GeneID:905925;gbkey=misc_feature;Note=PS00225 Crystallins beta and gamma 27Greek key 27 motif signature ### NC_002163.1 RefSeq CDS 1576853 1577311 . - 0 ID=cds1505;Parent=gene1589;Name=YP_002345022.1;Dbxref=GOA:Q0P7X5 InterPro:IPR000064 UniProtKB FTrEMBL:Q0P7X5 Genbank:YP_002345022.1 GeneID:905926;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj1653c 2C probable lipoprotein 2C len: 152 aa 3B similar to hypothetical proteins e.g. NLPC_ECOLI probable lipoprotein NLPC precursor 28154 aa 29 2C fasta scores 3B opt: 381 z-score: 485.2 E 28 29: 1e-19 2C40.3 25 identity in 154 aa overlap 2C and SPR_ECOLI lipoprotein SPR precursor 28188 aa 29 2C fasta scores 3B opt: 355 z-score: 451.8 E 28 29: 7.6e-18 2C 44.7 25 identity in 123 aa overlap. No Hp match. Contains probable N-terminal signal sequence with appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site 2C and Pfam match to entry PF00877 NLPC_P60 2C NLP 2FP60 family. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 1576853 1577311 . - . ID=gene1589;Name=Cj1653c;locus_tag=Cj1653c;Dbxref=GeneID:905926;gbkey=Gene NC_002163.1 RefSeq region 1576859 1577176 . - . ID=id2910;Name=id2910;Dbxref=GeneID:905926;gbkey=misc_feature;Note=HMMPfam hit to PF00877 2C NlpC 2FP60 family 2C score 7.8e-40 NC_002163.1 RefSeq region 1577243 1577302 . - . ID=id2911;Name=id2911;Dbxref=GeneID:905926;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1653c by TMHMM2.0 at aa 4-23 NC_002163.1 RefSeq region 1577261 1577293 . - . ID=id2912;Name=id2912;Dbxref=GeneID:905926;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq CDS 1577320 1578489 . - 0 ID=cds1506;Parent=gene1590;gene=nhaA;Name=YP_002345023.1;Dbxref=GOA:Q0P7X4 InterPro:IPR000215 InterPro:IPR004670 UniProtKB FSwiss-Prot:Q0P7X4 Genbank:YP_002345023.1 GeneID:905927;gbkey=CDS;product=pH-dependent sodium 2Fproton antiporter;Note=exports sodium by using the electrochemical proton gradient to allow protons into the cell 3B functions in adaptation to high salinity and alkaline pH 3B activity increases at higher pH 3B downregulated at acidic pH NC_002163.1 RefSeq gene 1577320 1578489 . - . ID=gene1590;gene=nhaA;Name=nhaA;locus_tag=Cj1654c;Dbxref=GeneID:905927;gbkey=Gene NC_002163.1 RefSeq region 1577329 1577397 . - . ID=id147;gene=nhaA;Name=id147;Dbxref=GeneID:905927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1654c by TMHMM2.0 at aa 12-34 2C 61-83 2C 96-118 2C 128-145 2C157-179 2C 183-205 2C 218-240 2C 260-282 2C 293-315 2C 330-352 and 365-387 NC_002163.1 RefSeq region 1577344 1578468 . - . ID=id2913;gene=nhaA;Name=id2913;Dbxref=GeneID:905927;gbkey=misc_feature;Note=HMMPfam hit to PF06965 2C Na 2B 2FH 2B antiporter 2C score 2.2e-229 NC_002163.1 RefSeq region 1577434 1577502 . - . ID=id147;gene=nhaA;Name=id147;Dbxref=GeneID:905927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1654c by TMHMM2.0 at aa 12-34 2C 61-83 2C 96-118 2C 128-145 2C157-179 2C 183-205 2C 218-240 2C 260-282 2C 293-315 2C 330-352 and 365-387 NC_002163.1 RefSeq region 1577545 1577613 . - . ID=id147;gene=nhaA;Name=id147;Dbxref=GeneID:905927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1654c by TMHMM2.0 at aa 12-34 2C 61-83 2C 96-118 2C 128-145 2C157-179 2C 183-205 2C 218-240 2C 260-282 2C 293-315 2C 330-352 and 365-387 NC_002163.1 RefSeq region 1577644 1577712 . - . ID=id147;gene=nhaA;Name=id147;Dbxref=GeneID:905927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1654c by TMHMM2.0 at aa 12-34 2C 61-83 2C 96-118 2C 128-145 2C157-179 2C 183-205 2C 218-240 2C 260-282 2C 293-315 2C 330-352 and 365-387 NC_002163.1 RefSeq region 1577770 1577838 . - . ID=id147;gene=nhaA;Name=id147;Dbxref=GeneID:905927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1654c by TMHMM2.0 at aa 12-34 2C 61-83 2C 96-118 2C 128-145 2C157-179 2C 183-205 2C 218-240 2C 260-282 2C 293-315 2C 330-352 and 365-387 NC_002163.1 RefSeq region 1577875 1577943 . - . ID=id147;gene=nhaA;Name=id147;Dbxref=GeneID:905927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1654c by TMHMM2.0 at aa 12-34 2C 61-83 2C 96-118 2C 128-145 2C157-179 2C 183-205 2C 218-240 2C 260-282 2C 293-315 2C 330-352 and 365-387 NC_002163.1 RefSeq region 1577953 1578021 . - . ID=id147;gene=nhaA;Name=id147;Dbxref=GeneID:905927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1654c by TMHMM2.0 at aa 12-34 2C 61-83 2C 96-118 2C 128-145 2C157-179 2C 183-205 2C 218-240 2C 260-282 2C 293-315 2C 330-352 and 365-387 NC_002163.1 RefSeq region 1578055 1578108 . - . ID=id147;gene=nhaA;Name=id147;Dbxref=GeneID:905927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1654c by TMHMM2.0 at aa 12-34 2C 61-83 2C 96-118 2C 128-145 2C157-179 2C 183-205 2C 218-240 2C 260-282 2C 293-315 2C 330-352 and 365-387 NC_002163.1 RefSeq region 1578136 1578204 . - . ID=id147;gene=nhaA;Name=id147;Dbxref=GeneID:905927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1654c by TMHMM2.0 at aa 12-34 2C 61-83 2C 96-118 2C 128-145 2C157-179 2C 183-205 2C 218-240 2C 260-282 2C 293-315 2C 330-352 and 365-387 NC_002163.1 RefSeq region 1578241 1578309 . - . ID=id147;gene=nhaA;Name=id147;Dbxref=GeneID:905927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1654c by TMHMM2.0 at aa 12-34 2C 61-83 2C 96-118 2C 128-145 2C157-179 2C 183-205 2C 218-240 2C 260-282 2C 293-315 2C 330-352 and 365-387 NC_002163.1 RefSeq region 1578292 1578324 . - . ID=id2914;gene=nhaA;Name=id2914;Dbxref=GeneID:905927;gbkey=misc_feature;Note=PS00284 Serpins signature NC_002163.1 RefSeq region 1578388 1578456 . - . ID=id147;gene=nhaA;Name=id147;Dbxref=GeneID:905927;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1654c by TMHMM2.0 at aa 12-34 2C 61-83 2C 96-118 2C 128-145 2C157-179 2C 183-205 2C 218-240 2C 260-282 2C 293-315 2C 330-352 and 365-387 NC_002163.1 RefSeq gene 1578486 1579634 . - . ID=gene1591;gene=nhaA1;Name=nhaA1;locus_tag=Cj1655c;Dbxref=GeneID:905928;gbkey=Gene NC_002163.1 RefSeq CDS 1578486 1579634 . - 0 ID=cds1507;Parent=gene1591;gene=nhaA1;Name=YP_002345024.1;Dbxref=GOA:Q0P7X3 InterPro:IPR004670 UniProtKB FSwiss-Prot:Q0P7X3 Genbank:YP_002345024.1 GeneID:905928;gbkey=CDS;product=Na 28 2B 29 2FH 28 2B 29 antiporter;Note=Original 282000 29 note: Cj1655c 2C nhaA1 2C probable Na 28 2B 29 2FH 28 2B 29 antiporter 2C len: 382 aa 3B similar to e.g. NHAA_ECOLI Na 28 2B 29 2FH 28 2B 29 antiporter 1 28388 aa 29 2C fasta scores 3B opt: 1165 z-score: 1343.6 E 28 29: 0 2C 47.3 25 identity in 383 aa overlap. 41.0 25 identity to HP1552. Also similar to Cj1654c nhaA2 2856.3 25 identity in 378 aa overlap 29 7EUpdated 282006 29 note: Pfam domain PF06965 Na 2B 2FH 2B antiporter identified within CDS. Further support given to product function. Also 2C ten probable transmembrane helices predicted by TMHMM2.0. Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification - Transport 2Fbinding proteins - Cations 7EPMID:1645730 2C PMID:1657980 2C PMID:9507001 NC_002163.1 RefSeq region 1578501 1578554 . - . ID=id148;gene=nhaA1;Name=id148;Dbxref=GeneID:905928;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1655c by TMHMM2.0 at aa 16-38 2C 58-80 2C 92-114 2C 124-146 2C153-175 2C 180-199 2C 206-228 2C 289-311 2C 324-346 and 361-378 NC_002163.1 RefSeq region 1578501 1579625 . - . ID=id2915;gene=nhaA1;Name=id2915;Dbxref=GeneID:905928;gbkey=misc_feature;Note=HMMPfam hit to PF06965 2C Na 2B 2FH 2B antiporter 2C score 1.1e-239 NC_002163.1 RefSeq region 1578597 1578665 . - . ID=id148;gene=nhaA1;Name=id148;Dbxref=GeneID:905928;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1655c by TMHMM2.0 at aa 16-38 2C 58-80 2C 92-114 2C 124-146 2C153-175 2C 180-199 2C 206-228 2C 289-311 2C 324-346 and 361-378 NC_002163.1 RefSeq region 1578702 1578770 . - . ID=id148;gene=nhaA1;Name=id148;Dbxref=GeneID:905928;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1655c by TMHMM2.0 at aa 16-38 2C 58-80 2C 92-114 2C 124-146 2C153-175 2C 180-199 2C 206-228 2C 289-311 2C 324-346 and 361-378 NC_002163.1 RefSeq region 1578951 1579019 . - . ID=id148;gene=nhaA1;Name=id148;Dbxref=GeneID:905928;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1655c by TMHMM2.0 at aa 16-38 2C 58-80 2C 92-114 2C 124-146 2C153-175 2C 180-199 2C 206-228 2C 289-311 2C 324-346 and 361-378 NC_002163.1 RefSeq region 1579038 1579097 . - . ID=id148;gene=nhaA1;Name=id148;Dbxref=GeneID:905928;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1655c by TMHMM2.0 at aa 16-38 2C 58-80 2C 92-114 2C 124-146 2C153-175 2C 180-199 2C 206-228 2C 289-311 2C 324-346 and 361-378 NC_002163.1 RefSeq region 1579110 1579178 . - . ID=id148;gene=nhaA1;Name=id148;Dbxref=GeneID:905928;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1655c by TMHMM2.0 at aa 16-38 2C 58-80 2C 92-114 2C 124-146 2C153-175 2C 180-199 2C 206-228 2C 289-311 2C 324-346 and 361-378 NC_002163.1 RefSeq region 1579197 1579265 . - . ID=id148;gene=nhaA1;Name=id148;Dbxref=GeneID:905928;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1655c by TMHMM2.0 at aa 16-38 2C 58-80 2C 92-114 2C 124-146 2C153-175 2C 180-199 2C 206-228 2C 289-311 2C 324-346 and 361-378 NC_002163.1 RefSeq region 1579293 1579361 . - . ID=id148;gene=nhaA1;Name=id148;Dbxref=GeneID:905928;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1655c by TMHMM2.0 at aa 16-38 2C 58-80 2C 92-114 2C 124-146 2C153-175 2C 180-199 2C 206-228 2C 289-311 2C 324-346 and 361-378 NC_002163.1 RefSeq region 1579395 1579463 . - . ID=id148;gene=nhaA1;Name=id148;Dbxref=GeneID:905928;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1655c by TMHMM2.0 at aa 16-38 2C 58-80 2C 92-114 2C 124-146 2C153-175 2C 180-199 2C 206-228 2C 289-311 2C 324-346 and 361-378 NC_002163.1 RefSeq region 1579521 1579589 . - . ID=id148;gene=nhaA1;Name=id148;Dbxref=GeneID:905928;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1655c by TMHMM2.0 at aa 16-38 2C 58-80 2C 92-114 2C 124-146 2C153-175 2C 180-199 2C 206-228 2C 289-311 2C 324-346 and 361-378 ### NC_002163.1 UTR_Extractor 5'-UTR 1579635 1579683 . - . ID=utr604;locus_tag=Cj1655c;product=Na 28 2B 29 2FH 28 2B 29 antiporter NC_002163.1 RefSeq gene 1579777 1579959 . - . ID=gene1592;Name=Cj1656c;locus_tag=Cj1656c;Dbxref=GeneID:905929;gbkey=Gene NC_002163.1 RefSeq CDS 1579777 1579959 . - 0 ID=cds1508;Parent=gene1592;Name=YP_002345025.1;Dbxref=UniProtKB FTrEMBL:Q0P7X2 Genbank:YP_002345025.1 GeneID:905929;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1656c 2C unknown 2C len: 180 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 UTR_Extractor 5'-UTR 1579960 1579989 . - . ID=utr605;locus_tag=Cj1656c;product=hypothetical protein NC_002163.1 UTR_Extractor 5'-UTR 1580782 1580835 . + . ID=utr606;locus_tag=Cj1658;product=putative iron permease NC_002163.1 RefSeq CDS 1580836 1582926 . + 0 ID=cds1509;Parent=gene1593;Name=YP_002345026.1;Dbxref=GOA:Q0P7X1 InterPro:IPR004923 UniProtKB FTrEMBL:Q0P7X1 Genbank:YP_002345026.1 GeneID:905930;gbkey=CDS;product=iron permease;Note=Original 282000 29 note: Cj1658 2C probable integral membrane protein 2C len: 696 aa 3B similar to TR:CAA21360 28EMBL:AL031866 29 Yersinia pestis ORF37 upstream of p19 homolog in 102 kbases unstable region 28639 aa 29 2C fasta scores 3B opt: 1055 z-score: 1112.1 E 28 29: 0 2C 31.6 25 identity in 706 aa overlap. Contains possible N-terminal signal sequence 2C followed by non-membrane domain with three coiled-coil regions to aa 440. C-terminal domain contains six possible membrane spanning sequences 2C and is similar to hypothetical membrane proteins e.g. YWBL_BACSU 28481 aa 29 2C fasta scores 3B opt: 439 z-score: 466.4 E 28 29: 1.2e-18 2C26.5 25 identity in 449 aa overlap. No Hp match 7EUpdated 282006 29 note: Pfam domain PF03239 Iron permease FTR1 family identified within CDS. Also 2C seven probable transmembrane helices predicted by TMHMM2.0. Product modified to more specific family member based on motif match. No specific characterisation has been carried out yet 2C so kept within product function. Literature search identified paper giving further clues to product function. Functional classification -Transport 2Fbinding proteins - Cations 7EPMID:15632442 NC_002163.1 RefSeq gene 1580836 1582926 . + . ID=gene1593;Name=Cj1658;locus_tag=Cj1658;Dbxref=GeneID:905930;gbkey=Gene NC_002163.1 RefSeq region 1581730 1582671 . + . ID=id2916;Name=id2916;Dbxref=GeneID:905930;gbkey=misc_feature;Note=HMMPfam hit to PF03239 2C Iron permease FTR1 family 2Cscore 2.3e-08 NC_002163.1 RefSeq region 1582150 1582209 . + . ID=id2917;Name=id2917;Dbxref=GeneID:905930;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1658 by TMHMM2.0 at aa 439-458 2C 470-492 2C 502-524 2C551-573 2C 583-604 2C 616-633 and 668-685 NC_002163.1 RefSeq region 1582243 1582311 . + . ID=id2917;Name=id2917;Dbxref=GeneID:905930;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1658 by TMHMM2.0 at aa 439-458 2C 470-492 2C 502-524 2C551-573 2C 583-604 2C 616-633 and 668-685 NC_002163.1 RefSeq region 1582339 1582407 . + . ID=id2917;Name=id2917;Dbxref=GeneID:905930;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1658 by TMHMM2.0 at aa 439-458 2C 470-492 2C 502-524 2C551-573 2C 583-604 2C 616-633 and 668-685 NC_002163.1 RefSeq region 1582486 1582554 . + . ID=id2917;Name=id2917;Dbxref=GeneID:905930;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1658 by TMHMM2.0 at aa 439-458 2C 470-492 2C 502-524 2C551-573 2C 583-604 2C 616-633 and 668-685 NC_002163.1 RefSeq region 1582582 1582647 . + . ID=id2917;Name=id2917;Dbxref=GeneID:905930;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1658 by TMHMM2.0 at aa 439-458 2C 470-492 2C 502-524 2C551-573 2C 583-604 2C 616-633 and 668-685 NC_002163.1 RefSeq region 1582681 1582734 . + . ID=id2917;Name=id2917;Dbxref=GeneID:905930;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1658 by TMHMM2.0 at aa 439-458 2C 470-492 2C 502-524 2C551-573 2C 583-604 2C 616-633 and 668-685 NC_002163.1 RefSeq region 1582837 1582890 . + . ID=id2917;Name=id2917;Dbxref=GeneID:905930;gbkey=misc_feature;Note=7 probable transmembrane helices predicted for Cj1658 by TMHMM2.0 at aa 439-458 2C 470-492 2C 502-524 2C551-573 2C 583-604 2C 616-633 and 668-685 NC_002163.1 RefSeq CDS 1582923 1583462 . + 0 ID=cds1510;Parent=gene1594;gene=p19;Name=YP_002345027.1;Dbxref=UniProtKB FTrEMBL:Q0P7X0 Genbank:YP_002345027.1 GeneID:905931;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1659 2C p19 2C periplasmic protein 2C len: 179 aa 3B identical to TR:O07089 28EMBL:Y13641 29 C. jejuni 19 kDa periplamic protein 28fragment 29 28152 aa 29 2Cand similar to TR:CAA21359 28EMBL:AL031866 29 Yersinia pestis ORF36 in 102 kbases unstable region 28175 aa 29 2C fasta scores 3B opt: 677 z-score: 805.8 E 28 29: 0 2C 57.9 25 identity in 178 aa overlap 2C and TA34_TREPA 34 kD membrane antigen precursor 28pathogen-specific membrane antigen 29 28204 aa 29 2Cfasta scores 3B opt: 353 z-score: 425.6 E 28 29: 2.2e-16 2C 35.8 25 identity in 159 aa overlap. No Hp match. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: One probable transmembrane helix predicted by TMHMM2.0. Characterised within Campylobacter jejuni 2C so not added to product function. Paper identified linking protein to glycoprotein. Functional classification - Miscellaneous periplasmic proteins 7EPMID:12186869 2C PMID:9766213 NC_002163.1 RefSeq gene 1582923 1583462 . + . ID=gene1594;gene=p19;Name=p19;locus_tag=Cj1659;Dbxref=GeneID:905931;gbkey=Gene NC_002163.1 RefSeq region 1582935 1583003 . + . ID=id2918;gene=p19;Name=id2918;Dbxref=GeneID:905931;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1659 by TMHMM2.0 at aa 5-27 ### NC_002163.1 RefSeq gene 1583545 1584948 . + . ID=gene1595;Name=Cj1660;locus_tag=Cj1660;Dbxref=GeneID:905932;gbkey=Gene NC_002163.1 RefSeq CDS 1583545 1584948 . + 0 ID=cds1511;Parent=gene1595;Name=YP_002345028.1;Dbxref=GOA:Q0P7W9 InterPro:IPR007029 UniProtKB FTrEMBL:Q0P7W9 Genbank:YP_002345028.1 GeneID:905932;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj1660 2C probable integral membrane protein 2C len: 467 aa 3B 97.3 25 identity to TR:O07090 28EMBL:Y13641 29 C. jejuni hypothetical protein 28fragment 29 2873 aa 29 2C and similar to TR:CAA21358 28EMBL:AL031866 29 Yersinia pestis ORF35 in 102 kbases unstable region 28469 aa 29 2C fasta scores 3B opt: 687 z-score: 761.3 E 28 29: 0 2C 27.5 25 identity in 465 aa overlap. No Hp match 7EUpdated 282006 29 note: Eight probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Pfam domain PF04945 YHS domain identified within CDS. No specific characterisation with acceptable identity score has been carried out yet 2C so kept within product function. Literature search identified paper giving further clues to product function. Functional classification - Membranes 2C lipoproteins and porins 7EPMID:15632442 NC_002163.1 RefSeq region 1583554 1583607 . + . ID=id2919;Name=id2919;Dbxref=GeneID:905932;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1660 by TMHMM2.0 at aa 4-21 2C 28-50 2C 60-79 2C 86-105 2C120-142 2C 154-176 2C 196-218 and 244-266 NC_002163.1 RefSeq region 1583626 1583694 . + . ID=id2919;Name=id2919;Dbxref=GeneID:905932;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1660 by TMHMM2.0 at aa 4-21 2C 28-50 2C 60-79 2C 86-105 2C120-142 2C 154-176 2C 196-218 and 244-266 NC_002163.1 RefSeq region 1583722 1583781 . + . ID=id2919;Name=id2919;Dbxref=GeneID:905932;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1660 by TMHMM2.0 at aa 4-21 2C 28-50 2C 60-79 2C 86-105 2C120-142 2C 154-176 2C 196-218 and 244-266 NC_002163.1 RefSeq region 1583800 1583859 . + . ID=id2919;Name=id2919;Dbxref=GeneID:905932;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1660 by TMHMM2.0 at aa 4-21 2C 28-50 2C 60-79 2C 86-105 2C120-142 2C 154-176 2C 196-218 and 244-266 NC_002163.1 RefSeq region 1583902 1583970 . + . ID=id2919;Name=id2919;Dbxref=GeneID:905932;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1660 by TMHMM2.0 at aa 4-21 2C 28-50 2C 60-79 2C 86-105 2C120-142 2C 154-176 2C 196-218 and 244-266 NC_002163.1 RefSeq region 1584004 1584072 . + . ID=id2919;Name=id2919;Dbxref=GeneID:905932;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1660 by TMHMM2.0 at aa 4-21 2C 28-50 2C 60-79 2C 86-105 2C120-142 2C 154-176 2C 196-218 and 244-266 NC_002163.1 RefSeq region 1584130 1584198 . + . ID=id2919;Name=id2919;Dbxref=GeneID:905932;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1660 by TMHMM2.0 at aa 4-21 2C 28-50 2C 60-79 2C 86-105 2C120-142 2C 154-176 2C 196-218 and 244-266 NC_002163.1 RefSeq region 1584274 1584342 . + . ID=id2919;Name=id2919;Dbxref=GeneID:905932;gbkey=misc_feature;Note=8 probable transmembrane helices predicted for Cj1660 by TMHMM2.0 at aa 4-21 2C 28-50 2C 60-79 2C 86-105 2C120-142 2C 154-176 2C 196-218 and 244-266 NC_002163.1 RefSeq region 1584772 1584906 . + . ID=id2920;Name=id2920;Dbxref=GeneID:905932;gbkey=misc_feature;Note=HMMPfam hit to PF04945 2C YHS domain 2C score 1.1e-17 NC_002163.1 RefSeq gene 1584935 1586227 . + . ID=gene1596;Name=Cj1661;locus_tag=Cj1661;Dbxref=GeneID:905933;gbkey=Gene NC_002163.1 RefSeq CDS 1584935 1586227 . + 0 ID=cds1512;Parent=gene1596;Name=YP_002345029.1;Dbxref=GOA:Q0P7W8 InterPro:IPR003838 UniProtKB FTrEMBL:Q0P7W8 Genbank:YP_002345029.1 GeneID:905933;gbkey=CDS;product=ABC transporter permease;Note=Original 282000 29 note: Cj1661 2C possible ABC transport system permease 2C len: 430 aa 3B similar to hypothetical membrane proteins e.g. TR:CAA21357 28EMBL:AL031866 29 Yersinia pestis ORF34 in 102 kbases unstable region 28430 aa 29 2C fasta scores 3B opt: 929 z-score: 1043.7 E 28 29: 0 2C 36.1 25 identity in 435 aa overlap 2C and to the membrane domain of hypothetical ACB-transporters e.g. YBJZ_ECOLI hypothetical ABC transporter ATP-binding protein 28648 aa 29 2C fasta scores 3B opt: 189 z-score: 214.0 E 28 29: 0.00014 2C 22.0 25 identity in 241 aa overlap. No Hp match. Also similar to Cj1662 2828.1 25 identity in 437 aa overlap 29 7EUpdated 282006 29 note: Four probable transmembrane helices predicted by TMHMM2.0. Pfam domain PF02687 Predicted permease identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score has been carried out yet 2Cso kept within product function. Functional classification - Transport 2Fbinding proteins - Other NC_002163.1 RefSeq region 1584992 1585060 . + . ID=id2921;Name=id2921;Dbxref=GeneID:905933;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1661 by TMHMM2.0 at aa 20-42 2C 303-325 2C 359-381 and 391-413 NC_002163.1 RefSeq region 1585715 1586203 . + . ID=id2922;Name=id2922;Dbxref=GeneID:905933;gbkey=misc_feature;Note=HMMPfam hit to PF02687 2C Predicted permease 2C score 2.3e-29 NC_002163.1 RefSeq region 1585841 1585909 . + . ID=id2921;Name=id2921;Dbxref=GeneID:905933;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1661 by TMHMM2.0 at aa 20-42 2C 303-325 2C 359-381 and 391-413 NC_002163.1 RefSeq region 1586009 1586077 . + . ID=id2921;Name=id2921;Dbxref=GeneID:905933;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1661 by TMHMM2.0 at aa 20-42 2C 303-325 2C 359-381 and 391-413 NC_002163.1 RefSeq region 1586105 1586173 . + . ID=id2921;Name=id2921;Dbxref=GeneID:905933;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1661 by TMHMM2.0 at aa 20-42 2C 303-325 2C 359-381 and 391-413 NC_002163.1 RefSeq region 1586135 1586167 . + . ID=id2923;Name=id2923;Dbxref=GeneID:905933;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq gene 1586217 1587335 . + . ID=gene1597;Name=Cj1662;locus_tag=Cj1662;Dbxref=GeneID:905934;gbkey=Gene NC_002163.1 RefSeq CDS 1586217 1587335 . + 0 ID=cds1513;Parent=gene1597;Name=YP_002345030.1;Dbxref=GOA:Q0P7W7 InterPro:IPR003838 UniProtKB FTrEMBL:Q0P7W7 Genbank:YP_002345030.1 GeneID:905934;gbkey=CDS;product=integral membrane protein;Note=Original 282000 29 note: Cj1662 2C probable integral membrane protein 2C len: 372 aa 3B similar to hypothetical membrane proteins e.g. TR:CAA21356 28EMBL:AL031866 29 Yersinia pestis ORF33 in 102 kbases unstable region 28387 aa 29 2C fasta scores 3B opt: 637 z-score: 710.8 E 28 29: 2.9e-32 2C32.5 25 identity in 375 aa overlap. No Hp match. Also similar to Cj1661 2828.1 25 identity in 437 aa overlap 29. Possibly a permease for an ABC transport system 3B ABC-binding protein is downstream 7EUpdated 282006 29 note: Four probable transmembrane helices predicted by TMHMM2.0. Pfam domain PF02687 Predicted permease identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score has been carried out yet 2Cso kept within product function. Functional classification - Transport 2Fbinding proteins - Other NC_002163.1 RefSeq region 1586277 1586345 . + . ID=id2924;Name=id2924;Dbxref=GeneID:905934;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1662 by TMHMM2.0 at aa 21-43 2C 250-272 2C 301-323 and 333-355 NC_002163.1 RefSeq region 1586820 1587311 . + . ID=id2925;Name=id2925;Dbxref=GeneID:905934;gbkey=misc_feature;Note=HMMPfam hit to PF02687 2C Predicted permease 2C score 1.4e-30 NC_002163.1 RefSeq region 1586964 1587032 . + . ID=id2924;Name=id2924;Dbxref=GeneID:905934;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1662 by TMHMM2.0 at aa 21-43 2C 250-272 2C 301-323 and 333-355 NC_002163.1 RefSeq region 1587117 1587185 . + . ID=id2924;Name=id2924;Dbxref=GeneID:905934;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1662 by TMHMM2.0 at aa 21-43 2C 250-272 2C 301-323 and 333-355 NC_002163.1 RefSeq region 1587213 1587281 . + . ID=id2924;Name=id2924;Dbxref=GeneID:905934;gbkey=misc_feature;Note=4 probable transmembrane helices predicted for Cj1662 by TMHMM2.0 at aa 21-43 2C 250-272 2C 301-323 and 333-355 NC_002163.1 RefSeq CDS 1587332 1587985 . + 0 ID=cds1514;Parent=gene1598;Name=YP_002345031.1;Dbxref=GOA:Q0P7W6 InterPro:IPR003439 InterPro:IPR003593 UniProtKB FTrEMBL:Q0P7W6 Genbank:YP_002345031.1 GeneID:905935;gbkey=CDS;product=ABC transporter ATP-binding protein;Note=Original 282000 29 note: Cj1663 2C probable ABC transport system ATP-binding protein 2C len: 217 aa 3B similar to many e.g. TR:CAA21355 28EMBL:AL031866 29 Yersinia pestis ORF32 in 102 kbases unstable region 28237 aa 29 2C fasta scores 3B opt: 859 z-score: 985.9 E 28 29: 0 2C 60.8 25 identity in 209 aa overlap 2C and GLNQ_ECOLI glutamine transport ATP-binding protein 28240 aa 29 2C fasta scores 3B opt: 555 z-score: 641.1 E 28 29: 2.2e-28 2C 43.5 25 identity in 214 aa overlap. No Hp ortholog. Contains PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 2C PS00211 ABC transporters family signature 2C and Pfam match to entry PF00005 ABC_tran 2C ABC transporters 7EUpdated 282006 29 note: kept within product function as similar to more than one transport system. Functional classification - Transport 2Fbinding proteins -Other NC_002163.1 RefSeq gene 1587332 1587985 . + . ID=gene1598;Name=Cj1663;locus_tag=Cj1663;Dbxref=GeneID:905935;gbkey=Gene NC_002163.1 RefSeq region 1587425 1587973 . + . ID=id2926;Name=id2926;Dbxref=GeneID:905935;gbkey=misc_feature;Note=HMMPfam hit to PF00005 2C ABC transporter 2C score 1.1e-63 NC_002163.1 RefSeq region 1587446 1587469 . + . ID=id2927;Name=id2927;Dbxref=GeneID:905935;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 1587749 1587793 . + . ID=id2928;Name=id2928;Dbxref=GeneID:905935;gbkey=misc_feature;Note=PS00211 ABC transporters family signature NC_002163.1 RefSeq CDS 1587982 1588470 . + 0 ID=cds1515;Parent=gene1599;Name=YP_002345032.1;Dbxref=GOA:Q0P7W5 InterPro:IPR006662 InterPro:IPR012335 InterPro:IPR013740 UniProtKB FTrEMBL:Q0P7W5 Genbank:YP_002345032.1 GeneID:905936;gbkey=CDS;product=thiredoxin;Note=Original 282000 29 note: Cj1664 2C possible periplasmic thiredoxin 2C len: 162 aa 3B similar to e.g. TR:CAA21354 28EMBL:AL031866 29 Yersinia pestis ORF31 in 102 kbases unstable region 28165 aa 29 2C fast scores 3B opt: 225 z-score: 278.4 E 28 29: 3.5e-08 2C 33.3 25 identity in 141 aa overlap 2C and weakly to RESA_BACSU RESA protein 28contains thiredoxin domain 29 28181 aa 29 2C fasta scores 3B opt: 124 z-score: 159.5 E 28 29: 0.15 2C 25.0 25 identity in 112 aa overlap. No Hp match. Contains PS00194 Thioredoxin family active site and probable N-terminal signal sequence 7EUpdated 282006 29 note: Specific characterisation with acceptable identity score has not been carried out yet. kept within product function. Literature search identified paper giving further clues to product function 28PMID:15632442 29. Functional classification - Energy metabolism - Respiration - Electron transport 7EPMID:15322369 2C PMID:15632442 NC_002163.1 RefSeq gene 1587982 1588470 . + . ID=gene1599;Name=Cj1664;locus_tag=Cj1664;Dbxref=GeneID:905936;gbkey=Gene NC_002163.1 RefSeq region 1588147 1588203 . + . ID=id2929;Name=id2929;Dbxref=GeneID:905936;gbkey=misc_feature;Note=PS00194 Thioredoxin family active site NC_002163.1 UTR_Extractor 5'-UTR 1588342 1588430 . + . ID=utr607;locus_tag=Cj1665;product=putative lipoprotein thiredoxin NC_002163.1 RefSeq gene 1588431 1588934 . + . ID=gene1600;Name=Cj1665;locus_tag=Cj1665;Dbxref=GeneID:905937;gbkey=Gene NC_002163.1 RefSeq CDS 1588431 1588934 . + 0 ID=cds1516;Parent=gene1600;Name=YP_002345033.1;Dbxref=GOA:Q0P7W4 InterPro:IPR006662 InterPro:IPR012335 InterPro:IPR013740 UniProtKB FTrEMBL:Q0P7W4 Genbank:YP_002345033.1 GeneID:905937;gbkey=CDS;product=lipoprotein thiredoxin;Note=Original 282000 29 note: Cj1665 2C possible lipoprotein thiredoxin 2C len: 167 aa 3B similar to TR:O33920 28EMBL:U75949 29 Salmonella typhimurium suppressor for copper-sensitivity D 28168 aa 29 2C fasta scores 3B opt: 121 z-score: 163.1 E 28 29: 0.093 2C 27.5 25 identity in 153 aa overlap 2C and weakly to many thiredoxins 2C e.g. THIO_BUCAP thioredoxin 28108 aa 29 2C fasta scores 3B opt: 108 z-score: 149.9 E 28 29: 0.5 2C 28.6 25 identity in 112 aa overlap. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. No Hp match 7EUpdated 282006 29 note: Specific characterisation with acceptable identity score has not been carried out yet. kept within product function. Literature search identified paper giving further clues to product function 28PMID:15632442 29. Functional classification - Energy metabolism - Respiration - Electron transport 7EPMID:15632442 NC_002163.1 RefSeq region 1588464 1588496 . + . ID=id2930;Name=id2930;Dbxref=GeneID:905937;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq gene 1588944 1589381 . - . ID=gene1601;Name=Cj1666c;locus_tag=Cj1666c;Dbxref=GeneID:905938;gbkey=Gene NC_002163.1 RefSeq CDS 1588944 1589381 . - 0 ID=cds1517;Parent=gene1601;Name=YP_002345034.1;Dbxref=InterPro:IPR007332 UniProtKB FTrEMBL:Q0P7W3 Genbank:YP_002345034.1 GeneID:905938;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1666c 2C probable periplasmic protein 2C len: 145 aa 3B similar to TR:AAD11752 28EMBL:AF067954 29 Salmonella typhimurium ORF105 in silver resistance cluster 28105 aa 29 2C fasta scores 3B opt: 244 z-score: 293.2 E 28 29: 5.2e-09 2C 39.2 25 identity in 102 aa overlap 2C and TR:O67205 28EMBL:AE000724 29 Aquifex aeolicus AQ_1129 28122 aa 29 2C fats scores 3B opt: 231 z-score: 277.7 E 28 29: 3.8e-08 2C 33.3 25 identity in 117 aa overlap. No Hp match. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Pfam domain PF04214 Protein of unknown function 2C DUF identified within CDS. Functional classification - Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 1589004 1589270 . - . ID=id2931;Name=id2931;Dbxref=GeneID:905938;gbkey=misc_feature;Note=HMMPfam hit to PF04214 2C Protein of unknown function 2C DUF 2C score 4.7e-60 ### NC_002163.1 UTR_Extractor 5'-UTR 1589382 1589404 . - . ID=utr608;locus_tag=Cj1666c;product=putative periplasmic protein NC_002163.1 RefSeq gene 1589598 1589666 . + . ID=NC_002163.1:CJas_Cj1667c;Name=NC_002163.1:CJas_Cj1667c;locus_tag=CJas_Cj1667c NC_002163.1 RefSeq sRNA 1589598 1589666 . + . ID=NC_002163.1:CJas_Cj1667c:unknown_transcript_1;Parent=NC_002163.1:CJas_Cj1667c;Name=NC_002163.1:CJas_Cj1667c:unknown_transcript_1;locus_tag=CJas_Cj1667c;gbkey=misc_RNA;product=CJas_Cj1667c NC_002163.1 RefSeq gene 1589680 1590096 . - . ID=gene1602;Name=Cj1668c;locus_tag=Cj1668c;Dbxref=GeneID:905940;gbkey=Gene NC_002163.1 RefSeq CDS 1589680 1590096 . - 0 ID=cds1518;Parent=gene1602;Name=YP_002345036.1;Dbxref=UniProtKB FTrEMBL:Q0P7W1 Genbank:YP_002345036.1 GeneID:905940;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1668c 2C probable periplasmic protein 2C len: 138 aa 3B no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq region 1590019 1590087 . - . ID=id2932;Name=id2932;Dbxref=GeneID:905940;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1668c by TMHMM2.0 at aa 4-26 ### NC_002163.1 RefSeq gene 1590271 1590355 . - . ID=gene1603;gene=tRNALeu;Name=tRNALeu;locus_tag=Cjt05;Dbxref=GeneID:3245052;gbkey=Gene NC_002163.1 RefSeq tRNA 1590271 1590355 . - . ID=rna47;Parent=gene1603;gene=tRNALeu;Name=rna47;Dbxref=GeneID:3245052;gbkey=tRNA;product=tRNA-Leu;Note=tRNA Leu anticodon TAG 2C Cove score 76.79 NC_002163.1 RefSeq exon 1590271 1590355 . - . ID=id2933;Parent=rna47;gene=tRNALeu;Name=id2933;Dbxref=GeneID:3245052;gbkey=tRNA;product=tRNA-Leu;Note=tRNA Leu anticodon TAG 2C Cove score 76.79 NC_002163.1 RefSeq gene 1590360 1590436 . - . ID=gene1604;gene=tRNAArg;Name=tRNAArg;locus_tag=Cjt3;Dbxref=GeneID:3245047;gbkey=Gene NC_002163.1 RefSeq tRNA 1590360 1590436 . - . ID=rna48;Parent=gene1604;gene=tRNAArg;Name=rna48;Dbxref=GeneID:3245047;gbkey=tRNA;product=tRNA-Arg;Note=tRNA Arg anticodon TCT 2C Cove score 87.94 NC_002163.1 RefSeq exon 1590360 1590436 . - . ID=id2934;Parent=rna48;gene=tRNAArg;Name=id2934;Dbxref=GeneID:3245047;gbkey=tRNA;product=tRNA-Arg;Note=tRNA Arg anticodon TCT 2C Cove score 87.94 NC_002163.1 RefSeq gene 1590451 1590527 . - . ID=gene1605;gene=tRNAArg;Name=tRNAArg;locus_tag=Cjt4;Dbxref=GeneID:3245057;gbkey=Gene NC_002163.1 RefSeq tRNA 1590451 1590527 . - . ID=rna49;Parent=gene1605;gene=tRNAArg;Name=rna49;Dbxref=GeneID:3245057;gbkey=tRNA;product=tRNA-Arg;Note=tRNA Arg anticodon TCG 2C Cove score 83.86 NC_002163.1 RefSeq exon 1590451 1590527 . - . ID=id2935;Parent=rna49;gene=tRNAArg;Name=id2935;Dbxref=GeneID:3245057;gbkey=tRNA;product=tRNA-Arg;Note=tRNA Arg anticodon TCG 2C Cove score 83.86 NC_002163.1 RefSeq gene 1590531 1590607 . - . ID=gene1606;gene=tRNAHis;Name=tRNAHis;locus_tag=Cjp32;Dbxref=GeneID:905942;gbkey=Gene NC_002163.1 RefSeq tRNA 1590531 1590607 . - . ID=rna50;Parent=gene1606;gene=tRNAHis;Name=rna50;Dbxref=GeneID:905942;gbkey=tRNA;product=tRNA-His;Note=tRNA His anticodon GTG 2C Cove score 77.53 NC_002163.1 RefSeq exon 1590531 1590607 . - . ID=id2936;Parent=rna50;gene=tRNAHis;Name=id2936;Dbxref=GeneID:905942;gbkey=tRNA;product=tRNA-His;Note=tRNA His anticodon GTG 2C Cove score 77.53 NC_002163.1 RefSeq gene 1590632 1590709 . - . ID=gene1607;gene=tRNAPro;Name=tRNAPro;locus_tag=Cjp33;Dbxref=GeneID:905943;gbkey=Gene NC_002163.1 RefSeq tRNA 1590632 1590709 . - . ID=rna51;Parent=gene1607;gene=tRNAPro;Name=rna51;Dbxref=GeneID:905943;gbkey=tRNA;product=tRNA-Pro;Note=tRNA Pro anticodon TGG 2C Cove score 88.47 NC_002163.1 RefSeq exon 1590632 1590709 . - . ID=id2937;Parent=rna51;gene=tRNAPro;Name=id2937;Dbxref=GeneID:905943;gbkey=tRNA;product=tRNA-Pro;Note=tRNA Pro anticodon TGG 2C Cove score 88.47 NC_002163.1 RefSeq CDS 1590752 1591600 . - 0 ID=cds1519;Parent=gene1608;Name=YP_002345037.1;Dbxref=GOA:Q0P7W0 InterPro:IPR012310 InterPro:IPR012340 InterPro:IPR016059 UniProtKB FTrEMBL:Q0P7W0 Genbank:YP_002345037.1 GeneID:905944;gbkey=CDS;product=DNA ligase;Note=catalyzes the formation of a phosphodiester at the site of a single-strand break in duplex DNA NC_002163.1 RefSeq gene 1590752 1591600 . - . ID=gene1608;Name=Cj1669c;locus_tag=Cj1669c;Dbxref=GeneID:905944;gbkey=Gene NC_002163.1 RefSeq region 1591004 1591075 . - . ID=id2939;Name=id2939;Dbxref=GeneID:905944;gbkey=misc_feature;Note=PS00333 ATP-dependent DNA ligase signature 2 NC_002163.1 RefSeq region 1591004 1591555 . - . ID=id2938;Name=id2938;Dbxref=GeneID:905944;gbkey=misc_feature;Note=HMMPfam hit to PF01068 2C ATP dependent DNA ligase domain 2C score 8.1e-08 NC_002163.1 RefSeq gene 1591600 1592262 . - . ID=gene1609;gene=cgpA;Name=cgpA;locus_tag=Cj1670c;Dbxref=GeneID:905945;gbkey=Gene NC_002163.1 RefSeq CDS 1591600 1592262 . - 0 ID=cds1520;Parent=gene1609;gene=cgpA;Name=YP_002345038.1;Dbxref=UniProtKB FTrEMBL:Q0P7V9 Genbank:YP_002345038.1 GeneID:905945;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1670c 2C probable periplasmic protein 2C len: 220 aa 3B 27.3 25 identity to HP0156. Contains probable N-terminal signal sequence 7EUpdated 282006 29 note: Characterisation paper within Campylobacter jejuni identified new gene name. Papers identified linking protein to glycoprotein 28PMID:12186869 29. Functional classification - Miscellaneous periplasmic proteins 7EPMID:12186869 2C PMID:11985725 NC_002163.1 RefSeq gene 1592252 1592455 . - . ID=gene1610;gene=Cj1671c;Name=Cj1671c;locus_tag=Cj1671c;Dbxref=GeneID:905946;gbkey=Gene NC_002163.1 RefSeq CDS 1592252 1592455 . - 0 ID=cds1521;Parent=gene1610;Name=YP_002345039.1;Dbxref=UniProtKB FTrEMBL:Q0P7V8 Genbank:YP_002345039.1 GeneID:905946;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1671c 2C unknown 2C len: 67 aa 3B 38.7 25 identity to HP0155 7EUpdated 282006 29 note: One probable transmembrane helix predicted by TMHMM2.0. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq region 1592393 1592452 . - . ID=id2940;Name=id2940;Dbxref=GeneID:905946;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1671c by TMHMM2.0 at aa 2-21 ### NC_002163.1 RefSeq CDS 1592521 1593765 . - 0 ID=cds1522;Parent=gene1611;gene=eno;Name=YP_002345040.1;Dbxref=GOA:P42448 HSSP:Q9NDH8 InterPro:IPR000941 UniProtKB FSwiss-Prot:P42448 Genbank:YP_002345040.1 GeneID:905947;gbkey=CDS;product=phosphopyruvate hydratase;Note=enolase 3B catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis NC_002163.1 RefSeq gene 1592521 1593765 . - . ID=gene1611;gene=eno;Name=eno;locus_tag=Cj1672c;Dbxref=GeneID:905947;gbkey=Gene NC_002163.1 RefSeq region 1592524 1593354 . - . ID=id2941;gene=eno;Name=id2941;Dbxref=GeneID:905947;gbkey=misc_feature;Note=HMMPfam hit to PF00113 2C Enolase 2C C-terminal TIM barrel domain 2C score 5e-135 NC_002163.1 RefSeq region 1593367 1593759 . - . ID=id2942;gene=eno;Name=id2942;Dbxref=GeneID:905947;gbkey=misc_feature;Note=HMMPfam hit to PF03952 2C Enolase 2C N-terminal domain 2Cscore 8.4e-59 NC_002163.1 RefSeq gene 1593765 1594796 . - . ID=gene1612;gene=recA;Name=recA;locus_tag=Cj1673c;Dbxref=GeneID:905948;gbkey=Gene NC_002163.1 RefSeq CDS 1593765 1594796 . - 0 ID=cds1523;Parent=gene1612;gene=recA;Name=YP_002345041.1;Dbxref=GOA:Q0P7V6 HSSP:P26345 InterPro:IPR001553 InterPro:IPR003593 InterPro:IPR013765 UniProtKB FSwiss-Prot:Q0P7V6 Genbank:YP_002345041.1 GeneID:905948;gbkey=CDS;product=recombinase A;Note=catalyzes the hydrolysis of ATP in the presence of single-stranded DNA 2C the ATP-dependent uptake of single-stranded DNA by duplex DNA 2C and the ATP-dependent hybridization of homologous single-stranded DNAs NC_002163.1 RefSeq region 1593810 1594778 . - . ID=id2943;gene=recA;Name=id2943;Dbxref=GeneID:905948;gbkey=misc_feature;Note=HMMPfam hit to PF00154 2C recA bacterial DNA recombination protein 2C score 1.2e-237 NC_002163.1 RefSeq region 1594131 1594157 . - . ID=id2944;gene=recA;Name=id2944;Dbxref=GeneID:905948;gbkey=misc_feature;Note=PS00321 recA signature NC_002163.1 RefSeq region 1594581 1594604 . - . ID=id2945;gene=recA;Name=id2945;Dbxref=GeneID:905948;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 ### NC_002163.1 UTR_Extractor 5'-UTR 1594797 1594824 . - . ID=utr609;locus_tag=Cj1673c;product=recombinase A NC_002163.1 UTR_Extractor 5'-UTR 1594881 1594901 . + . ID=utr610;locus_tag=Cj1674;product=hypothetical protein NC_002163.1 RefSeq gene 1594902 1595762 . + . ID=gene1613;Name=Cj1674;locus_tag=Cj1674;Dbxref=GeneID:905949;gbkey=Gene NC_002163.1 RefSeq CDS 1594902 1595762 . + 0 ID=cds1524;Parent=gene1613;Name=YP_002345042.1;Dbxref=InterPro:IPR003794 UniProtKB FTrEMBL:Q0P7V5 Genbank:YP_002345042.1 GeneID:905949;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1674 2C unknown 2C len: 286 aa 3B similar to hypothetical proteins e.g. TR:AE000683 28EMBL:AE000683 29 28279 aa 29 2C fasta scores 3B opt: 489 z-score: 599.3 E 28 29: 4.7e-26 2C 35.4 25 identity in 260 aa overlap. 58.7 25 identity to HP0152 7EUpdated 282006 29 note: Pfam domain PF02642 Uncharacterized ACR 2C COG2107 identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins NC_002163.1 RefSeq region 1594908 1595696 . + . ID=id2946;Name=id2946;Dbxref=GeneID:905949;gbkey=misc_feature;Note=HMMPfam hit to PF02642 2C Uncharacterized ACR 2CCOG2107 2C score 1.9e-107 ### NC_002163.1 RefSeq CDS 1595774 1596043 . + 0 ID=cds1525;Parent=gene1614;gene=fliQ;Name=YP_002345043.1;Dbxref=GOA:Q0P7V4 InterPro:IPR002191 InterPro:IPR006305 UniProtKB FTrEMBL:Q0P7V4 Genbank:YP_002345043.1 GeneID:905950;gbkey=CDS;product=flagellar biosynthesis protein FliQ;Note=with proteins FliP and FliR forms the core of the central channel in the flagella export apparatus NC_002163.1 RefSeq gene 1595774 1596043 . + . ID=gene1614;gene=fliQ;Name=fliQ;locus_tag=Cj1675;Dbxref=GeneID:905950;gbkey=Gene NC_002163.1 RefSeq region 1595783 1596010 . + . ID=id2947;gene=fliQ;Name=id2947;Dbxref=GeneID:905950;gbkey=misc_feature;Note=HMMPfam hit to PF01313 2C Bacterial export proteins 2Cfamily 2C score 4.6e-32 NC_002163.1 RefSeq region 1595816 1595884 . + . ID=id2948;gene=fliQ;Name=id2948;Dbxref=GeneID:905950;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1675 by TMHMM2.0 at aa 15-37 and 49-71 NC_002163.1 RefSeq region 1595918 1595986 . + . ID=id2948;gene=fliQ;Name=id2948;Dbxref=GeneID:905950;gbkey=misc_feature;Note=2 probable transmembrane helices predicted for Cj1675 by TMHMM2.0 at aa 15-37 and 49-71 NC_002163.1 RefSeq gene 1596040 1596816 . + . ID=gene1615;gene=murB;Name=murB;locus_tag=Cj1676;Dbxref=GeneID:905951;gbkey=Gene NC_002163.1 RefSeq CDS 1596040 1596816 . + 0 ID=cds1526;Parent=gene1615;gene=murB;Name=YP_002345044.1;Dbxref=GOA:Q9PM01 InterPro:IPR003170 InterPro:IPR011601 InterPro:IPR016169 UniProtKB FSwiss-Prot:Q9PM01 Genbank:YP_002345044.1 GeneID:905951;gbkey=CDS;product=UDP-N-acetylenolpyruvoylglucosamine reductase;Note=catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis NC_002163.1 RefSeq region 1596532 1596813 . + . ID=id2949;gene=murB;Name=id2949;Dbxref=GeneID:905951;gbkey=misc_feature;Note=HMMPfam hit to PF02873 2CUDP-N-acetylenolpyruvoylglucosamine reductas 2C score 6.6e-30 ### NC_002163.1 RefSeq stem_loop 1596867 1596953 . + . ID=id2950;Name=id2950;gbkey=stem_loop NC_002163.1 RefSeq CDS 1597008 1597589 . + 0 ID=cds1527a;Parent=gene1616;Name=YP_002345045.1;Dbxref=InterPro:IPR005546 UniProtKB FTrEMBL:Q0P7V2 Genbank:YP_002345045.1 GeneID:905952;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj1678 2C possible lipoprotein 2Clen: 928 aa 3B no Hp match. Contains a poly-T tract at aa 1 which 2C if variable 2C would allow translation from Cj1677 28which contains a signal sequence and lipid attachment site 29. Otherwise translation could start at aa 46. Highly similar to Cj0629 2890.7 25 identity in 901 aa overlap 29. Cj0629 has a non-variable poly-T tract in an quivalent position 2C which could allow translation from Cj0628 28similar to Cj1677 29 7EOriginal 282000 29 note: Cj1677 2C probable lipoprotein 2Clen: 216 aa 3B no Hp match. Contains N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. There is a poly-T tract at the C-terminus 28aa 194 29 which 2C if variable 2C would allow translation into the downstream ORF Cj1678. Similar to Cj0628 which does have a variable poly-T tract at the smae position which could allow translation into Cj0629 28highly similar to Cj1678 29 7EUpdated 282006 29 note: Coding sequences have been merged to reflect the complete amino acid sequence for this gene regardless of phase. Previous annotation gave Cj1677 and Cj1678 as seperate CDSs. Merging of these CDSs has lead to loss of the downstream CDS. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq gene 1597008 1600372 . + . ID=gene1616;Name=Cj1677;locus_tag=Cj1677;Dbxref=GeneID:905952;gbkey=Gene NC_002163.1 RefSeq repeat_region 1597585 1597591 . + . ID=id2951;Name=id2951;Dbxref=GeneID:905952;gbkey=repeat_region;Note=T 287 29 NC_002163.1 RefSeq CDS 1597592 1600372 . + 0 ID=cds1527b;Parent=gene1616;Name=YP_002345045.1;Dbxref=InterPro:IPR005546 UniProtKB FTrEMBL:Q0P7V2 Genbank:YP_002345045.1 GeneID:905952;gbkey=CDS;product=lipoprotein;Note=Original 282000 29 note: Cj1678 2C possible lipoprotein 2Clen: 928 aa 3B no Hp match. Contains a poly-T tract at aa 1 which 2C if variable 2C would allow translation from Cj1677 28which contains a signal sequence and lipid attachment site 29. Otherwise translation could start at aa 46. Highly similar to Cj0629 2890.7 25 identity in 901 aa overlap 29. Cj0629 has a non-variable poly-T tract in an quivalent position 2C which could allow translation from Cj0628 28similar to Cj1677 29 7EOriginal 282000 29 note: Cj1677 2C probable lipoprotein 2Clen: 216 aa 3B no Hp match. Contains N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. There is a poly-T tract at the C-terminus 28aa 194 29 which 2C if variable 2C would allow translation into the downstream ORF Cj1678. Similar to Cj0628 which does have a variable poly-T tract at the smae position which could allow translation into Cj0629 28highly similar to Cj1678 29 7EUpdated 282006 29 note: Coding sequences have been merged to reflect the complete amino acid sequence for this gene regardless of phase. Previous annotation gave Cj1677 and Cj1678 as seperate CDSs. Merging of these CDSs has lead to loss of the downstream CDS. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 RefSeq repeat_region 1598049 1600469 . + . ID=id2952;Name=id2952;gbkey=repeat_region;Note=repeat 2: identical to 588981..591400 NC_002163.1 RefSeq region 1599548 1600345 . + . ID=id2953;Name=id2953;Dbxref=GeneID:905952;gbkey=misc_feature;Note=HMMPfam hit to PF03797 2C Autotransporter beta-domain 2C score 5.9e-38 NC_002163.1 RefSeq gene 1600382 1600468 . + . ID=NC_002163.1:CJnc210;Name=NC_002163.1:CJnc210;locus_tag=CJnc210 NC_002163.1 RefSeq sRNA 1600382 1600468 . + . ID=NC_002163.1:CJnc210:unknown_transcript_1;Parent=NC_002163.1:CJnc210;Name=NC_002163.1:CJnc210:unknown_transcript_1;locus_tag=CJnc210;gbkey=misc_RNA;product=CJnc210 ### NC_002163.1 UTR_Extractor 5'-UTR 1600548 1600573 . + . ID=utr611;locus_tag=Cj1679;product=hypothetical protein NC_002163.1 RefSeq CDS 1600574 1602328 . + 0 ID=cds1528;Parent=gene1617;Name=YP_002345046.1;Dbxref=GOA:Q0P7V1 InterPro:IPR011990 InterPro:IPR013026 InterPro:IPR013105 UniProtKB FTrEMBL:Q0P7V1 Genbank:YP_002345046.1 GeneID:905954;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1679 2C unknown 2C len: 584 aa 3B no Hp match 7EUpdated 282006 29 note: Pfam domain x2 PF07719 Tetratricopeptide repeat identified within CDS. Functional classification - Unknown NC_002163.1 RefSeq gene 1600574 1602328 . + . ID=gene1617;Name=Cj1679;locus_tag=Cj1679;Dbxref=GeneID:905954;gbkey=Gene NC_002163.1 RefSeq region 1600865 1600966 . + . ID=id2954;Name=id2954;Dbxref=GeneID:905954;gbkey=misc_feature;Note=HMMPfam hit to PF07719 2C Tetratricopeptide repeat 2Cscore 2.8 NC_002163.1 RefSeq region 1601294 1601395 . + . ID=id2955;Name=id2955;Dbxref=GeneID:905954;gbkey=misc_feature;Note=HMMPfam hit to PF07719 2C Tetratricopeptide repeat 2Cscore 0.00092 ### NC_002163.1 RefSeq gene 1602332 1603099 . - . ID=gene1618;Name=Cj1680c;locus_tag=Cj1680c;Dbxref=GeneID:905955;gbkey=Gene NC_002163.1 RefSeq CDS 1602332 1603099 . - 0 ID=cds1529;Parent=gene1618;Name=YP_002345047.1;Dbxref=GOA:Q0P7V0 UniProtKB FTrEMBL:Q0P7V0 Genbank:YP_002345047.1 GeneID:905955;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1680c 2C probable periplasmic protein 2C len: 255 aa 3B no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 UTR_Extractor 5'-UTR 1603100 1603118 . - . ID=utr612;locus_tag=Cj1680c;product=putative periplasmic protein NC_002163.1 RefSeq CDS 1603139 1603903 . - 0 ID=cds1530;Parent=gene1619;gene=cysQ;Name=YP_002345048.1;Dbxref=GOA:Q0P7U9 InterPro:IPR000760 UniProtKB FTrEMBL:Q0P7U9 Genbank:YP_002345048.1 GeneID:905956;gbkey=CDS;product=3 27 282 27 29 2C5 27-bisphosphate nucleotidase CysQ;Note=Original 282000 29 note: Cj1681c 2C cysQ 2C probable cysQ protein homolog 2C len: 254 aa 3B similar to e.g. CYSQ_ECOLI CYSQ protein 28246 aa 29 2C fasta scores 3B opt: 421 z-score: 500.9 E 28 29: 1.4e-20 2C 32.4 25 identity in 247 aa overlap. No Hp match. Contains Pfam match to entry PF00459 inositol_P 2CInositol monophosphatase family 2C and PS00629 Inositol monophosphatase family signature 1. Functional classification - Central intermediary metabolism - Sulphur metabolism 7EPMID:1729235 2C PMID:7493934 NC_002163.1 RefSeq gene 1603139 1603903 . - . ID=gene1619;gene=cysQ;Name=cysQ;locus_tag=Cj1681c;Dbxref=GeneID:905956;gbkey=Gene NC_002163.1 RefSeq region 1603148 1603897 . - . ID=id2956;gene=cysQ;Name=id2956;Dbxref=GeneID:905956;gbkey=misc_feature;Note=HMMPfam hit to PF00459 2C Inositol monophosphatase family 2C score 3.5e-29 NC_002163.1 RefSeq region 1603622 1603663 . - . ID=id2957;gene=cysQ;Name=id2957;Dbxref=GeneID:905956;gbkey=misc_feature;Note=PS00629 Inositol monophosphatase family signature 1 ### NC_002163.1 RefSeq CDS 1603983 1605251 . - 0 ID=cds1531;Parent=gene1620;gene=gltA;Name=YP_002345049.1;Dbxref=GOA:Q0P7U8 InterPro:IPR002020 InterPro:IPR010953 InterPro:IPR016142 UniProtKB FTrEMBL:Q0P7U8 Genbank:YP_002345049.1 GeneID:905957;gbkey=CDS;product=citrate synthase;Note=Original 282000 29 note: Cj1682c 2C gltA 2C probable citrate synthase 2C len: 422 aa 3B similar to many e.g. CISY_PSEAE citrate synthase 28EC 4.1.3.7 29 28428 aa 29 2C fasta scores 3B opt: 1520 z-score: 1734.6 E 28 29: 0 2C 53.8 25 identity in 405 aa overlap. 52.8 25 identity to HP0026. Contains PS00480 Citrate synthase signature 2C and Pfam match to entry PF00285 citrate_synt 2C Citrate synthase 7EUpdated 282006 29 note: Characterised within Pseudomonas aeruginosa with acceptable identity score. Appropriate motifs present. not added to product function. EC number has been updated. Functional classification - Energy metabolism - Tricarboxylic acid cycle 7EPMID:2507528 NC_002163.1 RefSeq gene 1603983 1605251 . - . ID=gene1620;gene=gltA;Name=gltA;locus_tag=Cj1682c;Dbxref=GeneID:905957;gbkey=Gene NC_002163.1 RefSeq region 1604019 1605113 . - . ID=id2958;gene=gltA;Name=id2958;Dbxref=GeneID:905957;gbkey=misc_feature;Note=HMMPfam hit to PF00285 2C Citrate synthase 2C score 2.2e-174 NC_002163.1 RefSeq region 1604304 1604342 . - . ID=id2959;gene=gltA;Name=id2959;Dbxref=GeneID:905957;gbkey=misc_feature;Note=PS00480 Citrate synthase signature ### NC_002163.1 UTR_Extractor 5'-UTR 1605252 1605278 . - . ID=utr613;locus_tag=Cj1682c;product=citrate synthase NC_002163.1 RefSeq CDS 1605366 1606541 . - 0 ID=cds1532;Parent=gene1621;Name=YP_002345050.1;Dbxref=GOA:Q0P7U7 InterPro:IPR006153 UniProtKB FTrEMBL:Q0P7U7 Genbank:YP_002345050.1 GeneID:905958;gbkey=CDS;product=transmembrane transport protein;Note=Original 282000 29 note: Cj1684c 2C probable transmembrane transport protein 2C len: 391 aa 3B simlar to many predicted Na 2B 2FH 2B antiporters 2C and to KEFB_ECOLI Glutathione-regulated potassium-efflux system protein 28601 aa 29 2C fasta scores 3B opt: 197 z-score: 237.9 E 28 29: 6.2e-06 2C21.9 25 identity in 324 aa overlap 2C and NAPA_ENTHR Na 28 2B 29 2FH 28 2B 29 antiporter 28383 aa 29 2C blastp scores 3B E 3D 3.1e-10 2C22 25 identity in 372 aa overlap. 35.9 25 identity to HP1183 28called NA 2B 2FH 2B antiporter 28napA 29 on basis of match to NAPA_ENTHR 29 7EUpdated 282006 29 note: Eleven probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation yet with acceptable identity score. kept within product function. Functional classification - Transport 2Fbinding proteins - Other NC_002163.1 RefSeq gene 1605366 1606541 . - . ID=gene1621;Name=Cj1684c;locus_tag=Cj1684c;Dbxref=GeneID:905958;gbkey=Gene NC_002163.1 RefSeq region 1605381 1605449 . - . ID=id149;Name=id149;Dbxref=GeneID:905958;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1684c by TMHMM2.0 at aa 10-27 2C 34-56 2C 61-83 2C 96-129 2C149-171 2C 184-206 2C 232-254 2C 275-292 2C 302-324 2C 333-355 and 365-387 NC_002163.1 RefSeq region 1605477 1605545 . - . ID=id149;Name=id149;Dbxref=GeneID:905958;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1684c by TMHMM2.0 at aa 10-27 2C 34-56 2C 61-83 2C 96-129 2C149-171 2C 184-206 2C 232-254 2C 275-292 2C 302-324 2C 333-355 and 365-387 NC_002163.1 RefSeq region 1605570 1605638 . - . ID=id149;Name=id149;Dbxref=GeneID:905958;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1684c by TMHMM2.0 at aa 10-27 2C 34-56 2C 61-83 2C 96-129 2C149-171 2C 184-206 2C 232-254 2C 275-292 2C 302-324 2C 333-355 and 365-387 NC_002163.1 RefSeq region 1605666 1605719 . - . ID=id149;Name=id149;Dbxref=GeneID:905958;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1684c by TMHMM2.0 at aa 10-27 2C 34-56 2C 61-83 2C 96-129 2C149-171 2C 184-206 2C 232-254 2C 275-292 2C 302-324 2C 333-355 and 365-387 NC_002163.1 RefSeq region 1605780 1605848 . - . ID=id149;Name=id149;Dbxref=GeneID:905958;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1684c by TMHMM2.0 at aa 10-27 2C 34-56 2C 61-83 2C 96-129 2C149-171 2C 184-206 2C 232-254 2C 275-292 2C 302-324 2C 333-355 and 365-387 NC_002163.1 RefSeq region 1605924 1605992 . - . ID=id149;Name=id149;Dbxref=GeneID:905958;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1684c by TMHMM2.0 at aa 10-27 2C 34-56 2C 61-83 2C 96-129 2C149-171 2C 184-206 2C 232-254 2C 275-292 2C 302-324 2C 333-355 and 365-387 NC_002163.1 RefSeq region 1606029 1606097 . - . ID=id149;Name=id149;Dbxref=GeneID:905958;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1684c by TMHMM2.0 at aa 10-27 2C 34-56 2C 61-83 2C 96-129 2C149-171 2C 184-206 2C 232-254 2C 275-292 2C 302-324 2C 333-355 and 365-387 NC_002163.1 RefSeq region 1606155 1606256 . - . ID=id149;Name=id149;Dbxref=GeneID:905958;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1684c by TMHMM2.0 at aa 10-27 2C 34-56 2C 61-83 2C 96-129 2C149-171 2C 184-206 2C 232-254 2C 275-292 2C 302-324 2C 333-355 and 365-387 NC_002163.1 RefSeq region 1606293 1606361 . - . ID=id149;Name=id149;Dbxref=GeneID:905958;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1684c by TMHMM2.0 at aa 10-27 2C 34-56 2C 61-83 2C 96-129 2C149-171 2C 184-206 2C 232-254 2C 275-292 2C 302-324 2C 333-355 and 365-387 NC_002163.1 RefSeq region 1606374 1606442 . - . ID=id149;Name=id149;Dbxref=GeneID:905958;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1684c by TMHMM2.0 at aa 10-27 2C 34-56 2C 61-83 2C 96-129 2C149-171 2C 184-206 2C 232-254 2C 275-292 2C 302-324 2C 333-355 and 365-387 NC_002163.1 RefSeq region 1606461 1606514 . - . ID=id149;Name=id149;Dbxref=GeneID:905958;gbkey=misc_feature;Note=11 probable transmembrane helices predicted for Cj1684c by TMHMM2.0 at aa 10-27 2C 34-56 2C 61-83 2C 96-129 2C149-171 2C 184-206 2C 232-254 2C 275-292 2C 302-324 2C 333-355 and 365-387 NC_002163.1 RefSeq gene 1606522 1607358 . - . ID=gene1622;gene=bioB;Name=bioB;locus_tag=Cj1685c;Dbxref=GeneID:905959;gbkey=Gene NC_002163.1 RefSeq CDS 1606522 1607358 . - 0 ID=cds1533;Parent=gene1622;gene=bioB;Name=YP_002345051.1;Dbxref=GOA:Q0P7U6 InterPro:IPR002684 InterPro:IPR006638 InterPro:IPR007197 InterPro:IPR010722 InterPro:IPR013785 UniProtKB FTrEMBL:Q0P7U6 Genbank:YP_002345051.1 GeneID:905959;gbkey=CDS;product=biotin synthase;Note=catalyzes the formation of biotin from dethiobiotin and sulfur NC_002163.1 RefSeq region 1606540 1606812 . - . ID=id2960;gene=bioB;Name=id2960;Dbxref=GeneID:905959;gbkey=misc_feature;Note=HMMPfam hit to PF06968 2C Biotin and Thiamin Synthesis associated d 2C score 1e-25 NC_002163.1 RefSeq region 1606837 1607331 . - . ID=id2961;gene=bioB;Name=id2961;Dbxref=GeneID:905959;gbkey=misc_feature;Note=HMMPfam hit to PF04055 2C Radical SAM superfamily 2Cscore 9.8e-20 ### NC_002163.1 RefSeq CDS 1607360 1609462 . - 0 ID=cds1534;Parent=gene1623;gene=topA;Name=YP_002345052.1;Dbxref=GOA:Q9PLZ2 HSSP:P06612 InterPro:IPR000380 InterPro:IPR003601 InterPro:IPR003602 InterPro:IPR005733 InterPro:IPR006154 InterPro:IPR006171 InterPro:IPR013497 InterPro:IPR013498 InterPro:IPR013824 InterPro:IPR013826 UniProtKB FSwiss-Prot:Q9PLZ2 Genbank:YP_002345052.1 GeneID:905960;gbkey=CDS;product=DNA topoisomerase I;Note=catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining 2C maintains net negative superhelicity NC_002163.1 RefSeq gene 1607360 1609462 . - . ID=gene1623;gene=topA;Name=topA;locus_tag=Cj1686c;Dbxref=GeneID:905960;gbkey=Gene NC_002163.1 RefSeq region 1607372 1607467 . - . ID=id2962;gene=topA;Name=id2962;Dbxref=GeneID:905960;gbkey=misc_feature;Note=HMMPfam hit to PF01396 2C Topoisomerase DNA binding C4 zinc fing 2C score 0.0034 NC_002163.1 RefSeq region 1607468 1607587 . - . ID=id2963;gene=topA;Name=id2963;Dbxref=GeneID:905960;gbkey=misc_feature;Note=HMMPfam hit to PF01396 2C Topoisomerase DNA binding C4 zinc fing 2C score 8.7e-14 NC_002163.1 RefSeq region 1607639 1607755 . - . ID=id2964;gene=topA;Name=id2964;Dbxref=GeneID:905960;gbkey=misc_feature;Note=HMMPfam hit to PF01396 2C Topoisomerase DNA binding C4 zinc fing 2C score 4e-17 NC_002163.1 RefSeq region 1607870 1609087 . - . ID=id2965;gene=topA;Name=id2965;Dbxref=GeneID:905960;gbkey=misc_feature;Note=HMMPfam hit to PF01131 2C DNA topoisomerase 2C score 3.7e-168 NC_002163.1 RefSeq region 1608557 1608625 . - . ID=id2966;gene=topA;Name=id2966;Dbxref=GeneID:905960;gbkey=misc_feature;Note=PS00396 Prokaryotic DNA topoisomerase I active site NC_002163.1 RefSeq region 1609127 1609456 . - . ID=id2967;gene=topA;Name=id2967;Dbxref=GeneID:905960;gbkey=misc_feature;Note=HMMPfam hit to PF01751 2C Toprim domain 2C score 4.5e-32 ### NC_002163.1 RefSeq CDS 1609657 1610928 . + 0 ID=cds1535;Parent=gene1624;Name=YP_002345053.1;Dbxref=GOA:Q0P7U4 InterPro:IPR007114 InterPro:IPR011701 UniProtKB FTrEMBL:Q0P7U4 Genbank:YP_002345053.1 GeneID:905961;gbkey=CDS;product=efflux protein;Note=Original 282000 29 note: Cj1687 2C possible efflux protein 2C len: 423 aa 3B similar to members of the major facilitator family e.g. NORA_STAAU quinolone resistance NORA protein 28388 aa 29 2C fasta scores 3B opt: 333 z-score: 386.0 E 28 29: 3.5e-14 2C 23.1 25 identity in 350 aa overlap 2C and BMR1_BACSU multidrug resistance protein 1 28389 aa 29 2C fasta scores 3B opt: 282 z-score: 327.8 E 28 29: 6.1e-11 2C 24.6 25 identity in 305 aa overlap. No Hp match. Contains Pfam match to entry PF00083 sugar_tr 2C Sugar 28and other 29 transporters 7EUpdated 282006 29 note: Pfam domain PF07690 Major Facilitator Superfamily identified within CDS. Also 2Ctwelve probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity score has been carried out yet. Literature search identified paper giving further clues to product function. Functional classification - Antibiotic resistance 7EPMID:16048946 NC_002163.1 RefSeq gene 1609657 1610928 . + . ID=gene1624;Name=Cj1687;locus_tag=Cj1687;Dbxref=GeneID:905961;gbkey=Gene NC_002163.1 RefSeq region 1609747 1609815 . + . ID=id2968;Name=id2968;Dbxref=GeneID:905961;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1687 by TMHMM2.0 at aa 31-53 2C 80-102 2C 115-137 2C 141-160 2C172-194 2C 199-221 2C 240-259 2C 279-301 2C 308-327 2C 332-354 2C367-389 and 399-416 NC_002163.1 RefSeq region 1609750 1610829 . + . ID=id2969;Name=id2969;Dbxref=GeneID:905961;gbkey=misc_feature;Note=HMMPfam hit to PF07690 2C Major Facilitator Superfamily 2C score 2.5e-47 NC_002163.1 RefSeq region 1609894 1609962 . + . ID=id2968;Name=id2968;Dbxref=GeneID:905961;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1687 by TMHMM2.0 at aa 31-53 2C 80-102 2C 115-137 2C 141-160 2C172-194 2C 199-221 2C 240-259 2C 279-301 2C 308-327 2C 332-354 2C367-389 and 399-416 NC_002163.1 RefSeq region 1609999 1610067 . + . ID=id2968;Name=id2968;Dbxref=GeneID:905961;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1687 by TMHMM2.0 at aa 31-53 2C 80-102 2C 115-137 2C 141-160 2C172-194 2C 199-221 2C 240-259 2C 279-301 2C 308-327 2C 332-354 2C367-389 and 399-416 NC_002163.1 RefSeq region 1610077 1610136 . + . ID=id2968;Name=id2968;Dbxref=GeneID:905961;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1687 by TMHMM2.0 at aa 31-53 2C 80-102 2C 115-137 2C 141-160 2C172-194 2C 199-221 2C 240-259 2C 279-301 2C 308-327 2C 332-354 2C367-389 and 399-416 NC_002163.1 RefSeq region 1610170 1610238 . + . ID=id2968;Name=id2968;Dbxref=GeneID:905961;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1687 by TMHMM2.0 at aa 31-53 2C 80-102 2C 115-137 2C 141-160 2C172-194 2C 199-221 2C 240-259 2C 279-301 2C 308-327 2C 332-354 2C367-389 and 399-416 NC_002163.1 RefSeq region 1610251 1610319 . + . ID=id2968;Name=id2968;Dbxref=GeneID:905961;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1687 by TMHMM2.0 at aa 31-53 2C 80-102 2C 115-137 2C 141-160 2C172-194 2C 199-221 2C 240-259 2C 279-301 2C 308-327 2C 332-354 2C367-389 and 399-416 NC_002163.1 RefSeq region 1610374 1610433 . + . ID=id2968;Name=id2968;Dbxref=GeneID:905961;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1687 by TMHMM2.0 at aa 31-53 2C 80-102 2C 115-137 2C 141-160 2C172-194 2C 199-221 2C 240-259 2C 279-301 2C 308-327 2C 332-354 2C367-389 and 399-416 NC_002163.1 RefSeq region 1610491 1610559 . + . ID=id2968;Name=id2968;Dbxref=GeneID:905961;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1687 by TMHMM2.0 at aa 31-53 2C 80-102 2C 115-137 2C 141-160 2C172-194 2C 199-221 2C 240-259 2C 279-301 2C 308-327 2C 332-354 2C367-389 and 399-416 NC_002163.1 RefSeq region 1610578 1610637 . + . ID=id2968;Name=id2968;Dbxref=GeneID:905961;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1687 by TMHMM2.0 at aa 31-53 2C 80-102 2C 115-137 2C 141-160 2C172-194 2C 199-221 2C 240-259 2C 279-301 2C 308-327 2C 332-354 2C367-389 and 399-416 NC_002163.1 RefSeq region 1610581 1610613 . + . ID=id2970;Name=id2970;Dbxref=GeneID:905961;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1610650 1610718 . + . ID=id2968;Name=id2968;Dbxref=GeneID:905961;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1687 by TMHMM2.0 at aa 31-53 2C 80-102 2C 115-137 2C 141-160 2C172-194 2C 199-221 2C 240-259 2C 279-301 2C 308-327 2C 332-354 2C367-389 and 399-416 NC_002163.1 RefSeq region 1610755 1610823 . + . ID=id2968;Name=id2968;Dbxref=GeneID:905961;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1687 by TMHMM2.0 at aa 31-53 2C 80-102 2C 115-137 2C 141-160 2C172-194 2C 199-221 2C 240-259 2C 279-301 2C 308-327 2C 332-354 2C367-389 and 399-416 NC_002163.1 RefSeq region 1610851 1610904 . + . ID=id2968;Name=id2968;Dbxref=GeneID:905961;gbkey=misc_feature;Note=12 probable transmembrane helices predicted for Cj1687 by TMHMM2.0 at aa 31-53 2C 80-102 2C 115-137 2C 141-160 2C172-194 2C 199-221 2C 240-259 2C 279-301 2C 308-327 2C 332-354 2C367-389 and 399-416 ### NC_002163.1 RefSeq CDS 1610956 1612221 . - 0 ID=cds1536;Parent=gene1625;gene=secY;Name=YP_002345054.1;Dbxref=GOA:Q0P7U3 InterPro:IPR002208 UniProtKB FTrEMBL:Q0P7U3 Genbank:YP_002345054.1 GeneID:905962;gbkey=CDS;product=preprotein translocase subunit SecY;Note=forms heterotrimeric complex in the membrane 3B in bacteria the complex consists of SecY which forms the channel pore and SecE and SecG 3B the SecG subunit is not essential 3B in bacteria translocation is driven via the SecA ATPase NC_002163.1 RefSeq gene 1610956 1612221 . - . ID=gene1625;gene=secY;Name=secY;locus_tag=Cj1688c;Dbxref=GeneID:905962;gbkey=Gene NC_002163.1 RefSeq region 1611013 1612038 . - . ID=id2971;gene=secY;Name=id2971;Dbxref=GeneID:905962;gbkey=misc_feature;Note=HMMPfam hit to PF00344 2C eubacterial secY protein 2Cscore 5.2e-113 NC_002163.1 RefSeq region 1611028 1611081 . - . ID=id150;gene=secY;Name=id150;Dbxref=GeneID:905962;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1688c by TMHMM2.0 at aa 9-31 2C 61-83 2C 104-126 2C 141-163 2C170-191 2C 206-228 2C 257-279 2C 299-321 2C 357-376 and 381-398 NC_002163.1 RefSeq region 1611094 1611153 . - . ID=id150;gene=secY;Name=id150;Dbxref=GeneID:905962;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1688c by TMHMM2.0 at aa 9-31 2C 61-83 2C 104-126 2C 141-163 2C170-191 2C 206-228 2C 257-279 2C 299-321 2C 357-376 and 381-398 NC_002163.1 RefSeq region 1611259 1611327 . - . ID=id150;gene=secY;Name=id150;Dbxref=GeneID:905962;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1688c by TMHMM2.0 at aa 9-31 2C 61-83 2C 104-126 2C 141-163 2C170-191 2C 206-228 2C 257-279 2C 299-321 2C 357-376 and 381-398 NC_002163.1 RefSeq region 1611385 1611453 . - . ID=id150;gene=secY;Name=id150;Dbxref=GeneID:905962;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1688c by TMHMM2.0 at aa 9-31 2C 61-83 2C 104-126 2C 141-163 2C170-191 2C 206-228 2C 257-279 2C 299-321 2C 357-376 and 381-398 NC_002163.1 RefSeq region 1611538 1611606 . - . ID=id150;gene=secY;Name=id150;Dbxref=GeneID:905962;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1688c by TMHMM2.0 at aa 9-31 2C 61-83 2C 104-126 2C 141-163 2C170-191 2C 206-228 2C 257-279 2C 299-321 2C 357-376 and 381-398 NC_002163.1 RefSeq region 1611649 1611714 . - . ID=id150;gene=secY;Name=id150;Dbxref=GeneID:905962;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1688c by TMHMM2.0 at aa 9-31 2C 61-83 2C 104-126 2C 141-163 2C170-191 2C 206-228 2C 257-279 2C 299-321 2C 357-376 and 381-398 NC_002163.1 RefSeq region 1611661 1611717 . - . ID=id2972;gene=secY;Name=id2972;Dbxref=GeneID:905962;gbkey=misc_feature;Note=PS00095 C-5 cytosine-specific DNA methylases C-terminal signature NC_002163.1 RefSeq region 1611685 1611741 . - . ID=id2973;gene=secY;Name=id2973;Dbxref=GeneID:905962;gbkey=misc_feature;Note=PS00756 Protein secY signature 2 NC_002163.1 RefSeq region 1611733 1611801 . - . ID=id150;gene=secY;Name=id150;Dbxref=GeneID:905962;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1688c by TMHMM2.0 at aa 9-31 2C 61-83 2C 104-126 2C 141-163 2C170-191 2C 206-228 2C 257-279 2C 299-321 2C 357-376 and 381-398 NC_002163.1 RefSeq region 1611844 1611912 . - . ID=id150;gene=secY;Name=id150;Dbxref=GeneID:905962;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1688c by TMHMM2.0 at aa 9-31 2C 61-83 2C 104-126 2C 141-163 2C170-191 2C 206-228 2C 257-279 2C 299-321 2C 357-376 and 381-398 NC_002163.1 RefSeq region 1611973 1612041 . - . ID=id150;gene=secY;Name=id150;Dbxref=GeneID:905962;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1688c by TMHMM2.0 at aa 9-31 2C 61-83 2C 104-126 2C 141-163 2C170-191 2C 206-228 2C 257-279 2C 299-321 2C 357-376 and 381-398 NC_002163.1 RefSeq region 1612129 1612197 . - . ID=id150;gene=secY;Name=id150;Dbxref=GeneID:905962;gbkey=misc_feature;Note=10 probable transmembrane helices predicted for Cj1688c by TMHMM2.0 at aa 9-31 2C 61-83 2C 104-126 2C 141-163 2C170-191 2C 206-228 2C 257-279 2C 299-321 2C 357-376 and 381-398 NC_002163.1 RefSeq gene 1612221 1612613 . - . ID=gene1626;gene=rplO;Name=rplO;locus_tag=Cj1689c;Dbxref=GeneID:905963;gbkey=Gene NC_002163.1 RefSeq CDS 1612221 1612613 . - 0 ID=cds1537;Parent=gene1626;gene=rplO;Name=YP_002345055.1;Dbxref=GOA:Q0P7U2 InterPro:IPR001196 InterPro:IPR005749 UniProtKB FTrEMBL:Q0P7U2 Genbank:YP_002345055.1 GeneID:905963;gbkey=CDS;product=50S ribosomal protein L15;Note=late assembly protein NC_002163.1 RefSeq region 1612320 1612610 . - . ID=id2974;gene=rplO;Name=id2974;Dbxref=GeneID:905963;gbkey=misc_feature;Note=HMMPfam hit to PF01305 2C Ribosomal protein L15 amino terminal re 2C score 1.5e-41 ### NC_002163.1 RefSeq CDS 1612618 1613061 . - 0 ID=cds1538;Parent=gene1627;gene=rpsE;Name=YP_002345056.1;Dbxref=GOA:Q9PLY8 HSSP:P02357 InterPro:IPR000851 InterPro:IPR005324 InterPro:IPR005712 InterPro:IPR013810 InterPro:IPR014720 InterPro:IPR014721 UniProtKB FSwiss-Prot:Q9PLY8 Genbank:YP_002345056.1 GeneID:905964;gbkey=CDS;product=30S ribosomal protein S5;Note=located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body 3B contacts S4 and S8 3B with S4 and S12 plays a role in translational accuracy 3B mutations in this gene result in spectinomycin resistance NC_002163.1 RefSeq gene 1612618 1613061 . - . ID=gene1627;gene=rpsE;Name=rpsE;locus_tag=Cj1690c;Dbxref=GeneID:905964;gbkey=Gene NC_002163.1 RefSeq region 1612621 1612815 . - . ID=id2975;gene=rpsE;Name=id2975;Dbxref=GeneID:905964;gbkey=misc_feature;Note=HMMPfam hit to PF03719 2C Ribosomal protein S5 2CC-terminal domai 2C score 1.8e-23 NC_002163.1 RefSeq region 1612840 1613040 . - . ID=id2976;gene=rpsE;Name=id2976;Dbxref=GeneID:905964;gbkey=misc_feature;Note=HMMPfam hit to PF00333 2C Ribosomal protein S5 2CN-terminal domai 2C score 6.4e-34 NC_002163.1 RefSeq region 1612888 1612986 . - . ID=id2977;gene=rpsE;Name=id2977;Dbxref=GeneID:905964;gbkey=misc_feature;Note=PS00585 Ribosomal protein S5 signature ### NC_002163.1 RefSeq gene 1613073 1613429 . - . ID=gene1628;gene=rplR;Name=rplR;locus_tag=Cj1691c;Dbxref=GeneID:905965;gbkey=Gene NC_002163.1 RefSeq CDS 1613073 1613429 . - 0 ID=cds1539;Parent=gene1628;gene=rplR;Name=YP_002345057.1;Dbxref=GOA:Q9PLY7 HSSP:P09415 InterPro:IPR004389 InterPro:IPR005484 UniProtKB FSwiss-Prot:Q9PLY7 Genbank:YP_002345057.1 GeneID:905965;gbkey=CDS;product=50S ribosomal protein L18;Note=binds 5S rRNA along with protein L5 and L25 NC_002163.1 RefSeq region 1613076 1613408 . - . ID=id2978;gene=rplR;Name=id2978;Dbxref=GeneID:905965;gbkey=misc_feature;Note=HMMPfam hit to PF00861 2C Ribosomal L18p 2FL5e family 2Cscore 8.6e-27 ### NC_002163.1 RefSeq CDS 1613439 1613975 . - 0 ID=cds1540;Parent=gene1629;gene=rplF;Name=YP_002345058.1;Dbxref=GOA:Q0P7T9 InterPro:IPR000702 InterPro:IPR002358 UniProtKB FSwiss-Prot:Q0P7T9 Genbank:YP_002345058.1 GeneID:905966;gbkey=CDS;product=50S ribosomal protein L6;Note=ribosomal protein L6 appears to have arisen as a result of an ancient gene duplication as based on structural comparison of the Bacillus stearothermophilus protein 3B RNA-binding appears to be in the C-terminal domain 3B mutations in the L6 gene confer resistance to aminoglycoside antibiotics such as gentamicin and these occur in truncations of the C-terminal domain 3B it has been localized to a region between the base of the L7 2FL12 stalk and the central protuberance NC_002163.1 RefSeq gene 1613439 1613975 . - . ID=gene1629;gene=rplF;Name=rplF;locus_tag=Cj1692c;Dbxref=GeneID:905966;gbkey=Gene NC_002163.1 RefSeq region 1613484 1613708 . - . ID=id2979;gene=rplF;Name=id2979;Dbxref=GeneID:905966;gbkey=misc_feature;Note=HMMPfam hit to PF00347 2C Ribosomal protein L6 2C score 2.6e-30 NC_002163.1 RefSeq region 1613493 1613519 . - . ID=id2980;gene=rplF;Name=id2980;Dbxref=GeneID:905966;gbkey=misc_feature;Note=PS00525 Ribosomal protein L6 signature 1 NC_002163.1 RefSeq region 1613730 1613945 . - . ID=id2981;gene=rplF;Name=id2981;Dbxref=GeneID:905966;gbkey=misc_feature;Note=HMMPfam hit to PF00347 2C Ribosomal protein L6 2C score 3e-07 ### NC_002163.1 RefSeq CDS 1614054 1614449 . - 0 ID=cds1541;Parent=gene1630;gene=rpsH;Name=YP_002345059.1;Dbxref=GOA:Q9PLY5 HSSP:P24319 InterPro:IPR000630 UniProtKB FSwiss-Prot:Q9PLY5 Genbank:YP_002345059.1 GeneID:905967;gbkey=CDS;product=30S ribosomal protein S8;Note=binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit NC_002163.1 RefSeq gene 1614054 1614449 . - . ID=gene1630;gene=rpsH;Name=rpsH;locus_tag=Cj1693c;Dbxref=GeneID:905967;gbkey=Gene NC_002163.1 RefSeq region 1614057 1614068 . - . ID=id2983;gene=rpsH;Name=id2983;Dbxref=GeneID:905967;gbkey=misc_feature;Note=PS00294 Prenyl group binding site 28CAAX box 29 NC_002163.1 RefSeq region 1614057 1614440 . - . ID=id2982;gene=rpsH;Name=id2982;Dbxref=GeneID:905967;gbkey=misc_feature;Note=HMMPfam hit to PF00410 2C Ribosomal protein S8 2C score 2.7e-52 NC_002163.1 RefSeq region 1614096 1614149 . - . ID=id2984;gene=rpsH;Name=id2984;Dbxref=GeneID:905967;gbkey=misc_feature;Note=PS00053 Ribosomal protein S8 signature ### NC_002163.1 RefSeq CDS 1614459 1614644 . - 0 ID=cds1542;Parent=gene1631;gene=rpsN;Name=YP_002345060.1;Dbxref=GOA:Q9PLY4 InterPro:IPR001209 UniProtKB FSwiss-Prot:Q9PLY4 Genbank:YP_002345060.1 GeneID:905968;gbkey=CDS;product=30S ribosomal protein S14;Note=located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit 3B similar to what is observed with proteins L31 and L33 2C some proteins in this family contain CXXC motifs that are involved in zinc binding 3B if two copies are present in a genome 2C then the duplicated copy appears to have lost the zinc-binding motif and is instead regulated by zinc 3B the proteins in this group appear to contain the zinc-binding motif NC_002163.1 RefSeq gene 1614459 1614644 . - . ID=gene1631;gene=rpsN;Name=rpsN;locus_tag=Cj1694c;Dbxref=GeneID:905968;gbkey=Gene NC_002163.1 RefSeq region 1614465 1614629 . - . ID=id2985;gene=rpsN;Name=id2985;Dbxref=GeneID:905968;gbkey=misc_feature;Note=HMMPfam hit to PF00253 2C Ribosomal protein S14p 2FS29e 2C score 6.5e-20 NC_002163.1 RefSeq region 1614510 1614578 . - . ID=id2986;gene=rpsN;Name=id2986;Dbxref=GeneID:905968;gbkey=misc_feature;Note=PS00527 Ribosomal protein S14 signature ### NC_002163.1 RefSeq CDS 1614646 1615191 . - 0 ID=cds1543;Parent=gene1632;gene=rplE;Name=YP_002345061.1;Dbxref=GOA:Q9PLY3 HSSP:P08895 InterPro:IPR002132 UniProtKB FSwiss-Prot:Q9PLY3 Genbank:YP_002345061.1 GeneID:905969;gbkey=CDS;product=50S ribosomal protein L5;Note=part of 50S and 5S 2FL5 2FL18 2FL25 subcomplex 3B contacts 5S rRNA and P site tRNA 3B forms a bridge to the 30S subunit in the ribosome by binding to S13 NC_002163.1 RefSeq gene 1614646 1615191 . - . ID=gene1632;gene=rplE;Name=rplE;locus_tag=Cj1695c;Dbxref=GeneID:905969;gbkey=Gene NC_002163.1 RefSeq region 1614658 1614942 . - . ID=id2987;gene=rplE;Name=id2987;Dbxref=GeneID:905969;gbkey=misc_feature;Note=HMMPfam hit to PF00673 2C ribosomal L5P family C-terminus 2C score 6e-47 NC_002163.1 RefSeq region 1614952 1615122 . - . ID=id2988;gene=rplE;Name=id2988;Dbxref=GeneID:905969;gbkey=misc_feature;Note=HMMPfam hit to PF00281 2C Ribosomal protein L5 2C score 2.1e-21 NC_002163.1 RefSeq region 1614973 1615023 . - . ID=id2989;gene=rplE;Name=id2989;Dbxref=GeneID:905969;gbkey=misc_feature;Note=PS00358 Ribosomal protein L5 signature ### NC_002163.1 RefSeq CDS 1615195 1615428 . - 0 ID=cds1544;Parent=gene1633;gene=rplX;Name=YP_002345062.1;Dbxref=GOA:Q9PLY2 InterPro:IPR003256 InterPro:IPR005824 InterPro:IPR005825 InterPro:IPR014723 UniProtKB FSwiss-Prot:Q9PLY2 Genbank:YP_002345062.1 GeneID:905970;gbkey=CDS;product=50S ribosomal protein L24;Note=assembly initiator protein 3B binds to 5 27 end of 23S rRNA and nucleates assembly of the 50S 3B surrounds polypeptide exit tunnel NC_002163.1 RefSeq gene 1615195 1615428 . - . ID=gene1633;gene=rplX;Name=rplX;locus_tag=Cj1696c;Dbxref=GeneID:905970;gbkey=Gene NC_002163.1 RefSeq region 1615309 1615410 . - . ID=id2990;gene=rplX;Name=id2990;Dbxref=GeneID:905970;gbkey=misc_feature;Note=HMMPfam hit to PF00467 2C KOW motif 2C score 9.3e-11 NC_002163.1 RefSeq region 1615348 1615401 . - . ID=id2991;gene=rplX;Name=id2991;Dbxref=GeneID:905970;gbkey=misc_feature;Note=PS01108 Ribosomal protein L24 signature NC_002163.1 RefSeq CDS 1615428 1615796 . - 0 ID=cds1545;Parent=gene1634;gene=rplN;Name=YP_002345063.1;Dbxref=GOA:Q0P7T4 InterPro:IPR000218 InterPro:IPR005745 UniProtKB FSwiss-Prot:Q0P7T4 Genbank:YP_002345063.1 GeneID:905971;gbkey=CDS;product=50S ribosomal protein L14;Note=binds to the 23S rRNA between the centers for peptidyl transferase and GTPase NC_002163.1 RefSeq gene 1615428 1615796 . - . ID=gene1634;gene=rplN;Name=rplN;locus_tag=Cj1697c;Dbxref=GeneID:905971;gbkey=Gene NC_002163.1 RefSeq region 1615431 1615796 . - . ID=id2992;gene=rplN;Name=id2992;Dbxref=GeneID:905971;gbkey=misc_feature;Note=HMMPfam hit to PF00238 2C Ribosomal protein L14p 2FL23e 2C score 3.4e-77 NC_002163.1 RefSeq region 1615539 1615619 . - . ID=id2993;gene=rplN;Name=id2993;Dbxref=GeneID:905971;gbkey=misc_feature;Note=PS00049 Ribosomal protein L14 signature NC_002163.1 RefSeq gene 1615796 1616047 . - . ID=gene1635;gene=rpsQ;Name=rpsQ;locus_tag=Cj1698c;Dbxref=GeneID:905972;gbkey=Gene NC_002163.1 RefSeq CDS 1615796 1616047 . - 0 ID=cds1546;Parent=gene1635;gene=rpsQ;Name=YP_002345064.1;Dbxref=GOA:Q9PLY0 HSSP:P23828 InterPro:IPR000266 InterPro:IPR012340 UniProtKB FSwiss-Prot:Q9PLY0 Genbank:YP_002345064.1 GeneID:905972;gbkey=CDS;product=30S ribosomal protein S17;Note=primary binding protein 3B helps mediate assembly 3B involved in translation fidelity NC_002163.1 RefSeq region 1615817 1616023 . - . ID=id2994;gene=rpsQ;Name=id2994;Dbxref=GeneID:905972;gbkey=misc_feature;Note=HMMPfam hit to PF00366 2C Ribosomal protein S17 2Cscore 1.1e-23 NC_002163.1 RefSeq region 1615847 1615885 . - . ID=id2995;gene=rpsQ;Name=id2995;Dbxref=GeneID:905972;gbkey=misc_feature;Note=PS00056 Ribosomal protein S17 signature ### NC_002163.1 RefSeq CDS 1616057 1616242 . - 0 ID=cds1547;Parent=gene1636;gene=rpmC;Name=YP_002345065.1;Dbxref=GOA:Q9PLX9 InterPro:IPR001854 UniProtKB FSwiss-Prot:Q9PLX9 Genbank:YP_002345065.1 GeneID:905973;gbkey=CDS;product=50S ribosomal protein L29;Note=one of the stabilizing components for the large ribosomal subunit NC_002163.1 RefSeq gene 1616057 1616242 . - . ID=gene1636;gene=rpmC;Name=rpmC;locus_tag=Cj1699c;Dbxref=GeneID:905973;gbkey=Gene NC_002163.1 RefSeq region 1616063 1616236 . - . ID=id2996;gene=rpmC;Name=id2996;Dbxref=GeneID:905973;gbkey=misc_feature;Note=HMMPfam hit to PF00831 2C Ribosomal L29 protein 2Cscore 1.5e-19 NC_002163.1 RefSeq region 1616084 1616128 . - . ID=id2997;gene=rpmC;Name=id2997;Dbxref=GeneID:905973;gbkey=misc_feature;Note=PS00579 Ribosomal protein L29 signature NC_002163.1 RefSeq gene 1616229 1616654 . - . ID=gene1637;gene=rplP;Name=rplP;locus_tag=Cj1700c;Dbxref=GeneID:905974;gbkey=Gene NC_002163.1 RefSeq CDS 1616229 1616654 . - 0 ID=cds1548;Parent=gene1637;gene=rplP;Name=YP_002345066.1;Dbxref=GOA:Q9PLX8 InterPro:IPR000114 UniProtKB FSwiss-Prot:Q9PLX8 Genbank:YP_002345066.1 GeneID:905974;gbkey=CDS;product=50S ribosomal protein L16;Note=located in the peptidyl transferase center and may be involved in peptidyl transferase activity 3B similar to archaeal L10e NC_002163.1 RefSeq region 1616259 1616654 . - . ID=id2998;gene=rplP;Name=id2998;Dbxref=GeneID:905974;gbkey=misc_feature;Note=HMMPfam hit to PF00252 2C Ribosomal protein L16 2Cscore 2.7e-82 NC_002163.1 RefSeq region 1616376 1616411 . - . ID=id2999;gene=rplP;Name=id2999;Dbxref=GeneID:905974;gbkey=misc_feature;Note=PS00701 Ribosomal protein L16 signature 2 ### NC_002163.1 RefSeq CDS 1616657 1617358 . - 0 ID=cds1549;Parent=gene1638;gene=rpsC;Name=YP_002345067.1;Dbxref=GOA:Q9PLX7 InterPro:IPR001351 InterPro:IPR004044 InterPro:IPR004087 InterPro:IPR005704 InterPro:IPR008282 InterPro:IPR015946 UniProtKB FSwiss-Prot:Q9PLX7 Genbank:YP_002345067.1 GeneID:905975;gbkey=CDS;product=30S ribosomal protein S3;Note=forms a complex with S10 and S14 3B binds the lower part of the 30S subunit head and the mRNA in the complete ribosome to position it for translation NC_002163.1 RefSeq gene 1616657 1617358 . - . ID=gene1638;gene=rpsC;Name=rpsC;locus_tag=Cj1701c;Dbxref=GeneID:905975;gbkey=Gene NC_002163.1 RefSeq region 1616753 1617004 . - . ID=id3000;gene=rpsC;Name=id3000;Dbxref=GeneID:905975;gbkey=misc_feature;Note=HMMPfam hit to PF00189 2C Ribosomal protein S3 2CC-terminal domai 2C score 2.8e-49 NC_002163.1 RefSeq region 1616768 1616872 . - . ID=id3001;gene=rpsC;Name=id3001;Dbxref=GeneID:905975;gbkey=misc_feature;Note=PS00548 Ribosomal protein S3 signature NC_002163.1 RefSeq region 1617008 1617172 . - . ID=id3002;gene=rpsC;Name=id3002;Dbxref=GeneID:905975;gbkey=misc_feature;Note=HMMPfam hit to PF07650 2C KH domain 2C score 1.4e-17 NC_002163.1 RefSeq region 1617173 1617358 . - . ID=id3003;gene=rpsC;Name=id3003;Dbxref=GeneID:905975;gbkey=misc_feature;Note=HMMPfam hit to PF00417 2C Ribosomal protein S3 2CN-terminal domai 2C score 1.9e-24 NC_002163.1 RefSeq gene 1617358 1617783 . - . ID=gene1639;gene=rplV;Name=rplV;locus_tag=Cj1702c;Dbxref=GeneID:905976;gbkey=Gene NC_002163.1 RefSeq CDS 1617358 1617783 . - 0 ID=cds1550;Parent=gene1639;gene=rplV;Name=YP_002345068.1;Dbxref=GOA:Q9PLX6 HSSP:P48286 InterPro:IPR001063 InterPro:IPR005727 UniProtKB FSwiss-Prot:Q9PLX6 Genbank:YP_002345068.1 GeneID:905976;gbkey=CDS;product=50S ribosomal protein L22;Note=binds specifically to 23S rRNA during the early stages of 50S assembly 3B makes contact with all 6 domains of the 23S rRNA in the assembled 50S subunit and ribosome 3B mutations in this gene result in erythromycin resistance 3B located near peptidyl-transferase center NC_002163.1 RefSeq region 1617472 1617774 . - . ID=id3004;gene=rplV;Name=id3004;Dbxref=GeneID:905976;gbkey=misc_feature;Note=HMMPfam hit to PF00237 2C Ribosomal protein L22p 2FL17e 2C score 3.7e-29 NC_002163.1 RefSeq region 1617478 1617552 . - . ID=id3005;gene=rplV;Name=id3005;Dbxref=GeneID:905976;gbkey=misc_feature;Note=PS00464 Ribosomal protein L22 signature ### NC_002163.1 RefSeq CDS 1617794 1618075 . - 0 ID=cds1551;Parent=gene1640;gene=rpsS;Name=YP_002345069.1;Dbxref=GOA:Q9PLX5 HSSP:P80381 InterPro:IPR002222 InterPro:IPR005732 UniProtKB FSwiss-Prot:Q9PLX5 Genbank:YP_002345069.1 GeneID:905977;gbkey=CDS;product=30S ribosomal protein S19;Note=protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA NC_002163.1 RefSeq gene 1617794 1618075 . - . ID=gene1640;gene=rpsS;Name=rpsS;locus_tag=Cj1703c;Dbxref=GeneID:905977;gbkey=Gene NC_002163.1 RefSeq region 1617827 1618069 . - . ID=id3006;gene=rpsS;Name=id3006;Dbxref=GeneID:905977;gbkey=misc_feature;Note=HMMPfam hit to PF00203 2C Ribosomal protein S19 2Cscore 1.7e-43 NC_002163.1 RefSeq region 1617845 1617919 . - . ID=id3007;gene=rpsS;Name=id3007;Dbxref=GeneID:905977;gbkey=misc_feature;Note=PS00323 Ribosomal protein S19 signature ### NC_002163.1 RefSeq CDS 1618077 1618907 . - 0 ID=cds1552;Parent=gene1641;gene=rplB;Name=YP_002345070.1;Dbxref=GOA:Q9PLX4 HSSP:P04257 InterPro:IPR002171 InterPro:IPR005880 InterPro:IPR012340 InterPro:IPR014722 UniProtKB FSwiss-Prot:Q9PLX4 Genbank:YP_002345070.1 GeneID:905978;gbkey=CDS;product=50S ribosomal protein L2;Note=one of the primary rRNA-binding proteins 3B required for association of the 30S and 50S subunits to form the 70S ribosome 2C for tRNA binding and peptide bond formation NC_002163.1 RefSeq gene 1618077 1618907 . - . ID=gene1641;gene=rplB;Name=rplB;locus_tag=Cj1704c;Dbxref=GeneID:905978;gbkey=Gene NC_002163.1 RefSeq region 1618149 1618535 . - . ID=id3008;gene=rplB;Name=id3008;Dbxref=GeneID:905978;gbkey=misc_feature;Note=HMMPfam hit to PF03947 2C Ribosomal Proteins L2 2CC-terminal doma 2C score 1.7e-85 NC_002163.1 RefSeq region 1618218 1618253 . - . ID=id3009;gene=rplB;Name=id3009;Dbxref=GeneID:905978;gbkey=misc_feature;Note=PS00467 Ribosomal protein L2 signature NC_002163.1 RefSeq region 1618554 1618784 . - . ID=id3010;gene=rplB;Name=id3010;Dbxref=GeneID:905978;gbkey=misc_feature;Note=HMMPfam hit to PF00181 2C Ribosomal Proteins L2 2C RNA binding dom 2C score 4.1e-40 ### NC_002163.1 RefSeq gene 1618909 1619190 . - . ID=gene1642;gene=rplW;Name=rplW;locus_tag=Cj1705c;Dbxref=GeneID:905979;gbkey=Gene NC_002163.1 RefSeq CDS 1618909 1619190 . - 0 ID=cds1553;Parent=gene1642;gene=rplW;Name=YP_002345071.1;Dbxref=GOA:Q0P7S6 InterPro:IPR001014 InterPro:IPR012677 InterPro:IPR013025 UniProtKB FSwiss-Prot:Q0P7S6 Genbank:YP_002345071.1 GeneID:905979;gbkey=CDS;product=50S ribosomal protein L23;Note=binds third domain of 23S rRNA and protein L29 3B part of exit tunnel NC_002163.1 RefSeq region 1618912 1619172 . - . ID=id3011;gene=rplW;Name=id3011;Dbxref=GeneID:905979;gbkey=misc_feature;Note=HMMPfam hit to PF00276 2C Ribosomal protein L23 2Cscore 2.7e-09 ### NC_002163.1 RefSeq CDS 1619193 1619807 . - 0 ID=cds1554;Parent=gene1643;gene=rplD;Name=YP_002345072.1;Dbxref=GOA:Q9PLX2 InterPro:IPR002136 InterPro:IPR013005 InterPro:IPR015498 UniProtKB FSwiss-Prot:Q9PLX2 Genbank:YP_002345072.1 GeneID:905980;gbkey=CDS;product=50S ribosomal protein L4;Note=L4 is important during the early stages of 50S assembly 3B it initially binds near the 5 27 end of the 23S rRNA NC_002163.1 RefSeq gene 1619193 1619807 . - . ID=gene1643;gene=rplD;Name=rplD;locus_tag=Cj1706c;Dbxref=GeneID:905980;gbkey=Gene NC_002163.1 RefSeq region 1619199 1619765 . - . ID=id3012;gene=rplD;Name=id3012;Dbxref=GeneID:905980;gbkey=misc_feature;Note=HMMPfam hit to PF00573 2C Ribosomal protein L4 2FL1 family 2C score 1.6e-49 NC_002163.1 RefSeq CDS 1619804 1620379 . - 0 ID=cds1555;Parent=gene1644;gene=rplC;Name=YP_002345073.1;Dbxref=GOA:Q9PLX1 InterPro:IPR000597 UniProtKB FSwiss-Prot:Q9PLX1 Genbank:YP_002345073.1 GeneID:905981;gbkey=CDS;product=50S ribosomal protein L3;Note=binds directly near the 3 27 end of the 23S rRNA 2C where it nucleates assembly of the 50S subunit 3B essential for peptidyltransferase activity 3B mutations in this gene confer resistance to tiamulin NC_002163.1 RefSeq gene 1619804 1620379 . - . ID=gene1644;gene=rplC;Name=rplC;locus_tag=Cj1707c;Dbxref=GeneID:905981;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 1619808 1619830 . - . ID=utr614;locus_tag=Cj1706c;product=50S ribosomal protein L4 NC_002163.1 RefSeq region 1619816 1620361 . - . ID=id3013;gene=rplC;Name=id3013;Dbxref=GeneID:905981;gbkey=misc_feature;Note=HMMPfam hit to PF00297 2C Ribosomal protein L3 2C score 2.3e-18 ### NC_002163.1 RefSeq CDS 1620389 1620700 . - 0 ID=cds1556;Parent=gene1645;gene=rpsJ;Name=YP_002345074.1;Dbxref=GOA:Q9PLX0 InterPro:IPR001848 InterPro:IPR005731 UniProtKB FSwiss-Prot:Q9PLX0 Genbank:YP_002345074.1 GeneID:905982;gbkey=CDS;product=30S ribosomal protein S10;Note=NusE 3B involved in assembly of the 30S subunit 3B in the ribosome 2C this protein is involved in the binding of tRNA 3B in Escherichia coli this protein was also found to be involved in transcription antitermination 3B NusB 2FS10 heterodimers bind boxA sequences in the leader RNA of rrn operons which is required for antitermination 3B binding of NusB 2FS10 to boxA nucleates assembly of the antitermination complex NC_002163.1 RefSeq gene 1620389 1620700 . - . ID=gene1645;gene=rpsJ;Name=rpsJ;locus_tag=Cj1708c;Dbxref=GeneID:905982;gbkey=Gene NC_002163.1 RefSeq region 1620407 1620694 . - . ID=id3014;gene=rpsJ;Name=id3014;Dbxref=GeneID:905982;gbkey=misc_feature;Note=HMMPfam hit to PF00338 2C Ribosomal protein S10p 2FS20e 2C score 9.1e-49 NC_002163.1 RefSeq region 1620575 1620622 . - . ID=id3015;gene=rpsJ;Name=id3015;Dbxref=GeneID:905982;gbkey=misc_feature;Note=PS00361 Ribosomal protein S10 signature ### NC_002163.1 UTR_Extractor 5'-UTR 1620701 1620758 . - . ID=utr615;locus_tag=Cj1708c;product=30S ribosomal protein S10 NC_002163.1 RefSeq CDS 1620899 1621660 . - 0 ID=cds1557;Parent=gene1646;Name=YP_002345075.1;Dbxref=GOA:Q0P7S2 InterPro:IPR000748 InterPro:IPR002942 InterPro:IPR006145 UniProtKB FTrEMBL:Q0P7S2 Genbank:YP_002345075.1 GeneID:905983;gbkey=CDS;product=ribosomal pseudouridine synthase;Note=Original 282000 29 note: Cj1709c 2C probable ribosomal pseudouridine synthase 2C len: 253 aa 3B similar to e.g. RLUB_BACSU ribosomal large subunit pseudouridine synthase B 28EC 4.2.1.70 29 28229 aa 29 2C fasta scores 3B opt: 338 z-score: 414.2 E 28 29: 9.5e-16 2C 33.9 25 identity in 236 aa overlap. 50.4 25 identity to HP1459. Contains PS01149 RsuA family of pseudouridine synthase signature 7EUpdated 282006 29 note: Pfam domain PF00849 RNA pseudouridylate synthase and PF01479 S4 domain were identified within CDS. Further support given to product function. Characterisation work within Bacillus subtilis and others with marginal identity scores. kept in product function. Functional classification - Ribosome maturation and modification 7EPMID:9888802 NC_002163.1 RefSeq gene 1620899 1621660 . - . ID=gene1646;Name=Cj1709c;locus_tag=Cj1709c;Dbxref=GeneID:905983;gbkey=Gene NC_002163.1 RefSeq region 1621046 1621483 . - . ID=id3016;Name=id3016;Dbxref=GeneID:905983;gbkey=misc_feature;Note=HMMPfam hit to PF00849 2C RNA pseudouridylate synthase 2C score 2.2e-07 NC_002163.1 RefSeq region 1621325 1621369 . - . ID=id3017;Name=id3017;Dbxref=GeneID:905983;gbkey=misc_feature;Note=PS01149 Rsu family of pseudouridine synthase signature NC_002163.1 RefSeq region 1621523 1621660 . - . ID=id3018;Name=id3018;Dbxref=GeneID:905983;gbkey=misc_feature;Note=HMMPfam hit to PF01479 2C S4 domain 2C score 3.6e-09 NC_002163.1 RefSeq region 1621628 1621651 . - . ID=id3019;Name=id3019;Dbxref=GeneID:905983;gbkey=misc_feature;Note=PS00881 Protein splicing signature ### NC_002163.1 RefSeq CDS 1621696 1623690 . - 0 ID=cds1558;Parent=gene1647;Name=YP_002345076.1;Dbxref=GOA:Q0P7S1 InterPro:IPR001279 InterPro:IPR001587 InterPro:IPR004613 InterPro:IPR011108 UniProtKB FTrEMBL:Q0P7S1 Genbank:YP_002345076.1 GeneID:905984;gbkey=CDS;product=metallo-beta-lactamase family protein;Note=Original 282000 29 note: Cj1710c 2C unknown 2C len: 664 aa 3B similar to hypothetical proteins e.g. YKQC_BACSU 28555 aa 29 2C fasta scores 3B opt: 1429 z-score: 1605.6 E 28 29: 0 2C 39.5 25 identity in 544 aa overlap. N-terminal 100 aa is evry hydrophilic 2C and is conserved only with the Hp homolog and YOR4_CORGL 28645 aa 29 2C fasta scores 3B opt: 1223 z-score: 1373.2 E 28 29: 0 2C 34.4 25 identity in 613 aa overlap. 55.3 25 identity to HP1430. Contains S01292 Uncharacterized protein family UPF0036 signature 2C and fam match to entry PF00753 lactamase_B 2C Metallo-beta-lactamase superfamily 7EUpdated 282006 29 note: Pfam domains PF07521 RNA-metabolising metallo-beta-lactamase and PF00753 Metallo-beta-lactamase superfamily identified within CDS. Product modified to more specific family member based on motif match. No specific characterisation has been carried out yet with acceptable simiarity score. Thus 2C kept within product function. Functional classification -Misc NC_002163.1 RefSeq gene 1621696 1623690 . - . ID=gene1647;Name=Cj1710c;locus_tag=Cj1710c;Dbxref=GeneID:905984;gbkey=Gene NC_002163.1 RefSeq region 1622182 1622304 . - . ID=id3020;Name=id3020;Dbxref=GeneID:905984;gbkey=misc_feature;Note=HMMPfam hit to PF07521 2C RNA-metabolising metallo-beta-lactamase 2C score 4.4e-11 NC_002163.1 RefSeq region 1622188 1622274 . - . ID=id3021;Name=id3021;Dbxref=GeneID:905984;gbkey=misc_feature;Note=PS01292 Uncharacterized protein family UPF0036 signature NC_002163.1 RefSeq region 1622719 1623309 . - . ID=id3022;Name=id3022;Dbxref=GeneID:905984;gbkey=misc_feature;Note=HMMPfam hit to PF00753 2C Metallo-beta-lactamase superfamily 2C score 1.8e-26 NC_002163.1 RefSeq CDS 1623659 1624459 . - 0 ID=cds1559;Parent=gene1648;gene=ksgA;Name=YP_002345077.1;Dbxref=GOA:Q9PLW7 InterPro:IPR001737 InterPro:IPR011530 UniProtKB FSwiss-Prot:Q9PLW7 Genbank:YP_002345077.1 GeneID:905985;gbkey=CDS;product=dimethyladenosine transferase;Note=catalyzes the transfer of a total of four methyl groups from S-adenosyl-l-methionine 28S-AdoMet 29 to two adjacent adenosine bases A1518 and A1519 in 16S rRNA 3B mutations in ksgA causes resistance to the translation initiation inhibitor kasugamycin NC_002163.1 RefSeq gene 1623659 1624459 . - . ID=gene1648;gene=ksgA;Name=ksgA;locus_tag=Cj1711c;Dbxref=GeneID:905985;gbkey=Gene NC_002163.1 RefSeq region 1623689 1624459 . - . ID=id3023;gene=ksgA;Name=id3023;Dbxref=GeneID:905985;gbkey=misc_feature;Note=HMMPfam hit to PF00398 2C Ribosomal RNA adenine dimethylase 2C score 1.4e-42 NC_002163.1 RefSeq region 1623818 1623838 . - . ID=id3024;gene=ksgA;Name=id3024;Dbxref=GeneID:905985;gbkey=misc_feature;Note=PS00322 Histone H3 signature 1 ### NC_002163.1 UTR_Extractor 5'-UTR 1624460 1624461 . - . ID=utr616;locus_tag=Cj1711c;product=dimethyladenosine transferase NC_002163.1 RefSeq stem_loop 1624460 1624517 . + . ID=id3025;Name=id3025;gbkey=stem_loop ### NC_002163.1 RefSeq gene 1624541 1625077 . + . ID=gene1649;Name=Cj1712;locus_tag=Cj1712;Dbxref=GeneID:905986;gbkey=Gene NC_002163.1 RefSeq CDS 1624541 1625077 . + 0 ID=cds1560;Parent=gene1649;Name=YP_002345078.1;Dbxref=UniProtKB FTrEMBL:Q0P7R9 Genbank:YP_002345078.1 GeneID:905986;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1712 2C unknown 2C len: 178 aa 3B 40.9 25 identity to HP1530 28called purine nucleoside phosphorylase 28punB 29. Functional classification -Conserved hypothetical proteins NC_002163.1 RefSeq CDS 1625100 1626170 . + 0 ID=cds1561;Parent=gene1650;Name=YP_002345079.1;Dbxref=GOA:Q0P7R8 InterPro:IPR004383 InterPro:IPR006638 InterPro:IPR007197 UniProtKB FSwiss-Prot:Q0P7R8 Genbank:YP_002345079.1 GeneID:905987;gbkey=CDS;product=ribosomal RNA large subunit methyltransferase N;Note=23S rRNA m2A2503 methyltransferase 3B methylates the C2 position of the A2530 nucleotide in 23S rRNA 3B may be involved in antibiotic resistance NC_002163.1 RefSeq gene 1625100 1626170 . + . ID=gene1650;Name=Cj1713;locus_tag=Cj1713;Dbxref=GeneID:905987;gbkey=Gene NC_002163.1 RefSeq region 1625445 1625960 . + . ID=id3026;Name=id3026;Dbxref=GeneID:905987;gbkey=misc_feature;Note=HMMPfam hit to PF04055 2C Radical SAM superfamily 2Cscore 1.9e-13 NC_002163.1 RefSeq gene 1626167 1626265 . + . ID=gene1651;Name=Cj1714;locus_tag=Cj1714;Dbxref=GeneID:905988;gbkey=Gene NC_002163.1 RefSeq CDS 1626167 1626265 . + 0 ID=cds1562;Parent=gene1651;Name=YP_002345080.1;Dbxref=GOA:Q0P7R7 UniProtKB FTrEMBL:Q0P7R7 Genbank:YP_002345080.1 GeneID:905988;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1714 2C small hydrophobic protein 2C len: 32 aa 3B no Hp match 7EUpdated 282006 29 note: One probable transmembrane helix predicted by TMHMM2.0. Functional classification -Unknown NC_002163.1 RefSeq region 1626182 1626250 . + . ID=id3027;Name=id3027;Dbxref=GeneID:905988;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1714 by TMHMM2.0 at aa 6-28 ### NC_002163.1 RefSeq gene 1626279 1626355 . - . ID=gene1652;gene=tRNAMet;Name=tRNAMet;locus_tag=Cjp34;Dbxref=GeneID:905989;gbkey=Gene NC_002163.1 RefSeq tRNA 1626279 1626355 . - . ID=rna52;Parent=gene1652;gene=tRNAMet;Name=rna52;Dbxref=GeneID:905989;gbkey=tRNA;product=tRNA-Met;Note=tRNA Met anticodon CAT 2C Cove score 81.03 NC_002163.1 RefSeq exon 1626279 1626355 . - . ID=id3028;Parent=rna52;gene=tRNAMet;Name=id3028;Dbxref=GeneID:905989;gbkey=tRNA;product=tRNA-Met;Note=tRNA Met anticodon CAT 2C Cove score 81.03 NC_002163.1 RefSeq gene 1626491 1626578 . + . ID=gene1653;gene=tRNASer;Name=tRNASer;locus_tag=Cjt06;Dbxref=GeneID:3245049;gbkey=Gene NC_002163.1 RefSeq tRNA 1626491 1626578 . + . ID=rna53;Parent=gene1653;gene=tRNASer;Name=rna53;Dbxref=GeneID:3245049;gbkey=tRNA;product=tRNA-Ser;Note=tRNA Ser anticodon GGA 2C Cove score 63.73 NC_002163.1 RefSeq exon 1626491 1626578 . + . ID=id3029;Parent=rna53;gene=tRNASer;Name=id3029;Dbxref=GeneID:3245049;gbkey=tRNA;product=tRNA-Ser;Note=tRNA Ser anticodon GGA 2C Cove score 63.73 NC_002163.1 RefSeq gene 1626625 1626700 . + . ID=gene1654;gene=tRNAAla;Name=tRNAAla;locus_tag=Cjp35;Dbxref=GeneID:905990;gbkey=Gene NC_002163.1 RefSeq tRNA 1626625 1626700 . + . ID=rna54;Parent=gene1654;gene=tRNAAla;Name=rna54;Dbxref=GeneID:905990;gbkey=tRNA;product=tRNA-Ala;Note=tRNA Ala anticodon GGC 2C Cove score 84.81 NC_002163.1 RefSeq exon 1626625 1626700 . + . ID=id3030;Parent=rna54;gene=tRNAAla;Name=id3030;Dbxref=GeneID:905990;gbkey=tRNA;product=tRNA-Ala;Note=tRNA Ala anticodon GGC 2C Cove score 84.81 NC_002163.1 RefSeq gene 1626704 1626779 . + . ID=gene1655;gene=tRNAVal;Name=tRNAVal;locus_tag=Cjp36;Dbxref=GeneID:905991;gbkey=Gene NC_002163.1 RefSeq tRNA 1626704 1626779 . + . ID=rna55;Parent=gene1655;gene=tRNAVal;Name=rna55;Dbxref=GeneID:905991;gbkey=tRNA;product=tRNA-Val;Note=tRNA Val anticodon GAC 2C Cove score 82.27 NC_002163.1 RefSeq exon 1626704 1626779 . + . ID=id3031;Parent=rna55;gene=tRNAVal;Name=id3031;Dbxref=GeneID:905991;gbkey=tRNA;product=tRNA-Val;Note=tRNA Val anticodon GAC 2C Cove score 82.27 NC_002163.1 RefSeq CDS 1626807 1627337 . + 0 ID=cds1563;Parent=gene1656;Name=YP_002345081.1;Dbxref=GOA:Q0P7R6 InterPro:IPR000182 InterPro:IPR016181 UniProtKB FTrEMBL:Q0P7R6 Genbank:YP_002345081.1 GeneID:905992;gbkey=CDS;product=acetyltransferase;Note=Original 282000 29 note: Cj1715 2C possible acetyltransferase 2C len: 176 aa 3B similar to several plasmid- or integron-encoded genes e.g. STA_ECOLI streptothricin acetyltransferase 28174 aa 29 2C fasta scores 3B opt: 149 z-score: 192.6 E 28 29: 0.0021 2C 21.7 25 identity in 161 aa overlap 2C and TR:P75025 28EMBL:P75025 29 plasmid PVS1 hypothetical protein 28166 aa 29 2C fasta scores 3B opt: 201 z-score: 255.1 E 28 29: 6.9e-07 2C 26.1 25 identity in 161 aa overlap. Also simlilar to TR:O31513 28EMBL:Z99107 29 Bacillus subtilis chromosomal YESJ protein 28180 aa 29 2C fasta scores 3B opt: 157 z-score: 202.0 E 28 29: 0.00063 2C 20.6 25 identity in 155 aa overlap. No Hp match. Contains Pfam match to entry PF00583 Acetyltransf 2C Acetyltransferase 28GNAT 29 family 7EUpdated 282006 29 note: Specific characterisation with acceptable identity score has not been carried out yet. Thus 2C kept within product function. Functional classification - Antibiotic resistance NC_002163.1 RefSeq gene 1626807 1627337 . + . ID=gene1656;Name=Cj1715;locus_tag=Cj1715;Dbxref=GeneID:905992;gbkey=Gene NC_002163.1 RefSeq region 1626972 1627256 . + . ID=id3032;Name=id3032;Dbxref=GeneID:905992;gbkey=misc_feature;Note=HMMPfam hit to PF00583 2C Acetyltransferase 28GNAT 29 family 2C score 1.7e-13 NC_002163.1 RefSeq gene 1627317 1627919 . - . ID=gene1657;gene=leuD;Name=leuD;locus_tag=Cj1716c;Dbxref=GeneID:905993;gbkey=Gene NC_002163.1 RefSeq CDS 1627317 1627919 . - 0 ID=cds1564;Parent=gene1657;gene=leuD;Name=YP_002345082.1;Dbxref=GOA:Q9PLW2 InterPro:IPR000573 InterPro:IPR004431 InterPro:IPR012305 InterPro:IPR015928 InterPro:IPR015937 UniProtKB FSwiss-Prot:Q9PLW2 Genbank:YP_002345082.1 GeneID:905993;gbkey=CDS;product=isopropylmalate isomerase small subunit;Note=catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis 3B forms a heterodimer of LeuC 2FD NC_002163.1 RefSeq region 1627542 1627919 . - . ID=id3033;gene=leuD;Name=id3033;Dbxref=GeneID:905993;gbkey=misc_feature;Note=HMMPfam hit to PF00694 2C Aconitase C-terminal domain 2C score 7.2e-54 ### NC_002163.1 RefSeq CDS 1627921 1629333 . - 0 ID=cds1565;Parent=gene1658;gene=leuC;Name=YP_002345083.1;Dbxref=GOA:Q9PLW1 InterPro:IPR001030 InterPro:IPR004430 InterPro:IPR015931 InterPro:IPR015932 InterPro:IPR015936 InterPro:IPR015937 UniProtKB FSwiss-Prot:Q9PLW1 Genbank:YP_002345083.1 GeneID:905994;gbkey=CDS;product=isopropylmalate isomerase large subunit;Note=dehydratase component 2C catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate NC_002163.1 RefSeq gene 1627921 1629333 . - . ID=gene1658;gene=leuC;Name=leuC;locus_tag=Cj1717c;Dbxref=GeneID:905994;gbkey=Gene NC_002163.1 RefSeq region 1627957 1629318 . - . ID=id3034;gene=leuC;Name=id3034;Dbxref=GeneID:905994;gbkey=misc_feature;Note=HMMPfam hit to PF00330 2C Aconitase family 28aconitate hydratase 29 2C score 3.1e-218 NC_002163.1 RefSeq region 1627969 1628001 . - . ID=id3035;gene=leuC;Name=id3035;Dbxref=GeneID:905994;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site NC_002163.1 RefSeq region 1628092 1628133 . - . ID=id3036;gene=leuC;Name=id3036;Dbxref=GeneID:905994;gbkey=misc_feature;Note=PS01244 Aconitase family signature 2 NC_002163.1 RefSeq region 1628263 1628313 . - . ID=id3037;gene=leuC;Name=id3037;Dbxref=GeneID:905994;gbkey=misc_feature;Note=PS00450 Aconitase family signature 1 NC_002163.1 RefSeq gene 1629320 1630396 . - . ID=gene1659;gene=leuB;Name=leuB;locus_tag=Cj1718c;Dbxref=GeneID:905995;gbkey=Gene NC_002163.1 RefSeq CDS 1629320 1630396 . - 0 ID=cds1566;Parent=gene1659;gene=leuB;Name=YP_002345084.1;Dbxref=GOA:Q9PLW0 HSSP:P37412 InterPro:IPR001804 InterPro:IPR004429 UniProtKB FSwiss-Prot:Q9PLW0 Genbank:YP_002345084.1 GeneID:905995;gbkey=CDS;product=3-isopropylmalate dehydrogenase;Note=catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis NC_002163.1 RefSeq region 1629353 1630384 . - . ID=id3038;gene=leuB;Name=id3038;Dbxref=GeneID:905995;gbkey=misc_feature;Note=HMMPfam hit to PF00180 2C Isocitrate 2Fisopropylmalate dehydrogenase 2C score 2.3e-191 NC_002163.1 RefSeq region 1629617 1629676 . - . ID=id3039;gene=leuB;Name=id3039;Dbxref=GeneID:905995;gbkey=misc_feature;Note=PS00470 Isocitrate and isopropylmalate dehydrogenases signature NC_002163.1 RefSeq CDS 1630393 1631928 . - 0 ID=cds1567;Parent=gene1660;gene=leuA;Name=YP_002345085.1;Dbxref=GOA:Q9PLV9 InterPro:IPR000891 InterPro:IPR002034 InterPro:IPR005671 InterPro:IPR013709 InterPro:IPR013785 UniProtKB FSwiss-Prot:Q9PLV9 Genbank:YP_002345085.1 GeneID:905996;gbkey=CDS;product=2-isopropylmalate synthase;Note=catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis NC_002163.1 RefSeq gene 1630393 1631928 . - . ID=gene1660;gene=leuA;Name=leuA;locus_tag=Cj1719c;Dbxref=GeneID:905996;gbkey=Gene NC_002163.1 RefSeq region 1631086 1631889 . - . ID=id3040;gene=leuA;Name=id3040;Dbxref=GeneID:905996;gbkey=misc_feature;Note=HMMPfam hit to PF00682 2C HMGL-like 2C score 3.1e-133 NC_002163.1 RefSeq region 1631290 1631331 . - . ID=id3041;gene=leuA;Name=id3041;Dbxref=GeneID:905996;gbkey=misc_feature;Note=PS00816 Alpha-isopropylmalate and homocitrate synthases signature 2 NC_002163.1 RefSeq region 1631842 1631892 . - . ID=id3042;gene=leuA;Name=id3042;Dbxref=GeneID:905996;gbkey=misc_feature;Note=PS00815 Alpha-isopropylmalate and homocitrate synthases signature 1 ### NC_002163.1 UTR_Extractor 5'-UTR 1631929 1632146 . - . ID=utr617;locus_tag=Cj1719c;product=2-isopropylmalate synthase NC_002163.1 UTR_Extractor 5'-UTR 1632224 1632247 . + . ID=utr618;locus_tag=Cj1720;product=hypothetical protein NC_002163.1 RefSeq gene 1632248 1632877 . + . ID=gene1661;Name=Cj1720;locus_tag=Cj1720;Dbxref=GeneID:905997;gbkey=Gene NC_002163.1 RefSeq CDS 1632248 1632877 . + 0 ID=cds1568;Parent=gene1661;Name=YP_002345086.1;Dbxref=UniProtKB FTrEMBL:Q0P7R1 Genbank:YP_002345086.1 GeneID:905997;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1720 2C unknown 2C len: 209 aa 3B no Hp match. Functional classification - Unknown NC_002163.1 RefSeq gene 1632901 1633545 . - . ID=gene1662;Name=Cj1721c;locus_tag=Cj1721c;Dbxref=GeneID:905998;gbkey=Gene NC_002163.1 RefSeq CDS 1632901 1633545 . - 0 ID=cds1569;Parent=gene1662;Name=YP_002345087.1;Dbxref=UniProtKB FTrEMBL:Q0P7R0 Genbank:YP_002345087.1 GeneID:905998;gbkey=CDS;product=outer membrane protein;Note=Original 282000 29 note: Cj1721c 2C possible outer membrane protein 2C len: 214 aa 3B very weak similarity to several e.g. TR:P95343 28EMBL:U52069 29 Neisseria gonorrhoeae outer membrane protein precursor 28174 aa 29 2C blastp scores 3B E 3D 0.0043 2C 29 25 identity in 176 aa overlap. Contains probable N-terminal signal sequence. 22.3 25 identity to HP0706 28outer membrane protein 28omp15 29 29. Functional classification - Membranes 2C lipoproteins and porins NC_002163.1 UTR_Extractor 5'-UTR 1633546 1633591 . - . ID=utr619;locus_tag=Cj1721c;product=putative outer membrane protein NC_002163.1 RefSeq pseudogene 1633791 1634119 . - . ID=gene1663;Name=Cj1723c;locus_tag=Cj1723c;Dbxref=GeneID:906000;gbkey=Gene NC_002163.1 UTR_Extractor 5'-UTR 1634120 1634144 . - . ID=utr620;locus_tag=Cj1723c;product=putative periplasmic protein NC_002163.1 RefSeq gene 1634296 1634679 . - . ID=gene1664;Name=Cj1724c;locus_tag=Cj1724c;Dbxref=GeneID:905900;gbkey=Gene NC_002163.1 RefSeq CDS 1634296 1634679 . - 0 ID=cds1570;Parent=gene1664;Name=YP_002345090.1;Dbxref=GOA:Q9PLV4 InterPro:IPR001474 InterPro:IPR016856 UniProtKB FSwiss-Prot:Q9PLV4 Genbank:YP_002345090.1 GeneID:905900;gbkey=CDS;product=7-cyano-7-deazaguanine reductase;Note=NADPH-dependent 3B catalyzes the reduction of 7-cyano-7-deazaguanine to 7-aminomethyl-7-deazaguanine in queuosine biosynthesis NC_002163.1 RefSeq region 1634302 1634601 . - . ID=id3043;Name=id3043;Dbxref=GeneID:905900;gbkey=misc_feature;Note=HMMPfam hit to PF01227 2C GTP cyclohydrolase I 2C score 1.1e-55 ### NC_002163.1 RefSeq CDS 1634839 1635438 . + 0 ID=cds1571;Parent=gene1665;Name=YP_002345091.1;Dbxref=InterPro:IPR013027 UniProtKB FTrEMBL:Q0P7Q6 Genbank:YP_002345091.1 GeneID:905202;gbkey=CDS;product=hypothetical protein;Note=Original 282000 29 note: Cj1725 2C probable periplasmic protein 2C len: 199 aa 3B similar to TR:O66724 28EMBL:AE000688 29 Aquifex aeolicus AQ_407 28203 aa 29 2C fasta scores 3B opt: 411 z-score: 483.0 E 28 29: 1.4e-19 2C 34.0 25 identity in 203 aa overlap. No Hp match. Functional classification -Miscellaneous periplasmic proteins NC_002163.1 RefSeq gene 1634839 1635438 . + . ID=gene1665;Name=Cj1725;locus_tag=Cj1725;Dbxref=GeneID:905202;gbkey=Gene NC_002163.1 RefSeq region 1634851 1634910 . + . ID=id3044;Name=id3044;Dbxref=GeneID:905202;gbkey=misc_feature;Note=1 probable transmembrane helix predicted for Cj1725 by TMHMM2.0 at aa 5-24 NC_002163.1 RefSeq region 1635310 1635342 . + . ID=id3045;Name=id3045;Dbxref=GeneID:905202;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 RefSeq gene 1635443 1636324 . - . ID=gene1666;gene=metA;Name=metA;locus_tag=Cj1726c;Dbxref=GeneID:906001;gbkey=Gene NC_002163.1 RefSeq CDS 1635443 1636324 . - 0 ID=cds1572;Parent=gene1666;gene=metA;Name=YP_002345092.1;Dbxref=GOA:Q9PLV2 InterPro:IPR005697 UniProtKB FSwiss-Prot:Q9PLV2 Genbank:YP_002345092.1 GeneID:906001;gbkey=CDS;product=homoserine O-succinyltransferase;Note=catalyzes the formation of O-succinyl-L-homoserine from succinyl-CoA and L-homoserine in methionine biosynthesis NC_002163.1 RefSeq region 1635452 1636321 . - . ID=id3046;gene=metA;Name=id3046;Dbxref=GeneID:906001;gbkey=misc_feature;Note=HMMPfam hit to PF04204 2C Homoserine O-succinyltransferase 2C score 6.7e-185 ### NC_002163.1 RefSeq CDS 1636407 1637678 . - 0 ID=cds1573;Parent=gene1667;gene=metB;Name=YP_002345093.1;Dbxref=GOA:Q0P7Q4 InterPro:IPR000277 InterPro:IPR006235 InterPro:IPR015421 InterPro:IPR015422 UniProtKB FTrEMBL:Q0P7Q4 Genbank:YP_002345093.1 GeneID:906002;gbkey=CDS;product=O-acetylhomoserine 28thiol 29-lyase;Note=Original 282000 29 note: Cj1727c 2C metY 2C possible O-acetylhomoserine 28thiol 29-lyase 2C len: 423 aa 3B TR:P94890 28EMBL:Y10744 29 Leptospira meyeri O-acetylhomoserine sulfhydrylase 28metY 29 28442 aa 29 2C fasta scores 3B opt: 1198 z-score: 1372.4 E 28 29: 0 2C 43.0 25 identity in 433 aa overlap 2Cand CYSD_EMENI O-acetylhomoserine 28thiol 29-lyase 28EC 4.2.99.10 29 28437 aa 29 2C fasta scores 3B opt: 1001 z-score: 1147.5 E 28 29: 0 2C 39.4 25 identity in 419 aa overlap. No Hp ortholog. Also similar to Cj1393 metC 2830.0 25 identity in 363 aa overlap 29. Contains Pfam match to entry PF01053 Cys_Met_Meta_PP 2C Gamma-family of PLP-dependent enzymes 7EUpdated 282006 29 note: No specific characterisation in related bacteria with acceptable identity score. kept within product function. Functional classification - Amino acid biosynthesis - Aspartate family NC_002163.1 RefSeq gene 1636407 1637678 . - . ID=gene1667;gene=metB;Name=metB;locus_tag=Cj1727c;Dbxref=GeneID:906002;gbkey=Gene NC_002163.1 RefSeq region 1636413 1637663 . - . ID=id3047;gene=metB;Name=id3047;Dbxref=GeneID:906002;gbkey=misc_feature;Note=HMMPfam hit to PF01053 2C Cys 2FMet metabolism PLP-dependent enzy 2C score 1.3e-159 NC_002163.1 RefSeq region 1637418 1637450 . - . ID=id3048;gene=metB;Name=id3048;Dbxref=GeneID:906002;gbkey=misc_feature;Note=PS00013 Prokaryotic membrane lipoprotein lipid attachment site ### NC_002163.1 UTR_Extractor 5'-UTR 1637679 1637874 . - . ID=utr621;locus_tag=Cj1727c;product=putative O-acetylhomoserine 28thiol 29-lyase NC_002163.1 RefSeq gene 1637942 1638039 . - . ID=NC_002163.1:CJnc230;Name=NC_002163.1:CJnc230;locus_tag=CJnc230 NC_002163.1 RefSeq sRNA 1637942 1638039 . - . ID=NC_002163.1:CJnc230:unknown_transcript_1;Parent=NC_002163.1:CJnc230;Name=NC_002163.1:CJnc230:unknown_transcript_1;locus_tag=CJnc230;gbkey=misc_RNA;product=CJnc230 NC_002163.1 RefSeq CDS 1638104 1640701 . - 0 ID=cds1574;Parent=gene1668;gene=flgE;Name=YP_002345095.1;Dbxref=GOA:Q0P7Q2 InterPro:IPR001444 InterPro:IPR010810 InterPro:IPR010930 InterPro:IPR011491 InterPro:IPR012835 UniProtKB FTrEMBL:Q0P7Q2 Genbank:YP_002345095.1 GeneID:906004;gbkey=CDS;product=flagellar hook protein FlgE;Note=the hook connects flagellar basal body to the flagellar filament NC_002163.1 RefSeq gene 1638104 1640701 . - . ID=gene1668;gene=flgE;Name=flgE;locus_tag=Cj1729c;Dbxref=GeneID:906004;gbkey=Gene NC_002163.1 RefSeq region 1638113 1638229 . - . ID=id3049;gene=flgE;Name=id3049;Dbxref=GeneID:906004;gbkey=misc_feature;Note=HMMPfam hit to PF06429 2C Domain of unknown function 28DUF1078 29 2C score 2e-20 NC_002163.1 RefSeq region 1638392 1638415 . - . ID=id3050;gene=flgE;Name=id3050;Dbxref=GeneID:906004;gbkey=misc_feature;Note=PS00017 ATP 2FGTP-binding site motif A 28P-loop 29 NC_002163.1 RefSeq region 1638473 1638859 . - . ID=id3051;gene=flgE;Name=id3051;Dbxref=GeneID:906004;gbkey=misc_feature;Note=HMMPfam hit to PF07559 2C Flagellar basal body protein FlaE 2C score 5.2e-32 NC_002163.1 RefSeq region 1639646 1639813 . - . ID=id3052;gene=flgE;Name=id3052;Dbxref=GeneID:906004;gbkey=misc_feature;Note=HMMPfam hit to PF07196 2C Flagellin hook IN motif 2Cscore 9.5e-08 NC_002163.1 RefSeq region 1640597 1640689 . - . ID=id3053;gene=flgE;Name=id3053;Dbxref=GeneID:906004;gbkey=misc_feature;Note=HMMPfam hit to PF00460 2C Flagella basal body rod protein 2C score 8.2e-12 ### NC_002163.1 RefSeq gene 1640904 1641386 . - . ID=gene1669;gene=ruvC;Name=ruvC;locus_tag=Cj1731c;Dbxref=GeneID:906005;gbkey=Gene NC_002163.1 RefSeq CDS 1640904 1641386 . - 0 ID=cds1575;Parent=gene1669;gene=ruvC;Name=YP_002345096.1;Dbxref=GOA:Q9PLU8 HSSP:P24239 InterPro:IPR002176 UniProtKB FSwiss-Prot:Q9PLU8 Genbank:YP_002345096.1 GeneID:906005;gbkey=CDS;product=Holliday junction resolvase;Note=endonuclease 3B resolves Holliday structures 3B forms a complex of RuvABC 3B the junction binding protein RuvA forms a hexameric ring along with the RuvB helicase and catalyzes branch migration 3B RuvC then interacts with RuvAB to resolve the Holliday junction by nicking DNA strands of like polarity NC_002163.1 RefSeq region 1640931 1641374 . - . ID=id3054;gene=ruvC;Name=id3054;Dbxref=GeneID:906005;gbkey=misc_feature;Note=HMMPfam hit to PF02075 2C Crossover junction endodeoxyribonuclease Ruv 2C score 7.9e-66 ###