-- dump date 20120504_140600 -- class Genbank::Feature -- table feature -- table main -- field 1 id -- field 2 type -- field 3 name -- field 4 contig -- field 5 start_pos -- field 6 end_pos -- field 7 strand -- field 8 description -- field 9 chrom_position -- field 10 organism -- field 11 GeneID -- header -- id type name contig start_pos end_pos strand description chrom_position organism GeneID 192222000001 SEQ_END SEQ_END NC_002163.1 1641481 1641481 DR NC_002163.1; contig end 1641481..1641481 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 YP_002343473.1 CDS dnaA NC_002163.1 1 1323 D binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication; can also affect transcription of multiple genes including itself.; chromosomal replication initiation protein 1..1323 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904342 YP_002343474.1 CDS dnaN NC_002163.1 1483 2550 D binds the polymerase to DNA and acts as a sliding clamp; DNA polymerase III subunit beta 1483..2550 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904340 YP_002343475.1 CDS gyrB NC_002163.1 2579 4888 D negatively supercoils closed circular double-stranded DNA; DNA gyrase subunit B 2579..4888 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904343 YP_002343476.1 CDS Cj0004c NC_002163.1 4916 5257 R Original (2000) note: Cj0004c, possible periplasmic protein, len: 113 aa. No Hp match. Contains possible N-terminal signal sequence; Updated (2006) note: NCTC11168 Cj0004c encodes a monohaem cytochrome C (PMID:15632441). Together with Cj0005 (molybdopterin oxidoreductase), they are homologous to sulphite:cytochrome C oxidoreductase (SOR) of Starkeya novella (PMID:11557133). 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 (552nm) after addition of sulphite, demonstrating the reduction of cytochrome C. No cytochrome C reduction was observed after addition of sulphite to periplasmic extracts of the Cj0004c mutant (PMID:15632441). Characterised within Campylobacter jejuni, so not added to product function. Functional classification - Energy metabolism -Respiration - Electron transport; PMID:15632441; monohaem cytochrome C complement(4916..5257) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904344 YP_002343477.1 CDS Cj0005c NC_002163.1 5260 6498 R Original (2000) note: Cj0005c, possible molybdenum containing oxidoreductase, len: 412 aa; similar to many eukaryotic oxidoreductases e.g. SUOX_HUMAN sulfite oxidase precursor (488 aa), fasta scores; opt: 543 z-score: 338.2 E(): 1.4e-11, 29.8% identity in 372 aa overlap and NIA_PETHY nitrate reductase from Petunia hybrida (909 aa),fasta scores; opt: 281 z-score: 312.5 E(): 3.8e-10, 28.9% identity in 395 aa overlap. No Hp match. Contains Pfam match to entry PF00174 oxidored_molyb, Oxidoreductase molybdopterin binding domain, score 45.20, E-value 1e-12; Updated (2006) 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 (PMID:15632441). Product function modified to more specific family member based on characterisation paper. Functional classification - Misc; PMID:15632441; molydopterin containing oxidoreductase complement(5260..6498) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904345 YP_002343478.1 CDS Cj0006 NC_002163.1 6703 8010 D Original (2000) note: Cj0006, probable integral membrane protein, len: 435 aa; similar to e.g. Y325_HAEIN hypothetical protein HI0325 (450 aa), fasta scores; opt: 757 z-score: 1654.9 E(): 0, 44.0% identity in 450 aa overlap. 47.2% identity to HP0758; Updated (2006) note: Pfam domain PF03553 Na+/H+ antiporter family identified within CDS. Product modified to more specific family member due to motif match. Also,eleven 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, kept within product function. Functional classification -Transport/binding proteins - Cations; Na+/H+ antiporter family protein 6703..8010 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904346 YP_002343479.1 CDS gltB NC_002163.1 8144 12634 D Original (2000) note: Cj0007, gltB, probable glutamate synthase (NADPH) large subunit, len: 1496 aa; similar to many e.g. GLTB_ECOLI glutamate synthase (NADPH) large chain (1517 aa), fasta scores; opt: 3846 z-score: 3828.3 E(): 0, 42.5% identity in 1488 aa overlap. No Hp match; Updated (2006) note: Pfam domains PF00310 Glutamine amidotransferases class-II, PF04898 Glutamate synthase central domain, 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, not added to product function. Functional classification - Central intermediary metabolism - General; PMID:2548995, PMID:11029411; glutamate synthase large subunit 8144..12634 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904339 YP_002343480.1 CDS Cj0008 NC_002163.1 12644 14395 D Original (2000) note: Cj0008, unknown, len: 583 aa; similar to Y686_METJA hypothetical protein MJ0686 (580 aa), fasta scores; opt: 171 z-score: 228.3 E(): 1.9e-05,22.8% identity in 609 aa overlap. 37.5% identity in N-term to HP0938, 30.0% identity in C-term to HP0937; Updated (2006) note: Pfam PF03235 Protein of unknown function (DUF262), was present within CDS. Conserved added to product function as motif was identified. Functional classification - Conserved hypothetical proteins; hypothetical protein 12644..14395 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904337 YP_002343481.1 CDS gltD NC_002163.1 14398 15843 D glutamate synthase is composed of subunits alpha and beta; beta subunit is a flavin adenine dinucleotide-NADPH dependent oxidoreductase; provides electrons to the alpha subunit, which binds L-glutamine and 2-oxoglutarate and forms L-glutamate; glutamate synthase subunit beta 14398..15843 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904336 YP_002343482.1 CDS rnhB NC_002163.1 15844 16419 R RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids; ribonuclease HII complement(15844..16419) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904334 YP_002343483.1 CDS Cj0011c NC_002163.1 16452 16691 R Updated (2006) note: Characterisation work carried out within Bacillus subtilis, however, sequence alignment was only partial. kept within product function; Original (2000) note: Cj0011c, possible non-specific DNA binding protein, len: 79 aa; similar to the C-terminus of CME1_BACSU comE operon protein 1 (comeA) (205 aa), fasta scores; opt: 223 z-score: 359.5 E(): 9e-13, 56.9% identity in 65 aa overlap. No Hp match. Contains Pfam match to entry PF00633 HHH,Helix-hairpin-helix motif., score 31.80, E-value 1.6e-05; PMID:7968523, PMID:7768800; non-specific DNA binding protein complement(16452..16691) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904332 YP_002343484.1 CDS rrc NC_002163.1 16756 17403 R Original (2000) note: Cj0012c, non-haem iron protein, len: 215 aa; has three possible iron-binding domains; C-terminus is similar to rubrerythrins e.g. RUBY_DESVH rubrerythrin (191 aa), fasta scores; opt: 454 z-score: 746.8 E(): 0, 39.5% identity in 190 aa overlap,with 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 (125 aa), fasta scores; opt: 161 z-score: 275.8 E(): 4.2e-08,68.8% identity in 32 aa overlap, with the iron-binding residues conserved. No Hp match; Updated (2006) note: Pfam domains PF00301 Rubredoxin, PF02915 Rubrerythrin and PF06397 Desulfoferrodoxin, 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 (Rbo/Rbr-like protein of C. jejuni) protein. Thus, not added to product function. Functional classification - Transport/binding proteins - Cations; PMID:15158262; non-haem iron protein complement(16756..17403) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904330 YP_002343485.1 CDS ilvD NC_002163.1 17563 19239 D catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis; dihydroxy-acid dehydratase 17563..19239 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904349 YP_002343486.1 CDS Cj0014c NC_002163.1 19251 19775 R Original (2000) note: Cj0014c, probable integral membrane protein, len: 174 aa; similar to YAGU_ECOLI hypothetical 23.0 kd protein in intF-eaeH intergenic region (204 aa), fasta scores; opt: 402 z-score: 821.6 E(): 0, 45.1% identity in 184 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF07274 Protein of unknown function (DUF1440) identified within CDS. Also,three probable transmembrane helices identified by TMHMM2.0. Further support given to product function. No specific characterisation has been carried out yet. Thus, kept within product function. Functional classification - Central intermediary metabolism -General; integral membrane protein complement(19251..19775) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904347 YP_002343487.1 CDS Cj0015c NC_002163.1 19867 21093 R Original (2000) note: Cj0015c, unknown, len: 408 aa; 35.4% identity to HP0711; Updated (2006) note: Literature search identified paper (PMID:15647906) giving potential clues to product functionality. Functional classification - Conserved hypothetical proteins; PMID:15647906; hypothetical protein complement(19867..21093) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904352 YP_002343488.1 CDS Cj0016 NC_002163.1 21159 21833 D Original (2000) note: Cj0016, possible transcriptional regulatory protein, len: 224 aa; similar to many hypothetical proteins and to TR:Q52925 (EMBL:Z50189) Rhizobium meliloti succinoglycan biosynthesis regulator exsB (234 aa), fasta scores; opt: 284 z-score: 395.5 E(): 9e-15, 33.5% identity in 191 aa overlap. 33.9% identity to HP0639 conserved hypothetical protein; Updated (2006) note: Pfam domain PF06508 ExsB identified within CDS. Further support given to product function. Characterisation work carried out within Pseudomonas aeruginosa, however, identity scores were not acceptable. Thus, kept within product function. Functional classification - Broad regulatory functions; PMID:9045825, PMID:8544814; transcriptional regulatory protein 21159..21833 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904353 YP_002343489.1 CDS dsbI NC_002163.1 21854 23380 R Original (2000) note: Cj0017c, probable ATP/GTP binding protein, len: 508 aa; 37.4% identity to HP0595 hypothetical protein. Contains PS00017 ATP/GTP-binding site motif A (P-loop); Updated (2006) 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 (disulfide bond) proteins found in the periplasm and in the inner membrane. Supporting paper (PMID:15632440) 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 (PMID:15632440). This information along with motif identification has led to a new product function designation. In addition, this coding sequence has 100% amino acid identity with DsbI from C. jejuni 81-176 (CJJ81-176_0044). Characterisation paper within Campylobacter jejuni has led to being removed from product function. Functional classification -Synthesis and modification of macromolecules - Protein translation and modification; PMID:15632440; disulphide bond formation protein complement(21854..23380) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904354 YP_002343490.1 CDS dba NC_002163.1 23392 23559 R Original (2000) note: Cj0018c, small hydrophobic protein, len: 55 aa; similar to TR:E1314390 (EMBL:AL031184) small hydrophobic protein SC2A11.18 from Streptomyces coelicolor (55 aa), fasta scores; opt: 72 z-score: 141.4 E(): 1.3, 32.7% identity in 49 aa overlap. 49.1% identity to HP0594 hypothetical protein; Updated (2006) note: Gram negative bacterial cells have disulfide bond formation occuring in the oxidative environment of the periplasm and are catalysed by Dsb (disulfide bond) proteins found in the periplasm and in the inner membrance. Supporting paper (PMID:15632440) 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% amino acid identity with Dba from 81-176 (CJJ81176_0045). Characterisation paper within Campylobacter jejuni has led to being removed from product function. Functional classification - Synthesis and modification of macromolecules - Protein translation and modification; PMID:15632440; disulphide bond formation protein complement(23392..23559) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904356 YP_002343491.1 CDS Cj0019c NC_002163.1 23665 25443 R Original (2000) note: Cj0019c, probable MCP-domain signal transduction protein, len: 592 aa; similar to other proteins containing the MCP domain e.g. HLYB_VIBCH hemolysin secretion protein precursor (548 aa), fasta scores; opt: 418 z-score: 492.5 E(): 3.5e-20, 22.7% identity in 565 aa overlap, and AER_ECOLI aerotaxis receptor (506 aa), fasta scores; opt: 299 z-score: 391.2 E(): 1.6e-14, 25.5% identity in 357 aa overlap. 27.5% identity to HP0103. Contains N-terminal signal sequence and transmembrane anchor around aa 250. Also contains Pfam match to entry PF00015 MCPsignal, Methyl-accepting chemotaxis protein (MCP) signaling domain, score 104.90,E-value 1.7e-28; Updated (2006) 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, kept within product function. Functional classification - Signal transduction; MCP-domain signal transduction protein complement(23665..25443) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904357 YP_002343492.1 CDS Cj0020c NC_002163.1 25433 26347 R Original (2000) note: Cj0020c, probable cytochrome C551 peroxidase, len: 304 aa; similar to CCPR_PSEAE cytochrome C551 peroxidase precursor (EC 1.11.1.5) (346 aa), fasta scores; opt: 775 z-score: 1167.7 E(): 0, 42.3% identity in 298 aa overlap. No Hp ortholog. Contains 2x PS00190 Cytochrome c family heme-binding site signature and probable N-terminal signal sequence; Updated (2006) 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; PMID:7781769, PMID:8591033, PMID:1657179; cytochrome C551 peroxidase complement(25433..26347) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904360 YP_002343493.1 CDS Cj0021c NC_002163.1 26411 27289 R Original (2000) note: Cj0021c, unknown, len: 292 aa; similar to hypothetical proteins e.g. TR:O06724 (EMBL:Z99109) B. subtilis yisK (301 aa), fasta scores; opt: 665 z-score: 1018.0 E(): 0, 43.1% identity in 255 aa overlap, and to C-terminal half of HPCE_ECOLI 2-hydroxyhepta-2,4-diene-1,7-dioate isomeraase/5-carboxymethyl-2-oxo-hex-3-ene-1,7-dioate decarboxylase (405 aa), fasta scores; opt: 328 z-score: 381.2 E(): 5.6e-14, 31.2% identity in 199 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF01557 Fumarylacetoacetate (FAA) 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, kept within product function. Functional classification - Misc; fumarylacetoacetate (FAA) hydrolase family protein complement(26411..27289) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904361 YP_002343494.1 CDS Cj0022c NC_002163.1 27402 28304 R Original (2000) note: Cj0022c, possible ribosomal pseudouridine synthase, len: 300 aa; similar to e.g. RLUD_ECOLI ribosomal large subunit pseudouridine synthase D (EC 4.2.1.70) (326 aa), fasta scores; opt: 344 z-score: 412.1 E(): 1.2e-15, 29.6% identity in 243 aa overlap. 41.1% identity to HP0347. Contains PS01129 Hypothetical yabO/yceC/sfhB family signature and Pfam match to entry PF00849 YABO, Hypothetical yabO/yceC/sfhB family, score 182.90, E-value 5e-51. Also similar to Cj1280c (31.0% identity) and Cj0708 (28.0% identity); Updated (2006) note: Characterisation has been carried out within Escherichia coli, however, 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; PMID:11453071, PMID:11087118, PMID:9814761,PMID:14501142; ribosomal pseudouridine synthase complement(27402..28304) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904362 YP_002343495.1 CDS purB NC_002163.1 28382 29710 D Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide; adenylosuccinate lyase 28382..29710 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904425 YP_002343496.1 CDS nrdA NC_002163.1 29726 32095 D Catalyzes the rate-limiting step in dNTP synthesis; ribonucleotide-diphosphate reductase subunit alpha 29726..32095 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904363 YP_002343497.1 CDS Cj0025c NC_002163.1 32134 33519 R Original (2000) note: Cj0025c, probable transmembrane symporter (possibly glutamate), len: 461 aa; similar to many e.g. YB54_HAEIN hypothetical symporter HI1154 (440 aa), fasta scores; opt: 650 z-score: 890.6 E(): 0, 33.7% identity in 454 aa overlap, and TR:Q46202 (EMBL:X86516) Clostridium perfringens gluT-R gene (fragment) (132 aa), fasta scores; opt: 406 z-score: 569.0 E(): 1.9e-24, 49.6% identity in 119 aa overlap. No Hp match. Contains Pfam match to entry PF00375 SDF,Sodium:dicarboxylate symporter family, score 142.20,E-value 9.4e-39; Updated (2006) 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, kept within product function. Functional classification - Transport/binding proteins - Other; sodium:dicarboxylate family transmembrane symporter complement(32134..33519) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904364 YP_002343498.1 CDS thyX NC_002163.1 33639 34262 R flavin dependent thymidylate synthase; ThyX; thymidylate synthase complementing protein; catalyzes the formation of dTMP and tetrahydrofolate from dUMP and methylenetetrahydrofolate; the enzyme from Mycobacterium tuberculosis forms homotetramers; uses FAD as a cofactor; FAD-dependent thymidylate synthase complement(33639..34262) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904365 YP_002343499.1 CDS pyrG NC_002163.1 34382 36013 D CTP synthase; cytidine triphosphate synthetase; catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen; in Escherichia coli this enzyme forms a homotetramer; CTP synthetase 34382..36013 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904367 YP_002343500.1 CDS recJ NC_002163.1 36000 37571 D Original (2000) note: Cj0028, recJ, probable single-stranded-DNA-specific exonuclease, len: 523 aa; similar to e.g. RECJ_ECOLI single-stranded-DNA-specific exonuclease (EC 3.1.-.-) (577 aa), fasta scores; opt: 385 z-score: 861.6 E(): 0, 29.8% identity in 526 aa overlap. 39.0% identity to HP0348; Updated (2006) 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, however,marginal identity score was obtained. kept within product function. Functional classification - Synthesis and modification of macromolecules - DNA replication,restriction/modification, recombination and repair; PMID:2649886; single-stranded-DNA-specific exonuclease 36000..37571 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904450 YP_002343501.1 CDS ansA NC_002163.1 37667 38662 D Original (2000) note: Cj0029, ansA, probable cytoplasmic L-asparaginase, len: 331 aa; similar to many e.g. ASG2_ECOLI L-asparaginase II precursor (EC 3.5.1.1) (348 aa), fasta scores; opt: 1044 z-score: 1510.6 E(): 0,52.0% identity in 327 aa overlap, but with no signal sequence. 45.8% identity to HP0723. Contains PS00144 and PS00917 Asparaginase/glutaminase active site signatures 1 and 2 and Pfam match to entry PF00710 Asparaginase,Asparaginase, score 449.90, E-value 2.2e-131; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. Thus, not added to product function. Functional classification - Degradation - Amino acids; PMID:2407723, PMID:1287659, PMID:8706862; cytoplasmic L-asparaginase 37667..38662 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904872 YP_002343502.1 CDS Cj0030 NC_002163.1 44966 46363 D Original (2000) note: Cj0030, unknown, len: 465 aa. No Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein 44966..46363 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904369 YP_002343503.1 CDS Cj0031 NC_002163.1 46424 50156 D Original (2000) note: Cj0031, probable DNA restriction/modification enzyme, N-terminal half, len: 867 aa; similar to N-terminus of T257_ECOLI type IIS restriction enzyme Eco57I (which contains an adenine-specific methyltransferase activity) (997 aa),fasta scores; opt: 126 z-score: 218.0 E(): 6.9e-05, 24.0% identity in 516 aa overlap. 40.9% identity to N-terminus of HP1517. Some similarity to N-terminus of Cj0690c (24.8% identity in 858 aa overlap). 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, 9, or 10 bases. G10 (the most common in our shotgun) causes a termination here, G9 causes a termination 6 aa earlier. G8 allows translation to continue into Cj0032; Original (2000) note: Cj0032, probable DNA restriction/modification enzyme, C-terminal half, len: 867 aa; similar to C-terminus of MTB3_BACAR modification methylase BanIII (580 aa), fasta scores; opt: 132 z-score: 220.8 E(): 4.9e-05, 24.6% identity in 402 aa overlap. 47.4% identity to C-terminus of HP1517. Note that there is a polymorphic poly-G tract at the N-terminus of this ORF with 8, 9, or 10 bases. G10 (the most common in our shotgun) or G9 will not allow translation into this ORF,G8 allows translation to continue from Cj0031. Alternative downstram start at 49059; Updated (2006) 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,restriction/modification, recombination and repair; type IIS restriction/modification enzyme join(46424..49000,49002..50156) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904370 YP_002343504.1 CDS Cj0033 NC_002163.1 50156 51937 D Original (2000) note: Cj0033, probable integral membrane protein, len: 593 aa; contains 6 possible transmembrane domains in C-terminal half. No Hp match. Functional classification - Membranes, lipoproteins and porins; integral membrane protein 50156..51937 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904331 YP_002343505.1 CDS Cj0034c NC_002163.1 51967 52668 R Original (2000) note: Cj0034c, probable periplasmic protein, len: 233 aa; similar to e.g. TR:O50817 (EMBL:AE000788) Borrelia burgdorferi conserved hypothetical protein BBK13 (238 aa), fasta scores; opt: 306 z-score: 257.5 E(): 4.4e-07, 28.1% identity in 231 aa overlap. No Hp match. Contains possible N-terminal signal sequence. Functional classification - Miscellaneous periplasmic proteins; periplasmic protein complement(51967..52668) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904372 YP_002343506.1 CDS Cj0035c NC_002163.1 52665 53867 R Original (2000) note: Cj0035c, possible efflux protein, len: 400 aa; similar to many members of the bcr/cmlA subfamily of the major facilitator family e.g. BCR_ECOLI bicyclomycin resistance protein (396 aa), fasta scores; opt: 717 z-score: 1046.3 E(): 0, 28.1% identity in 398 aa overlap. No Hp ortholog. Contains 12 possible transmembrane domains. Also similar to Cj1375 (25.5% identity in 373 aa overlap); Updated (2006) note: Pfam domain PF07690 Major Facilitator Superfamily was identified within CDS. Further support given to product function. Some characterisation work within different bacteria, however, identity scores were marginal. Thus, kept within product function. Functional classification - Antibiotic resistance; PMID:2694948, PMID:8486276; efflux protein complement(52665..53867) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904517 YP_002343507.1 CDS Cj0036 NC_002163.1 53970 55319 D Original (2000) note: Cj0036, unknown, len: 449 aa; 37.8% identity to HP1143 hypothetical protein. Functional classification - Conserved hypothetical proteins; hypothetical protein 53970..55319 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904813 YP_002343508.1 CDS Cj0037c NC_002163.1 55343 56386 R Original (2000) note: Cj0037c, possible cytochrome C, len: 347 aa; weak simlarity to e.g. TR:O69780 (EMBL:U76906) di-heme cytochrome c (fixP) from Rhizobium etli (287 aa), fasta scores; opt: 97 z-score: 205.7 E(): 0.00034, 27.2% 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,Cytochrome c, score 5.90, E-value 0.11; Updated (2006) note: No specific characterisation with acceptable identity scores has been carried out yet. Thus, kept within product function. Functional classification - Energy metabolism - Respiration -Electron transport; cytochrome C complement(55343..56386) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904547 YP_002343509.1 CDS Cj0038c NC_002163.1 56564 57211 R Original (2000) note: Cj0038c, possible membrane protein, len: 215 aa; no HP match. Contains two possible transmembrane domains at the N-terminus; Updated (2006) 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, such as Poly(A) polymerase,which adds the poly(A) tail to mRNA (EC:2.7.7.19). This family also includes the tRNA nucleotidyltransferase that adds the CCA to the 3' of the tRNA (EC:2.7.7.25). Product modified to more specific family member due to motif match. No specific characterisation has been carried out yet. Thus, kept within product function. Functional classification - Synthesis and modification of macromolecules - DNA replication,restriction/modification, recombination and repair; poly(A) polymerase family protein complement(56564..57211) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904373 YP_002343510.1 CDS typA NC_002163.1 57211 59019 R Original (2000) note: Cj0039c, typA, GTP-binding protein typA homolog, len: 602 aa; similar to TYPA_ECOLI GTP-binding protein typA/bipA (591 aa), fasta scores; opt: 2145 z-score: 2659.1 E(): 0, 54.2% identity in 592 aa overlap, and to many EF-G proteins e.g. EFG_AGRTU elongation factor G (EF-G) (699 aa), fasta scores; opt: 344 z-score: 797.3 E(): 0, 26.2% identity in 715 aa overlap. 77.3% identity to HP0480. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00301 GTP-binding elongation factors signature and Pfam match to entry PF00009 GTP_EFTU, Elongation factor Tu family (contains ATP/GTP binding P-loop), score 282.90, E-value 4e-81; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. Thus, not added to product function. Homolog designation kept within product function. Functional classification - Synthesis and modification of macromolecules - Protein translation and modification; PMID:7783627, PMID:9642082, PMID:14560797; GTP-binding protein TypA complement(57211..59019) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904374 YP_002343511.1 CDS Cj0040 NC_002163.1 59154 59477 D Original (2000) note: Cj0040, unknown, len: 107 aa; no Hp match; Updated (2006) note: Literature search identified paper giving clues to product function. Functional classification - Unknown; PMID:14985343; hypothetical protein 59154..59477 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904375 YP_002343512.1 CDS fliK NC_002163.1 59493 61289 D Original (2000) note: Cj0041, unknown, len: 598 aa; 25.2% identity to HP0906, but shorter at N-term; Updated (2006) note: Literature search identified papers linking product function to be involved in motility and invasion. Unpublished observation by N.Kamal & C. Penn have predicted this CDS to be fliK. Literature search identified work carried out in Campylobacter jejuni,Helicobacter 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; PMID:12379703, PMID:14985343, PMID:15812042,PMID:11895937, PMID:16077121, PMID:15276839; flagellar hook-length control protein 59493..61289 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904378 YP_002343513.1 CDS flgD NC_002163.1 61343 62227 D acts as a scaffold for the assembly of hook proteins onto the flagellar basal body rod; flagellar basal body rod modification protein 61343..62227 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904379 YP_002343514.1 CDS flgE NC_002163.1 62231 63868 D Original (2000) note: Cj0043, flgE, probable flagellar hook protein, len: 545 aa; similar to e.g. FLGE_BORBU flagellar hook protein flgE (442 aa), fasta scores; opt: 350 z-score: 665.8 E(): 7.9e-30, 27.5% identity in 553 aa overlap. 24.5% identity to HP0908. Contains PS00588 Flagella basal body rod proteins signature and Pfam match to entry PF00460 flg_bb_rod,Flagella basal body rod proteins, score 37.00, E-value 6.7e-08; Updated (2006) 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, not added to product function. Functional classification - Surface structures; PMID:9658019, PMID:9244248, PMID:9079915; flagellar hook protein 62231..63868 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 906016 YP_002343515.1 CDS Cj0044c NC_002163.1 63872 65743 R Original (2000) note: Cj0044c, unknown, len: 623 aa; no Hp ortholog, Also similar to Cj0800c (28.5% identity in 625 aa overlap). Preceeded by a C(9-11) polymorphic region; C11 would allow the translation of Cj0045c to extend by another 15aa, overlapping the start of this CDS; C9 and C10 (consensus) have no effect; Updated (2006) note: Literature search identified paper giving further clues to product function. Functional classification - Conserved hypothetical proteins; PMID:14985343; hypothetical protein complement(63872..65743) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904380 YP_002343516.1 CDS Cj0045c NC_002163.1 65744 66466 R Original (2000) note: Cj0045c, possible iron-binding protein, len: 240 aa; weak similarity to members of the eukaryotic iron-binding hemerythrin family,e.g. HEMT_LINUN hemerythrin alpha chain (117 aa), fasta scores; opt: 105 z-score: 137.1 E(): 2.5, 23.8% identity in 122 aa overlap. Note that all of the iron-binding residues are conserved. No Hp match, similar to Cj0072c (pseudogene), Cj0241c (30.9% identity in 123 aa overlap) and Cj1224 (27.7% identity in 202 aa overlap). Contains a C(9-11) polymorphic region at the N-terminus; C11 would allow the translation of this CDS to extend by another 15aa, overlapping the start of Cj0044c; C9 and C10 (consensus) have little effect; Updated (2006) 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, kept within product function. Literature search identified paper giving further clues to product function. Functional classification - Transport/binding proteins - Cations; PMID:14985343; iron-binding protein complement(65744..66466) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904381 YP_002343517.1 CDS mnmA NC_002163.1 68532 69548 R catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs; tRNA-specific 2-thiouridylase MnmA complement(68532..69548) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904383 YP_002343518.1 CDS Cj0054c NC_002163.1 69548 70153 R Original (2000) note: Cj0054c, unknown, len: 201 aa; similar to hypothetical proteins e.g. TR:Q46063 (EMBL:X81379) Corynebacterium glutamicum hypothetucal protein (211 aa), fasta scores; opt: 426 z-score: 696.2 E(): 1.6e-31, 44.2% identity in 156 aa overlap. No Hp match; Updated (2006) 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, kept within product function. Functional classification -Misc; lysine decarboxylase family protein complement(69548..70153) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904384 YP_002343519.1 CDS Cj0055c NC_002163.1 70274 71098 R Original (2000) note: Cj0055c, unknown, len: 274 aa; no Hp match, similar in C-terminus to Cj0122 (46.6% identity in 148 aa overlap); Updated (2006) note: Contains Prosite match PS01164 COPPER_AMINE_OXID, 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 2,4,5-trihydroxyphenylalanine quinone (or topaquinone) (TPQ) cofactor (PMID:8591028). Functional classification -Unknown; PMID:8591028; hypothetical protein complement(70274..71098) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904386 YP_002343520.1 CDS Cj0056c NC_002163.1 71155 71571 R Original (2000) note: Cj0056c, unknown, len: 138 aa. No Hp match; Updated (2006) note: Literature search identified paper giving clues to product function. Functional classification - Unknown; PMID:14702320; hypothetical protein complement(71155..71571) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904387 YP_002343521.1 CDS Cj0057 NC_002163.1 72005 72859 D Original (2000) note: Cj0057, possible periplasmic protein, len: 284 aa; no Hp match. Contains possible N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein 72005..72859 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904388 YP_002343522.1 CDS Cj0058 NC_002163.1 72844 73443 D Original (2000) note: Cj0058, possible periplasmic protein, len: 199 aa; no Hp match. Contains possible N-terminal signal sequence; Updated (2006) 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, kept within product function. Functional classification - Degradation of macromolecules - Proteins, peptides and glycopeptides; peptidase C39 family protein 72844..73443 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904390 YP_002343523.1 CDS fliY NC_002163.1 73492 74334 R One of three proteins involved in switching the direction of the flagellar rotation; flagellar motor switch protein FliY complement(73492..74334) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904391 YP_002343524.1 CDS fliM NC_002163.1 74331 75410 R with FliG and FliN makes up the switch complex which is involved in switching the direction of the flagella rotation; flagellar motor switch protein FliM complement(74331..75410) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904392 YP_002343525.1 CDS fliA NC_002163.1 75410 76126 R sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this sigma factor directs late flagellar biosynthesis genes; flagellar biosynthesis sigma factor complement(75410..76126) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904393 YP_002343526.1 CDS Cj0062c NC_002163.1 76083 76439 R Original (2000) note: Cj0062c, probable integral membrane protein, len: 118 aa; no Hp match. Contains two possible transmembrane domains. Functional classification - Cell envelope - Membranes, lipoproteins and porins; integral membrane protein complement(76083..76439) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904394 YP_002343527.1 CDS Cj0063c NC_002163.1 76458 77324 R Original (2000) note: Cj0063c, probable ATP-binding protein, len: 288 aa; similar to hypothetical proteins in other flagellar operons e.g. YLXH_BACSU hypothetical 33.2 kd protein in flhF-cheB intergenic region (298 aa), fasta scores; opt: 390 z-score: 493.5 E(): 3.1e-20, 29.0% identity in 293 aa overlap, and to cell division proteins e.g. MIND_BACSU septum site-determining protein minD (268 aa), fasta scores; opt: 323 z-score: 417.6 E(): 5.3e-16,32.9% identity in 249 aa overlap. 45.7% identity to HP1034. Contains PS00017 ATP/GTP-binding site motif A (P-loop) and Pfam match to entry PF00991 ParA, ParA family ATPase, score 34.80, E-value 1.3e-06; Updated (2006) note: No specific characterisation with acceptable identity score carried out yet. Thus, kept within product function. Functional classification - Cell envelope - Surface structures; ATP-binding protein complement(76458..77324) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904395 YP_002343528.1 CDS flhF NC_002163.1 77317 78771 R positive regulator of class III flagellar genes; flagellar biosynthesis regulator FlhF complement(77317..78771) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904464 YP_002343529.1 CDS folK NC_002163.1 78781 79254 R Original (2000) note: Cj0065c, folK, possible 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase, len: 157 aa, similar to e.g. HPPK_BACSU 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (EC 2.7.6.3) (167 aa), fasta scores; opt: 194 z-score: 370.0 E(): 2.4e-13, 28.7% identity in 129 aa overlap. 35.6% identity to HP1036. Contains Pfam match to entry PF01288 HPPK,7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK), score 4.10, E-value 1.1e-06; Updated (2006) note: Characterised within Bacillus subtilis and Escherichia coli, however, identity scores were marginal. Thus, kept within product function. Functional classification - Biosynthesis of cofactors, prosthetic groups and carriers - Folic acid; PMID:1325970; 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase complement(78781..79254) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904396 YP_002343530.1 CDS aroQ NC_002163.1 79257 79736 R catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis; 3-dehydroquinate dehydratase complement(79257..79736) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904397 YP_002343531.1 CDS Cj0067 NC_002163.1 79827 81056 D Catalyzes the hydrolytic cleavage of a carbon-halogen bond in N-ethylammeline; chlorohydrolase 79827..81056 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904398 YP_002343532.1 CDS pspA NC_002163.1 81044 81940 D Original (2000) note: Cj0068, pspA, probable protease required for pilus-like appendage formation, len: 298 aa; almost identical to TR:P71127 (EMBL:U38524) pspA (298 aa) (99.0% identity in 298 aa overlap) and similar to the C-terminus of e.g. SPPA_ECOLI protease IV (618 aa),fasta scores; opt: 285 z-score: 266.8 E(): 1.3e-07, 24.7% identity in 251 aa overlap. 42.0% identity to HP1435; Updated (2006) note: Pfam domain PF01343 Peptidase family S49 identified within CDS. Product function based on direct submission with paper (PMID:8793884). not added to product function due to characterisation work within Campylobacter jejuni. Functional classification -Degradation of macromolecules - Surface structures; PMID:8793884, PMID:3522590; protease 81044..81940 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905251 YP_002343533.1 CDS Cj0069 NC_002163.1 82019 83050 D Original (2000) note: Cj0069, unknown, len: 343 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Literature search identified paper giving further clues to product function. Functional classification - Unknown; PMID:14702320; hypothetical protein 82019..83050 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905192 YP_002343534.1 CDS Cj0070c NC_002163.1 83047 83205 R Original (2000) note: Cj0070c, questionable CDS,len: 52 aa; no Hp match; Updated (2006) note: Similar to proteins in other bacteria. Functional classification - Unknown; hypothetical protein complement(83047..83205) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904429 YP_002343535.1 CDS Cj0073c NC_002163.1 84087 84743 R Original (2000) note: Cj0073c, unknown, len: 218 aa; similar to hypothetical proteins e.g. YKGG_ECOLI (282 aa), fasta scores; opt: 215 z-score: 231.0 E(): 1.3e-05,32.2% identity in 146 aa overlap. 41.8% identity to HP0137; Updated (2006) note: Pfam domain PF02589 Uncharacterized ACR, 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; PMID:15773975; hypothetical protein complement(84087..84743) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904400 YP_002343536.1 CDS Cj0074c NC_002163.1 84736 86175 R Original (2000) note: Cj0074c, probable iron-sulfur protein, len: 479 aa; similar to hypothetical proteins e.g. YKGF_ECOLI (475 aa), fasta scores; opt: 1142 z-score: 1335.9 E(): 0, 38.3% identity in 462 aa overlap. 58.1% identity to HP0138. Contains 2x PS00198 4Fe-4S ferredoxins, iron-sulfur binding region signature and 2x Pfam match to entry PF00037 fer4, 4Fe-4S ferredoxins and related iron-sulfur cluster binding domains., scores 13.80, E-value 0.0095, and 12.30, E-value 0.026; Updated (2006) note: No specific characterisation with acceptable identity scores. Thus, kept within product function. Functional classification -Energy metabolism - Electron transport; PMID:15773975; iron-sulfur protein complement(84736..86175) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904401 YP_002343537.1 CDS Cj0075c NC_002163.1 86172 86912 R Original (2000) note: Cj0075c, possible oxidoreductase iron-sulfur subunit, len: 246 aa; similar to hypothetical proteins and to the C-terminus of e.g. TR:O53142 (EMBL:AJ000942) Methanobacterium thermoautotrophicum strain Marburg, Thiol:fumarate reductase subunit B (488 aa), fasta scores; opt: 217 z-score: 476.0 E(): 3e-1, 24.3% identity in 235 aa overlap. 60.7% identity to HP0139; Updated (2006) 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, kept within product function. Functional classification - Energy metabolism - Electron transport; PMID:15773975; oxidoreductase iron-sulfur subunit complement(86172..86912) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904402 YP_002343538.1 CDS lctP NC_002163.1 87036 88718 R Original (2000) note: Cj0076c, lctP, probable L-lactate permease, len: 560 aa; highly similar to many e.g. LLDP_ECOLI L-lactate permease (551 aa), fasta scores; opt: 1957 z-score: 2614.5 E(): 0, 54.0% identity in 556 aa overlap. 61.2% identity to HP0141 and 60.6% identity to HP0140; Updated (2006) 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, not added to product function. Functional classification - Transport/binding proteins -Carbohydrates, organic acids and alcohols; PMID:8407843, PMID:11283302, PMID:11785976; L-lactate permease complement(87036..88718) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904403 YP_002343539.1 CDS cdtC NC_002163.1 88890 89459 R Original (2000) note: Cj0077c, cdtC, cytolethal distending toxin, len: 189 aa, identical to TR:Q46102 (EMBL:U51121) cdtC (189 aa). No Hp match. Contains N-terminal signal sequence; Updated (2006) 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, so not added to product function. Functional classification -Pathogenicity; PMID:10688204, PMID:8675309, PMID:11083762; cytolethal distending toxin C complement(88890..89459) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904404 YP_002343540.1 CDS cdtB NC_002163.1 89470 90267 R Original (2000) note: Cj0078c, cdtB, cytolethal distending toxin, len: 265 aa; identical toTR:Q46101 (EMBL:U51121) cdtB (265 aa) and similar to e.g. TR:Q47089 (EMBL:U03293) Escherichia coli cdtB (273 aa), fasta scores; opt: 946 z-score: 1533.6 E(): 0, 55.2% identity in 268 aa overlap. No Hp match. Contains N-terminal signal sequence; Updated (2006) note: Prosite domain PRO1388 CDTOXINB, Cytolethal distending toxin B signature identified within CDS. Product modified to more specific family member due to motif match. Characterised within Campylobacter jejuni, so not added to product function. Functional classification - Pathogenicity; PMID:10688204, PMID:8675309, PMID:11083762; cytolethal distending toxin B complement(89470..90267) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904405 YP_002343541.1 CDS cdtA NC_002163.1 90264 91070 R Original (2000) note: Cj0079c, cdtA, cytolethal distending toxin, len: 268 aa; identical to TR:Q46100 (EMBL:U51121) cdtB (268 aa) and similar to e.g. TR:Q47088 (EMBL:U03293) Escherichia coli cdtA (237 aa), fasta scores; opt: 310 z-score: 408.0 E(): 1.8e-15, 32.7% identity in 159 aa overlap. No Hp match. Contains N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site; Updated (2006) 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, so not added to product function. Functional classification -Pathogenicity; PMID:10688204, PMID:8675309, PMID:11083762; cytolethal distending toxin A complement(90264..91070) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904406 YP_002343542.1 CDS Cj0080 NC_002163.1 91147 91416 D Original (2000) note: Cj0080, possible membrane protein, len: 267 aa; no Hp match; Contains one possible transmembrane domain; Updated (2006) note: Two probable transmembrane helices predicted by TMHMM2.0; hypothetical protein 91147..91416 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904407 YP_002343543.1 CDS cydA NC_002163.1 91417 92979 D Original (2000) note: Cj0081, cydA, probable cytochrome bd oxidase subunit I, len: 520 aa;similar to many e.g. APPC_ECOLI cytochrome bd-ii oxidase subunit I (EC 1.10.3.-) (514 aa), fasta scores; opt: 1412 z-score: 1888.2 E(): 0, 45.7% identity in 530 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF01654 Bacterial Cytochrome Ubiquinol Oxidase identified within CDS. Also,nine probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. Thus, not added to product function. Functional classification - Energy metabolism - Electron transport; PMID:8626304, PMID:9068659, PMID:9852001; cytochrome bd oxidase subunit I 91417..92979 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904408 YP_002343544.1 CDS cydB NC_002163.1 92979 94103 D Original (2000) note: Cj0082, cydB, probable cytochrome bd oxidase subunit II, len: 520 aa;similar to many e.g. CYDB_ECOLI cytochrome d ubiquinol oxidase subunit II (EC 1.10.3.-) (379 aa), fasta scores; opt: 466 z-score: 449.6 E(): 8.7e-18, 27.7% identity in 386 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF02322 Cytochrome oxidase subunit II identified within CDS. Also, 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; PMID:8626304, PMID:9068659, PMID:9852001,PMID:15470119; cytochrome bd oxidase subunit II 92979..94103 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904409 YP_002343545.1 CDS Cj0085c NC_002163.1 94297 94992 R Original (2000) note: Cj0085c, probable amino acid recemase, len: 231 aa; similar to members of the aspartate/glutamate racemases family e.g. YGEA_ECOLI (230 aa), fasta scores; opt: 667 z-score: 1155.6 E(): 0, 46.7% identity in 225 aa overlap, and RACD_STRTR aspartate racemase (243 aa), fasta scores; opt: 254 z-score: 230.9 E(): 1.3e-05, 25.4% identity in 232 aa overlap. No Hp match. Contains PS00924 Aspartate and glutamate racemases signature 2 andPfam match to entry PF01177 Asp_Glu_race,Aspartate / glutamate racemase, score 108.40, E-value 1.3e-28; Updated (2006) note: Pfam domain PF01177 Asp/Glu/Hydantoin racemase identified within CDS. No specific characterisation with acceptable identity score identified. Thus, kept within product function. Functional classification - Misc; amino acid recemase complement(94297..94992) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904410 YP_002343546.1 CDS ung NC_002163.1 95108 95803 R 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; uracil-DNA glycosylase complement(95108..95803) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904411 YP_002343547.1 CDS aspA NC_002163.1 96074 97480 D catalyzes the formation of fumarate from aspartate; aspartate ammonia-lyase 96074..97480 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904412 YP_002343548.1 CDS dcuA NC_002163.1 97496 98833 D functions in anaerobic transport of C4-dicarboxylate compounds such as fumarate; similar to dcuB; anaerobic C4-dicarboxylate transporter 97496..98833 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904413 YP_002343549.1 CDS Cj0089 NC_002163.1 98941 100302 D Original (2000) note: Cj0089, probable lipoprotein,len: 453 aa; 27.4% identity to HP0018. Contains N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes, lipoproteins and porins; lipoprotein 98941..100302 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904416 YP_002343550.1 CDS Cj0090 NC_002163.1 100312 100680 D Original (2000) note: Cj0090, probable lipoprotein,len: 122 aa; no Hp match. Contains N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes, lipoproteins and porins; lipoprotein 100312..100680 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904418 YP_002343551.1 CDS Cj0091 NC_002163.1 100704 101327 D Original (2000) note: Cj0091, probable lipoprotein,len: 207 aa; 33.5% identity to HP1457. Contains N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes, lipoproteins and porins; lipoprotein 100704..101327 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904419 YP_002343552.1 CDS Cj0092 NC_002163.1 101410 102747 D Original (2000) note: Cj0092, probable periplasmic protein, len: 445 aa; no Hp match. Contains probable N-terminal signal sequence and PS00017 ATP/GTP-binding site motif A (P-loop). Functional classification -Miscellaneous periplasmic proteins; periplasmic protein 101410..102747 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904420 YP_002343553.1 CDS Cj0093 NC_002163.1 102757 103959 D Original (2000) note: Cj0093, probable periplasmic protein, len: 400 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein 102757..103959 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904421 YP_002343554.1 CDS rplU NC_002163.1 104118 104426 D Original (2000) note: Cj0094, rplU, 50S ribosomal protein L21, len: 102 aa; similar to many e.g. RL21_ECOLI 50S ribosomal protein L21 (103 aa), fasta scores; opt: 268 z-score: 457.7 E(): 3.1e-18, 40.8% identity in 103 aa overlap. 58.8% identity to HP0296. Contains PS01169 Ribosomal protein L21 signature and Pfam match to entry PF00829 Ribosomal_L21p, Ribosomal prokaryotic L21 protein,score 152.80, E-value 5.7e-42; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. Thus, not added to product function. Functional classification - Ribosomal protein synthesis and modification; PMID:378941, 8312607; 50S ribosomal protein L21 104118..104426 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904422 YP_002343555.1 CDS rpmA NC_002163.1 104437 104691 D involved in the peptidyltransferase reaction during translation; 50S ribosomal protein L27 104437..104691 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904423 YP_002343556.1 CDS obgE NC_002163.1 104798 105850 D essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication; GTPase ObgE 104798..105850 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905891 YP_002343557.1 CDS proB NC_002163.1 105955 106710 D catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis; gamma-glutamyl kinase 105955..106710 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904426 YP_002343558.1 CDS fmt NC_002163.1 106784 107701 D modifies the free amino group of the aminoacyl moiety of methionyl-tRNA(fMet) which is important in translation initiation; inactivation of this gene in Escherichia coli severely impairs growth; methionyl-tRNA formyltransferase 106784..107701 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904427 YP_002343559.1 CDS birA NC_002163.1 107664 108317 D catalyzes the formation of biotinyl-5'-AMP, also acts as a transcriptional repressor of the biotin operon; biotin--protein ligase 107664..108317 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904428 YP_002343560.1 CDS Cj0100 NC_002163.1 108314 109099 D Original (2000) note: Cj0100, parA family protein, len: 261 aa; similar to members of the parA family e.g. SOJ_BACSU soj protein (253 aa) fasta scores; opt: 762 z-score: 1251.6 E(): 0, 46.3% identity in 259 aa overlap. 61.1% identity to HP1139. Contains Pfam match to entry PF00991 ParA, ParA family ATPase, score 118.40,E-value 1.3e-31; Updated (2006) note: Pfam domain PF01656 CobQ/CobB/MinD/ParA nucleotide binding domain identified within CDS. This family consists of cobyrinic acid a,c-diamide synthases family protein. Some characterisation work within Bacillus subtilis with acceptable identity score. not added to product function. Functional classification - Cell division; PMID:8071208; parA family protein 108314..109099 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904430 YP_002343561.1 CDS Cj0101 NC_002163.1 109105 109941 D Original (2000) note: Cj0101, parB family protein, len: 278 aa; similar to members of the parB family e.g.SP0J_BACSU stage 0 sporulation protein J (282 aa), fasta scores; opt: 563 z-score: 842.8 E(): 0, 36.1% identity in 288 aa overlap. 41.7% identity to HP1138 plasmid replication-partition related protein. Contains helix-turn-helix motif (Score 1486, +4.25 SD); Updated (2006) 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; PMID:1900505, PMID:8071208; parB family protein 109105..109941 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904366 YP_002343562.1 CDS atpF' NC_002163.1 110002 110427 D Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B' is part of the membrane proton channel.; F0F1 ATP synthase subunit B' 110002..110427 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904431 YP_002343563.1 CDS atpF NC_002163.1 110438 110950 D Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel.; F0F1 ATP synthase subunit B 110438..110950 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904432 YP_002343564.1 CDS atpH NC_002163.1 110953 111474 D 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; F0F1 ATP synthase subunit delta 110953..111474 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904434 YP_002343565.1 CDS atpA NC_002163.1 111488 112993 D produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit; F0F1 ATP synthase subunit alpha 111488..112993 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904435 YP_002343566.1 CDS atpG NC_002163.1 113002 113886 D Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit; F0F1 ATP synthase subunit gamma 113002..113886 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904436 YP_002343567.1 CDS atpD NC_002163.1 113912 115309 D Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit; F0F1 ATP synthase subunit beta 113912..115309 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904437 YP_002343568.1 CDS atpC NC_002163.1 115313 115702 D part of catalytic core of ATP synthase; alpha(3)beta(3)gamma(1)delta(1)epsilon(1); involved in producing ATP from ADP in the presence of the proton motive force across the membrane; F0F1 ATP synthase subunit epsilon 115313..115702 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904438 YP_002343569.1 CDS exbB3 NC_002163.1 115702 116256 D Original (2000) note: Cj0109, exbB3, probable exbB/tolQ family transport protein, len: 184 aa; similar to members of the exbB/tolQ family, e.g. EXBB_ECOLI biopolymer transport exbB protein (244 aa), fasta scores; opt: 208 z-score: 287.0 E(): 9.9e-09, 33.6% identity in 128 aa overlap, and TOLQ_ECOLI tolQ protein (230 aa),fasta scores; opt: 187 z-score: 280.1 E(): 2.4e-08, 48.4% identity in 62 aa overlap. 42.6% identity to HP1130. Also similar to Cj0179 (30.6% identity in 186 aa overlap) and Cj1628 (44.4% identity in 81 aa overlap); Updated (2006) note: Pfam domain PF01618,MotA/TolQ/ExbB 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, kept within product function. Functional classification - Transport/binding proteins - Other; PMID:8437515, PMID:9371459; MotA/TolQ/ExbB proton channel family protein 115702..116256 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904439 YP_002343570.1 CDS exbD3 NC_002163.1 116265 116654 D Original (2000) note: Cj0110, exbD3, probable exbD/tolR family transport protein, len: 129 aa; similar to members of the exbD/tolR family, e.g. EXBD_ECOLI biopolymer transport exbD protein (141 aa), fasta scores; opt: 225 z-score: 240.1 E(): 4e-06, 31.1% identity in 132 aa overlap, and TOLR_ECOLI tolR protein (142 aa), fasta scores; opt: 191 z-score: 240.1 E(): 4.1e-06, 27.7% identity in 130 aa overlap. 46.8% identity to HP1129. Also similar to Cj0180 (34.1% identity in 126 aa overlap) and Cj1629 (26.4% identity in 121 aa overlap); Updated (2006) note: Pfam domain PF02472 Biopolymer transport protein ExbD/TolR identified within CDS. Further support given to product function. No specific characterisation with acceptable identity scores were identified. Thus, kept within product function. Functional classification - Transport/binding proteins -Other; PMID:9371459; exbD/tolR family transport protein 116265..116654 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904440 YP_002343571.1 CDS Cj0111 NC_002163.1 116657 117436 D Original (2000) note: Cj0111, possible periplasmic protein, len: 259 aa; no Hp match. Contains possible N-terminal signal sequence; Updated (2006) note: Literature search identified paper (PMID:15231804) suggesting a number of differentially expressed genes (e.g. Cj0111) 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; PMID:15231804; periplasmic protein 116657..117436 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904442 YP_002343572.1 CDS tolB NC_002163.1 117446 118654 D forms dimers; may be involved in cell envelope integrity; interacts with outer membrane proteins and with the C-terminal domain of inner membrane protein TolA; translocation protein TolB 117446..118654 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904443 YP_002343573.1 CDS pal NC_002163.1 118731 119228 D Original (2000) note: Cj0113, pal, peptidoglycan associated lipoprotein (omp18), len: 165 aa; identical to TR:Q46123 (EMBL:X83374) precursor of peptidoglycan associated lipoprotein (165 aa), almost identical to TR:Q46099 omp18 (165 aa) (93.9% identity). Similar to e.g. PAL_ECOLI peptidoglycan-associated lipoprotein precursor (173 aa), fasta scores; opt: 322 z-score: 491.5 E(): 4e-20, 38.5% identity in 169 aa overlap. 42.2% identity (in 109 aa overlap) to HP1125. Contains N-terminal signal sequence with appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site and Pfam match to entry PF00691 OmpA, OmpA family, score 100.60, E-value 3.2e-26; Updated (2006) note: Characterised within Campylobacter jejuni (PMID:8576327). not added to product function. Functional classification - Membranes,lipoproteins and porins; PMID:8576327; peptidoglycan associated lipoprotein 118731..119228 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904444 YP_002343574.1 CDS Cj0114 NC_002163.1 119232 120179 D Original (2000) note: Cj0114, possible periplasmic protein, len: 315 aa; similar to hypothetical protein YBGF_ECOLI hypothetical 28.2 kd protein in pal-lysT intergenic region (263 aa), fasta scores; opt: 144 z-score: 238.8 E(): 4.8e-06, 21.3% identity in 249 aa overlap. 28.6% identity to HP1124. Contains possible N-terminal signal sequence; Updated (2006) note: Prosite PS50005 TPR_REPEAT,Tetratricopeptide region identified within CDS. Supporting paper identifies protein as a glycoprotein. Functional classification - Miscellaneous periplasmic proteins; PMID:12186869; periplasmic protein 119232..120179 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904445 YP_002343575.1 CDS slyD NC_002163.1 120194 120763 D Original (2000) note: Cj0115, slyD, probable peptidyl-prolyl cis-trans isomerase, len: 189 aa; similar to many of the FKBP-type e.g. SLYD_ECOLI FKBP-type peptidyl-prolyl cis-trans isomerase (196 aa), fasta scores; opt: 478 z-score: 296.9 E(): 2.8e-09, 38.5% identity in 200 aa overlap. 39.2% identity to HP1123; Updated (2006) note: Prosite PS50059 FKBP_PPIASE,Peptidylprolyl isomerase, 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; PMID:9188461; FKBP-type peptidyl-prolyl cis-trans isomerase 120194..120763 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904446 YP_002343576.1 CDS fabD NC_002163.1 120763 121683 D Original (2000) note: Cj0116, fabD, probable malonyl CoA-acyl carrier protein transacylase, len: 306 aa; similar to many e.g. FABD_ECOLI malonyl CoA-acyl carrier protein transacylase (EC 2.3.1.39) (308 aa), fasta scores; opt: 555 z-score: 655.2 E(): 3.1e-29, 36.1% identity in 296 aa overlap. 49.5% identity to HP0090. Contains Pfam match to entry PF00698 Acyl_transf, Acyl transferase domain, score 58.10, E-value 1.9e-13; Updated (2006) note: Characterised within Escherichia coli with acceptable identity scores. Thus, not added to product function. Functional classification - Fatty acid biosynthesis; PMID:1339356, PMID:7768883, PMID:8759840; malonyl CoA-acyl carrier protein transacylase 120763..121683 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904447 YP_002343577.1 CDS pfs NC_002163.1 121680 122369 D enables the cleavage of the glycosidic bond in both 5'-methylthioadenosine and S-adenosylhomocysteine; 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase 121680..122369 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904448 YP_002343578.1 CDS Cj0118 NC_002163.1 122366 123121 D Original (2000) note: Cj0118, unknown, len: 251 aa; similar to hypothetical proteins from many organisms e.g. YDAO_ECOLI (311 aa), fasta scores; opt: 447 z-score: 465.6 E(): 1.1e-18, 32.5% identity in 240 aa overlap. 49.4% identity to HP1182. Contains Pfam match to entry PF01171 UPF0021, Uncharacterized protein family UPF0021, score -88.80, E-value 9.9e-05; Updated (2006) note: Pfam domain PF01171 PP-loop family identified within CDS. No specific characterisation has been carried out. Thus, kept within product function. Conserved added to product function. Functional classification - Conserved hypothetical proteins; hypothetical protein 122366..123121 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904449 YP_002343579.1 CDS Cj0119 NC_002163.1 123126 123647 D Original (2000) note: Cj0119, unknown, len: 173 aa; similar to a hypothetical protein from B. subtilis TR:O32091 (EMBL:Z99120) YUEJ protein (183 aa), fasta scores; opt: 172 z-score: 282.5 E(): 1.8e-08, 29.5% identity in 166 aa overlap. No Hp match; Updated (2006) note: Motif match (IPR000868) 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; hydrolase 123126..123647 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904451 YP_002343580.1 CDS Cj0120 NC_002163.1 123647 124261 D Original (2000) note: Cj0120, unknown, len: 204 aa; 41.7% identity to HP0951. Functional classification -Conserved hypothetical proteins; recombination protein RecO 123647..124261 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904452 YP_002343581.1 CDS Cj0121 NC_002163.1 124258 124665 D Original (2000) note: Cj0121, unknown, len: 135 aa; similar to hypothetical proteins from many organisms e.g. YBEY_ECOLI (155 aa) fasta scores; opt: 218 z-score: 353.9 E(): 1.9e-12, 37.8% identity in 111 aa overlap. 59.8% identity to HP1160; Updated (2006) note: Pfam PF02130 Uncharacterized protein family UPF0054 was present within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins; metalloprotease 124258..124665 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904453 YP_002343582.1 CDS Cj0122 NC_002163.1 124789 125478 D Original (2000) note: Cj0122, unknown, len: 229 aa; no Hp match. Similar in C-terminus to Cj0055c (46.6% identity in 148 aa overlap), and in N-terminus to Cj0416 (88.2% identity in 34 aa overlap); Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein 124789..125478 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904454 YP_002343583.1 CDS Cj0123c NC_002163.1 125503 126429 R Original (2000) note: Cj0123c, possible transcriptional regulator, len: 308 aa; similar to hypothetical proteins e.g. YACF_BACSU (333 aa), fasta scores; opt: 566 z-score: 916.8 E(): 0, 37.2% identity in 312 aa overlap, and to e.g. NIR3_RHOCA nitrogen regulation protein nifR3 (324 aa), fasta scores; opt: 517 z-score: 616.2 E(): 4.6e-27, 34.4% identity in 317 aa overlap. 49.5% identity to HP0727. Contains Pfam match to entry PF01207 UPF0034, Uncharacterized protein family UPF0034,score 260.90, E-value 1.7e-74; Updated (2006) note: Pfam domain PF01207 Dihydrouridine synthase (Dus) 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, kept within product function. Functional classification - Misc; tRNA-dihydrouridine synthase complement(125503..126429) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904455 YP_002343584.1 CDS Cj0124c NC_002163.1 126426 127412 R Original (2000) note: Cj0124c, probable membrane protein, len: 328 aa; 21.1% identity to HP0948. Contains two possible transmembrane domains. Functional classification - Membranes, lipoproteins and porins; hypothetical protein complement(126426..127412) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904457 YP_002343585.1 CDS Cj0125c NC_002163.1 127402 127764 R Original (2000) note: Cj0125c, unknown, len: 120 aa; some similarity to e.g. DKSA_ECOLI dnaK suppressor protein (151 aa), fasta scores; opt: 186 z-score: 276.6 E(): 3.8e-08, 26.3% identity in 118 aa overlap. No Hp match. Contains PS01102 Prokaryotic dksA/traR C4-type zinc finger and Pfam match to entry PF01258 zf_dskA_traR,Prokaryotic dksA/traR C4-type zinc finger, score 39.20,E-value 9.7e-08; Updated (2006) note: No specific characterisation has been carried out yet. Functional classification -Conserved hypothetical proteins; hypothetical protein complement(127402..127764) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904459 YP_002343586.1 CDS Cj0126c NC_002163.1 127776 128237 R Original (2000) note: Cj0126c, unknown, len: 153 aa; similar to hypotheticals e.g. YBEA_ECOLI (155 aa),fasta scores; opt: 189 z-score: 288.6 E(): 8.1e-09, 28.1% identity in 153 aa overlap. 37.2% identity to HP0949; Updated (2006) note: Pfam PF02590 Uncharacterized ACR family was present within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins; hypothetical protein complement(127776..128237) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904460 YP_002343587.1 CDS accD NC_002163.1 128227 129069 R catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer of AccA2D2 subunits; acetyl-CoA carboxylase subunit beta complement(128227..129069) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904461 YP_002343588.1 CDS Cj0128c NC_002163.1 129078 129800 R Original (2000) note: Cj0128c, unknown, len: 240 aa; some similarity to e.g. SUHB_ECOLI extragenic suppressor protein suhB (267 aa), fasta scores; opt: 168 z-score: 229.0 E(): 1.7e-05, 29.9% identity in 134 aa overlap. No Hp match; Updated (2006) 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, however,identity scores were not acceptable. Functional classification - Misc; PMID:10747806, PMID:8002619; inositol monophosphatase family protein complement(129078..129800) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904462 YP_002343589.1 CDS Cj0129c NC_002163.1 129800 132019 R Original (2000) note: Cj0129c, probable outer membrane protein, len: 739 aa; similar to e.g. TR:O30912 (EMBL:AF021245) Neisseria meningitidis outer membrane protein omp85 (797 aa), fasta scores; opt: 643 z-score: 886.3 E(): 0, 25.3% identity in 782 aa overlap, and D152_HAEIN protective surface antigen d15 precursor (795 aa), fasta scores; opt: 523 z-score: 548.2 E(): 2.8e-23,24.3% identity in 807 aa overlap. 34.2% identity to HP0655. Contains N-terminbal signal sequence and Pfam match to entry PF01103 Bac_suface_Ag, Bacterial surface antigen, score 404.10, E-value 1.3e-117; Updated (2006) 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, however,identity scores were marginal. Appropriate motifs were present. not added to product function. Functional classification - Membranes, lipoproteins and porins; PMID:11422558, PMID:16102012; outer membrane protein complement(129800..132019) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904463 YP_002343590.1 CDS tyrA NC_002163.1 132096 132923 D catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate; prephenate dehydrogenase 132096..132923 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904465 YP_002343591.1 CDS Cj0131 NC_002163.1 133003 134376 D Original (2000) note: Cj0131, probable periplasmic protein, len: 457 aa; similar to hypothetical proteins e.g.TR:O25694 (EMBL:AE000754) Aquifex aeolicus AQ_1743 (422 aa), fasta scores; opt: 401 z-score: 635.2 E(): 4e-28, 30.0% identity in 420 aa overlap. 30.0% identity to HP1054. Contains probable N-terminal signal sequence. Also similar in C-terminus to Cj1235 (30.2% identity in 222 aa overlap); Updated (2006) 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, kept within product function. Functional classification - Degradation of macromolecules - Proteins, peptides and glycopeptides; peptidase M23 family protein 133003..134376 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904466 YP_002343592.1 CDS lpxC NC_002163.1 134376 135260 D zinc-dependent; catalyzes the deacetylation of UDP-(3-O-acyl)-N-acetylglucosamine to UDP-3-O-(3-hydroxytetradecanoyl)-glucosamine in the second step of lipid A biosynthesis; UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase 134376..135260 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904467 YP_002343593.1 CDS Cj0133 NC_002163.1 135299 135700 D Original (2000) note: Cj0133, unknown, len: 133 aa; 33.6% identity to HP1051; Updated (2006) 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,peptides and glycopeptides; glycoprotease family protein 135299..135700 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904469 YP_002343594.1 CDS thrB NC_002163.1 135709 136587 D catalyzes the formation of O-phospho-L-homoserine from L-homoserine in threonine biosynthesis from asparate; homoserine kinase 135709..136587 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904490 YP_002343595.1 CDS Cj0135 NC_002163.1 136612 136869 D Original (2000) note: Cj0135, unknown, len: 85 aa; 44.6% identity to HP1049; Updated (2006) note: Pfam PF04296 Protein of unknown function (DUF448) was present within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins; hypothetical protein 136612..136869 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904470 YP_002343596.1 CDS infB NC_002163.1 136856 139471 D 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; translation initiation factor IF-2 136856..139471 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904471 YP_002343597.1 CDS rbfA NC_002163.1 139468 139830 D associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock; ribosome-binding factor A 139468..139830 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904468 YP_002343598.1 CDS Cj0138 NC_002163.1 139820 140242 D Original (2000) note: Cj0138, unknown, len: 140 aa; similar to hypothetical proteins e.g. YHBC_ECOLI (152 aa),fasta scores; opt: 272 z-score: 436.7 E(): 4.5e-17, 41.4% identity in 116 aa overlap. 38.9% identity to HP1046; Updated (2006) note: Pfam PF02576 Uncharacterised BCR, YhbC family was present within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins; hypothetical protein 139820..140242 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904546 YP_002343599.1 CDS Cj0139 NC_002163.1 140289 142640 D Original (2000) note: Cj0139, possible endonuclease, len: 783 aa; similar in part to MCRB_ECOLI 5-methylcytosine-specific restriction enzyme B (465 aa),fasta scores; opt: 305 z-score: 505.4 E(): 6.7e-21, 40.9% identity in 186 aa overlap. No Hp match; Updated (2006) 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, kept within product function. Functional classification - DNA replication,restriction/modification, recombination and repair; PMID:7781618; endonuclease 140289..142640 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904929 YP_002343600.1 CDS Cj0140 NC_002163.1 142633 143964 D Original (2000) note: Cj0140, unknown, len: 443 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein 142633..143964 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904472 YP_002343601.1 CDS Cj0141c NC_002163.1 143953 144756 R Original (2000) note: Cj0141c, ABC transporter integral membrane protein, len: 267 aa; similar to many e.g. MNTB_SYNY3 manganese transport system membrane protein (306 aa), fasta scores; opt: 425 z-score: 449.6 E(): 8.7e-18, 25.8% identity in 264 aa overlap. No Hp match. Contains Pfam match to entry PF00950 ABC-3, ABC 3 transport family, score 276.20, E-value 4.3e-79; Updated (2006) note: Seven probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity score identified. Thus, added to product function. Functional classification -Transport/binding proteins - Other; ABC transporter integral membrane protein complement(143953..144756) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904473 YP_002343602.1 CDS Cj0142c NC_002163.1 144749 145603 R Original (2000) note: Cj0142c, ABC transporter ATP-binding protein, len: 284 aa; simlar to many e.g. MNTA_SYNY3 manganese transport system ATP-binding protein (260 aa), fasta scores; opt: 417 z-score: 613.7 E(): 6.2e-27, 32.9% identity in 252 aa overlap. No Hp ortholog but 30.4% identity to HP0250 oligopeptide ABC transporter. Contains PS00017 ATP/GTP-binding site motif A (P-loop),PS00211 ABC transporters family signature and Pfam match to entry PF00005 ABC_tran, ABC transporters, score 165.90,E-value 6.9e-46; Updated (2006) note: Some characterisation within Bacillus subtilis with acceptable identity score. Sequence alignment was only partial. Thus, added to product function. Functional classification -Transport/binding proteins - Other; PMID:10760146; ABC transporter ATP-binding protein complement(144749..145603) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904475 YP_002343603.1 CDS Cj0143c NC_002163.1 145616 146506 R Original (2000) note: Cj0143c, probable periplasmic solute binding protein for ABC transport system, len: 296 aa; similar to e.g. ZNUA_ECOLI high-affinity zinc uptake system protein znuA (328 aa), fasta scores; opt: 386 z-score: 471.6 E(): 5.2e-19, 26.4% identity in 288 aa overlap. No Hp match. Contains probable N-terminal signal sequence and Pfam match to entry PF01297 Lipoprotein_4,score 133.20, E-value 4.6e-36; Updated (2006) note: Pfam domain PPF01297 Periplasmic solute binding protein identified within CDS. Further support given to product function. Some characterisation within Eschericia coli, however, identity score was marginal. Thus, kept within product function. Paper identified linking protein to glycoprotein (PMID:12186869). Also, found to have adhesin family signature. Functional classification - Transport/binding proteins - Other; PMID:9680209, PMID:12186869; periplasmic solute binding protein complement(145616..146506) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904476 YP_002343604.1 CDS Cj0144 NC_002163.1 146705 148684 D Original (2000) note: Cj0144, probable methyl-accepting chemotaxis signal transduction protein,len: 659 aa; similar to mnay e.g. MCPS_ENTAE methyl-accepting chemotaxis serine transducer (557 aa),fasta scores; opt: 297 z-score: 493.4 E(): 3.2e-20, 28.6% identity in 377 aa overlap. No Hp ortholog. C-terminus contains repeat1, 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,Methyl-accepting chemotaxis protein (MCP) signaling domain, score 110.60, E-value 4.1e-30; Updated (2006) note: Some characterisation work within Bacillus subtilis and Escherichia coli, however,identity scores were unnacceptable. Thus, kept within product function. Functional classification -Chemotaxis and mobility; PMID:6213619, PMID:7921238; methyl-accepting chemotaxis signal transduction protein 146705..148684 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904478 YP_002343605.1 CDS Cj0145 NC_002163.1 148819 150600 D Original (2000) note: Cj0145, unknown, len: 593 aa; some similarity to a hypothetical protein from Streptomyces coelicolor TR:O69840 (EMBL:AL023517) SC1B5.12C (465 aa), fasta scores; opt: 124 z-score: 327.1 E(): 5.8e-11, 23.0% identity in 574 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF05787 Bacterial protein of unknown function (DUF83), identified within CDS. TIGRFAM TIGR01409 TAT_signal_seq, Tat (twin-arginine translocation) 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, kept within product function. Functional classification -Misc; PMID:10766774; TAT (Twin-Arginine Translocation) pathway signal sequence domain protein 148819..150600 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904480 YP_002343606.1 CDS trxB NC_002163.1 150638 151576 R Original (2000) note: Cj0146c, trxB, probable thioredoxin reductase, len: 312 aa; similar to many e.g. TRXB_LISMO thioredoxin reductase (EC 1.6.4.5) (319 aa),fasta scores; opt: 749 z-score: 926.7 E(): 0, 38.0% identity in 313 aa overlap. 64.2% identity to HP0825. Contains PS00573 Pyridine nucleotide-disulphide oxidoreductases class-II active site; Updated (2006) 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, not added to product function. Functional classification - Biosynthesis of cofactors, prosthetic groups and carriers - Thioredoxin; PMID:2644268, PMID:15358361; thioredoxin reductase complement(150638..151576) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904481 YP_002343607.1 CDS trxA NC_002163.1 151710 152024 R Original (2000) note: Cj0147c, trxA, thioredoxin,len: 104 aa; highly similar to many e.g. THIO_ECOLI thioredoxin 1 (108 aa), fasta scores; opt: 344 z-score: 590.5 E(): 1.2e-25, 45.7% identity in 105 aa overlap. 68.6% identity to HP0824. Contains PS00194 Thioredoxin family active site and Pfam match to entry PF00085 thiored, Thioredoxins, score 144.20, E-value 3.6e-42; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. Thus, not added to product function. Appropiate motifs present. Paper identified linking protein to glycoprotein. Functional classification - Biosynthesis of cofactors,prosthetic groups and carriers - Thioredoxin; PMID:12186869, PMID:15358361; thioredoxin complement(151710..152024) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904479 YP_002343608.1 CDS Cj0148c NC_002163.1 152081 152419 R Original (2000) note: Cj0148c, unknown, len: 112 aa; similar to hypothetical proteins e.g. TR:G3323225 (EMBL:AE001259) Treponema pallidum TP0913 (126 aa), fasta scores; opt: 156 z-score: 253.1 E(): 7.6e-07, 31.0% identity in 100 aa overlap. 47.1% identity to HP0823; Updated (2006) note: Pfam PF02021 Uncharacterised protein family was present within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins; hypothetical protein complement(152081..152419) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904489 YP_002343609.1 CDS hom NC_002163.1 152419 153666 R catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine; homoserine dehydrogenase complement(152419..153666) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904482 YP_002343610.1 CDS Cj0150c NC_002163.1 153670 154872 R catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate; aspartate aminotransferase complement(153670..154872) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904483 YP_002343611.1 CDS Cj0151c NC_002163.1 154884 155690 R Original (2000) note: Cj0151c, possible periplasmic protein, len: 268 aa; 26.0% identity to HP0555. Contains possible N-terminal signal sequence. Functional classification - Miscellaneous periplasmic proteins; periplasmic protein complement(154884..155690) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904484 YP_002343612.1 CDS Cj0152c NC_002163.1 155684 156622 R Original (2000) note: Cj0152c, possible membrane protein, len: 312 aa; 25.0% identity to HP0554. Contains one probable transmembrane domain around aa 110. Functional classification - Membranes, lipoproteins and porins; hypothetical protein complement(155684..156622) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904485 YP_002343613.1 CDS Cj0153c NC_002163.1 156615 157298 R Original (2000) note: Cj0153c, probable rRNA methylase, len: 227 aa; similar to members of the spoU family e.g. NHS_STRAS 23S rRNA methyltransferase (274 aa), fasta scores; opt: 197 z-score: 247.9 E(): 1.5e-06,29.9% identity in 157 aa overlap. 42.7% identity to HP0553. Contains Pfam match to entry PF00588 SpoU_methylase, SpoU rRNA Methylase family, score 106.90,E-value 3.8e-28; Updated (2006) note: Characterised within Escherichia coli with marginal identity score. kept within product function. Functional classification -RNA synthesis, RNA modification and DNA transcription; PMID:11698387; rRNA methylase complement(156615..157298) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904486 YP_002343614.1 CDS Cj0154c NC_002163.1 157312 158136 R Original (2000) note: Cj0154c, possible methylase,len: 274 aa; similar to hypotehtical proteins e.g. YABC_BACSU (292 aa), fasta scores; opt: 453 z-score: 741.0 E(): 0, 32.9% identity in 289 aa overlap. 42.3% identity to HP0552. Contains PS01296 Uncharacterized protein family UPF0011 signature and Pfam match to entry PF00590 TP_methylase, Tetrapyrrole (Corrin/Porphyrin) Methylases.,score 81.20, E-value 2.2e-20; Updated (2006) note: Pfam domain PF00590 Tetrapyrrole (Corrin/Porphyrin) 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, kept within product function. Functional classification - Misc; tetrapyrrole methylase family protein complement(157312..158136) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904487 YP_002343615.1 CDS rpmE NC_002163.1 158139 158339 R RpmE; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; the proteins in this cluster have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome; 50S ribosomal protein L31 complement(158139..158339) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904488 YP_002343616.1 CDS Cj0156c NC_002163.1 158418 159074 R in Escherichia coli RsmE methylates the N3 position of the U1498 base in 16S rRNA; cells lacking this function can grow, but are outcompeted by wild-type; SAM-dependent m(3)U1498 methyltransferase; 16S ribosomal RNA methyltransferase RsmE complement(158418..159074) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904493 YP_002343617.1 CDS Cj0157c NC_002163.1 159076 159483 R Original (2000) note: Cj0157c, probable integral membrane protein, len: 135 aa; no Hp match. Contains four probable transmembrane domains. Functional classification - Membranes, lipoproteins and porins; integral membrane protein complement(159076..159483) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904494 YP_002343618.1 CDS Cj0158c NC_002163.1 159483 159908 R Original (2000) note: Cj0158c, possible haem-binding lipoprotein, len: 141 aa; no Hp match. Contains N-terminal signal sequence with appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site, PS00190 Cytochrome c family heme-binding site signature, and Pfam match to entry PF00034 cytochrome_c, Cytochrome c, score -3.00, E-value 0.87; Updated (2006) note: No specific characterisation with acceptable identity scores identified yet. kept within product function. Functional classification -Membranes, lipoproteins and porins; heme-binding lipoprotein complement(159483..159908) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904474 YP_002343619.1 CDS Cj0159c NC_002163.1 159908 160489 R Original (2000) note: Cj0159c, unknown, len: 193 aa; similar in N-terminus to hypothetical proteins e.g.TR:O27296 (EMBL:AE000890) Methanobacterium thermoautotrophicum MTH1228 (161 aa), fasta scores; opt: 140 z-score: 234.0 E(): 8.9e-06, 37.9% identity in 66 aa overlap. 35.8% identity to HP0933; Updated (2006) 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, kept within product function. Functional classification - Misc; 6-pyruvoyl tetrahydropterin synthase complement(159908..160489) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904501 YP_002343620.1 CDS Cj0160c NC_002163.1 160486 161229 R Original (2000) note: Cj0160c, unknown, len: 247 aa; similar to hypothetical proteins e.g. TR:O67826 (EMBL:AE000769) Aquifex aeolicus AQ_2035 (219 aa), fasta scores; opt: 130 z-score: 282.9 E(): 1.7e-08, 28.8% identity in 233 aa overlap. 43.1% identity to HP0934; Updated (2006) 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, so kept within product function. Functional classification - Misc; radical SAM domain protein complement(160486..161229) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904496 YP_002343621.1 CDS moaA NC_002163.1 161232 162194 R together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z; molybdenum cofactor biosynthesis protein A complement(161232..162194) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904499 YP_002343622.1 CDS Cj0162c NC_002163.1 162207 162722 R Original (2000) note: Cj0162c, probable periplasmic protein, len: 171 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein complement(162207..162722) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904500 YP_002343623.1 CDS Cj0163c NC_002163.1 162719 163216 R Original (2000) note: Cj0163c, unknown, len: 165 aa; no Hp match. Functional classification - Unknown; hypothetical protein complement(162719..163216) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904502 YP_002343624.1 CDS ubiA NC_002163.1 163207 164091 R UbiA prenyltransferase family catalyzes the transfer of a prenyl group to various acceptors with hydrophobic ring structures in the biosynthesis of respiratory quinones, hemes, chlorophylls, vitamin E, and shikonin; prenyltransferase complement(163207..164091) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904503 YP_002343625.1 CDS miaA NC_002163.1 164162 165031 D IPP transferase; isopentenyltransferase; involved in tRNA modification; 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; further tRNA modifications may occur; mutations in miaA result in defects in translation efficiency and fidelity; tRNA delta(2)-isopentenylpyrophosphate transferase 164162..165031 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904521 YP_002343626.1 CDS Cj0167c NC_002163.1 165017 165580 R Original (2000) note: Cj0167c, probable integral membrane protein, len: 187 aa; similar to hypothetical proteins e.g. YEBN_ECOLI (206 aa), fasta scores; opt: 451 z-score: 792.0 E(): 0, 38.1% identity in 197 aa overlap. No Hp match; Updated (2006) note: Six probable transmembrane helices predicted by TMHMM2.0. Also, 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, so included in product function. Functional classification - Membranes,lipoproteins and porins; integral membrane protein complement(165017..165580) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904504 YP_002343627.1 CDS Cj0168c NC_002163.1 165938 166105 R Original (2000) note: Cj0168c, probable periplasmic protein, len: 55 aa; No Hp ortholog. Some similarity in C-term to Cj0909 (35.0% identity in 40 aa overlap). Contains probable N-terminal signal sequence; Updated (2006) note: Literature search identified paper giving further support to product function. N-terminal matches to Yersinia pestis, acid shock protein 2 precursor. Functional classification - Miscellaneous periplasmic proteins; PMID:15632442; periplasmic protein complement(165938..166105) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904507 YP_002343628.1 CDS sodB NC_002163.1 166373 167035 D Original (2000) note: Cj0169, sodB, superoxide dismutase (Fe), len: 220 aa; 99.1% identical to SODF_CAMJE, and highly simlar to many e.g. SODF_ECOLI superoxide dismutase (Fe) (EC 1.15.1.1) (192 aa), fasta scores; opt: 740 z-score: 1209.9 E(): 0, 57.9% identity in 195 aa overlap. 61.6% identity to HP0389. Contains PS00088 Manganese and iron superoxide dismutases signature and Pfam match to entry PF00081 sodfe, Iron/manganese superoxide dismutases (SODM), score 275.90, E-value 5.2e-79; Updated (2006) note: Characterised within Campylobacter jejuni, so not added. Paper identified linking protein to glycoprotein (PMID:12186869). Functional classification -Detoxification; PMID:12186869, PMID:8025686, PMID:8005660; superoxide dismutase 166373..167035 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904414 YP_002343629.1 CDS Cj0170 NC_002163.1 167050 167794 D Original (2000) note: Cj0171, unknown, len: 166 aa; no Hp match. Contains polyporphic sequence G(9,11) at N-terminus; G11 allows translation from the upstream CDS Cj0170, G9 (consensus) would only allow this CDS to start at aa 47. Similar to Cj1326 (51.9% identity in 135 aa overlap), which also contains a polymorphic sequence allowing possible translation from Cj1325; Original (2000) note: Cj0170, unknown, len: 90 aa; no Hp match. Contains polyporphic sequence G(9,11) at C-terminus; G9 (consensus) gives this translation stop,G11 allows translation into the downstream CDS Cj0171. Similar to Cj1325 (73.8% identity in 61 aa overlap), which also contains a polymorphic sequence allowing possible translation into Cj1326; Updated (2006) 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; hypothetical protein join(167050..167295,167297..167794) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904508 YP_002343630.1 CDS Cj0172c NC_002163.1 167807 169012 R Original (2000) note: Cj0172c, unknown, len: 401 aa; similar to hypothetical proteins e.g. TR:Q55131 (EMBL:D64001) Synechocystis sp. SLR0049 (398 aa), fasta scores; opt: 1534 z-score: 2324.2 E(): 0, 55.7% identity in 397 aa overlap. 63.8% identity to HP1507 conserved hypothetical ATP-binding protein; Updated (2006) 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; saccharopine dehydrogenase complement(167807..169012) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904510 YP_002343631.1 CDS cfbpC NC_002163.1 169054 169962 R Original (2000) note: Cj0173c, possible iron-uptake ABC transport system ATP-binding protein, len: 302 aa; similar to many e.g. HITC_HAEIN iron(iii)-transport ATP-binding protein hitC (356 aa), fasta scores; opt: 389 z-score: 783.2 E(): 0, 38.0% identity in 250 aa overlap. Contains PS00017 ATP/GTP-binding site motif A (P-loop),PS00211 ABC transporters family signature and Pfam match to entry PF00005 ABC_tran, ABC transporters, score 163.10,E-value 4.9e-45. No Hp ortholog; Updated (2006) note: Literature search identified many supporting papers within Campylobacter jejuni (PMID:12069882) and also paper carrying out the original work within Serratia marcescens. Designated as Campylobacter ferric binding protein (Cfbp) system. Characterisation with acceptable identity score yet to be carried out. Thus, kept within product function. Functional classification - Transport/binding proteins -Cations; PMID:15231804, PMID:12069882, PMID:15731081,PMID:2644190, PMID:7927717; iron-uptake ABC transporter ATP-binding protein complement(169054..169962) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904511 YP_002343632.1 CDS cfbpB NC_002163.1 169946 171562 R Original (2000) note: Cj0174c, possible iron-uptake ABC transport system permease, len: 538 aa; similar to e.g. SFUB_SERMA iron(iii)-transport system permease (527 aa), fasta scores; opt: 333 z-score: 335.6 E(): 1.9e-11, 21.5% identity in 522 aa overlap. No Hp match. Contains Pfam match to entry PF00528 BPD_transp,Binding-protein-dependent transport systems inner membrane component, score 27.90, E-value 0.00024; Updated (2006) note: Literature search identified many supporting papers within Campylobacter jejuni (PMID:12069882) and also paper carrying out the original work within Serratia marcescens. Designated as Campylobacter ferric binding protein (Cfbp) system. Characterisation with acceptable identity score yet to be carried out. Thus, kept within product function. Functional classification - Transport/binding proteins -Cations; PMID:15231804, PMID:12069882, PMID:15731081,PMID:2644190, PMID:7927717; iron-uptake ABC transporter permease complement(169946..171562) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904512 YP_002343633.1 CDS cfbpA NC_002163.1 171562 172566 R Original (2000) note: Cj0175c, possible iron-uptake ABC transport system periplasmic iron-binding protein,len: 334 aa; similar to e.g. HITA_HAEIN iron-utilization periplasmic protein precursor (332 aa), fasta scores; opt: 466 z-score: 500.8 E(): 1.2e-20, 29.8% identity in 332 aa overlap. No Hp match. Contains N-terminal signal sequence; Updated (2006) 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 (PMID:12069882) and also paper carrying out the original work within Serratia marcescens. Designated as Campylobacter ferric binding protein (Cfbp) system. Characterisation with acceptable identity score yet to be carried out. Thus, kept within product function. Paper identified linked protein to glycoprotein (PMID:15231804). Functional classification -Transport/binding proteins - Cations; PMID:15613474, PMID:15231804, PMID:12069882,PMID:12186869, PMID:2644190; iron-uptake ABC transporter,periplasmic iron-binding protein complement(171562..172566) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904513 YP_002343634.1 CDS Cj0176c NC_002163.1 172563 172694 R Original (2000) note: Cj0176c, probable lipoprotein, len: 43 aa; no Hp match. Contains N-terminal signal sequence with appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site; Updated (2006) note: Literature search identified papers giving further clues to product function. Functional classification - Membranes, lipoproteins and porins; lipoprotein complement(172563..172694) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904515 YP_002343635.1 CDS Cj0177 NC_002163.1 172916 173767 D Original (2000) note: Cj0177, probable lipoprotein,len: 283 aa; simlar to TR:O68876 (EMBL:AF055999) hypothetical protein PhuW from Pseudomonas aeruginosa hemin uptake locus (295 aa), fasta scores; opt: 375 z-score: 307.6 E(): 7.1e-10, 31.3% identity in 246 aa overlap. No Hp match. Contains N-terminal signal sequence with appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site; Updated (2006) note: Pfam domain PF04187 Protein of unknown function, 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, kept within product function. Functional classification -Transport/binding proteins - Cations; PMID:12069882, PMID:15231804, PMID:15231804; iron transport protein 172916..173767 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904516 YP_002343636.1 CDS Cj0178 NC_002163.1 173764 176031 D Original (2000) note: Cj0178, possible outer membrane siderophore receptor, len: 755 aa; similar to e.g. YC17_HAEIN probable tonB-dependent receptor HI1217 (913 aa), fasta scores; opt: 440 z-score: 1818.4 E(): 0,32.7% identity in 912 aa overlap, and TR:O68881 (EMBL:AF055999) outer membrane hemin receptor PhuR from Pseudomonas aeruginosa (764 aa), fasta scores; opt: 145 z-score: 207.4 E(): 0.00027 22.3% identity in 806 aa overlap. No Hp match. Contains N-terminal signal sequence; Updated (2006) 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, kept within product function. Functional classification - Transport/binding proteins - Cations; PMID:15731081, PMID:15632442, PMID:15231804,PMID:12069882; TonB-denpendent outer membrane receptor 173764..176031 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904518 YP_002343637.1 CDS exbB1 NC_002163.1 176043 176804 D Original (2000) note: Cj0179, exbB1, biopolymer transport protein, len: 253 aa; highly similar to e.g. EXBB_ECOLI biopolymer transport exbB protein (244 aa),fasta scores; opt: 537 z-score: 811.2 E(): 0, 46.3% identity in 216 aa overlap. No Hp ortholog; Updated (2006) note: Pfam domain PF01618 MotA/TolQ/ExbB proton channel family identified within CDS. Also, three probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli with acceptable identity score. Thus, not added. Cj0179-Cj0181 (exbB1, exbD1, tonB1) function as an outer-membrane energy transducer system. Functional classification -Transport/binding proteins - Other; PMID:7642501, PMID:8437515, PMID:15632442,PMID:12069882; biopolymer transport protein 176043..176804 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904520 YP_002343638.1 CDS exbD1 NC_002163.1 176791 177201 D Original (2000) note: Cj0180, exbD1, biopolymer transport protein, len: 136 aa; highly similar to e.g. EXBD_ECOLI biopolymer transport exbD protein (141 aa),fasta scores; opt: 356 z-score: 629.2 E(): 8.7e-28, 42.9% identity in 119 aa overlap. No Hp ortholog; Updated (2006) note: Pfam domain PF02472 Biopolymer transport protein ExbD/TolR identified within CDS. Also,one probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Escherichia coli with acceptable identity scores. Thus, not added. Cj0179-Cj0181 (exbB1, exbD1,tonB1) function as an outer-membrane energy transducer system. Functional classification - Transport/binding proteins - Other; PMID:7642501, PMID:8437515, PMID:15632442,PMID:12069882; biopolymer transport protein 176791..177201 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904523 YP_002343639.1 CDS tonB1 NC_002163.1 177203 177949 D Original (2000) note: Cj0181, tonB1, possible tonB transport protein, len 248 aa; similar to e.g. TONB_PSEPU tonB protein (243 aa), fasta scores; opt: 220 z-score: 317.2 E(): 2.1e-10, 29.5% identity in 149 aa overlap. No Hp match; Updated (2006) note: One probable transmembrane helices predicted by TMHMM2.0. Characterised within Pseudomonas putida with marginal identity score. not added. Cj0179-Cj0181 (exbB1, exbD1, tonB1) function as an outer-membrane energy transducer system. Functional classification - Transport/binding proteins - Other; PMID:7642501, PMID:8437515, PMID:15632442,PMID:12069882; TonB transport protein 177203..177949 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904524 YP_002343640.1 CDS Cj0182 NC_002163.1 177995 179200 D in Escherichia coli SbmA is involved in uptake of microcin J25; functions along with FhuA, TonB, and ExbB/D in this capacity; in Sinorhizobium meliloti, BacA is essential and required for symbiosis; defects appear to affect the cell envelope; transporter 177995..179200 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904525 YP_002343641.1 CDS Cj0183 NC_002163.1 179299 180657 D Original (2000) note: Cj0183, probable integral membrane protein with haemolysin domain, len: 452 aa; similar to many members of the UPF0053 family e.g. YUGS_BACSU (434 aa), fasta scores; opt: 999 z-score: 1508.9 E(): 0, 38.1% identity in 430 aa overlap. Also similar in C-terminal half to haemolysins e.g. HLYC_TREHY Treponema hyodysenteriae hemolysin C (268 aa), fasta scores; opt: 447 z-score: 468.1 E(): 8.1e-19, 32.5% identity in 237 aa overlap. 54.3% identity to HP1490. Contains 2x Pfam match to entry PF00571 CBS, CBS domain,scores 26.10, E-value 0.00082 and 40.50, E-value 3.7e-08; Updated (2006) note: Four probable transmembrane helices predicted by TMHMM2.0. No specific characterisation with acceptable identity scores identified yet. Thus, kept within product function. Functional classification - Pathogenicity; integral membrane protein 179299..180657 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904526 YP_002343642.1 CDS Cj0184c NC_002163.1 180702 181856 R Original (2000) note: Cj0184c, possible serine/threonine protein phosphatase, len: 384 aa; similar in part to many eukarotic serine/threonine protein phosphatases e.g. PP12_SCHPO serine/threonine protein phosphatase PP1-2 (322 aa), fasta scores; opt: 140 z-score: 290.0 E(): 6.8e-09, 31.3% identity in 131 aa overlap. No Hp match. Contains Pfam match to entry PF00149 STphosphatase, Ser/Thr protein phosphatases, score 6.90,E-value 0.39; Updated (2006) 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; serine/threonine protein phosphatase complement(180702..181856) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904527 YP_002343643.1 CDS Cj0185c NC_002163.1 181866 182075 R Original (2000) note: Cj0185c, unknown, len: 69 aa; similar to part of phnA proteins (involved in alkylphosphonate uptake) from several organisms e.g. PHNA_ECOLI phnA protein (111 aa), fasta scores; opt: 238 z-score: 482.4 E(): 1.3e-19, 55.9% identity in 68 aa overlap. 45.6% identity in 68 aa overlap to HP0872 (109 aa); Updated (2006) note: Pfam domain PF03831 PhnA protein was identified within CDS. Characterisation work within Escherichia coli has been carried out with acceptable identity scores. However, sequence alignment was only partial. Product changed from phnA-like protein to phnA domain protein. Functional classification - Transport/binding proteins - Other; PMID:9300819; phnA domain protein complement(181866..182075) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904528 YP_002343644.1 CDS Cj0186c NC_002163.1 182068 182787 R Original (2000) note: Cj0186c, probable integral membrane protein, len: 239 aa; similar to many hypothetical proteins e.g. YGDQ_HAEIN HI0056 (237 aa),fasta scores; opt: 964 z-score: 1727.7 E(): 0, 64.3% identity in 230 aa overlap. 50.0% identity to HP1343; Updated (2006) 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, kept within product function. Functional classification -Membranes, lipoproteins and porins; TerC family integral membrane protein complement(182068..182787) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904529 YP_002343645.1 CDS purN NC_002163.1 182859 183425 R Original (2000) note: Cj0187c, purN, probable phosphoribosylglycinamide formyltransferase, len: 188 aa; similar to e.g. PUR3_ECOLI phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) (212 aa), fasta scores; opt: 406 z-score: 654.6 E(): 3.3e-29, 38.6% identity in 189 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00551 formyl_transf, Formyl transferase, score 177.90, E-value 4.4e-50; Updated (2006) note: Characterised within Escherichia coli with acceptable identity scores. not added to product function. Functional classification -Purine ribonucleotide biosynthesis; PMID:3301838; phosphoribosylglycinamide formyltransferase complement(182859..183425) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904530 YP_002343646.1 CDS Cj0188c NC_002163.1 183416 184786 R Original (2000) note: Cj0188c, unknown, len: 456 aa; similar to members of the UPF0031 family e.g. YJEF_ECOLI (515 aa), fasta scores; opt: 267 z-score: 441.8 E(): 2.4e-17, 29.9% identity in 418 aa overlap. 35.9% identity to HP1363. Contains PS01050 Uncharacterized protein family UPF0031 signature 2 and Pfam match to entry PF01256 UPF0031, Uncharacterized protein family UPF0031,score 96.30, E-value 6e-25; Updated (2006) 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; kinase complement(183416..184786) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904531 YP_002343647.1 CDS Cj0189c NC_002163.1 184770 185468 R Original (2000) note: Cj0189c, unknown, len: 232 aa; similar to hypothetical proteins e.g. TR:P73622 (EMBL:D90908) Synechocystis sp. (249 aa), fasta scores; opt: 351 z-score: 629.7 E(): 8.1e-28, 30.1% identity in 246 aa overlap. No Hp match; Updated (2006) note: Pfam PF01936 Protein of unknown function (DUF88) was present within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins; hypothetical protein complement(184770..185468) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904532 YP_002343648.1 CDS Cj0190c NC_002163.1 185470 186975 R Original (2000) note: Cj0190c, unknown, len: 501 aa; similar to prokaryotic hypothetical proteins e.g. YIFB_ECOLI (516 aa), fasta scores; opt: 670 z-score: 1088.3 E(): 0, 34.0% identity in 497 aa overlap, and more distantly to members of the eukaryotic MCM family of DNA replication regulatory factors e.g. MCM6_RAT DNA replication licensing factor MCM6 (509 aa), fasta scores; opt: 152 z-score: 247.8 E(): 1.5e-06, 23.5% identity in 345 aa overlap. 47.7% identity to HP0792 (anotated as sigma-54 interacting protein). Contains PS00017 ATP/GTP-binding site motif A (P-loop) and Pfam match to entry PF01078 Mg_chelatase, Magnesium chelatase, subunit ChlI, score 127.80, E-value 2e-34. Functional classification - Misc; hypothetical protein complement(185470..186975) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904533 YP_002343649.1 CDS def NC_002163.1 186972 187499 R cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+); peptide deformylase complement(186972..187499) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904534 YP_002343650.1 CDS clpP NC_002163.1 187535 188119 R hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates; ATP-dependent Clp protease proteolytic subunit complement(187535..188119) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 906014 YP_002343651.1 CDS tig NC_002163.1 188119 189453 R Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer; trigger factor complement(188119..189453) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904535 YP_002343652.1 CDS folE NC_002163.1 189596 190168 D involved in the first step of tetrahydrofolate biosynthesis; catalyzes the formation of formate and 2-amino-4-hydroxy-6-(erythro-1,2, 3-trihydroxypropyl)dihydropteridine triphosphate from GTP and water; forms a homopolymer; GTP cyclohydrolase I 189596..190168 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904536 YP_002343653.1 CDS fliI NC_002163.1 190168 191553 D involved in type III protein export during flagellum assembly; flagellum-specific ATP synthase 190168..191553 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904537 YP_002343654.1 CDS purF NC_002163.1 191556 192893 R Catalyzes first step of the de novo purine nucleotide biosynthetic pathway; amidophosphoribosyltransferase complement(191556..192893) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904538 YP_002343655.1 CDS dapB NC_002163.1 192895 193623 R catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate reductase complement(192895..193623) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904539 YP_002343656.1 CDS Cj0198c NC_002163.1 193686 194867 R Original (2000) note: Cj0198c, unknown, len: 393 aa; similar to hypothetical proteins e.g. YCAJ_ECOLI (447 aa), fasta scores; opt: 339 z-score: 796.4 E(): 0, 32.8% identity in 381 aa overlap, and less strongly to several helicases e.g. RUVB_HELPY holliday junction DNA helicase ruvB (336 aa), fasta scores; opt: 204 z-score: 280.5 E(): 2.3e-08, 28.8% identity in 278 aa overlap. 49.9% identity to HP1026. Contains PS00017 ATP/GTP-binding site motif A (P-loop); Updated (2006) note: Pfam domain PF00004 ATPase family associated with various cellular activities (AAA),was identified within CDS. Further support given to product function. No specific characterisation has been carried out yet. Product function unchanged. Functional classification - DNA replication,restriction/modification, recombination and repair; recombination factor protein RarA complement(193686..194867) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904540 YP_002343657.1 CDS Cj0199c NC_002163.1 194867 195988 R Original (2000) note: Cj0199c, probable periplasmic protein, len: 373 aa; no Hp match. Contains N-terminal signal sequence. Functional classification - Miscellaneous periplasmic proteins; periplasmic protein complement(194867..195988) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904542 YP_002343658.1 CDS Cj0200c NC_002163.1 196123 196470 R Original (2000) note: Cj0200c, probable periplasmic protein, len: 115 aa; no Hp match. Contains N-terminal signal sequence; Updated (2006) note: Literature search papers giving further clues to product function. Paper (PMID:12186869) links protein to glycoprotein. Functional classification - Miscellaneous periplasmic proteins; PMID:15554967, PMID:12186869; periplasmic protein complement(196123..196470) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904543 YP_002343659.1 CDS Cj0201c NC_002163.1 196534 197139 R Original (2000) note: Cj0201c, probable integral membrane protein, len: 201 aa; no Hp match. Contains possible transmembrane domain at N-terminus and PS00216 Sugar transport proteins signature 1. Functional classification - Membranes, lipoproteins and porins; integral membrane protein complement(196534..197139) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904544 YP_002343660.1 CDS Cj0202c NC_002163.1 197123 197464 R Original (2000) note: Cj0202c, unknown, len: 113 aa. No Hp match. Functional classification - Unknown; hypothetical protein complement(197123..197464) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 906013 YP_002343661.1 CDS Cj0203 NC_002163.1 197707 199053 D Original (2000) note: Cj0203, probable transmembrane transport protein, len: 448 aa; some similarity to e.g. CITM_BACSU Mg2+/citrate complex secondary transporter (433 aa), fasta scores; opt: 702 z-score: 964.3 E(): 0, 28.7% identity in 449 aa overlap. No Hp match; Updated (2006) 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, however, identity scores were marginal. kept within product function. Functional classification - Transport/binding proteins -Other; PMID:8892821; citrate transporter 197707..199053 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904545 YP_002343662.1 CDS Cj0204 NC_002163.1 199236 201233 D Original (2000) note: Cj0204, probable integral membrane protein, len: 665 aa; 98.9% identity in 369 aa overlap to TR:Q46110 (EMBL:X76062) C. jejuni ORF CJO1.1 (381 aa). Similar to hypothetical proteins e.g. Y561_HAEIN HI0561/560 (633 aa), fasta scores; opt: 2119 z-score: 1501.8 E(): 0, 53.6% identity in 640 aa overlap, and in C-terminus to TR:Q51156 (EMBL:L09189) Neisseria meningitidis ORF associated with capsule gene complex (282 aa), fasta scores; opt: 880 z-score: 1097.6 E(): 0, 51.3% identity in 273 aa overlap. No Hp match; Updated (2006) 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/binding proteins -Other; PMID:7489896; oligopeptide transporter, OPT family 199236..201233 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904548 YP_002343663.1 CDS uppP NC_002163.1 201307 202110 D Original (2000) note: Cj0205, bacA, possible undecaprenol kinase (bacitracin resistance protein), len: 267 aa; 98.6% identity in 138 aa overlap to TR:Q46111 C. jejuni ORF CJO1.2 (138 aa). Simlar to e.g. BACA_ECOLI bacitracin resistance protein ( undecaprenol kinase) (273 aa), fasta scores; opt: 483 z-score: 947.5 E(): 0, 43.7% identity in 270 aa overlap. No Hp match; Updated (2006) 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 (PMID:15778224). Product function modified to more specific family member. Identity scores were acceptable. Thus, not added to product function. Functional classification -Drug/analogue sensitivity; PMID:7489896, PMID:8389741, PMID:15138271,PMID:15778224; UDP-diphosphatase 201307..202110 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904549 YP_002343664.1 CDS thrS NC_002163.1 202241 204049 D catalyzes the formation of threonyl-tRNA(Thr) from threonine and tRNA(Thr); catalyzes a two-step reaction, first charging a threonine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; threonyl-tRNA synthetase 202241..204049 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904952 YP_002343665.1 CDS infC NC_002163.1 204046 204564 D IF-3 has several functions that are required and promote translation initiation including; preventing association of 70S by binding to 30S; monitoring codon-anticodon interactions by promoting disassociation of fMet-tRNA(fMet) from initiation complexes formed on leaderless mRNAs or incorrectly bound noninitiatior tRNAs and complexes with noncanonical start sites; stimulates codon-anticodon interactions at P-site; involved in moving mRNA to the P-site; and in recycling subunits; translation initiation factor IF-3 204046..204564 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904550 YP_002343666.1 CDS Cj0208 NC_002163.1 204603 205694 D Original (2000) note: Cj0208, probable DNA modification methylase (adenine-specific methyltransferase), len: 363 aa; similar to many e.g. MTN3_NEILA modification methylase NlaIII (EC 2.1.1.72) (334 aa), fasta scores; opt: 215 z-score: 401.1 E(): 4.4e-15, 31.7% identity in 366 aa overlap. 29.6% identity to HP1208 ulcer associated adenine specific DNA methyltransferase. Contains PS00092 N-6 Adenine-specific DNA methylases signature; Updated (2006) 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,restriction/modification, recombination and repair; PMID:2277628; DNA modification methylase 204603..205694 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904551 YP_002343667.1 CDS argC NC_002163.1 209279 210307 D 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; involved in both the arginine and lysine biosynthetic pathways; lysine is produced via the AAA pathway, lysine from alpha-aminoadipate; N-acetyl-gamma-glutamyl-phosphate reductase 209279..210307 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 906012 YP_002343668.1 CDS Cj0225 NC_002163.1 210317 210763 D Original (2000) note: Cj0225, probable acetyltransferase, len: 148 aa; some simlarity to STA_ECOLI streptothricin acetyltransferase (plasmid borne)(EC 2.3.-.-) (174 aa), fasta scores; opt: 118 z-score: 186.2 E(): 0.0041, 27.3% identity in 110 aa overlap. No Hp match. Contains Pfam match to entry PF00583 Acetyltransf, Acetyltransferase (GNAT) family, score 57.00, E-value 4.1e-13; Updated (2006) note: Characterisation carried out within Escherichia coil, however, identity score was marginal. kept within product function. Functional classification - Misc; PMID:2157196; acetyltransferase 210317..210763 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904553 YP_002343669.1 CDS argB NC_002163.1 210767 211612 D catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate; acetylglutamate kinase 210767..211612 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904554 YP_002343670.1 CDS argD NC_002163.1 211616 212803 D Original (2000) note: Cj0227, argD, probable acetylornithine aminotransferase, len: 395 aa; simlar to many e.g. ARGD_ECOLI acetylornithine aminotransferase (EC 2.6.1.11) (406 aa), fasta scores; opt: 921 z-score: 1042.0 E(): 0, 36.6% identity in 385 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00202 aminotran_3,Aminotransferases class-III pyridoxal-phosphate, score 378.20, E-value 5.1e-131; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. Based on current literature, product function has been modified and additional EC number has been added. kept within product function. Functional classification - Amino acid biosynthesis - Glutamate family; PMID:10588044, PMID:10074354; acetylornithine/succinyldiaminopimelate aminotransferase 211616..212803 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904555 YP_002343671.1 CDS pcm NC_002163.1 212822 213451 R catalyzes the methyl esterification of L-isoaspartyl residues that are formed in damaged proteins; protein-L-isoaspartate O-methyltransferase complement(212822..213451) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 906010 YP_002343672.1 CDS Cj0229 NC_002163.1 213540 214088 D Original (2000) note: Cj0229, possible acetyltransferase, len: 182 aa; similar to e.g. CAIE_ECOLI carnitine operon protein caiE (203 aa), fasta scores; opt: 251 z-score: 517.5 E(): 1.4e-21, 33.1% identity in 169 aa overlap. No Hp ortholog. Contains 3x Pfam match to entry PF00132 hexapep, Bacterial transferase hexapeptide (four repeats), scores 16.60, E-value 0.0071; 9.10, E-value 0.97 and 24.70, E-value 3.7e-05; Updated (2006) note: Some characterisation work within Escherichia coli, however, identity score was marginal. kept within product function. Functional classification - Misc; PMID:7815937; acetyltransferase 213540..214088 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904556 YP_002343673.1 CDS Cj0230c NC_002163.1 214057 215430 R catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate; nicotinate phosphoribosyltransferase complement(214057..215430) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904557 YP_002343674.1 CDS nrdF NC_002163.1 215417 216439 R B2 or R2 protein; type 1b enzyme; catalyzes the rate-limiting step in dNTP synthesis; converts nucleotides to deoxynucleotides; forms a homodimer and then a multimeric complex with NrdE; ribonucleotide-diphosphate reductase subunit beta complement(215417..216439) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904558 YP_002343675.1 CDS Cj0232c NC_002163.1 216453 216863 R Original (2000) note: Cj0232c, probable integral membrane protein, len: 136 aa; 37.9% identity to HP1258 (called conserved hypothetical mitochondrial protein 4). Contains three possible transmembrane domains; Updated (2006) 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, hence the name of RDD family. This region contains two predicted transmembrane regions. Functional classification - Membranes, lipoproteins and porins; integral membrane protein complement(216453..216863) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904559 YP_002343676.1 CDS pyrE NC_002163.1 216864 217472 R involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate; orotate phosphoribosyltransferase complement(216864..217472) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904560 YP_002343677.1 CDS frr NC_002163.1 217475 218038 R Rrf; Frr; ribosome-recycling factor; release factor 4; RF4; recycles ribosomes upon translation termination along with release factor RF-3 and elongation factor EF-G; A GTPase-dependent process results in release of 50S from 70S; inhibited by release factor RF-1; essential for viability; structurally similar to tRNAs; ribosome recycling factor complement(217475..218038) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904561 YP_002343678.1 CDS secG NC_002163.1 218048 218419 R Original (2000) note: Cj0235c, secG, possible protein-export membrane protein, len: 123 aa; similar to e.g. SECG_PSESY protein-export membrane protein secG (126 aa), fasta scores; opt: 157 z-score: 210.5 E(): 0.00018,25.2% identity in 119 aa overlap. 48.8% identity to HP1255; Updated (2006) note: Pfam domain PF03840 Preprotein translocase SecG subunit was identified within CDS. Also,two 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; preprotein translocase subunit SecG complement(218048..218419) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904562 YP_002343679.1 CDS Cj0236c NC_002163.1 218523 219218 R Original (2000) note: Cj0236c, probable integral membrane protein, len: 231 aa similar to members of the UPF0005 family e.g. YCCA_PSEAE (222 aa), fasta scores; opt: 377 z-score: 628.9 E(): 8.9e-28, 37.7% identity in 207 aa overlap. 49.1% identity to HP0920. Contains Pfam match to entry PF01027 UPF0005, Uncharacterized protein family, score 128.30, E-value 1.4e-34; Updated (2006) note: Six probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; integral membrane protein complement(218523..219218) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904563 YP_002343680.1 CDS cynT NC_002163.1 219378 220013 D Original (2000) note: Cj0237, cynT, probable carbonic anyhydrase, len: 211 aa; similar to e.g. CYNT_ECOLI carbonic anhydrase (EC 4.2.1.1) (219 aa), fasta scores; opt: 541 z-score: 776.7 E(): 0, 41.2% identity in 204 aa overlap. 43.5% identity to HP0004. Contains PS00704 and PS00705 Prokaryotic-type carbonic anhydrases signatures 1 and 2, and Pfam match to entry PF00484 Pro_CA, Prokaryotic-type carbonic anhydrases, score 208.10, E-value 2.7e-59; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Central intermediary metabolism - General; PMID:1740425, PMID:14563877; carbonic anyhydrase 219378..220013 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904564 YP_002343681.1 CDS Cj0238 NC_002163.1 220010 221893 D Original (2000) note: Cj0238, probable integral membrane protein, len: 627 aa; similar in C-terminus to many hypothetical proteins, e.g. YB43_METJA MJ1143 (361 aa), fasta scores; opt: 413 z-score: 535.7 E(): 1.4e-22,23.9% identity in 372 aa overlap. 36.3% identity in 608 aa overlap to HP0415. Contains Pfam match to entry PF00924 UPF0003, Uncharacterized protein family UPF0003, score 145.90, E-value 6.9e-40; Updated (2006) 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, so kept within product function. Functional classification - Transport/binding proteins -Other; mechanosensitive ion channel family protein 220010..221893 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904565 YP_002343682.1 CDS Cj0239c NC_002163.1 221916 222887 R Original (2000) note: Cj0239c, nifU protein homolog, len: 323 aa; similar to many e.g. NIFU_AZOVI nifU protein (312 aa), fasta scores; opt: 627 z-score: 910.4 E(): 0, 37.0% identity in 330 aa overlap. 68.8% identity to HP0221. Also similar in C-terminus to Cj1639 (38.2% identity in 76 aa overlap). Contains Pfam match to entry PF01106 NifU-like, NifU-like domain, score 100.40, E-value 3.5e-26; Updated (2006) note: Pfam domains PF01592 NifU-like N terminal domain and PF04324 which is a BFD-like [2Fe-2S] binding domain identified within CDS. Further support given to product function. Functional classification -Conserved hypothetical proteins; PMID:7947754, PMID:10819462; NifU protein complement(221916..222887) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904566 YP_002343683.1 CDS iscS NC_002163.1 222897 224078 R Original (2000) note: Cj0240c, probable aminotransferase (nifS protein homolog), len: 393 aa; similar to many e.g. NIFS_KLEPN nifS protein (397 aa),fasta scores; opt: 1067 z-score: 1533.6 E(): 0, 47.0% identity in 383 aa overlap. 62.8% identity to HP0220. Contains PS00132 Zinc carboxypeptidases, zinc-binding region 1 signature, PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site, and Pfam match to entry PF00266 aminotran_5, Aminotransferases class-V,score 358.80, E-value 5.9e-104; Updated (2006) 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; PMID:10908675, PMID:10781607, PMID:12860127,PMID:3040672, PMID:8464885; cysteine desulfurase complement(222897..224078) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904567 YP_002343684.1 CDS Cj0241c NC_002163.1 224256 224657 R Original (2000) note: Cj0241c, possible iron-binding protein, len: 133 aa; Weak similarity to members of the eukaryotic iron-binding hemerythrin family,e.g. HEMT_LINUN hemerythrin alpha chain (117 aa), fasta scores; opt: 93 z-score: 135.4 E(): 3.1, 27.3% identity in 77 aa overlap. Note that all of the iron-binding residues are conserved. No Hp match. Also similar to Cj1224 (34.7% identity in 118 aa overlap), Cj0072c (40.5% identity in 79 aa overlap) and Cj0045c (30.9% identity in 123 aa overlap); Updated (2006) 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, kept within product function. Functional classification -Transport/binding proteins - Cations; iron-binding protein complement(224256..224657) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904568 YP_002343685.1 CDS Cj0243c NC_002163.1 224794 225960 R Original (2000) note: Cj0243c, unknown, len: 388 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein complement(224794..225960) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904569 YP_002343686.1 CDS rpmI NC_002163.1 226116 226307 D Original (2000) note: Cj0244, rpmI, 50s ribosomal protein L35, len: 63 aa; similar to many e.g. RL35_ECOLI 50s ribosomal protein L35 (64 aa), fasta scores; opt: 133 z-score: 282.3 E(): 1.8e-08. 45.6% identity in 57 aa overlap. 60.7% identity to HP0125; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Ribosomal protein synthesis and modification; PMID:16272117; 50S ribosomal protein L35 226116..226307 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904570 YP_002343687.1 CDS rplT NC_002163.1 226401 226754 D binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit; 50S ribosomal protein L20 226401..226754 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904571 YP_002343688.1 CDS Cj0246c NC_002163.1 226807 227934 R Original (2000) note: Cj0246c, probable MCP-domain signal transduction protein, len: 375 aa; similar in C-terminus to many MCP-domain containing proteins e.g. MCPA_BACSU methyl-accepting chemotaxis protein mcpA (661 aa), fasta scores; opt: 257 z-score: 408.0 E(): 1.8e-15,33.2% identity in 205 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00015 MCPsignal, Methyl-accepting chemotaxis protein (MCP) signaling domain, score 93.20,E-value 3.9e-25; Updated (2006) note: Characterisation within Bacillus subtilis, however, identity score was marginal. kept within product function. Functional classification - Signal transduction; PMID:8188684; MCP-domain signal transduction protein complement(226807..227934) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904572 YP_002343689.1 CDS Cj0247c NC_002163.1 227910 228443 R Original (2000) note: Cj0247c, unknown, len: 177 aa; no Hp match; Updated (2006) note: Similar to proteins from other bacteria. Functional classification - Unknown; hypothetical protein complement(227910..228443) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904573 YP_002343690.1 CDS Cj0248 NC_002163.1 228946 229803 D Original (2000) note: Cj0248, unknown, len: 285 aa; no Hp match; Updated (2006) 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; PMID:16287129, PMID:15066034, PMID:11298288; hypothetical protein 228946..229803 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904574 YP_002343691.1 CDS Cj0249 NC_002163.1 229831 230310 D Original (2000) note: Cj0249, unknown, len: 159 aa; no Hp match. Functional classification - Unknown; hypothetical protein 229831..230310 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904575 YP_002343692.1 CDS Cj0250c NC_002163.1 230279 231589 R Original (2000) note: Cj0250c, probable transmembrane transport protein, len: 436 aa; similar to many members of the sugar transport protein family, e.g. PROP_ECOLI proline/betaine transporter (500 aa), fasta scores; opt: 602 z-score: 791.3 E(): 0, 31.7% identity in 394 aa overlapCIT1_SALTY citrate-proton symport (citrate transporter) (434 aa), fasta scores; opt: 580 z-score: 734.9 E(): 0, 28.0% identity in 396 aa overlap. 50.9% identity to HP0936. Contains Pfam match to entry PF00083 sugar_tr, Sugar (and other) transporters, score 93.10,E-value 5.5e-24; Updated (2006) note: Pfam domain PF07690 Major Facilitator Superfamily was identified within CDS in addition to previous PF0083. Prosite domain PS50850 MFS,Major facilitator superfamily was also identified. Also,twelve 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/binding proteins -Other; MFS transport protein complement(230279..231589) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904576 YP_002343693.1 CDS Cj0251c NC_002163.1 231592 231747 R Original (2000) note: Cj0251c, highly acidic protein, len: 51 aa; 47.9% identity to HP0756. Functional classification - Conserved hypothetical proteins; highly acidic protein complement(231592..231747) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904577 YP_002343694.1 CDS moaC NC_002163.1 231840 232313 D MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis; molybdenum cofactor biosynthesis protein MoaC 231840..232313 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904578 YP_002343695.1 CDS Cj0253 NC_002163.1 232291 232554 D Original (2000) note: Cj0253, unknown, len: 87 aa; 33.8% identity to HP0495. Functional classification -Conserved hypothetical proteins; hypothetical protein 232291..232554 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904579 YP_002343696.1 CDS Cj0254 NC_002163.1 232544 233704 D Original (2000) note: Cj0254, unknown, len: 386 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein 232544..233704 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904580 YP_002343697.1 CDS exoA NC_002163.1 233723 234481 R Original (2000) note: Cj0255c, probable exodeoxyribonuclease, len: 252 aa; similar to many e.g. EXOA_BACSU exodeoxyribonuclease (EC 3.1.11.2)(252 aa),fasta scores; opt: 676 z-score: 868.1 E(): 0, 40.5% identity in 259 aa overlap. 41.1% identity to HP1526. Contains Pfam match to entry PF01260 AP_endonulease1, AP endonucleases family 1, score 282.10, E-value 7.3e-81; Updated (2006) note: Pfam domain PF03372,Endonuclease/Exonuclease/phosphatase 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,restriction/modification, recombination and repair; PMID:10540738; exodeoxyribonuclease complement(233723..234481) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904581 YP_002343698.1 CDS Cj0256 NC_002163.1 234599 236137 D Original (2000) note: Cj0256, probable integral membrane protein, len: 512 aa; similar to hypothetical proteins e.g. YJDB_ECOLI (547 aa), fasta scores; opt: 646 z-score: 1169.8 E(): 0, 38.9% identity in 530 aa overlap. 34.1% identity to HP0022; Updated (2006) note: Pfam domain PF00884 Sulfatase identified within CDS. Also, 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, so kept within product function. Literature search identified paper giving further clues to product function. Functional classification - Misc; PMID:11895937; sulfatase family protein 234599..236137 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904582 YP_002343699.1 CDS dgkA NC_002163.1 236134 236490 D Original (2000) note: Cj0257, dgkA, probale diacylglycerol kinase, len: 118 aa; similar to many e.g. KDGL_ECOLI diacylglycerol kinase (EC 2.7.1.107) (121 aa),fasta scores; opt: 263 z-score: 425.4 E(): 1.9e-16, 41.7% identity in 108 aa overlap. 38.7% identity to HP0700. Contains PS01069 Prokaryotic diacylglycerol kinase signature and Pfam match to entry PF01219 DAGK_prokar,Prokaryotic diacylglycerol kinase, score 114.40, E-value 2.2e-30; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Synthesis and modification of macromolecules -Phospholipids; PMID:2984194, PMID:3015952; diacylglycerol kinase 236134..236490 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904583 YP_002343700.1 CDS Cj0258 NC_002163.1 236487 236732 D Original (2000) note: Cj0258, possible DNA binding protein, len: 81 aa; no Hp match. Contains probable helix-turn-helix motif at aa 35-56 (Score 1128, +3.03 SD); Updated (2006) note: Pfam domain PF01022 Bacterial regulatory protein, 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, so kept within product function. Literature search identified paper with some additional information. Functional classification - Broad regulatory functions; PMID:15231810; ArsR family transcriptional regulator 236487..236732 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904584 YP_002343701.1 CDS pyrC NC_002163.1 236722 237729 D catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis; dihydroorotase 236722..237729 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904585 YP_002343702.1 CDS Cj0260c NC_002163.1 237761 237976 R Original (2000) note: Cj0260c, unknown, len: 71 aa; no Hp match, very hydrophobic; Updated (2006) note: Two probable transmembrane helices identified by TMHMM2.0. Functional classification - Unknown; hypothetical protein complement(237761..237976) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904586 YP_002343703.1 CDS Cj0261c NC_002163.1 238032 238751 R Original (2000) note: Cj0261c, unknown, len: 239 aa; some similarity in N-terminus to YC73_HAEIN hypothetical protein HI1273 (268 aa), fasta scores; opt: 208 z-score: 260.9 E(): 2.8e-07, 29.0% identity in 176 aa overlap. No Hp match; Updated (2006) 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, so kept within product function. Functional classification - Misc; SAM-dependent methyltransferase complement(238032..238751) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904587 YP_002343704.1 CDS Cj0262c NC_002163.1 238832 240829 R Original (2000) note: Cj0262c, probable methyl-accepting chemotaxis signal transduction protein,len: 665 aa; similar to many e.g. TR:O32443 (EMBL:D86947) Pseudomonas aeruginosa chemotactic transducer (629 aa),fasta scores; opt: 283 z-score: 635.0 E(): 4.1e-28, 25.3% identity in 667 aa overlap, and MCP1_ECOLI methyl-accepting chemotaxis protein I (551 aa), fasta scores; opt: 280 z-score: 519.1 E(): 1.2e-21. 29.1% identity in 302 aa overlap. No Hp ortholog. C-terminus contains repeat1, 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,Methyl-accepting chemotaxis protein (MCP) signaling domain, score 110.60, E-value 4.1e-30; Updated (2006) note: Pfam motifs PF05581 Vibrio chemotaxis protein N terminus, 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; PMID:14985343, PMID:15066034; methyl-accepting chemotaxis signal transduction protein complement(238832..240829) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904377 YP_002343705.1 CDS Cj0263 NC_002163.1 241022 241897 D Original (2000) note: Cj0263, probable integral membrane protein, len: 291 aa; similar to hypothetical proteins e.g. YGIE_ECOLI (257 aa), fasta scores; opt: 498 z-score: 952.9 E(): 0, 40.0% identity in 280 aa overlap and GUFA_MYXXA (254 aa), fasta scores; opt: 252 z-score: 298.8 E(): 2.2e-09, 26.3% identity in 285 aa overlap. No Hp match. Contains PS00107 Protein kinases ATP-binding region signature; Updated (2006) 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, not added. Functional classification - Transport/binding proteins -Other; PMID:11790762, PMID:15716430; zinc transporter ZupT 241022..241897 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904588 YP_002343706.1 CDS Cj0264c NC_002163.1 241921 244437 R Original (2000) note: Cj0264c, probable molybdopterin-containing oxidoreductase, len: 838 aa; highly similar to many e.g. DMSA_RHOSH dimethyl sulfoxide reductase precursor (822 aa), fasta scores; opt: 1343 z-score: 2990.1 E(): 0, 46.8% identity in 842 aa overlap,and BISC_ECOLI biotin sulfoxide reductase 1 (739 aa),fasta scores; opt: 1263 z-score: 2612.9 E(): 0, 46.7% identity in 766 aa overlap. 40.9% identity to HP0407. Contains PS00017 ATP/GTP-binding site motif A (P-loop),PS00932 Prokaryotic molybdopterin oxidoreductases signature 3, Pfam match to entry PF00384 molybdopterin,Prokaryotic molybdopterin oxidoreductases, score 110.50,E-value 9.4e-35 and N-terminal signal sequence; Updated (2006) 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 (TMAO) and dimethyl sulfoxide (DMSO) reduction. not added to product function. Functional classification - Misc; PMID:12107136, PMID:11004177, PMID:8645727; molybdopterin containing oxidoreductase complement(241921..244437) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904589 YP_002343707.1 CDS Cj0265c NC_002163.1 244448 245023 R Original (2000) note: Cj0265c, probable cytochrome C-type haem-binding periplasmic protein, len: 191 aa; 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 (366 aa), fasta scores; opt: 208 z-score: 216.4 E(): 8.5e-05, 27.0% identity in 163 aa overlap, and TORC_ECOLI cytochrome C-type protein torC (390 aa), fasta scores; opt: 264 z-score: 216.0 E(): 8.9e-05, 26.4% identity in 178 aa overlap. No Hp match. Contains N-terminal signal sequence and PS00190 Cytochrome c family heme-binding site signature; Updated (2006) note: Characterised within Escherichia coli, however, identity score was marginal. kept within product function. Functional classification - Energy metabolism - Electron transport; PMID:11562502, PMID:11056172; cytochrome C-type haem-binding periplasmic protein complement(244448..245023) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904590 YP_002343708.1 CDS Cj0266c NC_002163.1 245504 246013 R Original (2000) note: Cj0266c, probable integral membrane protein, len: 169 aa; no Hp match; Updated (2006) note: Two probable transmembrane helices identified by TMHMM2.0. Prosite PS00430 TONB_DEPENDENT_REC_1, TonB box, N-terminal also identified. No specific characterisation has been carried out yet. kept within product function. Functional classification - Membranes, lipoproteins and porins; integral membrane protein complement(245504..246013) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904591 YP_002343709.1 CDS Cj0267c NC_002163.1 246013 246543 R Original (2000) note: Cj0267c, probable integral membrane protein, len: 176 aa; no Hp match; Updated (2006) note: Two probable transmembrane helices identified by TMHMM2.0. Functional classification - Membranes, lipoproteins and porins; integral membrane protein complement(246013..246543) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904592 YP_002343710.1 CDS Cj0268c NC_002163.1 246555 247643 R Original (2000) note: Cj0268c, probable transmembrane protein, len: 362 aa; 55.9% identity to HP0248. Contains one transmembrane domain around aa 60; Updated (2006) note: Pfam domain PF01145 SPFH domain / 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, lipoproteins and porins; transmembrane protein complement(246555..247643) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904593 YP_002343711.1 CDS ilvE NC_002163.1 247656 248570 R catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids; branched-chain amino acid aminotransferase complement(247656..248570) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904594 YP_002343712.1 CDS Cj0270 NC_002163.1 248747 248953 D Original (2000) note: Cj0270, possible isomerase,len: 68 aa; some similarity hypothetical proteins and to to e.g. DMPI_PSESP 4-oxalocrotonate tautomerase (EC 5.3.2.-) ( (62 aa), fasta scores; opt: 91 z-score: 182.5 E(): 0.0066, 28.0% identity in 50 aa overlap, and XYLH_PSEPU 4-oxalocrotonate tautomerase (62 aa), fasta scores; opt: 86 z-score: 164.7 E(): 0.064, 25.8% identity in 62 aa overlap. No Hp ortholog, but 37.3% identity to HP0924. Also similar to Cj1255 (37.7% identity in 69 aa overlap); Updated (2006) 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, however, identity scores were marginal. kept within product function. Functional classification - Misc; tautomerase family protein 248747..248953 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904595 YP_002343713.1 CDS Cj0271 NC_002163.1 248950 249405 D Original (2000) note: Cj0271, bacterioferritin comigratory protein homolog, len: 151 aa; similar to many e.g. BCP_ECOLI bacterioferritin comigratory protein (156 aa), fasta scores; opt: 390 z-score: 675.8 E(): 2.2e-30,39.6% identity in 149 aa overlap. 57.0% identity to HP0136. Contains Pfam match to entry PF00578 AhpC-TSA,AhpC/TSA family, score 146.30, E-value 5.4e-40; Updated (2006) note: Some characterisation work within Escherichia coli shows Cj0271 to be peroxiredoxin; bcp. Literature search also identified work within Helicobacter pylori. Product function kept the same. Functional classification - Misc; PMID:15618175, PMID:12576586, PMID:14506251; bacterioferritin comigratory protein 248950..249405 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904596 YP_002343714.1 CDS Cj0272 NC_002163.1 249405 250496 D Original (2000) note: Cj0272, unknown, len: 363 aa; similar to hypothetical proteins e.g. TR:O66919 (EMBL:) Aquifex aeolicus AQ_701 (413 aa), fasta scores; opt: 830 z-score: 1296.8 E(): 0, 48.0% identity in 254 aa overlap. 37.4% identity to HP0100; Updated (2006) note: Pfam PF02677 Uncharacterized BCR was present within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins; hypothetical protein 249405..250496 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904597 YP_002343715.1 CDS fabZ NC_002163.1 250590 251030 D in Pseudomonas aeruginosa this enzyme is a trimer of dimers; essential for membrane formation; performs third step of type II fatty acid biosynthesis; catalyzes dehydration of (3R)-hydroxyacyl-ACP to trans-2-acyl-ACP; (3R)-hydroxymyristoyl-ACP dehydratase 250590..251030 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904598 YP_002343716.1 CDS lpxA NC_002163.1 251030 251821 D catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis; UDP-N-acetylglucosamine acyltransferase 251030..251821 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904599 YP_002343717.1 CDS clpX NC_002163.1 251784 253037 D binds and unfolds substrates as part of the ClpXP protease; ATP-dependent protease ATP-binding subunit ClpX 251784..253037 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904600 YP_002343718.1 CDS mreB NC_002163.1 253049 254089 D functions in MreBCD complex in some organisms; rod shape-determining protein MreB 253049..254089 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904601 YP_002343719.1 CDS mreC NC_002163.1 254079 254828 D in some organisms this protein is a transmembrane protein while in others it is periplasmic; involved in some organisms with other components of the MreBCD complex and with penicillin binding proteins in the periplasm or cell wall; rod shape-determining protein MreC 254079..254828 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904602 YP_002343720.1 CDS carB NC_002163.1 255089 258358 D four CarB-CarA dimers form the carbamoyl phosphate synthetase holoenzyme that catalyzes the production of carbamoyl phosphate; CarB is responsible for the amidotransferase activity; carbamoyl phosphate synthase large subunit 255089..258358 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904603 YP_002343721.1 CDS Cj0280 NC_002163.1 258355 258777 D Original (2000) note: Cj0280, unknown, len: 140 aa; 52.8% identity to HP0918. Functional classification -Conserved hypothetical proteins; hypothetical protein 258355..258777 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904604 YP_002343722.1 CDS tal NC_002163.1 258778 259755 R Important for the balance of metabolites in the pentose-phosphate pathway; transaldolase complement(258778..259755) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904605 YP_002343723.1 CDS serB NC_002163.1 259755 260378 R Original (2000) note: Cj0282c, serB, possible phosphoserine phosphatase, len: 207 aa; similar to C-terminus of SERB_ECOLI phosphoserine phosphatase (EC 3.1.3.3) (322 aa), fasta scores; opt: 361 z-score: 572.4 E(): 1.3e-24, 34.3% identity in 204 aa overlap. 48.8% identity to HP0652; Updated (2006) note: Pfam domain PF00702 haloacid dehalogenase-like hydrolase were identified within CDS. TIGRFAM motif TIGR00338, 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, however, alignment was only partial. kept in product function. Functional classification - Amino acid biosynthesis - Serine family; PMID:2997734; phosphoserine phosphatase complement(259755..260378) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904606 YP_002343724.1 CDS cheW NC_002163.1 260378 260899 R Original (2000) note: Cj0283c, cheW, probable chemotaxis protein, len: 173 aa; similar to many e.g. CHEW_ECOLI purine-binding chemotaxis protein (167 aa),fasta scores; opt: 236 z-score: 304.4 E(): 1.1e-09, 32.4% identity in 139 aa overlap. 51.4% identity to HP0391; Updated (2006) 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; PMID:2068106, PMID:3510184; chemotaxis protein complement(260378..260899) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904607 YP_002343725.1 CDS cheA NC_002163.1 260904 263213 R Original (2000) note: Cj0284c, cheA, probable chemotaxis histidine kinase, len: 769 aa; similar to many e.g. CHEA_ECOLI chemotaxis protein cheA (EC 2.7.3.-) (654 aa), fasta scores; opt: 1022 z-score: 1416.0 E(): 0, 35.7% identity in 658 aa overlap. 64.6% identity to HP0392. Contains Pfam matches to entry PF00072 response_reg,Response regulator receiver domain, score 103.80, E-value 3.4e-27 and to entry PF00512 signal, Signal carboxyl-terminal domain, score -12.30, E-value 0.00013; Updated (2006) note: Characterised within Escherichia coli with marginal identity scores. not added to product function. Functional classification -Chemotaxis and mobility; PMID:1938941, PMID:2068106; chemotaxis histidine kinase complement(260904..263213) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904608 YP_002343726.1 CDS cheV NC_002163.1 263217 264173 R Original (2000) note: Cj0285c, cheV, probable chemotaxis protein cheV, len: 318 aa; similar to e.g. CHEV_BACSU chemotaxis cheV protein (EC 2.7.3.-) (303 aa),fasta scores; opt: 414 z-score: 344.9 E(): 5.9e-12, 28.2% identity in 309 aa overlap. 50.8% identity to HP0393. Contains Pfam match to entry PF00072 response_reg,Response regulator receiver domain, score 50.70, E-value 3.1e-11; Updated (2006) 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; PMID:8169223, PMID:8169224; chemotaxis protein complement(263217..264173) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904609 YP_002343727.1 CDS Cj0286c NC_002163.1 264166 264783 R Original (2000) note: Cj0286c, unknown, len: 205 aa; 28.4% identity to HP0394 (252 aa). Functional classification - Conserved hypothetical proteins; hypothetical protein complement(264166..264783) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904610 YP_002343728.1 CDS greA NC_002163.1 264934 265419 R necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites; arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, 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'terminus; transcription elongation factor GreA complement(264934..265419) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904611 YP_002343729.1 CDS lpxB NC_002163.1 265431 266525 R catalyzes the formation of lipid A disaccharide from UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate, lipid A disaccharide is a precursor of lipid A that anchors LPS to the OM; ipid-A-disaccharide synthase complement(265431..266525) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904612 YP_002343730.1 CDS peb3 NC_002163.1 266622 267374 R Original (2000) note: Cj0289c, peb3, major antigenic peptide PEB3, len: 250 aa; 94.9% identical to TR:G234575, sequenced by direct peptide sequencing; see: Pei at al. J. Biol. Chem. 266:16363-16369 (1991). Also similar to TR:Q57410 (EMBL:U39068) Vibrio cholerae accessory colonization factor acfC (253 aa), fasta scores; opt: 855 z-score: 1301.2 E(): 0, 53.6% identity in 239 aa overlap and TR:P96759 (EMBL:U82533) anm (E. coli 045 attachment and effacement negative mutant) (251 aa), fasta scores; opt: 849 z-score: 824.0 E(): 0, 51.8% identity in 251 aa overlap. No Hp match. Also similar to Cj0778 (peb2) (32.4% identity in 256 aa overlap). Contains N-terminal signal sequence; Updated (2006) note: Characterised within Campylobacter jejuni. Paper identified linking protein to glycoprotein (PMID:12186869). Functional classification -Miscellaneous periplasmic proteins; PMID:1885571, PMID:12186869; major antigenic peptide PEB3 complement(266622..267374) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904613 YP_002343731.1 CDS surE NC_002163.1 269064 269840 D catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate; stationary phase survival protein SurE 269064..269840 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904617 YP_002343732.1 CDS Cj0294 NC_002163.1 269830 270489 D Original (2000) note: Cj0294, unknown, len: 219 aa; similar to members of the hesA/moeB/thiF family, e.g. YGDL_ECOLI (268 aa), fasta scores; opt: 219 z-score: 563.3 E(): 4e-24, 33.5% identity in 254 aa overlap. 48.3% identity to HP0755 (described as moeB). Contains Pfam match to entry PF00899 ThiF_family, ThiF family, score 33.10, E-value 2e-07. Also similar to Cj1046c (33.6% identity in 146 aa overlap); Updated (2006) note: No specific characterisation with acceptable identity scores carried out yet. kept within product function. Functional classification -Misc; MoeB/ThiF family protein 269830..270489 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904618 YP_002343733.1 CDS Cj0295 NC_002163.1 270473 270931 D Original (2000) note: Cj0295, possible acetyltransferase, len: 152 aa; similar to hypothetical proteins e.g. YAFP_ECOLI (150 aa), fasta scores; opt: 246 z-score: 340.4 E(): 1.1e-11, 27.8% identity in 144 aa overlap. No Hp match. Contains Pfam match to entry PF00583 Acetyltransf, Acetyltransferase (GNAT) family, score 20.20, E-value 0.011; Updated (2006) note: Some characterisation within Escherichia coli with marginal identity score. kept within product function. Functional classification -Misc; acetyltransferase 270473..270931 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904619 YP_002343734.1 CDS panD NC_002163.1 271041 271421 R 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 (vitamin B5); aspartate alpha-decarboxylase complement(271041..271421) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904620 YP_002343735.1 CDS panC NC_002163.1 271418 272266 R catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine; pantoate--beta-alanine ligase complement(271418..272266) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904621 YP_002343736.1 CDS panB NC_002163.1 272277 273101 R catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate; 3-methyl-2-oxobutanoate hydroxymethyltransferase complement(272277..273101) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904622 YP_002343737.1 CDS Cj0299 NC_002163.1 273321 274094 D Original (2000) note: Cj0299, possible periplasmic beta-lactamase, len: 257 aa; similar to members of the class-D beta-lactamase family e.g. BLL1_PSEAE BETA-LACTAMASE LCR-1 PRECURSOR (EC 3.5.2.6) (Pseudomonas aeruginosa plasmid PMG76) (260 aa), fasta scores; opt: 423 z-score: 305.2 E(): 9.6e-10, 33.7% identity in 255 aa overlap. No Hp match. Contains N-terminal signal sequence; Updated (2006) note: Some characterisation work within Pseudomonas aeruginosa and Escherichia coli with marginal identity scores. kept within product function. Functional classification - Antibiotic resistance; PMID:11188693, PMID:7574536; periplasmic beta-lactamase 273321..274094 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904623 YP_002343738.1 CDS modC NC_002163.1 274179 275063 R Original (2000) note: Cj0300c, modC, probable molybdenum transport ATP-binding protein, len: 294 aa; similar to many ABC-transporter ATP binding proteins, and to MODC_ECOLI molybdenum transport ATP-binding protein (352 aa), fasta scores; opt: 487 z-score: 700.9 E(): 8.7e-32, 34.8% identity in 270 aa overlap. Identification as modC is based on presence of probable molybdenum-specific permease and periplasmic binding proteins upstream. 46.8% identity to HP0475. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00211 ABC transporters family signature and Pfam match to entry PF00005 ABC_tran, ABC transporters, score 214.40, E-value 1.7e-60; Updated (2006) note: Characterised more than once within Escherichia coli with marginal identity scores. kept within product function. Functional classification - Transport/binding proteins - Anions; PMID:2188958, PMID:7665461, PMID:7665460; molybdenum transport ATP-binding protein complement(274179..275063) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904624 YP_002343739.1 CDS modB NC_002163.1 275060 275734 R Original (2000) note: Cj0301c, modB, probable molybdenum transport system permease, len: 224 aa; similar to e.g. MODC_AZOVI molybdenum transport system permease (226 aa), fasta scores; opt: 562 z-score: 889.7 E(): 0, 43.3% identity in 210 aa overlap and MODB_ECOLI (229 aa), fasta scores; opt: 390 z-score: 537.4 E(): 1.1e-22, 32.8% identity in 183 aa overlap. 55.2% identity to HP0474. Contains PS00017 ATP/GTP-binding site motif A (P-loop) and Pfam match to entry PF00528 BPD_transp, Binding-protein-dependent transport systems inner membrane component, score 43.10, E-value 6.1e-09; Updated (2006) note: Characterised in many e.g. Rhodobacter capsulatus and Azotobacter vinelandii with acceptable identity scores. kept within product function. Functional classification - Transport/binding proteins - Anions; PMID:8384683, PMID:8491722; molybdenum transport system permease complement(275060..275734) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904625 YP_002343740.1 CDS Cj0302c NC_002163.1 275727 276128 R Original (2000) note: Cj0302c, unknonw, len: 133 aa; no Hp match; Updated (2006) note: Pfam domain PF03459 TOBE domain identified within CDS. TOBE (Transport-associated OB) 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, however, identity scores were marginal and full length sequence alignment was not achieved. Functional classification - Miscellaneous periplasmic proteins; PMID:3540853, PMID:2820842; molybdenum-pterin binding protein complement(275727..276128) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904626 YP_002343741.1 CDS modA NC_002163.1 276125 276874 R Original (2000) note: Cj0303c, modA, probable molybdate-binding lipoprotein, len: 249 aa; similar to e.g. MODA_RHOCA molybdate-binding periplasmic protein precursor (252 aa), fasta scores; opt: 354 z-score: 449.0 E(): 9.4e-18, 30.8% identity in 224 aa overlap, and MODA_ECOLI (257 aa), fasta scores; opt: 220 z-score: 245.4 E(): 2.1e-06, 25.0% identity in 232 aa overlap. 42.3% identity to HP0473. Contains probable N-terminal signal sequence with appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site; Updated (2006) 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, Azotobacter vinelandii and Escherichia coli. Identity scores were marginal and sequence alignment was not full length. kept within product function. Functional classification - Transport/binding proteins -Anions; PMID:8491722, PMID:8384683, PMID:8564363; molybdate-binding lipoprotein complement(276125..276874) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904627 YP_002343742.1 CDS bioC NC_002163.1 276925 277611 R Original (2000) note: Cj0304c, bioC, possible biotin synthesis protein, len: 228 aa; similar to BIOC_HAEIN biotin synthesis protein bioC (260 aa), fasta scores; opt: 342 z-score: 595.7 E(): 6.4e-26,34.0% identity in 238 aa overlap. Also some similarity to BIOC_ECOLI (251 aa), wublastp scores; E= 0.00028, 24% identity in 193 aa overlap. No Hp match; Updated (2006) note: Some characterisation within Bacillus subtilis and Escherichia coli, however, identity scores were unnacceptable. kept within product function. Functional classification - Biosynthesis of cofactors, prosthetic groups and carriers - Biotin; PMID:3058702, PMID:8763940; biotin synthesis protein complement(276925..277611) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904628 YP_002343743.1 CDS Cj0305c NC_002163.1 277608 278219 R Original (2000) note: Cj0305c, unknown, len: 203 aa; similar to a hypothetical protein from H. infuenzae YF52_HAEIN HI1552 (215 aa), fasta scores; opt: 297 z-score: 372.7 E(): 1.7e-13, 29.8% identity in 215 aa overlap. No Hp match; Updated (2006) note: Pfam PF04301, Protein of unknown function (DUF452) was present within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins; hypothetical protein complement(277608..278219) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904629 YP_002343744.1 CDS bioF NC_002163.1 278216 279358 R Original (2000) note: Cj0306c, bioF, probable 8-amino-7-oxononanoate synthase, len: 380 aa; similar to many e.g. BIOF_ECOLI 8-amino-7-oxononanoate synthase (EC 2.3.1.47) (384 aa), fasta scores; opt: 525 z-score: 550.3 E(): 2.1e-23, 28.9% identity in 387 aa overlap. 29.0% identity to HP0598. Contains PS00599 Aminotransferases class-II pyridoxal-phosphate attachment site and Pfam match to entry PF00222 aminotran_2, Aminotransferases class-II, score 196.30, E-value 4.7e-55; Updated (2006) note: Characterised within Escherichia coli with marginal identity scores. not added to product function. Functional classification -Biosynthesis of cofactors, prosthetic groups and carriers - Biotin; PMID:9813126, PMID:1575677, PMID:1575677,PMID:3058702; 8-amino-7-oxononanoate synthase complement(278216..279358) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904630 YP_002343745.1 CDS bioA NC_002163.1 279426 280709 D catalyzes the formation of S-adenosyl-4-methylthionine-2-oxobutanoate and 7,8-diaminononanoate from S-adenosyl-L-methionine and 8-amino-7-oxononanoate; adenosylmethionine-8-amino-7-oxononanoate aminotransferase 279426..280709 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904631 YP_002343746.1 CDS bioD NC_002163.1 280696 281301 R Original (2000) note: Cj0308c, bioD, possible dethiobiotin synthetase, len: 201 aa; some similarity to many e.g. BIOD_BACSH dethiobiotin synthetase (EC 6.3.3.3) (234 aa), fasta scores; opt: 206 z-score: 260.4 E(): 3e-07, 29.8% identity in 215 aa overlap. 31.8% identity in 66 aa overlap to HP0029; Updated (2006) note: Some characterisation within Bacillus sphaericus, however, identity score was marginal. kept within product function. Functional classification - Biosynthesis of cofactors, prosthetic groups and carriers - Biotin; PMID:2110099, PMID:3058702, PMID:10455485; dethiobiotin synthetase complement(280696..281301) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904632 YP_002343747.1 CDS Cj0309c NC_002163.1 281311 281625 R Original (2000) note: Cj0309c, probable efflux protein, len: 104 aa; similar to many membrane protein of known and unknown function e.g. TR:O34690 (EMBL:AJ002571) Bacillus subtilis YKKD (105 aa), fasta scores; opt: 303 z-score: 547.1 E(): 3.2e-23, 44.2% identity in 104 aa overlap, and EBR_STAAU ethidium bromide resistance protein (multidrug resistance protein) (107 aa), fasta scores; opt: 187 z-score: 272.5 E(): 6.4e-08, 27.2% identity in 103 aa overlap. No Hp match. Also similar to upstream CDS Cj0310c (32.4% identity in 105 aa overlap), and to Cj1174 (28.7% identity in 94 aa overlap) and Cj1173 (24.7% identity in 93 aa overlap). Contains Pfam match to entry PF00893 DUF7, Integral membrane protein, score 109.20,E-value 7.7e-29, and four possible transmembrane domains; Updated (2006) note: Pfam domain PF00893 Small Multidrug Resistance (Smr) 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/analogue sensitivity; PMID:10735877, PMID:11566977; efflux protein complement(281311..281625) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904633 YP_002343748.1 CDS Cj0310c NC_002163.1 281629 281967 R Original (2000) note: Cj0310c, possible efflux protein, len: 104 aa; similar to many membrane proteins of known and unknown function e.g. YKKC_BACSU (112 aa), fasta scores; opt: 273 z-score: 458.2 E(): 2.9e-18, 40.8% identity in 103 aa overlap, and EBR_STAAU ethidium bromide resistance protein (107 aa), fasta scores; opt: 135 z-score: 198.9 E(): 0.00088, 27.4% identity in 84 aa overlap. No Hp match. Also similar to downstream CDS Cj0309c (32.4% identity in 105 aa overlap) and to Cj1173 (27.1% identity in 107 aa overlap). Contains Pfam match to entry PF00893 DUF7, Integral membrane protein, score 51.40, E-value 2e-11, and four possible transmembrane domains; Updated (2006) note: Pfam domain PF00893 Small Multidrug Resistance (Smr family) 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/analogue sensitivity; PMID:10735877, PMID:11948170; efflux protein complement(281629..281967) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904634 YP_002343749.1 CDS Cj0311 NC_002163.1 282101 282637 D the Ctc family of proteins consists of two types, 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; 50S ribosomal protein L25 282101..282637 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904635 YP_002343750.1 CDS pth NC_002163.1 282634 283179 D Enables the recycling of peptidyl-tRNAs produced at termination of translation; peptidyl-tRNA hydrolase 282634..283179 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904636 YP_002343751.1 CDS Cj0313 NC_002163.1 283181 284239 D Original (2000) note: Cj0313, probable integral membrane protein, len: 352 aa; 35.9% identity to HP1498; Updated (2006) note: Pfam domains PF03739 Predicted permease YjgP/YjgQ 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, lipoproteins and porins; integral membrane protein 283181..284239 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904637 YP_002343752.1 CDS lysA NC_002163.1 284283 285491 D Original (2000) note: Cj0314, lysA, probable diaminopimelate decarboxylase, len: 402 aa; highly similar to mnay e.g. DCDA_PSEAE diaminopimelate decarboxylase (EC 4.1.1.20) (415 aa), fasta scores; opt: 1077 z-score: 968.8 E(): 0, 44.7% identity in 394 aa overlap. 60.4% identity to HP0290. Contains Pfam match to entry PF00278 Orn_DAP_Arg_deC, Pyridoxal-dependent decarboxylase, score 381.60, E-value 2.3e-113; Updated (2006) note: Characterised within Pseudomonas aeruginosa with acceptable identity score. not added to product function. Functional classification - Amino acid biosynthesis - Aspartate family; PMID:3143046; diaminopimelate decarboxylase 284283..285491 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904638 YP_002343753.1 CDS Cj0315 NC_002163.1 285493 286260 D Original (2000) note: Cj0315, unknown, len: 255 aa; similar to the hypothetical proteins TR:O59622 (EMBL:AB009530) Pyrococcus horikoshii PHBR011 (263 aa),fasta scores; opt: 185 z-score: 375.5 E(): 1.2e-13, 28.1% identity in 267 aa overlapNAGD_ECOLI nagD protein (250 aa), fasta scores; opt: 259 z-score: 266.1 E(): 1.4e-07,26.0% identity in 250 aa overlap. No Hp match; Updated (2006) note: Pfam domains PF00702 haloacid dehalogenase-like hydrolase, PF02142 MGS-like domain and PF03558 TBSV core protein P21/P22 were identified with separate Pfam search. This family is a member of the HAD superfamily which includes L-2-haloacid dehalogenase,epoxide 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; HAD-superfamily hydrolase 285493..286260 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904639 YP_002343754.1 CDS pheA NC_002163.1 286248 287321 D Original (2000) note: Cj0316, pheA, probable chorismate mutase/prephenate dehydratase, len: 357 aa; similar to many e.g. PHEA_ECOLI chorismate mutase (EC 5.4.99.5)/prephenate dehydratase (EC 4.2.1.51) (386 aa),fasta scores; opt: 482 z-score: 733.8 E(): 0, 33.1% identity in 366 aa overlap. Similar in N-term to possible truncated pheA in Hp; HP0291 hypothetical protein (96 aa) 35.8% identity in 81 aa overlap. Contains PS00857 and PS00858 Prephenate dehydratase signatures 1 and 2, and Pfam match to entry PF00800 PDT, Prephenate dehydratase,score 268.20, E-value 1.1e-76; Updated (2006) 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; PMID:9497350; chorismate mutase/prephenate dehydratase 286248..287321 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904640 YP_002343755.1 CDS hisC NC_002163.1 287311 288405 D catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis; histidinol-phosphate aminotransferase 287311..288405 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904641 YP_002343756.1 CDS fliF NC_002163.1 288457 290139 D the MS-ring anchors the flagellum to the cytoplasmic membrane; part of the flagellar basal body which consists of four rings L, P, S, and M mounted on a central rod; flagellar MS-ring protein 288457..290139 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904642 YP_002343757.1 CDS fliG NC_002163.1 290139 291167 D One of three proteins involved in switching the direction of the flagellar rotation; flagellar motor switch protein G 290139..291167 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904643 YP_002343758.1 CDS fliH NC_002163.1 291175 292005 D binds to and inhibits the function of flagella specific ATPase FliI; flagellar assembly protein H 291175..292005 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904644 YP_002343759.1 CDS dxs NC_002163.1 291998 293845 D catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate; 1-deoxy-D-xylulose-5-phosphate synthase 291998..293845 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904645 YP_002343760.1 CDS perR NC_002163.1 293931 294341 D Original (2000) note: Cj0322, perR, regulator of peroxide stress regulon, len: 136 aa; similar to many members of the furR family e.g. FUR3_BACSU ferric uptake regulation protein homolog 3 (145 aa), fasta scores; opt: 258 z-score: 379.6 E(): 6.9e-14, 32.6% identity in 135 aa overlap. No Hp match; Updated (2006) 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; PMID:9701813, PMID:12100544; peroxide stress regulator 293931..294341 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904646 YP_002343761.1 CDS Cj0323 NC_002163.1 294387 295583 D Original (2000) note: Cj0323, unknown, len: 398 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein 294387..295583 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904647 YP_002343762.1 CDS ubiE NC_002163.1 295586 296293 D Catalyzes the carbon methylation reaction in the biosynthesis of ubiquinone; ubiquinone/menaquinone biosynthesis methyltransferase 295586..296293 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904648 YP_002343763.1 CDS xseA NC_002163.1 296290 297453 D bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides; exodeoxyribonuclease VII large subunit 296290..297453 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904649 YP_002343764.1 CDS serC NC_002163.1 297463 298539 D catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate; required both in major phosphorylated pathway of serine biosynthesis and in the biosynthesis of pyridoxine; phosphoserine aminotransferase 297463..298539 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904650 YP_002343765.1 CDS Cj0327 NC_002163.1 298536 298886 D Original (2000) note: Cj0327, unknown, len: 116 aa; similar to hypothetical proteins e.g. YABJ_BACSU (125 aa),fasta scores; opt: 211 z-score: 261.9 E(): 2.5e-07, 33.0% identity in 109 aa overlap, and to e.g. UK14_HUMAN 14.5 kd translational inhibitor protein (137 aa), fasta scores; opt: 173 z-score: 249.5 E(): 1.2e-06, 29.2% identity in 106 aa overlap. No Hp ortholog. Also similar to Cj1388 (33.3% identity in 96 aa overlap). Contains Pfam match to entry PF01042 DUF10, Domain of unknown function, score 69.30, E-value 8.4e-17; Updated (2006) note: Pfam domain PF01042 Endoribonuclease L-PSP identified within CDS (previously uncharacterised). 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; endoribonuclease L-PSP family protein 298536..298886 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904651 YP_002343766.1 CDS fabH NC_002163.1 298883 299857 R FabH; beta-ketoacyl-acyl carrier protein synthase III; catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation; differs from 3-oxoacyl-(acyl carrier protein) synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs; 3-oxoacyl-ACP synthase complement(298883..299857) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904652 YP_002343767.1 CDS plsX NC_002163.1 299850 300836 R involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY; glycerol-3-phosphate acyltransferase PlsX complement(299850..300836) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904653 YP_002343768.1 CDS rpmF NC_002163.1 300842 300988 R some L32 proteins have zinc finger motifs consisting of CXXC while others do not; 50S ribosomal protein L32 complement(300842..300988) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904654 YP_002343769.1 CDS Cj0331c NC_002163.1 301012 301365 R Original (2000) note: Cj0331c, unknown, len: 117 aa; 34.7% identity to HP0199. Functional classification -Conserved hypothetical proteins; hypothetical protein complement(301012..301365) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904655 YP_002343770.1 CDS ndk NC_002163.1 301366 301779 R catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate; nucleoside diphosphate kinase complement(301366..301779) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904656 YP_002343771.1 CDS fdxA NC_002163.1 301892 302176 R Original (2000) note: Cj0333c, fdxA, probable ferredoxin, len: 94 aa; similar to many e.g. FER_CLOTM ferredoxin (55 aa), fasta scores; opt: 142 z-score: 311.2 E(): 4.5e-10, 45.8% identity in 59 aa overlap. No Hp ortholog. Also similar to Cj0354c (38.8% identity in 67 aa overlap). Contains PS00198 4Fe-4S ferredoxins, iron-sulfur binding region signature and Pfam match to entry PF00037 fer4, 4Fe-4S ferredoxins and related iron-sulfur cluster binding domains., score 51.80, E-value 8.8e-14; Updated (2006) note: Similar to many e.g. Clostridium sp. with acceptable identity scores. not added to product function. Functional classification -Energy metabolism - Electron transport; PMID:4433520; ferredoxin complement(301892..302176) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904657 YP_002343772.1 CDS ahpC NC_002163.1 302383 302979 D Original (2000) note: Cj0334, ahpC, probable alkyl hydroperoxide reductase, len: 198 aa; highly simlar to e.g. TDX1_HUMAN thioredoxin peroxidase 1 (198 aa), fasta scores; opt: 615 z-score: 915.3 E(): 0, 46.1% identity in 193 aa overlap, and to e.g. AHPC_ECOLI P26427 alkyl hydroperoxide reductase C22 protein (EC 1.6.4.-) (186 aa),wublastp scores E= 8.9e-23, 34% identity in 149 aa overlap. 67.7% identity to HP1563 (Hp 26 kD antigen). Contains Pfam match to entry PF00578 AhpC-TSA, AhpC/TSA family, score 208.20, E-value 1.2e-58; Updated (2006) note: Characterised within Campylobacter jejuni. not added to product function. Literature search identified paper linking protein to glycoprotein (PMID:12186869). Functional classification - Detoxification; PMID:10438747, PMID:10515927, PMID:12186869; alkyl hydroperoxide reductase 302383..302979 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904658 YP_002343773.1 CDS flhB NC_002163.1 303098 304186 D membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export; flagellar biosynthesis protein FlhB 303098..304186 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904659 YP_002343774.1 CDS motB NC_002163.1 304192 304935 R with MotA forms the ion channels that couple flagellar rotation to proton/sodium motive force across the membrane and forms the stator elements of the rotary flagellar machine; flagellar motor protein MotB complement(304192..304935) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904660 YP_002343775.1 CDS motA NC_002163.1 304938 305714 R With MotB forms the ion channels that couple flagellar rotation to proton/sodium motive force across the membrane and forms the stator elements of the rotary flagellar machine; flagellar motor protein MotA complement(304938..305714) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904661 YP_002343776.1 CDS polA NC_002163.1 305730 308369 R has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair; DNA polymerase I complement(305730..308369) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904662 YP_002343777.1 CDS Cj0339 NC_002163.1 308533 309894 D Original (2000) note: Cj0339, probable transmembrane transport protein, len: 453 aa; similar to e.g. YDFJ_ECOLI hypothetical metabolite transport protein (427 aa), fasta scores; opt: 1214 z-score: 1428.6 E(): 0,42.5% identity in 416 aa overlap, and SHIA_ECOLI shikimate transporter (438 aa), fasta scores; opt: 876 z-score: 1104.0 E(): 0, 32.3% identity in 421 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00083 sugar_tr,Sugar (and other) transporters, score 123.20, E-value 4.9e-33; Updated (2006) note: Ten probable transmembrace helices identified by TMHMM2.0 within CDS. Pfam domain PF07690 Major Facilitator Superfamily protein identified within CDS. Prosite PS50850 MFS, 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/binding proteins - Other; PMID:15919996; MFS transport protein 308533..309894 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904663 YP_002343778.1 CDS Cj0340 NC_002163.1 309891 310898 D Original (2000) note: Cj0340, possible nucleoside hydrolase, len: 335 aa; similar to hypothetical proteins e.g. YAAF_ECOLI (304 aa), fasta scores; opt: 252 z-score: 377.2 E(): 9.4e-14, 25.9% identity in 309 aa overlap, and to the eukaryotic IUNH_CRIFA inosine-uridine preferring nucleoside hydrolase (314 aa), fasta scores; opt: 261 z-score: 363.4 E(): 5.5e-13, 25.3% identity in 296 aa overlap. No Hp match. Contains Pfam match to entry PF01156 IU_nuc_hydro, Inosine-uridine preferring nucleoside hydrolase, score -11.20, E-value 4.8e-12; Updated (2006) note: No specific characterisation with acceptable identity score has been carried out yet. kept within product function. Functional classification - Salvage of nucleosides and nucleotides; PMID:10409664; nucleoside hydrolase 309891..310898 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904664 YP_002343779.1 CDS Cj0341c NC_002163.1 310854 311297 R Original (2000) note: Cj0341c, possible integral membrane protein, len: 147 aa; similar to hypothetical membrane proteins e.g. Y489_HAEIN HI0489 (157 aa), fasta scores; opt: 252 z-score: 350.5 E(): 2.9e-12, 34.0% identity in 159 aa overlap. No Hp match; Updated (2006) note: Four probable transmembrace helices identified by TMHMM2.0 within CDS. Functional classification - Membranes, lipoproteins and porins; integral membrane protein complement(310854..311297) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904665 YP_002343780.1 CDS uvrA NC_002163.1 311302 314127 R 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, the uvrA molecules dissociate; excinuclease ABC subunit A complement(311302..314127) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904666 YP_002343781.1 CDS Cj0343c NC_002163.1 314200 314985 R Original (2000) note: Cj0343c, probable integral membrane protein, len: 261 aa; similar to many hypothetical membrane proteins e.g. Y441_METJA MJ0441 (267 aa), fasta scores; opt: 152 z-score: 301.8 E(): 1.5e-09,30.7% identity in 257 aa overlap. 45.1% identity to HP0677 and 44.0% identity to HP0226; Updated (2006) note: Nine probable transmembrace helices identified by TMHMM2.0 within CDS. Pfam PF01925 Domain of unknown function (DUF81) protein identified within CDS. Further support given to product function. Functional classification - Membranes, lipoproteins and porins; integral membrane protein complement(314200..314985) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904667 YP_002343782.1 CDS Cj0344 NC_002163.1 315108 315233 D Original (2000) note: Cj0344, unknown, len: 41 aa; no Hp match. Functional classification - Unknown; hypothetical protein 315108..315233 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904668 YP_002343783.1 CDS trpE NC_002163.1 315398 316648 D Original (2000) note: Cj0345, trpE, possible anthranilate synthase component I, len: 416 aa; similar in C-terminal half to many e.g. TRPE_CLOTM anthranilate synthase component I (EC 4.1.3.27) (494 aa), fasta scores; opt: 784 z-score: 1209.9 E(): 0, 47.0% identity in 281 aa overlap. 35.6% identity in 365 aa overlap to HP1282. Contains Pfam match to entry PF00425 chorismate_bind,chorismate binding enzyme, score 309.50, E-value 3.9e-89; Updated (2006) note: Characterised within Clostridium thermocellum with acceptable identity score,however, sequence alignment was only partial. Thus, kept within product function. Functional classification - Amino acid biosynthesis - Aromatic amino acid family; PMID:2732211, PMID:789357; anthranilate synthase component I 315398..316648 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904669 YP_002343784.1 CDS trpD NC_002163.1 316645 318246 D Original (2000) note: Cj0346, trpD (trpGD),probable anthranilate synthase component II, len: 533 aa; (contains glutamine amidotransferase and anthranilate phosphoribosyltransferase) similar to many e.g. TRPG_ECOLI anthranilate synthase component II (EC 4.1.3.27) (530 aa),fasta scores; opt: 866 z-score: 781.3 E(): 0, 32.6% identity in 528 aa overlap. N-terminus has 34.6% identity to HP1281, C-terminus is 33.2% identity to HP1280. Contains PS00442 Glutamine amidotransferases class-I active site and Pfam matches to entry PF00117 GATase,Glutamine amidotransferases class-I, score 252.00, E-value 8.4e-72 and to entry PF00591 Glycos_transf_3, glycosyl transferase family, score 138.60, E-value 1.1e-37; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Amino acid biosynthesis - Aromatic amino acid family; PMID:6283099, PMID:4594441, PMID:789357; anthranilate synthase component II 316645..318246 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904670 YP_002343785.1 CDS trpF NC_002163.1 318233 318832 D Original (2000) note: Cj0347, trpF, probable N-(5'-phosphoribosyl)anthranilate isomerase, len: 199 aa; similar to many trpF e.g. TRPF_LACCA N-(5'-phosphoribosyl)anthranilate isomerase (199 aa) (EC 5.3.1.24), fasta scores; opt: 271 z-score: 352.4 E(): 2.3e-12, 31.0% identity in 200 aa overlap, and to the trpF domain of many trpC proteins e.g. TRPC_SALTY indole-3-glycerol phosphate synthase, fasta scores; opt: 307 z-score: 394.5 E(): 1e-14, 30.8% identity in 201 aa overlap. 38.2% identity to C-terminus of HP1279 (trpC) Conatains Pfam match to entry PF00697 PRAI,N-(5'phosphoribosyl)antranilate (PRA) isomerase, score 102.30, E-value 9.5e-27; Updated (2006) 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; PMID:2299982, PMID:2184433, PMID:789357; N-(5'-phosphoribosyl)anthranilate isomerase 318233..318832 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904671 YP_002343786.1 CDS trpB NC_002163.1 318829 320007 D catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate; tryptophan synthase subunit beta 318829..320007 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904672 YP_002343787.1 CDS trpA NC_002163.1 320000 320749 D catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis; tryptophan synthase subunit alpha 320000..320749 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904673 YP_002343788.1 CDS Cj0350 NC_002163.1 320820 321242 D Original (2000) note: Cj0350, unknown, len: 140 aa; no Hp match. . Functional classification - Unknown; hypothetical protein 320820..321242 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904674 YP_002343789.1 CDS fliN NC_002163.1 321242 321550 D One of three proteins involved in switching the direction of the flagellar rotation; flagellar motor switch protein 321242..321550 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904675 YP_002343790.1 CDS Cj0352 NC_002163.1 321551 322348 D Original (2000) note: Cj0352, probable transmembrane protein, len: 265 aa; 99.6% identity to TR:O32371 (EMBL:AJ000400). No Hp match. Contains probable N-terminal signal sequence and transmembrane domain around aa 160; Updated (2006) 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, lipoproteins and porins; PMID:15817382, PMID:9894591; transmembrane protein 321551..322348 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904676 YP_002343791.1 CDS Cj0353c NC_002163.1 322345 323805 R Original (2000) note: Cj0353c, probable phosphatase, len: 486 aa; similar to e.g. GPPA_ECOLI guanosine-5'-triphosphate,3'-diphosphate pyrophosphatase (EC 3.6.1.40) (494 aa), fasta scores; opt: 368 z-score: 272.7 E(): 6.2e-08, 25.8% identity in 480 aa overlap, and to PPX_ECOLI EXOPOLYPHOSPHATASE (EC 3.6.1.11) (512 aa),fasta scores; opt: 340 z-score: 350.9 E(): 2.7e-12, 23.8% identity in 441 aa overlap. 41.0% identity to HP0278; Updated (2006) note: Pfam domain PF02541 Ppx/GppA 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; PMID:8394006; phosphatase complement(322345..323805) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904677 YP_002343792.1 CDS fdxB NC_002163.1 323805 324050 R Original (2000) note: Cj0354c, fdxB, probable ferredoxin, len: 81 aa; similar to many e.g. FER_CHRVI ferredoxin (82 aa), fasta scores; opt: 282 z-score: 445.5 E(): 1.5e-17, 45.3% identity in 75 aa overlap. 58.4% identity to HP0277. Also similar to Cj0333c (fdx); 38.8% identity in 67 aa overlap. Contains PS00198 4Fe-4S ferredoxins, iron-sulfur binding region signature and Pfam match to entry PF00037 fer4, 4Fe-4S ferredoxins and related iron-sulfur cluster binding domains., score 39.00,E-value 4.8e-10; Updated (2006) note: Characterised within Chromatium vinosum with acceptable identity scores. Appropriate motifs also present. not added to product function. Functional classification - Energy metabolism - Electron transport; PMID:8765743; ferredoxin complement(323805..324050) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904678 YP_002343793.1 CDS Cj0355c NC_002163.1 324163 324834 R Original (2000) note: Cj0355c, probable two-component regulator, len: 223 aa; similar to many e.g. CZCR_ALCEU transcriptional activator protein CZCR (225 aa), fasta scores; opt: 375 z-score: 570.8 E(): 1.5e-24,31.7% identity in 218 aa overlap. 59.9% identity to HP1043. Contains Pfam match to entry PF00072 response_reg,Response regulator receiver domain, score 70.70, E-value 3.1e-17 and Pfam match to entry PF00486 trans_reg_C,Transcriptional regulatory protein, C terminal, score 56.60, E-value 1.5e-15; Updated (2006) 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 (PMID:15901688). Functional classification - Signal transduction; PMID:9044283, PMID:15901688; two-component regulator complement(324163..324834) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904679 YP_002343794.1 CDS folB NC_002163.1 324913 325230 R Original (2000) note: Cj0356c, unknown, len: 105 aa; 31.0% identity to HP1510; Updated (2006) note: Pfam domain PF02152 FolB Dihydroneopterin aldolase was identified within CDS. This enzyme catalyses the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-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; dihydroneopterin aldolase complement(324913..325230) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904680 YP_002343795.1 CDS Cj0357c NC_002163.1 325215 325823 R involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsX; glycerol-3-phosphate acyltransferase PlsY complement(325215..325823) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904681 YP_002343796.1 CDS Cj0358 NC_002163.1 326024 327049 D Original (2000) note: Cj0358, probable cytochrome C551 peroxidase, len: 341 aa; similar to e.g. CCPR_PSEAE cytochrome C551 peroxidase precursor (EC 1.11.1.5) (346 aa), fasta scores; opt: 281 z-score: 1028.0 E(): 0, 48.9% identity in 313 aa overlap. 58.5% identity to HP1461. Also similar to Cj0020c (45.4% identity in 273 aa overlap). Contains 2x PS00190 Cytochrome c family heme-binding site signature and probable N-terminal signal sequence; Updated (2006) 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,however, only partial sequence alignment was achieved. kept within product function. Functional classification - Detoxification; PMID:7781769, PMID:8591033; cytochrome C551 peroxidase 326024..327049 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904682 YP_002343797.1 CDS glmM NC_002163.1 327143 328480 D catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate; phosphoglucosamine mutase 327143..328480 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904683 YP_002343798.1 CDS lspA NC_002163.1 328473 328943 D lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis; lipoprotein signal peptidase 328473..328943 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904684 YP_002343799.1 CDS Cj0362 NC_002163.1 328927 329379 D Original (2000) note: Cj0362, probable integral membrane protein, len: 150 aa; similar to hypothetical proteins e.g. TR:Q53231 (EMBL:L76097) from Rhodobacter sphaeroides (154 aa), fasta scores; opt: 301 z-score: 419.6 E(): 4.1e-16, 34.2% identity in 149 aa overlap. 47.6% identity to HP1484; Updated (2006) note: Four probable transmembrace helices identified by TMHMM2.0 within CDS. Pfam domain PF03653 Uncharacterised protein family (UPF0093) identified within CDS. Further support given to product function. Functional classification - Membranes,lipoproteins and porins; integral membrane protein 328927..329379 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904685 YP_002343800.1 CDS Cj0363c NC_002163.1 329376 330722 R catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase complement(329376..330722) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904686 YP_002343801.1 CDS Cj0364 NC_002163.1 330851 331102 D Original (2000) note: Cj0364, unknown, len: 83 aa; no Hp match; Updated (2006) note: Literature search identified paper giving further clues to product function. Functional classification - Unknown; hypothetical protein 330851..331102 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904687 YP_002343802.1 CDS cmeC NC_002163.1 331125 332603 R Original (2000) note: Cj0365c, possible outer membrane channel protein, len: 492 aa; similar to members of the nodT/fusA family e.g. TR:O31101 (EMBL:AF029405) Pseudomonas putida outer membrane channel protein SRPC (470 aa), fasta scores; opt: 645 z-score: 834.4 E(): 0,29.2% identity in 465 aa overlap. and TR:Q51006 (EMBL:X95635) Neisseria gonorrhoeae mtrE gene (467 aa,fasta scores; opt: 663 z-score: 829.8 E(): 0, 31.1% identity in 476 aa overlap. No Hp match. Also some similarity to Cj0608 (28.6% identity in 455 aa overlap). Contains N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site; Updated (2006) 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; PMID:12069964, PMID:15728904, PMID:16359189; outer membrane channel protein CmeC complement(331125..332603) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904688 YP_002343803.1 CDS cmeB NC_002163.1 332596 335718 R Original (2000) note: Cj0366c, probable transmembrane efflux protein, len: 1040 aa; similar to e.g. TR:P95422 (EMBL:X99514) Pseudomonas aeruginosa mexF (antibiotic efflux system protein) (1062 aa), fasta scores; opt: 1584 z-score: 3208.4 E(): 0, 41.2% identity in 1056 aa overlap, and ACRB_ECOLI acriflavin resistance protein B (1049 aa), fasta scores; opt: 2739 z-score: 3055.6 E(): 0, 41.7% identity in 1031 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00873 ACR_tran,AcrB/AcrD/AcrF family, score 1415.10, E-value 0; Updated (2006) note: Thirteen probable transmembrace helices identified by TMHMM2.0 within CDS. Prosite domain PS50156 SSD, 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; PMID:12069964, PMID:11814661, PMID:15728904,PMID:16359189, PMID:15201231; inner membrane efflux transporter CmeB complement(332596..335718) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904689 YP_002343804.1 CDS cmeA NC_002163.1 335718 336821 R Original (2000) note: Cj0367c, possible membrane fusion component of efflux system, len: 367 aa; similar to e.g. MTRC_NEIGO membrane fusion protein MTRC precursor (412 aa), fasta scores; opt: 592 z-score: 692.4 E(): 2.6e-31, 29.9% identity in 358 aa overlap, and TR:P95421 (EMBL:X99514) Pseudomonas aeruginosa mexE (antibiotic efflux system protein) (414 aa), fasta scores; opt: 460 z-score: 570.0 E(): 1.7e-24, 26.9% identity in 357 aa overlap. No Hp ortholog. Contains N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site; Updated (2006) 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; PMID:12069964, PMID:15728904, PMID:16359189; periplasmic fusion protein CmeA complement(335718..336821) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904690 YP_002343805.1 CDS cmeR NC_002163.1 336916 337548 R Original (2000) note: Cj0368c, probable transcriptional regulatory protein, len: 210 aa; similar to members of the tetR family e.g. TR:G3327947 (EMBL:AF053772) Staphylococcus aureus transcriptional regulator qacR (regulator of multidrug efflux protein QacB) (188 aa), fasta scores; opt: 162 z-score: 285.0 E(): 1.3e-08, 29.3% identity in 198 aa overlap, and MTRR_NEIGO regulatory protein MTRR (210 aa), fasta scores; opt: 137 z-score: 210.6 E(): 0.00018, 31.3% identity in 83 aa overlap. No Hp match. Contains Pfam match to entry PF00440 tetR, Bacterial regulatory proteins, tetR family, score 24.00, E-value 6.4e-05; Updated (2006) 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; PMID:15728904; transcriptional regulator CmeR complement(336916..337548) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904691 YP_002343806.1 CDS Cj0369c NC_002163.1 337535 338911 R Original (2000) note: Cj0369c, ferredoxin domain-containing integral membrane protein, len: 458 aa; some similarity to e.g. RDXA_RHOSH RDXA protein (469 aa),fasta scores; opt: 474 z-score: 657.7 E(): 2.2e-29, 24.9% identity in 402 aa overlap, and FIXG_RHIME nitrogen fixation protein FIXG (524 aa), fasta scores; opt: 476 z-score: 533.8 E(): 1.8e-22, 28.7% identity in 296 aa overlap. 45.7% identity to HP1508. Contains PS00198 4Fe-4S ferredoxins, iron-sulfur binding region signature and Pfam match to entry PF00037 fer4, 4Fe-4S ferredoxins and related iron-sulfur cluster binding domains., score 17.10,E-value 0.0011; Updated (2006) 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; ferredoxin domain-containing integral membrane protein complement(337535..338911) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904692 YP_002343807.1 CDS rpsU NC_002163.1 339071 339283 D a small basic protein that is one of the last in the subunit assembly; omission does not prevent assembly but the subunit is inactive; binds central domain of 16S rRNA; 30S ribosomal protein S21 339071..339283 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904693 YP_002343808.1 CDS Cj0371 NC_002163.1 339403 340008 D Original (2000) note: Cj0371, probable lipoprotein,len: 201 aa; similar to H. pylori gene fragment reported to be involved in flagellar motility TR:Q48273 (EMBL:Z68311) (122 aa), fasta scores; opt: 322 z-score: 449.5 E(): 8.8e-18, 46.1% identity in 115 aa overlap. 46.4% identity to HP0232. Contains N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site; Updated (2006) 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; PMID:8733234; hypothetical protein 339403..340008 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904694 YP_002343809.1 CDS Cj0372 NC_002163.1 340018 341187 D Original (2000) note: Cj0372, unknown, len: 389 aa; similar to hypothetical proteins e.g. YGIC_ECOLI (386 aa),fasta scores; opt: 552 z-score: 508.4 E(): 4.6e-21, 31.3% identity in 383 aa overlap. Also similar to N-terminus of GSP_ECOLI glutathionylspermidine synthase (619 aa), fasta scores; opt: 314 z-score: 248.3 E(): 1.4e-06, 24.4% identity in 381 aa overlap. 60.5% identity to HP0233; Updated (2006) 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; PMID:7775463, PMID:9398217; glutathionylspermidine synthase 340018..341187 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904695 YP_002343810.1 CDS Cj0373 NC_002163.1 341190 342125 D Involved in the metabolism of aromatic amino acids; 2-hydroxyacid dehydrogenase 341190..342125 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904696 YP_002343811.1 CDS Cj0374 NC_002163.1 342115 342606 D nucleotide binding property based on structural studies of Haemophilus influenzae crystallized protein in PDB Accession Number 1IN0 and NMR studies of Escherichia coli YajQ; the YajQ protein from Pseudomonas synringae appears to play a role in activation of bateriophage phi6 segment L transcription; nucleotide-binding protein 342115..342606 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904697 YP_002343812.1 CDS Cj0375 NC_002163.1 342615 343091 D Original (2000) note: Cj0375, probable lipoprotein,len: 158 aa; no Hp match. Contains N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification -Membranes, lipoproteins and porins; lipoprotein 342615..343091 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904698 YP_002343813.1 CDS Cj0376 NC_002163.1 343102 343926 D Original (2000) note: Cj0376, possible periplasmic protein, len: 274 aa; no Hp match. Contains probable N-terminal signal sequence; Updated (2006) note: Literature search identified paper linking protein to glycoprotein. Functional classification - Miscellaneous periplasmic proteins; PMID:12186869; periplasmic protein 343102..343926 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904699 YP_002343814.1 CDS Cj0377 NC_002163.1 343926 345638 D Original (2000) note: Cj0377, probable ATPase, len: 570 aa; weak similarity to many members of the AAA family e.g. TR:O28182 (EMBL:O28182) cell division control protein 48 (Archaeoglobus fulgidus AF2098) (811 aa), fasta scores; opt: 341 z-score: 312.6 E(): 3.7e-10, 26.4% identity in 435 aa overlap. No Hp match. Contains PS00017 ATP/GTP-binding site motif A (P-loop) and Pfam match to entry PF00004 AAA, ATPases associated with various cellular activities (AAA), score 106.20, E-value 6.3e-28; Updated (2006) note: Probable changed to . No specific characterisation with acceptable identity scores carried out yet. Functional classification - Misc; AAA family ATPase 343926..345638 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904700 YP_002343815.1 CDS Cj0378c NC_002163.1 345635 346174 R Original (2000) note: Cj0378c, probable integral membrane protein, len: 179 aa; no Hp match; Updated (2006) 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 (UPF0191) 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; PMID:15632442; ferric reductase-like transmembrane protein complement(345635..346174) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904701 YP_002343816.1 CDS Cj0379c NC_002163.1 346174 347067 R in Escherichia coli this periplasmic enzyme was found to encode the periplasmic catalytic subunit of an oxidoreductase; sulfite oxidase activity not demonstrated; requires inner membrane anchor protein YedZ; sulfite oxidase subunit YedY complement(346174..347067) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904702 YP_002343817.1 CDS Cj0380c NC_002163.1 347123 347908 R Original (2000) note: Cj0380c, unknonw, len: 261 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein complement(347123..347908) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904703 YP_002343818.1 CDS pyrF NC_002163.1 347905 348744 R type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase; orotidine 5'-phosphate decarboxylase complement(347905..348744) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904704 YP_002343819.1 CDS nusB NC_002163.1 348741 349139 R Regulates rRNA biosynthesis by transcriptional antitermination; transcription antitermination protein NusB complement(348741..349139) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904705 YP_002343820.1 CDS ribH NC_002163.1 349139 349603 R RibE; 6,7-diimethyl-8-ribityllumazine synthase; DMRL synthase; lumazine synthase; beta subunit of riboflavin synthase; condenses 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate to generate 6,6-dimethyl-8-lumazine (DMRL); riboflavin synthase then uses 2 molecules of DMRL to produce riboflavin (vitamin B12); involved in the last steps of riboflavin biosynthesis; forms a 60mer (icosahedral shell) in both Bacillus subtilis and Escherichia coli; in Bacillus subtilis this 60mer is associated with the riboflavin synthase subunit (alpha) while in Escherichia coli it is not; 6,7-dimethyl-8-ribityllumazine synthase complement(349139..349603) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904706 YP_002343821.1 CDS kdsA NC_002163.1 349600 350415 R catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis; 2-dehydro-3-deoxyphosphooctonate aldolase complement(349600..350415) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904707 YP_002343822.1 CDS Cj0385c NC_002163.1 350412 351344 R Original (2000) note: Cj0385c, probable integral membrane protein, len: 310 aa; similar to many hypothetical integral membrane proteins e.g. TR:O29973 (EMBL:AE001087) Archaeoglobus fulgidus AF0266 (276 aa),fasta scores; opt: 155 z-score: 221.8 E(): 4.5e-05, 26.9% identity in 279 aa overlap. 30.8% identity to HP1234. Contains Pfam match to entry PF00892 DUF6, Integral membrane protein, score 29.90, E-value 5.9e-05; Updated (2006) 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, lipoproteins and porins; integral membrane protein complement(350412..351344) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904708 YP_002343823.1 CDS engA NC_002163.1 351446 352828 D EngA; essential Neisserial GTPase; synchronizes cellular events by interacting with multiple targets with tandem G-domains; overexpression in Escherichia coli suppresses rrmJ mutation; structural analysis of the Thermotoga maritima ortholog shows different nucleotide binding affinities in the two binding domains; GTP-binding protein EngA 351446..352828 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904709 YP_002343824.1 CDS aroK NC_002163.1 352815 353312 D catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis; shikimate kinase 352815..353312 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904710 YP_002343825.1 CDS trpS NC_002163.1 353309 354268 D catalyzes a two-step reaction, first charging a tryptophan molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; tryptophanyl-tRNA synthetase 353309..354268 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904711 YP_002343826.1 CDS serS NC_002163.1 354279 355514 D catalyzes a two-step reaction, first charging a serine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; seryl-tRNA synthetase 354279..355514 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904712 YP_002343827.1 CDS Cj0390 NC_002163.1 355524 357986 D Original (2000) note: Cj0390, possible transmembrane protein, len: 820 aa; 28.7% identity in 703 aa overlap to HP1479. Contains possible transmembrane domain around aa 100 and Pfam match to entry PF00515 TPR,TPR Domain, score 26.90, E-value 0.00047; Updated (2006) note: Pfam domains x4 PF07719 Tetratricopeptide repeat were identified within CDS. Functional classification - Membranes, lipoproteins and porins; transmembrane protein 355524..357986 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904713 YP_002343828.1 CDS Cj0391c NC_002163.1 358017 358652 R Original (2000) note: Cj0391c, unknown, len: 211 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Literature search identified paper giving further clues to product function. Functional classification - Unknown; hypothetical protein complement(358017..358652) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904714 YP_002343829.1 CDS pyk NC_002163.1 358750 360192 R Original (2000) note: Cj0392c, pyk, probable pyruvate kinase, len: 480 aa; similar to e.g. KPYK_BACSU pyruvate kinase (EC 2.7.1.40) (585 aa), fasta scores; opt: 1111 z-score: 1494.8 E(): 0, 41.8% identity in 476 aa overlap. No Hp match. Contains PS00659 Glycosyl hydrolases family 5 signature and Pfam match to entry PF00224 PK,Pyruvate kinase, score 523.20, E-value 1.8e-153; Updated (2006) note: Pfam domain PF02887 Pyruvate kinase, alpha/beta 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; PMID:10932722; pyruvate kinase complement(358750..360192) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904715 YP_002343830.1 CDS mqo NC_002163.1 360241 361587 R Original (2000) note: Cj0393c, possible oxidoreductase, len: 448 aa; some simlarity to MQO_ECOLI probable malate:quinone oxidoreductase (548 aa), fasta scores; opt: 121 z-score: 223.1 E(): 3.8e-05, 24.6% identity in 455 aa overlap. 49.3% identity to HP0086. Contains PS00110 Pyruvate kinase active site signature; Updated (2006) note: Pfam domain PF06039 Malate:quinone oxidoreductase (Mqo) 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; PMID:10809701; malate:quinone oxidoreductase complement(360241..361587) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904716 YP_002343831.1 CDS Cj0394c NC_002163.1 361706 362335 R type III; catalyzes the formation of (R)-4'-phosphopantothenate from (R)-pantothenate in coenzyme A biosynthesis; type III pantothenate kinases are not subject to feedback inhibition from coenzyme A and have a high Km for ATP; pantothenate kinase complement(361706..362335) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904717 YP_002343832.1 CDS Cj0395c NC_002163.1 362322 362612 R Original (2000) note: Cj0395c, unknown, len: 96 aa; no Hp match. Functional classification - Unknown; hypothetical protein complement(362322..362612) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904718 YP_002343833.1 CDS Cj0396c NC_002163.1 362609 363607 R Original (2000) note: Cj0396c, probable lipoprotein, len: 332 aa; 28.9% identity to HP0863. Conatins N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes, lipoproteins and porins; lipoprotein complement(362609..363607) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904719 YP_002343834.1 CDS Cj0397c NC_002163.1 363604 364182 R Original (2000) note: Cj0397c, unknown, len: 192 aa; almost identical to C. jejuni hypothetical protein fragment TR:Q46096 (EMBL:U27272), 28.5% identity to HP0864; Updated (2006) 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; PMID:10913692; hypothetical protein complement(363604..364182) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904720 YP_002343835.1 CDS gatC NC_002163.1 364326 364610 D allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; some Mycoplasma proteins contain an N-terminal fusion to an unknown domain; aspartyl/glutamyl-tRNA amidotransferase subunit C 364326..364610 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904721 YP_002343836.1 CDS Cj0399 NC_002163.1 364678 365241 D Original (2000) note: Cj0399, probable integral membrane protein, len: 187 aa; identical to C. jejuni hypothetical protein fragment TR:O68605 (EMBL:AF052056) (123 aa). 26.9% identity in 171 aa overlap to HP0181 (224 aa); Updated (2006) 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; colicin V production protein 364678..365241 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904722 YP_002343837.1 CDS fur NC_002163.1 365243 365716 D Original (2000) note: Cj0400, fur, ferric uptake regulator, len: 157 aa; identical to FUR_CAMJE ferric uptake regulation protein, and highly simliar to many others e.g. FUR_BORPE (139 aa), fasta scores; opt: 354 z-score: 552.9 E(): 1.7e-23 41.6% identity in 137 aa overlap. 40.8% identity to HP1027; Updated (2006) 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; PMID:8083178, PMID:7590316, PMID:9765558; ferric uptake regulator 365243..365716 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904724 YP_002343838.1 CDS lysS NC_002163.1 365717 367222 D class II; LysRS2; catalyzes a two-step reaction, first charging a lysine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; in Methanosarcina barkeri, 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; lysyl-tRNA synthetase 365717..367222 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904725 YP_002343839.1 CDS glyA NC_002163.1 367219 368463 D catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate; serine hydroxymethyltransferase 367219..368463 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904726 YP_002343840.1 CDS Cj0403 NC_002163.1 368460 369005 D Original (2000) note: Cj0403, unknown, len: 181 aa; 57.8% identity to HP0184; Updated (2006) note: Literature search identified paper giving further clues to product function. Functional classification - Conserved hypothetical proteins; PMID:12595250; hypothetical protein 368460..369005 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904727 YP_002343841.1 CDS Cj0404 NC_002163.1 369019 369855 D Original (2000) note: Cj0404, probable transmembrane protein, len: 278 aa; no Hp match. Contains probable transmembrane domain around 40 aa; Updated (2006) note: Literature search identified paper giving further clues to product function. Functional classification - Membranes, lipoproteins and porins; PMID:12595250; transmembrane protein 369019..369855 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904728 YP_002343842.1 CDS aroE NC_002163.1 369852 370640 D AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate; shikimate 5-dehydrogenase 369852..370640 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904729 YP_002343843.1 CDS Cj0406c NC_002163.1 370715 371614 R Original (2000) note: Cj0406c, probable lipoprotein, len: 299 aa; no Hp match. Contains N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes, lipoproteins and porins; lipoprotein complement(370715..371614) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904730 YP_002343844.1 CDS lgt NC_002163.1 371704 372519 D transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein; prolipoprotein diacylglyceryl transferase 371704..372519 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904731 YP_002343845.1 CDS frdC NC_002163.1 372589 373371 D part of three member fumarate reductase enzyme complex FrdABC which catalyzes the reduction of fumarate to succinate during anaerobic respiration; FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit, respectively; FrdC is the cytochrome b-556 subunit; fumarate reductase cytochrome b-556 subunit 372589..373371 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904732 YP_002343846.1 CDS frdA NC_002163.1 373355 375346 D part of three member fumarate reductase enzyme complex FrdABC which catalyzes the reduction of fumarate to succinate during anaerobic respiration; FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit, respectively; FrdC is the cytochrome b-556 subunit; the catalytic subunits are similar to succinate dehydrogenase SdhAB; fumarate reductase flavoprotein subunit 373355..375346 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904733 YP_002343847.1 CDS frdB NC_002163.1 375339 376064 D part of three member fumarate reductase enzyme complex FrdABC which catalyzes the reduction of fumarate to succinate during anaerobic respiration; FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit, respectively; FrdC is the cytochrome b-556 subunit; the catalytic subunits are similar to succinate dehydrogenase SdhAB; fumarate reductase iron-sulfur subunit 375339..376064 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904734 YP_002343848.1 CDS Cj0411 NC_002163.1 376092 378278 D Original (2000) note: Cj0411, probable ATP/GTP binding protein, len: 728 aa; some similarity in C-term to YOR6_CALSR hypothetical protein (402 aa), fasta scores; opt: 220 z-score: 284.9 E(): 1.4e-08, 25.2% identity in 425 aa overlap, and to C-term of YPBR_BACSU hypothetical protein (1193 aa), fasta scores; opt: 173 z-score: 275.1 E(): 5e-08, 20.1% identity in 722 aa overlap. No Hp match. Contains PS00017 ATP/GTP-binding site motif A (P-loop); Updated (2006) note: Pfam domain PF00350 Dynamin family protein was identified within CDS. Dynamin is a member of the G-protein superfamily clan. ATP/GTP 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; ATP/GTP binding protein 376092..378278 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904735 YP_002343849.1 CDS Cj0412 NC_002163.1 378268 380097 D Original (2000) note: Cj0412, probable ATP/GTP binding protein, len: 609 aa; some similarity to YPBR_BACSU hypothetical protein (1193 aa), fasta scores; opt: 172 z-score: 237.5 E(): 6.2e-06, 23.7% identity in 439 aa overlap. No Hp match. Contains PS00017 ATP/GTP-binding site motif A (P-loop); Updated (2006) note: Pfam domain PF00350 Dynamin family protein was identified within CDS. Dynamin is a member of the G-protein superfamily clan. ATP/GTP 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; ATP/GTP binding protein 378268..380097 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904736 YP_002343850.1 CDS Cj0413 NC_002163.1 380097 380801 D Original (2000) note: Cj0413, probable periplasmic protein, len: 234 aa; similar to several Hp proteins; HP0160, 30.3% identity; HP0211, 32.6% identity; HP1098 31.1% identity; HP0336 31.3% identity; HP0235 30.9% identity; HP0628 26.5% identity; and HP1117 26.9% identity. This is the only copy in C. jejuni; Updated (2006) note: Pfam domain PF07719 Tetratricopeptide repeat was identified within CDS. Functional classification - Miscellaneous periplasmic proteins; periplasmic protein 380097..380801 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904737 YP_002343851.1 CDS Cj0414 NC_002163.1 380937 381665 D Original (2000) note: Cj0414, possible oxidoreductase subunit, len: 242 aa; some similarity to TR:O34213 (EMBL:U97665) Erwinia cypripedii gluconate dehydrogenase subunit III precursor (220 aa), fasta scores; opt: 343 z-score: 502.3 E(): 1.1e-20, 32.6% identity in 193 aa overlap. No Hp match; Updated (2006) 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; PMID:15231804; oxidoreductase subunit 380937..381665 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904738 YP_002343852.1 CDS Cj0415 NC_002163.1 381667 383388 D Original (2000) note: Cj0415, possible oxidoreductase subunit, len: 573 aa; similar to e.g. TR:O34214 (EMBL:U97665) Erwinia cypripedii gluconate dehydrogenase subunit precursor (615 aa), fasta scores; opt: 1025 z-score: 1674.4 E(): 0, 40.8% identity in 583 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF00732 GMC (glucose-methanol-choline) oxidoreductase was identified within CDS when carrying out own Pfam search. This family is a member of the FAD/NAD(P)-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, so kept within product function. Literature search identified paper linking protein to glycoprotein (PMID:12186869). Functional classification -Misc; PMID:15231804, PMID:12186869; GMC oxidoreductase subunit 381667..383388 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904739 YP_002343853.1 CDS Cj0416 NC_002163.1 383559 383657 D Original (2000) note: Cj0416, unknown, len: 32 aa; no Hp match, highly simlar to N-terminus of Cj0122 (88.2% identity in 34 aa overlap). Functional classification -Unknown; hypothetical protein 383559..383657 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904740 YP_002343854.1 CDS Cj0417 NC_002163.1 383677 383823 D Original (2000) note: Cj0417, unknown, len: 48 aa; no Hp match. Functional classification - Unknown; hypothetical protein 383677..383823 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904741 YP_002343855.1 CDS Cj0418c NC_002163.1 383947 384651 R Original (2000) note: Cj0418c, unknown, len: 234 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein complement(383947..384651) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904742 YP_002343856.1 CDS Cj0419 NC_002163.1 384759 385121 D Original (2000) note: Cj0419, unknown, len: 120 aa; no Hp match; Updated (2006) note: Pfam domain PF01230 HIT (histidine triad) 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; PMID:1472710, PMID:9164465; histidine triad (HIT) family protein 384759..385121 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904743 YP_002343857.1 CDS Cj0420 NC_002163.1 385195 385767 D Original (2000) note: Cj0420, probable periplasmic protein, len: 190 aa; similar to hypothetical proteins e.g. YCEI_ECOLI (191 aa), fasta scores; opt: 377 z-score: 504.2 E(): 8.7e-21, 37.4% identity in 195 aa overlap. 37.8% identity to HP1286. Contains probable N-terminal signal sequence; Updated (2006) 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; PMID:15231804; periplasmic protein 385195..385767 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904744 YP_002343858.1 CDS Cj0421c NC_002163.1 385772 386728 R Original (2000) note: Cj0421c, probable integral membrane protein, len: 318 aa; no Hp match; Updated (2006) note: Six probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; integral membrane protein complement(385772..386728) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904745 YP_002343859.1 CDS Cj0422c NC_002163.1 386790 386999 R Original (2000) note: Cj0422c, unknown, len: 69 aa; no Hp match. Contains probable helix-turn-helix motif at aa 5-26 (Score 1410, +3.99 SD). Functional classification - Broad regulatory functions; H-T-H containing protein complement(386790..386999) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904746 YP_002343860.1 CDS Cj0423 NC_002163.1 387168 387395 D Original (2000) note: Cj0423, probable integral membrane protein, len: 75 aa; similar to immunity proteins of T4 and T2 phage e.g. IMM_BPT4 immunity protein (83 aa),fasta scores; opt: 174 z-score: 240.8 E(): 4e-06, 40.2% identity in 82 aa overlap. No Hp match; Updated (2006) note: Two probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; integral membrane protein 387168..387395 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904747 YP_002343861.1 CDS Cj0424 NC_002163.1 387404 388036 D Original (2000) note: Cj0424, probable acidic periplasmic protein, len: 210 aa; no Hp match. Contains probable N-terminal signal sequence; Updated (2006) note: Pfam domain PF07661 MORN repeat variant was identified within CDS. The MORN (Membrane Occupation and Recognition Nexus) 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; PMID:15632442; acidic periplasmic protein 387404..388036 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904748 YP_002343862.1 CDS Cj0425 NC_002163.1 388049 388465 D Original (2000) note: Cj0425, probable periplasmic protein, len: 138 aa; no Hp match. Contains probable N-terminal signal sequence; Updated (2006) note: Literature search identified paper giving functional link to iron stimulation. Functional classification - Miscellaneous periplasmic proteins; PMID:15632442; periplasmic protein 388049..388465 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904749 YP_002343863.1 CDS Cj0426 NC_002163.1 388595 390172 D Original (2000) note: Cj0426, probable ABC transporter ATP-binding protein, len: 525 aa; simlar to many e.g. YBIT_ECOLI hypothetical ABC transporter ATP-binding protein (530 aa), fasta scores; opt: 1461 z-score: 1750.6 E(): 0, 42.8% identity in 526 aa overlap. 60.5% identity to HP0853. Contains 2x PS00017 ATP/GTP-binding site motif A (P-loop) and Pfam match to entry PF00005 ABC_tran, ABC transporters, scores 115.00, E-value 1.4e-30, and 120.70, E-value 2.7e-32; Updated (2006) note: Some characterisation within Escherichia coli with acceptable identity score. added to product function as original designation was only hypothetical. Functional classification -Transport/binding proteins - Other; ABC transporter ATP-binding protein 388595..390172 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904750 YP_002343864.1 CDS Cj0427 NC_002163.1 390162 390497 D Original (2000) note: Cj0427, unknown, len: 111 aa; no Hp match. Functional classification - Unknown; hypothetical protein 390162..390497 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904751 YP_002343865.1 CDS Cj0428 NC_002163.1 390572 390955 D Original (2000) note: Cj0428, unknown, len: 127 aa; no Hp match; Updated (2006) note: Literature search identified papers linking product function to be involved with motility. Functional classification - Unknown; PMID:15812042, PMID:14985343; hypothetical protein 390572..390955 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904752 YP_002343866.1 CDS Cj0429c NC_002163.1 390999 391583 R Original (2000) note: Cj0429c, unknown, len: 194 aa; similar to hypothetical proteins e.g. YIGZ_ECOLI (205 aa), fasta scores; opt: 241 z-score: 370.8 E(): 2.3e-13,40.2% identity in 112 aa overlap. 39.1% identity to HP1485 (misannotated as proline dipeptidase); Updated (2006) note: Pfam domain PF01205 Uncharacterized protein family (UPF0029) was identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins; hypothetical protein complement(390999..391583) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904753 YP_002343867.1 CDS Cj0430 NC_002163.1 391711 392937 D Original (2000) note: Cj0430, probable integral membrane protein, len: 408 aa; 33.8% identity to HP1235; Updated (2006) 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, lipoproteins and porins; PMID:16045618; integral membrane protein 391711..392937 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904754 YP_002343868.1 CDS Cj0431 NC_002163.1 392930 393544 D Original (2000) note: Cj0431, possible periplasmic ATP/GTP-binding protein, len: 204 aa; no Hp match; contains possible N-terminal signal sequence and PS00017 ATP/GTP-binding site motif A (P-loop); Updated (2006) note: One probable transmembrane helices predicted by TMHMM2.0. Functional classification -Miscellaneous periplasmic proteins; periplasmic ATP/GTP-binding protein 392930..393544 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904723 YP_002343869.1 CDS murD NC_002163.1 399936 401144 R UDP-N-acetylmuramoylalanine--D-glutamate ligase; involved in peptidoglycan biosynthesis; cytoplasmic; catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine during cell wall formation; UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase complement(399936..401144) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904757 YP_002343870.1 CDS mraY NC_002163.1 401144 402205 R First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan; phospho-N-acetylmuramoyl-pentapeptide- transferase complement(401144..402205) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904758 YP_002343871.1 CDS pgm NC_002163.1 402285 403763 D catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate; phosphoglyceromutase 402285..403763 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904759 YP_002343872.1 CDS fabG NC_002163.1 403835 404578 D Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis; 3-ketoacyl-ACP reductase 403835..404578 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904760 YP_002343873.1 CDS Cj0436 NC_002163.1 404585 404995 D Original (2000) note: Cj0436, unknown, len: 136 aa; no Hp match; Updated (2006) note: Pfam domain PF01243 Pyridoxamine 5'-phosphate oxidase was identified within CDS. Product function modified to more specific family member based on motif match. Pyridoxamine 5'-phosphate oxidase (1.4.3.5) is a FMN flavoprotein involved in the de novo synthesis of pyridoxine (vitamin B6) and pyridoxal phosphate. It oxidizes pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) 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,prosthetic groups and carriers - Pyridoxine; pyridoxamine 5'-phosphate oxidase 404585..404995 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904761 YP_002343874.1 CDS sdhA NC_002163.1 405333 407168 D Original (2000) note: Cj0437, sdhA, probable succinate dehydrogenase flavoprotein subunit, len: 611 aa; similar to many e.g. DHSA_ECOLI succinate dehydrogenase flavoprotein subunit (EC 1.3.99.1) (588 aa), fasta scores; opt: 1036 z-score: 1136.5 E(): 0, 37.3% identity in 569 aa overlap and to e.g. FRDA_WOLSU fumarate reductase flavoprotein subunit (656 aa), fasta scores; opt: 862 z-score: 1211.2 E(): 0, 33.3% identity in 595 aa overlap. No Hp ortholog, but 32.3% identity to HP0192 fumarate reductase, flavoprotein subunit (frdA), and 33.8% identity to C. jejuni frdA (Cj0409). Contains Pfam match to entry PF00890 FAD_binding_2, FAD binding domain, score 386.60,E-value 2.5e-112; Updated (2006) note: Pfam domain PF02910 Fumarate reductase/succinate 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; PMID:1556094, PMID:2987185; succinate dehydrogenase flavoprotein subunit 405333..407168 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904762 YP_002343875.1 CDS sdhB NC_002163.1 407165 408130 D Original (2000) note: Cj0438, sdhB, possibleble succinate dehydrogenase iron-sulfur protein, len: 321 aa; similar to e.g. DHSB_MYCGR succinate dehydrogenase (ubiquinone) iron-sulfur protein (EC 1.3.5.1) (297 aa),fasta scores; opt: 352 z-score: 442.4 E(): 2.4e-17, 29.3% identity in 215 aa overlap. No Hp ortholog, but 28.1% identical to HP0191 fumarate reductase, iron-sulfur subunit (frdB). Contains PS00197 2Fe-2S ferredoxins,iron-sulfur binding region signature, PS00198 4Fe-4S ferredoxins, iron-sulfur binding region signature, and Pfam match to entry PF00037 fer4, 4Fe-4S ferredoxins and related iron-sulfur cluster binding domains., score 13.70,E-value 0.01; Updated (2006) 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; succinate dehydrogenase iron-sulfur protein 407165..408130 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904763 YP_002343876.1 CDS sdhC NC_002163.1 408134 408991 D Original (2000) note: Cj0439, sdhC, probable succinate dehydrogenase subunit C, len: 285 aa; similar to e.g. TR:P77945 (EMBL:Y09041) Sulfolobus acidocaldarius succinate dehydrogenase subunit C (EC 1.3.99.1) (290 aa),fasta scores; opt: 612 z-score: 739.6 E(): 0, 34.2% identity in 275 aa overlap. No Hp match; Updated (2006) 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; succinate dehydrogenase subunit C 408134..408991 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904764 YP_002343877.1 CDS Cj0440c NC_002163.1 409015 409683 R Original (2000) note: Cj0440c, probable transcriptional regulator, len: 222 aa; similar to many regulators and to TENA_BACSU transcriptional activator TENA (236 aa), fasta scores; opt: 250 z-score: 275.4 E(): 4.8e-08, 28.8% identity in 215 aa overlap. 30.7% identity to HP1287; Updated (2006) note: Pfam domain PF03070 TENA/THI-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; transcriptional regulator complement(409015..409683) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904765 YP_002343878.1 CDS acpP NC_002163.1 409793 410026 D carries the fatty acid chain in fatty acid biosynthesis; acyl carrier protein 409793..410026 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904766 YP_002343879.1 CDS fabF NC_002163.1 410053 411267 D FabF; beta-ketoacyl-ACP synthase II, KASII; catalyzes a condensation reaction in fatty acid biosynthesis: addition of an acyl acceptor of two carbons from malonyl-ACP; required for the elongation of short-chain unsaturated acyl-ACP; 3-oxoacyl-ACP synthase 410053..411267 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904767 YP_002343880.1 CDS accA NC_002163.1 411269 412207 D catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer composed of two alpha (AccA) and two beta (AccD) subunits; one of the two catalytic subunits that can form the acetyl CoA carboxylase enzyme together with a carrier protein; acetyl-CoA carboxylase carboxyltransferase subunit alpha 411269..412207 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904768 YP_002343881.1 CDS Cj0447 NC_002163.1 414516 415112 D Original (2000) note: Cj0447, unknown, len: 198 aa; similar to a hypothetical protein from E. coli; YFFH_ECOLI (191 aa), fasta scores; opt: 168 z-score: 344.6 E(): 6.7e-12, 31.1% identity in 122 aa overlap; and to part of a hypothetical protein from C. elegans TR:Q18745 (EMBL:Z70750) C50F4.11 (1092 aa), fasta scores; opt: 133 z-score: 491.0 E(): 4.7e-20, 35.3% identity in 215 aa overlap. 45.7% identity to HP0507; Updated (2006) note: Pfam domain PF00293 NUDIX was identified within CDS. The generic name 'NUDIX hydrolases' (NUcleoside DIphosphate linked to some other moiety X) has been coined for this domain family . The family can be divided into a number of subgroups, of which MutT anti-mutagenic activity represents only one type; most of the rest hydrolyse diverse nucleoside diphosphate derivatives (including ADP-ribose, GDP- mannose, TDP-glucose, NADH,UDP-sugars, dNTP and NTP). Product modified to more specific family member due to motif match. Functional classification - Misc; NUDIX hydrolase family protein 414516..415112 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904770 YP_002343882.1 CDS Cj0448c NC_002163.1 415144 416241 R Original (2000) note: Cj0448c, probable MCP-type signal transduction protein, len: 365 aa; similar to many proteins with MCP domains e.g. TR:Q56633 (EMBL:L25660) Vibrio cholerae acfB accessory colonization factor (626 aa), fasta scores; opt: 364 z-score: 455.7 E(): 4.4e-18,29.9% identity in 278 aa overlap, and PILJ_PSEAE PILJ protein (682 aa), fasta scores; opt: 314 z-score: 451.9 E(): 7.1e-18, 30.7% identity in 189 aa overlap. 31.9% identity to HP0599 (called hemolysin secretion protein precursor (hylB), but previously sequenced as TR:P94847 H.pylori 48 kDa antigen (433 aa), fasta scores; opt: 580 z-score: 833.7 E(): 0, 32.4% identity in 370 aa overlap). Contains Pfam match to entry PF00015 MCPsignal,Methyl-accepting chemotaxis protein (MCP) signaling domain, score 122.40, E-value 1.7e-33; Updated (2006) note: Prosite domain PS50111 CHEMOTAXIS_TRANSDUC_2, 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; MCP-type signal transduction protein complement(415144..416241) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904771 YP_002343883.1 CDS Cj0449c NC_002163.1 416251 416466 R Original (2000) note: Cj0449c, unknown, len: 71 aa; similar to E. coli hypothetical protein YDCH_ECOLI (55 aa), fasta scores; opt: 112 z-score: 209.2 E(): 0.00023,42.6% identity in 47 aa overlap. 45.1% identity to HP1242; Updated (2006) note: Pfam domain PF04325 Protein of unknown function (DUF465) was identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins; hypothetical protein complement(416251..416466) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904772 YP_002343884.1 CDS rpmB NC_002163.1 416651 416845 R required for 70S ribosome assembly; 50S ribosomal protein L28 complement(416651..416845) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904773 YP_002343885.1 CDS rep NC_002163.1 416985 417632 D catalyzes the interconversion of D-ribulose 5-phosphate to xylulose 5-phosphate; ribulose-phosphate 3-epimerase 416985..417632 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904774 YP_002343886.1 CDS dnaQ NC_002163.1 417629 418390 D 3'-5' exonuclease of DNA polymerase III; DNA polymerase III subunit epsilon 417629..418390 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904775 YP_002343887.1 CDS thiC NC_002163.1 418573 419865 D required for the synthesis of the hydromethylpyrimidine moiety of thiamine; thiamine biosynthesis protein ThiC 418573..419865 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904776 YP_002343888.1 CDS Cj0454c NC_002163.1 419857 420426 R Original (2000) note: Cj0454c, possible membrane protein, len: 189 aa; no Hp match; Updated (2006) note: One probable transmembrane helices predicted by TMHMM2.0 within CDS. Literature search identified paper linking product function to motility. Functional classification - Membranes,lipoproteins and porins; PMID:15066034; hypothetical protein complement(419857..420426) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904777 YP_002343889.1 CDS Cj0455c NC_002163.1 420548 420892 R Original (2000) note: Cj0455c, possible membrane protein, len: 114 aa; no Hp match; Updated (2006) note: One probable transmembrane helices predicted by TMHMM2.0 within CDS. Functional classification - Membranes, lipoproteins and porins; hypothetical protein complement(420548..420892) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904778 YP_002343890.1 CDS Cj0456c NC_002163.1 420889 421848 R Original (2000) note: Cj0456c, unknown, len: 319 aa; no Hp match. Functional classification - Unknown; hypothetical protein complement(420889..421848) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904779 YP_002343891.1 CDS Cj0457c NC_002163.1 421850 422479 R Original (2000) note: Cj0457c, probable lipoprotein, len: 209 aa; similar to hypothetical protein fromRICKETTSIA PROWAZEKII TR:E1342403 (EMBL:AJ235270) RP090 (218 aa), fasta scores; opt: 372 z-score: 531.3 E(): 2.7e-22, 33.0% identity in 212 aa overlap. 35.9% identity in 153 aa overlap to HP0270. Contains N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site; Updated (2006) note: Pfam domain PF04028 Domain of unknown function (DUF374) identified within CDS. One probable transmembrane helices predicted by TMHMM2.0 within CDS. Further support given to product function. Functional classification - Membranes, lipoproteins and porins; lipoprotein complement(421850..422479) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904780 YP_002343892.1 CDS miaB NC_002163.1 422463 423764 R catalyzes the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine from N6-(dimethylallyl)adenosine (i(6)A); (dimethylallyl)adenosine tRNA methylthiotransferase complement(422463..423764) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904781 YP_002343893.1 CDS Cj0459c NC_002163.1 423761 424027 R Original (2000) note: Cj0459c, unknown, len: 88 aa; 32.5% identical to HP0268. Functional classification -Conserved hypothetical proteins; hypothetical protein complement(423761..424027) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904782 YP_002343894.1 CDS nusA NC_002163.1 424131 425219 D modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination; transcription elongation factor NusA 424131..425219 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904783 YP_002343895.1 CDS Cj0461c NC_002163.1 425235 426422 R Original (2000) note: Cj0461c, probable integral membrane protein, len: 395 aa; some similarity to a hypothetical protein from B. subtilis TR:O31400 (EMBL:AJ222587) YKUC (430 aa), fasta scores; opt: 172 z-score: 369.7 E(): 2.7e-13, 23.8% identity in 407 aa overlap. No Hp match; Updated (2006) note: Pfam domains PF07690 Major Facilitator Superfamily (MFS) and PF04332 Protein of unknown function (DUF475) 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, lipoproteins and porins; MFS transport protein complement(425235..426422) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904784 YP_002343896.1 CDS Cj0462 NC_002163.1 426496 427542 D Original (2000) note: Cj0462, unknown, len: 348 aa; similar to many hypothetical proteins e.g. TR:O66979 (EMBL:AE000707) Aquifex aeolicus AQ_789 (361 aa), fasta scores; opt: 1202 z-score: 1804.1 E(): 0, 51.4% identity in 348 aa overlap. 66.2% identity to HP0656. Also similar to Cj1368 (35.5% identity in 349 aa overlap); Updated (2006) note: Pfam domain PF04055 Radical SAM superfamily identified within CDS. Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, 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, such as a phosphorylation receiver or oxygen sensing domain. Product modified to more specific family member due to motif match. Functional classification - Misc; hypothetical protein 426496..427542 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904785 YP_002343897.1 CDS Cj0463 NC_002163.1 427542 428762 D Original (2000) note: Cj0463, zinc protease-like protein, len: 406 aa; some similarity to members of the peptidase M16 (insulinase) family e.g. Y4WB_RHISN hypothetical zinc protease-like protein Y4WB (447 aa),fasta scores; opt: 375 z-score: 306.4 E(): 9.1e-10, 22.7% identity in 396 aa overlap. 39.3% identity to HP0657; Updated (2006) 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, peptides and glycopeptides; zinc protease-like protein 427542..428762 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904786 YP_002343898.1 CDS recG NC_002163.1 428752 430575 D catalyzes branch migration in Holliday junction intermediates; ATP-dependent DNA helicase RecG 428752..430575 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904787 YP_002343899.1 CDS ctb NC_002163.1 430572 430955 R Original (2000) note: Cj0465c, unknown, len: 127 aa; identical to C. jejuni hypothetical protein TR:O52917 (EMBL:CJAJ2417) clone 1g9 ORF1 (fragment) (74 aa). No Hp match; Updated (2006) 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 (Nitrosative stress sensing Regulator - Cj0466) controls the expression of a nitrosative stress-responsive regulon in Campylobacter jejuni which includes ctb (Cj0465c) and cgb (Cj1586). not added to product function. Functional classification - Energy metabolism - Electron transport; PMID:16681372, PMID:16339953, PMID:16045618,PMID:15292134; group III truncated haemoglobin complement(430572..430955) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904788 YP_002343900.1 CDS nssR NC_002163.1 431050 431646 D Original (2000) note: Cj0466, probable transcriptional regulator, len: 198 aa; similar to members of the crp/fnr family e.g. CRP_SALTY catabolite gene activator (210 aa), fasta scores; opt: 191 z-score: 236.7 E(): 6.9e-06, 24.1% identity in 195 aa overlap, and FNR_BACSU anaerobic regulatory protein (238 aa), fasta scores; opt: 182 z-score: 215.5 E(): 0.0001, 23.0% identity in 209 aa overlap. No Hp match. Contains helix-turn-helix motif at aa 150-171 (Score 1452, +4.13 SD); Updated (2006) note: Pfam domain PF00027 Cyclic nucleotide-binding domain identified within CDS. Prosite PS50042 CNMP_BINDING_3, Cyclic nucleotide-binding identified within CDS. Characterised within Campylobacter jejuni. NssR (Nitrosative stress sensing Regulator) controls the expression of a nitrosative stress-responsive regulon in Campylobacter jejuni which includes ctb (Cj0465c) and cgb (Cj1586). not added to product function. Functional classification - Broad regulatory functions; PMID:16045618, PMID:15292134, PMID:16339953,PMID:16681372; transcriptional regulator 431050..431646 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904789 YP_002343901.1 CDS Cj0467 NC_002163.1 431662 432363 D Original (2000) note: Cj0467, probable amino-acid ABC transporter integral membrane protein, len: 233 aa; similar to many e.g. GLNP_ECOLI glutamine transport system permease (219 aa), fasta scores; opt: 237 z-score: 468.8 E(): 8.1e-19, 32.6% identity in 233 aa overlap. 45.3% identity to HP1169. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp sign. and Pfam match to entry PF00528 BPD_transp,Binding-protein-dependent transport systems inner membrane component, score 50.10, E-value 4.9e-11; Updated (2006) note: Literature search identified paper within Campylobacter jejuni linking Cj0467, Cj0468 and Cj0469 as cysteine transporters. Three probable transmembrane helices predicted by TMHMM2.0. not added to product function. Functional classification - Transport/binding proteins - Amino acids and amines; PMID:15948956; amino-acid ABC transporter integral membrane protein 431662..432363 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904790 YP_002343902.1 CDS Cj0468 NC_002163.1 432356 433012 D Original (2000) note: Cj0468, probable amino-acid ABC transporter integral membrane protein, len: 218 aa; similar to many e.g. GLTJ_ECOLI glutamate/aspartate transport system permease (246 aa), fasta scores; opt: 194 z-score: 425.1 E(): 2.2e-16, 25.7% identity in 222 aa overlap. 49.3% identity to HP1170. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp sign. and Pfam match to entry PF00528 BPD_transp,Binding-protein-dependent transport systems inner membrane component, score 52.80, E-value 7.6e-12; Updated (2006) note: Literature search identified paper within Campylobacter jejuni linking Cj0467, Cj0468 and Cj0469 as cysteine transporters. Five probable transmembrane helices predicted by TMHMM2.0. not added to product function. Functional classification - Transport/binding proteins - Amino acids and amines; PMID:15948956; amino-acid ABC transporter integral membrane protein 432356..433012 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904791 YP_002343903.1 CDS Cj0469 NC_002163.1 433014 433775 D Original (2000) note: Cj0469, probable amino-acid ABC transporter ATP-binding protein, len: 2t53 aa; highly similar to many e.g. GLNQ_BACST glutamine transport ATP-binding protein (242 aa), fasta scores; opt: 902 z-score: 1279.6 E(): 0, 55.4% identity in 242 aa overlap. 61.4% identity to HP1171. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00211 ABC transporters family signature, and Pfam match to entry PF00005 ABC_tran, ABC transporters, score 227.80, E-value 1.6e-64; Updated (2006) note: Literature search identified paper within Campylobacter jejuni linking Cj0467, Cj0468 and Cj0469 as cysteine transporters. not added to product function. Functional classification -Transport/binding proteins - Amino acids and amines; PMID:15948956; amino-acid ABC transporter ATP-binding protein 433014..433775 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904792 YP_002343904.1 CDS tuf NC_002163.1 434408 435607 D EF-Tu; promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis; when the tRNA anticodon matches the mRNA codon, GTP hydrolysis results; the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts; many prokaryotes have two copies of the gene encoding EF-Tu; elongation factor Tu 434408..435607 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904796 YP_002343905.1 CDS rpmG NC_002163.1 435660 435818 D in Escherichia coli BM108, a mutation that results in lack of L33 synthesis had no effect on ribosome synthesis or function; there are paralogous genes in several bacterial genomes, 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; the proteins in this group lack the CXXC motif; 50S ribosomal protein L33 435660..435818 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904797 YP_002343906.1 CDS secE NC_002163.1 435925 436104 D forms a complex with SecY and SecG; SecYEG forms a protein-conducting channel to which secA binds and translocates targeted polypeptides across the cytoplasmic membrane, a process driven by ATP and a proton-motive force; preprotein translocase subunit SecE 435925..436104 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904799 YP_002343907.1 CDS nusG NC_002163.1 436114 436647 D Modulates Rho-dependent transcription termination; transcription antitermination protein NusG 436114..436647 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904801 YP_002343908.1 CDS rplK NC_002163.1 436673 437098 D binds directly to 23S ribosomal RNA; 50S ribosomal protein L11 436673..437098 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904802 YP_002343909.1 CDS rplA NC_002163.1 437153 437854 D in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA; 50S ribosomal protein L1 437153..437854 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904803 YP_002343910.1 CDS rplJ NC_002163.1 438006 438485 D binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit; 50S ribosomal protein L10 438006..438485 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904804 YP_002343911.1 CDS rplL NC_002163.1 438506 438883 D present in two forms; L12 is normal, while L7 is aminoacylated at the N-terminal serine; the only multicopy ribosomal protein; 4:1 ratio of L7/L12 per ribosome; two L12 dimers bind L10; critically important for translation efficiency and fidelity; stimulates GTPase activity of translation factors; 50S ribosomal protein L7/L12 438506..438883 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904805 YP_002343912.1 CDS rpoB NC_002163.1 438992 443128 D DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates; beta subunit is part of the catalytic core which binds with a sigma factor to produce the holoenzyme; DNA-directed RNA polymerase subunit beta 438992..443128 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904806 YP_002343913.1 CDS rpoC NC_002163.1 443121 447674 D Original (2000) note: Cj0479, rpoC, DNA-directed RNA polymerase beta' chain, len: 1517 aa; highly similar to many e.g. RPOC_ECOLI DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (1407 aa), fasta scores; opt: 1505 z-score: 5793.8 E(): 0, 46.1% identity in 1541 aa overlap. 69.7% identity to C-terminus of HP1198. Contains Pfam match to entry PF00623 RNA_pol_A, RNA polymerase alpha subunit, score 779.40, E-value 1.4e-230; Updated (2006) note: A total of five Pfam domains have now been identified all encoding the same motif; 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, RNA modification and DNA transcription; PMID:6287430, PMID:6278450; DNA-directed RNA polymerase subunit beta' 443121..447674 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904807 YP_002343914.1 CDS Cj0480c NC_002163.1 447705 448466 R Original (2000) note: Cj0480c, probable transcriptional regulator, len: 253 aa; similar to many e.g. KDGR_ECOLI transcriptional regulator KDGR (263 aa),fasta scores; opt: 305 z-score: 319.1 E(): 1.8e-10, 24.1% identity in 212 aa overlap. No Hp match. Contains helix-turn-helix motif at aa 21-42 (Score 1424, +4.04 SD); Updated (2006) 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; transcriptional regulator complement(447705..448466) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904808 YP_002343915.1 CDS dapA NC_002163.1 448697 449605 D Original (2000) note: Cj0481, probable lyase, len: 302 aa; similar to members of the DHDPS family; e.g. DAPA_BACSU dihydrodipicolinate synthase (290 aa), fasta scores; opt: 444 z-score: 557.2 E(): 9.6e-24, 27.6% identity in 275 aa overlap, and NPL_HAEIN probable N-acetylneuraminate lyase subunit (293 aa), fasta scores; opt: 358 z-score: 428.6 E(): 1.4e-16, 28.5% identity in 291 aa overlap. No Hp match. Also similar to C. jejuni dapA, Cj0806; 26.1% identity in 295 aa overlap. ContainsPfam match to entry PF00701 DHDPS,Dihydrodipicolinate synthetase, score 70.30, E-value 4e-17; Updated (2006) note: Based on similarity search results, product modified to more specific family member. Characterised within Bacillus subtilis and Eschereichia coli, however identity scores were marginal. kept within product function. Functional classification - Misc; PMID:8098035, PMID:P9047371; dihydrodipicolinate synthase 448697..449605 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904809 YP_002343916.1 CDS uxaA' NC_002163.1 449602 449865 D Original (2000) note: Cj0482, uxaA' possible altronate hydrolase N-terminus, len: 87 aa; similar to N-terminus of e.g. UXAA_ECOLI altronate hydrolase (495 aa), fasta scores; opt: 199 z-score: 322.2 E(): 1.2e-10. 46.2% identity in 78 aa overlap. Simlarity continues in downstream ORF Cj0485. No Hp match. Note that B. subtilis paralog of uxaA, YCBI_BACSU, also has a separate N-terminus (YCBH_BACSU); Updated (2006) note: Pfam domain PF04292 D-galactarate dehydratase / 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 ' denoting two separate terminals for the same CDS. May well be a pseudogene. kept within product function. Functional classification - Central intermediary metabolism - General; PMID:3038546, PMID:10762278; altronate hydrolase N-terminus 449602..449865 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 5066041 YP_002343917.1 CDS uxaA' NC_002163.1 449862 451034 D Original (2000) note: Cj0483, uxaA' possible altronate hydrolase C-terminus, len: 390 aa; similar to C-terminus of e.g. UXAA_ECOLI altronate hydrolase (495 aa), fasta scores; opt: 832 z-score: 1121.7 E(): 0, 36.1% identity in 391 aa overlap. Simlarity continues from upstream ORF Cj0482. No Hp match. Note that B. subtilis paralog of uxaA, YCBI_BACSU, also has a separate N-terminus (YCBH_BACSU); Updated (2006) note: Pfam domain PF04295 D-galactarate dehydratase / 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 ' denoting two separate terminals for the same CDS. May well be a pseudogene. kept within product function. Functional classification - Central intermediary metabolism - General; PMID:3038546, PMID:10762278; altronate hydrolase C-terminus 449862..451034 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904810 YP_002343918.1 CDS Cj0484 NC_002163.1 451046 452278 D Original (2000) note: Cj0484, probable transmembrane transport protein, len: 410 aa; similar to members of the phalate transporter family e.g. TR:Q44470 (EMBL:U25634) Agrobacterium vitis tartrate transporter (433 aa), fasta scores; opt: 1004 z-score: 1322.2 E(): 0, 40.4% identity in 408 aa overlap, and PHT1_PSEPU phthalate transporter (451 aa), fasta scores; opt: 663 z-score: 835.4 E(): 0, 29.8% identity in 413 aa overlap. No Hp ortholog; Updated (2006) note: Pfam domain PF07690 Major Facilitator Superfamily (MFS) identified within CDS. Eleven probable transmembrane helices predicted by TMHMM2.0. Product modified to more specific family member due to motif match. Functional classification -Transport/binding proteins - Other; MFS transport protein 451046..452278 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904811 YP_002343919.1 CDS Cj0485 NC_002163.1 452320 453108 D Original (2000) note: Cj0485, probable oxidoreductase, len: 262 aa; similar to many e.g. FABG_AQUAE 3-oxoacyl-[acyl-carrier protein] reductase (248 aa), fasta scores; opt: 384 z-score: 465.5 E(): 1.2e-18,34.3% identity in 254 aa overlap, and BA71_EUBSP 7-alpha-hydroxysteroid dehydrogenase (249 aa), fasta scores; opt: 349 z-score: 421.2 E(): 3.6e-16, 32.3% identity in 254 aa overlap. No Hp ortholog. Also similar to C. jejuni fabG, Cj0435 (31.7% identity in 252 aa overlap). Contains Pfam matches to entry PF00106 adh_short, Alcohol/other dehydrogenases, short chain type,score 143.40, E-value 4e-39 and to entry PF00678 adh_short_C2, Short chain dehydrogenase /reductase C-terminus, score 31.00, E-value 2.7e-05; Updated (2006) note: Characterisation work in more than one species with marginal identity scores. kept within product function. Functional classification -Misc; short chain dehydrogenase 452320..453108 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904812 YP_002343920.1 CDS Cj0486 NC_002163.1 453119 454375 D Original (2000) note: Cj0486, probable sugar transporter, len: 418 aa; simlar to members of the FHS family e.g. FUCP_ECOLI L-fucose permease (438 aa), fasta scores; opt: 848 z-score: 1022.1 E(): 0, 37.2% identity in 390 aa overlap, and GLUP_BRUAB glucose/galactose transporter (412 aa), fasta scores; opt: 456 z-score: 830.5 E(): 0, 33.4% identity in 410 aa overlap. 32.6% identity to HP1174; Updated (2006) note: Pfam domain PF07690 Major Facilitator Superfamily identified within CDS. Prosite PS50850 MFS, 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 (L-fucose permease). This permease mediates the uptake of L-fucose across the boundary membrane with the concomitant transport of protons into the cell (symport system). It can also transport L-galactose and D-arabinose, but at reduced rates compared with L-fucose. Other sugar transporters also identified. Product function kept the same along with . Functional classification - Transport/binding proteins - Carbohydrates, organic acids and alcohols; PMID:15919996, PMID:7783647, PMID:8052131; sugar transporter 453119..454375 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904814 YP_002343921.1 CDS Cj0487 NC_002163.1 454359 455129 D Original (2000) note: Cj0487, unknown, len: 256 aa; some similarity to Y4MH_RHISN hypothetical protein Y4MH (297 aa), fasta scores; opt: 98 z-score: 200.8 E(): 0.00069, 22.7% identity in 295 aa overlap. No Hp match; Updated (2006) 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, kept within product function. Functional classification - Misc; amidohydrolase 454359..455129 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904815 YP_002343922.1 CDS Cj0488 NC_002163.1 455130 455447 D Original (2000) note: Cj0488, unknown, len: ; similar to a hypothetical protein from B. subtilis TR:O05263 (EMBL:Z93938) YULD(104 aa), fasta scores; opt: 183 z-score: 266.1 E(): 1.6e-07, 33.6% identity in 107 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF05336 Protein of unknown function (DUF718) identified within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins; hypothetical protein 455130..455447 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904816 YP_002343923.1 CDS ald' NC_002163.1 455461 455682 D Original (2000) note: Cj0489, ald', aldehyde dehydrogenase N-terminus, len: 73 aa; highly similar to ALDA_ECOLI aldehyde dehydrogenase A (EC 1.2.1.22) (478 aa), fasta scores; opt: 229 z-score: 319.3 E(): 1.7e-10,51.5% identity in 68 aa overlap. Similarity continues into downstream ORF Cj0490. No error in the sequence can be found. No Hp match; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. Gene names for Cj0489 and Cj0490 are identical with a ' denoting two separate terminals for the same CDS. May well be a pseudogene. kept within product function. Functional classification - Central intermediary metabolism - General; PMID:3308886; aldehyde dehydrogenase N-terminus 455461..455682 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 5066042 YP_002343924.1 CDS ald' NC_002163.1 455718 456899 D Original (2000) note: Cj0490, ald', aldehyde dehydrogenase C-terminus, len: 393 aa; highly similar to ALDA_ECOLI aldehyde dehydrogenase A (EC 1.2.1.22) (478 aa), fasta scores; opt: 1653 z-score: 2398.4 E(): 0, 63.7% identity in 388 aa overlap. Similarity continues from upstream ORF Cj0489. No error in the sequence can be found. No Hp match. Contains PS00687 Aldehyde dehydrogenases glutamic acid active site and Pfam match to entry PF00171 aldedh, Aldehyde dehydrogenase, score 433.60, E-value 1.8e-126; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. Gene names for Cj0489 and Cj0490 are identical with a ' denoting two separate terminals for the same CDS. May well be a pseudogene. kept within product function. Functional classification - Central intermediary metabolism - General; PMID:3308886; aldehyde dehydrogenase C-terminus 455718..456899 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904817 YP_002343925.1 CDS rpsL NC_002163.1 457227 457613 D interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone; located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side; mutations in the S12 gene confer streptomycin resistance; 30S ribosomal protein S12 457227..457613 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904818 YP_002343926.1 CDS rpsG NC_002163.1 457683 458153 D binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit; 30S ribosomal protein S7 457683..458153 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904819 YP_002343927.1 CDS fusA NC_002163.1 458166 460241 D EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene; elongation factor G 458166..460241 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904822 YP_002343928.1 CDS Cj0494 NC_002163.1 460364 460513 D Original (2000) note: Cj0494, small hydrophobic protein, len: 49 aa; no Hp match; Updated (2006) note: Product function modified to more specific family member based on SignalP 2.0 HMM results. kept within product function. Functional classification - Transport/binding proteins - Other; exporting protein 460364..460513 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904824 YP_002343929.1 CDS Cj0495 NC_002163.1 460519 461220 D Original (2000) note: Cj0495, unknown, len: 233 aa; some simillarity to hypothetical proteins e.g. YABB_BACSU (247 aa), fasta scores; opt: 295 z-score: 352.0 E(): 2.6e-12, 23.9% identity in 230 aa overlap. 36.9% identity to HP1504. Contains PS00092 N-6 Adenine-specific DNA methylases signature; Updated (2006) 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, SAM (and some other nucleotide) 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; PMID:9873033; methyltransferase domain protein 460519..461220 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904825 YP_002343930.1 CDS Cj0496 NC_002163.1 461210 461584 D Original (2000) note: Cj0496, unknown, len: 124 aa; similar to hypothetical proteins e.g. TR:O59308 (EMBL:AB009522) Pyrococcus horikoshii PHAV002 (141 aa),fasta scores; opt: 154 z-score: 270.6 E(): 8.8e-08,30.1% identity in 113 aa overlap. 47.5% identity to HP0274; Updated (2006) note: Pfam domain PF03692 Uncharacterised protein family (UPF0153) identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins; hypothetical protein 461210..461584 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904826 YP_002343931.1 CDS Cj0497 NC_002163.1 461557 462834 D Original (2000) note: Cj0497, probable lipoprotein,len: 425 aa; some similarity to hypothetical prteins e.g. TR:O67021 (EMBL:AE000710) Aquifex aeolicus AQ_854 (545 aa), fasta scores; opt: 266 z-score: 326.7 E(): 6.7e-11,29.1% identity in 412 aa overlap. 26.7% identity to HP0275 (misannotated as ATP-dependent nuclease (addB)). Contains N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes, lipoproteins and porins; lipoprotein 461557..462834 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904827 YP_002343932.1 CDS trpC NC_002163.1 462831 463607 D involved in tryptophan biosynthesis; amino acid biosynthesis; converts 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate to C(1)-(3-indolyl)-glycerol 3-phosphate and carbon dioxide and water; indole-3-glycerol-phosphate synthase 462831..463607 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904828 YP_002343933.1 CDS Cj0499 NC_002163.1 463617 464102 D Original (2000) note: Cj0499, unknown, len: 161 aa; similar to many members of the HIT family e.g. HIT_BACSU HIT protein (145 aa), fasta scores; opt: 176 z-score: 274.7 E(): 5.2e-08, 26.1% identity in 111 aa overlap. 42.6% identity to HP0741. Contains Pfam match to entry PF01230 HIT, HIT family, score 19.90, E-value 3.6e-06; Updated (2006) 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; histidine triad (HIT) family protein 463617..464102 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904829 YP_002343934.1 CDS Cj0500 NC_002163.1 464092 465090 D catalyzes the selenophosphate-dependent transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA; tRNA 2-selenouridine synthase 464092..465090 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904830 YP_002343935.1 CDS hemH NC_002163.1 466660 467571 R protoheme ferro-lyase; catalyzes the insertion of a ferrous ion into protoporphyrin IX to form protoheme; involved in protoheme biosynthesis; in some organisms this protein is membrane-associated while in others it is cytosolic; ferrochelatase complement(466660..467571) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904832 YP_002343936.1 CDS Cj0504c NC_002163.1 467568 468434 R Original (2000) note: Cj0504c, unknown, len: 288 aa; similar to hypothetical proteins e.g. YISS_BACSU 342 aa), fasta scores; opt: 224 z-score: 359.9 E(): 9.4e-13,28.1% identity in 192 aa overlap. 26.4% identity to HP0679; Updated (2006) note: Pfam domain PF01408 Oxidoreductase family, 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; oxidoreductase complement(467568..468434) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904833 YP_002343937.1 CDS Cj0505c NC_002163.1 468439 469512 R Updated (2006) note: Some characterisation work carried out within Bacillus stearothermophilus with acceptable identity score. kept within product function; Original (2000) note: Cj0505c, possible aminotransferase, len: 357 aa; similar to members of the degT family e.g. DEGT_BACST (372 aa), fasta scores; opt: 857 z-score: 1253.3 E(): 0, 38.8% identity in 356 aa overlap. No Hp ortholog. Contains Pfam match to entry PF01041 DegT_DnrJ_EryC1, DegT/DnrJ/EryC1/StrS family,score 441.40, E-value 7.9e-129; PMID:2104607; DegT family aminotransferase complement(468439..469512) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904834 YP_002343938.1 CDS alaS NC_002163.1 469627 472155 D Catalyzes a two-step reaction, first charging an alanyl molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; alanyl-tRNA synthetase 469627..472155 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904835 YP_002343939.1 CDS maf NC_002163.1 472155 472706 D Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell; Maf-like protein 472155..472706 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904836 YP_002343940.1 CDS pbpA NC_002163.1 472703 474634 D Original (2000) note: Cj0508, pbpA, probable penicillin-binding protein, len: 643 aa; similar to many e.g. PBPB_ECOLI penicillin-binding protein 1B (PBP-1B) (844 aa), fasta scores; opt: 774 z-score: 915.8 E(): 0,32.5% identity in 616 aa overlap. 48.0% identity to HP0597. Also similar to Cj0525c (22.9% identity in 407 aa overlap). Contains Pfam matches to entry PF00912 Transglycosyl, Transglycosylase, score 299.40, E-value 4.5e-86 and Pfam match to entry PF00905 Transpeptidase,Penicillin binding protein transpeptidase domain, score 103.80, E-value 3.3e-27; Updated (2006) note: Characterised within Escherichia coli with marginal identity score. not added to product function. Functional classification -Murein sacculus and peptidoglycan; PMID:11181392, PMID:9841666, PMID:8335642; penicillin-binding protein 472703..474634 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904837 YP_002343941.1 CDS clpB NC_002163.1 474662 477235 R Original (2000) note: Cj0509c, clpB, ATP-dependent CLP protease ATP-binding subunit, len: 857 aa; 98.9% identical to C. jejuni TR:O69287 (EMBL:Y13333) and similar to many e.g. CLAA_LYCES ATP-dependent CLP protease ATP-binding subunit (926 aa), fasta scores; opt: 1130 z-score: 2439.8 E(): 0, 45.0% identity in 845 aa overlap. 61.2% identity to HP0264. Also simlar to C. jejuni clpA (Cj1108); 36.6% identity in 836 aa overlap. Contains 2x PS00017 ATP/GTP-binding site motif A (P-loop), PS00870 and PS00871 Chaperonins clpA/B signatures 1 and 2, and Pfam match to entry PF00495 clpA_B, Chaperonins clpA/B, score 1257.60, E-value 0; Updated (2006) note: Characterised within Campylobacter jejuni. not added to product function. Functional classification - Chaperones,chaperonins, heat shock; PMID:10196475; ATP-dependent Clp protease ATP-binding subunit complement(474662..477235) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904838 YP_002343942.1 CDS Cj0510c NC_002163.1 477347 477637 R Original (2000) note: Cj0510c, unknown, len: 96 aa; similar to hypothetical proteins e.g. TR:O32222 (EMBL:Z99121) B. subtilis YVGZ protein (101 aa), fasta scores; opt: 212 z-score: 338.9 E(): 1.4e-11, 40.0% identity in 95 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF02583 Uncharacterised BCR, COG1937 identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins; hypothetical protein complement(477347..477637) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904839 YP_002343943.1 CDS Cj0511 NC_002163.1 477755 479089 D Original (2000) note: Cj0511, probable secreted protease, len: 444 aa; similar to many e.g. PRC_ECOLI tail-specific protease precursor (682 aa), fasta scores; opt: 357 z-score: 500.2 E(): 1.4e-20, 29.9% identity in 388 aa overlap. 54.3% identity to HP1350. Contains possible N-terminal signal sequence and Pfam match to entry PF00595 PDZ, PDZ domain (Also known as DHR or GLGF)., score 52.00, E-value 1.3e-11; Updated (2006) 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 (PMID:12186869). Functional classification - Protein translation and modification; PMID:8576225, PMID:12186869; secreted protease 477755..479089 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904840 YP_002343944.1 CDS purC NC_002163.1 479091 479801 D catalyzes the formation of (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxamido)succinate from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate and L-aspartate in purine biosynthesis; SAICAR synthase; phosphoribosylaminoimidazole-succinocarboxamide synthase 479091..479801 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904841 YP_002343945.1 CDS purS NC_002163.1 479810 480055 D Original (2000) note: Cj0513, unknown, len: 81 aa; similar to many e.g. YEXA_BACSU hypothetical 9.7 kd protein in PURC-PURL intergenic region (84 aa), fasta scores; opt: 248 z-score: 331.6 E(): 3.6e-11, 48.1% identity in 79 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF02700 Phosphoribosylformylglycinamidine (FGAM) 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; PMID:15301532, PMID:10071207; phosphoribosylformylglycinamidine synthase 479810..480055 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904842 YP_002343946.1 CDS purQ NC_002163.1 480057 480728 D catalyzes the formation of 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine from N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide and L-glutamine in purine biosynthesis; phosphoribosylformylglycinamidine synthase I 480057..480728 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904843 YP_002343947.1 CDS Cj0515 NC_002163.1 480700 481896 D Original (2000) note: Cj0515, possible periplasmic protein, len: 398 aa; 27.2% identity to HP1349; Updated (2006) note: One probable transmembrane helices predicted by TMHMM2.0 within CDS. Functional classification - Miscellaneous periplasmic proteins; periplasmic protein 480700..481896 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904844 YP_002343948.1 CDS plsC NC_002163.1 481877 482569 D Original (2000) note: Cj0516, plsC, possible 1-acyl-SN-glycerol-3-phosphate acyltransferase, len: 230 aa; similar to e.g. PLCB_HUMAN 1-acyl-SN-glycerol-3-phosphate acyltransferase (EC 2.3.1.51) (278 aa), fasta scores; opt: 227 z-score: 328.0 E(): 5.7e-11, 25.7% identity in 210 aa overlap. 38.4% identity to HP1348; Updated (2006) note: Pfam domain PF01553 Acyltransferase along with Prosite domains PS50239 GLYCEROL_ACYLTRANS, Phospholipid/glycerol acyltransferase and PS00989 CLAT_ADAPTOR_S, Clathrin adaptor complex,small 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; PMID:1557036; 1-acyl-SN-glycerol-3-phosphate acyltransferase 481877..482569 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904845 YP_002343949.1 CDS crcB NC_002163.1 482563 482931 D Original (2000) note: Cj0517, crcB, probable integral membrane protein, len: 122 aa; similar to e.g. CRCB_ECOLI CRCB protein (127 aa), fasta scores; opt: 245 z-score: 278.4 E(): 3.2e-08, 37.9% identity in 124 aa overlap. 33.9% identity to HP1225; Updated (2006) 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, lipoproteins and porins; PMID:2904550; CrcB protein 482563..482931 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904846 YP_002343950.1 CDS htpG NC_002163.1 483003 484829 D molecular chaperone; heat shock protein 90 483003..484829 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904847 YP_002343951.1 CDS Cj0519 NC_002163.1 484826 485143 D Original (2000) note: Cj0519, unknown, len: 105 aa; similar to hypothetical proteins e.g. TR:E1342888 (EMBL:AJ235272) Rickettsia prowazekii RP600 (123 aa),fasta scores; opt: 151 z-score: 214.9 E(): 0.00011, 41.6% identity in 89 aa overlap. 34.3% identity to HP1223; Updated (2006) note: Prosite domain PS50206 RHODANESE_3, Rhodanese domain profile also identified within CDS. Rhodanese, 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, including phosphatases and ubiquitin C-terminal hydrolases. Product modified to new function based on motif identification. No specific characterisation has been carried out yet, so kept within product function. Functional classification -Misc; rhodanese-like domain protein 484826..485143 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904848 YP_002343952.1 CDS Cj0520 NC_002163.1 485143 485577 D Original (2000) note: Cj0520, possible membrane protein, len: 144 aa; no Hp match. Contains one possible transmembrane domain at N-terminus. Functional classification - Membranes, lipoproteins and porins; hypothetical protein 485143..485577 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904849 YP_002343953.1 CDS Cj0522 NC_002163.1 485698 486201 D Original (2000) note: Cj0522, possible membrane protein, len: 167 aa; no Hp match. May be fragment of pseudogene; Updated (2006) note: Pfam domain PF02690 Na+/Pi-cotransporter identified within CDS. Three 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 - Transport/binding proteins - Cations; Na+/Pi cotransporter protein 485698..486201 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904850 YP_002343954.1 CDS Cj0523 NC_002163.1 486213 486488 D Original (2000) note: Cj0523, possible membrane protein, len: 91 aa; no Hp match. May be fragment of pseudogene; Updated (2006) note: Three probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; hypothetical protein 486213..486488 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904851 YP_002343955.1 CDS Cj0524 NC_002163.1 486642 487343 D Original (2000) note: Cj0524, unknown, len: 233 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins and cotransporter family proteins from other bacteria. Functional classification - Unknown; hypothetical protein 486642..487343 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904852 YP_002343956.1 CDS pbpB NC_002163.1 487340 489148 R Original (2000) note: Cj0525c, pbpB, probable penicillin-binding protein, len: 602 aa; similar to many e.g. PBP2_NEIME penicillin-binding protein 2 (581 aa),fasta scores; opt: 184 z-score: 511.3 E(): 3.5e-21. 28.9% identity in 443 aa overlap. 35.8% identity to HP1556 (misannotated as cell division protein (ftsI)). Also similar to Cj0508 (22.6% identity in 407 aa overlap). Contains PS00017 ATP/GTP-binding site motif A (P-loop),Pfam match to entry PF00905 Transpeptidase, Penicillin binding protein transpeptidase domain, score 259.30,E-value 5.2e-74 and N-terminal signal sequence; Updated (2006) 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; PMID:8244929, PMID:8289242; penicillin-binding protein complement(487340..489148) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904853 YP_002343957.1 CDS fliE NC_002163.1 489155 489451 R forms a junction between the M-ring and FlgB during flagella biosynthesis; flagellar hook-basal body protein FliE complement(489155..489451) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904854 YP_002343958.1 CDS flgC NC_002163.1 489458 489952 R with FlgF and B makes up the proximal portion of the flagellar basal body rod; flagellar basal body rod protein FlgC complement(489458..489952) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904855 YP_002343959.1 CDS flgB NC_002163.1 489962 490393 R with FlgF and C makes up the proximal portion of the flagellar basal body rod; Vibrio parahaemolyticus protein is associated with the polar flagella; flagellar basal body rod protein FlgB complement(489962..490393) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904856 YP_002343960.1 CDS Cj0529c NC_002163.1 490474 491475 R Original (2000) note: Cj0529c, unknown, len: 333 aa; similar to hypothetical proteins e.g.YCEG_ECOLI hypothetical 38.2 kd protein in PABC-HOLB intergenic region (340 aa), fasta scores; opt: 326 z-score: 408.1 E(): 1.9e-15, 31.3% identity in 252 aa overlap. 43.0% identity to HP0587 (misannotated as aminodeoxychorismate lyase (pabC)); Updated (2006) 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'-phosphate-dependent enzyme that converts 4-aminodeoxychorismate to pyruvate and p-aminobenzoate, a precursor of folic acid in bacteria (PMID:11011151). 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; PMID:11011151; aminodeoxychorismate lyase family protein complement(490474..491475) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904857 YP_002343961.1 CDS Cj0530 NC_002163.1 491390 493960 D Original (2000) note: Cj0530, probable periplasmic protein, len: 856 aa; 22.7% identity to HP0586. Contains N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein 491390..493960 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904858 YP_002343962.1 CDS icd NC_002163.1 494077 496281 D Original (2000) note: Cj0531, icd, probable isocitrate dehydrogenase, len: 734 aa; highly similar to e.g. IDH2_VIBA1 isocitrate dehydrogenase (NADP) 2 (EC 1.1.1.42) (741 aa), fasta scores; opt: 2534 z-score: 3250.7 E(): 0, 53.3% identity in 733 aa overlap. No Hp match; Updated (2006) 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; PMID:8226630, PMID:14702320; isocitrate dehydrogenase 494077..496281 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904859 YP_002343963.1 CDS mdh NC_002163.1 496278 497180 D Original (2000) note: Cj0532, mdh, probable malate dehydrogenase, len: 300 aa; MDH_CHLTE malate dehydrogenase (EC 1.1.1.37) (310 aa), fasta scores; opt: 652 z-score: 1151.6 E(): 0, 35.4% identity in 294 aa overlap. No Hp match. Also similar toCj1167 ldh (25.4% identity in 311 aa overlap). Contains Pfam match to entry PF00056 ldh,L-lactate dehydrogenases, score 153.00, E-value 1e-42; Updated (2006) note: Pfam domain PF02866 lactate/malate dehydrogenase, alpha/beta 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; PMID:1735722, PMID:8550482, PMID:14702320; malate dehydrogenase 496278..497180 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904860 YP_002343964.1 CDS sucC NC_002163.1 497181 498344 D catalyzes the interconversion of succinyl-CoA and succinate; succinyl-CoA synthetase subunit beta 497181..498344 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904861 YP_002343965.1 CDS sucD NC_002163.1 498354 499223 D Original (2000) note: Cj0534, sucD, probable succinyl-coA synthetase alpha chain, len: 289 aa; highly similar to many e.g. SUCD_ECOLI succinyl-coA synthetase alpha chain (EC 6.2.1.5) (288 aa), fasta scores; opt: 1101 z-score: 1532.0 E(): 0, 58.5% identity in 287 aa overlap. No Hp match. Contains PS01216 ATP-citrate lyase / succinyl-CoA ligases family signature 1, PS00399 ATP-citrate lyase / succinyl-CoA ligases family active site, and Pfam match to entry PF00549 ligase-CoA,CoA-ligases, score 142.30, E-value 8.6e-39; Updated (2006) 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; PMID:3543212, PMID:14702320; succinyl-coA synthetase alpha chain 498354..499223 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904862 YP_002343966.1 CDS oorD NC_002163.1 499238 499549 D Original (2000) note: Cj0535, oorD, probable OORD subunit of 2-oxoglutarate:acceptor oxidoreductase, len: 103 aa; similar to TR:O68227 (EMBL:AF021094) H. pylori OORD subunit of 2-oxoglutarate:acceptor oxidoreductase (113 aa), fasta scores; opt: 436 z-score: 768.9 E(): 0,59.8% identity in 97 aa overlap. 59.8% identity to HP0588. Contains 2x PS00198 4Fe-4S ferredoxins, iron-sulfur binding region signature and Pfam match to entry PF00037 fer4, 4Fe-4S ferredoxins and related iron-sulfur cluster binding domains., score 17.40, E-value 0.00091; Updated (2006) note: Characterised within Helicobacter pylori with acceptable identity score. not added to product function. Functional classification - Energy metabolism - Electron transport; PMID:9495749, PMID:7608066, PMID:14702320; 2-oxoglutarate-acceptor oxidoreductase subunit OorD 499238..499549 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904863 YP_002343967.1 CDS oorA NC_002163.1 499558 500682 D Original (2000) note: Cj0536, oorA, probable OORA subunit of 2-oxoglutarate:acceptor oxidoreductase, len: 374 aa; similar to TR:O68228 (EMBL:AF021094) H. pylori OORA subunit of 2-oxoglutarate:acceptor oxidoreductase (371 aa), fasta scores; opt: 1447 z-score: 2256.7 E(): 0,62.7% identity in 351 aa overlap. 63.2% identity to HP0589; Updated (2006) note: Pfam domain PF01855 Pyruvate flavodoxin/ferredoxin 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; PMID:9495749, PMID:7608066, PMID:14702320; 2-oxoglutarate-acceptor oxidoreductase subunit OorA 499558..500682 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904864 YP_002343968.1 CDS oorB NC_002163.1 500683 501528 D Original (2000) note: Cj0537, oorB, probable OORB subunit of 2-oxoglutarate:acceptor oxidoreductase, len: 281 aa; similar to TR:O68229 (EMBL:AF021094) H. pylori OORB subunit of 2-oxoglutarate:acceptor oxidoreductase (274 aa), fasta scores; opt: 1356 z-score: 2118.6 E(): 0,69.7% identity in 274 aa overlap. 72.9% identity to HP0590; Updated (2006) note: Pfam domain PF02775 Thiamine pyrophosphate enzyme, 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; PMID:9495749, PMID:7608066, PMID:14702320; 2-oxoglutarate-acceptor oxidoreductase subunit OorB 500683..501528 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904963 YP_002343969.1 CDS oorC NC_002163.1 501525 502082 D Original (2000) note: Cj0538, oorC, probable OORC subunit of 2-oxoglutarate:acceptor oxidoreductase, len: 185 aa; similar to TR:O68230 (EMBL:AF021094) H. pylori OORC subunit of 2-oxoglutarate:acceptor oxidoreductase (184 aa), fasta scores; opt: 714 z-score: 1191.4 E(): 0,59.7% identity in 181 aa overlap. 60.8% identity to HP0591; Updated (2006) note: Pfam domain PF01558 Pyruvate ferredoxin/flavodoxin 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; PMID:9495749, PMID:7608066, PMID:14702320; 2-oxoglutarate-acceptor oxidoreductase subunit OorC 501525..502082 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905096 YP_002343970.1 CDS Cj0539 NC_002163.1 502221 502484 D Original (2000) note: Cj0539, unknown, len: 87 aa; no Hp match. Functional classification - Unknown; hypothetical protein 502221..502484 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904865 YP_002343971.1 CDS Cj0540 NC_002163.1 502487 503023 D Original (2000) note: Cj0540, unknown, len: 178 aa; 30.6% identity in 72 aa overlap (N-terminus) to HP0241; Updated (2006) 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; exporting protein 502487..503023 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904866 YP_002343972.1 CDS Cj0541 NC_002163.1 503037 503930 D Original (2000) note: Cj0541, probable polyprenyl synthetase, len: 297 aa; similar to many e.g. ISPB_ECOLI octaprenyl-diphosphate synthase (EC 2.5.1.-) (323 aa),fasta scores; opt: 514 z-score: 753.9 E(): 0, 35.2% identity in 281 aa overlap, IDSA_METTM bifunctional short chain isoprenyl diphosphate synthase (324 aa), fasta scores; opt: 549 z-score: 676.0 E(): 2.3e-30, 36.5% identity in 277 aa overlap, and GGPP_SULAC geranylgeranyl pyrophosphate synthetase (330 aa), fasta scores; opt: 330 z-score: 653.2 E(): 4.4e-29, 32.9% identity in 292 aa overlap. 44.6% identity to HP0240. Also similar to Cj1644 (27.6% identity in 268 aa overlap). Contains PS00723 and PS00444 Polyprenyl synthetases signatures 1 and 2, and Pfam match to entry PF00348 polyprenyl_synt, Polyprenyl synthetases, score 153.40, E-value 3.8e-42; Updated (2006) note: Similarity to more than one characterised genus with acceptable identity scores. not added to product function. Functional classification - Biosynthesis of cofactors, prosthetic groups and carriers - Menaquinone and ubiquinine; PMID:8037730; polyprenyl synthetase 503037..503930 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904867 YP_002343973.1 CDS hemA NC_002163.1 503930 505228 D catalyzes the formation of glutamate-1-semialdehyde from glutamyl-tRNA(Glu) and NADPH; the second step of the pathway is catalyzed by glutamate-1-semialdehyde aminomutase which results in the formation of 5-aminolevulinic acid; functions in porphyrin (tetrapyrroles) biosynthesis; the crystal structure showed a C-terminal dimerization domain that appears to be absent in Chlamydial proteins; glutamyl-tRNA reductase 503930..505228 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904868 YP_002343974.1 CDS proS NC_002163.1 505212 506921 D catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro); prolyl-tRNA synthetase 505212..506921 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904869 YP_002343975.1 CDS Cj0544 NC_002163.1 506918 507307 D Original (2000) note: Cj0544, probable integral membrane protein, len: 129 aa; no Hp match; Updated (2006) note: Three probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; integral memnbrane protein 506918..507307 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904870 YP_002343976.1 CDS hemC NC_002163.1 507304 508227 D transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis; porphobilinogen deaminase 507304..508227 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904871 YP_002343977.1 CDS ubiD NC_002163.1 508224 510026 D Original (2000) note: Cj0546, unknown, len: 600 aa; similar to many hypothetical proteins e.g. YIGC_ECOLI (497 aa), fasta scores; opt: 837 z-score: 852.4 E(): 0, 32.7% identity in 459 aa overlap. 51.6% identity to HP0396; Updated (2006) 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; PMID:782527, PMID:11029449; 3-octaprenyl-4-hydroxybenzoate carboxylyase 508224..510026 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904873 YP_002343978.1 CDS flaG NC_002163.1 510184 510549 D possibly involved in flagella export; flagellar protein FlaG 510184..510549 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904874 YP_002343979.1 CDS fliD NC_002163.1 510552 512480 D Also called hook-associated protein 2; involved in flagellin assembly; flagellar capping protein 510552..512480 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904875 YP_002343980.1 CDS fliS NC_002163.1 512492 512878 D flagellin specific chaperone; flagellar protein FliS 512492..512878 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904876 YP_002343981.1 CDS Cj0550 NC_002163.1 512859 513134 D Original (2000) note: Cj0550, unknown, len: 91 aa; no Hp match. Functional classification - Unknown; hypothetical protein 512859..513134 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904877 YP_002343982.1 CDS efp NC_002163.1 513566 514135 D Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA; elongation factor P 513566..514135 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904879 YP_002343983.1 CDS Cj0552 NC_002163.1 514295 514987 D Original (2000) note: Cj0552, unknown, len: 230 aa; no Hp match. Hydrophobic; Updated (2006) note: Pfam domain PF06149 Protein of unknown function (DUF969) 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, lipoproteins and porins; hypothetical protein 514295..514987 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904880 YP_002343984.1 CDS Cj0553 NC_002163.1 514974 515927 D Original (2000) note: Cj0553, probable integral membrane protein, len: 317 aa; no Hp match; Updated (2006) note: Pfam domain PF06166 Protein of unknown function (DUF979) 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,lipoproteins and porins; integral membrane protein 514974..515927 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904881 YP_002343985.1 CDS Cj0554 NC_002163.1 515937 516941 D Original (2000) note: Cj0554, unknown, len: 334 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein 515937..516941 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904341 YP_002343986.1 CDS Cj0555 NC_002163.1 517060 518352 D Original (2000) note: Cj0555, probable integral membrane protein, len: 430 aa; similar in N-terminus to an ORF within the Streptococcus pneumoniae cps3E and rpt pseudogene region TR:P72556 (EMBL:U66846) orf5 (197 aa),fasta scores; opt: 493 z-score: 726.3 E(): 3.7e-33, 47.4% identity in 152 aa overlap. No Hp match; Updated (2006) 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 (PMID:9826185). 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, so kept within product function. Functional classification - Carbohydrates, organic acids and alcohols; PMID:9826185; dicarboxylate carrier protein MatC 517060..518352 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904882 YP_002343987.1 CDS Cj0556 NC_002163.1 518363 519160 D Original (2000) note: Cj0556, unknown, len: 265 aa; no Hp match; Updated (2006) 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; amidohydrolase family protein 518363..519160 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904883 YP_002343988.1 CDS Cj0557c NC_002163.1 519157 520242 R Original (2000) note: Cj0557c, probable integral membrane protein, len: 361 aa; similar in C terminus to hypothetical proteins from B. subtilis and E. coli: TR:O32225 (EMBL:O32225) YVAC (631 aa), fasta scores; opt: 271 z-score: 562.0 E(): 5.2e-24, 29.9% identity in 187 aa overlap, and YHFK_ECOLI (696 aa), fasta scores; opt: 182 z-score: 212.9 E(): 0.00015, 27.8% identity in 133 aa overlap. No Hp match; Updated (2006) note: Nine probable transmembrane helices predicted by TMHMM2.0. Further support added to product function. Functional classification - Membranes,lipoproteins and porins; integral membrane protein complement(519157..520242) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904884 YP_002343989.1 CDS proA NC_002163.1 520239 521471 R Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway; gamma-glutamyl phosphate reductase complement(520239..521471) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904885 YP_002343990.1 CDS Cj0559 NC_002163.1 521542 522477 D Original (2000) note: Cj0559, probable oxidoreductase, len: 311 aa; similar to members of the pyridine nucleotide-disulfide oxidoreductases class-II family e.g. R34K_CLOPA 34.2 KD protein in rubredoxin operon (308 aa), fasta scores; opt: 217 z-score: 335.8 E(): 2.1e-11, 23.2% identity in 314 aa overlap, and TRXB_BACSU thioredoxin reductase (315 aa), fasta scores; opt: 192 z-score: 279.9 E(): 2.7e-08, 25.9% identity in 313 aa overlap. 46.3% identity to HP1164. Contains possible N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site; Updated (2006) 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; pyridine nucleotide-disulphide oxidoreductase 521542..522477 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905160 YP_002343991.1 CDS Cj0560 NC_002163.1 522658 523986 D Original (2000) note: Cj0560, probable integral membrane protein, len: 442 aa; similar to many hypothetical proteins e.g. Y709_METJA MJ0709 (450 aa),fasta scores; opt: 402 z-score: 324.8 E(): 8.5e-11, 21.0% identity in 429 aa overlap. 26.3% identity to HP1184; Updated (2006) note: Pfam domain PF01554 MatE identified within CDS. Prosite domain PS00589 PTS_HPR_SER,Phosphotransferase system, HPr serine phosphorylation site also identified. Twelve probable transmembrane helices predicted by TMHMM2.0. Characterised members of the Multi Antimicrobial Extrusion (MATE) family function as drug/sodium antiporters. These proteins mediate resistance to a wide range of cationic dyes, fluroquinolones,aminoglycosides and other structurally diverse antibodies and drugs. MATE proteins are found in bacteria, archaea and eukaryotes. These proteins are predicted to have 12 alpha-helical transmembrane regions (which this one does). 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; PMID:16048946; MATE family transport protein 522658..523986 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905129 YP_002343992.1 CDS Cj0561c NC_002163.1 524034 524963 R Original (2000) note: Cj0561c, possible periplasmic protein, len: 309 aa; no Hp match; Updated (2006) note: possible changed to . Functional classification - Miscellaneous periplasmic proteins; periplasmic protein complement(524034..524963) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905206 YP_002343993.1 CDS dnaB NC_002163.1 525117 526493 D unwinds double stranded DNA; replicative DNA helicase 525117..526493 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904886 YP_002343994.1 CDS Cj0563 NC_002163.1 526556 527158 D Original (2000) note: Cj0563, unknown, len: 200 aa; no Hp match. Functional classification - Unknown; hypothetical protein 526556..527158 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905136 YP_002343995.1 CDS Cj0564 NC_002163.1 527149 527355 D Original (2000) note: Cj0564, probable integral membrane protein, len: 68 aa; no Hp match; Updated (2006) note: Two probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; integral membrane protein 527149..527355 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904359 YP_002343996.1 CDS Cj0566 NC_002163.1 528182 529648 D Original (2000) note: Cj0566, unknown, len: 488 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein 528182..529648 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904889 YP_002343997.1 CDS Cj0567 NC_002163.1 529659 529772 D Original (2000) note: Cj0567, unknown, len: 37 aa; no Hp match; Updated (2006) note: Paper identified linking product function to iron transport or metabolism. Functional classification - Unknown; PMID:15632442; hypothetical protein 529659..529772 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904890 YP_002343998.1 CDS Cj0568 NC_002163.1 529974 530255 D Original (2000) note: Cj0568, unknown, len: 93 aa; no Hp match; Updated (2006) note: One probable transmembrane helices predicted by TMHMM2.0. Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein 529974..530255 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904891 YP_002343999.1 CDS Cj0569 NC_002163.1 530261 531130 D Original (2000) note: Cj0569, unknown, len: 289 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein 530261..531130 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904892 YP_002344000.1 CDS Cj0570 NC_002163.1 531139 532206 D Original (2000) note: Cj0570, probable ATP/GTP binding protein, len: 355 aa; 85.1% identity to HP0729. Contains PS00017 ATP/GTP-binding site motif A (P-loop). Functional classification - Conserved hypothetical proteins; ATP/GTP binding protein 531139..532206 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904893 YP_002344001.1 CDS Cj0571 NC_002163.1 532203 533075 D Original (2000) note: Cj0571, possible transcriptional regulator; len: 290 aa; similar in C-terminus to two hypothetical deoR family transcriptional regulators from E. coli; YFJR_ECOLI (233 aa), fasta scores; opt: 279 z-score: 374.9 E(): 1.4e-13, 27.7% identity in 202 aa overlap, and YAFY_ECOLI (285 aa), fasta scores; opt: 167 z-score: 203.3 E(): 0.0005, 40.4% identity in 57 aa overlap. No Hp match, Contains probable helix-turn-helix motif at aa 25-46 (Score 1541, +4.44 SD); Updated (2006) 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; PMID:15731081; transcriptional regulator 532203..533075 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904894 YP_002344002.1 CDS ribA NC_002163.1 533373 534392 D bifunctional enzyme DHBP synthase/GTP cyclohydrolase II; functions in riboflavin synthesis; converts GTP to 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine; converts ribulose 5-phopshate to 3,4-dihydroxy-2-butanone 4-phosphate; bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein 533373..534392 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904897 YP_002344003.1 CDS Cj0573 NC_002163.1 534404 534847 D Original (2000) note: Cj0573, unknown, len: 147 aa; similar to several hypothetical proteins e.g.YQEY_BACSU (148 aa), fasta scores; opt: 265 z-score: 348.7 E(): 4e-12, 32.9% identity in 140 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF02637 GatB/Yqey 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; GatB/Yqey family protein 534404..534847 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904898 YP_002344004.1 CDS ilvI NC_002163.1 534865 536565 D catalyzes the formation of 2-acetolactate from pyruvate, leucine resistant; also known as acetolactate synthase 3 large subunit; acetolactate synthase 3 catalytic subunit 534865..536565 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904899 YP_002344005.1 CDS ilvH NC_002163.1 536562 537026 D with IlvI catalyzes the formation of 2-acetolactate from pyruvate, the small subunit is required for full activity and valine sensitivity; E.coli produces 3 isoenzymes of acetolactate synthase which differ in specificity to substrates, valine sensitivity and affinity for cofactors; also known as acetolactate synthase 3 small subunit; acetolactate synthase 3 regulatory subunit 536562..537026 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904900 YP_002344006.1 CDS lpxD NC_002163.1 537023 537988 D adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis; UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase 537023..537988 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904901 YP_002344007.1 CDS queA NC_002163.1 537977 539005 R Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step; S-adenosylmethionine:tRNA ribosyltransferase-isomerase complement(537977..539005) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904902 YP_002344008.1 CDS tatC NC_002163.1 538998 539735 R Original (2000) note: Cj0578c, mttB, probable sec-independant protein translocase, len: 245 aa; similar to e.g. TR:G3193219 (EMBL:AF067848) E. coli MTTB (258 aa),fasta scores; opt: 523 z-score: 804.5 E(): 0,36.2% identity in 246 aa overlap. 49.6% identity to HP1061. Contains Pfam match to entry PF00902 UPF0032, Integral membrane protein of unknown function; Updated (2006) 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 (S/T-R-R-X-F-L-K). 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; PMID:9649434, PMID:10652088, PMID:11781311; sec-independent protein translocase complement(538998..539735) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904903 YP_002344009.1 CDS Cj0579c NC_002163.1 539728 540144 R mediates the export of protein precursors bearing twin-arginine signal peptides; sec-independent translocase complement(539728..540144) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904904 YP_002344010.1 CDS Cj0580c NC_002163.1 540202 541269 R catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase complement(540202..541269) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905215 YP_002344011.1 CDS Cj0581 NC_002163.1 541371 541841 D hydrolyzes diadenosine polyphosphate; dinucleoside polyphosphate hydrolase 541371..541841 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905255 YP_002344012.1 CDS lysC NC_002163.1 541843 543045 D catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation.; aspartate kinase 541843..543045 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904905 YP_002344013.1 CDS Cj0583 NC_002163.1 543046 543582 D Original (2000) note: Cj0583, unknown, len: 178 aa; 30.8% identity to HP1230. Functional classification -Conserved hypothetical proteins; hypothetical protein 543046..543582 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904906 YP_002344014.1 CDS Cj0584 NC_002163.1 543588 544187 D catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the delta' subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA; DNA polymerase III subunit delta' 543588..544187 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904907 YP_002344015.1 CDS folP NC_002163.1 544189 545331 D Original (2000) note: Cj0585, folP, probable dihydropteroate synthase, len: 380 aa; simliar in C-terminus to e.g. DHPS_ECOLI dihydropteroate synthase (EC 2.5.1.15) (282 aa), fasta scores; opt: 508 z-score: 504.3 E(): 8.5e-21, 35.8% identity in 274 aa overlap. 41.6% identity to HP1232. Contains Pfam match to entry PF00809 DHPS, Dihydropteroate synthase; Updated (2006) note: Pfam domain PF00809 DHPS,Dihydropteroate 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, prosthetic groups and carriers - Folic acid; PMID:10471557, PMID:8244950; dihydropteroate synthase 544189..545331 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904908 YP_002344016.1 CDS ligA NC_002163.1 545332 547275 D this protein catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction; essential for DNA replication and repair of damaged DNA; similar to ligase LigB; NAD-dependent DNA ligase LigA 545332..547275 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904909 YP_002344017.1 CDS Cj0587 NC_002163.1 547256 548260 D Original (2000) note: Cj0587, probable integral membrane protein, len: 334 aa; no Hp match; Updated (2006) note: Eight probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; integral membrane protein 547256..548260 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904911 YP_002344018.1 CDS tlyA NC_002163.1 548257 549018 D Original (2000) note: Cj0588, tlyA, possible haemolysin, len: 253 aa; similar to e.g. HLYA_TREHY hemolysin A from Treponema hyodysenteriae (Serpulina hyodysenteriae) (240 aa), fasta scores; opt: 342 z-score: 596.3 E(): 6.4e-26, 33.7% identity in 261 aa overlap. 40.7% identity to HP1086; Updated (2006) 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; PMID:1730486; hemolysin 548257..549018 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904912 YP_002344019.1 CDS ribF NC_002163.1 548984 549838 D catalyzes the formation of FMN from riboflavin and the formation of FAD from FMN; in Bacillus the ribC gene has both flavokinase and FAD synthetase activities; bifunctional riboflavin kinase/FMN adenylyltransferase 548984..549838 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904913 YP_002344020.1 CDS Cj0590 NC_002163.1 549825 550535 D Original (2000) note: Cj0590, unknown, len: 236 aa; similar to hypothetical proteins e.g. YECO_ECOLI (247 aa),fasta scores; opt: 476 z-score: 737.5 E(): 0, 35.6% identity in 239 aa overlap. 45.3% identity to HP0388; Updated (2006) note: Prosite domain PS50193 SAM_BIND, SAM (and some other nucleotide) 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; SAM-dependent methyltransferase 549825..550535 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904914 YP_002344021.1 CDS Cj0591c NC_002163.1 550525 550746 R Original (2000) note: Cj0591c, probable lipoprotein, len: 73 aa; no Hp match. Contains N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Some similarity to upstream gene Cj0592c (39.7% identity in 63 aa overlap). Functional classification - Membranes, lipoproteins and porins; lipoprotein complement(550525..550746) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904916 YP_002344022.1 CDS Cj0592c NC_002163.1 550743 551177 R Original (2000) note: Cj0592c, probable periplasmic protein, len: 144 aa; no Hp match. Contains N-terminal signal sequence. Some similarity to downstream gene Cj0591c (39.7% identity in 63 aa overlap). Functional classification - Miscellaneous periplasmic proteins; periplasmic protein complement(550743..551177) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904917 YP_002344023.1 CDS Cj0593c NC_002163.1 551235 551867 R Original (2000) note: Cj0593c, probable integral membrane protein, len: 210 aa; similar to hypothetical proteins e.g. YICG_ECOLI (205 aa), fasta scores; opt: 783 z-score: 1285.7 E(): 0, 57.4% identity in 204 aa overlap. No Hp match; Updated (2006) 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, lipoproteins and porins; integral membrane protein complement(551235..551867) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904918 YP_002344024.1 CDS Cj0594c NC_002163.1 551878 552528 R Original (2000) note: Cj0594c, probable periplasmic protein, len: 216 aa; no Hp match. Contains N-terminal signal sequence; Updated (2006) note: Pfam domain PF01223 DNA/RNA 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, kept within product function. Functional classification -DNA replication, restriction/modification, recombination and repair; DNA/RNA non-specific endonuclease complement(551878..552528) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904919 YP_002344025.1 CDS nth NC_002163.1 552525 553151 R Original (2000) note: Cj0595c, nth, probable endonuclease III, len 208 aa; similar to many e.g. END3_ECOLI endonuclease III (EC 4.2.99.18) (211 aa), fasta scores; opt: 488 z-score: 749.2 E(): 0, 39.7% identity in 204 aa overlap. 57.4% identity to HP0585. Contains PS00764 Endonuclease III iron-sulfur binding region signature and Pfam match to entry PF00730 Endonuclease_3, Endonuclease III; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -DNA replication, restriction/modification, recombination and repair; PMID:2669955; endonuclease III complement(552525..553151) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904920 YP_002344026.1 CDS peb4cbf2 NC_002163.1 553232 554053 D Original (2000) note: Cj0596, peb4-cbf2, major antigenic peptide PEB4-cell binding factor 2, len: 273 aa; identical to CBF2_CAMJE cell binding factor 2 precursor,and TR:G451285 peb4=major antigenic peptide (34 aa). Also similar to memebers of the PPIC-parvulin family of rotamases e.g. PRTM_LACPA protease maturation protein precursor (299 aa), fasta scores; opt: 238 z-score: 303.5 E(): 1.3e-09, 31.3% identity in 240 aa overlap, and CYPD_ECOLI peptidyl-prolyl cis-trans isomerase D (623 aa),fasta scores; opt: 244 z-score: 293.9 E(): 4.5e-09, 27.1% identity in 221 aa overlap. 35.7% identity to HP0175. Contains PS01096 PpiC-type peptidyl-prolyl cis-trans isomerase signature and Pfam match to entry PF00639 Rotamase, PPIC-type PPIASE domain; Updated (2006) note: Characterised within Campylobacter jejuni. Functional classification -Miscellaneous periplasmic proteins; PMID:8525063; major antigenic peptide PEB-cell binding factor 553232..554053 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904921 YP_002344027.1 CDS fba NC_002163.1 554053 555117 D catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1,6, bisphosphate; fructose-bisphosphate aldolase 554053..555117 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904922 YP_002344028.1 CDS Cj0598 NC_002163.1 555212 556654 D Original (2000) note: Cj0598, probable membrane protein, len: 480 aa; no Hp match; Updated (2006) note: Four probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; hypothetical protein 555212..556654 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904923 YP_002344029.1 CDS Cj0599 NC_002163.1 556651 557604 D Original (2000) note: Cj0599, probable periplasmic protein, len: 317 aa; no Hp match. Contains N-terminal signal sequence; Updated (2006) note: Pfam domain PF00691 OmpA family protein was identified within CDS. Also, 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; OmpA family membrane protein 556651..557604 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904924 YP_002344030.1 CDS Cj0600 NC_002163.1 557591 558466 D Original (2000) note: Cj0600, unknown, len: 291 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein 557591..558466 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904925 YP_002344031.1 CDS Cj0601c NC_002163.1 558458 559801 R Original (2000) note: Cj0601c, probable sodium-dependent transmembrane transport protein, len: 447 aa; similar to members of the sodium:neurotransmitter symporter family e.g. YG90_HAEIN hypothetical sodium-dependent transporter HI1690 (457 aa), fasta scores; opt: 1380 z-score: 2645.2 E(): 0, 61.0% identity in 456 aa overlap, and NTSE_RAT sodium-dependent serotonin transporter (630 aa), fasta scores; opt: 265 z-score: 744.2 E(): 0. 25.8% identity in 488 aa overlap. No Hp ortholog. Also similar to Cj0935c (32.4% identity in 451 aa overlap), and Cj0934c (28.0% identity in 454 aa overlap). Contains PS00610 Sodium:neurotransmitter symporter family signature 1 and Pfam match to entry PF00209 SNF, Sodium:neurotransmitter symporter family; Updated (2006) 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/binding proteins - Other; sodium-dependent transmembrane transport protein complement(558458..559801) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904927 YP_002344032.1 CDS Cj0602c NC_002163.1 559852 560520 R Original (2000) note: Cj0602c, unknown, len: 222 aa; similar to hypothetical proteins e.g. YIIM_ECOLI (234 aa), fasta scores; opt: 298 z-score: 406.4 E(): 2.4e-15,30.4% identity in 207 aa overlap. No Hp match; Updated (2006) 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; MOSC-domain containing protein complement(559852..560520) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904928 YP_002344033.1 CDS dsbD NC_002163.1 560517 562220 R Original (2000) note: Cj0603c, dsbD, possible thiol:disulfide interchange protein, len: 567 aa; similar to e.g. DSBD_ECOLI thiol:disulfide interchange protein DSBD (488 aa), fasta scores; opt: 795 z-score: 977.8 E(): 0, 31.5% identity in 496 aa overlap. 27.1% identity to HP0265; Updated (2006) note: Pfam domain PF02683 Cytochrome C biogenesis protein transmembrane was identified within CDS. Also, Prosite domain PS50223 THIOREDOXIN_2,Thioredoxin 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, 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; PMID:7628442, PMID:11085993; thiol:disulphide interchange protein complement(560517..562220) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904931 YP_002344034.1 CDS Cj0604 NC_002163.1 562315 563196 D Original (2000) note: Cj0604, unknown, len: 293 aa; similar to hypothetical proteins e.g. TR:O05877 (EMBL:O05877) Mycobacterium tuberculosis Rv3232c (MTCY20B11.07c) (295 aa), fasta scores; opt: 858 z-score: 1317.7 E(): 0, 52.0% identity in 227 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF03976 Domain of unknown function (DUF344) 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; PMID:12486232; polyphosphate kinase 562315..563196 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904932 YP_002344035.1 CDS Cj0605 NC_002163.1 563205 564395 D Original (2000) note: Cj0605, probable amidohydrolase, len: 396 aa; similar to members of the AMA/HIPO/HYUC family of hydrolases (peptidase family M40) e.g. AMAA_BACST N-acyl-L-amino acid amidohydrolase (370 aa), fasta scores; opt: 805 z-score: 1165.8 E(): 0, 41.4% identity in 307 aa overlap. Also similar to HIPO_CAMJE hippurate hydrolase (Cj0985c) (383 aa) (39.1% identity in 376 aa overlap). No Hp match. Contains PS00070 Aldehyde dehydrogenases cysteine active site; Updated (2006) note: Pfam domain PF01546 Peptidase family M20/M25/M40 was identified within CDS. Further support given to product function. kept within product function. Functional classification - Misc; amidohydrolase 563205..564395 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904933 YP_002344036.1 CDS Cj0606 NC_002163.1 564474 565646 D Original (2000) note: Cj0606, probable periplasmic protein, len: 390 aa; similar to hypothetical proteins e.g. E. coli TR:P75830 (EMBL:AE000189) (380 aa), fasta scores; opt: 522 z-score: 648.1 E(): 8.4e-29, 31.3% identity in 386 aa overlap. No Hp ortholog. Contains probable N-terminal signal sequence and poly-Serine tract from aa 211 to 225; Updated (2006) note: Pfam domain PF00529 HlyD family secretion protein was identified within CDS. Literature search identified paper linking the three-gene operon Cj0606-0608) to a type-one secretion system. Each of the three CDSs show characteristics similar to the alpha-haemolysin secretion system of Escherichia coli (PMID:8137117). Product modified to more specific family member due to motif match. Some characterisation work carried out within Escherichia coli (marginal identity score) and designated as macrolide-specific ABC-type efflux transporter. kept within product function. Functional classification - Protein and peptide secretion; PMID:15554967, PMID:8137117, PMID:11544226; secretion protein HlyD 564474..565646 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904934 YP_002344037.1 CDS Cj0607 NC_002163.1 565646 567571 D Original (2000) note: Cj0607, probable ABC-type transmembrane transport protein, len: 641 aa; similar to many predicted ABC transporters e.g. YBJZ_ECOLI (648 aa),fasta scores; opt: 1729 z-score: 1619.1 E(): 0, 44.3% identity in 632 aa overlap. No Hp ortholog. Contains 2x PS00017 ATP/GTP-binding site motif A (P-loop), PS00211 ABC transporters family signature, Pfam match to entry PF00005 ABC_tran, ABC transporters, and two possible membrane-spanning regions; Updated (2006) note: Literature search identified paper linking the three-gene operon (Cj0606-0608) to a type-one secretion system. Each of the three CDSs show characteristics similar to the alpha-haemolysin secretion system of E.coli (PMID:8137117). Some characterisation work carried out within Escherichia coli (marginal identity score) and designated as macrolide-specific ABC-type efflux transporter. not added to product function. Functional classification -Transport/binding proteins - Other; PMID:15554967, PMID:8137117, PMID:11544226; ABC transporter transmembrane protein 565646..567571 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904935 YP_002344038.1 CDS Cj0608 NC_002163.1 567573 568943 D Original (2000) note: Cj0608, possible outer membrane protein, len: 456 aa; similar to hypothetical proteins e.g. YE62_HAEIN HI1462 (454 aa), fasta scores; opt: 711 z-score: 933.7 E(): 0, 29.8% identity in 450 aa overlap, and weakly to outer membrene proteins e.g. TR:Q51006 (EMBL:X95635) Neisseria gonorrhoeae MTRE gene (fragment) (467 aa), fasta scores; opt: 289 z-score: 325.5 E(): 8.3e-11, 22.8% identity in 465 aa overlap. No Hp match. Also similar to Cj0365c (28.6% identity in 455 aa overlap). Contains N-terminal signal sequence, PS00013 Prokaryotic membrane lipoprotein lipid attachment site and PS00217 Sugar transport proteins signature 2; Updated (2006) 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 (Cj0606-0608) to a type-one secretion system. Each of the three CDSs show characteristics similar to the alpha-haemolysin secretion system of E.coli (PMID:8137117). kept within product function. Functional classification -Transport/binding proteins - Other; PMID:15554967, PMID:8137117, PMID:11544226; outer membrane efflux protein 567573..568943 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904936 YP_002344039.1 CDS Cj0609c NC_002163.1 568946 570124 R Original (2000) note: Cj0609c, possible periplasmic protein, len: 392 aa; no Hp match. Contains possible N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein complement(568946..570124) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904937 YP_002344040.1 CDS Cj0610c NC_002163.1 570111 571121 R Original (2000) note: Cj0610c, probable periplasmic protein, len: 336 aa; no Hp match. Contains probable N-terminal signal sequence; Updated (2006) note: Pfam domain PF04311 Protein of unknown function (DUF459) was identified within CDS. Product function kept the same. Functional classification - Miscellaneous periplasmic proteins; periplasmic protein complement(570111..571121) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904522 YP_002344041.1 CDS Cj0611c NC_002163.1 571122 572498 R Original (2000) note: Cj0611c, probable transmembrane transport protein, len: 458 aa; similar to e.g. TR:Q51392 (EMBL:U50202) Pseudomonas aeruginosa ALGI (520 aa), fasta scores; opt: 729 z-score: 779.3 E(): 0,32.5% identity in 428 aa overlap, and DLTB_BACSU DLTB protein (395 aa), fasta scores; opt: 431 z-score: 482.4 E(): 1.4e-19, 29.6% identity in 361 aa overlap. 32.9% identity to HP0855; Updated (2006) note: Pfam domain PF03062 MBOAT family identified within CDS. Also, 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; PMID:8636017, PMID:11208804; acyltransferase family protein complement(571122..572498) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904938 YP_002344042.1 CDS cft NC_002163.1 572541 573044 R Original (2000) note: Cj0612c, cft, probable ferritin, len: 167 aa; identical to TR:Q46106 (EMBL:D64082), and similar to many e.g. FTN_ECOLI ferritin (165 aa), fasta scores; opt: 535 z-score: 957.6 E(): 0,47.2% identity in 161 aa overlap. 63.9% identity to HP0653. Contains Pfam match to entry PF00210 ferritin; Updated (2006) note: Characterised within Campylobacter jejuni. Functional classification -Transport/binding proteins - Cations; PMID:8809765; ferritin complement(572541..573044) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904939 YP_002344043.1 CDS pstS NC_002163.1 573224 574219 D Original (2000) note: Cj0613, pstS, possible periplasmic phosphate binding protein, len: 167 aa; similar to e.g. SPHX_SYNP7 SPHX protein precursor (337 aa), fasta scores; opt: 346 z-score: 602.6 E(): 2.9e-26,33.2% identity in 301 aa overlap. No Hp match. Contains probable N-terminal signal sequence; Updated (2006) note: Characterised within Escherichia coli, however, identity score was unnacceptable. kept within product function. Functional classification - Transport/binding proteins -Anions; PMID:2651888, PMID:7741855; periplasmic phosphate binding protein 573224..574219 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904940 YP_002344044.1 CDS pstC NC_002163.1 574229 575143 D Original (2000) note: Cj0614, pstC, probable phosphate transport system permease, len: 304 aa; similar to e.g. PSTC_ECOLI phosphate transport system permease (319 aa), fasta scores; opt: 289 z-score: 590.3 E(): 1.4e-25, 28.9% identity in 305 aa overlap. No Hp ortholog. Also similar to downstream gene Cj0615 (30.7% identity in 254 aa overlap). Contains Pfam match to entry PF00528 BPD_transp, Binding-protein-dependent transport systems inner membrane component; Updated (2006) note: Six probable transmembrane helices predicted by TMHMM2.0. Characterised within Pseudomonas putida and Escherichia coli, however, identity scores were unnacceptable. kept within product function. Functional classification - Transport/binding proteins - Anions; PMID:16232467, PMID:2646285; phosphate transport system permease 574229..575143 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904941 YP_002344045.1 CDS pstA NC_002163.1 575140 576228 D Original (2000) note: Cj0615, pstA, probable phosphate transport system permease, len: 362 aa; similar to e.g. PSTA_ECOLI phosphate transport system permease (296 aa), fasta scores; opt: 346 z-score: 447.5 E(): 1.3e-17, 29.2% identity in 226 aa overlap. No Hp ortholog. Also similar to upstream gene Cj0614 (30.7% identity in 254 aa overlap). Contains Pfam match to entry PF00528 BPD_transp, Binding-protein-dependent transport systems inner membrane component; Updated (2006) note: Six probable transmembrane helices predicted by TMHMM2.0. Characterised within Escherichia coli, however, identity scores were unnacceptable. kept within product function. Functional classification - Transport/binding proteins -Anions; PMID:2993631, PMID:2896188; phosphate transport system permease 575140..576228 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904942 YP_002344046.1 CDS pstB NC_002163.1 576225 576965 D ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation; phosphate ABC transporter ATP-binding protein 576225..576965 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904943 YP_002344047.1 CDS Cj0617 NC_002163.1 577027 577638 D Original (2000) note: Cj0617, unknown, len: 203 aa; no Hp match. A member of the 617 family of C.j. proteins containing homopolymeric tracts; similar to N-terminus of Cj1305c (38.9% identity in 180 aa overlap), Cj1306c (39.2% identity in 181 aa overlap), Cj1310c (37.4% identity in 182 aa overlap) and Cj1342c (49.7% identity in 191 aa overlap). The similarities continue in the downstream ORF Cj0618, suggesting that these two ORFs may encode a single protein, but are frameshifted w.r.t. each other. There is a poly-G tract at the site of the possible frameshift (577586..577594) and all of the similar genes contain variable poly-G tracts at this position. Functional classification - Unknown; hypothetical protein 577027..577638 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904944 YP_002344048.1 CDS Cj0618 NC_002163.1 577608 578255 D Original (2000) note: Cj0618, unknown, len: 215 aa; no Hp match. A member of the 617 family of C.j. proteins containing homopolymeric tracts; similar to C-terminus of Cj1305c (36.7% identity in 221 aa overlap), Cj1306c (39.1% identity in 220 aa overlap), Cj1310c (33.6% identity in 220 aa overlap) and Cj1342c (43.4% identity in 221 aa overlap). The similarities continue from the upstream ORF Cj0617, suggesting that these two ORFs may encode a single protein, but are frameshifted w.r.t. each other. There is a poly-G tract at thesite of the possible frameshift (577586..577594) and all of the similar genes contain variable poly-G tracts at this position; Updated (2006) note: Literature search identified paper giving functional link to motility. Functional classification - Unknown; PMID:15066034; hypothetical protein 577608..578255 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904945 YP_002344049.1 CDS Cj0619 NC_002163.1 578345 579661 D Original (2000) note: Cj0619, probable integral membrane protein, len: 438 aa; similar to hypothetical proteins e.g. TR:O07940 B. subtilis YISQ (455 aa), fasta scores; opt: 880 z-score: 1364.9 E(): 0, 32.1% identity in 446 aa overlap, and YEEO_ECOLI (547 aa), fasta scores; opt: 164 z-score: 529.6 E(): 3.3e-22, 22.7% identity in 437 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF01554 MatE was identified within CDS. This family of protein function as drug/sodium antiporters. These proteins mediate resistance to a wide range of cationic dyes, fluroquinolones,aminoglycosides and other structurally diverse antibodies and drugs. MatE proteins are found in bacteria, archaea and eukaryotes. These proteins are predicted to have 12 alpha-helical transmembrane regions (which this CDS has). Product modified to more specific family member due to motif match. Literature search identified paper giving further support. Functional classification -Membranes, lipoproteins and porins; PMID:16048946; MATE family transport protein 578345..579661 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904946 YP_002344050.1 CDS Cj0620 NC_002163.1 579637 580284 D Original (2000) note: Cj0620, unknown, len: 215 aa; some simlarity to TR:O58443 (EMBL:AB009490) Pyrococcus horikoshii PHCF016 (230 aa), fasta scores; opt: 229 z-score: 237.3 E(): 6.4e-06, 26.9% identity in 197 aa overlap. 33.7% identity to HP0806, 25.0% identity to HP1401; Updated (2006) note: Pfam domain PF01863 Protein of unknown function DUF45 identified within CDS. This motif has no known function. Members are found in some archaebacteria, as well as Helicobacter pylori (Epsilon Proteobacteria). The proteins are 190-240 amino acids long, with the C terminus being the most conserved region,containing three conserved histidines. This motif is similar to that found in Zinc proteases, suggesting a possible role as a protease. Conserved added to product function. Functional classification - Conserved hypothetical proteins; hypothetical protein 579637..580284 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904947 YP_002344051.1 CDS Cj0621 NC_002163.1 580326 581846 D Original (2000) note: Cj0621, unknown, len: 506 aa; similar to TR:E1186594 (EMBL:AJ003049) hypothetical protein HYDE from Wolinella succinogenes (546 aa), fasta scores; opt: 207 z-score: 285.3 E(): 1.3e-08, 25.8% identity in 551 aa overlap. 23.2% identity to HP0635; Updated (2006) note: Literature search identified paper linking product function to hydE-like protein. Functional classification - Conserved hypothetical proteins; PMID:10533287; hypothetical protein 580326..581846 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904948 YP_002344052.1 CDS hypF NC_002163.1 581827 584016 D Original (2000) note: Cj0622, hypF, probable transcriptional regulatory protein, len: 729 aa; similar to many e.g. HYPF_ECOLI transcriptional regulatory protein HYPF (750 aa), fasta scores; opt: 1166 z-score: 1359.5 E(): 0, 34.1% identity in 747 aa overlap. 35.0% identity to HP0048. Contains PS00150 Acylphosphatase signature 1 and Pfam match to entry PF01300 Sua5_yciO_yrdC,SUA5/yciO/yrdC family; Updated (2006) 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; PMID:15504408, PMID:1849603; carbamoyltransferase 581827..584016 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904949 YP_002344053.1 CDS hypB NC_002163.1 584094 584837 D Original (2000) note: Cj0623, hypB, probable hydrogenase isoenzymes formation protein, len: 247 aa; similar to many e.g. HYPB_ECOLI hydrogenase isoenzymes formation protein (290 aa), fasta scores; opt: 691 z-score: 1142.3 E(): 0, 46.1% identity in 230 aa overlap. 44.2% identity to HP0900. Contains PS00028 Zinc finger,C2H2 type, domain; Updated (2006) note: Pfam domain PF02492 CobW/HypB/UreG, 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; PMID:7601092, PMID:1849603; hydrogenase isoenzymes formation protein 584094..584837 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904950 YP_002344054.1 CDS hypC NC_002163.1 584837 585118 D Original (2000) note: Cj0624, hypC, probable hydrogenase isoenzymes formation protein, len: 93 aa; similar to many e.g. HYPC_ECOLI hydrogenase isoenzymes formation protein (90 aa), fasta scores; opt: 145 z-score: 173.2 E(): 0.024, 35.9% identity in 78 aa overlap. 53.3% identity to HP0899; Updated (2006) note: Pfam domain PF01455 HupF/HypC 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; PMID:8021226, PMID:1849603; hydrogenase isoenzymes formation protein 584837..585118 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904953 YP_002344055.1 CDS hypD NC_002163.1 585102 586193 D Original (2000) note: Cj0625, hypD, probable hydrogenase isoenzymes formation protein, len: 363 aa; similar to many e.g. HYPD_ECOLI hydrogenase isoenzymes formation protein (373 aa), fasta scores; opt: 1097 z-score: 1671.2 E(): 0, 41.3% identity in 368 aa overlap. 58.5% identity to HP0898; Updated (2006) 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; PMID:1849603; hydrogenase isoenzymes formation protein 585102..586193 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904954 YP_002344056.1 CDS hypE NC_002163.1 586190 587164 D Original (2000) note: Cj0626, hypE, probable hydrogenase isoenzymes formation protein, len: 324 aa; similar to many e.g. HYPE_ECOLI hydrogenase isoenzymes formation protein (322 aa), fasta scores; opt: 705 z-score: 923.2 E(): 0, 40.4% identity in 327 aa overlap. 46.8% identity to HP0047. Contains Pfam match to entry PF00586 AIRS, AIR synthase related proteins; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Energy metabolism - Respiration; PMID:1849603; hydrogenase isoenzymes formation protein 586190..587164 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904955 YP_002344057.1 CDS hypA NC_002163.1 587164 587508 D Original (2000) note: Cj0627, hypA, probable hydrogenase isoenzymes formation protein, len: 114 aa; similar to e.g. HYPA_AZOVI hydrogenase expression/formation protein (113 aa), fasta scores; opt: 228 z-score: 397.9 E(): 7.2e-15, 32.4% identity in 111 aa overlap. 39.7% identity to HP0869. Contains Pfam match to entry PF01155 HypA, Hydrogenase expression/synthesis hypA family; Updated (2006) note: Characterised within Azotobacter vinelandii and Escherichia coli with marginal identity scores. not added to product function. Functional classification - Energy metabolism -Respiration; PMID:1849603, PMID:1610901; hydrogenase expression/formation protein 587164..587508 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904956 YP_002344058.1 CDS Cj0628 NC_002163.1 587868 591303 D Original (2000) note: Cj0628, probable lipoprotein,len: 171 aa; 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(4-5). T5 causes the ORF to stop here, T4 allows translation into the downstream ORF Cj0629. Similar to Cj1677 (42.4% identity in 172 aa overlap). Cj1677 has a non-variable poly-T tract in an quivalent position, which could allow translation into Cj1678 (highly similar to Cj0629); Original (2000) note: Cj0629, possible lipoprotein,len: 978 aa; no Hp match. Contains a variable poly-T tract at the N-terminus T(4-5). T5 causes the ORF to start here,T4 allows translation from the upstream ORF Cj0628 (which contains a signal sequence and lipid attachment site). Highly similar to Cj1678 (90.7% identity in 901 aa overlap). Cj1678 has a non-variable poly-T tract in an quivalent position, which could allow translation from Cj1677 (similar to Cj0628); Updated (2006) 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, lipoproteins and porins; lipoprotein join(587868..588371,588373..591303) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904958 YP_002344059.1 CDS Cj0630c NC_002163.1 591537 592502 R required for the assembly and function of the DNAX complex which is required for the assembly of the beta subunit onto primed DNA; DNA polymerase III subunit delta complement(591537..592502) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904888 YP_002344060.1 CDS Cj0631c NC_002163.1 592495 594429 R Original (2000) note: Cj0631c, possible ribonuclease, len: 644 aa; similar to members of the ribonuclease II (RNB) family, e.g. VACB_ECOLI VACB protein (813 aa), fasta scores; opt: 503 z-score: 829.1 E(): 0,31.0% identity in 580 aa overlap. 35.1% identity to HP1248. Contains PS01175 Ribonuclease II family signature,and Pfam match to entry PF00773 RNB, RNB-like proteins; Updated (2006) note: Some characterisation within Escherichia coli, however, identity scores were marginal. kept within product function. Functional classification - Degradation of macromolecules; PMID:9603904; ribonuclease complement(592495..594429) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904960 YP_002344061.1 CDS ilvC NC_002163.1 594548 595570 D catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis; ketol-acid reductoisomerase 594548..595570 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904961 YP_002344062.1 CDS Cj0633 NC_002163.1 595574 596656 D Original (2000) note: Cj0633, probable periplasmic protein, len: 360 aa; similar in C-terminus to hypothetical proteins e.g. TR:O51711 (EMBL:AE001176) Borrelia burgdorferi BB0770 (293 aa), fasta scores; opt: 425 z-score: 553.2 E(): 1.6e-23, 36.3% identity in 237 aa overlap. No Hp match. Contains probable N-terminal signal sequence; Updated (2006) 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; periplasmic protein 595574..596656 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904962 YP_002344063.1 CDS dprA NC_002163.1 596646 597419 D Original (2000) note: Cj0634, unknown, len: 257 aa; similar, in part, to members of the SMF family e.g. SMF_HAEIN SMF protein (DNA processing chain A) (373 aa),fasta scores; opt: 329 z-score: 487.6 E(): 7.2e-20, 31.5% identity in 213 aa overlap. 48.8% identity to HP0333; Updated (2006) 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, restriction/modification, recombination and repair; PMID:16194595; DNA processing protein A 596646..597419 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904964 YP_002344064.1 CDS Cj0635 NC_002163.1 597416 597799 D similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function; Holliday junction resolvase-like protein 597416..597799 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904965 YP_002344065.1 CDS Cj0636 NC_002163.1 597828 598667 D Original (2000) note: Cj0636, unknown, len: 279 aa; similar to members of the NOL1/NOP2/sun family e.g. Y026_METJA MJ0026 (274 aa), fasta scores; opt: 422 z-score: 688.4 E(): 4.8e-31, 33.9% identity in 280 aa overlap. No Hp match. Contains Pfam match to entry PF01189 Nol1_Nop2_Sun, NOL1/NOP2/sun family. Functional classification - Conserved hypothetical proteins; NOL1/NOP2/sun family protein 597828..598667 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904966 YP_002344066.1 CDS mrsA NC_002163.1 598843 599340 R this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; provides protection against oxidative stress; methionine sulfoxide reductase A complement(598843..599340) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904967 YP_002344067.1 CDS ppa NC_002163.1 599381 599899 R Original (2000) note: Cj0638c, ppa, probable inorganic pyrophosphatase, len: 172 aa; highly similar to many e.g. IPYR_ECOLI inorganic pyrophosphatase (EC 3.6.1.1) (175 aa), fasta scores; opt: 564 z-score: 990.9 E(): 0, 54.0% identity in 161 aa overlap. 59.3% identity to HP0620. Contains PS00387 Inorganic pyrophosphatase signature and Pfam match to entry PF00719 Pyrophosphatase,Inorganic pyrophosphatase; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Literature search identified paper linking protein to glycoprotein (PMID:12186869). Functional classification - Central intermediary metabolism - General; PMID:12186869, PMID:2848015, PMID:9201917; inorganic pyrophosphatase complement(599381..599899) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904968 YP_002344068.1 CDS adk NC_002163.1 599909 600487 R essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP; adenylate kinase complement(599909..600487) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904969 YP_002344069.1 CDS aspS NC_002163.1 600484 602235 R catalyzes a two-step reaction, first charging an aspartate molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; contains discriminating and non-discriminating subtypes; aspartyl-tRNA synthetase complement(600484..602235) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904820 YP_002344070.1 CDS pnk NC_002163.1 602326 603186 D catalyzes the phosphorylation of NAD to NADP; inorganic polyphosphate/ATP-NAD kinase 602326..603186 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905135 YP_002344071.1 CDS recN NC_002163.1 603186 604709 D Original (2000) note: Cj0642, recN, possible DNA repair protein, len: 507 aa; some similarity to e.g. RECN_BACSU DNA repair protein RECN (576 aa), fasta scores; opt: 272 z-score: 353.1 E(): 2.3e-12, 24.5% identity in 559 aa overlap. 36.1% identity to HP1393. Contains PS00017 ATP/GTP-binding site motif A (P-loop); Updated (2006) note: Characterised within Bacillus subtilis, however, identity score was unnacceptable. kept within product function. Functional classification - DNA replication,restriction/modification, recombination and repair; PMID:9044256; DNA repair protein 603186..604709 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905122 YP_002344072.1 CDS cbrR NC_002163.1 604815 606059 D Original (2000) note: Cj0643, probable two-component response regulator, len: 414 aa; similar to e.g. TR:P97018 (EMBL:U67070) Aeromonas jandaei response regulator protein RRPX (415 aa), fasta scores; opt: 597 z-score: 530.0 E(): 3.2e-22, 25.8% identity in 414 aa overlap, andTR:Q46020 (EMBL:L42554) Caulobacter crescentus response regulator PLED (454 aa), fasta scores; opt: 286 z-score: 309.9 E(): 5.8e-10, 22.0% identity in 451 aa overlap. No Hp ortholog. Contains 2x Pfam match to entry PF00072 response_reg, Response regulator receiver domain and Pfam match to entry PF00990 DUF9, Domain of unknown function; Updated (2006) 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 (Campylobacter bile resistance Regulator) protein. Functional classification - Signal transduction; PMID:15901688; two-component response regulator 604815..606059 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904970 YP_002344073.1 CDS Cj0644 NC_002163.1 606050 606865 D Original (2000) note: Cj0644, unknown, len: 271 aa; similar to hypothetical proteins e.g. YABD_BACSU (255 aa),fasta scores; opt: 614 z-score: 1024.7 E(): 0, 38.6% identity in 259 aa overlap. 49.2% identity to HP1573. Contains PS01137 Uncharacterized protein family UPF0006 signature 1 and Pfam match to entry PF01026 UPF0006,Uncharacterized protein family; Updated (2006) note: Pfam domain PF01026 TatD related DNase and Prosite domain PS01137 TATD_1,TatD-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; TatD-related deoxyribonuclease 606050..606865 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904971 YP_002344074.1 CDS Cj0645 NC_002163.1 606865 607983 D Original (2000) note: Cj0645, possible secreted transglycosylase, len: 372 aa; similar to members of the SLT family e.g. MLTD_ECOLI membrane-bound lytic murein transglycosylase D precursor (EC 3.2.1.-) (452 aa), fasta scores; opt: 425 z-score: 431.3 E(): 1e-16, 28.4% identity in 348 aa overlap. 37.5% identity to HP1572. Contains N-terminal signal sequence; Updated (2006) 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; PMID:10843862; secreted transglycosylase 606865..607983 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904972 YP_002344075.1 CDS Cj0646 NC_002163.1 607943 608770 D Original (2000) note: Cj0646, probable lipoprotein,len: 275 aa; similar to e.g. RLPA_ECOLI rare lipoprotein A precursor (362 aa), fasta scores; opt: 251 z-score: 431.7 E(): 9.4e-17, 33.6% identity in 131 aa overlap. 50.2% identity to HP1571. Contains N-terminal signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site; Updated (2006) note: Pfam domain PF03330 Rare lipoprotein A (RlpA)-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, lipoproteins and porins; lipoprotein 607943..608770 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904973 YP_002344076.1 CDS Cj0647 NC_002163.1 608776 609264 D Original (2000) note: Cj0647, unknown, len: 162 aa; similar to hypothetical proteins e.g. YRBI_ECOLI (188 aa), fasta scores; opt: 322 z-score: 399.6 E(): 5.8e-15,40.0% identity in 155 aa overlap. 40.9% identity to HP1570; Updated (2006) 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, KdsC, however, alignment was only partial. Functional classification - Misc; PMID:12639950; HAD-superfamily hydrolase 608776..609264 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904974 YP_002344077.1 CDS Cj0648 NC_002163.1 609255 609770 D Original (2000) note: Cj0648, unknwn, len: 171 aa; no Hp match; Updated (2006) note: One probable transmembrane helix predicted by TMHMM2.0. Also, 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, lipoproteins and porins; hypothetical protein 609255..609770 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904975 YP_002344078.1 CDS Cj0649 NC_002163.1 609752 610213 D Original (2000) note: Cj0649, unknown, len: 153 aa; 31.6% identity to HP1568; Updated (2006) 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; PMID:7811102; OstA family protein 609752..610213 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904976 YP_002344079.1 CDS engB NC_002163.1 610210 610806 D binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential; ribosome biogenesis GTP-binding protein YsxC 610210..610806 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904977 YP_002344080.1 CDS Cj0651 NC_002163.1 610803 611297 D Original (2000) note: Cj0651, possible integral membrane protein, len: 164 aa; no Hp match; Updated (2006) note: Five probable transmembrane helices predicted by TMHMM2.0 identified within CDS. Functional classification - Membranes, lipoproteins and porins; integral membrane protein 610803..611297 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904978 YP_002344081.1 CDS pbpC NC_002163.1 611298 613103 D Original (2000) note: Cj0652, pbpC, probable penicillin-binding protein, len: 601 aa; similar to many e.g. PBP2_ECOLI penicillin-binding protein 2 (PBP-2) (633 aa), fasta scores; opt: 954 z-score: 1474.4 E(): 0, 32.7% identity in 609 aa overlap. 43.5% identity to HP1565. Contains Pfam match to entry PF00905 Transpeptidase,Penicillin binding protein transpeptidase domain; Updated (2006) 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; PMID:9045804; penicillin-binding protein 611298..613103 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904979 YP_002344082.1 CDS Cj0653c NC_002163.1 613224 615014 R Original (2000) note: Cj0653c, probable aminopeptidase, len: 596 aa; similar to e.g. TR:O54975 (EMBL:AF038591) rattus norvegicus cytoplasmic aminopeptidase P (623 aa), fasta scores; opt: 763 z-score: 1470.5 E(): 0, 36.8% identity in 612 aa overlap, and TR:O51094 (EMBL:AE001119) Borrelia burgdorferi peptidase BB0067 (592 aa), fasta scores; opt: 1234 z-score: 1316.7 E(): 0, 41.1% identity in 609 aa overlap. 25.8% identity to HP1037. Contains Pfam match to entry PF00557 pep_M24, metallopeptidase family M24; Updated (2006) note: No specific characterisation with acceptable identity scores carried out yet. kept within product function. Functional classification -Degradation of macromolecules - Proteins, peptides and glycopeptides; aminopeptidase complement(613224..615014) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904980 YP_002344083.1 CDS Cj0659c NC_002163.1 616572 617120 R Original (2000) note: Cj0659c, possible periplasmic protein, len: 182 aa; no Hp match. Contains probable N-terminal signal sequence; Updated (2006) note: One probable transmembrane helices predicted by TMHMM2.0 identified within CDS. Functional classification - Miscellaneous periplasmic proteins; periplasmic protein complement(616572..617120) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904910 YP_002344084.1 CDS Cj0660c NC_002163.1 617113 618219 R Original (2000) note: Cj0660c, possible transmembrane protein, len: 368 aa; no Hp match. Contains a possible transmembrane domain around aa 220; Updated (2006) note: One probable transmembrane helices predicted by TMHMM2.0 identified within CDS. Functional classification - Membranes, lipoproteins and porins; transmembrane protein complement(617113..618219) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904982 YP_002344085.1 CDS era NC_002163.1 618206 619081 R Era; Escherichia coli Ras-like protein; Bex; Bacillus Era-complementing segment; essential protein in Escherichia coli that is involved in many cellular processes; GTPase; binds the cell membrane through apparent C-terminal domain; mutants are arrested during the cell cycle; Streptococcus pneumoniae Era binds to RNA and Escherichia coli Era binds 16S rRNA and 30S ribosome; GTP-binding protein Era complement(618206..619081) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904983 YP_002344086.1 CDS hslU NC_002163.1 619078 620397 R heat shock protein involved in degradation of misfolded proteins; ATP-dependent protease ATP-binding subunit HslU complement(619078..620397) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904984 YP_002344087.1 CDS hslV NC_002163.1 620394 620936 R heat shock protein involved in degradation of misfolded proteins; ATP-dependent protease peptidase subunit complement(620394..620936) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904986 YP_002344088.1 CDS rplI NC_002163.1 620936 621379 R in Escherichia coli this protein is wrapped around the base of the L1 stalk; 50S ribosomal protein L9 complement(620936..621379) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904987 YP_002344089.1 CDS argG NC_002163.1 621392 622612 R catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming; argininosuccinate synthase complement(621392..622612) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904988 YP_002344090.1 CDS Cj0667 NC_002163.1 622768 623013 D Original (2000) note: Cj0667, unknown, len: 81 aa; similar to many hypothetical proteins e.g. YABO_BACSU (86 aa), fasta scores; opt: 149 z-score: 259.2 E(): 3.8e-07,35.4% identity in 79 aa overlap. 43.6% identity to HP1423; Updated (2006) 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; S4 domain protein 622768..623013 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904989 YP_002344091.1 CDS Cj0668 NC_002163.1 623010 623417 D Original (2000) note: Cj0668, probable ATP/GTP-binding protein, len: 135 aa; similar to hypothetical proteins e.g. YJEE_ECOLI (153 aa), fasta scores; opt: 164 z-score: 205.3 E(): 0.00039, 33.8% identity in 80 aa overlap. 44.2% identity to HP0716. Contains PS00017 ATP/GTP-binding site motif A (P-loop); Updated (2006) 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; ATP/GTP-binding protein 623010..623417 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904990 YP_002344092.1 CDS Cj0669 NC_002163.1 623410 624138 D Original (2000) note: Cj0669, probable ABC-transporter ATP-binding protein, len: 242 aa; highly similar to many e.g. YHBG_ECOLI probable ABC transporter ATP-binding protein (240 aa), fasta scores; opt: 840 z-score: 1144.2 E(): 0, 54.2% identity in 236 aa overlap. 65.8% identity to HP0715. Contains PS00017 ATP/GTP-binding site motif A (P-loop) and Pfam match to entry PF00005 ABC_tran, ABC transporters; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. Appropriate motifs also present. not added to product function. Functional classification -Transport/binding proteins - Other; PMID:16079137; ABC-transporter ATP-binding protein 623410..624138 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905196 YP_002344093.1 CDS rpoN NC_002163.1 624138 625388 D sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; sigma 54 factor is responsible for the expression of enzymes involved in nitrogen assimilation and metabolism; the rhizobia often have 2 copies of this sigma factor; 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; in Bradyrhizobium both RpoN1 and N2 are functional in free-living and symbiotic conditions, rpoN1 gene was regulated in response to oxygen; RNA polymerase factor sigma-54 624138..625388 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904991 YP_002344094.1 CDS dcuB NC_002163.1 625552 626976 D functions in anaerobic transport of C4-dicarboxylate compounds such as fumarate; similar to DcuA; DcuA and DcuB function as independent and mutually redundant C4-dicarboxylate (aspartate, malate, fumarate and succinate) transporters; anaerobic C4-dicarboxylate transporter 625552..626976 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904992 YP_002344095.1 CDS Cj0672 NC_002163.1 627118 627306 D Original (2000) note: Cj0672, possible periplasmic protein, len: 62 aa; no Hp match. Contains possible N-terminal signal sequence and second hydrophobic domain; Updated (2006) note: Two probable transmembrane helices predicted by TMHMM2.0. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein 627118..627306 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904993 YP_002344096.1 CDS kdpB NC_002163.1 629020 631065 D One of the components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions; potassium-transporting ATPase subunit B 629020..631065 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904995 YP_002344097.1 CDS kdpD NC_002163.1 631667 633487 D Original (2000) note: Cj0679, kdpD', truncated KdpD protein, len: 606 aa; similar to other kdpD sensor proteins, but lacking the C-terminal two-component histidine kinase domain, e.g. KDPD_ECOLI sensor protein KDPD (EC 2.7.3.-) (894 aa), fasta scores; opt: 883 z-score: 1523.9 E(): 0, 34.8% identity in 604 aa overlap. No Hp match. Note that C. jejuni apparently lacks a kdpE two-component regulator homolog; Updated (2006) note: Pfam domain PF02702 Osmosensitive K+ channel His kinase sensor domain was identified within CDS. Five probable transmembrane helices predicted by TMHMM2.0. Further support for product function. not added to product function. Functional classification - Transport/binding proteins -Cations; PMID:9226259, PMID:7499326, PMID:1532388; truncated KdpD protein 631667..633487 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904997 YP_002344098.1 CDS uvrB NC_002163.1 633589 635562 R 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, where it probes for the presence of a lesion; excinuclease ABC subunit B complement(633589..635562) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904998 YP_002344099.1 CDS Cj0681 NC_002163.1 635716 635946 D Original (2000) note: Cj0681, unknown, len: 76 aa; 36.2% identity to HP0385. Functional classification -Conserved hypothetical proteins; hypothetical protein 635716..635946 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904999 YP_002344100.1 CDS Cj0682 NC_002163.1 635936 636178 D Original (2000) note: Cj0682, unknown, len: 80 aa; no Hp match. Functional classification - Unknown; hypothetical protein 635936..636178 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905000 YP_002344101.1 CDS Cj0683 NC_002163.1 636175 636612 D Original (2000) note: Cj0683, probable periplasmic protein, len: 145 aa; no Hp match; Updated (2006) 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; periplasmic protein 636175..636612 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905001 YP_002344102.1 CDS priA NC_002163.1 636594 638447 D binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity; primosome assembly protein PriA 636594..638447 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905002 YP_002344103.1 CDS cipA NC_002163.1 638540 639892 R Original (2000) note: Cj0685c, possible sugar transferase, len: 450 aa; no Hp match. Contains variable poly-G tract near C-terminus; G9 (consensus) allows complete translation, G10 would cause truncation at aa 233. Some similarity to Cj1421c (28.0% identity in 404 aa overlap) and Cj1422c (25.3% identity in 442 aa overlap),both of which contain variable polyG tracts, though in different positions. functional assignment is based on family clustering (BLASTP) with other C. jejuni predicted sugar transferases e,g, Cj1434c, and Cj1438c; Updated (2006) 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, work has been carried out within a PhD thesis. Functional classification - Surface polysaccharides, lipopolysaccharides and antigens; http://www.freepatentsonline.com/6087105.html; http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape9/PQDD_ 0004/MQ46044.pdf#search=%22cipA%20AND%20campylobacter%22; invasion protein CipA complement(638540..639892) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905003 YP_002344104.1 CDS ispG NC_002163.1 639998 641071 D catalyzes the conversion of 2C-methyl-D-erythritol 2,4-cyclodiphosphate into 4-hydroxy-3-methyl-2-en-1-yl diphosphate; involved in isoprenoid synthesis; 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase 639998..641071 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905004 YP_002344105.1 CDS flgH NC_002163.1 641102 641800 R part of the flagellar basal body which consists of four rings L,P, S and M mounted on a central rod; flagellar basal body L-ring protein complement(641102..641800) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905006 YP_002344106.1 CDS pta NC_002163.1 641890 643395 D Original (2000) note: Cj0688, pta, probable phosphate acetyltransferase, len: 501 aa; highly similar in C-terminus to e.g. PTA_ECOLI phosphate acetyltransferase (EC 2.3.1.8) (713 aa), fasta scores; opt: 1012 z-score: 1161.8 E(): 0, 48.8% identity in 326 aa overlap. 24.8% identity in N-terminus to HP0905; Updated (2006) note: Pfam domain PF01515 Phosphate acetyl/butaryl transferase was identified within CDS. Further support given to product function. Characterised within Escherichia coli with acceptable identity score,however, sequence alignment was only partial. kept within product function. Literature search identified paper linking product function to biofilm formation (PMID:16436427). Functional classification - Degradation -Carbon compounds; PMID:16436427, PMID:7883769; phosphate acetyltransferase 641890..643395 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905007 YP_002344107.1 CDS ackA NC_002163.1 643409 644599 D AckA utilizes acetate and can acetylate CheY which increases signal strength during flagellar rotation; utilizes magnesium and ATP; also involved in conversion of acetate to aceyl-CoA; acetate kinase 643409..644599 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905008 YP_002344108.1 CDS Cj0690c NC_002163.1 644627 648379 R Original (2000) note: Cj0690c, possible restriction/modification enzyme, len: 1250 aa; similar to Borrelia burgdorferi plasmid TR:O50698 (EMBL:AE000785) hypotheticalprotein BBE02 (1277 aa), fasta scores; opt: 1517 z-score: 1607.6 E(): 0, 35.0% identity in 1304 aa overlap. Very weak similarity to T257_ECOLI type IIS restriction enzyme ECO57I (997 aa), fasta scores; opt: 156 z-score: 163.4 E(): 0.083, 19.6% identity in 981 aa overlap. No Hp ortholog. Some simlarity to Cj0031 (25.0% identity in 859 aa overlap). Contains PS00092 N-6 Adenine-specific DNA methylases signature; Updated (2006) 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,restriction/modification, recombination and repair; restriction/modification enzyme complement(644627..648379) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905009 YP_002344109.1 CDS Cj0691 NC_002163.1 648529 649020 D Original (2000) note: Cj0691, possible membrane protein, len: 163 aa; no Hp match. Contains two possible transmembrane domains. Functional classification -Membranes, lipoproteins and porins; hypothetical protein 648529..649020 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905010 YP_002344110.1 CDS Cj0692c NC_002163.1 649008 649946 R Original (2000) note: Cj0692c, possible membrane protein, len: 312 aa; 34.7% identity in N-terminus to HP0708 (114 aa). Contains one possible transmembrane domain. Functional classification - Membranes,lipoproteins and porins; hypothetical protein complement(649008..649946) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905011 YP_002344111.1 CDS mraW NC_002163.1 649946 650884 R Original (2000) note: Cj0693c, unknown, len: 312 aa; similar to members of the YABC/YLXA family of hypothetical proteins e.g. YLXA_BACSU (311 aa), fasta scores; opt: 584 z-score: 670.8 E(): 4.6e-30, 39.8% identity in 304 aa overlap. 47.4% identity to HP0707; Updated (2006) 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; PMID:10572301; S-adenosyl-methyltransferase MraW complement(649946..650884) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905012 YP_002344112.1 CDS Cj0694 NC_002163.1 651043 652533 D Original (2000) note: Cj0694, probable periplasmic protein, len: 496 aa; C-terminus is almost identical to C. jejuni ORF TR:Q46115 (EMBL:X95910). 31.9% identity toHP0977. Contains probable N-terminal signal sequence; Updated (2006) note: Literature search identified paper linking product function to glycoprotein. Functional classification - Miscellaneous periplasmic proteins; PMID:12186869; periplasmic protein 651043..652533 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905013 YP_002344113.1 CDS ftsA NC_002163.1 652530 653918 D Original (2000) note: Cj0695, ftsA, probable cell division protein, len: 462; identical, except for a small frameshift, to C. jejuni ftsA TR:Q46116 (EMBL:X95910). Similar to many e.g. FTSA_ECOLI cell division protein FTSA (420 aa), fasta scores; opt: 570 z-score: 635.2 E(): 4.4e-28, 27.7% identity in 382 aa overlap. 37.2% identity to HP0978; Updated (2006) note: Pfam domains PF02491 (x2) 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; PMID:8807806; cell division protein FtsA 652530..653918 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905014 YP_002344114.1 CDS ftsZ NC_002163.1 653934 655046 D GTPase; similar structure to tubulin; forms ring-shaped polymers at the site of cell division; other proteins such as FtsA, ZipA, and ZapA, interact with and regulate FtsZ function; cell division protein FtsZ 653934..655046 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905015 YP_002344115.1 CDS flgG2 NC_002163.1 655202 656014 D Original (2000) note: Cj0697, flgG2, probable flagellar basal-body rod protein, len: 270 aa; similar to e.g. FLGG_ECOLI flagellar basal-body rod protein FLGG (260 aa), fasta scores; opt: 290 z-score: 318.7 E(): 1.9e-10,28.7% identity in 272 aa overlap. 42.6% identity to HP1092. Also similar to downstream gene Cj0698 (flgG,29.9% identity in 281 aa overlap). Contains PS00588 Flagella basal body rod proteins signature and Pfam match to entry PF00460 flg_bb_rod, Flagella basal body rod proteins; Updated (2006) note: Characterised within Escherichia coli with marginal identity score. Also,characterisation work within Campylobacter jejuni. removed from product function. Functional classification - Surface structures; PMID:9931471, PMID:15228533; flagellar basal-body rod protein 655202..656014 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905016 YP_002344116.1 CDS flgG NC_002163.1 656043 656834 D makes up the distal portion of the flagellar basal body rod; flagellar basal body rod protein FlgG 656043..656834 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905017 YP_002344117.1 CDS glnA NC_002163.1 656901 658331 R Original (2000) note: Cj0699c, glnA, probable glutamine synthetase, len: 476 aa; highly similar to many e.g. GLNA_ECOLI glutamine synthetase (EC 6.3.1.2) (468 aa), fasta scores; opt: 1529 z-score: 1812.8 E(): 0,51.5% identity in 462 aa overlap. 63.6% identity to HP0512. Contains PS00180 Glutamine synthetase signature 1,PS00181 Glutamine synthetase ATP-binding region signature, and Pfam match to entry PF00120 gln-synt; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Amino acid biosynthesis - Glutamate family; PMID:2882477; glutamine synthetase complement(656901..658331) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905018 YP_002344118.1 CDS Cj0700 NC_002163.1 658534 659229 D Original (2000) note: Cj0700, unknown, len: 231 aa; 49.4% identity to HP0170. Functional classification -Conserved hypothetical proteins; hypothetical protein 658534..659229 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905019 YP_002344119.1 CDS Cj0701 NC_002163.1 659226 660479 D Original (2000) note: Cj0701, probable protease,len: 417 aa; similar to many proteases belonging to the peptidase family U32, e.g. YEGQ_ECOLI protease in baer-ogrk intergenic Region (453 aa), fasta scores; opt: 567 z-score: 648.6 E(): 7.9e-29, 34.9% identity in 404 aa overlap. 55.5% identity to HP0169. Contains PS01276 Peptidase family U32 signature and Pfam match to entry PF01136 Peptidase_U32; Updated (2006) note: Similar to many with marginal identity scores. kept within product function. Functional classification - Degradation of macromolecules - Proteins, peptides and glycopeptides; protease 659226..660479 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905020 YP_002344120.1 CDS purE NC_002163.1 660480 660974 D Original (2000) note: Cj0702, purE, probable phosphoribosylaminoimidazole carboxylase catalytic subunit, len: 164 aa; similar to many e.g. PUR6_ECOLI phosphoribosylaminoimidazole carboxylase catalytic subunit (EC 4.1.1.21) (168 aa), fasta scores; opt: 485 z-score: 562.6 E(): 4.9e-24, 55.2% identity in 143 aa overlap. No Hp match. Contains Pfam match to entry PF00731 AIRC, AIR carboxylase; Updated (2006) note: Characterised within Escherichia coli and Bacillus subtilus with acceptable identity scores. not added to product function. Functional classification - Purine ribonucleotide biosynthesis; PMID:10074353, PMID:2464576; phosphoribosylaminoimidazole carboxylase catalytic subunit 660480..660974 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905021 YP_002344121.1 CDS Cj0703 NC_002163.1 660984 661520 D Original (2000) note: Cj0703, unknown, len: 178 aa; 51.0% identity to HP0406. Functional classification -Conserved hypothetical proteins; hypothetical protein 660984..661520 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905022 YP_002344122.1 CDS glyQ NC_002163.1 661532 662395 D glycine--tRNA ligase alpha chain; GlyRS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA; glycyl-tRNA synthetase subunit alpha 661532..662395 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905023 YP_002344123.1 CDS Cj0705 NC_002163.1 662382 663107 D Original (2000) note: Cj0705, unknown, len: 241 aa; similar to hypothetical proteins e.g. TR:O51424 (EMBL:AE001151) Borrelia burgdorferi BB0468 (248 aa),fasta scores; opt: 240 z-score: 292.4 E(): 5.5e-09, 27.0% identity in 244 aa overlap. 42.7% identity to HP0959; Updated (2006) note: Pfam domain PF01784 NIF3 (NGG1p interacting factor 3) identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins; hypothetical protein 662382..663107 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905024 YP_002344124.1 CDS Cj0706 NC_002163.1 663117 663833 D Original (2000) note: Cj0706, unknown, len: 238 aa; similar to hypothetical proteins e.g. TR:O67273 (EMBL:AE000729) Aquifex aeolicus AQ_1223 (235 aa), fasta scores; opt: 298 z-score: 287.3 E(): 1.1e-08, 30.1% identity in 236 aa overlap. 37.4% identity to HP0958; Updated (2006) note: Pfam domain PF02591 Uncharacterized ACR, COG1579 identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins; hypothetical protein 663117..663833 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905025 YP_002344125.1 CDS kdtA NC_002163.1 663830 664987 D catalyzes the transfer of 2-keto-3-deoxy-D-manno-octulosonic acid to lipid A; 3-deoxy-D-manno-octulosonic-acid transferase 663830..664987 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905026 YP_002344126.1 CDS Cj0708 NC_002163.1 664968 665720 D Original (2000) note: Cj0708, possible ribosomal pseudouridine synthase, len: 250 aa; similar to many hypothetical proteins and to e.g. RLUC_ECOLI ribosomal large subunit pseudouridine synthase D (EC 4.2.1.70) (319 aa), fasta scores; opt: 202 z-score: 252.9 E(): 8.6e-07,29.7% identity in 175 aa overlap. 47.0% identity to HP0956. Contains PS01129 Hypothetical yabO/yceC/sfhB family signature and Pfam match to entry PF00849 YABO,Hypothetical yabO/yceC/sfhB family. Also similar to Cj1280c (26.9% identity in 223 aa overlap) and Cj0022c (27.6% identity in 275 aa overlap); Updated (2006) 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; PMID:10089432; ribosomal pseudouridine synthase 664968..665720 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905027 YP_002344127.1 CDS ffh NC_002163.1 665788 667125 D Original (2000) note: Cj0709, ffh, probable signal recognition particle protein, len: 445 aa; highly similar to many e.g. SR54_ECOLI signal recognition particle protein (453 aa), fasta scores; opt: 1136 z-score: 1195.2 E(): 0, 41.5% identity in 441 aa overlap. 61.0% identity to HP1152. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00300 SRP54-type proteins GTP-binding domain signature, and Pfam match to entry PF00448 SRP54,SRP54-type protein; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Protein and peptide secretion; PMID:1331806, PMID:11976293; signal recognition particle protein 665788..667125 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905028 YP_002344128.1 CDS rpsP NC_002163.1 667190 667417 D binds to lower part of 30S body where it stabilizes two domains; required for efficient assembly of 30S; in Escherichia coli this protein has nuclease activity; 30S ribosomal protein S16 667190..667417 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905030 YP_002344129.1 CDS Cj0711 NC_002163.1 667420 667662 D Original (2000) note: Cj0711, unknown, len: 80 aa; simlar to small hypothetical proteins downstream of rpsP in many organisms e.g. TR:O31738 (EMBL:Z99112) Bacillus subtilis YLQC (81 aa), fasta scores; opt: 115 z-score: 178.5 E(): 0.012, 32.3% identity in 62 aa overlap. 37.7% identity to HP1150. Functional classification - Conserved hypothetical proteins; hypothetical protein 667420..667662 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904497 YP_002344130.1 CDS rimM NC_002163.1 667655 668194 D Original (2000) note: Cj0712, rimM, possible 16S rRNA processing protein, len: 179 aa; similar to e.g. RIMM_ECOLI 16S rRNA processing protein RIMM (185 aa),fasta scores; opt: 202 z-score: 255.1 E(): 6.6e-07, 24.1% identity in 174 aa overlap. 37.8% identity to HP1149; Updated (2006) 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; PMID:9422595; 16S rRNA processing protein 667655..668194 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904519 YP_002344131.1 CDS trmD NC_002163.1 668191 668895 D methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA; tRNA (guanine-N(1)-)-methyltransferase 668191..668895 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904477 YP_002344132.1 CDS rplS NC_002163.1 668906 669262 D 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; 50S ribosomal protein L19 668906..669262 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905031 YP_002344133.1 CDS Cj0715 NC_002163.1 669395 669808 D Original (2000) note: Cj0715, transthyretin-like periplasmic protein, len: 137 aa; similar to members of the transthyretin family e.g. YEDX_ECOLI hypothetical transthyretin-like protein precursor (137 aa), fasta scores; opt: 305 z-score: 409.7 E(): 1.6e-15, 38.9% identity in 126 aa overlap, and TTHY_BOVIN Cow transthyretin precursor (prealbumin) (147 aa), fasta scores; opt: 205 z-score: 279.8 E(): 2.8e-08, 33.8% identity in 142 aa overlap. No Hp match. Contains Pfam match to entry PF00576 Transthyretin and probable N-terminal signal sequence; Updated (2006) note: Prosite domains PS00768 TRANSTHYRETIN_1, Transthyretin and PS00769 TRANSTHYRETIN_2, 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; PMID:12186869; transthyretin-like periplasmic protein 669395..669808 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905032 YP_002344134.1 CDS Cj0716 NC_002163.1 669832 671172 D Original (2000) note: Cj0716, probable phospho-2-dehydro-3-deoxyheptonate aldolase, len: 446 aa; similar to enzymes from plants e.g. AROF_ARATH phospho-2-dehydro-3-deoxyheptonate aldolase (EC 4.1.2.15) (525 aa), fasta scores; opt: 1680 z-score: 1935.9 E(): 0,54.2% identity in 445 aa overlap. 59.6% identity to HP0134; Updated (2006) note: Pfam domain PF01474 Class-II DAHP synthetase family identified within CDS. Product function kept the same (along with ), as no specific characterisation within related bacteria has been carried out. Functional classification - Amino acid biosynthesis - Aromatic amino acid family; phospho-2-dehydro-3-deoxyheptonate aldolase 669832..671172 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905033 YP_002344135.1 CDS Cj0717 NC_002163.1 671169 671498 D Original (2000) note: Cj0717, unknown, len: aa; similar to hypothetical proteins e.g. YFFB_ECOLI (118 aa),fasta scores; opt: 164 z-score: 215.8 E(): 0.0001, 32.3% identity in 93 aa overlap. No Hp match; Updated (2006) 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; PMID:1704144; ArsC family protein 671169..671498 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905035 YP_002344136.1 CDS dnaE NC_002163.1 671946 675548 D catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase; DNA polymerase III subunit alpha 671946..675548 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905036 YP_002344137.1 CDS Cj0719c NC_002163.1 675560 676192 R Original (2000) note: Cj0719c, unknown, len: 210 aa; similar to hypothetical proteins from many organisms e.g. YGGS_ECOLI (234 aa), fasta scores; opt: 307 z-score: 380.4 E(): 6.9e-14, 34.0% identity in 206 aa overlap. 47.5% identity to HP0395. Contains PS01211 Uncharacterized protein family UPF0001 signature and Pfam match to entry PF01168 UPF0001; Updated (2006) note: Pfam domain PF01168 Alanine racemase, 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; PMID:15228533; hypothetical protein complement(675560..676192) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905037 YP_002344138.1 CDS flaC NC_002163.1 676227 676976 R Original (2000) note: Cj0720c, flaC, flagellin,len: 249 aa; 99.6% identical to TR:P96747 (EMBL:U85622) C. jejuni flaC, and similar to the N-terminus of e.g. FLAB_CAMJE flagellin B (CJ1338) (575 aa), fasta scores; opt: 236 z-score: 261.7 E(): 2.8e-07, 27.2% identity in 202 aa overlap. No Hp ortholog; Updated (2006) 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; PMID:15228533, PMID:16740937; flagellin complement(676227..676976) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905038 YP_002344139.1 CDS Cj0721c NC_002163.1 677015 677485 R Original (2000) note: Cj0721c, probable integral membrane protein, len: 156 aa; 35.9% identity to HP0288; Updated (2006) note: Four probable transmembrane helices predicted by TMHMM2.0; integral membrane protein complement(677015..677485) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905039 YP_002344140.1 CDS Cj0722c NC_002163.1 677498 678313 R Original (2000) note: Cj0722c, probable DNA methylase, len: 271 aa; similar to members of the hemK family of methylases, e.g. HEMK_ECOLI HEMK protein (277 aa), fasta scores; opt: 262 z-score: 315.7 E(): 2.7e-10,26.1% identity in 276 aa overlap. 36.9% identity to HP0381. Contains PS00092 N-6 Adenine-specific DNA methylases signature; Updated (2006) note: Prosite domain PS50193 SAM_BIND, SAM (and some other nucleotide) 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, restriction/modification, recombination and repair; DNA methylase complement(677498..678313) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905040 YP_002344141.1 CDS Cj0723c NC_002163.1 678310 679497 R Original (2000) note: Cj0723c, probable integral membrane zinc-metalloprotease, len: 395 aa; simimlar to yeast proteases e.g. ST24_YEAST CAAX prenyl protease 1 (453 aa), fasta scores; opt: 494 z-score: 565.5 E(): 3.4e-24, 31.6% identity in 430 aa overlap, and to prokaryotic htpX, e.g. HTPX_ECOLI heat shock protein HTPX (293 aa), fasta scores; opt: 183 z-score: 216.0 E(): 9.9e-05, 24.1% identity in 295 aa overlap. 38.6% identity to HP0382. Contains PS00142 Neutral zinc metallopeptidases, zinc-binding region signature; Updated (2006) note: Pfam domain PF01435 Peptidase family M48 and Prosite domain PS00142 ZINC_PROTEASE,Peptidase M, neutral zinc metallopeptidases, zinc-binding site were identified within CDS. Also, 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,peptides and glycopeptides; integral membrane zinc-metalloprotease complement(678310..679497) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905041 YP_002344142.1 CDS Cj0724 NC_002163.1 679624 679809 D Original (2000) note: Cj0724, unknown, len: 61 aa; no Hp match. Functional classification - Unknown; hypothetical protein 679624..679809 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905042 YP_002344143.1 CDS mogA NC_002163.1 679806 680348 R forms a trimer; related to eukaryotic protein gephyrin; functions during molybdenum cofactor biosynthesis; molybdenum cofactor biosynthesis protein MogA complement(679806..680348) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905043 YP_002344144.1 CDS corA NC_002163.1 680369 681352 R Original (2000) note: Cj0726c, corA, probable magnesium and cobalt transport protein, len: 327 aa; similar to e.g. CORA_ECOLI magnesium and cobalt transport protein CORA (316 aa), fasta scores; opt: 559 z-score: 616.2 E(): 5.1e-27, 31.3% identity in 329 aa overlap. 49.4% identity to HP1344; Updated (2006) note: Pfam domain PF01544 CorA-like Mg2+ transporter protein identified within CDS. Also, 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/binding proteins - Cations; PMID:1779764, PMID:9775386; magnesium and cobalt transport protein complement(680369..681352) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905044 YP_002344145.1 CDS Cj0727 NC_002163.1 681469 682515 D Original (2000) note: Cj0727, probable periplasmic solute-binding protein, len: 348 aa; similar to e.g. SUBI_ECOLI sulfate-binding protein precursor (329 aa),fasta scores; opt: 220 z-score: 256.1 E(): 5.8e-07, 25.0% identity in 220 aa overlap. No Hp match. Contains N-terminal signal sequence; Updated (2006) note: Pfam domain PF01547 Bacterial extracellular solute-binding protein identified within CDS. Further support given to product function. Characterised within Escherichia coli, however, identity scores were unnacceptable. kept within product function. Functional classification - Transport/binding proteins - Other; periplasmic solute-binding protein 681469..682515 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905045 YP_002344146.1 CDS Cj0728 NC_002163.1 682526 683851 D Original (2000) note: Cj0728, probable periplasmic protein, len: 441 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein 682526..683851 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905046 YP_002344147.1 CDS Cj0729 NC_002163.1 683848 684657 D Original (2000) note: Cj0729, unknown, len: 269 aa; no Hp match; Updated (2006) note: Pfam domain PF01663 Type I phosphodiesterase / nucleotide pyrophosphatase identified within CDS. Product modified to more specific family member due to motif match. No specific characterisation has been carried out yet, so kept within product function. Functional classification - Purines,pyrimidines, nucleosides and nucleotides - Miscellaneous nucleoside/nucleotide reactions; type I phosphodiesterase/nucleotide pyrophosphatase 683848..684657 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905047 YP_002344148.1 CDS Cj0730 NC_002163.1 684654 685493 D Original (2000) note: Cj0730, probable ABC transport system permease, len: 279 aa; similar to members of the binding protein-dependent permease family e.g. UGPA_ECOLI SN-glycerol-3-phosphate transport system permease (295 aa), fasta scores; opt: 273 z-score: 324.4 E(): 9.1e-11, 25.0% identity in 280 aa overlap. No Hp match. Contains Pfam match to entry PF00528 BPD_transp,Binding-protein-dependent transport systems inner membrane component; Updated (2006) 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/binding proteins - Other; ABC transporter permease 684654..685493 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905048 YP_002344149.1 CDS Cj0731 NC_002163.1 685494 686273 D Original (2000) note: Cj0731, probable ABC transport system permease, len: 259 aa; similar to members of the binding protein-dependent permease family e.g. POTC_ECOLI spermidine/putrescine transport system permease (264 aa), fasta scores; opt: 271 z-score: 337.3 E(): 1.7e-11, 24.1% identity in 241 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00528 BPD_transp,Binding-protein-dependent transport systems inner membrane component; Updated (2006) 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/binding proteins - Other; ABC transporter permease 685494..686273 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905049 YP_002344150.1 CDS Cj0732 NC_002163.1 686277 687266 D Original (2000) note: Cj0732, probable ABC transport system ATP-binding protein, len: 329 aa; similar to many e.g. POTA_ECOLI spermidine/putrescine transport ATP-binding protein (378 aa), fasta scores; opt: 802 z-score: 857.8 E(): 0, 43.2% identity in 292 aa overlap. No Hp otholog. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00211 ABC transporters family signature and Pfam match to entry PF00005 ABC_tran; Updated (2006) note: Similar to more than one species with acceptable identity score. not added to product function. Functional classification -Transport/binding proteins - Other; ABC transporter ATP-binding protein 686277..687266 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905050 YP_002344151.1 CDS Cj0733 NC_002163.1 687263 687901 D Original (2000) note: Cj0733, unknown, len: 212 aa; some similarity to hypotheical proteins from Actinomycetes e.g. TR:O69629 (EMBL:AL022121) Rv3661 (MTV025.009) (287 aa), fasta scores; opt: 264 z-score: 321.7 E(): 1.3e-10,28.4% identity in 215 aa overlap. No Hp match; Updated (2006) 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; HAD-superfamily hydrolase 687263..687901 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905051 YP_002344152.1 CDS hisJ NC_002163.1 687925 688680 R Original (2000) note: Cj0734c, hisJ, probable histidine-binding protein precursor, len: 251 aa; almost identical to HISJ_CAMJE histidine-binding protein precursor (256 aa) (88.7% identity in 256 aa overlap) and similar to many priplasmic amino-acid binding proteins e.g. HISJ_ECOLI histidine-binding periplasmic protein precursor (260 aa), fasta scores; opt: 343 z-score: 390.5 E(): 1.9e-14. 33.5% identity in 263 aa overlap. No Hp ortholog. Contains N-terminal signal sequence, PS00013 Prokaryotic membrane lipoprotein lipid attachment site,PS01039 Bacterial extracellular solute-binding proteins,family 3 signature, and Pfam match to entry PF00497 SBP_bac_3, Bacterial extracellular solute-binding proteins, family 3; Updated (2006) note: Characterised in Campylobacter jejuni. not added to product function. Functional classification - Transport/binding proteins - Amino acids and amines; PMID:9489038, PMID:15063560, PMID:9395059; histidine-binding protein precursor complement(687925..688680) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905052 YP_002344153.1 CDS Cj0735 NC_002163.1 689007 689726 D Original (2000) note: Cj0735, probable periplasmic protein, len: 239 aa; no Hp match. Similar to N-terminus of Cj0967 (E(): 6.7e-15, 34.5% identity in 116 aa overlap); similarity continues in downstream CDS Cj0736. Contains probable N-terminal signal sequence; Updated (2006) note: One probable transmembrane helix predicted by TMHMM2.0. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein 689007..689726 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905053 YP_002344154.1 CDS Cj0736 NC_002163.1 689656 691584 D Original (2000) note: Cj0736, unknown, len: 239 aa; no Hp match. Similar to C-terminus of Cj0967(E(): 0, 42.3% identity in 562 aa overlap); similarity continues from upstream CDS Cj0735; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein 689656..691584 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905054 YP_002344155.1 CDS Cj0737 NC_002163.1 691596 692672 D Original (2000) note: Cj0737, probable periplasmic protein, len: 358 aa; simlar to the N-terminus of HXA3_HAEIN heme:hemopexin-binding protein precursor (hxuA) (917 aa), fasta scores; opt: 236 z-score: 251.5 E(): 1e-06, 32.8% identity in 180 aa overlap, and N-terminus of TR:Q48028 H. influenzae adhesin (1477 aa), fasta scores; opt: 292 z-score: 307.3 E(): 8.1e-10, 28.9% identity in 381 aa overlap. No Hp match. Similar in part to Cj0968 and Cj0969, probably representing a pseudogene copy of this CDS; Updated (2006) note: Pfam domain PF05860 haemagglutination activity domain identified within CDS. One probable transmembrane helix predicted by TMHMM2.0. Product modified to more specific family member due to motif match. kept as no specific characterisation. Functional classification - Misc; hemagglutination activity domain-containing protein 691596..692672 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905055 YP_002344156.1 CDS Cj0738 NC_002163.1 692726 692890 D Original (2000) note: Cj0738, unknown, len: 54 aa; no Hp match. Functional classification - Unknown; hypothetical protein 692726..692890 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905056 YP_002344157.1 CDS Cj0739 NC_002163.1 692878 693051 D Original (2000) note: Cj0739, unknown, len: 57 aa; no Hp match. Functional classification - Unknown; hypothetical protein 692878..693051 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905057 YP_002344158.1 CDS Cj0740 NC_002163.1 693048 693212 D Original (2000) note: Cj0740, unknown, len: 54 aa; no Hp match. Functional classification - . Functional classification - Unknown; hypothetical protein 693048..693212 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905058 YP_002344159.1 CDS Cj0741 NC_002163.1 693191 694117 D Original (2000) note: Cj0741, unknown, len: 308 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein 693191..694117 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905059 YP_002344160.1 CDS Cj0747 NC_002163.1 702810 702917 D Original (2000) note: Cj0747, unknown, len: 35 aa; no Hp match. Functional classification - Unknown; hypothetical protein 702810..702917 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905062 YP_002344161.1 CDS Cj0748 NC_002163.1 703027 703119 D Original (2000) note: Cj0748, unknown, len: 30 aa; no Hp match. Functional classification - Unknown; hypothetical protein 703027..703119 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905063 YP_002344162.1 CDS tonB3 NC_002163.1 704442 705125 R Original (2000) note: Cj0753c, tonB3, probable tonB transport protein, len: 227 aa; almost identical to TONB_CAMCO C. coli tonB protein (232 aa); 96.6% identity in 232 aa overlap, and similar to e.g. TONB_ECOLI (239 aa,fasta scores; opt: 154 z-score: 170.4 E(): 0.034, 29.6% identity in 162 aa overlap. 34.6% identity to HP1341. Also similar to tonB2, Cj1630 (41.7% identity in 230 aa overlap); Updated (2006) 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/binding proteins - Other; PMID:9190817, PMID:11395459; TonB transport protein complement(704442..705125) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905065 YP_002344163.1 CDS cfrA NC_002163.1 705450 707540 D Original (2000) note: Cj0755, cfrA, probable iron uptake protein (ferric receptor), len: 696 aa; almost identical to TR:O07651 (EMBL:U80812) C. coli ferric receptor CFRA (696 aa); 98.7% identity in 696 aa overlap. Also simimlar to e.g. TR:O87518 (EMBL:AF081285) E. coli exogenous ferric siderophore receptor R4 (669 aa), fasta scores; opt: 1127 z-score: 1247.0 E(): 0, 34.5% identity in 693 aa overlap. 23.4% identity to HP0686; Updated (2006) 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 (following on from Campylobacter coli), has led to product function being modified to more specfic family member. not added to product function. Functional classification - Transport/binding proteins - Cations; PMID:9190817, PMID:9765558, PMID:15231804,PMID:15632442; ferric enterobactin uptake receptor 705450..707540 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905066 YP_002344164.1 CDS hrcA NC_002163.1 707840 708634 D Acts as a negative regulator of the grpE-dnaK-dnaJ and groELS class I heat shock operons by preventing heat-shock induction; heat-inducible transcription repressor 707840..708634 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905067 YP_002344165.1 CDS grpE NC_002163.1 708631 709161 D with DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins; may act as a thermosensor; heat shock protein GrpE 708631..709161 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905068 YP_002344166.1 CDS dnaK NC_002163.1 709183 711054 D heat shock protein 70; assists in folding of nascent polypeptide chains; refolding of misfolded proteins; utilizes ATPase activity to help fold; co-chaperones are DnaJ and GrpE; multiple copies in some bacteria; molecular chaperone DnaK 709183..711054 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905069 YP_002344167.1 CDS Cj0760 NC_002163.1 711314 712336 D Original (2000) note: Cj0760, unknown, len: 340 aa; similar to hypothetical proteins e.g. YZ34_MYCTU Rv0906,(MTCY31.34) (372 aa), fasta scores; opt: 598 z-score: 724.2 E(): 4.8e-33, 29.9% identity in 335 aa overlap. Some similarity in C-terminus to ROMA_KLEPN outer membrane protein roma (fragment) (132 aa), fasta scores; opt: 335 z-score: 415.0 E(): 8.1e-16, 43.0% identity in 114 aa overlap. No Hp match; Updated (2006) 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; PMID:15758238; hypothetical protein 711314..712336 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905070 YP_002344168.1 CDS Cj0761 NC_002163.1 712406 712747 D Original (2000) note: Cj0761, unknown, len: aa; similar to hypothetical proteins e.g. TR:O67079 (EMBL:AE000715) Aquifex aeolicus AQ_943 (107 aa), fasta scores; opt: 130 z-score: 186.5 E(): 0.0043, 28.6% identity in 84 aa overlap. 55.8% identity to HP0902; Updated (2006) note: Literature search identified paper giving clues to product function. Functional classification - Conserved hypothetical proteins; PMID:15758235; hypothetical protein 712406..712747 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905071 YP_002344169.1 CDS aspB NC_002163.1 712797 713966 R catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate; aspartate aminotransferase complement(712797..713966) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905072 YP_002344170.1 CDS cysE NC_002163.1 714138 714776 R Original (2000) note: Cj0763c, cysE, probable serine acetyltransferase, len: 212 aa; highly similar to many e.g. CYSE_BACSU serine acetyltransferase (EC 2.3.1.30) (217 aa), fasta scores; opt: 598 z-score: 700.2 E(): 1e-31, 46.6% identity in 204 aa overlap. 50.9% identity to HP1210. Contains PS00101 Hexapeptide-repeat containing-transferases signature and 2x Pfam match to entry PF00132 hexapep, Bacterial transferase hexapeptide (four repeats); Updated (2006) note: Characterised in Bacillus subtilis with acceptable identity score. not added to product function. Functional classification -Amino acid biosynthesis - Serine family; PMID:7510287; serine acetyltransferase complement(714138..714776) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905073 YP_002344171.1 CDS speA NC_002163.1 714777 716612 R catalyzes the formation of agmatine from arginine in putrescine and spermidine biosynthesis; arginine decarboxylase complement(714777..716612) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905074 YP_002344172.1 CDS hisS NC_002163.1 716609 717835 R catalyzes a two-step reaction, first charging a histidine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class II aminoacyl-tRNA synthetase; forms homodimers; some organisms have a paralogous gene, hisZ, that is similar to hisS and produces a protein that performs the first step in histidine biosynthesis along with HisG; histidyl-tRNA synthetase complement(716609..717835) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905075 YP_002344173.1 CDS tmk NC_002163.1 717832 718410 R catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP); thymidylate kinase complement(717832..718410) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905076 YP_002344174.1 CDS coaD NC_002163.1 718401 718877 R Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA; phosphopantetheine adenylyltransferase complement(718401..718877) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905077 YP_002344175.1 CDS Cj0768c NC_002163.1 718917 719480 R catalyzes the formation of 2-octaprenylphenol from 3-octaprenyl-4-hydroxybenzoate; 3-octaprenyl-4-hydroxybenzoate carboxy-lyase complement(718917..719480) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905078 YP_002344176.1 CDS flgA NC_002163.1 719477 720139 R required for the assembly of the flagellar basal body P-ring; flagellar basal body P-ring biosynthesis protein FlgA complement(719477..720139) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905079 YP_002344177.1 CDS Cj0770c NC_002163.1 720223 720999 R Original (2000) note: Cj0770c, probable periplasmic protein, len: 258 aa; similar to lipoproteins from other organisms e.g. PLPC_PASHA outer membrane lipoprotein 3 precursor (263 aa), fasta scores; opt: 569 z-score: 657.0 E(): 2.7e-29, 38.9% identity in 265 aa overlap, and TR:O69441 (EMBL:AJ005668) Legionella pneumophila 29 kda immunogenic protein (259 aa), fasta scores; opt: 584 z-score: 674.2 E(): 3e-30, 41.0% identity in 261 aa overlap. Also similar to Cj0772c (55.0% identity), Cj0771c (54.8% identity) and Cj1200 (44.9% identity). Single copy in Hp (HP1564); Updated (2006) note: Pfam domain PF03180 NLPA lipoprotein identified within CDS. NLPA lipoproteins are a family of bacterial lipoproteins that contain many antigenic members, 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; PMID:12169620; NLPA family lipoprotein complement(720223..720999) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905080 YP_002344178.1 CDS Cj0771c NC_002163.1 721009 721779 R Original (2000) note: Cj0771c, probable periplasmic protein, len: 258 aa; similar to lipoproteins from other organisms e.g. NLPA_ECOLI lipoprotein-28 precursor (272 aa), fasta scores; opt: 623 z-score: 705.2 E(): 5.6e-32,46.4% identity in 237 aa overlap, and TR:O69441 (EMBL:AJ005668) Legionella pneumophila 29 kda immunogenic protein (259 aa), fasta scores; opt: 661 z-score: 747.9 E(): 0, 44.2% identity in 258 aa overlap. Also similar to Cj0772c (52.5% identity), Cj0770c (54.8% identity) and Cj1200 (45.6% identity). Single copy in Hp (HP1564); Updated (2006) note: Pfam domain PF03180 NLPA lipoprotein identified within CDS. NLPA lipoproteins are a family of bacterial lipoproteins that contain many antigenic members, 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; PMID:12169620; NLPA family lipoprotein complement(721009..721779) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905081 YP_002344179.1 CDS Cj0772c NC_002163.1 721828 722601 R Original (2000) note: Cj0772c, probable periplasmic protein, len: 258 aa; similar to lipoproteins from other organisms e.g. PLPC_PASHA outer membrane lipoprotein 3 precursor (263 aa), fasta scores; opt: 642 z-score: 721.7 E(): 6.7e-33. 40.8% identity in 260 aa overlap, and TR:O69441 (EMBL:AJ005668) Legionella pneumophila 29 kda immunogenic protein (259 aa), fasta scores; opt: 638 z-score: 717.3 E(): 1.2e-32. 39.8% identity in 259 aa overlap. Also similar to Cj0770c (55.0% identity), Cj0771c (52.5% identity) and Cj1200 (57.5% identity). Single copy in Hp (HP1564; 47.7% identity in 243 aa overlap); Updated (2006) note: Pfam domain PF03180 NLPA lipoprotein identified within CDS. NLPA lipoproteins are a family of bacterial lipoproteins that contain many antigenic members, 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; PMID:12169620; NLPA family lipoprotein complement(721828..722601) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905082 YP_002344180.1 CDS Cj0773c NC_002163.1 722791 723702 R Original (2000) note: Cj0773c, probable binding-protein dependent transport system permease, len: 303 aa; similar to many e.g. PROW_BACSU glycine betaine/L-proline transport system permease (217 aa), fasta scores; opt: 212 z-score: 249.9 E(): 1.3e-06, 30.0% identity in 190 aa overlap. 43.9% identity in 205 aa overlap to HP1577. Contains Pfam match to entry PF00528 BPD_transp, Binding-protein-dependent transport systems inner membrane component; Updated (2006) 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/binding proteins - Other; PMID:12169620; binding-protein dependent transport system permease complement(722791..723702) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905083 YP_002344181.1 CDS Cj0774c NC_002163.1 723699 724709 R Original (2000) note: Cj0774c, probable ABC transport system ATP-binding protein, len: 336 aa; similar to many e.g. HISP_ECOLI histidine transport ATP-binding protein (257 aa), fasta scores; opt: 497 z-score: 566.5 E(): 2.9e-24, 38.5% identity in 262 aa overlap, and OCCP_AGRT6 octopine permease ATP-binding protein P (262 aa), fasta scores; opt: 511 z-score: 582.1 E(): 4e-25,36.9% identity in 260 aa overlap. 38.9% identity to HP1576. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00211 ABC transporters family signature, and Pfam match to entry PF00005 ABC_tran; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Transport/binding proteins - Other; PMID:3313284; ABC transporter ATP-binding protein complement(723699..724709) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905084 YP_002344182.1 CDS valS NC_002163.1 724714 727326 R valine--tRNA ligase; ValRS; converts valine ATP and tRNA(Val) to AMP PPi and valyl-tRNA(Val); class-I aminoacyl-tRNA synthetase type 1 subfamily; has a posttransfer editing process to hydrolyze mischarged Thr-tRNA(Val) which is done by the editing domain; valyl-tRNA synthetase complement(724714..727326) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904417 YP_002344183.1 CDS Cj0776c NC_002163.1 727349 728371 R Original (2000) note: Cj0776c, probable periplasmic protein, len: 340 aa; no Hp match. Contains N-terminal signal sequence. Functional classification - Miscellaneous periplasmic proteins; periplasmic protein complement(727349..728371) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905085 YP_002344184.1 CDS Cj0777 NC_002163.1 728500 730530 D Original (2000) note: Cj0777, probable ATP-dependent DNA helicase, len: 676 aa; similar to many members of the uvrD family of helicases, e.g. PCRA_STAAU ATP-dependent helicase PCRA (675 aa), fasta scores; opt: 561 z-score: 634.4 E(): 4.9e-28, 29.0% identity in 694 aa overlap, and REP_ECOLI ATP-dependent DNA helicase REP (673 aa), fasta scores; opt: 423 z-score: 478.5 E(): 2.4e-19,27.3% identity in 682 aa overlap. 47.5% identity to HP0911. Contains PS00017 ATP/GTP-binding site motif A (P-loop) and Pfam match to entry PF00580 UvrD-helicase,UvrD/REP helicase; Updated (2006) note: Characterisation work carried out within more than one species with marginal identity score. kept within product function. Functional classification - DNA replication,restriction/modification, recombination and repair; ATP-dependent DNA helicase 728500..730530 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905086 YP_002344185.1 CDS peb2 NC_002163.1 730569 731306 D Original (2000) note: Cj0778, peb2, major antigenic peptide PEB2, len: 245 aa; 94.9% identical to TR:G234576,sequenced by direct peptide sequencing; see: J. Biol. Chem. 266:16363-16369 (1991). Also similar to TR:Q57410 (EMBL:U39068, U15606) Vibrio cholerae accessory colonization factor ACFC (253 aa), fasta scores; opt: 430 z-score: 499.2 E(): 1.7e-20, 33.9% identity in 248 aa overlap, and TR:P96759 (EMBL:U82533)E. coli O45 ANM protein (251 aa), fasta scores; opt: 417 z-score: 484.4 E(): 1.1e-19, 33.2% identity in 247 aa overlap. Contains N-terminal signal sequence; Updated (2006) note: Characterised in Campylobacter jejuni in 1991. not added to product function. Functional classification - Miscellaneous periplasmic proteins; PMID:1885571; major antigenic peptide PEB2 730569..731306 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905087 YP_002344186.1 CDS tpx NC_002163.1 731405 731932 D Original (2000) note: Cj0779, tpx, probable thiol peroxidase, len: 175 aa; similar to e.g. TPX_ECOLI thiol peroxidase (EC 1.11.1.-) (167 aa), fasta scores; opt: 407 z-score: 489.0 E(): 6.1e-20, 44.2% identity in 154 aa overlap, and TAGD_VIBCH TAGD protein (164 aa), fasta scores; opt: 381 z-score: 458.8 E(): 3e-18, 39.9% identity in 158 aa overlap. 42.2% identity to HP0390. Contains PS01265 Tpx family signature, and Pfam match to entry PF00578 AhpC-TSA, AhpC/TSA family; Updated (2006) 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 (PMID:12186869). Functional classification -Detoxification; PMID:15632442, PMID:12069882, PMID:12186869; thiol peroxidase 731405..731932 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905088 YP_002344187.1 CDS napA NC_002163.1 732179 734953 D periplasmic; catalytic subunit; with NapBC catalyzes the reduction of nitrate to nitrite; NapAB receives electrons from NapC; nitrate reductase catalytic subunit 732179..734953 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905089 YP_002344188.1 CDS napG NC_002163.1 734971 735711 D part of NapHG quinol dehydrogenase; couples electron transfer from ubiquinone-ubiquinol couple via NapC/B to NapA; secreted by twin arginine translocation pathway; quinol dehydrogenase periplasmic component 734971..735711 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904514 YP_002344189.1 CDS napH NC_002163.1 735708 736490 D part of NapHG quinol dehydrogenase; couples electron transfer from ubiquinone-ubiquinol couple via NapC/B to NapA; quinol dehydrogenase membrane component 735708..736490 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904348 YP_002344190.1 CDS napB NC_002163.1 736487 737011 D Original (2000) note: Cj0783, napB, probable cytochrome C-type protein (periplasmic nitrate reductase small subunit), len: 174 aa; similar to e.g. NAPB_ECOLI cytochrome C-type protein NAPB precursor (149 aa), fasta scores; opt: 269 z-score: 327.2 E(): 6.3e-11,38.1% identity in 97 aa overlap. No Hp match. Contains 2x PS00190 Cytochrome c family heme-binding site signature,N-terminla signal sequence and PS00013 Prokaryotic membrane lipoprotein lipid attachment site; Updated (2006) 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, thus not needed. Literature search identified paper given further information on product function. Functional classification - Respiration - Electron transport; PMID:12107136, PMID:16436444, PMID:12823811; periplasmic nitrate reductase small subunit 736487..737011 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904951 YP_002344191.1 CDS napL NC_002163.1 737016 737930 D Original (2000) note: Cj0784, probable periplasmic protein, len: 304 aa; no Hp match. Contains N-terminal signal sequence; Updated (2006) note: Some characterisation work within Wolinella succinogenes with acceptable identity score. Functional classification - Miscellaneous periplasmic proteins; PMID:12823811; periplasmic protein 737016..737930 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905090 YP_002344192.1 CDS napD NC_002163.1 737923 738261 D Original (2000) note: Cj0785, napD, possible napD protein, len: 112 aa; very weak similarity to e.g. NAPD_PARDT NAPD protein (112 aa), fasta scores; opt: 102 z-score: 146.1 E(): 0.77, 22.9% identity in 83 aa overlap,and NAPD_ECOLI NAPD protein (87 aa), blastp scores; E = 4.7e-05, 23% identity in 72 bp overlap. No Hp match; Updated (2006) 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; PMID:12107136, PMID:12823811; NapD protein 737923..738261 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905091 YP_002344193.1 CDS Cj0786 NC_002163.1 738274 738447 D Original (2000) note: Cj0786, small hydrophobic protein, len: 57 aa; no Hp match; Updated (2006) note: One probable transmembrane helix predicted by TMHMM2.0. Functional classification -Unknown; hypothetical protein 738274..738447 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905092 YP_002344194.1 CDS Cj0787 NC_002163.1 738526 738774 D Original (2000) note: Cj0787, unknown, len: 82 aa; 38.1% identity to HP0168; Updated (2006) note: Prosite domain PS50293 TPR_REGION, Tetratricopeptide region identified within CDS. Functional classification - Conserved hypothetical proteins; hypothetical protein 738526..738774 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905224 YP_002344195.1 CDS Cj0788 NC_002163.1 738771 739262 D Original (2000) note: Cj0788, unknown, len: 163 aa; 30.8% identity to HP0167. Functional classification -Conserved hypothetical proteins; hypothetical protein 738771..739262 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905093 YP_002344196.1 CDS cca NC_002163.1 739231 740349 D Original (2000) note: Cj0789, probable RNA nucleotidyltransferase, len: 372 aa;p similar in C-terminus to C-terminus of e.g. CCA_ECOLI tRNA nucleotidyltransferase (412 aa), fasta scores; opt: 343 z-score: 412.9 E(): 1.1e-15, 35.4% identity in 212 aa overlap, and PAPS_BACSU poly(A) polymerase (397 aa), fasta scores; opt: 338 z-score: 407.2 E(): 2.2e-15, 29.3% identity in 294 aa overlap. 24.9% identity to HP0640. Contains PS00017 ATP/GTP-binding site motif A (P-loop); Updated (2006) 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, RNA modification and DNA transcription; PMID:3009457, PMID:3516995, PMID:15210699; multifunctional Cca protein 739231..740349 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905094 YP_002344197.1 CDS purU NC_002163.1 740346 741170 D produces formate from formyl-tetrahydrofolate which is the major source of formate for PurT in de novo purine nucleotide biosynthesis; has a role in one-carbon metabolism; forms a homohexamer; activated by methionine and inhibited by glycine; formyltetrahydrofolate deformylase 740346..741170 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905095 YP_002344198.1 CDS Cj0791c NC_002163.1 741167 742441 R Original (2000) note: Cj0791c, probable aminotransferase, len: 424 aa; similar to many members of the nifS family e.g. TR:O32164 (EMBL:Z99120) B. subtilis YURW protein (406 aa), fasta scores; opt: 289 z-score: 340.6 E(): 1.1e-11, 23.9% identity in 431 aa overlap. 45.4% identity to HP0405. Contains PS00455 AMP-binding domain signature and PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site; Updated (2006) note: No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification -Misc; aminotransferase complement(741167..742441) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905097 YP_002344199.1 CDS Cj0792 NC_002163.1 742477 743355 D Original (2000) note: Cj0792, unknown, len: 292 aa; some similarity to hypothetical proteins e.g. YZ04_METJA hypothetical protein MJECL04 (439 aa), fasta scores; opt: 175 z-score: 208.0 E(): 0.00027, 26.5% identity in 309 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF03008 Archaea bacterial proteins of unknown function identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins; hypothetical protein 742477..743355 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905098 YP_002344200.1 CDS flgS NC_002163.1 743359 744378 D Original (2000) note: Cj0793, probable signal transduction histidine kinase, len: 339 aa; similar to e.g. the C-terminus of ATOS_ECOLI sensor protein ATOS (608 aa), fasta scores; opt: 357 z-score: 408.3 E(): 1.9e-15,33.3% identity in 222 aa overlap. 42.4% identity to HP0244. Contains Pfam match to entry PF00512 signal,Signal carboxyl-terminal domain; Updated (2006) 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 (FlgS/FlgR) that regulates the fla regulon in Campylobacter jejuni (similar to that found in Helicobacter pylori). Functional classification - Signal transduction; PMID:14960570, PMID:15231786, PMID:14617189; signal transduction histidine kinase 743359..744378 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905099 YP_002344201.1 CDS Cj0794 NC_002163.1 744495 745775 D Original (2000) note: Cj0794, unknown, len: 426 aa; no Hp match. Has consecutive regions of near-identity to Cj0814 (73.9% identity in 253 aa overlap), Cj0815 (61.6% identity in 86 aa overlap) and Cj0816 (63.6% identity in 44 aa overlap), which may represent a pseudogene copy of this CDS; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein 744495..745775 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905100 YP_002344202.1 CDS murF NC_002163.1 745833 747260 R Original (2000) note: Cj0795c, murF, possible UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate -- ligase, len: 475 aa; some similarity to e.g. MURF_BACSU UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate -- ligase (EC 6.3.2.15) (457 aa), fasta scores; opt: 235 z-score: 258.7 E(): 4.1e-07, 26.7% identity in 348 aa overlap. 41.5% identity to HP0740; Updated (2006) note: Pfam domains PF01225 Mur ligase family, catalytic domain and PF02875 Mur ligase family, glutamate ligase domain were identified within CDS. Also, 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; PMID:11090285, PMID:2668880, PMID:9305945; UDP-N-acetylmuramoyl-tripeptide D-alanyl-D-alanine ligase complement(745833..747260) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905101 YP_002344203.1 CDS Cj0796c NC_002163.1 747261 747980 R Original (2000) note: Cj0796c, unknown, len: 239 aa; 46.3% identity to HP0739 (annotated as 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase); Updated (2006) note: Pfam domain PF00561 alpha/beta hydrolase fold and Prosite domain PS50187 Esterase/lipase/thioesterase active site serine identified within CDS. The latter are found in alpha/beta 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; hydrolase complement(747261..747980) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905199 YP_002344204.1 CDS Cj0797c NC_002163.1 747982 748197 R Original (2000) note: Cj0797c, unknown, len: 71 aa; weak similarity to TR:O68849 (EMBL:AF055586) ORF10 in Vibrio cholerae integron InVch (80 aa), fasta scores; opt: 95 z-score: 151.4 E(): 0.39, 39.2% identity in 51 aa overlap. No Hp match. Functional classification -Conserved hypothetical proteins; hypothetical protein complement(747982..748197) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905230 YP_002344205.1 CDS ddl NC_002163.1 748257 749297 R D-alanine--D-alanine ligase; DdlA; DdlB; cytoplasmic; catalyzes the formation of D-alanyl-D-alanine from two D-alanines in peptidoglycan synthesis; there are two forms of this enzyme in Escherichia coli; D-alanyl-alanine synthetase A complement(748257..749297) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905128 YP_002344206.1 CDS ruvA NC_002163.1 749307 749858 R plays an essential role in ATP-dependent branch migration of the Holliday junction; Holliday junction DNA helicase RuvA complement(749307..749858) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905102 YP_002344207.1 CDS Cj0800c NC_002163.1 749834 751693 R Original (2000) note: Cj0800c, unknown, len: 619 aa; 24.7% identity to HP0884. Also similar to Cj0044c (28.6% identity in 622 aa overlap); Updated (2006) note: Prosite domain PS00389 ATPase,F1 complex, OSCP/delta 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; ATPase complement(749834..751693) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905103 YP_002344208.1 CDS Cj0801 NC_002163.1 751797 753248 D Original (2000) note: Cj0801, probable integral membrane protein, len: 483 aa; similar to MVIN_SALTY virulence factor MVIN (524 aa), fasta scores; opt: 725 z-score: 828.0 E(): 0, 32.4% identity in 463 aa overlap,and to homologs from other organisms. 45.8% identity to HP0885; Updated (2006) note: Eleven probable transmembrane helices predicted by TMHMM2.0. Also, Pfam domain PF03023 MviN-like protein identified within CDS. Still not functionally characterised. Homolog designation kept within product function. Functional classification -Membranes, lipoproteins and porins; integral membrane protein 751797..753248 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905104 YP_002344209.1 CDS cysS NC_002163.1 753248 754636 D catalyzes a two-step reaction; charges a cysteine by linking its carboxyl group to the alpha-phosphate of ATP then transfers the aminoacyl-adenylate to its tRNA; cysteinyl-tRNA synthetase 753248..754636 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905105 YP_002344210.1 CDS msbA NC_002163.1 754629 756371 D Original (2000) note: Cj0803, msbA, probable lipid export ABC transport protein, len: 580 aa; similar to lipid export protein MSBA_ECOLI probable transport ATP-binding protein MSBA (582 aa), fasta scores; opt: 1032 z-score: 1135.9 E(): 0, 29.6% identity in 575 aa overlap,and to other members of the mutidrug-resistance family of ABC transporters. 42.7% identity to HP1082. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00211 ABC transporters family signature, Pfam match to entry PF00664 ABC_membrane, ABC transporter transmembrane region, and Pfam match to entry PF00005 ABC_tran, ABC transporters; Updated (2006) note: Characterised in Escherichia coli with marginal identity score. Appropriate motifs present. not needed to product function. Functional classification - Transport/binding proteins -Other; PMID:16159769, PMID:12119303; lipid export ABC transport protein 754629..756371 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905106 YP_002344211.1 CDS pyrD NC_002163.1 756403 757461 D catalyzes the conversion of dihydroorotate to orotate in the pyrimidine biosynthesis pathway; uses a flavin nucleotide as an essential cofactor; class 2 enzymes are monomeric and compared to the class 1 class 2 possess an extended N terminus, 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; dihydroorotate dehydrogenase 2 756403..757461 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905107 YP_002344212.1 CDS Cj0805 NC_002163.1 757458 758708 D Original (2000) note: Cj0805, probable zinc protease, len: 416 aa; similar to many members of the insulinase family e.g. Y4WA_RHISN hypothetical zinc protease Y4WA (512 aa), fasta scores; opt: 664 z-score: 739.8 E(): 0, 31.8% identity in 415 aa overlap. 57.2% identity to HP1012. Contains PS00143 Insulinase family,zinc-binding region signature, and Pfam match to entry PF00675 Insulinase, Insulinase (proteinase M16); Updated (2006) 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, peptides and glycopeptides; zinc protease 757458..758708 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905108 YP_002344213.1 CDS dapA NC_002163.1 758701 759597 D catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis; dihydrodipicolinate synthase 758701..759597 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905109 YP_002344214.1 CDS Cj0807 NC_002163.1 759597 760376 D Acts on the hydroxyl group at position 7 of the steroid frame; 7-alpha-hydroxysteroid dehydrogenase 759597..760376 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905110 YP_002344215.1 CDS Cj0808c NC_002163.1 760417 760722 R Original (2000) note: Cj0808c, small hydrophobic protein, len: 101 aa; no Hp match; Updated (2006) note: Three probable transmembrane helices predicted by TMHMM2.0. Functional classification -Unknown; hypothetical protein complement(760417..760722) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905112 YP_002344216.1 CDS Cj0809c NC_002163.1 760734 761330 R Original (2000) note: Cj0809c, possible hydrolase,len: 198 aa; similar to many hypothetical proteins belonging to the glyoxalase II family e.g. YQGX_BACSU (211 aa), fasta scores; opt: 289 z-score: 365.7 E(): 4.5e-13,32.8% identity in 204 aa overlap. 44.3% identity to HP0813. Contains Pfam match to entry PF00753 lactamase_B,Metallo-beta-lactamase superfamily; Updated (2006) note: No specific characterisation with acceptable identity scores carried out yet. kept within product function. Functional classification -Misc; hydrolase complement(760734..761330) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905113 YP_002344217.1 CDS nadE NC_002163.1 761404 762144 D catalyzes the formation of nicotinamide adenine dinucleotide (NAD) from nicotinic acid adenine dinucleotide (NAAD) using either ammonia or glutamine as the amide donor and ATP; ammonia-utilizing enzymes include the ones from Bacillus and Escherichia coli while glutamine-utilizing enzymes include the Mycobacterial one; forms homodimers; NAD synthetase 761404..762144 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 906011 YP_002344218.1 CDS lpxK NC_002163.1 762148 763074 D transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate; tetraacyldisaccharide 4'-kinase 762148..763074 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905114 YP_002344219.1 CDS thrC NC_002163.1 763071 764483 D catalyzes the formation of L-threonine from O-phospho-L-homoserine; threonine synthase 763071..764483 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905115 YP_002344220.1 CDS kdsB NC_002163.1 764480 765199 D CMP-2-keto-3-deoxyoctulosonic acid synthetase; catalyzes the formation of CMP-3-deoxy-D-manno-octulosonate from CTP and 3-deoxy-D-manno-octulosonate which is incorporated into LPS; 3-deoxy-manno-octulosonate cytidylyltransferase 764480..765199 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905116 YP_002344221.1 CDS Cj0814 NC_002163.1 765304 766059 D Original (2000) note: Cj0814, unknown, len: 251 aa; no Hp match. Almost identical to the N-teminus of Cj0794; similarity continues in Cj0815 and Cj0816: may represent a pseudogene fragment; Updated (2006) note: Similar to hypothetical proteins from other bacteria; hypothetical protein 765304..766059 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905117 YP_002344222.1 CDS Cj0815 NC_002163.1 766075 766419 D Original (2000) note: Cj0815, unknown, len: 114 aa; no Hp match. Almost identical to the centre of Cj0794; similarity continues from Cj0814 and into Cj0816: may represent a pseudogene fragment. Functional classification - Unknown; hypothetical protein 766075..766419 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905118 YP_002344223.1 CDS Cj0816 NC_002163.1 766427 766597 D Original (2000) note: Cj0816, unknown, len: 56 aa; no Hp match. Almost identical to the C-terminus of Cj0794; similarity continues from Cj0814 and Cj0815: may represent a pseudogene fragment. Functional classification -Unknown; hypothetical protein 766427..766597 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905119 YP_002344224.1 CDS glnH NC_002163.1 766692 767462 D Original (2000) note: Cj0817, glnH, probable glutamine-binding periplasmic protein, len: 256 aa; similar to e.g. GLNH_ECOLI glutamine-binding periplasmic protein precursor (248 aa), fasta scores; opt: 382 z-score: 441.9 E(): 2.6e-17, 32.5% identity in 243 aa overlap. 29.0% identity to HP0940. Contains Pfam match to entry PF00497 SBP_bac_3, Bacterial extracellular solute-binding proteins, family 3; Updated (2006) note: Characterised with marginal identity scores in more than one bacteria. Prosite domain PS50121, Solute binding protein/glutamate receptor domain identified within CDS. Further support given to product function. added to product function. Functional classification - Transport/binding proteins - Amino acids and amines; PMID:3027504, PMID:9571045, PMID:9142743; glutamine binding periplasmic protein 766692..767462 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905120 YP_002344225.1 CDS Cj0818 NC_002163.1 767555 767782 D Original (2000) note: Cj0818, probable lipoprotein,len: 75 aa; no Hp match. Contains N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes, lipoproteins and porins; lipoprotein 767555..767782 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905121 YP_002344226.1 CDS Cj0819 NC_002163.1 767808 768032 D Original (2000) note: Cj0819, small hydrophobic protein, len 74 aa; no Hp match; Updated (2006) note: Two probable transmembrane helices predicted by TMHMM2.0. Functional classification -Unknown; hypothetical protein 767808..768032 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905123 YP_002344227.1 CDS fliP NC_002163.1 768029 768763 R FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus; flagellar biosynthesis protein FliP complement(768029..768763) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905124 YP_002344228.1 CDS glmU NC_002163.1 768906 770195 D forms a homotrimer; catalyzes the acetylation of glucosamine-1-phosphate and uridylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc; function in cell wall synthesis; bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase 768906..770195 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905125 YP_002344229.1 CDS dfp NC_002163.1 770192 771346 D catalyzes the conjugation of cysteine to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, which is then decarboxylated to form 4'-phosphopantotheine; bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase 770192..771346 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905213 YP_002344230.1 CDS Cj0823 NC_002163.1 771343 771960 D Original (2000) note: Cj0823, unknown, len: 205 aa; 24.3% identity to HP0842; Updated (2006) note: One probable transmembrane helix predicted by TMHMM2.0. Functional classification -Unknown; hypothetical protein 771343..771960 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905126 YP_002344231.1 CDS uppS NC_002163.1 771964 772632 D Original (2000) note: Cj0824, uppS, probable UDP diphosphate synthase, len: 222 aa; similar to TR:O82827 (EMBL:AB004319) Micrococcus luteus UDP diphosphate synthase (249 aa), fasta scores; opt: 365 z-score: 445.7 E(): 1.6e-17, 35.2% identity in 227 aa overlap, and to other members of the UPF0015 family e.g. YAES_ECOLI (252 aa), fasta scores; opt: 371 z-score: 452.7 E(): 6.4e-18, 37.2% identity in 226 aa overlap. 42.6% identity to HP1221. Contains Pfam match to entry PF01255 UPF0015; Updated (2006) 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 (UDP pyrophosphate synthase) catalyses consecutive condensation reactions of FPP (farnesyl pyrophosphate) with eight isopentenyl pyrophosphates to generate C55 UPP, which serves as a lipid carrier for bacterial peptidoglycan biosynthesis. removed from product function. Functional classification - Synthesis and modification of macromolecules - Phospholipids; PMID:9882662, PMID:12756244, PMID:15447632; UDP diphosphate synthase 771964..772632 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905127 YP_002344232.1 CDS Cj0825 NC_002163.1 772629 773405 D Original (2000) note: Cj0825, possible processing peptidase, len: 258 aa; similar to e.g. LEP3_VIBCH type 4 prepilin-like protein specific leader peptidase (253 aa),fasta scores; opt: 261 z-score: 323.9 E(): 9.7e-11, 28.5% identity in 260 aa overlap. No Hp match. Contains several probable membrane spanning domains; Updated (2006) 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; PMID:12949093, PMID:2553669; processing peptidase 772629..773405 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905130 YP_002344233.1 CDS Cj0826 NC_002163.1 773405 774430 D Original (2000) note: Cj0826, probable integral membrane protein, len: 341 aa; similar to hypothetical membrane proteins e.g. YJGP_HAEIN (372 aa), fasta scores; opt: 203 z-score: 236.9 E(): 6.8e-06, 21.7% identity in 314 aa overlap. 32.3% identity to HP0362; Updated (2006) note: Pfam domain PF03739 Predicted permease YjgP/YjgQ family identified within CDS. Members of this family are predicted integral membrane proteins of unknown function. Also, six probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; integral membrane protein 773405..774430 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905219 YP_002344234.1 CDS truA NC_002163.1 774427 775152 D mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability; tRNA pseudouridine synthase A 774427..775152 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904389 YP_002344235.1 CDS ilvA NC_002163.1 775149 776360 R catalyzes the formation of 2-oxobutanoate from L-threonine; threonine dehydratase complement(775149..776360) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904335 YP_002344236.1 CDS Cj0829c NC_002163.1 776360 776773 R Original (2000) note: Cj0829c, unknown, len: 137 aa; similar to hypothetical proteins e.g. TR:P75874 (EMBL:AE000198) E. coli b0965 (164 aa), fasta scores; opt: 240 z-score: 312.1 E(): 4.4e-10, 30.3% identity in 132 aa overlap. No Hp match; Updated (2006) 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; CoA binding domain containing protein complement(776360..776773) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905131 YP_002344237.1 CDS Cj0830 NC_002163.1 776892 777308 D Original (2000) note: Cj0830, probable integral membrane protein, len: 138 aa; 42.7% identity to HP1502; Updated (2006) note: Pfam domain PF04323 Protein of unknown function (DUF474) identified within CDS. Also,four probable transmembrane helices predicted by TMHMM2.0. Literature search identified paper giving potential clues to product function. Functional classification -Membranes, lipoproteins and porins; PMID:16045618; integral membrane protein 776892..777308 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904930 YP_002344238.1 CDS trmA NC_002163.1 777295 778368 R catalyzes the formation of 5-methyl-uridine at position 54 in all tRNAs; tRNA (uracil-5-)-methyltransferase complement(777295..778368) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905134 YP_002344239.1 CDS Cj0832c NC_002163.1 778365 780098 R Original (2000) note: Cj0832c, probable integral membrane protein, len: 577 aa; similar to hypothetical proteins e.g. TR:O59530 (EMBL:AP000007) Pyrococcus horikoshii PH1889 (533 aa), fasta scores; opt: 628 z-score: 744.4 E(): 0, 39.2% identity in 558 aa overlap. 26.9% identity to HP0946; Updated (2006) note: Pfam domain PF03553 Na+/H+ antiporter family identified within CDS. Also, thirteen probable transmembrane helices predicted by TMHMM2. Product modified to more specific family member based on motif match. No specific characterisation carried out yet,so kept within product function. Functional classification - Transport/binding proteins - Cations; Na+/H+ antiporter family protein complement(778365..780098) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904915 YP_002344240.1 CDS Cj0833c NC_002163.1 780095 780844 R Original (2000) note: Cj0833c, probable oxidoreductase, len: 249 aa; simlar to e.g. YDFG_ECOLI probable oxidoreductase (248 aa), fasta scores; opt: 796 z-score: 943.5 E(): 0, 48.8% identity in 244 aa overlap. 47.3% identity to HP0357. Contains PS00061 Short-chain dehydrogenases/reductases family signature, and Pfam match to entry PF00106 adh_short, Alcohol/other dehydrogenases,short chain type; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. kept within product function. Functional classification -Misc; PMID:12535615; oxidoreductase complement(780095..780844) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905132 YP_002344241.1 CDS Cj0834c NC_002163.1 780841 782079 R Original (2000) note: Cj0834c, possible periplasmic protein, len: 412 aa; similar in C-terminus to ankyrin repeat-containing proteins e.g. ANKH_CHRVI ankyrin homolog precursor (323 aa), fasta scores; opt: 194 z-score: 229.9 E(): 1.7e-05, 28.9% identity in 194 aa overlap. No Hp match. Some similarity to ankyrin repeats in Cj1386 (29.3% identity in 99 aa overlap). Contains 2x Pfam match to entry PF00023 ank, Ank repeat, and possible N-terminal signal sequence; Updated (2006) note: No specific characterisation with acceptable identity scores carried out yet. kept within product function. Functional classification -Miscellaneous periplasmic proteins; ankyrin repeat-containing periplasmic protein complement(780841..782079) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905133 YP_002344242.1 CDS acnB NC_002163.1 782129 784675 R catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase complement(782129..784675) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905137 YP_002344243.1 CDS ogt NC_002163.1 784730 785182 D Original (2000) note: Cj0836, ogt, probable methylated-DNA--protein-cysteine methyltransferase, len: 150 aa; similar to many e.g. OGT_ECOLI methylated-DNA--protein-cysteine methyltransferase (EC 2.1.1.63) (171 aa), fasta scores; opt: 274 z-score: 355.6 E(): 1.6e-12, 43.7% identity in 103 aa overlap, and DAT1_BACSU methylated-DNA--protein-cysteine methyltransferase (165 aa), fasta scores; opt: 358 z-score: 460.7 E(): 2.3e-18, 44.5% identity in 137 aa overlap. 45.3% identity to HP0676. Contains PS00374 Methylated-DNA--protein-cysteine methyltransferase active site and Pfam match to entry PF01035 Methyltrans,6-O-methylguanine DNA methyltransferase; Updated (2006) note: Characterised in Escherichia coli and Bacillus subtilis with acceptable identity score. not added to product function. Functional classification - DNA replication,restriction/modification, recombination and repair; PMID:2506524; methylated-DNA--protein-cysteine methyltransferase 784730..785182 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904456 YP_002344244.1 CDS Cj0837c NC_002163.1 785174 786115 R Original (2000) note: Cj0837c, unknown, len: 313 aa; no Hp match. Contains PS00179 Aminoacyl-transfer RNA synthetases class-II signature 1, and PS00030 Eukaryotic RNA-binding region RNP-1 signature. Functional classification - Unknown; hypothetical protein complement(785174..786115) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905005 YP_002344245.1 CDS metG NC_002163.1 786119 788005 R methionine--tRNA ligase; MetRS; adds methionine to tRNA(Met) with cleavage of ATP to AMP and diphosphate; 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; four subfamilies exist based on sequence motifs and zinc content; methionyl-tRNA synthetase complement(786119..788005) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905186 YP_002344246.1 CDS Cj0839c NC_002163.1 788015 788212 R Original (2000) note: Cj0839c, unknown, len: 65 aa; 43.1% identity to HP1384. Functional classification -Conserved hypothetical proteins; hypothetical protein complement(788015..788212) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905138 YP_002344247.1 CDS fbp NC_002163.1 788205 789047 R catalyzes the formation of D-fructose 6-phosphate from fructose-1,6-bisphosphate; fructose-1,6-bisphosphatase complement(788205..789047) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905148 YP_002344248.1 CDS mobB NC_002163.1 789049 789540 R Original (2000) note: Cj0841c, probable ATP/GTP binding protein, len: 163 aa; some similarity to e.g. MOBB_ECOLI molybdopterin-guanine dinucleotide biosynthesis protein B (174 aa), fasta scores; opt: 148 z-score: 194.1 E(): 0.0016, 25.6% identity in 168 aa overlap. No Hp match. Contains S00017 ATP/GTP-binding site motif A (P-loop); Updated (2006) 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, prosthetic groups and carriers - Molybdopterin; PMID:12372836, PMID:9219527; molybdopterin-guanine dinucleotide biosynthesis protein complement(789049..789540) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904424 YP_002344249.1 CDS Cj0842 NC_002163.1 789636 790121 D Original (2000) note: Cj0842, probable lipoprotein,len: 161 aa; no Hp match. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes, lipoproteins and porins; lipoprotein 789636..790121 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905139 YP_002344250.1 CDS Cj0843c NC_002163.1 790018 791643 R Original (2000) note: Cj0843c, probable secreted transglycosylase, len: 541 aa; some simialarity in C-terminus to SLT_ECOLI soluble lytic murein transglycosylase precursor (645 aa), fasta scores; opt: 257 z-score: 285.7 E(): 1.3e-08, 29.3% identity in 208 aa overlap. 31.4% identity to HP0645. Contains PS00922 Prokaryotic transglycosylases signature and N-terminal signal sequence; Updated (2006) 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,peptides and glycopeptides; PMID:12186869; secreted transglycosylase complement(790018..791643) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905140 YP_002344251.1 CDS Cj0844c NC_002163.1 791640 791921 R Original (2000) note: Cj0844c, possible integral membrane protein, len: 93 aa; 38.4% identity to HP0644; Updated (2006) 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, two probable transmembrane helices predicted by TMHMM2.0. Functional classification - Membranes, lipoproteins and porins; integral membrane protein complement(791640..791921) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905141 YP_002344252.1 CDS gltX NC_002163.1 791924 793219 R charges one glutamine molecule and pairs it with tRNA(Gln); glutamylglutaminyl-tRNA synthetase complement(791924..793219) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905144 YP_002344253.1 CDS Cj0846 NC_002163.1 793305 794429 D Original (2000) note: Cj0846, probable integral membrane protein, len: 374 aa; contains several probable membrane spanning regions in N-terminal half, C-terminal half is simalar to several hypothetical proteins e.g. YPBG_BACSU (259 aa), fasta scores; opt: 197 z-score: 233.7 E(): 1e-05, 28.6% identity in 238 aa overlap. 38.8% identity to HP1044; Updated (2006) note: Pfam domain PF00149 Calcineurin-like phosphoesterase and Prosite domain PS00142 Peptidase M, neutral zinc metallopeptidases,zinc-binding site identified within CDS. Also, 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; metallophosphoesterase 793305..794429 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905145 YP_002344254.1 CDS psd NC_002163.1 794426 795226 D catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine; phosphatidylserine decarboxylase 794426..795226 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904800 YP_002344255.1 CDS Cj0848c NC_002163.1 795223 795504 R Original (2000) note: Cj0848c, unknown, len: 93 aa; similar to hypothetical proteins e.g. TR:O34867 (EMBL:AJ000975) B. subtilis YLQH protein (93 aa), fasta scores; opt: 284 z-score: 365.6 E(): 4.5e-13, 47.3% identity in 91 aa overlap. Also similar to C-terminus of flhB possible flagellar transport proteins e.g. FLHB_ECOLI flagellar biosynthetic protein FLHB (382 aa), fasta scores; opt: 182 z-score: 232.8 E(): 1.1e-05, 41.6% identity in 77 aa overlap. 39.2% identity to HP1575 (annotated as flhB). Also similar to C-terminus of Cj0335,flhB (40.7% identity in 81 aa overlap); Updated (2006) note: Pfam domain PF01312 Bac_export_2, 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; hypothetical protein complement(795223..795504) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905149 YP_002344256.1 CDS Cj0849c NC_002163.1 795501 797660 R Original (2000) note: Cj0849c, unknown, len: 719 aa; no Hp ortholog, some similarity to Cj0041 (23.1% identity in 566 aa overlap). Contain Asn-rich region near centre; Updated (2006) note: Prosite domain PS00063 Aldo/keto reductase family active site signature found within CDS. Functional classification - Conserved hypothetical proteins; hypothetical protein complement(795501..797660) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905146 YP_002344257.1 CDS Cj0850c NC_002163.1 797653 798840 R Original (2000) note: Cj0850c, transmembrane transport protein, len: 395 aa; similar to hypothetical transport proteins e.g. YCAD_ECOLI (382 aa), fasta scores; opt: 431 z-score: 481.6 E(): 1.6e-19, 27.6% identity in 366 aa overlap. No Hp ortholog. Contains S00216 Sugar transport proteins signature 1, and Pfam match to entry PF00083 sugar_tr, Sugar (and other) transporters; Updated (2006) note: Pfam domain PF07690 Major Facilitator Superfamily identified within CDS. Also,twelve probable transmembrane helices predicted by TMHMM2.0. The MFS family contains functions such as uniporters, symporters or antiporters. MFS proteins typically contain 12 transmembrane regions. Product modified to more specific family based on motif match. Functional classification - Transport/binding proteins -Other; MFS transport protein complement(797653..798840) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905150 YP_002344258.1 CDS Cj0851c NC_002163.1 798818 799321 R Original (2000) note: Cj0851c, probable integral membrane protein, len: 167 aa; some similarity to YCIB_BUCAP integral membrane protein from Buchnera aphidicola (177 aa), fasta scores; opt: 139 z-score: 180.5 E(): 0.0093, 30.0% identity in 160 aa overlap. No Hp match; Updated (2006) note: Four probable transmembrane helices predicted by TMHMM2.0. Paper identified giving further clues to product function. Functional classification - Membranes, lipoproteins and porins; PMID:16045618; integral membrane protein complement(798818..799321) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905151 YP_002344259.1 CDS Cj0852c NC_002163.1 799321 799650 R Original (2000) note: Cj0852c, possible integral membrane protein, len: 109 aa; some similarity to hypothetical proteins e.g. TR:O27758 (EMBL:AE000929) Methanobacterium thermoautotrophicum MTH1725 (92 aa),fasta scores; opt: 123 z-score: 165.5 E(): 0.064, 32.7% identity in 98 aa overlap. 55.0% identity to HP0307; Updated (2006) note: Two probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; integral membrane protein complement(799321..799650) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905153 YP_002344260.1 CDS hemL NC_002163.1 799647 800921 R Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway; glutamate-1-semialdehyde aminotransferase complement(799647..800921) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905185 YP_002344261.1 CDS Cj0854c NC_002163.1 800918 801265 R Original (2000) note: Cj0854c, probable periplasmic protein, len: 115 aa; 37.9% identity to HP0236. Contains N-terminal signal sequence and PS00190 Cytochrome c family heme-binding site signature. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein complement(800918..801265) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905154 YP_002344262.1 CDS folD NC_002163.1 801345 802193 D catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate; bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase 801345..802193 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905155 YP_002344263.1 CDS lepP NC_002163.1 802203 803051 D Original (2000) note: Cj0856, lepP, probable signal peptidase I, len: 282 aa; similar to many e.g. LEP_ECOLI signal peptidase I (EC 3.4.21.89) (324 aa), fasta scores; opt: 339 z-score: 395.2 E(): 1e-14, 33.7% identity in 270 aa overlap. 46.2% identity to HP0576. Contains PS00761 Signal peptidases I signature 3 and Pfam match to entry PF00461 signal_pept_I, Signal peptidases I; Updated (2006) note: Pfam domain PF00717 Peptidase S24-like identified within CDS. Also, 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; PMID:9823901; signal peptidase I 802203..803051 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905156 YP_002344264.1 CDS moeA NC_002163.1 803073 804233 R Original (2000) note: Cj0857c, moeA, possible molybdopterin biosynthesis protein, len: 386 aa; similar to many e.g. MOEA_ECOLI molybdopterin biosynthesis MOEA protein (411 aa), fasta scores; opt: 602 z-score: 691.1 E(): 3.4e-31, 29.2% identity in 387 aa overlap. 37.0% identity to HP0172. Also similar to Cj1519 (33.3% identity in 378 aa overlap). Contains Pfam match to entry PF00994 MoCF_biosynth, Molybdenum cofactor biosynthesis protein; Updated (2006) note: Pfam domains PF03454 MoeA C-terminal region (domain IV) and PF03453 MoeA N-terminal region (domain I and II) 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, prosthetic groups and carriers - Molybdopterin; PMID:9515915, PMID:12719427; molybdopterin biosynthesis protein complement(803073..804233) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905221 YP_002344265.1 CDS murA NC_002163.1 804230 805486 R adds enolpyruvyl to UDP-N-acetylglucosamine as a component of cell wall formation; gram-positive bacteria have 2 copies of MurA which are active; UDP-N-acetylglucosamine 1-carboxyvinyltransferase complement(804230..805486) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905157 YP_002344266.1 CDS Cj0859c NC_002163.1 805552 805980 R Original (2000) note: Cj0859c, unknown, len: 142 aa; no Hp match. Gln-rich in C-term; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein complement(805552..805980) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905158 YP_002344267.1 CDS Cj0860 NC_002163.1 806075 806947 D Updated (2006) note: Ten probable transmembrane helices predicted by TMHMM2.0; Original (2000) note: Cj0860, probable integral membrane protein, len: 290 aa; similar to hypothetical proteins e.g. YICL_ECOLI (307 aa), fasta scores; opt: 516 z-score: 611.4 E(): 9.3e-27, 32.0% identity in 284 aa overlap. No Hp match. Contains 2x Pfam match to entry PF00892 DUF6, Integral membrane protein. Functional classification - Membranes, lipoproteins and porins; integral membrane protein 806075..806947 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905161 YP_002344268.1 CDS pabA NC_002163.1 806934 807500 R Original (2000) note: Cj0861c, pabA, probable para-aminobenzoate synthase glutamine amidotransferase component II, len: 188 aa; simlar to e.g. PABA_BACSU para-aminobenzoate synthase glutamine amidotransferase component II (EC 4.1.3.-) (194 aa), fasta scores; opt: 534 z-score: 632.3 E(): 6.4e-28, 44.6% identity in 186 aa overlap, and PABA_ECOLI (187 aa), fasta scores; opt: 475 z-score: 564.2 E(): 4e-24, 36.8% identity in 185 aa overlap. 38.6% identity to HP1281 annotated as anthranilate synthase component II (trpD). Contains Pfam match to entry PF00117 GATase, Glutamine amidotransferases class-I; Updated (2006) note: Characterised in Escherichia coli with acceptable identity score. not added to product function. Functional classification - Biosynthesis of cofactors, prosthetic groups and carriers - Folic acid; PMID:8096767, PMID:2123867; para-aminobenzoate synthase glutamine amidotransferase component II complement(806934..807500) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905163 YP_002344269.1 CDS pabB NC_002163.1 807497 809281 R Original (2000) note: Cj0862c, pabB, probable para-aminobenzoate synthase component I, len: 594 aa; simlar to e.g. PABB_ECOLI para-aminobenzoate synthase component I (EC 4.1.3.-) (453 aa), fasta scores; opt: 541 z-score: 604.3 E(): 2.3e-26, 35.7% identity in 252 aa overlap. 39.3% identity to HP0293. Contains Pfam match to entry PF00425 chorismate_bind, chorismate binding enzyme; Updated (2006) note: Characterised in Escherichia coli with acceptable identity score. not added to product function. Functional classification - Biosynthesis of cofactors, prosthetic groups and carriers - Folic acid; PMID:11841211, PMID:2251281; para-aminobenzoate synthase component I complement(807497..809281) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905164 YP_002344270.1 CDS xerD NC_002163.1 809271 810335 R Original (2000) note: Cj0863c, xerD, probable DNA recombinase, len: 354 aa; similar to e.g. XERD_ECOLI integrase/recombinase XERD (298 aa), fasta scores; opt: 336 z-score: 389.2 E(): 2.2e-14, 29.5% identity in 298 aa overlap. 47.5% identity to HP0675 (xerC) and 30.5% identity to HP0995 (xerD). Contains Pfam match to entry PF00589 Phage_integrase, 'Phage' integrase family; Updated (2006) note: Characterised in Escherichia coli with acceptable identity score. not added to product function. Functional classification - DNA replication, restriction/modification, recombination and repair; PMID:9311978, PMID10635320, PMID11832210; DNA recombinase complement(809271..810335) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905165 YP_002344271.1 CDS Cj0864 NC_002163.1 810963 811322 D Original (2000) note: Cj0864, probable periplasmic protein, len: 119 aa; some similarity in C-terminus to C-terminus of thiol:disulfide interchange proteins (not including active site) e.g. TR:P97037 (EMBL:U32616) Klebsiella pneumoniae disulfide isomerase (222 aa), fasta scores; opt: 184 z-score: 240.3 E(): 4.4e-06, 36.9% identity in 84 aa overlap. No Hp match. Also similar to C-term of Cj0872 dsbA (57.3% identity in 82 aa overlap); Updated (2006) note: Interpro result (ipr012335) 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; periplasmic protein 810963..811322 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904441 YP_002344272.1 CDS dsbB NC_002163.1 811319 812119 D Original (2000) note: Cj0865, dsbB, possible disulfide oxidoreductase, len: 266 aa; similar to e.g. DSBB_ECOLI disulfide bond formation protein B (disulfide oxidoreductase) (176 aa), fasta scores; opt: 200 z-score: 250.0 E(): 1.3e-06, 29.9% identity in 137 aa overlap (the essential Cysteine residues are conserved). No Hp match; Updated (2006) note: Four probable transmembrane helices predicted by TMHMM2.0. This CDS has been characterised as DsbB protein (PMID:15632440). 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 (including Cj0865) with prediction of 5 transmembranehelises (not 4 as stated in annotation); (P24-A39; F60-I74; S87-L101; F194-A214; F231-G246). There are some differences in amino acid sequences between Cj0865 and its ortholog from 81-176 (CJJ81176_0881). It is stated that its translation starts from the second Met (although the predicted N-terminal amino acid sequences of both proteins are identical), there is also an insertion of 3 amino acids at the COOH end of protein. Thus, not added to protein function. Functional classification -Protein translation and modification; PMID:15632440, PMID:7957076; disulfide oxidoreductase 811319..812119 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905166 YP_002344273.1 CDS dsbA NC_002163.1 813675 814316 D Original (2000) note: Cj0872, dsbA, possible protein disulphide isomerase, len: 213 aa; some similarity to e.g. DSBA_ECOLI thiol:disulfide interchange protein DSBA precursor (208 aa), fasta scores; opt: 128 z-score: 159.8 E(): 0.13, 23.1% identity in 216 aa overlap (active site is conserved). No Hp match; Updated (2006) 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; PMID:8494885; protein disulphide isomerase 813675..814316 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905167 YP_002344274.1 CDS Cj0873c NC_002163.1 814351 814563 R Original (2000) note: Cj0873c, unknown, len: 70 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein complement(814351..814563) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905147 YP_002344275.1 CDS Cj0874c NC_002163.1 814539 815099 R Original (2000) note: Cj0874c, possible cytochrome C, len: 186 aa; very weak similarity to many cytochrome C proteins e.g. CYC_APIME cytochrome C (107 aa), fasta scores; opt: 106 z-score: 137.1 E(): 2.5, 36.5% identity in 52 aa overlap. No Hp match. Contains 2x PS00190 Cytochrome c family heme-binding site signature. Also some similarity to Cj0037c possible cytochrome C (36.0% identity in 178 aa overlap); Updated (2006) note: No specific characterisation in related bacteria with acceptable identity score. Appropriate motifs present. added to product function. Functional classification - Energy metabolism -Electron transport; cytochrome C complement(814539..815099) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905168 YP_002344276.1 CDS Cj0876c NC_002163.1 815050 815337 R Original (2000) note: Cj0876c, probable periplasmic protein, len: 96 aa; no Hp match. Functional classification - Miscellaneous periplasmic proteins; periplasmic protein complement(815050..815337) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905169 YP_002344277.1 CDS Cj0877c NC_002163.1 815432 815524 R Original (2000) note: Cj0877c, questionable ORF,len: 30 aa; no Hp match. Functional classification -Unknown; hypothetical protein complement(815432..815524) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905171 YP_002344278.1 CDS Cj0878 NC_002163.1 815545 815691 D Original (2000) note: Cj0878, unknown, len: 48 aa; no Hp match. Functional classification - Unknown; hypothetical protein 815545..815691 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905143 YP_002344279.1 CDS Cj0879c NC_002163.1 815669 816301 R Original (2000) note: Cj0879c, probable periplasmic protein, len: 210 aa; no Hp match. Functional classification - Miscellaneous periplasmic proteins; periplasmic protein complement(815669..816301) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904821 YP_002344280.1 CDS Cj0880c NC_002163.1 816298 816540 R Original (2000) note: Cj0880c, unknown, len: 240 aa; no Hp match. Functional classification - Unknown; hypothetical protein complement(816298..816540) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905170 YP_002344281.1 CDS Cj0881c NC_002163.1 816524 817570 R Original (2000) note: Cj0881c, unknown, len: 348 aa; 40.6% identity to HP1042. Functional classification -Conserved hypothetical proteins; hypothetical protein complement(816524..817570) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905173 YP_002344282.1 CDS flhA NC_002163.1 817579 819753 R membrane protein involved in the flagellar export apparatus; flagellar biosynthesis protein FlhA complement(817579..819753) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905174 YP_002344283.1 CDS Cj0883c NC_002163.1 819740 820150 R Original (2000) note: Cj0883c, unknown, len: 136 aa; identical to TR:Q46090 (EMBL:U06951) Campylobacter jejuni 81-176 ORF3 in region upstream of the flhA gene. (136 aa), and similar to hypothetical proteins e.g. Y379_HAEIN (150 aa), fasta scores; opt: 174 z-score: 226.5 E(): 2.6e-05, 28.3% identity in 138 aa overlap. No Hp match; Updated (2006) 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, so kept in product function. Literature search identified papers giving further clues to product function. Functional classification - Broad regulatory functions; PMID:8063102, PMID:15066034, PMID:14985343; transcriptional regulator complement(819740..820150) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905175 YP_002344284.1 CDS rpsO NC_002163.1 820325 820597 D primary rRNA binding protein; helps nucleate assembly of 30S; binds directly to the 16S rRNA and an intersubunit bridge to the 23S rRNA; autoregulates translation through interactions with the mRNA leader sequence; 30S ribosomal protein S15 820325..820597 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905176 YP_002344285.1 CDS ftsK NC_002163.1 820683 823523 R Original (2000) note: Cj0886c, ftsK, probable cell division protein, len: 946 aa; 96.7% identity to YRO1_CAMJE (941 aa), and similar to e.g. FTSK_ECOLI cell division protein FTSK (1329 aa), fasta scores; opt: 803 z-score: 772.9 E(): 0, 45.2% identity in 522 aa overlap,and SP3E_BACSU stage III sporulation protein E (787 aa),fasta scores; opt: 1488 z-score: 1436.1 E(): 0, 48.3% identity in 476 aa overlap. 52.0% identity to HP1090. Contains PS00017 ATP/GTP-binding site motif A (P-loop); Updated (2006) note: Pfam domain PF01580 FtsK/SpoIIIE 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; PMID:8063102, PMID:11778051, PMID:7592387; cell division protein complement(820683..823523) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905152 YP_002344286.1 CDS flgL NC_002163.1 823633 825885 R with FlgK acts as a hook filament junction protein to join the flagellar filament to the hook; lagellar hook-associated protein FlgL complement(823633..825885) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905178 YP_002344287.1 CDS Cj0888c NC_002163.1 826268 828199 R Original (2000) note: Cj0888c, ABC transport system ATP-binding protein, len: 643 aa; similar to UUP_ECOLI ABC transporter atp-binding protein UUP (635 aa), fasta scores; opt: 744 z-score: 763.9 E(): 0, 37.1% identity in 634 aa overlap. No Hp ortholog. Contains 2x PS00017 ATP/GTP-binding site motif A (P-loop), 2x PS00211 ABC transporters family signature, and 2x Pfam match to entry PF00005 ABC_tran; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Transport/binding proteins - Other; PMID:9139905; ABC transporter ATP-binding protein complement(826268..828199) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904350 YP_002344288.1 CDS Cj0889c NC_002163.1 828203 829492 R Original (2000) note: Cj0889c, probable sensory transduction histidine kinase, len: 429 aa; similar in C-terminus to many e.g. ENVZ_ECOLI osmolarity sensor protein ENVZ (450 aa), fasta scores; opt: 210 z-score: 229.3 E(): 1.8e-05. 26.5% identity in 204 aa overlap No Hp ortholog. Contains two probable transmembrane domains in N-terminus and Pfam match to entry PF00512 signal, Signal carboxyl-terminal domain; Updated (2006) note: Pfam domain PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase identified within CDS. Further support given to product function. Some characterisation in Bacillus subtilitis, however,identity score not acceptable. kept in product function. Functional classification - Signal transduction; PMID:8002614, PMID:14612242, PMID:12890034; sensory trasnduction histidine kinase complement(828203..829492) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905181 YP_002344289.1 CDS Cj0890c NC_002163.1 829486 830148 R Original (2000) note: Cj0890c, probable sensory transduction transcriptional regulator, len: 220 aa; similar to many e.g. PHOB_SHIFL phosphate regulon transcriptional regulator (229 aa), fasta scores; opt: 396 z-score: 471.5 E(): 5.8e-19, 29.3% identity in 222 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00072 response_reg, Response regulator receiver domain and Pfam match to entry PF00486 trans_reg_C,Transcriptional regulatory protein, C terminal; Updated (2006) note: Characterisation within more than one genus, however, identity scores were marginal. kept within product function. Functional classification - Signal transduction; PMID:9141682; sensory transduction transcriptional regulator complement(829486..830148) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905187 YP_002344290.1 CDS serA NC_002163.1 830135 831718 R catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate; D-3-phosphoglycerate dehydrogenase complement(830135..831718) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905182 YP_002344291.1 CDS Cj0892c NC_002163.1 831715 832203 R Original (2000) note: Cj0892c, probable periplasmic protein, len: 162 aa; no Hp match. Functional classification - Miscellaneous periplasmic proteins; periplasmic protein complement(831715..832203) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905183 YP_002344292.1 CDS rpsA NC_002163.1 832203 833873 R in Escherichia coli this protein is involved in binding to the leader sequence of mRNAs and is itself bound to the 30S subunit; autoregulates expression via a C-terminal domain; in most gram negative organisms this protein is composed of 6 repeats of the S1 domain while in gram positive there are 4 repeats; the S1 nucleic acid-binding domain is found associated with other proteins; 30S ribosomal protein S1 complement(832203..833873) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905184 YP_002344293.1 CDS ispH NC_002163.1 834005 834838 R catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP); functions in the nonmevalonate isoprenoid biosynthesis pathway; 4-hydroxy-3-methylbut-2-enyl diphosphate reductase complement(834005..834838) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905189 YP_002344294.1 CDS aroA NC_002163.1 834828 836114 R catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis; 3-phosphoshikimate 1-carboxyvinyltransferase complement(834828..836114) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904338 YP_002344295.1 CDS pheT NC_002163.1 836111 838432 R catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a tetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 2 subfamily; phenylalanyl-tRNA synthetase subunit beta complement(836111..838432) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905191 YP_002344296.1 CDS pheS NC_002163.1 838429 839421 R catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a heterotetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 1 subfamily; phenylalanyl-tRNA synthetase subunit alpha complement(838429..839421) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905193 YP_002344297.1 CDS Cj0898 NC_002163.1 839544 839909 D Original (2000) note: Cj0898, HIT-family protein,len: 121 aa; similar to many members of the HIT family e.g. IPK1_HUMAN HINT protein (protein kinase C inhibitor 1) (125 aa), fasta scores; opt: 286 z-score: 385.9 E(): 3.4e-14, 40.6% identity in 106 aa overlap, and YCFF_ECOLI HYPOTHETICAL 13.2 KD PROTEIN HIT-LIKE PROTE (119 aa),fasta scores; opt: 276 z-score: 373.2 E(): 1.7e-13, 38.2% identity in 110 aa overlap. 56.6% identity to HP0404. Contains Pfam match to entry PF01230 HIT, HIT family; Updated (2006) note: Specific characterisation has not been carried out, so kept in product function. Functional classification - Misc; histidine triad (HIT) family protein 839544..839909 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905194 YP_002344298.1 CDS thiJ NC_002163.1 839939 840508 R Original (2000) note: Cj0899c, thiJ, probable 4-methyl-5(beta-hydroxyethyl)-thiazole monophosphate synthesis protein, len: 189 aa; simlar to e.g. THIJ_ECOLI 4-methyl-5(b-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme (198 aa), fasta scores; opt: 265 z-score: 330.3 E(): 4.2e-11, 32.6% identity in 181 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF01965 DJ-1/PfpI 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, prosthetic groups and carriers - Thiamine; PMID:10075431; 4-methyl-5(beta-hydroxyethyl)-thiazole monophosphate synthesis protein complement(839939..840508) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905197 YP_002344299.1 CDS Cj0900c NC_002163.1 840501 840680 R Original (2000) note: Cj0900c, small hydrophobic protein, len: 59 aa; 29.8% identity to HP0085. Functional classification - Conserved hypothetical proteins; hypothetical protein complement(840501..840680) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905195 YP_002344300.1 CDS Cj0901 NC_002163.1 840763 841506 D Original (2000) note: Cj0901, probable amino acid ABC tansporter permease, len: 247 aa; similar to many e.g. YQIY_BACSU probable amino-acid ABC transporter permease (219 aa), fasta scores; opt: 552 z-score: 683.2 E(): 9.3e-31, 43.6% identity in 204 aa overlap. 28.6% identity to HP0939. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp signature, and Pfam match to entry PF00528 BPD_transp, Binding-protein-dependent transport systems inner membrane component; Updated (2006) 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/binding proteins - Amino acids and amines; amino acid ABC tansporter permease 840763..841506 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905200 YP_002344301.1 CDS glnQ NC_002163.1 841499 842227 D Original (2000) note: Cj0902, glnQ, probable glutamine transport ATP-binding protein, len: 247 aa; highly similar to e.g. GLNQ_BACST glutamine transport ATP-binding protein (242 aa), fasta scores; opt: 940 z-score: 1074.4 E(): 0, 56.2% identity in 242 aa overlap. No Hp ortholog. Also similar to Cj0469 (52.9% identity in 238 aa overlap). Contains S00017 ATP/GTP-binding site motif A (P-loop), S00211 ABC transporters family signature, and Pfam match to entry PF00005 ABC_tran, ABC transporters; Updated (2006) 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/binding proteins -Amino acids and amines; PMID:1856180; glutamine transport ATP-binding protein 841499..842227 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905198 YP_002344302.1 CDS Cj0903c NC_002163.1 842255 843721 R Original (2000) note: Cj0903c, probable amino-acid transport protein, len: 488 aa; simlar to many hypothetical membaer of the sodium:alanine symporter family e.g. ALST_BACSU amino acid carrier protein ALST (465 aa), fasta scores; opt: 821 z-score: 946.6 E(): 0,41.9% identity in 473 aa overlap. 33.6% identity to HP0942. Contains PS00873 Sodium:alanine symporter family signature, and Pfam match to entry PF01235 Na_Ala_symp,Sodium:alanine symporter family; Updated (2006) 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/binding proteins - Amino acids and amines; PMID:15066034; amino-acid transport protein complement(842255..843721) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905201 YP_002344303.1 CDS Cj0904c NC_002163.1 843825 844292 R Original (2000) note: Cj0904c, probable RNA methylase, len: 155 aa; similar to members of the spoU family e.g. YIBK_ECOLI (157 aa), fasta scores; opt: 373 z-score: 490.5 E(): 5e-20, 43.3% identity in 150 aa overlap. No Hp match. Contains Pfam match to entry PF00588 SpoU_methylase, SpoU rRNA Methylase family; Updated (2006) note: kept within product function, as full characterisation has not been carried out. Functional classification - RNA synthesis, RNA modification and DNA transcription; RNA methylase complement(843825..844292) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905203 YP_002344304.1 CDS alr NC_002163.1 844295 845281 R converts L-alanine to D-alanine which is used in cell wall biosynthesis; binds one pyridoxal phosphate per monomer; forms a homodimer; alanine racemase complement(844295..845281) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905209 YP_002344305.1 CDS Cj0906c NC_002163.1 845282 846259 R Original (2000) note: Cj0906c, probable periplasmic protein, len: 325 aa; similar to hypothetical proteins e.g. TR:O66569 (EMBL:AE000677) Aquifex aeolicus AQ_183 (397 aa), fasta scores; opt: 380 z-score: 432.9 E(): 8.2e-17, 31.1% identity in 270 aa overlap. 36.6% identity to HP0518. Contains probable N-terminal signal sequence; Updated (2006) note: Paper identified linking protein to glycoprotein. Functional classification -Miscellaneous periplasmic proteins; PMID:12186869; periplasmic protein complement(845282..846259) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905204 YP_002344306.1 CDS Cj0908 NC_002163.1 846415 846885 D Original (2000) note: Cj0908, probable periplasmic protein, len: 156 aa; no Hp match. Contains probable N-terminal signal sequence. Similar to downstream gene Cj0910 (41.3% identity in 143 aa overlap). Functional classification - Miscellaneous periplasmic proteins; periplasmic protein 846415..846885 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905208 YP_002344307.1 CDS Cj0909 NC_002163.1 846971 847390 D Original (2000) note: Cj0909, probable periplasmic protein, len: 139 aa; similar to TR:O67294 (EMBL:AE000731) Aquifex aeolicus AQ_1253 (151 aa), fasta scores; opt: 208 z-score: 273.4 E(): 6.3e-08, 34.3% identity in 134 aa overlap. No Hp match. Contains probable N-terminal signal sequence; Updated (2006) note: Pfam domain PF04314 Protein of unknown function (DUF461) identified within CDS. This Pfam is linked to being a membrane or periplasmic protein. Functional classification - Miscellaneous periplasmic proteins; periplasmic protein 846971..847390 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905210 YP_002344308.1 CDS Cj0910 NC_002163.1 847394 847846 D Original (2000) note: Cj0910, probable periplasmic protein, len: 150 aa; no Hp match. Contains probable N-terminal signal sequence. Similar to downstream gene Cj0908 (41.3% identity in 145 aa overlap). Functional classification - Miscellaneous periplasmic proteins; periplasmic protein 847394..847846 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905190 YP_002344309.1 CDS Cj0911 NC_002163.1 847843 848403 D Original (2000) note: Cj0911, probable periplasmic protein, len: 186 aa; similar to bacterial hypotheticals e.g. TR:O67113 (EMBL:AE000717) Aquifex aeolicus AQ_988 (197 aa), fasta scores; opt: 260 z-score: 314.1 E(): 3.4e-10, 28.1% identity in 167 aa overlap, and to N-terminus of eukaryotic proteins e.g. SCO1_YEAST SCO1 protein precursor (295 aa), opt: 213 z-score: 257.2 E(): 5e-07, 32.1% identity in 137 aa overlap. No Hp match. Contains probable N-terminal signal sequence; Updated (2006) note: Pfam domain PF02630 SCO1/SenC identified within CDS. Characterization has been carried out in Rhodobacter capsulatus, however, identity scores was unnacceptable. kept in product function. Functional classification - Miscellaneous periplasmic proteins; PMID:7592491; periplasmic protein 847843..848403 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905211 YP_002344310.1 CDS cysM NC_002163.1 848410 849309 R Original (2000) note: Cj0912c, cysM, cysteine synthase, len: 299 aa; 98.7% identical to CYSM_CAMJE cysteine synthase B (EC 4.2.99.8) (299 aa), and similar to many e.g. CYSK_BACSU CYSTEINE SYNTHASE (EC 4.2.99.8) (307 aa), fasta scores; opt: 907 z-score: 1020.2 E(): 0, 48.5% identity in 305 aa overlap. 38.9% identity to HP0107. Contains PS00165 Serine/threonine dehydratases pyridoxal-phosphate attachment site, PS00901 Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site, and Pfam match to entry PF00291 S_T_dehydratase, Pyridoxal-phosphate dependant enzymes; Updated (2006) note: Characterised in Campylobacter jejuni, so not added to product function. Functional classification - Amino acid biosynthesis -Serine family; PMID:9034314; cysteine synthase complement(848410..849309) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 906009 YP_002344311.1 CDS hupB NC_002163.1 849436 849732 R Original (2000) note: Cj0913c, hupB, DNA-binding protein HU homolog, len: 98 aa; identical to TR:Q46121 (EMBL:L25627) DNA-binding protein HU homolog (98 aa), and highly similar to many e.g. DBHB_ECOLI DNA-binding protein HU-beta (90 aa), fasta scores; opt: 272 z-score: 356.7 E(): 1.4e-12, 44.9% identity in 89 aa overlap. 42.2% identity to HP0835. Contains Pfam match to entry PF00216 Bac_DNA_binding, Bacterial DNA-binding protein; Updated (2006) note: Characterised in Campylobacter jejuni and many others. not added to product function. Functional classification - Synthesis and modification of macromolecules - Nucleoproteins; PMID:8063109; DNA-binding protein HU complement(849436..849732) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905212 YP_002344312.1 CDS ciaB NC_002163.1 849834 851666 R Original (2000) note: Cj0914c, ciaB, unknown function, len: 610 aa; no Hp match. Product is translocated into host cells. Mutants fail to translocate,and fail to translocate other proteins. Contains PS00142 Neutral zinc metallopeptidases, zinc-binding region signature; Updated (2006) note: Papers attached giving further information regarding this CDS. Functional classification - Pathogenicity; PMID:10361274, PMID:10540297, PMID:10659361,PMID:15722140; CiaB protein complement(849834..851666) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905214 YP_002344313.1 CDS Cj0915 NC_002163.1 851728 852141 D Original (2000) note: Cj0915, possible hydrolase,len: 137 aa; similar to prokaryotic hypotheticals e.g. YCIA_ECOLI (132 aa), fasta scores; opt: 351 z-score: 440.7 E(): 3e-17, 41.5% identity in 123 aa overlap, and to eukaryotic acyl-CoA hydrolases e.g. THCC_HUMAN cytosolic acyl coenzyme A thioester hydrolase (372 aa), fasta scores; opt: 174 z-score: 220.2 E(): 5.7e-05, 31.6% identity in 114 aa overlap. 25.4% identity to HP0891 (VDLD_HELPY); Updated (2006) 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; PMID:12426338; hydrolase 851728..852141 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905254 YP_002344314.1 CDS Cj0916c NC_002163.1 852181 852378 R Original (2000) note: Cj0916c, unknown, len: 65 aa; similar to two hypothetical E. coli proteins; YBDD_ECOLI (65 aa), fasta scores; opt: 154 z-score: 227.0 E(): 2.5e-05, 41.3% identity in 46 aa overlap, and YJIX_ECOLI (67 aa), fasta scores; opt: 141 z-score: 209.5 E(): 0.00023, 35.8% identity in 67 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF04328 Protein of unknown function (DUF466) identified within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins; hypothetical protein complement(852181..852378) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905180 YP_002344315.1 CDS cstA NC_002163.1 852359 854470 R Original (2000) note: Cj0917c, cstA, integral membrane protein, homolog of carbon starvation protein A,len: 703 aa; highly similar to e.g. CSTA_ECOLI carbon starvation protein A (701 aa), fasta scores; opt: 2523 z-score: 2823.2 E(): 0, 56.0% identity in 707 aa overlap. 65.6% identity to HP1168; Updated (2006) 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, lipoproteins and porins; PMID:1848300; integral membrane protein complement(852359..854470) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905216 YP_002344316.1 CDS prsA NC_002163.1 854637 855566 R catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP; ribose-phosphate pyrophosphokinase complement(854637..855566) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905217 YP_002344317.1 CDS Cj0919c NC_002163.1 855674 856333 R Original (2000) note: Cj0919c, probable ABC-type amino-acid transporter permease, len: 219 aa; similar to many e.g. GLTK_ECOLI glutamate/aspartate transport system permease (224 aa), fasta scores; opt: 380 z-score: 457.9 E(): 3.3e-18, 32.6% identity in 221 aa overlap. No Hp ortholog. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp sign., and Pfam match to entry PF00528 BPD_transp,Binding-protein-dependent transport systems inner membrane component; Updated (2006) 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/binding proteins - Amino acids and amines; PMID:16689801; ABC-type amino-acid transporter permease complement(855674..856333) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904985 YP_002344318.1 CDS Cj0920c NC_002163.1 856344 857096 R Original (2000) note: Cj0920c, probable ABC-type amino-acid transporter permease, len: 250 aa; similar to many e.g. YCKA_BACSU probable amino-acid ABC transporter permease (226 aa), fasta scores; opt: 448 z-score: 560.9 E(): 6e-24, 32.0% identity in 219 aa overlap. No Hp ortholog. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp sign., and Pfam match to entry PF00528 BPD_transp,Binding-protein-dependent transport systems inner membrane component; Updated (2006) note: Three probable transmembrane helices predicted by TMHMM2.0. No specific characterisation has been carried out yet. kept within product function. Functional classification -Transport/binding proteins - Amino acids and amines; PMID:16689801; ABC-type amino-acid transporter permease complement(856344..857096) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905218 YP_002344319.1 CDS peb1A NC_002163.1 857098 857877 R PEB1; bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein complement(857098..857877) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 906008 YP_002344320.1 CDS pebC NC_002163.1 857899 858627 R Original (2000) note: Cj0922c, pebC, probable ABC-type amino-acid transporter ATP-binding protein, len: 242 aa; 98.8% identical to PEBC_CAMJE, and similar to many e.g. GLNQ_BACST glutamine transport ATP-binding protein (242 aa), fasta scores; opt: 1013 z-score: 1161.8 E(): 0,64.6% identity in 243 aa overlap. No Hp ortholog. Contains PS00211 ABC transporters family signature, PS00017 ATP/GTP-binding site motif A (P-loop), and Pfam match to entry PF00005 ABC_tran, ABC transporters; Updated (2006) note: Characterised within Campylobacter jejuni. not added to product function. Functional classification - Transport/binding proteins - Amino acids and amines; PMID:16689801; amino-acid ABC transporter ATP-binding protein complement(857899..858627) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905220 YP_002344321.1 CDS cheR NC_002163.1 858763 859551 R Original (2000) note: Cj0923c, cheR, probable MCP protein methyltransferase, len: 262 aa; identical to YPEB_CAMJE, and similar to e.g. CHER_BACSU chemotaxis protein methyltransferase (EC 2.1.1.80) (256 aa), fasta scores; opt: 357 z-score: 432.6 E(): 8.5e-17, 31.6% identity in 231 aa overlap. No Hp match; Updated (2006) note: Pfam domains PF01739 CheR methyltransferase, SAM binding domain and PF03705 CheR methyltransferase, all-alpha domain were identified within CDS. Further support given to product function. Characterised in more than one genus, however, identity scores were marginal. kept within product function. Functional classification - Chemotaxis and mobility; PMID:8244966, PMID:8360165, PMID:3510184,PMID:11669626; MCP protein methyltransferase complement(858763..859551) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905222 YP_002344322.1 CDS cheB' NC_002163.1 859567 860121 R Original (2000) note: Cj0924c, cheB' probable MCP protein-glutamate methylesterase, len: 184 aa; similar to the methylesterase domain of e.g. CHEB_ECOLI protein-glutamate methylesterase (EC 3.1.1.61) (349 aa),fasta scores; opt: 339 z-score: 430.2 E(): 1.1e-16, 34.4% identity in 183 aa overlap. Note that the 'response reciever domain' normally found in cheB is not present. No Hp match; Updated (2006) note: Characterised within Escherichia coli, however, identity scores were marginal. Possible truncated protein as missing receiver domain of CheB protein. kept within product function. Functional classification - Chemotaxis and mobility; PMID:3280143, PMID:3510184, PMID:2188960,PMID:8244966; MCP protein-glutamate methylesterase complement(859567..860121) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904926 YP_002344323.1 CDS rpiB NC_002163.1 860287 860724 D Original (2000) note: Cj0925, rpiB, probable ribose 5-phosphate isomerase, len: 145 aa; highly similar to e.g. RPIB_ECOLI ribose 5-phosphate isomerase B (EC 5.3.1.6) (149 aa), fasta scores; opt: 399 z-score: 505.9 E(): 7e-21, 45.0% identity in 140 aa overlap. 45.0% identity to HP0574, misannotated as galactosidase acetyltransferase (lacA); Updated (2006) note: Prosite domain PS00237 G_PROTEIN_RECEP_F1_1, Rhodopsin-like GPCR superfamily and Pfam domain PF02502 Ribose/Galactose 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; PMID:8576032,PMID:14499611; ribose 5-phosphate isomerase 860287..860724 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905223 YP_002344324.1 CDS Cj0926 NC_002163.1 860724 861056 D Original (2000) note: Cj0926, possible membrane protein, len: 110 aa; 50.0% identity to HP0573. Contains possible transmembrane domain at N-terminus; Updated (2006) note: One probable transmembrane helix predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; hypothetical protein 860724..861056 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905225 YP_002344325.1 CDS apt NC_002163.1 861053 861601 D catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis; adenine phosphoribosyltransferase 861053..861601 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905205 YP_002344326.1 CDS Cj0928 NC_002163.1 861620 862216 D Original (2000) note: Cj0928, probable integral membrane protein, len: 198 aa; similar to members of the dedA family of hypothetical integral membrane proteins e.g. YOHD_ECOLI (192 aa), fasta scores; opt: 303 z-score: 394.8 E(): 1.1e-14, 29.1% identity in 172 aa overlap, and DEDA_ECOLI DEDA protein (219 aa), fasta scores; opt: 169 z-score: 224.4 E(): 3.3e-05, 25.3% identity in 162 aa overlap. 61.4% identity to HP0571. Contains Pfam match to entry PF00597 DedA, DedA family. Also similar to Cj1210 (27.1% identity in 177 aa overlap); Updated (2006) note: Five probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; integral membrane protein 861620..862216 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905226 YP_002344327.1 CDS pepA NC_002163.1 862213 863664 D catalyzes the removal of N-terminal amino acids preferably leucine from various peptides; leucyl aminopeptidase 862213..863664 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904492 YP_002344328.1 CDS Cj0930 NC_002163.1 863661 864764 D translation-associated GTPase; the crystal structure of the Haemophilus influenzae YchF protein showed similarity to the yeast structure (PDB: 1NI3); fluorescence spectroscopy revealed nucleic acid binding; the yeast protein YBR025c interacts with the translation elongation factor eEF1; GTP-dependent nucleic acid-binding protein EngD 863661..864764 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904351 YP_002344329.1 CDS argH NC_002163.1 864786 866168 R catalyzes the formation of arginine from (N-L-arginino)succinate; argininosuccinate lyase complement(864786..866168) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905111 YP_002344330.1 CDS pckA NC_002163.1 866178 867752 R PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP; phosphoenolpyruvate carboxykinase complement(866178..867752) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905227 YP_002344331.1 CDS pycB NC_002163.1 867765 869564 R Original (2000) note: Cj0933c, pycB, possible possible pyruvate carboxylase B subunit, len: 599 aa; similar to TR:O27179 (EMBL:AE000942) Methanobacterium thermoautotrophicum characterised pyruvate carboxylase B (EC 6.4.1.1) (568 aa), fasta scores; opt: 425 z-score: 482.7 E(): 1.4e-19, 29.1% identity in 601 aa overlap. Also similar to other biotin-requiring decarboxlases e.g. DCOA_SALTY oxaloacetate decarboxylase alpha chain (590 aa), fasta scores; opt: 515 z-score: 584.5 E(): 2.9e-25,27.3% identity in 605 aa overlap, and C-terminus of PYC1_YEAST pyruvate carboxylase 1 (1178 aa), fasta scores; opt: 434 z-score: 488.3 E(): 6.7e-20, 24.2% identity in 631 aa overlap. No Hp match. Contains S00188 Biotin-requiring enzymes attachment site and Pfam match to entry PF00364 biotin_req_enzy, Biotin-requiring enzymes; Updated (2006) note: No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification -Central intermediary metabolism - Gluconeogenesis; pyruvate carboxylase B subunit complement(867765..869564) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905229 YP_002344332.1 CDS Cj0934c NC_002163.1 869596 870936 R Original (2000) note: Cj0934c, probable transmembrane transport protein, len: 446 aa; similar to members of the sodium:neurotransmitter symporter family e.g. YD19_METJA hypothetical sodium-dependent transporter MJ1319 (492 aa), fasta scores; opt: 628 z-score: 711.7 E(): 2.4e-32, 27.4% identity in 457 aa overlap. 42.6% identity to HP0498. Also similar to Cj0935c (51.0% identity in 441 aa overlap) and Cj0601c (28.2% identity in 454 aa overlap); Updated (2006) note: Pfam domain PF00209 Sodium:neurotransmitter symporter family identified within CDS. Also, 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, so has kept within product function. Functional classification -Transport/binding proteins - Other; sodium:amino-acid symporter family protein complement(869596..870936) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905237 YP_002344333.1 CDS Cj0935c NC_002163.1 870949 872283 R Original (2000) note: Cj0935c, probable transmembrane transport protein, len: 444 aa; similar to members of the sodium:neurotransmitter symporter family e.g. YG90_HAEIN hypothetical sodium-dependent transporter HI1690 (457 aa), fasta scores; opt: 694 z-score: 771.9 E(): 0, 33.0% identity in 449 aa overlap. 40.4% identity to HP0497. Pfam match to entry PF00209 SNF,Sodium:neurotransmitter symporter family. Also similar to Cj0934c (51.0% identity in 441 aa overlap) and Cj0601c (32.6% identity in 451 aa overlap); Updated (2006) note: Pfam domain PF00209 Sodium:neurotransmitter symporter family identified within CDS. Also, 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, so has kept within product function. Functional classification -Transport/binding proteins - Other; sodium:amino-acid symporter family protein complement(870949..872283) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 906006 YP_002344334.1 CDS atpE NC_002163.1 872516 872854 D Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit C is part of the membrane proton channel F0; F0F1 ATP synthase subunit C 872516..872854 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905243 YP_002344335.1 CDS Cj0937 NC_002163.1 873171 874082 D Original (2000) note: Cj0937, probable integral membrane protein, len: 303 aa; simimlar to hypothetical membrane proteins e.g. YA31_METJA MJ1031 (308 aa), fasta scores; opt: 379 z-score: 446.4 E(): 1.4e-17, 26.1% identity in 318 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF03547 Auxin Efflux Carrier identified within CDS. Also, ten probable transmembrane helices predicted by TMHMM2.0. PProteins in this group are mostly uncharacterised and of unknown function. Functional classification - Membranes,lipoproteins and porins; integral membrane protein 873171..874082 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905231 YP_002344336.1 CDS aas NC_002163.1 874090 877602 R Original (2000) note: Cj0938c, aas, probable 2-acylglycerophosphoethanolamine acyltransferase / acyl-acyl carrier protein synthetase, len: 1170 aa; contains 2 domains; C-terminal domain (420 aa to end) is simlar to the bifunctional enzyme AAS_ECOLI 2-acylglycerophosphoethanolamine acyltransferase / acyl-acyl carrier protein synthetase (719 aa), fasta scores; opt: 438 z-score: 471.6 E(): 5.7e-19, 31.0% identity in 762 aa overlap; N-terminal domain contains approx 12 transmembrane domains, and is similar to the hypothetical membrane protein immediately upstreram of the E. coli aas; YGED_ECOLI; wublastp scores E= 3.5e-12, 25% in 192 aa overlap and 31% identity in 146 aa overlap. No Hp match. Contains PS00455 AMP-binding domain signature, and Pfam match to entry PF00501 AMP-binding,AMP-binding enzyme; Updated (2006) note: Now contains additional Pfam domains in centre of CDS, PF01553 Acyltransferase and N-terminal domain PF07690 Major Facilitator Superfamily. Characterisation has been carried out within Escherichia coli, however, sequence alignment is only partial. kept within product function. Functional classification - Fatty acid biosynthesis; PMID:10733890; 2-acyl-glycerophospho-ethanolamine acyltransferase complement(874090..877602) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905232 YP_002344337.1 CDS Cj0939c NC_002163.1 877647 878027 R Original (2000) note: Cj0939c, unknown, len: 126 aa; 29.5% identity to HP1065. Functional classification -Conserved hypothetical proteins; hypothetical protein complement(877647..878027) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905233 YP_002344338.1 CDS glnP NC_002163.1 878828 879613 R Original (2000) note: Cj0940c, glnP, probable glutamine transport system permease, len: 261 aa; similar to many e.g. GLNP_ECOLI glutamine transport system permease (219 aa), fasta scores; opt: 414 z-score: 509.0 E(): 4.7e-21, 37.5% identity in 216 aa overlap. No Hp otholog. Contains PS00402 Binding-protein-dependent transport systems inner membrane comp sign., and Pfam match to entry PF00528 BPD_transp,Binding-protein-dependent transport systems inner membrane component; Updated (2006) note: Six probable transmembrane helices predicted by TMHMM2.0. Not fully characterised, so kept in product function. Functional classification - Transport/binding proteins - Amino acids and amines; glutamine transport system permease complement(878828..879613) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905236 YP_002344339.1 CDS Cj0941c NC_002163.1 879636 880841 R Original (2000) note: Cj0941c, probable integral membrane protein, len: 401 aa; similar to many hypothetical membrane proteins e.g. YCFU_ECOLI(399 aa),fasta scores; opt: 414 z-score: 478.9 E(): 2.2e-19, 22.1% identity in 408 aa overlap. 53.5% identity to HP0787; Updated (2006) note: Pfam domain PF02687 Predicted permease identified within CDS. Also, 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, so kept within product function. Functional classification - Transport/binding proteins - Other; permease complement(879636..880841) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904433 YP_002344340.1 CDS secA NC_002163.1 880838 883426 R functions in protein export; can interact with acidic membrane phospholipids and the SecYEG protein complex; binds to preproteins; binds to ATP and undergoes a conformational change to promote membrane insertion of SecA/bound preprotein; ATP hydrolysis appears to drive release of the preprotein from SecA and deinsertion of SecA from the membrane; additional proteins SecD/F/YajC aid SecA recycling; exists in an equilibrium between monomers and dimers; may possibly form higher order oligomers; proteins in this cluster correspond SecA1; SecA2 is not essential and seems to play a role in secretion of a subset of proteins; preprotein translocase subunit SecA complement(880838..883426) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905172 YP_002344341.1 CDS lolA NC_002163.1 883526 884035 D participates with LolB in the incorporation of lipoprotein into the outer membrane; outer-membrane lipoprotein carrier protein 883526..884035 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905238 YP_002344342.1 CDS Cj0944c NC_002163.1 884032 884766 R Original (2000) note: Cj0944c, probable periplasmic protein, len: 244 aa; no Hp match; Updated (2006) note: Paper identified linking protein to glycoprotein. Functional classification -Miscellaneous periplasmic proteins; PMID:12186869; periplasmic protein complement(884032..884766) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904376 YP_002344343.1 CDS Cj0945c NC_002163.1 884776 886119 R Original (2000) note: Cj0945c, possible helicase,len: 447 aa; similar to the C-terminus of members of the eukaryotic RAD3/XPD helicase subfamily, e.g. PIF1_YEAST mitochondrial DNA repair and recombination protein (857 aa), fasta scores; opt: 193 z-score: 220.7 E(): 5.4e-05,29.6% identity in 324 aa overlap. No Hp match. Contains S00017 ATP/GTP-binding site motif A (P-loop); Updated (2006) note: No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification -DNA replication, restriction/modification, recombination and repair; helicase complement(884776..886119) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905207 YP_002344344.1 CDS Cj0946 NC_002163.1 886168 887514 D Original (2000) note: Cj0946, probable lipoprotein,len: 448 aa; 29.0% identity to HP0087. Contains probable N-terminal signal sequence with appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site, and Pfam match to entry PF00877 NLPC_P60, NLP/P60 family. Functional classification - Membranes,lipoproteins and porins; lipoprotein 886168..887514 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905239 YP_002344345.1 CDS Cj0947c NC_002163.1 887526 888398 R Original (2000) note: Cj0947c, probable hydrolase,len: 290 aa; similar to prokaryotic hypothetical hydrolases, and to e.g. BUP_RAT beta-ureidopropionase (393 aa), fasta scores; opt: 319 z-score: 392.0 E(): 1.6e-14,26.0% identity in 304 aa overlap. 60.9% identity to HP0757; Updated (2006) 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,so kept in product funciton. Functional classification - Misc; carbon-nitrogen hydrolase complement(887526..888398) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905240 YP_002344346.1 CDS Cj0948c NC_002163.1 888395 889282 R Original (2000) note: Cj0948c, possible transmembrane transport protein, len: 295 aa; similar to members of the UPF0018 family, e.g. YIIP_ECOLI (300 aa),fasta scores; opt: 564 z-score: 671.3 E(): 4.3e-30, 31.8% identity in 292 aa overlap, and to cation efflux proteins e.g. CZCD_ALCEU cation efflux system protein CZCD (316 aa), fasta scores; opt: 262 z-score: 316.4 E(): 2.5e-10,22.3% identity in 273 aa overlap. No Hp match. Also similar to Cj1163c (24.7% identity in 279 aa overlap); Updated (2006) 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/analogue sensitivity; PMID:12019132, PMID:15549269; cation efflux family protein complement(888395..889282) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905780 YP_002344347.1 CDS Cj0949c NC_002163.1 889279 890256 R Original (2000) note: Cj0949c, unknown, len: 325 aa; similar to hypothetical proteins e.g. TR:O86509 (EMBL:AL031124) Streptomyces coelicolor SC1C2.08 (339 aa),fasta scores; opt: 283 z-score: 328.5 E(): 5.3e-11, 24.3% identity in 333 aa overlap. 45.5% identity to HP0049; Updated (2006) 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,so kept within product function. Functional classification - Misc; peptidyl-arginine deiminase family protein complement(889279..890256) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905241 YP_002344348.1 CDS Cj0950c NC_002163.1 890355 890789 R Original (2000) note: Cj0950c, probable lipoprotein, len: 144 aa; some similarity to HSLJ_ECOLI heat shock protein HSLJ (140 aa), fasta scores; opt: 152 z-score: 202.3 E(): 0.00057, 26.2% identity in 145 aa overlap. 33.3% identity to HP1462 (secreted protein involved in flagellar motility). Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site; Updated (2006) note: Pfam domain PF03724 Domain of unknown function (306) identified within CDS. Functional classification - Membranes, lipoproteins and porins; lipoprotein complement(890355..890789) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905242 YP_002344349.1 CDS Cj0951c NC_002163.1 890799 891473 R Original (2000) note: Cj0951c, probable MCP-domain signal transduction protein, len: 224 aa; similar to MCP domains in many proteins e.g. CPS_CLOTM sensory transducer protein (557 aa), fasta scores; opt: 270 z-score: 283.0 E(): 1.8e-08, 30.3% identity in 198 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00015 MCPsignal, Methyl-accepting chemotaxis protein (MCP) signaling domain. The ORF continues upstream of this start, and contains BLASTX hits to other MCP proteins,suggesting that this may be a pseudogene, and should be read through from the upstream CDS. The sequence has been checked, and is believed to be correct; Updated (2006) note: No specific characterisation has been carried out yet. kept in product function. Functional classification - Signal transduction; MCP-domain signal transduction protein complement(890799..891473) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905244 YP_002344350.1 CDS Cj0952c NC_002163.1 891663 892382 R Original (2000) note: Cj0952c, probable membrane protein, len: 239 aa; some simlarity to TR:O66691 (EMBL:AE000686) Aquifex aeolicus AQ_367 (850 aa), fasta scores; opt: 229 z-score: 256.9 E(): 5.2e-07, 26.4% identity in 208 aa overlap. No Hp match. Contains PS00190 Cytochrome c family heme-binding site signature. BLASTX hits to MCP proteins in the C-terminus of this CDS continue into the downstream ORF, suggesting that this may be a pseudogene, and should be read through into the downstream CDS. The sequence has been checked, and is believed to be correct; Updated (2006) note: Two probable transmembrane helices predicted by TMHMM2.0. Running own Pfam search identified PF00672 HAMP domain. This domain is known as the HAMP domain for histidine kinases, adenylyl cyclases,methyl binding proteins and phosphatases. They are found in bacterial sensor and chemotaxis proteins. The bacterial proteins are usually integral membrane proteins and part of a two-component signal transduction pathway. Product function modified to more specific family member based on motif search results. Functional classification -Membranes, lipoproteins and porins; HAMP containing membrane protein complement(891663..892382) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905245 YP_002344351.1 CDS purH NC_002163.1 892478 894010 R involved in de novo purine biosynthesis; bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase complement(892478..894010) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905247 YP_002344352.1 CDS Cj0954c NC_002163.1 894013 894783 R Original (2000) note: Cj0954c, possible dnaJ-like protein, len: 256 aa; weak similarity to e.g. DJLA_COXBU DNAJ-like protein DJLA (270 aa), fasta scores; opt: 167 z-score: 193.0 E(): 0.0019, 26.9% identity in 201 aa overlap. No Hp match. Contains Pfam match to entry PF00226 DnaJ, DnaJ domain; Updated (2006) note: No specific characterisation with acceptable identity scores carried out yet. kept within product function. Functional classification -Chaperones, chaperonins, heat shock; DnaJ-like protein complement(894013..894783) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905248 YP_002344353.1 CDS purL NC_002163.1 894780 896966 R catalyzes the formation of 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine from N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide and L-glutamine in purine biosynthesis; phosphoribosylformylglycinamidine synthase II complement(894780..896966) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904957 YP_002344354.1 CDS trmE NC_002163.1 896977 898305 R in Escherichia coli this protein is involved in the biosynthesis of the hypermodified nucleoside 5-methylaminomethyl-2-thiouridine, which is found in the wobble position of some tRNAs and affects ribosomal frameshifting; shows potassium-dependent dimerization and GTP hydrolysis; also involved in regulation of glutamate-dependent acid resistance and activation of gadE; tRNA modification GTPase TrmE complement(896977..898305) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905249 YP_002344355.1 CDS Cj0957c NC_002163.1 898298 899116 R Original (2000) note: Cj0957c, unknown, len: 272 aa; 42.5% identity to HP1451. Functional classification -Conserved hypothetical proteins; hypothetical protein complement(898298..899116) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 906015 YP_002344356.1 CDS Cj0958c NC_002163.1 899120 900706 R functions to insert inner membrane proteins into the IM in Escherichia coli; interacts with transmembrane segments; functions in both Sec-dependent and -independent membrane insertion; similar to Oxa1p in mitochondria; inner membrane protein translocase component YidC complement(899120..900706) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904358 YP_002344357.1 CDS Cj0959c NC_002163.1 900703 901044 R Original (2000) note: Cj0959c, unknown, len: 113 aa; similar to hypothetical proteins from a wide range of organisms, e.g. YIDD_BUCAP (85 aa), fasta scores; opt: 168 z-score: 234.3 E(): 9.5e-06, 32.3% identity in 65 aa overlap, and YIDD_ECOLI (85 aa), fasta scores; opt: 156 z-score: 218.9 E(): 6.8e-05, 31.7% identity in 63 aa overlap. Also similar to TR:Q44066 (EMBL:L36462) Aeromonas hydrophila ALPHA-HEMOLYSIN (85 aa), fasta scores; opt: 156 z-score: 218.9 E(): 6.8e-05, 31.7% identity in 63 aa overlap. 34.2% identity to HP1449; Updated (2006) note: Pfam domain PF01809 Domain of unknown function DUF37 identified within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins; hypothetical protein complement(900703..901044) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905228 YP_002344358.1 CDS rnpA NC_002163.1 901041 901367 R Original (2000) note: Cj0960c, rnpA, probable ribonuclease P protein component, len: 108 aa; similar to e.g. RNPA_BACSU ribonuclease P protein component (EC 3.1.26.5) (116 aa), fasta scores; opt: 195 z-score: 280.1 E(): 2.6e-08, 27.9% identity in 111 aa overlap. 31.9% identity to HP1448. Contains Pfam match to entry PF00825 Ribonuclease_P, Ribonuclease P; Updated (2006) note: Prosite domain PS00648 RIBONUCLEASE_P, Bacterial ribonuclease P protein identified within CDS. Further support given to product function. Characterised in Bacillus subtilis, however,identity score was marginal. not added to product function. Functional classification - RNA synthesis, RNA modification and DNA transcription; PMID:9628904; ribonuclease P protein component complement(901041..901367) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905252 YP_002344359.1 CDS rpmH NC_002163.1 901364 901498 R in Escherichia coli transcription of this gene is enhanced by polyamines; 50S ribosomal protein L34 complement(901364..901498) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905034 YP_002344360.1 CDS Cj0962 NC_002163.1 901629 902108 D Original (2000) note: Cj0962, possible acetyltransferase, len: 159 aa; most similar to eukaryotic acetyltransferases, e.g. TR:P79081 (EMBL:U82218) Schizosaccharomyces pombe acetyltransferase ATS1 (168 aa), fasta scores; opt: 317 z-score: 406.2 E(): 2.5e-15, 34.6% identity in 162 aa overlap, and ATDA_MOUSE diamine acetyltransferase (171 aa), fasta scores; opt: 211 z-score: 274.9 E(): 5.2e-08, 27.4% identity in 168 aa overlap. No Hp match. Contains Pfam match to entry PF00583 Acetyltransf, Acetyltransferase (GNAT) family; Updated (2006) note: No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification -Misc; acetyltransferase 901629..902108 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905253 YP_002344361.1 CDS Cj0963 NC_002163.1 902105 902713 D Original (2000) note: Cj0963, unknown, len: 202 aa; similar to hypothetical proteins e.g. TR:O67598 (EMBL:AE000751) Aquifex aeolicus DPLF (195 aa), fasta scores; opt: 234 z-score: 301.4 E(): 1.7e-09, 27.2% identity in 184 aa overlap. 21.4% identity to HP0650. Functional classification - Conserved hypothetical proteins; hypothetical protein 902105..902713 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905142 YP_002344362.1 CDS Cj0964 NC_002163.1 902710 903900 D Original (2000) note: Cj0964, probable periplasmic protein, len: 396 aa; 26.6% identity to HP0781. Contains probable N-terminal signal sequence. Functional classification - Miscellaneous periplasmic proteins; periplasmic protein 902710..903900 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905256 YP_002344363.1 CDS Cj0965c NC_002163.1 903892 904266 R Original (2000) note: Cj0965c, unknown, len: 124 aa; similar to hypothetical proteins e.g. YBGC_ECOLI (134 aa), fasta scores; opt: 235 z-score: 313.7 E(): 3.5e-10,38.1% identity in 113 aa overlap. 40.6% identity to HP0496; Updated (2006) note: Pfam domain PF03061 Thioesterase superfamily and Prosite domain PS01328 4HBCOA_THIOESTERASE, 4-hydroxybenzoyl-CoA thioesterase,active 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; PMID:15808744; acyl-CoA thioester hydrolase complement(903892..904266) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905257 YP_002344364.1 CDS Cj0967 NC_002163.1 904409 906697 D Original (2000) note: Cj0967, possible periplasmic protein, len: 762 aa; no Hp match. N- and C- termini are similar to two consecutive genes Cj0735 (37.8% identity in 214 aa overlap) and Cj0736 (42.3% identity in 562 aa overlap). Contains probable N-terminal signal sequence. Note that an ATA initiation codon has been used: this is consistent with the RBS, the similarity to Cj0735, and measures of coding likelyhood based on aa usage. Contains S00639 Eukaryotic thiol (cysteine) proteases histidine active site, PS00133 Zinc carboxypeptidases, zinc-binding region 2 signature, and PS00017 ATP/GTP-binding site motif A (P-loop). Functional classification - Miscellaneous periplasmic proteins; periplasmic protein 904409..906697 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905258 YP_002344365.1 CDS Cj0970 NC_002163.1 907408 907710 D Original (2000) note: Cj0970, unknown, len: 100 aa; no Hp match. Functional classification - Unknown; hypothetical protein 907408..907710 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905261 YP_002344366.1 CDS Cj0971 NC_002163.1 907713 908105 D Original (2000) note: Cj0971, unknown, len: 130 aa; no Hp match. Functional classification - Unknown; hypothetical protein 907713..908105 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905262 YP_002344367.1 CDS Cj0972 NC_002163.1 908107 908430 D Original (2000) note: Cj0972, unknown, len: 107 aa; no Hp match. Functional classification - Unknown; hypothetical protein 908107..908430 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905263 YP_002344368.1 CDS Cj0973 NC_002163.1 908554 908664 D Original (2000) note: Cj0973, unknown, len: 36 aa; no Hp match. Functional classification - Unknown; hypothetical protein 908554..908664 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905264 YP_002344369.1 CDS Cj0974 NC_002163.1 908693 908833 D Original (2000) note: Cj0974, questionable CDS, len 46 aa; no Hp match. Functional classification - Unknown; hypothetical protein 908693..908833 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905265 YP_002344370.1 CDS Cj0975 NC_002163.1 908891 910615 D Original (2000) note: Cj0975, probable outer-membrane protein, len: 584 aa; similar to OM proteins involved in specific protein secretion/activation e.g. HXB1_HAEIN heme-hemopexin utilization protein B precursor (565 aa), fasta scores; opt: 489 z-score: 539.9 E(): 9e-23, 23.9% identity in 570 aa overlap, and HLYB_PROMI hemolysin activator protein precursor (561 aa),fasta scores; opt: 220 z-score: 244.2 E(): 2.7e-06, 21.0% identity in 539 aa overlap. No Hp match. Apparently a complete copy of pseudogene Cj0742; Updated (2006) note: No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification -Protein and peptide secretion; outer-membrane protein 908891..910615 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905266 YP_002344371.1 CDS Cj0976 NC_002163.1 910711 911601 D Original (2000) note: Cj0976, unknown, len: 296 aa; similar to hypothetical proteins e.g. YECP_ECOLI (323 aa),fatsta scores; opt: 649 z-score: 775.1 E(): 0, 35.7% identity in 291 aa overlap. 51.2% identity to HP0419; Updated (2006) 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; methyltransferase 910711..911601 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905267 YP_002344372.1 CDS Cj0977 NC_002163.1 911674 912252 D Original (2000) note: Cj0977, unknown, len: 192 aa; 29.2% identity to HP0420; Updated (2006) note: Literature search identified paper linking product function to be involved with invasion of intestinal epithelial cells. Functional classification - Conserved hypothetical proteins; PMID:16369037; hypothetical protein 911674..912252 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905268 YP_002344373.1 CDS Cj0978c NC_002163.1 912253 912426 R Original (2000) note: Cj0978c, probable lipoprotein, len: 57 aa; no Hp match. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes, lipoproteins and porins; lipoprotein complement(912253..912426) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905269 YP_002344374.1 CDS Cj0979c NC_002163.1 912435 912962 R Original (2000) note: Cj0979c, probable secreted nuclease, len: 175 aa; similar to many e.g. NUC_STAHY thermonuclease precursor (EC 3.1.31.1) (169 aa), fasta scores; opt: 206 z-score: 261.7 E(): 2.8e-07, 36.9% identity in 122 aa overlap. No Hp match. Contains possible N-terminal signal sequence and Pfam match to entry PF00565 SNase, Staphylococcal nuclease homologues; Updated (2006) note: Some characterisation work in Staphylococcus spp. kept in product function. Functional classification - Degradation of macromolecules - DNA; PMID:67041918; secreted nuclease complement(912435..912962) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905270 YP_002344375.1 CDS Cj0980 NC_002163.1 913030 914298 D Original (2000) note: Cj0980, possible peptidase,len: 422 aa; similar to e.g. PEPD_ECOLI aminoacyl-histidine dipeptidase (484 aa), fasta scores; opt: 175 z-score: 206.9 E(): 0.00032, 31.1% identity in 476 aa overlap. No Hp match; Updated (2006) note: No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification -Degradation of macromolecules - Proteins, peptides and glycopeptides; PMID:2651887; peptidase 913030..914298 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905271 YP_002344376.1 CDS cjaB NC_002163.1 914281 915528 R Original (2000) note: Cj0981c, transmembrane transport protein, len: 415 aa; similar to many members of the sugar transporter family e.g. YHJE_ECOLI hypothetical metabolite transport protein I (440 aa), fasta scores; opt: 548 z-score: 610.3 E(): 1.1e-26, 30.4% identity in 418 aa overlap, and PROP_ECOLI proline/betaine transporter (500 aa), fasta scores; opt: 474 z-score: 528.2 E(): 4e-22, 28.0% identity in 421 aa overlap. No Hp ortholog. Contains PS00216 Sugar transport protein; Updated (2006) note: Pfam domains PF07690 Major Facilitator Superfamily and PF00083 Sugar (and other) transporter, 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, so kept in product function. Some characterisation work carried out within Campylobacter jejuni. Gene name has been added. Functional classification - Transport/binding proteins - Other; PMID:9395059; MFS transport protein complement(914281..915528) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905272 YP_002344377.1 CDS cjaA NC_002163.1 915568 916407 R Original (2000) note: Cj0982c, probable amino-acid transporter periplasmic solute-binding protein, len: 279 aa; similar to e.g. GLNH_BACST glutamine-binding protein precursor (262 aa), fasta scores; opt: 410 z-score: 484.3 E(): 1.1e-19, 32.4% identity in 253 aa overlap. 98.2% identical to TR:O05414 (EMBL:U93169) C. jejuni OMPH1, and 89.2% identical to TR:P94643 (EMBL:U93169) C. jejuni CjaA. 56.1% identity to HP1172. Contains Pfam match to entry PF00497 SBP_bac_3, Bacterial extracellular solute-binding proteins, N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site; Updated (2006) 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/binding proteins -Other; PMID:9395059; amino-acid transporter periplasmic solute-binding protein complement(915568..916407) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905273 YP_002344378.1 CDS Cj0983 NC_002163.1 916626 917744 D Original (2000) note: Cj0983, probable lipoprotein,len: 372 aa; 97.0% 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, lipoproteins and porins; lipoprotein 916626..917744 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905274 YP_002344379.1 CDS Cj0984 NC_002163.1 917836 918576 D Original (2000) note: Cj0984, unknown, len: 246 aa; 97.2% identical to YHI3_CAMJE. No Hp match. Weak similarity to TR:O66885 (EMBL:AE000700) Aquifex aeolicus AQ_644 (227 aa), fasta scores; opt: 154 z-score: 190.3 E(): 0.0027, 23.6% identity in 212 aa overlap; Updated (2006) note: Pfam domain PF03883 Protein of unknown function (DUF328) identified within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins; hypothetical protein 917836..918576 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905275 YP_002344380.1 CDS hipO NC_002163.1 918580 919731 R Original (2000) note: Cj0985c, hipO, hippurate hydrolase, len: 383 aa; 99.0% identical to HIPO_CAMJE hippurate hydrolase (EC 3.5.1.32), and similar to other hydrolases belinging to the peptidase M40 family (AMA/HIPO/HYUC hydrolase family) e.g. CBPX_SULSO thermostable carboxypeptidase (393 aa), fasta scores; opt: 805 z-score: 949.5 E(): 0, 38.2% identity in 398 aa overlap; Updated (2006) note: Pfam domains PF01546 Peptidase family M20/M25/M40 and PF07687 Peptidase dimerisation domain identified within CDS. Characterised in Campylobacter jejuni, so not added to product function. Functional classification - Misc; PMID:7730270; hippurate hydrolase complement(918580..919731) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905276 YP_002344381.1 CDS Cj0986c NC_002163.1 919733 919921 R Original (2000) note: Cj0986c, possible integral membrane protein, len: 62 aa; 98.4% identical to C-terminus of YHI2_CAMJE hypothetical protein (203 aa). No Hp match; Updated (2006) note: Two probable transmembrane helices predicted for Cj0986c by TMHMM2.0. Functional classification - Membranes, lipoproteins and porins; integral membrane protein complement(919733..919921) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905277 YP_002344382.1 CDS Cj0987c NC_002163.1 919988 920953 R Original (2000) note: Cj0987c, probable integral membrane protein, len: 321 aa; identical to N- and C-terminus of YHI2_CAMJE hypothetical protein (203 aa),which has a central deletion relative to this CDS. Some similarity to hypothetical membrane proteins e.g. YJHB_ECOLI (405 aa), fasta scores; opt: 239 z-score: 285.2 E(): 1.4e-08, 24.6% identity in 301 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF07690 Major Facilitator Superfamily identified within CDS. Also, nine probable transmembrane helices predicted by TMHMM2.0. Product modified to more specific family member based on motif match. Not specifically characterised yet, so kept in product function. Functional classification - Transport/binding proteins - Other; MFS transport protein complement(919988..920953) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905278 YP_002344383.1 CDS Cj0988c NC_002163.1 920967 921203 R Original (2000) note: Cj0988c, questionable CDS,len: 78 aa; 98.3% identical to TR:Q46117 (EMBL:Z36940) C. jejuni hypothetical protein. No Hp match; Updated (2006) note: One probable transmembrane helix predicted by TMHMM2.0. Functional classification -Unknown; hypothetical protein complement(920967..921203) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905279 YP_002344384.1 CDS Cj0989 NC_002163.1 921188 921394 D Original (2000) note: Cj0989, possible membrane protein, len: 68 aa; identical to TR:Q46118 (EMBL:Z36940) C. jejuni hypothetical protein. No Hp match; Updated (2006) note: One probable transmembrane helix predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; hypothetical protein 921188..921394 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905280 YP_002344385.1 CDS Cj0990c NC_002163.1 921397 922158 R Original (2000) note: Cj0990c, unknown, len: 253 aa; identical in C-terminus to YHI1_CAMJE C. jejuni hypothetical protein fragment (94 aa). No Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein complement(921397..922158) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905281 YP_002344386.1 CDS Cj0991c NC_002163.1 922155 923420 R Original (2000) note: Cj0991c, probable oxidoreductase ferredoxin-type electron transport protein,len: 421; weak similarity to e.g. GLPC_ECOLI anaerobic glycerol-3-phosphate dehydrogenase subunit C (396 aa),fasta scores; opt: 280 z-score: 323.3 E(): 1e-10, 23.3% identity in 425 aa overlap, and GLCF_ECOLI glycolate oxidase iron-sulfur subunit (407 aa), fasta scores; opt: 199 z-score: 231.5 E(): 1.4e-05, 22.3% identity in 413 aa overlap. 44.7% identity to HP0666 (annotated as glpC, but there are no homologs of glpA or glpB in Hp or Cj). Contains PS00198 4Fe-4S ferredoxins, iron-sulfur binding region signature, and 2x Pfam match to entry PF00037 fer4,4Fe-4S ferredoxins and related iron-sulfur cluster binding domains; Updated (2006) 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; oxidoreductase ferredoxin-type electron transport protein complement(922155..923420) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905282 YP_002344387.1 CDS hemN NC_002163.1 923422 924777 R catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III; coproporphyrinogen III oxidase complement(923422..924777) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905283 YP_002344388.1 CDS Cj0993c NC_002163.1 924764 925255 R Original (2000) note: Cj0993c, unknown, len: 163 aa; 30.1% identity to HP0664. Functional classification -Conserved hypothetical proteins; hypothetical protein complement(924764..925255) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905284 YP_002344389.1 CDS argF NC_002163.1 925252 926172 R catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation; ornithine carbamoyltransferase complement(925252..926172) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905285 YP_002344390.1 CDS hemB NC_002163.1 926169 927152 R catalyzes the formation of porphobilinogen from 5-aminolevulinate; delta-aminolevulinic acid dehydratase complement(926169..927152) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905286 YP_002344391.1 CDS ribA NC_002163.1 927210 927770 D catalyzes the conversion of GTP to formate and 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine and diphosphate; GTP cyclohydrolase II 927210..927770 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905287 YP_002344392.1 CDS Cj0997 NC_002163.1 927771 928337 D Original (2000) note: Cj0997, probable gidB homolog. len: 188 aa; similar to gidB proteins from many organisms e.g. GIDB_ECOLI glucose inhibited division protein B (207 aa), fasta scores; opt: 212 z-score: 265.9 E(): 1.6e-07, 24.7% identity in 182 aa overlap. 37.3% identity to HP1063; Updated (2006) 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 (PMID:12001236). Thus, product function has now been modified to more specific family member. Functional classification - Misc; PMID:12001236; methyltransferase 927771..928337 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905288 YP_002344393.1 CDS Cj0998c NC_002163.1 928353 928925 R Original (2000) note: Cj0998c, probable periplasmic protein, len: 190 aa; 33.9% identity to HP0305. Contains probable N-terminal signal sequence; Updated (2006) note: Paper identified linking protein to glycoprotein. Functional classification -Miscellaneous periplasmic proteins; PMID:12186869; periplasmic protein complement(928353..928925) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905289 YP_002344394.1 CDS Cj0999c NC_002163.1 929020 930117 R Original (2000) note: Cj0999c, probable integral membrane protein, len: 365 aa; similar to hypothetical membrane proteins e.g. YEIH_ECOLI (349 aa), fasta scores; opt: 631 z-score: 729.2 E(): 0, 35.7% identity in 347 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF03601 Conserved hypothetical protein identified within CDS. Also, eleven probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Functional classification - Membranes, lipoproteins and porins; integral membrane protein complement(929020..930117) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905290 YP_002344395.1 CDS Cj1000 NC_002163.1 930230 931111 D Original (2000) note: Cj1000, probable transcriptional regulator, len: 293 aa; similar to members of the lysR family e.g. YEIE_ECOLI hypothetical transcriptional regulator (293 aa), fasta scores; opt: 332 z-score: 390.5 E(): 1.9e-14, 24.3% identity in 288 aa overlap. No Hp match. Contains Pfam match to entry PF00126 HTH_1, Bacterial regulatory helix-turn-helix proteins,lysR family, and probable helix-turn-helix motif at aa 17-38 (Score 1147, +3.09 SD); Updated (2006) 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, so kept in product function. Functional classification - Broad regulatory functions; transcriptional regulator 930230..931111 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905291 YP_002344396.1 CDS rpoD NC_002163.1 931191 933059 D sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this is the primary sigma factor of bacteria; RNA polymerase sigma factor RpoD 931191..933059 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905292 YP_002344397.1 CDS Cj1002c NC_002163.1 933075 933587 R Original (2000) note: Cj1002c, unknown, len: 170 aa; similar to hypothetical proteins e.g. TR:O67234 (EMBL:AE000727) Aquifex aeolicus AQ_1173 (149 aa), fasta scores; opt: 185 z-score: 235.0 E(): 8.6e-06, 34.2% identity in 117 aa overlap. No Hp match; Updated (2006) 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, so kept in product function. Functional classification - Energy metabolism -Glycolysis; phosphoglycerate/bisphosphoglycerate mutase complement(933075..933587) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905293 YP_002344398.1 CDS Cj1003c NC_002163.1 933584 934102 R Original (2000) note: Cj1003c, probable integral membrane protein, len: 172 aa; similar to hypothetical proteins e.g. TR:O59166 (EMBL:AP000006) Pyrococcus horikoshii PH1497 (197 aa), fasta scores; opt: 233 z-score: 292.8 E(): 5.2e-09, 30.8% identity in 172 aa overlap. No Hp ortholog; Updated (2006) note: Pfam domain PF01694 Rhomboid family identified within CDS. Also, five probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific charactersation carried out yet, so kept in product function. Functional classification - Membranes,lipoproteins and porins; integral membrane protein complement(933584..934102) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905294 YP_002344399.1 CDS Cj1004 NC_002163.1 934201 934617 D Original (2000) note: Cj1004, probable periplasmic protein, len: 138 aa; very weak similarity to TR:P75137 (EMBL:AE000019) Mycoplasma pneumoniae lipoprotein E09_orf129 (129 aa), fasta scores; opt: 110 z-score: 147.3 E(): 0.66, 34.9% identity in 129 aa overlap. No Hp match. Also similar to Cj1626c (38.6% identity in 140 aa overlap); Updated (2006) note: Literature search identified paper giving further clues on product funciton. Functional classification - Miscellaneous periplasmic proteins; PMID:15554967; periplasmic protein 934201..934617 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905295 YP_002344400.1 CDS Cj1005c NC_002163.1 934626 936242 R Original (2000) note: Cj1005c, probable membrane bound ATPase, len: 538 aa; similar to many members of the AAA family e.g. FTSH_BACSU cell division protein FTSH homolog (EC 3.4.24.-) (637 aa), fasta scores; opt: 901 z-score: 909.6 E(): 0, 36.3% identity in 518 aa overlap. 43.8% identity to HP0286. Also similar to ftsH Cj1116c (36.2% identity in 578 aa overlap). Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00674 AAA-protein family signature, and Pfam match to entry PF00004 AAA,ATPases associated with various cellular activities (AAA); Updated (2006) 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; PMID:8892813, PMID:9244252 and PMID:96132941; membrane bound ATPase complement(934626..936242) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905296 YP_002344401.1 CDS Cj1006c NC_002163.1 936246 937496 R Original (2000) note: Cj1006c, unknown, len: 416 aa; similar to hypothetical proteins belonging to the UPF0004 family e.g. Y16R_MYCIO (438 aa), fasta scores; opt: 580 z-score: 664.7 E(): 1e-29, 30.5% identity in 413 aa overlap. 50.1% identity to HP0285. Also similar to Cj0458c (28.6% identity in 391 aa overlap) and Cj1454c (28.4% identity in 419 aa overlap). Contains PS01278 Uncharacterized protein family UPF0004 signature and Pfam match to entry PF00919 UPF0004; Updated (2006) 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, however, kept within product function. Functional classification - RNA synthesis, RNA modification and DNA transcription; PMID:10572129, PMID:11882645 and PMID:11313137; MiaB-like tRNA modifying enzyme complement(936246..937496) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905297 YP_002344402.1 CDS Cj1007c NC_002163.1 937493 939064 R Original (2000) note: Cj1007c, probable membrane protein, len: 523 aa; similar in C-terminus to hypothetical proteins e.g. Y700_METJA hypothetical protein MJ0700 (324 aa), fasta scores; opt: 281 z-score: 300.2 E(): 2e-09, 29.0% identity in 276 aa overlap. 37.4% identity to HP0284; Updated (2006) note: Pfam domain PF00924 Mechanosensitive ion channel identified within CDS. Also,three 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/binding proteins - Other; PMID:12446901; mechanosensitive ion channel family protein complement(937493..939064) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905298 YP_002344403.1 CDS aroB NC_002163.1 939061 940116 R catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis; 3-dehydroquinate synthase complement(939061..940116) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905299 YP_002344404.1 CDS Cj1009c NC_002163.1 940162 941562 R Original (2000) note: Cj1009c, unknown, len: 466 aa; 29.1% identity to HP0282; Updated (2006) 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; hypothetical protein complement(940162..941562) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905300 YP_002344405.1 CDS tgt NC_002163.1 941592 942713 D Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr); queuine tRNA-ribosyltransferase 941592..942713 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905301 YP_002344406.1 CDS Cj1011 NC_002163.1 942715 943482 D Original (2000) note: Cj1011, probable membrane protein, len: 255 aa; no Hp match; Updated (2006) note: Two probable transmembrane helices predicted by TMHMM2.0. Running own Pfam search identified PF01544 CorA-like Mg2+ 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/binding proteins - Cations; CorA-like Mg2+ transporter protein 942715..943482 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905302 YP_002344407.1 CDS Cj1012c NC_002163.1 943614 944063 R Original (2000) note: Cj1012c, possible membrane protein, len: 149 aa; no Hp match; Updated (2006) note: One probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; hypothetical protein complement(943614..944063) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905304 YP_002344408.1 CDS Cj1013c NC_002163.1 944080 947325 R Original (2000) note: Cj1013c, probable membrane protein, len: 1081 aa; contains three domains; aa 1-90 contains three membrane spanning domains; aa 90-780 is non-membrane, 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 (353 aa), fasta scores; opt: 459 z-score: 515.4 E(): 2.1e-21, 36.0% identity in 267 aa overlap, and to prokaryotic equivalents e.g. CCMF_ECOLI cytochrome C-type biogenesis protein CCMF (647 aa); BLASTP scores; E = 0.20, 24% identity in 293 aa overlap. 39.0% identity to HP0378 (domains 2+3 only); Updated (2006) 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, however, identity scores were marginal. kept within product function. Functional classification - Energy metabolism - Electron transport; PMID:10672190, PMID:11069671, PMID:16629661; cytochrome C biogenesis protein complement(944080..947325) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905305 YP_002344409.1 CDS livF NC_002163.1 947343 948038 R Original (2000) note: Cj1014c, livF, probable branched-chain amino-acid ABC transport system ATP-binding protein, len: 231 aa; similar to e.g. LIVF_ECOLI high-affinity branched-chain amino acid transport ATP-binding protein (237 aa), fasta scores; opt: 686 z-score: 797.6 E(): 0, 46.4% identity in 233 aa overlap. No Hp ortholog. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00211 ABC transporters family signature, and Pfam match to entry PF00005 ABC_tran; Updated (2006) note: Characterised within Pseudomonas aeruginosa and Escherichia coli with acceptable identity scores. not added to product function. Functional classification - Transport/binding proteins - Amino acids and amines; PMID:2120183, PMID:1429514, PMID:2195019; branched-chain amino-acid ABC transporter ATP-binding protein complement(947343..948038) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905306 YP_002344410.1 CDS livG NC_002163.1 948025 948795 R Original (2000) note: Cj1015c, livG, probable branched-chain amino-acid ABC transport system ATP-binding protein, len: 256 aa; similar to e.g. LIVG_ECOLI high-affinity branched-chain amino acid transport ATP-binding protein (255 aa), fasta scores; opt: 680 z-score: 800.2 E(): 0, 41.2% identity in 250 aa overlap. No Hp ortholog. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00211 ABC transporters family signature, and Pfam match to entry PF00005 ABC_tran; Updated (2006) note: Characterised within Pseudomonas aeruginosa and Escherichia coli with acceptable identity scores. not added to product function. Functional classification - Transport/binding proteins - Amino acids and amines; PMID:2120183, PMID:1429514, PMID:2195019; branched-chain amino-acid ABC transporter ATP-binding protein complement(948025..948795) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905307 YP_002344411.1 CDS livM NC_002163.1 948792 949844 R Original (2000) note: Cj1016c, livM, probable branched-chain amino-acid ABC transport system permease, len: 350 aa; similar to e.g. LIVM_ECOLI high-affinity branched-chain amino acid transport permease (425 aa) fasta scores; opt: 239 z-score: 284.9 E(): 1.4e-08, 31.5% identity in 321 aa overlap. No Hp ortholog; Updated (2006) note: Eight probable transmembrane helices predicted by TMHMM2.0. Pfam domain PF02653 Branched-chain amino acid transport system / permease component. Characterised in Escherichia coli with marginal identity score. Appropriate motifs present. removed from product function. Functional classification - Transport/binding proteins - Amino acids and amines; PMID:2120183, PMID:1429514, PMID:2195019; branched-chain amino-acid ABC transporter permease complement(948792..949844) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905308 YP_002344412.1 CDS livH NC_002163.1 949844 950740 R Original (2000) note: Cj1017c, livH, probable branched-chain amino-acid ABC transport system permease, len: 298 aa; similar to e.g. LIVH_ECOLI high-affinity branched-chain amino acid transport permease (308 aa) fasta scores; opt: 538 z-score: 595.2 E(): 7.4e-26, 40.8% identity in 299 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF02653 Branched-chain amino acid transport system / permease component identified within CDS. Also, 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/binding proteins -Amino acids and amines; PMID:2120183, PMID:1429514, PMID:2195019; branched-chain amino-acid ABC transporter permease complement(949844..950740) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905309 YP_002344413.1 CDS livK NC_002163.1 950759 951868 R Original (2000) note: Cj1018c, livK, probable branched-chain amino-acid ABC transport system periplasmic binding protein, len: 369 aa; similar to e.g. LIVK_ECOLI LEU/ILE/VAL-binding protein precursor (367 aa), fasta scores; opt: 386 z-score: 436.5 E(): 5.1e-17, 28.3% identity in 272 aa overlap. No Hp match. Highly similar to Cj1019c (62.0% identity in 371 aa overlap); Updated (2006) note: Pfam domain PF01094 Receptor family ligand binding region identified within CDS. Further support given to product function. Paper identified linking protein to glycoprotein (PMID:12186869). Characterised in Escherichia coli with marginal identity score. Appropriate motifs present. removed from product function. Functional classification - Transport/binding proteins - Amino acids and amines; PMID:2649683, PMID:2195019; branched-chain amino-acid ABC transporter periplasmic binding protein complement(950759..951868) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905310 YP_002344414.1 CDS livJ NC_002163.1 951890 953005 R Original (2000) note: Cj1019c, livJ, probable branched-chain amino-acid ABC transport system periplasmic binding protein, len: 369 aa; similar to e.g. LIVJ_ECOLI LEU/ILE/VAL-binding protein precursor (367 aa), fasta scores; opt: 419 z-score: 465.8 E(): 1.2e-18, 27.8% identity in 352 aa overlap. No Hp match. Highly similar to Cj1018c (62.0% identity in 371 aa overlap); Updated (2006) 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/binding proteins - Amino acids and amines; PMID:15850393, PMID:2195019; branched-chain amino-acid ABC transporter periplasmic binding protein complement(951890..953005) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905311 YP_002344415.1 CDS Cj1020c NC_002163.1 953036 953470 R Original (2000) note: Cj1020c, probable cytochrome C, len: 144 aa; similar to e.g.C553_DESDN cytochrome C-553 (80 aa), fasta scores; opt: 142 z-score: 184.4 E(): 0.0056, 30.8% identity in 78 aa overlap. Also similar to Cj1153 (27.6% identity in 76 aa overlap). No Hp ortholog. Contains N-terminal signal sequence, PS00190 Cytochrome c family heme-binding site signature, and Pfam match to entry PF00034 cytochrome_c; Updated (2006) note: kept in product function as no specific characterisation has been carried out. Functional classification - Energy metabolism -Electron transport; cytochrome C complement(953036..953470) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905312 YP_002344416.1 CDS Cj1021c NC_002163.1 953479 953670 R Original (2000) note: Cj1021c, probable periplasmic protein, len: 63 aa; similar to the N-terminus of C. jejuni major outer membrane protein TR:G2529699 (EMBL:U96452) (MOMP_CAMJE) momp, porA, Cj1259 (424 aa),fasta scores; opt: 110 z-score: 165.3 E(): 0.066, 36.4% identity in 55 aa overlap. No Hp match. Contains probable N-terminal signal sequence; Updated (2006) note: Pfam domain PF05538 Campylobacter major outer membrane protein identified when running own Pfam search. Some characterisation work within Cj1259, however, alignment was only partial. kept within product function. Psort was also ran with no additional results. Functional classification -Miscellaneous periplasmic proteins; PMID:10992471, PMID:754346, PMID:99163918; periplasmic protein complement(953479..953670) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905313 YP_002344417.1 CDS Cj1022c NC_002163.1 953723 954229 R Original (2000) note: Cj1022c, probable integral membrane protein, len: 168 aa; similar to e.g. TR:O66639 (EMBL:AE000682) Aquifex aeolicus AQ_286 (175 aa), fasta scores; opt: 354 z-score: 451.1 E(): 7.9e-18, 34.3% identity in 166 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF07053 Protein of unknown function (DUF1334) identified within CDS. Also,four probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Functional classification - Membranes, lipoproteins and porins; integral membrane protein complement(953723..954229) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905314 YP_002344418.1 CDS asd NC_002163.1 954238 955269 R catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde; aspartate-semialdehyde dehydrogenase complement(954238..955269) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905315 YP_002344419.1 CDS flgR NC_002163.1 955269 956570 R Original (2000) note: Cj1024c, probable signal-transduction regulatory protein, len: 433 aa; similar to e.g. NTRC_PROVU nitrogen regulation protein NR(I) (473 aa), fasta scores; opt: 957 z-score: 1002.5 E(): 0, 38.8% identity in 397 aa overlap, and ATOC_ECOLI acetoacetate metabolism regulatory protein (461 aa), fasta scores; opt: 929 z-score: 973.5 E(): 0, 38.2% identity in 453 aa overlap. 57.1% identity to HP0703. Contains Pfam match to entry PF00072 response_reg, Response regulator receiver domain, PS00675 and PS00676 Sigma-54 interaction domain ATP-binding regions A and B signatures, and Pfam match to entry PF00158 sigma54, Sigma-54 transcription factors; Updated (2006) 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 (FlgS/FlgR) that regulates the fla regulon in Campylobacter jejuni. Similar to that found in Helicobacter pylori. Functional classification - Signal transduction; PMID:11292815, PMID:14617189, PMID:14960570; sigma-54 associated transcriptional activator complement(955269..956570) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905316 YP_002344420.1 CDS Cj1025c NC_002163.1 956627 957076 R Original (2000) note: Cj1025c, unknown, len: 149 aa; no Hp match. Functional classification - Unknown; hypothetical protein complement(956627..957076) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905317 YP_002344421.1 CDS Cj1026c NC_002163.1 957052 957567 R Original (2000) note: Cj1026c, probable lipoprotein, len: 171 aa; 51.0% identity in N-terminus to HP0837 (102 aa). Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site; Updated (2006) note: Pfam domain PF04164 Protein of unknown function, DUF400 identified within CDS. Literature search identified paper linking product to motility. Functional classification - Membranes, lipoproteins and porins; PMID:14985343; lipoprotein complement(957052..957567) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905318 YP_002344422.1 CDS gyrA NC_002163.1 957631 960222 R negatively supercoils closed circular double-stranded DNA; DNA gyrase subunit A complement(957631..960222) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905319 YP_002344423.1 CDS Cj1028c NC_002163.1 960263 960838 R Original (2000) note: Cj1028c, possible purine/pyrimidine phosphoribosyltransferase, len: 191 aa; weak similarity to e.g. orotate phosphoribosyltransferase domain of PYR5_HUMAN uridine 5'-monophosphate synthase (480 aa), fasta scores; opt: 114 z-score: 145.4 E(): 0.85,25.5% identity in 149 aa overlap. 37.3% identity to HP1473. Contains PS00103 Purine/pyrimidine phosphoribosyl transferases signature; Updated (2006) 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/nucleotide reactions; PMID:16048946, PMID:12949093; purine/pyrimidine phosphoribosyltransferase complement(960263..960838) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905320 YP_002344424.1 CDS mapA NC_002163.1 960835 961479 R Original (2000) note: Cj1029c, mapA, probable lipoprotein, len: 214 aa; identical to TR:Q46122 (EMBL:X80135) C. jeuni species specific mapA gene (214 aa). No Hp match. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site; Updated (2006) note: Studied in Campylobacter jejuni. No specific characterisation has been carried out yet. Functional classification - Membranes, lipoproteins and porins; PMID:7790451; liproprotein complement(960835..961479) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905321 YP_002344425.1 CDS lepA NC_002163.1 961556 963352 R binds to the ribosome on the universally-conserved alpha-sarcin loop; GTP-binding protein LepA complement(961556..963352) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905322 YP_002344426.1 CDS cmeD NC_002163.1 963479 964753 D Original (2000) note: Cj1031, possible outer membrane component of efflux system, len: 424 aa; similar to members of the PRTF family of secretion proteins e.g. TR:O68960 (EMBL:AF059041) outer membrane pore protein hefA (=HP0605) (477 aa), fasta scores; opt: 238 z-score: 261.5 E(): 2.9e-07, 25.2% identity in 409 aa overlap, and TOLC_SALEN outer membrane protein TOLC precursor (491 aa), fasta scores; opt: 174 z-score: 192.9 E(): 0.0019, 21.5% identity in 437 aa overlap. 24.8% identity to HP0605. Contains probable N-terminal signal sequence; Updated (2006) note: Pfam domains x2 PF02321 Outer membrane efflux protein were identified within CDS. Further support given to product function. Characterised in Campylobacter jejuni, so removed from product function. Functional classification - Antibiotic resistance; PMID:16048946, PMID:15793099, PMID:12069964,PMID:15201231, PMID:16303882; multidrug efflux system outer membrane protein 963479..964753 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905323 YP_002344427.1 CDS cmeE NC_002163.1 964750 965490 D Original (2000) note: Cj1032, possible membrane fusion component of efflux system, len: 246 aa; similar to e.g. TR:O68961 EMBL:AF059041) H. pylori membrane fusion protein hefB (=HP0606) (241 aa), fasta scores; opt: 318 z-score: 369.4 E(): 2.8e-13, 35.5% identity in 248 aa overlap, and part of CZCB_ALCSP cation efflux system protein CZCB (520 aa), fasta scores; opt: 224 z-score: 258.9 E(): 4e-07, 28.6% identity in 213 aa overlap. Contains probable N-terminal signal sequence; Updated (2006) note: Pfam domain identified by running own Pfam search, PF00529 HlyD family secretion protein. Further support given to product function. Characterised in Campylobacter jejuni, so removed from product function. Functional classification -Antibiotic resistance; PMID:16048946, PMID:15793099, PMID:12069964,PMID:15201231, PMID:16303882; mutlidrug efflux system membrane fusion protein 964750..965490 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905324 YP_002344428.1 CDS cmeF NC_002163.1 965493 968510 D Original (2000) note: Cj1033, probable integral membrane component of efflux system, len: 1005 aa; similar to members of the ACRB/ACRD/ACRF family e.g. TR:O68962 (EMBL:AF059041) H. pylori RND pump protein hefC (=HP0607) (1026 aa), fasta scores; opt: 1372 z-score: 1439.0 E(): 0, 36.9% identity in 1027 aa overlap, and ACRD_ECOLI acriflavin resistance protein D (1037 aa),fasta scores; opt: 571 z-score: 598.0 E(): 5.2e-26, 25.7% identity in 1033 aa overlap. 37.1% identity to HP0607. Contains PS00017 ATP/GTP-binding site motif A (P-loop),and Pfam match to entry PF00873 ACR_tran, AcrB/AcrD/AcrF family; Updated (2006) note: Twelve probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised in Campylobacter jejuni,so removed from product function. Functional classification - Antibiotic resistance; PMID:16048946, PMID:15793099, PMID:12069964,PMID:15201231, PMID:16303882; multidrug efflux system membrane protein 965493..968510 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905325 YP_002344429.1 CDS Cj1034c NC_002163.1 968534 969340 R Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide; adenylosuccinate lyase complement(968534..969340) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905326 YP_002344430.1 CDS Cj1035c NC_002163.1 969341 970060 R Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate; arginyl-tRNA-protein transferase complement(969341..970060) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905327 YP_002344431.1 CDS Cj1036c NC_002163.1 970060 970311 R Original (2000) note: Cj1036c, possible transcriptional regulator, len: 83 aa; no Hp match. Contains probable helix-turn-helix motif at aa 19-40 (Score 1070, +2.83 SD); Updated (2006) note: Conserved added to product function. Functional classification - Broad regulatory functions; hypothetical protein complement(970060..970311) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905328 YP_002344432.1 CDS pycA NC_002163.1 970315 971760 R biotin carboxylase; catalyses the carboxylation of the carrier protein which then transfers the carboxyl group to form malonyl-CoA, which in turn controls the rate of fatty acid metabolism; acetyl-CoA carboxylase subunit A complement(970315..971760) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905329 YP_002344433.1 CDS Cj1038 NC_002163.1 971900 973063 D Original (2000) note: Cj1038, probable cell division/peptidoglycan biosynthesis protein, len: 387 aa; similar to members of the FTSW/RODA/SPOVE family e.g. RODA_ECOLi rod shape-determining protein RODA (370 aa),fasta scores; opt: 297 z-score: 358.2 E(): 1.2e-12, 27.1% identity in 388 aa overlap, and FTSW_ECOLI cell division protein FTSW (414 aa), fasta scores; opt: 288 z-score: 346.8 E(): 5.1e-12, 28.4% identity in 394 aa overlap. 46.4% identity to HP1560. Contains Pfam match to entry PF01098 FTSW_RODA_SPOVE, Cell cycle protein; Updated (2006) note: Ten probable transmembrane helices predicted by TMHMM2.0. Specific characterisation not yet carried out, so kept in product function. Functional classification - Cell division; cell division/peptidoglycan biosynthesis protein 971900..973063 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905330 YP_002344434.1 CDS murG NC_002163.1 973060 974088 D UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase; involved in cell wall formation; inner membrane-associated; last step of peptidoglycan synthesis; UDPdiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase 973060..974088 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905331 YP_002344435.1 CDS Cj1040c NC_002163.1 974059 975222 R Original (2000) note: Cj1040c, probable transmembrane transport protein, len: 387 aa; simlar to hypothetical membrane proteins e.g. YEAN_ECOLI (393 aa),fasta scores; opt: 641 z-score: 726.5 E(): 0, 31.2% identity in 381 aa overlap, and to CYNX_ECOLI cyanate transport protein CYNX (384 aa), fasta scores; opt: 421 z-score: 480.1 E(): 1.9e-19, 23.9% identity in 368 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF07690 Major Facilitator Superfamily (MFS) protein identified within CDS. Also, Twelve probable transmembrane helices predicted by TMHMM2.0. Specific characterisation has not been carried out yet, so kept in product function. Functional classification - Transport/binding proteins -Other; MFS transport protein complement(974059..975222) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905332 YP_002344436.1 CDS Cj1041c NC_002163.1 975230 976081 R Original (2000) note: Cj1041c, probable periplasmic ATP/GTP-binding protein, len: 283 aa; no Hp match. Contains probable N-terminal signal sequence and PS00017 ATP/GTP-binding site motif A (P-loop). Functional classification - Miscellaneous periplasmic proteins; periplasmic ATP/GTP-binding protein complement(975230..976081) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905333 YP_002344437.1 CDS Cj1042c NC_002163.1 976144 977034 R Original (2000) note: Cj1042c, probable transcriptional regulatory protein, len: 296 aa; similar to many members of the ARAC/XYLS family e.g. VIRF_YEREN VIRULENCE regulon transcriptional activator (271 aa),fasta scores; opt: 220 z-score: 270.6 E(): 9e-08, 23.9% identity in 247 aa overlap, and LCRF_YERPE thermoregulatory protein LCRF (271 aa), fasta scores; opt: 219 z-score: 269.4 E(): 1e-07, 23.5% identity in 247 aa overlap. No Hp match. Contains PS00041 Bacterial regulatory proteins, araC family signature, and Pfam match to entry PF00165 HTH_2, Bacterial regulatory helix-turn-helix proteins, araC family; Updated (2006) note: No characterisation with acceptable identity score has been identified, so kept in product function. Literature search identified paper giving further clues to product function. Functional classification - Broad regulatory functions; PMID:15201231; transcriptional regulatory protein complement(976144..977034) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905334 YP_002344438.1 CDS Cj1043c NC_002163.1 977031 977636 R Original (2000) note: Cj1043c, possible transferase, len: 201 aa; similar to e.g. TENI_BACSU regulatory protein TENI (205 aa), fasta scores; opt: 217 z-score: 277.4 E(): 3.8e-08, 26.3% identity in 171 aa overlap, and THIE_ECOLI thiamin-phosphate pyrophosphorylase (211 aa), fasta scores; opt: 146 z-score: 190.3 E(): 0.0026, 27.9% identity in 154 aa overlap. No Hp ortholog. Also similar to Cj1081c (30.0% identity in 190 aa overlap); Updated (2006) note: Pfam domain PF02581 Thiamine monophosphate synthase/TENI 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, so kept in product function. Functional classification - Biosynthesis of cofactors, prosthetic groups and carriers - Thiamine; thiamine-phosphate pyrophosphorylase complement(977031..977636) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905335 YP_002344439.1 CDS thiH NC_002163.1 977626 978771 R in Escherichia coli this enzyme functions in thiamine biosynthesis along with thiFSGI and iscS; with ThiFSG catalyzes the formation of thiazole phosphate from tyrosine, cysteine and 1-deoxy-D-xylulose-5-phosphate; forms a complex with ThiG; contains an iron-sulfur center; thiamine biosynthesis protein ThiH complement(977626..978771) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905336 YP_002344440.1 CDS thiG NC_002163.1 978774 979550 R functions in thiamine (vitamin B1) biosynthesis; in Bacillus subtilis this enzyme catalyzes the formation of thiazole from dehydroxyglycine and 1-deoxy-D-xylulose-5-phosphate and ThiS-thiocarboxylate; thiazole synthase complement(978774..979550) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905337 YP_002344441.1 CDS moeB NC_002163.1 979553 980356 R catalyzes the adenylation of ThiS which is involved in the formation of 5-methyl-4-(beta-hydroxyethyl)thiazole phosphate; thiamine biosynthesis protein ThiF complement(979553..980356) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905338 YP_002344442.1 CDS thiS NC_002163.1 980353 980544 R Original (2000) note: Cj1047c, unknown, len: 63 aa; similar to hypothetical proteins e.g. YC40_ODOSI (73 aa),fasta scores; opt: 131 z-score: 200.4 E(): 0.00072, 37.1% identity in 62 aa overlap. No Hp match; Updated (2006) 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, prosthetic groups and carriers - Thiamine; PMID:15489164, PMID:15362849; thiamine biosynthesis protein complement(980353..980544) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905339 YP_002344443.1 CDS dapE NC_002163.1 980554 981651 R dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE), catalyzes the hydrolysis of N-succinyl-L,Ldiaminopimelate L,L-SDAP to L,L-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.; succinyl-diaminopimelate desuccinylase complement(980554..981651) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905340 YP_002344444.1 CDS Cj1049c NC_002163.1 981655 982254 R Original (2000) note: Cj1049c, probable integral membrane protein, len: 199 aa; similar to hypothetical membrane proteins belonging to the UPF0056 (MARC) family e.g. YVBG_BACSU (211 aa), fasta scores; opt: 173 z-score: 220.6 E(): 5.4e-05, 32.8% identity in 189 aa overlap. No Hp match; Updated (2006) note: Six probable transmembrane helices predicted by TMHMM2.0. Also, 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, so kept in product function. Functional classification - Transport/binding proteins - Other; LysE family transporter protein complement(981655..982254) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905341 YP_002344445.1 CDS npdA NC_002163.1 982247 982948 R Original (2000) note: Cj1050c, possible transferase, len: 233 aa; similar to hypothetical proteins and to TR:G2996605 (EMBL:U89687) nicotinic acid mononucleotide:5,6-dimethylbenzimidazole (DMB) phosphoribosyltransferase (cobB) gene (237 aa), fasta scores; opt: 486 z-score: 586.6 E(): 2.2e-25, 37.7% identity in 207 aa overlap. 42.4% identity to HP1259; Updated (2006) note: Pfam domain PF02146 Sir2 family identified within CDS. These sequences represent the Sir2 family of NAD+-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; PMID:10811920, PMID:15019790; NAD-dependent deacetylase complement(982247..982948) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905342 YP_002344446.1 CDS cjeI NC_002163.1 982991 987010 R Original (2000) note: Cj1051c, probable restriction modification enzyme, len: 1339 aa; similar in N-terminal 70% to TR:O85299 (EMBL:AF060542) Haemophilus influenzae biogroup aegyptius HaeIV restriction/modification system (953 aa), fasta scores; opt: 1818 z-score: 1949.8 E(): 0 42.7% identity in 976 aa overlap, and in extreme C-terminus to e.g. T1SA_ECOLI type I restriction enzyme ECOAI specificity protein (589 aa), fasta scores; opt: 393 z-score: 422.5 E(): 3.1e-16, 40.4% identity in 178 aa overlap. No Hp ortholog. Contains PS00092 N-6 Adenine-specific DNA methylases signature; Updated (2006) note: Pfam domains PF01420 x2 Type I restriction modification DNA specificity domain was identified within CDS. Prosite domain PS00290 IG_MHC,Immunoglobulins 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, restriction/modification, recombination and repair; PMID:2642743, PMID:12879741, PMID:15699185; restriction modification enzyme complement(982991..987010) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905343 YP_002344447.1 CDS mutS NC_002163.1 987019 989229 R MutS2; MutS-II; involved in blocking homologous and homeologous recombination; has ATPase activity stimulated by recombination intermediates; inhibits DNA strand exchange; recombination and DNA strand exchange inhibitor protein complement(987019..989229) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905344 YP_002344448.1 CDS Cj1053c NC_002163.1 989219 989569 R Original (2000) note: Cj1053c, possible integral membrane protein, len: 116 aa; 25.4% identity to HP0622; Updated (2006) note: Two probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; integral membrane protein complement(989219..989569) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905345 YP_002344449.1 CDS murC NC_002163.1 989562 990860 R Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis; UDP-N-acetylmuramate--L-alanine ligase complement(989562..990860) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905346 YP_002344450.1 CDS Cj1055c NC_002163.1 990924 992897 R Original (2000) note: Cj1055c, probable integral membrane protein, len: 657 aa; weakly similar to hypothetical proteins, e.g. YQGS_BACSU (638 aa), fasta scores; opt: 197 z-score: 215.2 E(): 0.00011, 22.1% identity in 602 aa overlap. 24.3% identity to HP0578. Contains PS00044 Bacterial regulatory proteins, lysR family signature, though this may be spurious; Updated (2006) 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, so kept in product function. Functional classification - Transport/binding proteins - Other; sulfatase family protein complement(990924..992897) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905347 YP_002344451.1 CDS Cj1056c NC_002163.1 992909 993685 R Original (2000) note: Cj1056c, unknown, len: 258 aa; similar to hypothetical proteins e.g. TR:O59829 (EMBL:AL023590) Schizosaccharomyces pombe nitrilase SPCC965.09 (272 aa), fasta scores; opt: 175 z-score: 224.3 E(): 3.4e-05, 25.1% identity in 187 aa overlap. 38.8% identity to HP1481; Updated (2006) note: Prosite domain PS50263 CN_HYDROLASE, Carbon-nitrogen hydrolase domain,Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase identified within CDS. Product modified to more specific family member due to motif match. No specific characterisation yet, so kept within product function. Functional classification - Misc; carbon-nitrogen hydrolase family protein complement(992909..993685) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905348 YP_002344452.1 CDS Cj1057c NC_002163.1 993678 993851 R Original (2000) note: Cj1057c, probable coiled-coil protein, len: 57 aa; 31.5% identity to HP1482. Contains coiled-coil prediction for entire length. Functional classification - Conserved hypothetical proteins; coiled-coil protein complement(993678..993851) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905349 YP_002344453.1 CDS guaB NC_002163.1 993848 995305 R catalyzes the synthesis of xanthosine monophosphate by the NAD+ dependent oxidation of inosine monophosphate; inosine 5'-monophosphate dehydrogenase complement(993848..995305) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905350 YP_002344454.1 CDS gatA NC_002163.1 995315 996676 R allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; aspartyl/glutamyl-tRNA amidotransferase subunit A complement(995315..996676) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905351 YP_002344455.1 CDS Cj1060c NC_002163.1 996673 996783 R Original (2000) note: Cj1060c, small hydrophobic protein, len: 36 aa. No Hp match; Updated (2006) note: One probable transmembrane helix predicted for TMHMM2.0. Also, one signal peptide predicted by SignalP 2.0 HMM. Product function modified to more specific family member. kept within product function. Functional classification - Membranes,lipoproteins and porins; hypothetical protein complement(996673..996783) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905352 YP_002344456.1 CDS ileS NC_002163.1 996777 999530 R IleRS; catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile); since isoleucine and other amino acids such as valine are similar, there are additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile); there are two active sites, one for aminoacylation and one for editing; class-I aminoacyl-tRNA synthetase family type 1 subfamily; some organisms carry two different copies of this enzyme; isoleucyl-tRNA synthetase complement(996777..999530) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905353 YP_002344457.1 CDS Cj1062 NC_002163.1 999629 1000717 D Original (2000) note: Cj1062, unknown, len: 362 aa; C-terminus is similar to hypothetical proteins e.g. YGAD_ENTAG (164 aa), fasta scores; opt: 326 z-score: 399.0 E(): 6.3e-15, 39.9% identity in 153 aa overlap. 33.5% identity in C-terminus to HP0952; Updated (2006) note: Pfam domain PF02464 Competence-damaged protein (CinA) identified within CDS. Product modified to more specific family member based on motif match. Specific characterisation not yet carried out, so kept within product function. Literature search identified paper (PMID:11895937), giving further clues to product function. Functional classification -Pathogenicity; PMID:11895937; CinA-like protein 999629..1000717 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905354 YP_002344458.1 CDS Cj1063 NC_002163.1 1000729 1001154 D Original (2000) note: Cj1063, possible acetyltransferase, len: 141 aa; very weak similarity to PHNO_ECOLI PHNO protein (involved in alkylphosphonate uptake) (144 aa), fasta scores; opt: 135 z-score: 184.7 E(): 0.0054, 26.8% identity in 138 aa overlap. No Hp match. Contains Pfam match to entry PF00583 Acetyltransf,Acetyltransferase (GNAT) family; Updated (2006) note: Specific characterisation with acceptable identity score has not been carried out yet, so was kept within product function. Functional classification - Misc; acetyltransferase 1000729..1001154 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905355 YP_002344459.1 CDS rdxA NC_002163.1 1001837 1002442 D Original (2000) note: Cj1066, rdxA, probable nitroreductase, len: 201 aa; similar to TR:O30585 (EMBL:AF012552) H. pylori NADPH-linked flavin nitroreductase RDXA (=HP0954) (210 aa), fasta scores; opt: 261 z-score: 325.6 E(): 7.8e-11, 29.1% identity in 199 aa overlap. 28.3% identity to HP0954. Also similar to upstream pseudogene Cj1064. Contains Pfam match to entry PF00881 Nitroreductase, Nitroreductase family; Updated (2006) note: Some characterisation in Helicobacter pylori. Appropriate motifs present. not added to product function. Functional classification -Misc; nitroreductase 1001837..1002442 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905357 YP_002344460.1 CDS pgsA NC_002163.1 1002567 1003103 D Original (2000) note: Cj1067, pgsA, probable CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, len: 201 aa; similar to many e.g. PGSA_ECOLI CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (EC 2.7.8.5) (181 aa), fasta scores; opt: 320 z-score: 405.9 E(): 2.6e-15, 35.8% identity in 176 aa overlap. 43.9% identity to HP1016. Contains PS00379 CDP-alcohol phosphatidyltransferases signature, and Pfam match to entry PF01066 CDP-OH_P_transf, CDP-alcohol phosphatidyltransferase; Updated (2006) note: Four probable transmembrane helices predicted by TMHMM2.0. Characterised in Escherichia coli with acceptable identity score, so not added to product function. Functional classification - Synthesis and modification of macromolecules - Phospholipids; PMID:6267013, PMID:9853401; CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase 1002567..1003103 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905358 YP_002344461.1 CDS Cj1068 NC_002163.1 1003100 1004206 D Original (2000) note: Cj1068, probable integral membrane protein, len: 368 aa; similar to hypothetical proteins e.g. YAEL_ECOLI (450 aa), fasta scores; opt: 341 z-score: 399.4 E(): 6e-15, 29.0% identity in 445 aa overlap. 39.6% identity to HP0258. Contains PS00142 Neutral zinc metallopeptidases, zinc-binding region signature, and Pfam match to entry PF00595 PDZ, PDZ domain (Also known as DHR or GLGF); Updated (2006) note: Pfam domain PF02163 Peptidase family M50 identified within CDS. Also, 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,peptides and glycopeptides; peptidase M50 family protein 1003100..1004206 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905359 YP_002344462.1 CDS Cj1069 NC_002163.1 1004199 1005065 D Original (2000) note: Cj1069, unknown, len: 288 aa; similar to hypothetical proteins e.g. YB19_HAEIN HI1119 (292 aa), fasta scores; opt: 428 z-score: 534.0 E(): 1.9e-22, 34.1% identity in 290 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF04393 Protein of unknown function (DUF535) identified within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins; hypothetical protein 1004199..1005065 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905360 YP_002344463.1 CDS rpsF NC_002163.1 1005152 1005529 D binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21; 30S ribosomal protein S6 1005152..1005529 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905361 YP_002344464.1 CDS ssb NC_002163.1 1005538 1006089 D binds to single stranded DNA and may facilitate the binding and interaction of other proteins to DNA; single-stranded DNA-binding protein 1005538..1006089 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905362 YP_002344465.1 CDS rpsR NC_002163.1 1006100 1006360 D binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit; 30S ribosomal protein S18 1006100..1006360 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905363 YP_002344466.1 CDS lon NC_002163.1 1006421 1008796 R Original (2000) note: Cj1073c, lon, ATP-dependent protease La, len: 791 aa; 99.7% identical to LON_CAMJE ATP-dependent protease La (EC 3.4.21.53) (791 aa), and similar to many e.g. LON_ECOLI (784 aa), fasta scores; opt: 1394 z-score: 1373.0 E(): 0, 39.9% identity in 782 aa overlap. 55.6% identity to HP1379. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS01046 ATP-dependent serine proteases, lon family, serine active site, and Pfam match to entry PF00004 AAA, ATPases associated with various cellular activities; Updated (2006) note: Characterised in Campylobacter jejuni, so not added to product function. Functional classification - Degradation of macromolecules - Proteins, peptides and glycopeptides; PMID:9742705; ATP-dependent protease La complement(1006421..1008796) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905364 YP_002344467.1 CDS Cj1074c NC_002163.1 1008813 1009460 R Original (2000) note: Cj1074c, probable lipoprotein, len: 215 aa; identical to partial TR:O69299 (EMBL:Y17166) C. jejuni (called comL), 34.1% identity to HP1378 (called comL, on basis of weak match to N. gonorrhoeae comL). 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, lipoproteins and porins; lipoprotein complement(1008813..1009460) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905365 YP_002344468.1 CDS Cj1075 NC_002163.1 1009621 1010010 D binds to flagellin and appears to stabilize flagellin during flagella assembly; flagellar assembly protein FliW 1009621..1010010 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905366 YP_002344469.1 CDS proC NC_002163.1 1010010 1010741 D catalyzes the formation of L-proline from pyrroline-5-carboxylate; pyrroline-5-carboxylate reductase 1010010..1010741 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905367 YP_002344470.1 CDS ctsT NC_002163.1 1010738 1011040 D Original (2000) note: Cj1077, probable periplasmic protein, len: 100 aa; no Hp match. Contains probable N-terminal signal sequence; Updated (2006) note: Some characterisation work carried out within Campylobacter jejuni. Product unchanged, but gene name added. Functional classification - Miscellaneous periplasmic proteins; PMID:12949093; periplasmic protein 1010738..1011040 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905368 YP_002344471.1 CDS Cj1078 NC_002163.1 1011037 1011699 D Original (2000) note: Cj1078, probable periplasmic protein, len: 220 aa; no Hp match. Contains probable N-terminal signal sequence and PS00572 Glycosyl hydrolases family 1 active site; Updated (2006) note: Some research carried out within Campylobacter jejuni. Product unchanged. Functional classification - Miscellaneous periplasmic proteins; PMID:12949093; periplasmic protein 1011037..1011699 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905369 YP_002344472.1 CDS Cj1079 NC_002163.1 1011696 1012148 D Original (2000) note: Cj1079, probable periplasmic protein, len: 150 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein 1011696..1012148 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905370 YP_002344473.1 CDS hemD NC_002163.1 1012145 1012774 R catalyzes the formation of uroporphyrinogen-III from hydroxymethylbilane; functions in tetrapyrrole and heme biosynthesis; uroporphyrinogen-III synthase complement(1012145..1012774) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905371 YP_002344474.1 CDS thiE NC_002163.1 1012752 1013384 R Original (2000) note: Cj1081c, thiE, probale thiamin-phosphate pyrophosphorylase, len: 210 aa; similar to many e.g. THIE_BACSU thiamin-phosphate pyrophosphorylase (EC 2.5.1.3) (222 aa), fasta scores; opt: 342 z-score: 426.6 E(): 1.8e-16, 31.6% identity in 206 aa overlap. 38.9% identity to HP0843. Also similar to Cj1043c (29.5% identity in 190 aa overlap); Updated (2006) note: Pfam domain PF02581 Thiamine monophosphate synthase/TENI 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, prosthetic groups and carriers - Thiamine; PMID:10350464; thiamin-phosphate pyrophosphorylase complement(1012752..1013384) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905372 YP_002344475.1 CDS thiD NC_002163.1 1013374 1014186 R Original (2000) note: Cj1082c, thiD, probable phosphomethylpyrimidine kinase, len: 270 aa; similar to many e.g. THID_ECOLI phosphomethylpyrimidine kinase (EC 2.7.4.7) (266 aa), fasta scores; opt: 582 z-score: 703.6 E(): 6.8e-32, 41.0% identity in 261 aa overlap. 43.4% identity to HP0844; Updated (2006) note: Characterised in Escherichia coli with acceptable identity score, so not added to product function. Functional classification -Biosynthesis of cofactors, prosthetic groups and carriers - Thiamine; PMID:10075431; phosphomethylpyrimidine kinase complement(1013374..1014186) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905373 YP_002344476.1 CDS Cj1083c NC_002163.1 1014183 1014869 R Original (2000) note: Cj1083c, possible nuclease,len: 228 aa; some similarity with predicted proteins showing similarity to endonucleases e.g. END3_RICPR endonuclease III (EC 4.2.99.18) (212 aa), fasta scores; opt: 147 z-score: 181.9 E(): 0.0078, 25.7% identity in 152 aa overlap. 43.0% identity to HP0602 (annotated as endonuclease III). No detectable similarity to C. jejuni endonuclease III (Cj0595c, equivalent to HP0585); Updated (2006) 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,restriction/modification, recombination and repair; nuclease complement(1014183..1014869) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905374 YP_002344477.1 CDS Cj1084c NC_002163.1 1014866 1015627 R Original (2000) note: Cj1084c, possible ATP/GTP-binding protein, len: 253 aa; similar to part of hypothetical proteins from Synechocystis TR:Q55502 (EMBL:D64006) (436 aa), fasta scores; opt: 586 z-score: 675.2 E(): 2.6e-30, 42.4% identity in 236 aa overlap, and Aquifex aeolicus TR:O66668 (EMBL:AE000684) AQ_336 (196 aa), fasta scores; opt: 383 z-score: 449.2 E(): 1e-17,40.4% identity in 136 aa overlap. No Hp match. Contains PS00017 ATP/GTP-binding site motif A (P-loop); Updated (2006) note: Pfam domain PF05673 Protein of unknown function (DUF815) identified within CDS. No specific characterisation has been carried out yet. kept within product function. Functional classification - Conserved hypothetical proteins; ATP/GTP-binding protein complement(1014866..1015627) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905375 YP_002344478.1 CDS mfd NC_002163.1 1015629 1018565 R Original (2000) note: Cj1085c, mfd, probable transcription-repair coupling factor, len: 978 aa; similar to many e.g. MFD_ECOLI transcription-repair coupling factor (1148 aa), fasta scores; opt: 1474 z-score: 1608.2 E(): 0, 31.5% identity in 967 aa overlap. 48.3% identity to HP1541. Contains PS00017 ATP/GTP-binding site motif A (P-loop), and Pfam match to entry PF00271 helicase_C,Helicases conserved C-terminal domain; Updated (2006) note: Pfam domains PF03461 TRCF domain, PF00270 DEAD/DEAH box helicase and PF02559 CarD-like/TRCF 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,restriction/modification, recombination and repair; PMID:16511235, PMID:12658334, PMID:12086674; transcription-repair coupling factor complement(1015629..1018565) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905376 YP_002344479.1 CDS Cj1086c NC_002163.1 1018565 1018960 R Original (2000) note: Cj1086c, unknown, len: 131 aa; some similarity to hypothetical proteins e.g. TR:O51261 (EMBL:AE001134) Borrelia burgdorferi BB0245 (184 aa), fasta scores; opt: 197 z-score: 255.1 E(): 6.6e-07,30.0% identity in 110 aa overlap. 39.8% identity to HP1542; Updated (2006) note: Pfam domain PF04519 Protein of unknown function, DUF583 are identified within CDS. Prosite domain PS00430 TONB_DEPENDENT_REC_1,TonB-dependent receptor proteins signature 1 was also identified. Functional classification - Conserved hypothetical proteins; hypothetical protein complement(1018565..1018960) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905377 YP_002344480.1 CDS Cj1087c NC_002163.1 1018897 1019799 R Original (2000) note: Cj1087c, possible periplasmic protein, len: 300 aa; similar to TR:Q57503 (EMBL:U39068) Vibrio cholerae ToxR activated gene (302 aa), fasta scores; opt: 575 z-score: 642.1 E(): 1.8e-28, 34.4% identity in 305 aa overlap. Also contains a segment of similarity to e.g. LSTP_STASI lysostaphin precursor (493 aa), fasta scores; opt: 262 z-score: 294.5 E(): 4.2e-09,28.8% identity in 208 aa overlap. 36.9% identity to HP1543. Also similar to Cj1215 (40.6% identity in 133 aa overlap), and Cj1235 (40.7% identity in 123 aa overlap). Contains possible N-terminal signal sequence; Updated (2006) 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,peptides and glycopeptides; peptidase complement(1018897..1019799) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905378 YP_002344481.1 CDS folC NC_002163.1 1019786 1020970 R Original (2000) note: Cj1088c, folC, probable folylpolyglutamate synthase/dihydrofolate synthase, len: 394 aa; similar to many e.g. FOLC_ECOLI folylpolyglutamate synthase (EC 6.3.2.17) / dihydrofolate synthase (EC 6.3.2.12) (422 aa), fasta sores; opt: 315 z-score: 360.4 E(): 8.9e-13, 30.7% identity in 313 aa overlap. 42.7% identity to HP1545. Contains Pfam match to entry PF01225 FPGS, Folylpolyglutamate synthase; Updated (2006) note: Characterised in Escherichia coli with marginal identity score. Appropriate motifs present. not added to product function. Functional classification - Biosynthesis of cofactors,prosthetic groups and carriers - Heme; PMID:3040739, PMID:1939056; folylpolyglutamate synthase/dihydrofolate synthase complement(1019786..1020970) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905379 YP_002344482.1 CDS Cj1089c NC_002163.1 1020936 1022333 R Original (2000) note: Cj1089c, unknown, len: 65 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein complement(1020936..1022333) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905380 YP_002344483.1 CDS Cj1090c NC_002163.1 1022317 1022829 R Original (2000) note: Cj1090c, probable lipoprotein, len: 170 aa; 26.5% identity to HP1546. Contains N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes,lipoproteins and porins; lipoprotein complement(1022317..1022829) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905381 YP_002344484.1 CDS leuS NC_002163.1 1022826 1025255 R leucine--tRNA ligase; LeuRS; class-I aminoacyl-tRNA synthetase; charges leucine by linking carboxyl group to alpha-phosphate of ATP and then transfers aminoacyl-adenylate to its tRNA; due to the large number of codons that tRNA(Leu) recognizes, the leucyl-tRNA synthetase does not recognize the anticodon loop of the tRNA, but instead recognition is dependent on a conserved discriminator base A37 and a long arm; an editing domain hydrolyzes misformed products; in Methanothermobacter thermautotrophicus this enzyme associates with prolyl-tRNA synthetase; leucyl-tRNA synthetase complement(1022826..1025255) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905382 YP_002344485.1 CDS secF NC_002163.1 1025265 1026236 R forms a complex with SecD and YajC; SecDFyajC stimulates the proton motive force-driven protein translocation; 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; in some organisms, such as Bacillus subtilis, SecD is fused to SecF; preprotein translocase subunit SecF complement(1025265..1026236) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905383 YP_002344486.1 CDS secD NC_002163.1 1026236 1027816 R part of the preprotein secretory system; when complexed with proteins SecF and YajC, SecDFyajC stimulates the proton motive force-driven protein translocation, and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane; preprotein translocase subunit SecD complement(1026236..1027816) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905384 YP_002344487.1 CDS yajC NC_002163.1 1027809 1028081 R member of preprotein translocase; forms a heterotrimer with SecD and SecF; links the SecD/SecF/YajC/YidC complex with the SecY/SecE/SecG complex; preprotein translocase subunit YajC complement(1027809..1028081) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905385 YP_002344488.1 CDS Cj1095 NC_002163.1 1028054 1029379 D Transfers the fatty acyl group on membrane lipoproteins; apolipoprotein N-acyltransferase 1028054..1029379 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905386 YP_002344489.1 CDS metK NC_002163.1 1029616 1030812 R catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase; S-adenosylmethionine synthetase complement(1029616..1030812) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905387 YP_002344490.1 CDS Cj1097 NC_002163.1 1030953 1032176 D involved in the import of serine and threonine coupled with the import of sodium; serine/threonine transporter SstT 1030953..1032176 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905388 YP_002344491.1 CDS pyrB NC_002163.1 1032186 1033073 D catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis; aspartate carbamoyltransferase 1032186..1033073 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905389 YP_002344492.1 CDS Cj1099 NC_002163.1 1033077 1034798 D Original (2000) note: Cj1099, probable peptidase,len: 573 aa; similar to many members of the peptidase family M3 (zinc metalloprotease) e.g. PEPF_LACLA oligoendopeptidase F (601 aa), fasta scores; opt: 603 z-score: 673.0 E(): 3.4e-30, 25.9% identity in 595 aa overlap. 53.5% identity to HP0470. Contains PS00142 Neutral zinc metallopeptidases, zinc-binding region signature; Updated (2006) 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, peptides and glycopeptides; peptidase 1033077..1034798 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905390 YP_002344493.1 CDS Cj1100 NC_002163.1 1034792 1035229 D Original (2000) note: Cj1100, unknown, len: 145 aa; 34.7% identity to HP0469. Functional classification -Conserved hypothetical proteins; hypothetical protein 1034792..1035229 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905391 YP_002344494.1 CDS Cj1101 NC_002163.1 1035226 1037301 D Original (2000) note: Cj1101, probable ATP-dependent DNA helicase, len: 691 aa; similar to many e.g REP_ECOLI ATP-dependent DNA helicase REP (EC 3.6.1.-) (673 aa), fasta scores; opt: 977 z-score: 1067.3 E(): 0,36.9% identity in 640 aa overlap, and UVRD_ECOLI DNA helicase II (EC 3.6.1.-) (720 aa), fasta scores; opt: 1129 z-score: 1232.6 E(): 0, 35.2% identity in 714 aa overlap. 43.7% identity to HP1478. Contains PS00017 ATP/GTP-binding site motif A (P-loop), and Pfam match to entry PF00580 UvrD-helicase, UvrD/REP helicase; Updated (2006) note: Similar to more than one helicase with acceptable identity scores. not added to product function. Functional classification - DNA replication, restriction/modification, recombination and repair; PMID:9288744, PMID:8419285; ATP-dependent DNA helicase 1035226..1037301 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905392 YP_002344495.1 CDS truB NC_002163.1 1037298 1038116 D catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs; tRNA pseudouridine synthase B 1037298..1038116 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905393 YP_002344496.1 CDS csrA NC_002163.1 1038110 1038337 D Original (2000) note: Cj1103, csrA, probable carbon storage regulator homolog, len: 75 aa; similar to many e.g. CSRA_ECOLI carbon storage regulator (61 aa), fasta scores; opt: 133 z-score: 202.6 E(): 0.00055, 33.3% identity in 54 aa overlap. 46.7% identity to HP1442; Updated (2006) 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; PMID:9211896, PMID:8393005; carbon storage regulator 1038110..1038337 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905394 YP_002344497.1 CDS Cj1104 NC_002163.1 1038334 1039101 D catalyzes the phosphorylation of 4-diphosphocytidyl-2-C-methyl-D-erythritol in the nonmevalonate pathway of isoprenoid biosynthesis; 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase 1038334..1039101 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905395 YP_002344498.1 CDS smpB NC_002163.1 1039098 1039550 D binds to ssrA RNA (tmRNA) and is required for its successful binding to ribosomes; also appears to function in the trans-translation step by promoting accommodation of tmRNA into the ribosomal A site; SmpB protects the tmRNA from RNase R degradation in Caulobacter crescentus; both the tmRNA and SmpB are regulated in cell cycle-dependent manner; functions in release of stalled ribosomes from damaged mRNAs and targeting proteins for degradation; SsrA-binding protein 1039098..1039550 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905396 YP_002344499.1 CDS Cj1106 NC_002163.1 1039561 1040163 D Original (2000) note: Cj1106, possible periplasmic thioredoxin, len: 200 aa; similar to active site region of thioredoxins e.g. THIO_BACSU thioredoxin (103 aa), fasta scores; opt: 112 z-score: 150.6 E(): 0.43, 37.7% identity in 69 aa overlap. Contains probable N-terminal signal sequence. No Hp match. Also similar to Cj1207c (29.4% identity in 201 aa overlap); Updated (2006) note: No specific characterisation with acceptable identity score has been carried out yet,so kept in product function. Functional classification - Energy metabolism - Electron transport; periplasmic thioredoxin 1039561..1040163 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905397 YP_002344500.1 CDS clpS NC_002163.1 1040163 1040453 D Original (2000) note: Cj1107, unknown, len: 96 aa; similar to hypothetical proteins e.g. YLJA_ECOLI (also upstream of clpA) (106 aa), fasta scores; opt: 255 z-score: 354.9 E(): 1.8e-12, 44.0% identity in 84 aa overlap. 38.2% identity to HP0032; Updated (2006) note: Pfam domain PF02617 ATP-dependent Clp protease adaptor protein Clps,identified 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,chaperonins, heat shock; PMID:12426582, PMID:12235156, PMID:9278503; ATP-dependent Clp protease adaptor protein 1040163..1040453 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905398 YP_002344501.1 CDS clpA NC_002163.1 1040450 1042579 D Original (2000) note: Cj1108, clpA, probable ATP-dependent CLP protease ATP-binding subunit, len: CLPA_ECOLI ATP-dependent CLP protease ATP-binding subunit (758 aa), fasta scores; opt: 1730 z-score: 1803.9 E(): 0,41.2% identity in 748 aa overlap. 41.7% identity to HP0033. Contains 2x PS00017 ATP/GTP-binding site motif A (P-loop), PS00871 Chaperonins clpA/B signature 2, and Pfam match to entry PF00495 clpA_B, Chaperonins clpA /B. Also similar to clpB Cj0509c (36.5% identity in 835 aa overlap); Updated (2006) note: Pfam domains PF02861 Clp amino terminal domain and PF00004 ATPase family associated with various cellular activities (AAA) 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, chaperonins, heat shock; PMID:11344323, PMID:11274130; ATP-dependent Clp protease ATP-binding subunit 1040450..1042579 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905399 YP_002344502.1 CDS aat NC_002163.1 1042554 1043201 D leucyltransferase; phenylalanyltransferse; functions in the N-end rule pathway; transfers Leu, Phe, Met, from aminoacyl-tRNAs to N-terminal of proteins with Arg or Lys; leucyl/phenylalanyl-tRNA--protein transferase 1042554..1043201 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905400 YP_002344503.1 CDS Cj1110c NC_002163.1 1043223 1044512 R Original (2000) note: Cj1110c, probable MCP-type signal transduction protein, len: 429 aa; similar to TR:O68016 (EMBL:AF010180) Agrobacterium tumefaciens plasmid pTiC58 MCPA (579 aa), fasta scores; opt: 749 z-score: 785.2 E(): 0, 34.5% identity in 496 aa overlap,and to many other proteins with MCP domains e.g. PILJ_PSEAE PILJ protein (682 aa), fasta scores; opt: 379 z-score: 399.1 E(): 6.3e-15, 26.9% identity in 443 aa overlap, and HLYB_VIBCH hemolysin secretion protein precursor (548 aa), fasta scores; opt: 357 z-score: 377.6 E(): 9.8e-14, 37.0% identity in 173 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00015 MCPsignal,Methyl-accepting chemotaxis protein (MCP) signaling domain; Updated (2006) note: Specific characterisation with acceptable identity score has not been carried out yet, so kept in product function. Functional classification - Signal transduction; MCP-type signal transduction protein complement(1043223..1044512) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905401 YP_002344504.1 CDS Cj1111c NC_002163.1 1044593 1045219 R Original (2000) note: Cj1111c, probable integral membrane protein, len: 208 aa; similar to many hypothetical membrane proteoins, e.g. YVBG_BACSU (211 aa),fasta scores; opt: 324 z-score: 391.8 E(): 1.6e-14, 28.8% identity in 198 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF01914 MarC family integral membrane protein identified within CDS. Also, 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, so kept within product function. Functional classification - Membranes,lipoproteins and porins; MarC family integral membrane protein complement(1044593..1045219) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905402 YP_002344505.1 CDS Cj1112c NC_002163.1 1045234 1045593 R this stereospecific enzymes reduces the R isomer of methionine sulfoxide while MsrA reduces the S form; a fusion protein of this enzyme with MsrA and thioredoxin provides protection against oxidative stress in Neisseria gonorrhoeae; methionine sulfoxide reductase B complement(1045234..1045593) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905403 YP_002344506.1 CDS Cj1113 NC_002163.1 1045683 1046480 D Original (2000) note: Cj1113, unknown, len: 265 aa; similar to a hypothetical protein from Haemophilus Y077_HAEIN HI0077 (288 aa), fasta scores; opt: 441 z-score: 521.9 E(): 9.1e-22, 34.5% identity in 275 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF04305 Protein of unknown function (DUF455) identified within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins; hypothetical protein 1045683..1046480 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905404 YP_002344507.1 CDS pssA NC_002163.1 1046471 1047199 R Original (2000) note: Cj1114c, pssA, probable CDP-diacylglycerol--serine O-phosphatidyltransferase, len: 242 aa; similar to the characterised PSS_HELPY CDP-diacylglycerol--serine O-phosphatidyltransferase (EC 2.7.8.8) (HP1071) (237 aa), fasta scores; opt: 754 z-score: 933.2 E(): 0, 50.9% identity in 226 aa overlap,and to others e.g. PSS_YEAST (275 aa), fasta scores; opt: 287 z-score: 360.8 E(): 8.5e-13, 38.2% identity in 165 aa overlap. Contains PS00379 CDP-alcohol phosphatidyltransferases signature; Updated (2006) note: Characterised within Helicobacter pylori with acceptable identity score. not added to product function. Functional classification - Synthesis and modification of macromolecules - Phospholipids; PMID:9244252, PMID:9260935; CDP-diacylglycerol--serine O-phosphatidyltransferase complement(1046471..1047199) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905405 YP_002344508.1 CDS Cj1115c NC_002163.1 1047209 1047826 R Original (2000) note: Cj1115c, probable membrane protein, len: 205 aa; simimlar to hypothetical proteins e.g. TR:Q50967 (EMBL:U34760) Neisseria gonorrhoeae ORF259 (259 aa), fasta scores; opt: 223 z-score: 281.2 E(): 2.3e-08, 24.6% identity in 191 aa overlap. No Hp match; Updated (2006) 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; PMID:361737, PMID:3042771; phosphatidylserine decarboxylase-related protein complement(1047209..1047826) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905406 YP_002344509.1 CDS ftsH NC_002163.1 1047823 1049760 R Original (2000) note: Cj1116c, ftsH, probable membrane bound zinc metallopeptidase, len: 645 aa; similar to many e.g. FTSH_ECOLI cell division protein FTSH (EC 3.4.24.-) (644 aa), fasta scores; opt: 1598 z-score: 1665.6 E(): 0, 43.3% identity in 609 aa overlap. 67.4% identity to HP1069. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00674 AAA-protein family signature,and Pfam match to entry PF00004 AAA, ATPases associated with various cellular activities (AAA); Updated (2006) 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, so not added to product function. Functional classification -Degradation of macromolecules - Proteins, peptides and glycopeptides; PMID:8892813, PMID:12037319, PMID:1925026,PMID:8444796; membrane bound zinc metallopeptidase complement(1047823..1049760) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905407 YP_002344510.1 CDS prmA NC_002163.1 1049764 1050609 R methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype; ribosomal protein L11 methyltransferase complement(1049764..1050609) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905408 YP_002344511.1 CDS cheY NC_002163.1 1050632 1051024 R Original (2000) note: Cj1118c, cheY, chemotaxis regulatory protein, len: 130 aa; identical to CHEY_CAMJE,and highly similar to e.g. CHEY_ECOLI (128 aa), fasta scores; opt: 376 z-score: 468.7 E(): 8.2e-19, 48.3% identity in 120 aa overlap. 82.8% identity to HP1067. Contains Pfam match to entry PF00072 response_reg,Response regulator receiver domain; Updated (2006) note: Characterised within Campylobacter jejuni. not added to product function. Functional classification - Chemotaxis and mobility; PMID:9076738, PMID:11912013; chemotaxis regulatory protein complement(1050632..1051024) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905409 YP_002344512.1 CDS pglG NC_002163.1 1051137 1052030 R Original (2000) note: Cj1119c, wlaM, pglG, probable integral membrane protein, len: 297 aa; 99.3% identical to TR:O86160 (EMBL:Y11648) C. jejuni 81116 wlaM (297 aa). Also contains short section of similarity to TR:Q56633 (EMBL:L25660) Vibrio cholerae accessory colonization factor (ACFB) (626 aa), fasta scores; opt: 165 z-score: 202.6 E(): 0.00055, 34.0% identity in 103 aa overlap. 37.6% identity to HP0158; Updated (2006) 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 (Cj1119c - Cj1130c). Functional classification - Membranes, lipoproteins and porins; PMID:15752194, PMID:16186480, PMID:16618123,PMID:16547029; integral membrane protein complement(1051137..1052030) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905410 YP_002344513.1 CDS pglF NC_002163.1 1052030 1053802 R Original (2000) note: Cj1120c, wlaL, pglF, possible sugar epimerase/dehydratase, len: 590 aa; 99.5% identical to TR:O86159 (EMBL:Y11648) C. jejuni 81116 wlaL (590 aa),and similar to e.g. CAPD_STAAU Staphylococcus aureus capsular polysaccharide biosynthesis CAPD protein (599 aa), fasta scores; opt: 1051 z-score: 1218.6 E(): 0, 38.4% identity in 614 aa overlap, and TR:O69130 (EMBL:AF064070) Burkholderia pseudomallei epimerase/dehydratase WBII (637 aa), fasta scores; opt: 961 z-score: 1113.9 E(): 0, 36.0% identity in 605 aa overlap. No Hp ortholog. Contains probable integral membrane domain at N-terminus; Updated (2006) 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-2,6-dideoxy-alpha-D-xylo-hexos-4-ulose. Identifed as part of Campylobacter jejuni N-linked glycosylation locus (Cj1119c - Cj1130c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:16421095 PMID:15752194, PMID:16186480,PMID:16618123, PMID:16547029, PMID:16286454; UDP-GlcNAc C4,6 dehydratase complement(1052030..1053802) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905411 YP_002344514.1 CDS pglE NC_002163.1 1053804 1054964 R Original (2000) note: Cj1121c, wlaK, pglE, possible aminotransferase, len: 386 aa; 98.7% identical to TR:O86158 (EMBL:Y11648) C. jejuni 81116 wlaK (386 aa), and similar to e.g. TR:O68392 (EMBL:AF036614) Brucella melitensis perosamine synthetase rfbE (367 aa), fasta scores; opt: 621 z-score: 742.5 E(): 0, 31.5% identity in 375 aa overlap, and TR:P72452 (EMBL:Y00459) Streptomyces griseus aminotransferase strS (378 aa), fasta scores; opt: 426 z-score: 510.6 E(): 3.8e-, 32.2% identity in 264 aa overlap. No Hp ortholog. Contains Pfam match to entry PF01041 DegT_DnrJ_EryC1, DegT/DnrJ/EryC1/StrS family; Updated (2006) note: Characterised in Campylobacter jejuni. Product function modified to more specific family member. This protein acts to form 2,4-diacetamido bacillosamine. Identifed as part of Campylobacter jejuni N-linked glycosylation locus (Cj1119c - Cj1130c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:15752194, PMID:16186480, PMID:16618123,PMID:16547029, PMID:16286454, PMID:16690622; UDP-4-keto-6-deoxy-GlcNAc C4 aminotransferase complement(1053804..1054964) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905412 YP_002344515.1 CDS Cj1122c NC_002163.1 1055060 1055713 R Original (2000) note: Cj1122c, wlaJ, possible integral membrane protein, len: 217 aa; 99.5% identical to TR:G4100601 (EMBL:AF001497) C. jejuni 11168 orfE (217 aa). Not present in C. jejuni 81116. No Hp match; Updated (2006) note: Three probable transmembrane helices predicted by TMHMM2.0; integral membrane protein complement(1055060..1055713) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905413 YP_002344516.1 CDS pglD NC_002163.1 1055670 1056257 R Original (2000) note: Cj1123c, wlaI, pglD, possible transferase, len: 195 aa; 98.0% identical to TR:O86157 (EMBL:Y11648) C. jejuni 81116 wlaI (203 aa), and similar to e.g. TR:Q46674 (EMBL:U05248) E. coli polysialic acid gene cluster region 2 neuD (207 aa), fasta scores; opt: 287 z-score: 358.6 E(): 1.1e-12, 28.6% identity in 203 aa overlap, and in the N-terminus to several acetyltransferases, e.g. LPXD_ECOLI UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase (340 aa), fasta scores; opt: 149 z-score: 188.9 E(): 0.0032, 31.7% identity in 82 aa overlap. No hp match. Also similar to Cj1321 (30.2% identity in 179 aa overlap). Contains 2x Pfam match to entry PF00132 hexapep, Bacterial transferase hexapeptide (four repeats); Updated (2006) note: Characterised in Campylobacter jejuni. Product function modified to more specific family member. This protein acts as an acetyltransferase to form 2,4-diacetamido bacillosamine. Identifed as part of Campylobacter jejuni N-linked glycosylation locus (Cj1119c - Cj1130c). Functional classification - Surface polysaccharides, lipopolysaccharides and antigens; PMID:15752194, PMID:16186480, PMID:16618123,PMID:16547029; acetyltransferase complement(1055670..1056257) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905414 YP_002344517.1 CDS pglC NC_002163.1 1056244 1056846 R Original (2000) note: Cj1124c, wlaH, pglC, probable galactosyltransferase, len: 200 aa; 99.0% identical to TR:O86156 (EMBL:Y11648) C. jejuni 81116 wlaH (200 aa),96.5% identical to TR:P71124 (EMBL:X91081) C. hyoilei galactosyltransferase RFBP (200 aa), and similar to e.g. RFBP_SALTY UDP-phosphate galactosephosphotransferase (476 aa), fasta scores; opt: 330 z-score: 406.2 E(): 2.5e-15, 38.0% identity in 200 aa overlap. No Hp match. Contains one possible transmembrane domain; Updated (2006) note: Pfam domain PF02397, Bacterial sugar transferase, 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 (Cj1119c - Cj1130c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:15752194, PMID:16186480, PMID:16618123,PMID:16547029; galactosyltransferase complement(1056244..1056846) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905415 YP_002344518.1 CDS pglA NC_002163.1 1056839 1057969 R Original (2000) note: Cj1125c, wlaG, pglA, probable galactosyltransferase, len: 376 aa; 98.4% identical to TR:O86155 (EMBL:Y11648) C. jejuni 81116 wlaG (376 aa),82.7% identical to TR:P71123 (EMBL:X91081) C. hyoileigalactosyltransferase RFBF (376 aa), and similar to e.g. TR:O87893 (EMBL:U73942) NEISSERIA MENINGITIDIS GLYCOSYLTRANSFERASE PGLA (376 aa), fasta scores; opt: 549 z-score: 651.7 E(): 5.3e-29, 29.5% identity in 387 aa overlap. No Hp match. Contains Pfam match to entry PF00534 Glycos_transf_1; Updated (2006) note: Pfam domain PF00534, Glycosyl transferase group, 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 (Cj1119c - Cj1130c). Functional classification - Surface polysaccharides, lipopolysaccharides and antigens; PMID:15752194, PMID:16186480, PMID:16618123,PMID:16547029; GalNAc transferase complement(1056839..1057969) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905416 YP_002344519.1 CDS pglB NC_002163.1 1057979 1060120 R Original (2000) note: Cj1126c, wlaF, pglB, probable integral membrane protein, possible oligosaccharyl transferase, len: 713 aa; 98.9% identical to TR:O86154 (EMBL:Y11648) C. jejuni 81116 wlaF (713 aa), very weak simlarity to e.g. STT3_HUMAN P46977 oligosaccharyl transferase STT3 subunit homolog (705 aa), blastp scores; E= 6.7e-05, 22% identity in 233 aa overlap and 32% identity in 56 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF02516,Oligosaccharyl transferase STT3 subunit, 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 (Cj1119c - Cj1130c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:15752194, PMID:16186480, PMID:16618123,PMID:16547029, PMID:16356848, PMID:16641107; oligosaccharide transferase to N-glycosylate proteins complement(1057979..1060120) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905417 YP_002344520.1 CDS pglJ NC_002163.1 1060124 1061221 R Original (2000) note: Cj1127c, wlaE, probable glycosyltransferase, len: 365 aa; 98.6% identical to TR:O86153 (EMBL:Y11648) C. jejuni 81116 wlaE (365 aa), and similar to e.g. AMSD_ERWAM amylovoran biosynthesis glycosyl transerase AMSD (351 aa), fasta scores; opt: 250 z-score: 309.4 E(): 6.2e-10, 27.1% identity in 351 aa overlap. No Hp match. Contains Pfam match to entry PF00534 Glycos_transf_1; Updated (2006) 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 (Cj1119c - Cj1130c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:15752194, PMID:16186480, PMID:16618123,PMID:16547029; GalNAc transferase complement(1060124..1061221) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905418 YP_002344521.1 CDS pglI NC_002163.1 1061209 1062138 R Original (2000) note: Cj1128c, wlaD, epsI, probable glycosyltransferase, len: 309 aa; 99.7% identical to TR:O86152 (EMBL:Y11648) C. jejuni 81116 wlaD (309 aa),99.7% identical to TR:O52906 (EMBL:AJ000854) C. jejuni 11168 epsI (309 aa), and similar to e.g. TR:O87182 (EMBL:AB017355) Streptococcus agalactiae N-acetylglucosaminyltransferase CPSH (333 aa), fasta scores; opt: 281 z-score: 324.3 E(): 9.1e-11, 23.5% identity in 281 aa overlap. No Hp match. Contains Pfam match to entry PF00535 Glycos_transf_2; Updated (2006) 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 (Cj1119c - Cj1130c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:15752194, PMID:16186480, PMID:16618123,PMID:16547029; glucosyl transferase complement(1061209..1062138) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905419 YP_002344522.1 CDS pglH NC_002163.1 1062131 1063210 R Original (2000) note: Cj1129c, wlaC, capM, probable glycosyltransferase, len: 359 aa; identical to TR:O52905 (EMBL:AJ000854) C. jejuni 11168 capM (358 aa), 97.2% identical to TR:O86151 (EMBL:Y11648) C. jejuni 81116 wlaC (358 aa), and similar to e.g. AMSD_ERWAM amylovoran biosynthesis glycosyl transerase (351 aa), fasta scores; opt: 360 z-score: 445.6 E(): 1.6e-17, 27.3% identity in 362 aa overlap. No Hp match. Contains Pfam match to entry PF00534 Glycos_transf_1; Updated (2006) note: Characterised in Campylobacter jejuni. Product function modified to more specific family member. This protein acts as the transferase/polymerase of GalNAc(s) to bacillosamine. not added to product function. Identifed as part of Campylobacter jejuni N-linked glycosylation locus (Cj1119c - Cj1130c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:15752194, PMID:16498400, PMID:15184581,PMID:16186480, PMID:16618123, PMID:16547029; GalNAc transferase/polymerase complement(1062131..1063210) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905420 YP_002344523.1 CDS pglK NC_002163.1 1063207 1064901 R Original (2000) note: Cj1130c, wlaB, ABC-type transport protein, len: 564 aa; 98.2% identical to TR:O86150 (EMBL:Y11648) C. jejuni 81116 wlaB (564 aa), and similar to e.g. HLY2_ECOLI hemolysin secretion atp-binding protein (707 aa), fasta scores; opt: 655 z-score: 715.2 E(): 1.5e-32, 29.0% identity in 572 aa overlap. Integral membrane domain in N-term contains Pfam match to entry PF00664 ABC_membrane, ABC transporter transmembrane region, ATP-binding domain in C-term contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00211 ABC transporters family signature, and Pfam match to entry PF00005 ABC_tran, ABC transporters. 38.3% identity to HP1206 (called multidrug resistance protein (hetA)); Updated (2006) 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 (Cj1119c - Cj1130c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:15752194, PMID:16547029, PMID:16498400,PMID:16481326; flippase complement(1063207..1064901) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905421 YP_002344524.1 CDS gne NC_002163.1 1064895 1065881 R Original (2000) note: Cj1131c, galE, probable UDP-glucose 4-epimerase, len: 328 aa; 98.2% identical to TR:O86149 (EMBL:Y11648) C. jejuni 81116 galE (328 aa), and similar to e.g. GALE_STRMU UDP-glucose 4-epimerase (EC 5.1.3.2) (333 aa), fasta scores; opt: 887 z-score: 1056.0 E(): 0, 43.7% identity in 327 aa overlap. 50.0% identity to HP0360; Updated (2006) note: Pfam domain PF01370, NAD dependent epimerase/dehydratase 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/Glc 4-epimerase for the LOS, capsule and N-linked glycan in 11168. Identifed as part of Campylobacter jejuni lipooligosaccharide locus (Cj1131c - Cj1152c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:9720026, PMID:14742567, PMID:10768949,PMID:15509570; UDP-GlcNAc/Glc 4-epimerase complement(1064895..1065881) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905422 YP_002344525.1 CDS Cj1132c NC_002163.1 1065939 1066733 R Original (2000) note: Cj1132c, unknown, len: 264 aa; some similarity to part of DNA polymerases e.g. DPOL_PYRFU DNA polymerase (775 aa), fasta scores; opt: 168 z-score: 197.4 E(): 0.0011, 29.6% identity in 247 aa overlap. Similar in N- and C-termini to sequential Hp CDSs; HP0688 (46.7% identity in 169 aa overlap), and HP0689 (47.4% identity in 95 aa overlap). Contains Pfam match to entry PF00136 DNA_pol_B, DNA polymerase family B; Updated (2006) note: Literature search identified paper giving further clues about product function. Conserved added to product function. Identifed as part of Campylobacter jejuni lipooligosaccharide locus (Cj1131c -Cj1152c). Functional classification - Conserved hypothetical proteins; PMID:15509570; hypothetical protein complement(1065939..1066733) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905423 YP_002344526.1 CDS waaC NC_002163.1 1066799 1067827 D Original (2000) note: Cj1133, waaC, probable lipopolysaccharide heptosyltransferase, len: 342 aa; 98.2% identical to TR:O87585 (EMBL:AF086705) C. jejuni heptosyltransferase WaaC (342 aa), and similar to e.g. RFAC_ECOLI lipopolysaccharide heptosyltransferase-1 (319 aa), fasta scores; opt: 212 z-score: 252.9 E(): 8.6e-07,26.2% identity in 302 aa overlap. 38.5% identity to HP0279. Contains Pfam match to entry PF01075 Heptosyltranf, Heptosyltransferase; Updated (2006) note: Characterised within Campylobacter jejuni. Product function further updated. not added to product function. Identifed as part of Campylobacter jejuni lipooligosaccharide locus (Cj1131c - Cj1152c). Functional classification - Surface polysaccharides, lipopolysaccharides and antigens; PMID:16621820, PMID:9831648, PMID:11689567,PMID:15808749, PMID:11083778, PMID:10660542; heptosyltransferase I 1066799..1067827 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905424 YP_002344527.1 CDS htrB NC_002163.1 1067817 1068704 D acylates the intermediate (KDO)2-lipid IVA to form (KDO)2-(lauroyl)-lipid IVA; essential for survival; plays a role in cell responses to environmental changes; lipid A biosynthesis lauroyl acyltransferase 1067817..1068704 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905425 YP_002344528.1 CDS Cj1135 NC_002163.1 1068701 1070248 D Original (2000) note: Cj1135, probable two-domain glycosyltransferase, len: 515 aa; contains similarities in N- and C-termini to glycosyltransferases e.g. TR:P95373 (EMBL:U58765) Neisseria meningitidis beta 1,4 glucosyltransferase lgtF (252 aa), fatsa scores; opt: 380 z-score: 453.4 E(): 5.9e-18, 30.9% identity in 262 aa overlap, and TR:O85457 Pasteurella multocida glycosyl transferase hyaD (864 aa), fasta scores; opt: 259 z-score: 302.8 E(): 1.4e-09, 28.0% identity in 239 aa overlap. No Hp match. Contains 2x Pfam match to entry PF00535 Glycos_transf_2, Glycosyl transferases; Updated (2006) note: Some characterisation within Neisseria meningitidis,however, 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 (Michel.Gilbert@nrc-cnrc.gc.ca) personal communication. Identifed as part of Campylobacter jejuni lipooligosaccharide locus (Cj1131c - Cj1152c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:11689567, PMID:15808749, PMID:11083778,PMID:10660542; two-domain glucosyltransferase 1068701..1070248 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905426 YP_002344529.1 CDS Cj1136 NC_002163.1 1070252 1071424 D Original (2000) note: Cj1136, probable galactosyltransferase, len: 390 aa; similar to e.g. TR:O07340 (EMBL:X85787) Streptococcus pneumoniae SS-1,4-galactosyltransferase CPS14J (318 aa), fasta scores; opt: 309 z-score: 361.4 E(): 7.8e-13, 29.0% identity in 290 aa overlap. No Hp match. Contains Pfam match to entry PF00535 Glycos_transf_2, Glycosyl transferases; Updated (2006) note: Pfam domain PF00535 Glycosyl transferase identified within CDS. Product function updated based on motif match. No specific characterisation has been carried out yet, so kept within product function. Identifed as part of Campylobacter jejuni lipooligosaccharide locus (Cj1131c - Cj1152c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:11689567, PMID:15808749, PMID:11083778,PMID:10660542, PMID:16594990; glycosyltransferase 1070252..1071424 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905427 YP_002344530.1 CDS Cj1137c NC_002163.1 1071408 1072403 R Original (2000) note: Cj1137c, unknown, len: 331 aa; similar to hypothetcal proteins in polysaccharide biosynthesis operons e.g. TR:O86892 (EMBL:AJ006986) Streptococcus pneumoniae CAPP33FI protein (322 aa), fasta scores; opt: 295 z-score: 346.5 E(): 5.3e-12, 26.5% identity in 294 aa overlap. No Hp match; Updated (2006) 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 (Michel.Gilbert@nrc-cnrc.gc.ca) personal communication. Identifed as part of Campylobacter jejuni lipooligosaccharide locus (Cj1131c - Cj1152c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:11689567, PMID:14742567, PMID:11083778,PMID:10660542; glycosyltransferase complement(1071408..1072403) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905428 YP_002344531.1 CDS Cj1138 NC_002163.1 1072461 1073630 D Original (2000) note: Cj1138, probable galactosyltransferase, len: 389 aa; similar to e.g. TR:O07340 (EMBL:X85787) Streptococcus pneumoniae SS-1,4-galactosyltransferase CPS14J (318 aa), fasta scores; opt: 304 z-score: 361.2 E(): 8e-13, 25.8% identity in 383 aa overlap. No Hp match. Contains Pfam match to entry PF00535 Glycos_transf_2, Glycosyl transferases; Updated (2006) 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 (Cj1131c - Cj1152c). Functional classification - Surface polysaccharides, lipopolysaccharides and antigens; PMID:16594990, PMID:11083778, PMID:10660542; glycosyltransferase 1072461..1073630 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905429 YP_002344532.1 CDS wlaN NC_002163.1 1073619 1074530 R Original (2000) note: Cj1139c, probable galactosyltransferase, len: 303 aa; similar to e.g. TR:O07340 (EMBL:X85787) Streptococcus pneumoniae SS-1,4-galactosyltransferase CPS14J (318 aa), fasta scores; opt: 309 z-score: 362.2 E(): 7.1e-13, 26.1% identity in 249 aa overlap. No Hp match. Contains Pfam match to entry PF00535 Glycos_transf_2, Glycosyl transferases. Contains C(8-9) polymorphic region at aa 111. C(8), the consensus, allows translation of the full length protein. C(9) would cause a premature truncation after a further 20 aa; Updated (2006) note: Characterised within Campylobacter jejuni. Product function modified to more specific family member. not added to product function. This protein carries out the beta-1,3 galactosyltransferase addition of terminal galactose to LOS. Identifed as part of Campylobacter jejuni lipooligosaccharide locus (Cj1131c - Cj1152c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:10931344, PMID:11083778, PMID:10660542; beta-1,3 galactosyltransferase complement(1073619..1074530) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905430 YP_002344533.1 CDS cstIII NC_002163.1 1074585 1075469 D Original (2000) note: Cj1140, unknown, len: 294 aa; similar to H. influenzae hypothetical protein in lipopolysaccharide biosynthesis gene cluster Y352_HAEIN HI0352 (ORF1) (231 aa), fasta scores; opt: 558 z-score: 672.8 E(): 3.5e-30, 41.5% identity in 229 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF06002 Alpha-2,3-sialyltransferase (CST-I) identified within CDS. Characterisation work carried out within Campylobacter jejuni, so product function modified to new family member. not added to product function. This protein transfers sialic acid from cytidine-5'-monophospho-N-acetyl-neuraminic acid (CMP-NeuAc) to LOS. Gilbert (Michel.Gilbert@nrc-cnrc.gc.ca) personal communication. Identifed as part of Campylobacter jejuni lipooligosaccharide locus (Cj1131c - Cj1152c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:11083778, PMID:11689567, PMID:10660542,PMID:14730352, PMID:16620397; alpha-2,3 sialyltransferase 1074585..1075469 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905431 YP_002344534.1 CDS neuB1 NC_002163.1 1075450 1076481 D Original (2000) note: Cj1141, neuB1, probable N-acetylneuraminic acid synthetase, len: 343 aa; highly similar to e.g. TR:Q57265 (EMBL:U40740) N-acetylneuraminic acid synthetase (EC 4.1.3.-) (349 aa), fasta scores; opt: 1327 z-score: 1554.1 E(): 0, 59.0% identity in 344 aa overlap. No Hp ortholog. Also similar to Cj1327 (37.1% identity in 329 aa overlap) and Cj1317 (34.4% identity in 340 aa overlap); Updated (2006) 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 (Cj1131c -Cj1152c). Functional classification - Surface polysaccharides, lipopolysaccharides and antigens; PMID:10712693, PMID:11689567, PMID:10660542,PMID:14742567, PMID:16567003; sialic acid synthase 1075450..1076481 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905432 YP_002344535.1 CDS neuC1 NC_002163.1 1076478 1077593 D Original (2000) note: Cj1142, neuC1, probable N-acetylglucosamine-6-phosphate 2-epimerase/N-acetylglucosamine-6-phosphatase, len: 371 aa; similar to e.g. TR:Q57141 (EMBL:X78068) Neisseria meningitidis N-acetylglucosamine-6-phosphate 2-epimerase (EC 5.1.3.-) / N-acetylglucosamine-6-phosphatase (EC 3.1.3.-) (377 aa),fatsta scores; opt: 1029 z-score: 1162.4 E(): 0, 44.0% identity in 377 aa overlap. No Hp match; Updated (2006) 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 (PMID:15518580). kept within product function. This protein plays a role in sialic acid biosysthesis. Gilbert (Michel.Gilbert@nrc-cnrc.gc.ca) personal communication. Identifed as part of Campylobacter jejuni lipooligosaccharide locus (Cj1131c - Cj1152c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:15518580, PMID:11083778, PMID:11689567,PMID:10688204, PMID:11796612; UDP-N-acetylglucosamine 2-epimerase 1076478..1077593 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905433 YP_002344536.1 CDS neuA1 NC_002163.1 1077590 1079200 D Original (2000) note: Cj1143, neuA1, probable acylneuraminate cytidylyltransferase (CMP-N-acetylneuraminic acid synthetase), len: 536 aa; N-terminus is similar to HP0217 (49.1% identity in 279 aa overlap), C-traminus is similar to NEUA_NEIME acylneuraminate cytidylyltransferase (EC 2.7.7.43) (228 aa), fasta scores; opt: 471 z-score: 550.3 E(): 2.3e-23,39.4% identity in 221 aa overlap, and to Cj1311 (31.6% identity in 215 aa overlap) and Cj1331 (34.7% identity in 219 aa overlap); Updated (2006) note: Pfam domains PF06306 Beta-1,4-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 (Cj1131c - Cj1152c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:15808749, PMID:11083778, PMID:16481326,PMID:12044670, PMID:10660542, PMID:11796612; bifunctional beta-1,4-N-acetylgalactosaminyltransferase/CMP-Neu5Ac synthase 1077590..1079200 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905434 YP_002344537.1 CDS Cj1145c NC_002163.1 1079195 1080041 R Original (2000) note: Cj1144c, unknown, len: 197 aa; no Hp match. Contains C(8-9) polymorphism at aa 15; C(8), the consnsus gives this CDS; C(9) would cause truncation after 4 aa, although a Met at aa 23 would allow translation to re-initiate. C(7) or C(10), although not seen in shotgun, would allow translation from upstream CDS Cj1145c; Original (2000) note: Cj1145c, unknown, len: 105 aa; no Hp match. Contains C(8-9) polymorphism at aa 99; C(8), the consnsus gives this CDS; C(9) would cause truncation after4 aa; C(7) or C(10), although not seen in shotgun, would allow translation into downstream CDS Cj1144c; Updated (2006) 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; hypothetical protein complement(join(1079195..1079743,1079745..1080041)) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905436 YP_002344538.1 CDS waaV NC_002163.1 1080025 1080849 R Original (2000) note: Cj1146c, waaV, possible glucosyltransferase, len: 274 aa; similar to e.g. TR:O87182 (EMBL:AB017355) Streptococcus agalactiae N-acetylglucosaminyltransferase CPSH (333 aa), fasta scores; opt: 339 z-score: 402.4 E(): 4.1e-15, 31.4% identity in 274 aa overlap. No Hp match. Contains Pfam match to entry PF00535 Glycos_transf_2, Glycosyl transferases; Updated (2006) note: Some characterisation within Escherichia coli, however, identity score was marginal. kept within product function. Identifed as part of Campylobacter jejuni lipooligosaccharide locus (Cj1131c - Cj1152c). Functional classification - Surface polysaccharides, lipopolysaccharides and antigens; PMID:9792656; glucosyltransferase complement(1080025..1080849) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905437 YP_002344539.1 CDS waaF NC_002163.1 1080908 1081867 D Original (2000) note: Cj1148, waaF, probable ADP-heptose--LPS heptosyltransferase, len: 319 aa; similar to e.g. TR:Q51063 (EMBL:Z37141) Neisseria gonorrhoeae ADP-heptose:LPS heptosyltransferase II (336 aa), fasta scores; opt: 384 z-score: 447.0 E(): 1.3e-17, 29.7% identity in 333 aa overlap, and RFAF_ECOLI ADP-heptose--LPS heptosyltransferase II (348 aa), fasta scores; opt: 292 z-score: 341.5 E(): 1e-11, 24.1% identity in 348 aa overlap. 37.6% identity to HP1191. Also similar to Cj1133 (24.8% identity in 351 aa overlap). Contains Pfam match to entry PF01075 Heptosyltranf,Heptosyltransferase; Updated (2006) note: Pfam domain now modified to Glycosyltransferase family 9 (heptosyltransferase). Characterisation work carried out within Campylobacter jejuni, so not added to product function. Identifed as part of Campylobacter jejuni lipooligosaccharide locus (Cj1131c - Cj1152c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:9446588, PMID:11054112, PMID:11914340; heptosyltransferase II 1080908..1081867 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905438 YP_002344540.1 CDS gmhA NC_002163.1 1081848 1082408 R catalyzes the isomerization of sedoheptulose 7-phosphate to D-glycero-D-manno-heptose 7-phosphate; phosphoheptose isomerase complement(1081848..1082408) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905439 YP_002344541.1 CDS hldE NC_002163.1 1082405 1083790 R Original (2000) note: Cj1150c, waaE, possible ADP-heptose synthase, len: 461 aa; similar to TR:Q48046 (EMBL:U17642) Haemophilus influenzae ADP-heptose synthase (342 aa), fasta scores; opt: 687 z-score: 784.6 E(): 0,40.8% identity in 306 aa overlap. Similar in N-term to RBSK_BACSU ribokinase (286 aa), fasta scores; opt: 204 z-score: 238.0 E(): 5.9e-06, 28.1% identity in 295 aa overlap, and in C-term to TAGD_BACSU glycerol-3-phosphate cytidylyltransferase (129 aa), fasta scores; opt: 208 z-score: 247.5 E(): 1.7e-06, 34.9% identity in 129 aa overlap. 50.8% identity to HP0858. Contains 2x Pfam match to entry PF00294 pfkB, pfkB family carbohydrate kinase; Updated (2006) 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 (Cj1131c -Cj1152c). Functional classification - Surface polysaccharides, lipopolysaccharides and antigens; PMID:10629197, PMID:11751812, PMID:16030223,PMID:11751812, PMID:12101286; D-beta-D-heptose 7-phosphate kinase/D-beta-D-heptose 1-phosphate adenylyltransferase complement(1082405..1083790) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905440 YP_002344542.1 CDS hldD NC_002163.1 1083783 1084736 R Original (2000) note: Cj1151c, waaD, probable ADP-L-glycero-D-manno-heptose-6-epimerase, len: 317 aa; similar to e.g. RFAD_ECOLI ADP-L-glycero-D-manno-heptose-6-epimerase (EC 5.1.3.20) (310 aa), fasta scores; opt: 533 z-score: 600.5 E(): 3.8e-26. 32.9% identity in 319 aa overlap. 48.3% identity to HP0859; Updated (2006) note: Pfam domain PF01370 NAD dependent epimerase/dehydratase 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 (Cj1131c - Cj1152c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:10896473, PMID:11751812, PMID:16481326,PMID:12101286; ADP-glyceromanno-heptose 6-epimerase complement(1083783..1084736) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905441 YP_002344543.1 CDS gmhB NC_002163.1 1084737 1085297 R Original (2000) note: Cj1152c, possible phosphatase, len: 186 aa; similar to hypothetical proteins e.g. YAED_ECOLI (191 aa), fasta scores; opt: 295 z-score: 372.3 E(): 1.9e-13, 45.1% identity in 153 aa overlap. 46.2% identity to HP0860. Some similarity to N-terminal histidinol-phosphatase domain of hisB proteins e.g. HIS7_ECOLI imidazoleglycerol-phosphate dehydratase/histidinol-phosphatase (355 aa), fasta scores; opt: 266 z-score: 332.8 E(): 3.1e-11, 30.8% identity in 146 aa overlap; Updated (2006) 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 (Cj1131c - Cj1152c). Functional classification - Misc; PMID:11751812, PMID:12101286; D,D-heptose 1,7-bisphosphate phosphatase complement(1084737..1085297) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905442 YP_002344544.1 CDS Cj1153 NC_002163.1 1085379 1085681 D Original (2000) note: Cj1153, probable periplasmic cytochrome C, len: 100 aa; similar to many e.g. 553_DESVH cytochrome C-553 precursor (103 aa), fasta scores; opt: 187 z-score: 243.8 E(): 2.8e-06, 34.6% identity in 107 aa overlap. 31.0% identity to HP1227. Contains PS00190 Cytochrome c family heme-binding site signature, and Pfam match to entry PF00034 cytochrome_c; Updated (2006) note: Characterisation work has been carried out in Helicobacter pylori, however, identity searches were marginal. kept in product function. Functional classification - Energy metabolism - Electron transport; PMID:10965034; periplasmic cytochrome C 1085379..1085681 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905443 YP_002344545.1 CDS Cj1154c NC_002163.1 1085704 1085910 R Original (2000) note: Cj1154c, small hydrophobic protein, len: 68 aa; 38.7% identity to HP1163; Updated (2006) note: Pfam domain PF03597 Cytochrome oxidase maturation protein cbb3-type identified within CDS. Also, 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, so kept within product function. Functional classification - Protein translation and modification; cytochrome oxidase maturation protein cbb3-type complement(1085704..1085910) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905444 YP_002344546.1 CDS Cj1155c NC_002163.1 1085907 1088264 R Original (2000) note: Cj1155c, probable cation-transporting ATPase, len: 785 aa; similar to members of the E1-E2 ATPase family e.g. ATCU_ECOLI probable copper-transporting ATPase (834 aa), fasta scores; opt: 708 z-score: 767.6 E(): 0, 28.9% identity in 830 aa overlap. 36.5% identity to HP1503. Contains 2x Pfam match to entry PF00122 E1-E2_ATPase; Updated (2006) 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/binding proteins - Cations; cation-transporting ATPase complement(1085907..1088264) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905445 YP_002344547.1 CDS rho NC_002163.1 1088373 1089671 D An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes; transcription termination factor Rho 1088373..1089671 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905446 YP_002344548.1 CDS dnaX NC_002163.1 1089675 1091204 D catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the tau chain serves as a scaffold to help in the dimerizaton of the alpha,epsilon and theta core complex; the gamma chain seems to interact with the delta and delta' subunits to transfer the beta subunit on the DNA; DNA polymerase III subunits gamma and tau 1089675..1091204 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905447 YP_002344549.1 CDS Cj1158c NC_002163.1 1091201 1091428 R Original (2000) note: Cj1158c, small hydrophobic protein, len: 75 aa; no Hp match; Updated (2006) note: Two probable transmembrane helices predicted by TMHMM2.0. Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein complement(1091201..1091428) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905448 YP_002344550.1 CDS Cj1159c NC_002163.1 1091407 1091529 R Original (2000) note: Cj1159c, small hydrophobic protein, len: 40 aa; no Hp match; Updated (2006) note: One probable transmembrane helices predicted by TMHMM2.0. Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein complement(1091407..1091529) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905449 YP_002344551.1 CDS Cj1160c NC_002163.1 1091544 1091723 R Original (2000) note: Cj1160c, small hydrophobic protein, len: 59 aa; no Hp match; Updated (2006) note: One probable transmembrane helix predicted for TMHMM2.0. Also, one signal peptide predicted by SignalP 2.0 HMM. Product function modified to more specific family member. kept within product function. Functional classification - Membranes,lipoproteins and porins; hypothetical protein complement(1091544..1091723) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905450 YP_002344552.1 CDS Cj1161c NC_002163.1 1091795 1093894 R Original (2000) note: Cj1161c, probable cation-transporting ATPase, len: 699 aa; similar to members of the E1-E2 ATPase family e.g. COPA_HELFE copper-transporting ATPase (732 aa), fasta scores; opt: 1106 z-score: 1124.4 E(): 0, 32.8% identity in 729 aa overlap. 33.2% identity to HP1072. Contains Pfam match to entry PF00403 HMA, Heavy-metal-associated domain containing proteins, 2x Pfam match to entry PF00122 E1-E2_ATPase, and PS00154 E1-E2 ATPases phosphorylation site; Updated (2006) note: Characterisation in more than one bacteria with marginal identity scores. kept within product function. Functional classification -Transport/binding proteins - Cations; PMID:9440521; cation-transporting ATPase complement(1091795..1093894) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905451 YP_002344553.1 CDS Cj1162c NC_002163.1 1093894 1094088 R Original (2000) note: Cj1162c, unknown, len: 64 aa; no Hp match; Updated (2006) note: Prosite domain PS50846 HMA_2,Heavy metal transport/detoxification protein within CDS. Product modified to more specific family member based on motif match. No specific characterisation carried out yet,so kept within product function. Functional classification - Conserved hypothetical proteins; heavy-metal-associated domain protein complement(1093894..1094088) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905452 YP_002344554.1 CDS Cj1163c NC_002163.1 1094078 1095028 R Original (2000) note: Cj1163c, possible cation transport protein, len: 316 aa; similar to e.g. CZCD_ALCEU cobalt-zinc-cadmium resistance protein CZCD (316 aa),fasta scores; opt: 609 z-score: 699.8 E(): 1.1e-31, 36.2% identity in 287 aa overlap. No Hp match. Contains His-rich regin at N-terminus. Also similar to Cj0948c (25.7% identity in 280 aa overlap); Updated (2006) note: Pfam domain PF01545 Cation efflux family domain identified within CDS. Also, 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/binding proteins - Cations; PMID:9044283; cation transport protein complement(1094078..1095028) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905453 YP_002344555.1 CDS Cj1164c NC_002163.1 1095104 1095367 R Original (2000) note: Cj1164c, unknown, len: 87 aa; no Hp match. Contains two Cys pairs; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein complement(1095104..1095367) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905454 YP_002344556.1 CDS Cj1165c NC_002163.1 1095437 1095931 R Original (2000) note: Cj1165c, probable integral membrane protein, len: 164 aa; some similarity to hypothetical proteins e.g. YJJB_ECOLI (128 aa), fasta scores; opt: 171 z-score: 229.8 E(): 1.7e-05, 29.2% identity in 106 aa overlap. No Hp match. Contains one Cys pair; Updated (2006) note: Five probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; integral membrane protein complement(1095437..1095931) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905455 YP_002344557.1 CDS Cj1166c NC_002163.1 1095928 1096704 R Original (2000) note: Cj1166c, probable integral membrane protein, len: 258 aa; some similarity to hypothetical proteins e.g. YJJP_ECOLI (277 aa), fasta scores; opt: 292 z-score: 367.7 E(): 3.5e-13, 25.8% identity in 236 aa overlap. No Hp match. Contains one Cys pair; Updated (2006) note: Pfam domain PF06738 Protein of unknown function (DUF1212) identified within CDS. Five probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Functional classification - Membranes, lipoproteins and porins; integral membrane protein complement(1095928..1096704) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905456 YP_002344558.1 CDS ldh NC_002163.1 1096771 1097697 D Original (2000) note: Cj1167, ldh, probable L-lactate dehydrogenase, len: LDH_LACLA L-lactate dehydrogenase (EC 1.1.1.27) (324 aa), fasta scores; opt: 579 z-score: 683.7 E(): 8.8e-31, 33.7% identity in 306 aa overlap. No Hp match. Also similar to Cj0532 mdh (25.4% identity in 311 aa overlap). Contains; Updated (2006) note: Pfam domains PF00056 lactate/malate dehydrogenase, NAD binding domain and PF02866 lactate/malate dehydrogenase, alpha/beta C-terminal were identified within CDS. Also, Prosite PS00064 L_LDH, 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; PMID:8081494, PMID:15644899; L-lactate dehydrogenase 1096771..1097697 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905457 YP_002344559.1 CDS Cj1168c NC_002163.1 1097694 1098296 R Updated (2006) note: Four probable transmembrane helices predicted by TMHMM2.0; Original (2000) note: Cj1168c, probable integral membrane protein (dedA homolog), len: 200 aa; similar to many members of the dedA family e.g. APL_LACLA alkaline phosphatase like protein (242 aa), fasta scores; opt: 424 z-score: 531.1 E(): 2.8e-22, 37.5% identity in 208 aa overlap, and DEDA_ECOLI DEDA protein (219 aa), fasta scores; opt: 240 z-score: 306.1 E(): 9.5e-10, 24.7% identity in 190 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00597 DedA. Also similar to Cj1210 (24.5% identity in 200 aa overlap). Functional classification -Membranes, lipoproteins and porins; integral membrane protein complement(1097694..1098296) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905458 YP_002344560.1 CDS Cj1169c NC_002163.1 1098377 1098604 R Original (2000) note: Cj1169c, probable periplasmic protein, len: 75 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein complement(1098377..1098604) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905459 YP_002344561.1 CDS omp50 NC_002163.1 1098615 1100036 R Original (2000) note: Cj1170c, omp50, outer membrane protein, len: 473 aa; 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 (Jean-Michel.Bolla@medicine.univ-mrs.fr) personal communication; Updated (2006) note: Further characterisation with attached papers give more information on protein naming. Functional classification - Membranes, lipoproteins and porins; PMID:11104668, PMID:15131219; 50 kda outer membrane protein precursor complement(1098615..1100036) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905460 YP_002344562.1 CDS ppi NC_002163.1 1100192 1100674 R Original (2000) note: Cj1171c, ppi, probable peptidyl-prolyl cis-trans isomerase, len: 480 aa; similar to many e.g. YPB_BACSU peptidyl-prolyl cis-trans isomerase B (EC 5.2.1.8) (143 aa), fasta scores; opt: 537 z-score: 643.2 E(): 1.6e-28, 56.2% identity in 137 aa overlap. 55.3% identity to HP1441. Contains PS00170 Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature, and Pfam match to entry PF00160 pro_isomerase,Peptidyl-prolyl cis-trans isomerases; Updated (2006) note: Characterised in Bacillus subtilis with acceptable identity score, so not added to product function. Functional classification -Protein translation and modification; PMID:8022278; peptidyl-prolyl cis-trans isomerase complement(1100192..1100674) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905461 YP_002344563.1 CDS Cj1172c NC_002163.1 1100684 1101391 R Original (2000) note: Cj1172c, unknown, len: 235 aa; similar to hypothetical proteins e.g. YEBC_ECOLI (246 aa), fasta scores; opt: 508 z-score: 579.3 E(): 5.7e-25,37.1% identity in 229 aa overlap. 58.1% identity to HP0162; Updated (2006) note: Pfam domain PF01709 Domain of unknown function DUF28 identified within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins; hypothetical protein complement(1100684..1101391) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905462 YP_002344564.1 CDS Cj1173 NC_002163.1 1101500 1101841 D Original (2000) note: Cj1173, possible efflux protein, len: 113 aa; similar to many e.g. EBR_STAAU ethidium bromide resistance protein (107 aa), fasta scores; opt: 232 z-score: 309.2 E(): 6.3e-10, 38.0% identity in 100 aa overlap. No Hp match. Contains Pfam match to entry PF00893 DUF7, Integral membrane protein. Also similar to Cj0310c (27.1% identity in 107 aa overlap); Updated (2006) note: Pfam domain PF00893 Small Multidrug Resistance protein identified within CDS. Also,four 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 (PMID:16048946) giving further information within Campylobacter spp. Functional classification - Drug/analogue sensitivity; PMID:11566977, PMID:15919996, PMID:16048946; multidrug resistance protein 1101500..1101841 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905463 YP_002344565.1 CDS Cj1174 NC_002163.1 1101841 1102149 D Original (2000) note: Cj1174, possible efflux protein, len: 102 aa; similar to many e.g. EBR_STAAU ethidium bromide resistance protein (107 aa), fasta scores; opt: 228 z-score: 302.9 E(): 1.4e-09, 33.0% identity in 100 aa overlap. No Hp match. Contains Pfam match to entry PF00893 DUF7, Integral membrane protein. Also similar to Cj0309c (28.7% identity in 94 aa overlap); Updated (2006) note: Pfam domain PF00893 Small Multidrug Resistance protein identified within CDS. Also,four 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 (PMID:16048946) giving further information within Campylobacter spp. Functional classification - Drug/analogue sensitivity; PMID:11566977, PMID:15919996, PMID:16048946; multidrug resistance protein 1101841..1102149 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905464 YP_002344566.1 CDS argS NC_002163.1 1102167 1103759 R catalyzes a two-step reaction, first charging an arginine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class-I aminoacyl-tRNA synthetase; arginyl-tRNA synthetase complement(1102167..1103759) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905465 YP_002344567.1 CDS tatA NC_002163.1 1103771 1104010 R Original (2000) note: Cj1176c, unknown, len: 79 aa; similar to hypothetical proteins e.g. YY34_MYCTU MTCY49.34C (83 aa), fasta scores; opt: 162 z-score: 221.6 E(): 4.8e-05, 42.9% identity in 56 aa overlap. 49.4% identity to HP0320; Updated (2006) note: Pfam domain PF02416 mttA/Hcf106 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,with acceptable identity score. Product function uses homolog description. Functional classification - Protein and peptide secretion; PMID:9649434, PMID:12427031, PMID:15571732,PMID:9546395, PMID:16027357; Sec-independent protein translocase complement(1103771..1104010) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905466 YP_002344568.1 CDS gmk NC_002163.1 1104012 1104635 R Essential for recycling GMP and indirectly, cGMP; guanylate kinase complement(1104012..1104635) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905467 YP_002344569.1 CDS Cj1178c NC_002163.1 1104632 1106260 R Original (2000) note: Cj1178c, highly acidic protein, len: 542 aa; no Hp match. Very Asp- Glu- rich; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; highly acidic protein complement(1104632..1106260) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905468 YP_002344570.1 CDS fliR NC_002163.1 1106317 1107084 R FliR, with proteins FliP and FliQ, forms the core of the central channel in the flagella export apparatus; flagellar biosynthesis protein FliR complement(1106317..1107084) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905469 YP_002344571.1 CDS Cj1180c NC_002163.1 1107071 1107706 R Original (2000) note: Cj1180c, probable ABC transporter ATP binding protein, len: 211 aa; similar to many e.g. YBBA_ECOLI hypothetical ABC transporter ATP-binding protein (228 aa), fasta scores; opt: 457 z-score: 554.6 E(): 1.4e-23, 39.7% identity in 199 aa overlap. 49.5% identity to HP0179. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00211 ABC transporters family signature, and Pfam match to entry PF00005 ABC_tran, ABC transporters; Updated (2006) note: Similar to many identified as lipoprotein-releasing system ATP-binding protein. kept within product function. Functional classification -Transport/binding proteins - Other; PMID:10783239, PMID:11844772, PMID:12823819; ABC transporter ATP-binding protein complement(1107071..1107706) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905470 YP_002344572.1 CDS tsf NC_002163.1 1107719 1108792 R EF-Ts; functions during elongation stage of protein translation; forms a dimer; associates with EF-Tu-GDP complex and promotes exchange of GDP to GTP resulting in regeneration of the active form of EF-Tu; elongation factor Ts complement(1107719..1108792) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905471 YP_002344573.1 CDS rpsB NC_002163.1 1108792 1109583 R one of the last subunits in the assembly of the 30S subunit; absence of S2 does not inhibit assembly but results in an inactive subunit; 30S ribosomal protein S2 complement(1108792..1109583) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905472 YP_002344574.1 CDS cfa NC_002163.1 1109699 1110862 R Original (2000) note: Cj1183c, cfa, probable cyclopropane-fatty-acyl-phospholipid synthase, len: 387 aa; CFA_ECOLI cyclopropane-fatty-acyl-phospholipid synthase (EC 2.1.1.79) (381 aa), fasta scores; opt: 721 z-score: 802.3 E(): 0, 38.7% identity in 362 aa overlap. 62.1% identity to HP0416; Updated (2006) 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; PMID:1445840; cyclopropane-fatty-acyl-phospholipid synthase complement(1109699..1110862) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905473 YP_002344575.1 CDS petC NC_002163.1 1110990 1112114 R Original (2000) note: Cj1184c, petC, possible ubiquinol-cytochrome C reductase cytochrome C subunit,len: 374 aa; some similarity to e.g. CYC_TETPY cytochrome C (109 aa), fasta scores; opt: 124 z-score: 145.5 E(): 0.83, 25.6% identity in 121 aa overlap. 36.4% identity to HP1538. Contains Pfam match to entry PF00034 cytochrome_c,Cytochrome c, probable N-terminal signal sequence, and possible membrane anchor at C-terminus; Updated (2006) note: Two probable transmembrane helices predicted by TMHMM2.0. Specific characterisation with acceptable identity score not carried out yet, so kept in product function. Literature search identified paper giving further clues to functionality within Campylobacter. Functional classification - Energy metabolism - Electron transport; PMID:16041056; ubiquinol-cytochrome C reductase cytochrome C subunit complement(1110990..1112114) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905474 YP_002344576.1 CDS petB NC_002163.1 1112111 1113361 R Original (2000) note: Cj1185c, petB, probable ubiquinol-cytochrome C reductase cytochrome B subunit,len: 416 aa; similar to e.g. CYB_RHOSH cytochrome B (EC 1.10.2.2) (444 aa), fasta scores; opt: 1023 z-score: 1190.8 E(): 0, 40.4% identity in 416 aa overlap. 70.9% identity to HP1539; Contains PS00193 Cytochrome b/b6 Qo site signature, Pfam match to entry PF00033 cytochrome_b_N, Cytochrome b(N-terminal)/b6/petB, and Pfam match to entry PF00032 cytochrome_b_C, Cytochrome b(C-terminal)/b6/petD; Updated (2006) 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 (PMID:16041056) giving further clues to functionality within Campylobacter. Functional classification - Energy metabolism - Electron transport; PMID:2176595, PMID:1645718, PMID:16041056; ubiquinol-cytochrome C reductase cytochrome B subunit complement(1112111..1113361) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905475 YP_002344577.1 CDS petA NC_002163.1 1113363 1113866 R Original (2000) note: Cj1186c, petA, probable ubiquinol-cytochrome C reductase iron-sulfur subunit, len: 167 aa; similar to e.g. UCRI_BRAJA ubiquinol-cytochrome C reductase iron-sulfur subunit (EC 1.10.2.2) (176 aa),fatsa scores; opt: 236 z-score: 291.2 E(): 6.4e-09, 39.2% identity in 171 aa overlap. 56.8% identity to HP1540. Contains PS00199 Rieske iron-sulfur protein signature 1,and Pfam match to entry PF00355 Rieske, Rieske iron-sulfur protein; Updated (2006) note: No specific characterisation with acceptable identity score, so kept within product function. Literature search identified paper giving further clues to functionality within Campylobacter. Functional classification - Energy metabolism - Electron transport; PMID:16041056; ubiquinol-cytochrome C reductase iron-sulfur subunit complement(1113363..1113866) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905476 YP_002344578.1 CDS arsB NC_002163.1 1113956 1115242 R Original (2000) note: Cj1187c, arsB, possible arsenical pump membrane protein, len: 428 aa; simlar to many e.g. ARSB_ECOLI arsenical pump membrane protein (429 aa), fasta scores; opt: 805 z-score: 920.7 E(): 0, 33.5% identity in 433 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF02040 Arsenical pump membrane protein identified within CDS. Also, 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/analogue sensitivity; PMID:7721697, PMID:1688427; arsenical pump membrane protein complement(1113956..1115242) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905477 YP_002344579.1 CDS gidA NC_002163.1 1115243 1117102 R GidA; glucose-inhibited cell division protein A; involved in the 5-carboxymethylaminomethyl modification (mnm(5)s(2)U) of the wobble uridine base in some tRNAs; tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA complement(1115243..1117102) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905478 YP_002344580.1 CDS cetB NC_002163.1 1117190 1117687 R Original (2000) note: Cj1189c, possible signal-transduction sensor protein, len: 165 aa; similar to N-terminus of genes involved in oxygen-sensing e.g. AER_ECOLI aerotaxis receptor (506 aa), fasta scores; opt: 342 z-score: 407.5 E(): 2.1e-15, 36.4% identity in 140 aa overlap, and NIFL_AZOVI nitrogen fixation regulatory protein (519 aa), fasta scores; opt: 175 z-score: 212.5 E(): 0.00015, 33.6% identity in 110 aa overlap. No Hp match. Also similar to Cj1191c (63.4% identity in 161 aa overlap); Updated (2006) 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, 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 (PMID:11298288). Gene name added. Functional classification - Signal transduction; PMID:9380671, PMID:11298288; bipartate energy taxis response protein CetB complement(1117190..1117687) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905479 YP_002344581.1 CDS cetA NC_002163.1 1117705 1119084 R Original (2000) note: Cj1190c, probable MCP-domain signal transduction protein, len: 459 aa; similar to many e.g. TLPC_BACSU methyl-accepting chemotaxis protein TLPC (573 aa), fasta scores; opt: 371 z-score: 397.9 E(): 7.3e-15, 26.2% identity in 404 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00015 MCPsignal,Methyl-accepting chemotaxis protein (MCP) signaling domain, and probable membrane spanning domain at N-terminus; Updated (2006) note: Characterisation work carried out in Campylobacter jejuni. Product function updated. Literature search identified paper giving further information to product functionality (PMID:11298288). New gene name has been added. Functional classification -Signal transduction; PMID:8188684, PMID:11298288; bipartate energy taxis response protein CetA complement(1117705..1119084) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905480 YP_002344582.1 CDS Cj1191c NC_002163.1 1119205 1119699 R Original (2000) note: Cj1191c, possible signal-transduction sensor protein, len: 164 aa; similar to N-terminus of genes involved in oxygen-sensing e.g. AER_ECOLI aerotaxis receptor (506 aa), fasta scores; opt: 297 z-score: 373.5 E(): 1.7e-13, 34.3% identity in 134 aa overlap, and NIFL_AZOVI nitrogen fixation regulatory protein (519 aa), fasta scores; opt: 178 z-score: 226.6 E(): 2.5e-05, 33.0% identity in 103 aa overlap. No Hp match. Also similar to Cj1189c (63.4% identity in 161 aa overlap); Updated (2006) 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, 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 (PMID:11298288). Functional classification - Signal transduction; PMID:9380671, PMID:11298288; PAS domain containing signal-transduction sensor protein complement(1119205..1119699) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905481 YP_002344583.1 CDS dctA NC_002163.1 1119968 1121344 D Original (2000) note: Cj1192, dctA, probable C4-dicarboxylate transport protein, len: 458 aa; similar to many e.g. DCTA_ECOLI C4-dicarboxylate transport protein (428 aa), fasta scores; opt: 1073 z-score: 1222.5 E(): 0,45.3% identity in 433 aa overlap. No Hp match. Contains Pfam match to entry PF00375 SDF, Sodium:dicarboxylate symporter family; Updated (2006) 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,organic acids and alcohols; PMID:8955389, PMID:10482502, PMID:15919996,PMID:11803016; C4-dicarboxylate transport protein 1119968..1121344 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905482 YP_002344584.1 CDS Cj1193c NC_002163.1 1121341 1122147 R Original (2000) note: Cj1193c, probable periplasmic protein, len: 268 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein complement(1121341..1122147) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905483 YP_002344585.1 CDS Cj1194 NC_002163.1 1122289 1123815 D Original (2000) note: Cj1194, possible phosphate permease, len: 508 aa; similar to many predicted phosphate permeases e.g. TR:Q50684 Mycobacterium tuberculosis phosphate permease Rv2281 MTCY339.29C (552 aa),fasta scores; opt: 900 z-score: 971.5 E(): 0, 46.6% identity in 511 aa overlap. 32.7% identity to HP1491; Updated (2006) note: Pfam domain PF01384 Phosphate transporter family identified within CDS. Also, thirteen probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation has been carried out yet, so kept within product function. Functional classification -Transport/binding proteins - Anions; phosphate permease 1122289..1123815 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905484 YP_002344586.1 CDS pyrC2 NC_002163.1 1123823 1125001 R Catalyzes the reversible hydrolysis of the amide bond within dihydroorotate. This metabolic intermediate is required for the biosynthesis of pyrimidine nucleotides; dihydroorotase complement(1123823..1125001) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905485 YP_002344587.1 CDS gpsA NC_002163.1 1125011 1125907 R NAD(P)+; catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate; NAD(P)H-dependent glycerol-3-phosphate dehydrogenase complement(1125011..1125907) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905486 YP_002344588.1 CDS gatB NC_002163.1 1125904 1127322 R allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; aspartyl/glutamyl-tRNA amidotransferase subunit B complement(1125904..1127322) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905487 YP_002344589.1 CDS Cj1198 NC_002163.1 1127437 1127931 D catalyzes the hydrolysis of S-ribosylhomocysteine to homocysteine and autoinducer-2; S-ribosylhomocysteinase 1127437..1127931 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905488 YP_002344590.1 CDS Cj1199 NC_002163.1 1128243 1129235 D Original (2000) note: Cj1199, probable iron/ascorbate-dependent oxidoreductase, len: 330 aa; similar to many eukaryotic oxidoreductases e.g. LDOX_MALSP Malus sp. (crab apple) leucoanthocyanidin dioxygenase (EC 1.-.-.-) (357 aa), fasta scores; opt: 334 z-score: 386.2 E(): 3.3e-14, 25.2% identity in 313 aa overlap, and ACCO_MALDO Malus domesticus (apple) 1-aminocyclopropane-1-carboxylate oxidase (314 aa), fasta scores; opt: 301 z-score: 349.6 E(): 3.6e-12, 26.7% identity in 303 aa overlap. No Hp match. Contains Pfam match to entry PF00671 Fe_Asc_oxidored, Iron/Ascorbate family of oxidoreductases; Updated (2006) note: Pfam domain PF03171 2OG-Fe(II) 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; iron/ascorbate-dependent oxidoreductase 1128243..1129235 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905489 YP_002344591.1 CDS Cj1200 NC_002163.1 1129228 1130016 D Original (2000) note: Cj1200, probable periplasmic protein, len: 262 aa; similar to members of the nlpA family of outem membrane lipoproteins, e.g. NLPA_ECOLI lipoprotein-28 precursor (272 aa), fasta scores; opt: 560 z-score: 650.6 E(): 6.1e-29, 39.7% identity in 239 aa overlap, and PLPC_PASHA outer membrane lipoprotein 3 precursor (263 aa), fasta scores; opt: 564 z-score: 655.4 E(): 3.3e-29, 38.6% identity in 259 aa overlap. No Hp ortholog. Contains probable N-terminal signal sequence. Also similar to Cj0772c (57.5% identity in 254 aa overlap), Cj0771c (45.6% identity in 259 aa overlap), and Cj0770c (44.9% identity in 256 aa overlap); Updated (2006) 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's as D-methionine-binding lipoprotein metQ precursor. Product function modified to more specific family member. kept within product function. Functional classification -Miscellaneous periplasmic proteins; PMID:3003106, PMID:12169620; NLPA family lipoprotein 1129228..1130016 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905490 YP_002344592.1 CDS metE NC_002163.1 1130028 1132292 D catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine to form methionine; 5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase 1130028..1132292 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905491 YP_002344593.1 CDS metF NC_002163.1 1132302 1133150 D Original (2000) note: Cj1202, metF, probable 5,10-methylenetetrahydrofolate reductase, len: 282 aa; similar to e.g. METF_ECOLI 5,10-methylenetetrahydrofolate reductase (EC 1.7.99.5) (296 aa), fasta scores; opt: 529 z-score: 613.4 E(): 7.2e-27 33.0% identity in 264 aa overlap. No Hp match; Updated (2006) 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; PMID:6356036, PMID:10201405; 5,10-methylenetetrahydrofolate reductase 1132302..1133150 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905492 YP_002344594.1 CDS Cj1203c NC_002163.1 1133172 1133363 R Original (2000) note: Cj1203c, probable integral membrane protein, len: 63 aa; no Hp match; Updated (2006) note: Two probable transmembrane helices predicted by TMHMM2.0. Functional classification -Central intermediary metabolism - General; integral membrane protein complement(1133172..1133363) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905493 YP_002344595.1 CDS atpB NC_002163.1 1133360 1134040 R Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit A is part of the membrane proton channel F0; F0F1 ATP synthase subunit A complement(1133360..1134040) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905494 YP_002344596.1 CDS radA NC_002163.1 1134109 1135449 R Sms; stabilizes the strand-invasion intermediate during the DNA repair; involved in recombination of donor DNA and plays an important role in DNA damage repair after exposure to mutagenic agents; DNA repair protein RadA complement(1134109..1135449) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905495 YP_002344597.1 CDS ftsY NC_002163.1 1135449 1136315 R Original (2000) note: Cj1206c, ftsY, probable signal recognition particle protein, len: 288 aa; similar to e.g. FTSY_ECOLI cell division protein FTSY (497 aa),fasta scores; opt: 663 z-score: 759.0 E(): 0, 43.3% identity in 298 aa overlap, and PILA_NEIME probable signal recognition particle protein (421 aa), fasta scores; opt: 633 z-score: 726.0 E(): 3.8e-33, 39.9% identity in 298 aa overlap. 48.6% identity to HP0763. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00300 SRP54-type proteins GTP-binding domain signature, and Pfam match to entry PF00448 SRP54, SRP54-type protein. Also similar to Cj0709 ffh (31.4% identity in 271 aa overlap); Updated (2006) note: Similar to more than one bacteria with acceptable identity score. kept within product function. Functional classification -Protein and peptide secretion; PMID:10048040, PMID:9188744, PMID:8194520; signal recognition particle protein complement(1135449..1136315) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905496 YP_002344598.1 CDS Cj1207c NC_002163.1 1136315 1136872 R Original (2000) note: Cj1207c, possible lipoprotein thiredoxin, len: 185 aa; some similarity to TR:G4100188 (EMBL:U95250) Treponema pallidum predicted thioredoxin (185 aa), fasta scores; opt: 196 z-score: 242.3 E(): 3.4e-06, 31.5% identity in 111 aa overlap, and HELX_RHOCA thiol:disulfide interchange protein(176 aa), fatsa scores; opt: 153 z-score: 192.6 E(): 0.002, 23.2% identity in 142 aa overlap. 23.7% identity to HP0762. Also similar to Cj1106 (29.4% identity in 201 aa overlap). Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site; Updated (2006) note: Prosite domain PS50223 THIOREDOXIN_2, Thioredoxin domain 2 was identified within CDS. Further support given to product function. kept within product function. Functional classification -Energy metabolism - Electron transport; lipoprotein thiredoxin complement(1136315..1136872) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905497 YP_002344599.1 CDS Cj1208 NC_002163.1 1136955 1137581 D Original (2000) note: Cj1208, unknown, len: 208 aa; similar to hypothetical proteins e.g. YGFA_HAEIN HI0858 (187 aa), fasta scores; opt: 150 z-score: 196.6 E(): 0.0012, 26.8% identity in 164 aa overlap. 27.8% identity to HP0761; Updated (2006) 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, so kept within product function. Functional classification -Purine ribonucleotide biosynthesis; 5-formyltetrahydrofolate cyclo-ligase family protein 1136955..1137581 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905498 YP_002344600.1 CDS Cj1209 NC_002163.1 1137502 1139055 D protein from Staphylococcus aureus has phosphodiesterase activity against 2'-3'-cAMP and 2'-3'-cGMP; phosphodiesterase 1137502..1139055 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905499 YP_002344601.1 CDS Cj1210 NC_002163.1 1139064 1139621 D Original (2000) note: Cj1210, probable integral membrane protein, len: 185 aa; similar to members of the dedA family e.g. DEDA_ECOLI DEDA protein (219 aa), fasta scores; opt: 193 z-score: 248.3 E(): 1.6e-06, 26.7% identity in 172 aa overlap. 35.6% identity to HP1162. Also similar to Cj0928 (27.7% identity in 177 aa overlap), and Cj1168c (23.0% identity in 200 aa overlap). Contains Pfam match to entry PF00597 DedA, DedA family; Updated (2006) note: Four probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; integral membrane protein 1139064..1139621 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905500 YP_002344602.1 CDS Cj1211 NC_002163.1 1139621 1140880 D Original (2000) note: Cj1211, probable integral membrane protein, len: 419 aa; similar to hypothetical membrane proteins e.g. TR:O51537 (EMBL:AE001160) BB0591 (416 aa), fasta scores; opt: 222 z-score: 251.2 E(): 1.1e-06, 26.4% identity in 405 aa overlap. 33.9% identity to HP1361 (called competence locus E (comE3)); Updated (2006) 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, so kept in product function. Functional classification - Membranes,lipoproteins and porins; PMID:7968523; competence family protein 1139621..1140880 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905501 YP_002344603.1 CDS rbn NC_002163.1 1140824 1141630 R Original (2000) note: Cj1212c, rbn, possible ribonuclease BN, len: RBN_ECOLI ribonuclease BN (EC 3.1.-.-) (290 aa), fasta scores; opt: 365 z-score: 430.3 E(): 1.1e-16, 28.5% identity in 242 aa overlap. 29.2% identity to HP1407; Updated (2006) 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; PMID:8955422; ribonuclease BN complement(1140824..1141630) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905502 YP_002344604.1 CDS glcD NC_002163.1 1141634 1143016 R Original (2000) note: Cj1213c, glcD, probable glycolate oxidase subunit D, len: 460 aa; similar to e.g. GLCD_ECOLI glycolate oxidase subunit GLCD (499 aa), fasta scores; opt: 952 z-score: 1099.5 E(): 0, 37.0% identity in 419 aa overlap. 64.8% identity to HP0509; Updated (2006) note: Pfam domains PF02913 FAD linked oxidases, 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; PMID:8606183, PMID:11283302; glycolate oxidase subunit D complement(1141634..1143016) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905503 YP_002344605.1 CDS Cj1214c NC_002163.1 1143019 1143744 R Original (2000) note: Cj1214c, unknown, len: 241 aa; similar to N-terminal half of HP0508 (452 aa) (24.9% identity in 245 aa overlap); Updated (2006) 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 (PMID:12186869). Functional classification -Transport/binding proteins - Other; PMID:12186869; exporting protein complement(1143019..1143744) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905504 YP_002344606.1 CDS Cj1215 NC_002163.1 1143866 1145026 D Original (2000) note: Cj1215, probable periplasmic protein, len: 386 aa; similar to hypothetical proteins e.g. YEBA_ECOLI (419 aa), fasta scores; opt: 491 z-score: 556.7 E(): 1e-23, 30.2% identity in 338 aa overlap. 44.0% identity to HP0506. Also similar, in part, to Cj1087c (40.6% identity in 133 aa overlap), and Cj1235 (29.6% identity in 206 aa overlap); Updated (2006) 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, so kept within product function. Functional classification -Degradation of macromolecules - Proteins, peptides and glycopeptides; peptidase M23 family protein 1143866..1145026 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905505 YP_002344607.1 CDS Cj1216c NC_002163.1 1145023 1145226 R Original (2000) note: Cj1216c, unknown, len: 67 aa; no Hp match. Functional classification - Unknown; hypothetical protein complement(1145023..1145226) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905506 YP_002344608.1 CDS Cj1217c NC_002163.1 1145228 1145908 R Original (2000) note: Cj1217c, unknown, len: 226 aa; similar to hypothetical proteins e.g. YFIH_ECOLI (243 aa), fasta scores; opt: 262 z-score: 319.9 E(): 1.6e-10,30.3% identity in 185 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF02578 Uncharacterised ACR, YfiH family COG1496 identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins; hypothetical protein complement(1145228..1145908) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905507 YP_002344609.1 CDS ribA NC_002163.1 1145872 1146483 R catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine; riboflavin synthase subunit alpha complement(1145872..1146483) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905508 YP_002344610.1 CDS Cj1219c NC_002163.1 1146492 1149032 R Original (2000) note: Cj1219c, probable periplasmic protein, len: 846 aa; 27.3% identity to HP0358. Weak similarity to FLID_ECOLI flagellar hook-associated protein 2 (467 aa), fasta scores; opt: 168 z-score: 180.0 E(): 0.0099, 24.2% identity in 446 aa overlap, and to Cj0530 (22.1% identity in 891 aa overlap). Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein complement(1146492..1149032) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905509 YP_002344611.1 CDS groES NC_002163.1 1149194 1149454 D 10 kDa chaperonin; Cpn10; GroES; forms homoheptameric ring; binds to one or both ends of the GroEL double barrel in the presence of adenine nucleotides capping it; folding of unfolded substrates initiates in a GroEL-substrate bound and capped by GroES; release of the folded substrate is dependent on ATP binding and hydrolysis in the trans ring; co-chaperonin GroES 1149194..1149454 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905510 YP_002344612.1 CDS groEL NC_002163.1 1149475 1151112 D 60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; many bacteria have multiple copies of the groEL gene which are active under different environmental conditions; the B.japonicum protein in this cluster is expressed constitutively; in Rhodobacter, Corynebacterium and Rhizobium this protein is essential for growth; molecular chaperone GroEL 1149475..1151112 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905511 YP_002344613.1 CDS dccS NC_002163.1 1151155 1152345 R Original (2000) note: Cj1222c, probable two-component sensor (histidine kinase), len: 396 aa; similar to many sensor proteins e.g. RSTB_ECOLI sensor protein RSTB (433 aa), fasta scores; opt: 226 z-score: 267.7 E(): 1.3e-07, 24.5% identity in 237 aa overlap. 28.5% identity to HP1364. Contains Pfam match to entry PF00512 signal, Signal carboxyl-terminal domain, and two possible membrane spanning domains; Updated (2006) note: Pfam domains PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase motif and PF00512 His Kinase A (phosphoacceptor) domain were identified within CDS. Prosite domain PS50109 HIS_KIN,Histidine kinase domain profile was also identified within CDS. Also, 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 (diminished capacity to colonize) two-component system. Functional classification - Signal transduction; PMID:15554967; two-component sensor histidine kinase complement(1151155..1152345) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905512 YP_002344614.1 CDS dccR NC_002163.1 1152338 1153003 R Original (2000) note: Cj1223c, probable two-component regulator, len: 221 aa; similar to many e.g. CIAR_STRPN transcriptional regulatory protein CIAR (224 aa), fasta scores; opt: 426 z-score: 522.6 E(): 8.2e-22,37.0% identity in 219 aa overlap. 39.4% identity to HP1365. Contains Pfam match to entry PF00072 response_reg,Response regulator receiver domain, and Pfam match to entry PF00486 trans_reg_C, Transcriptional regulatory protein, C terminal; Updated (2006) 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 (diminished capacity to colonize) two-component system. Functional classification - Signal transduction; PMID:15554967; two-component regulator complement(1152338..1153003) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905513 YP_002344615.1 CDS Cj1224 NC_002163.1 1153151 1153750 D Original (2000) note: Cj1224, possible iron-binding protein, len: 199 aa; some simlarity to TR:Q58157 (EMBL:U67520) Methanococcus jannaschii MJ0747 (169 aa),fasta scores; opt: 230 z-score: 274.3 E(): 5.6e-08, 33.9% identity in 127 aa overlap. Weak similarity to members of the eukaryotic oxygen-binding hemerythrin family, e.g. HEMM_THEZO myohemerythrin (118 aa), fasta scores; opt: 159 z-score: 196.6 E(): 0.0012, 30.5% identity in 118 aa overlap. Note that all of the iron-binding residues are conserved. No Hp match. Also similar to Cj0045c (29.2% identity in 202 aa overlap), Cj0072c (pseudogene), and Cj0241c (34.7% identity in 118 aa overlap); Updated (2006) note: Pfam domain (x2) PF01814 Hemerythrin HHE cation binding domain identified within CDS. Prosite domain PS00550 HEMERYTHRINS, Hemerythrin family signature also identified within CDS. Further support given to product function. Specific characterisation has not been carried out yet, so kept within product function. Functional classification -Transport/binding proteins - Cations; iron-binding protein 1153151..1153750 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905514 YP_002344616.1 CDS Cj1225 NC_002163.1 1153761 1154009 D Original (2000) note: Cj1225, unknown, len: 82 aa; weak similarity to CDS from Borrelia burgdorferi repeated DNA element TR:Q45025 (EMBL:X87127) (210 aa), fasta scores; opt: 117 z-score: 159.0 E(): 0.15, 33.3% identity in 78 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF01402 Ribbon-helix-helix protein, copG family identified within CDS. No specific characterisation has yet been carried out yet. Functional classification - Conserved hypothetical proteins; hypothetical protein 1153761..1154009 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905515 YP_002344617.1 CDS Cj1226c NC_002163.1 1154267 1155514 R Original (2000) note: Cj1226c, probable two-component sensor (histidine kinase), len: 415 aa; similar to many sensor proteins e.g. CPXA_ECOLI sensor protein CPXA (457 aa), fasta scores; opt: 205 z-score: 241.7 E(): 3.7e-06, 25.2% identity in 270 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00512 signal,Signal carboxyl-terminal domain, and two possible membrane spanning domains. Also similar to Cj1262 (31.0% identity in 410 aa overlap); Updated (2006) note: Pfam domains PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase motifs,PF00512 His Kinase A (phosphoacceptor) domain and PF00672 HAMP domain were all identified within CDS. Also, PS50109 HIS_KIN, 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, so kept within product function. Functional classification - Signal transduction; two-component sensor complement(1154267..1155514) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905517 YP_002344618.1 CDS Cj1227c NC_002163.1 1155511 1156185 R Original (2000) note: Cj1227c, probable two-component regulator, len: 224 aa; identical to TR:Q46095 (EMBL:U27271) C. jejuni CDS (called ompR) (198 aa), and similar to many e.g. YYCF_BACSU hypothetical 27.2 kd sensory transduction protein (235 aa), fasta scores; opt: 490 z-score: 561.1 E(): 5.9e-24, 36.4% identity in 225 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00072 response_reg, Response regulator receiver domain, and Pfam match to entry PF00486 trans_reg_C,Transcriptional regulatory protein, C terminal. Also similar to Cj1261 (50.7% identity in 223 aa overlap); Updated (2006) note: Similar to more than one type of two-component regulator with acceptable identity scores, so kept within product function. Literature search identified paper giving further clues to product function. Functional classification - Signal transduction; PMID:15901688, PMID:2402249; two-component regulator complement(1155511..1156185) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905518 YP_002344619.1 CDS htrA NC_002163.1 1156261 1157679 R Original (2000) note: Cj1228c, htrA, probable serine protease (protease DO), len: 472 aa; 99.2% identical to TR:Q46120 (EMBL:X82628) C. jejuni serine protease htrA (472 aa), and similar to e.g. HTRA_ECOLI protease DO precursor (EC 3.4.21.-) (474 aa), fasta scores; opt: 965 z-score: 1004.5 E(): 0, 39.5% identity in 461 aa overlap. 50.5% identity to HP1019. Contains Pfam match to entry PF00089 trypsin, and 2x Pfam match to entry PF00595 PDZ, PDZ domain; Updated (2006) note: Characterised in Escherichia coli and Campylobacter jejuni, so not added to product function. Functional classification - Degradation of macromolecules - Proteins, peptides and glycopeptides; PMID:15933023, PMID:16041056; serine protease complement(1156261..1157679) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905519 YP_002344620.1 CDS cbpA NC_002163.1 1157879 1158772 D Original (2000) note: Cj1229, cbpA, probable curved-DNA binding protein, len: 297 aa; similar to e.g. CBPA_ECOLI curved DNA-binding protein (306 aa), fatsa scores; opt: 514 z-score: 550.9 E(): 2.2e-23, 32.8% identity in 287 aa overlap. 52.0% identity to HP1024. Contains S00636 Nt-dnaJ domain signature, and Pfam match to entry PF00226 DnaJ, DnaJ domain; Updated (2006) 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,chaperonins, heat shock; PMID:15184371, PMID:10947847, PMID:10551881; curved-DNA binding protein 1157879..1158772 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905520 YP_002344621.1 CDS hspR NC_002163.1 1158788 1159162 D Original (2000) note: Cj1230, hspR, possible heat shock transcriptional regulator, len: 124 aa; similar to SPR_STRCO heat shock protein HSPR (151 aa), fatsa scores; opt: 309 z-score: 385.2 E(): 3.7e-14, 42.4% identity in 118 aa overlap, and to other members of the MerR family of transcriptional regulators. 63.3% identity to HP1025. Contains PS00552 Bacterial regulatory proteins,merR family signature, Pfam match to entry PF00376 merR,and probable helix-turn-helix motif at aa 11-32 (Score 1333, +3.73 SD); Updated (2006) note: Characterised in Campylobacter jejuni (PMID:15758235). removed from product function. Functional classification - Chaperones,chaperonins, heat shock; PMID: PMID:8801421, PMID:15758235,PMID:10564507, PMID:15720562; heat shock transcriptional regulator 1158788..1159162 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905521 YP_002344622.1 CDS kefB NC_002163.1 1159168 1160793 D Original (2000) note: Cj1231, kefB, probable glutathione-regulated potassium-efflux system protein,len: 541 aa; similar to e.g. KEFC_ECOLI glutathione-regulated potassium-efflux system protein (620 aa), fasta scores; opt: 803 z-score: 903.5 E(): 0, 30.8% identity in 494 aa overlap. 37.7% identity to HP0471; Updated (2006) note: Pfam domains PF02254 TrkA-N domain and PF00999 Sodium/hydrogen exchanger family were identified within CDS. Also, 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/binding proteins - Cations; PMID:2046548, PMID:1325937; glutathione-regulated potassium-efflux system protein 1159168..1160793 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905522 YP_002344623.1 CDS Cj1232 NC_002163.1 1160803 1161135 D Original (2000) note: Cj1232, unknown, len: 110 aa; no Hp match. Lys-rich. Functional classification -Unknown; hypothetical protein 1160803..1161135 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905523 YP_002344624.1 CDS Cj1233 NC_002163.1 1161132 1161752 D Original (2000) note: Cj1233, probable hydrolase,len: 206 aa; similar to e.g. GPH_ECOLI phosphoglycolate phosphatase (252 aa), fasta scores; opt: 177 z-score: 216.3 E(): 9.5e-05, 27.6% identity in 199 aa overlap. No Hp match. Contains Pfam match to entry PF00702 Hydrolase,haloacid dehalogenase-like hydrolase. Also similar to Cj1477c (27.3% identity in 205 aa overlap); Updated (2006) note: Characterisation work within Escherichia coli, however, identity scores were marginal. Product modified to more specific family member based on motif matches. kept within product function. Functional classification - Misc; PMID:13129953, PMID:10572959; HAD-superfamily hydrolase 1161132..1161752 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905524 YP_002344625.1 CDS glyS NC_002163.1 1161808 1163802 D glycine--tRNA ligase beta chain; glyS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking the carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA; glycyl-tRNA synthetase subunit beta 1161808..1163802 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905525 YP_002344626.1 CDS Cj1235 NC_002163.1 1163799 1164620 D Original (2000) note: Cj1235, probable periplasmic protein, len: 273 aa; similar to many e.g. TR:Q57503 (EMBL:U07173) Vibrio cholerae ToxR-activated gene, tagE (302 aa), fasta scores; opt: 319 z-score: 373.7 E(): 1.6e-13, 37.0% identity in 192 aa overlap, and YEBA_ECOLI (419 aa), fasta scores; opt: 299 z-score: 348.5 E(): 4.1e-12, 44.3% identity in 115 aa overlap. No Hp ortholog. Also similar to Cj0131 (30.2% identity in 222 aa overlap),Cj1087c (40.7% identity in 123 aa overlap), and Cj1215 (29.6% identity in 206 aa overlap); Updated (2006) 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, so kept within product function. Functional classification -Degradation of macromolecules - Proteins, peptides and glycopeptides; peptidase M23 family protein 1163799..1164620 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905526 YP_002344627.1 CDS Cj1236 NC_002163.1 1164617 1165567 D Original (2000) note: Cj1236, unknown, len: 316 aa; similar to hypothetical proteins e.g. TR:O66873 (EMBL:AE000698) Aquifex aeolicus AQ_622 (320 aa), fasta scores; opt: 263 z-score: 318.9 E(): 1.8e-10, 23.8% identity in 323 aa overlap. 32.4% identity to HP0812; Updated (2006) note: Pfam domain PF02636 Uncharacterized ACR, COG1565 identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins; hypothetical protein 1164617..1165567 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905527 YP_002344628.1 CDS Cj1237c NC_002163.1 1165564 1166538 R Original (2000) note: Cj1237c, possible phosphatase, len: 324 aa; weak similarity to e.g. GPPA_ECOLI guanosine-5'-triphosphate,3'-diphosphate pyrophosphatase (494 aa), fasta scores; opt: 174 z-score: 201.9 E(): 0.0006, 25.7% identity in 323 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF02541 Ppx/GppA phosphatase family was identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score carried out yet, so kept within product function (previously was posssible). Functional classification -Misc; phosphatase complement(1165564..1166538) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905528 YP_002344629.1 CDS pdxJ NC_002163.1 1166594 1167367 D involved in the de novo synthesis of pyridoxine (Vitamin B6); pyridoxine 5'-phosphate synthase 1166594..1167367 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905529 YP_002344630.1 CDS pdxA NC_002163.1 1167364 1168458 D catalyzes oxidation of 4-(phosphohydroxy)-L-threonine into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which decarboxylates to form 1-amino-3-(phosphohydroxy)propan-2-one (3-amino-2-oxopropyl phosphate); 4-hydroxythreonine-4-phosphate dehydrogenase 1167364..1168458 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905530 YP_002344631.1 CDS Cj1240c NC_002163.1 1168448 1169050 R Original (2000) note: Cj1240c, probable periplasmic protein, len: 200 aa; no Hp match. Functional classification - Miscellaneous periplasmic proteins; periplasmic protein complement(1168448..1169050) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905531 YP_002344632.1 CDS Cj1241 NC_002163.1 1169163 1170362 D Original (2000) note: Cj1241, probable transmembrane transport protein, len: 399 aa; similar to e.g. ARAJ_ECOLI protein ARAJ precursor (394 aa), fasta scores; opt: 579 z-score: 680.4 E(): 1.3e-30, 28.8% identity in 385 aa overlap, and CMLR_STRLI chloramphenicol resistance protein (392 aa), fasta scores; opt: 444 z-score: 523.2 E(): 7.6e-22, 25.5% identity in 380 aa overlap. 27.4% identity to HP1185; Updated (2006) note: Pfam domain PF07690 Major Facilitator Superfamily identified within CDS. Also,twelve 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, so kept within product function. Literature search identified paper giving further clues to product function. Functional classification - Transport/binding proteins - Other; PMID:16048946; MFS transport protein 1169163..1170362 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905532 YP_002344633.1 CDS Cj1242 NC_002163.1 1170418 1170738 D Original (2000) note: Cj1242, unknown, len: 106 aa; no Hp match; Updated (2006) note: Literature search identified papers giving potential clues to product function. Functional classification - Unknown; PMID:14985343, PMID:15812042; hypothetical protein 1170418..1170738 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905533 YP_002344634.1 CDS hemE NC_002163.1 1170922 1171944 D catalyzes the formation of coproporphyrinogen from uroporphyrinogen III; uroporphyrinogen decarboxylase 1170922..1171944 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905534 YP_002344635.1 CDS Cj1244 NC_002163.1 1171941 1172843 D Original (2000) note: Cj1244, unknown, len: 300 aa; similar to hypothetical proteins e.g. YD12_METJA Methanococcus jannaschii MJ1312 (321 aa), fasta scores; opt: 436 z-score: 499.9 E(): 1.5e-20, 30.7% identity in 313 aa overlap. 40.1% identity to HP0117; Updated (2006) 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, so kept within product function. Functional classification -Misc; radical SAM domain protein 1171941..1172843 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905535 YP_002344636.1 CDS Cj1245c NC_002163.1 1172840 1174036 R Original (2000) note: Cj1245c, possible membrane protein, len: 398 aa; no Hp match; Updated (2006) note: Two probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; hypothetical protein complement(1172840..1174036) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905536 YP_002344637.1 CDS uvrC NC_002163.1 1174038 1175840 R The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision; excinuclease ABC subunit C complement(1174038..1175840) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905537 YP_002344638.1 CDS Cj1247c NC_002163.1 1175833 1176327 R Original (2000) note: Cj1247c, unknown, len: 164 aa; 27.1% identity to HP0820. Functional classification -Conserved hypothetical proteins; hypothetical protein complement(1175833..1176327) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905538 YP_002344639.1 CDS guaA NC_002163.1 1176466 1178001 D contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway; GMP synthase 1176466..1178001 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905539 YP_002344640.1 CDS Cj1249 NC_002163.1 1178087 1179547 D Original (2000) note: Cj1249, unknown, len: 486 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein 1178087..1179547 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905540 YP_002344641.1 CDS purD NC_002163.1 1179787 1181037 D catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis; phosphoribosylamine--glycine ligase 1179787..1181037 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905541 YP_002344642.1 CDS Cj1251 NC_002163.1 1181034 1181486 D Original (2000) note: Cj1251, unknown, len: 150 aa; similar to hypothetical proteins e.g. TR:Q56614 (EMBL:U39068) Vibrio cholerae orfY (145 aa), fasta scores; opt: 220 z-score: 291.8 E(): 5.9e-09, 28.6% identity in 140 aa overlap. 27.9% identity to HP1217; Updated (2006) note: Pfam domain PF06271 RDD family identified within CDS. Also, two probable transmembrane helices predicted by TMHMM2.0. Functional classification -Conserved hypothetical proteins; hypothetical protein 1181034..1181486 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905542 YP_002344643.1 CDS Cj1252 NC_002163.1 1181476 1183524 D Original (2000) note: Cj1252, probable periplasmic protein, len: 682 aa; some similarity to proteins involved in outer membrane permeability e.g. OSTA_ECOLI organic solvent tolerance protein precursor (784 aa), fasta scores; opt: 223 z-score: 255.4 E(): 6.3e-07, 20.3% identity in 507 aa overlap. 27.9% identity to HP1216. Contains probable N-terminal signal sequence; Updated (2006) note: Pfam domain PF04453 Organic solvent tolerance protein identified within CDS. No specific characterisation with acceptable identity score identified yet, so kept within product function. Functional classification - Miscellaneous periplasmic proteins; periplasmic protein 1181476..1183524 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905543 YP_002344644.1 CDS pnp NC_002163.1 1183594 1185753 D Original (2000) note: Cj1253, pnp, probable polyribonucleotide nucleotidyltransferase, len: 719 aa; similar to e.g. PNP_ECOLI polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) (711 aa), fasta scores; opt: 1068 z-score: 1130.9 E(): 0, 38.9% identity in 730 aa overlap. 49.2% identity to HP1213. Contains Pfam match to entry PF00575 S1, S1 RNA binding domain, Pfam match to entry PF00013 KH-domain, KH domain family of RNA binding proteins, and Pfam match to entry PF01138 RNase_PH, Prokaryotic ribonuclease PH; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score, so not added to product function. Functional classification - RNA synthesis, RNA modification and DNA transcription; PMID:16079137, PMID:2432069, PMID:10931296; polynucleotide phosphorylase 1183594..1185753 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905544 YP_002344645.1 CDS Cj1254 NC_002163.1 1185750 1186232 D Original (2000) note: Cj1254, unknown, len: 160 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins and also to G/U mismatch-specific DNA glycosyl from other bacteria. Functional classification - Unknown; hypothetical protein 1185750..1186232 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905545 YP_002344646.1 CDS Cj1255 NC_002163.1 1186290 1186499 D Original (2000) note: Cj1255, possible isomerase,len: 69 aa; highly similar to hypothetical protein from Erwinia chrysanthemi YKDK_ERWCH in KDGK (pectin degradation) 5'region (73 aa), fasta scores; opt: 259 z-score: 374.4 E(): 1.5e-13, 61.2% identity in 67 aa overlap. Some similarity to plasmid-borne isomerases involed in toluene degradation e.g. XYLH_PSEPU 4-oxalocrotonate tautomerase (62 aa), fasta scores; opt: 104 z-score: 164.7 E(): 0.071, 30.8% identity in 65 aa overlap, and to chromosomal hypothetical proteins e.g. YDCE_ECOLI (77 aa), fasta scores; opt: 84 z-score: 136.1 E(): 2.8, 27.8% identity in 54 aa overlap. 64.2% identity to HP0924. Also similar to Cj0270 (37.7% identity in 69 aa overlap); Updated (2006) 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; isomerase 1186290..1186499 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905546 YP_002344647.1 CDS Cj1256c NC_002163.1 1186496 1187158 R Original (2000) note: Cj1256c, possible membrane protein, len: 220 aa; no Hp match. Contains possible membrane spanning domain at N-terminus. Functional classification - Membranes, lipoproteins and porins; hypothetical protein complement(1186496..1187158) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905547 YP_002344648.1 CDS Cj1257c NC_002163.1 1187176 1188360 R Original (2000) note: Cj1257c, possible efflux pump, len: 394 aa; similar to TR:CAA07482 (EMBL:AJ007367) Streptococcus pneumoniae multi-drug resistance efflux pump pmrA (399 aa), fasta scores; opt: 854 z-score: 1007.9 E(): 0, 37.6% identity in 380 aa overlap. Also similar hypothetical transporters e.g. YCEE_ECOLI (408 aa), fasta scores; opt: 830 z-score: 965.7 E(): 0, 35.8% identity in 383 aa overlap, and to other members of the major facilitator family, e.g. BMR1_BACSU multidrug resistance protein 1 (389 aa), fasta scores; opt: 345 z-score: 405.2 E(): 2.8e-15, 24.2% identity in 389 aa overlap. No Hp match. Contains Pfam match to entry PF00083 sugar_tr,Sugar (and other) transporters; Updated (2006) note: Pfam domain PF07690 Major Facilitator Superfamily identified within CDS. Also,twelve 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 (PMID:16048946). Functional classification -Drug/analogue sensitivity; PMID:1537791, PMID:11566977, PMID:16048946; efflux pump complement(1187176..1188360) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905548 YP_002344649.1 CDS Cj1258 NC_002163.1 1188414 1188869 D Original (2000) note: Cj1258, possible phosphotyrosine protein phosphatase, len: 151 aa; simlar to e.g. PPAL_YEAST low molecular weight phosphotyrosine protein phosphatase (EC 3.1.3.48) (161 aa), fasta scores; opt: 279 z-score: 343.4 E(): 7.9e-12, 37.6% identity in 149 aa overlap, and YWLE_BACSU low molecular weight protein-tyrosine protein phosphatase (150 aa),fasta scores; opt: 191 z-score: 240.4 E(): 4.3e-06, 27.7% identity in 148 aa overlap. No Hp match; Updated (2006) 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, so kept in product function. Functional classification -Protein translation and modification; phosphotyrosine protein phosphatase 1188414..1188869 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905549 YP_002344650.1 CDS porA NC_002163.1 1189121 1190395 D Original (2000) note: Cj1259, porA, major outer membrane protein (MOMP), len: 424 aa; 94.6% identical to TR:AAC82317 (EMBL:U96452) C. jejuni major outer membrane porin (424 aa), and 98.0% identity to MOMP_CAMJE major outer membrane protein (fragments) (399 aa). No hp match. Also simlar in part to Cj1021c (63 aa, 34.5% identity in 55 aa overlap); Updated (2006) note: Pfam domain PF05538 Campylobacter major outer membrane protein identified within CDS. Further support given to product function. Characterised within Campylobacter jejuni, so not added to product function. Functional classification -Membranes, lipoproteins and porins; PMID:7543469, PMID:9163918; major outer membrane protein 1189121..1190395 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905550 YP_002344651.1 CDS dnaJ NC_002163.1 1190510 1191631 R chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion; molecular chaperone DnaJ complement(1190510..1191631) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905551 YP_002344652.1 CDS racR NC_002163.1 1191788 1192459 D Original (2000) note: Cj1261, racR, two-component regulator, len: 223 aa; identical to TR:O68795 (EMBL:AF053960) C. jejuni response regulator protein (223 aa), and similar to e.g. BAER_ECOLI transcriptional regulatory protein BAER (240 aa), fasta scores; opt: 485 z-score: 583.5 E(): 3.3e-25, 37.4% identity in 219 aa overlap. 52.0% identity to HP0166. Also simlar to Cj1227c (50.7% identity in 223 aa overlap). Contains Pfam match to entry PF00072 response_reg, Response regulator receiver domain, and Pfam match to entry PF00486 trans_reg_C,Transcriptional regulatory protein, C terminal; Updated (2006) note: Characterisation work carried out in Campylobacter jejuni, so not added to product function. Literature search identified paper linking product function to be involved in virulence associated factors (PMID:16392901). Functional classification - Signal transduction; PMID:10322038, PMID:16392901; two-component regulator 1191788..1192459 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905552 YP_002344653.1 CDS racS NC_002163.1 1192456 1193691 D Original (2000) note: Cj1262, racS, probable two-component sensor (histidine kinase), len: 411 aa; 99.5% identical to TR:O68796 (EMBL:AF053961) C. jejuni histidine protein kinase (fragment) (189 aa), and similar to e.g. ENVZ_ECOLI osmolarity sensor protein ENVZ (450 aa), fast scores; opt: 188 z-score: 217.1 E(): 8.5e-05, 24.4% identity in 242 aa overlap. N-term has 28.2% identity to HP0165, C-term has 37.9% identity to HP0164. Also similar to Cj1226c (31.3% identity in 412 aa overlap). Contains Pfam match to entry PF00512 signal,Signal carboxyl-terminal domain, and Pfam match to entry PF00149 STphosphatase, Ser/Thr protein phosphatases; Updated (2006) note: Characterisation work carried out in Campylobacter jejuni, so not added to product function. Functional classification - Signal transduction; PMID:10322038; two-component sensor histidine kinase 1192456..1193691 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905553 YP_002344654.1 CDS recR NC_002163.1 1193691 1194263 D involved in a recombinational process of DNA repair, independent of the recBC complex; recombination protein RecR 1193691..1194263 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905554 YP_002344655.1 CDS hydD NC_002163.1 1194260 1194796 R Original (2000) note: Cj1264c, hydD, probable hydrogenase maturation protease, len: 178 aa; simlar to e.g. HYDD_WOLSU HYDD protein (159 aa), fasta scores; opt: 443 z-score: 561.5 E(): 5.6e-24, 42.5% identity in 160 aa overlap, and HYBD_ECOLI hydrogenase 2 maturation protease (164 aa), fasta scores; opt: 212 z-score: 275.6 E(): 4.7e-08, 28.1% identity in 128 aa overlap. 42.7% identity to HP0634; Updated (2006) 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; PMID:1587288, PMID:2180913, PMID:14726233; hydrogenase maturation protease complement(1194260..1194796) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905555 YP_002344656.1 CDS hydC NC_002163.1 1194793 1195485 R Original (2000) note: Cj1265c, hydC, probable Ni/Fe-hydrogenase B-type cytochrome subunit, len: 230 aa; similar to e.g. CYBH_WOLSU quinone-reactive Ni/Fe-hydrogenase B-type cytochrome subunit (230 aa),fasta scores; opt: 771 z-score: 968.2 E(): 0, 49.8% identity in 225 aa overlap, and CYBH_ECOLI probable Ni/Fe-hydrogenase B-type cytochrome subunit (235 aa),fasta scores; opt: 344 z-score: 437.4 E(): 4.6e-17, 25.5% identity in 231 aa overlap. 41.1% identity to HP0633. Contains PS00883 Nickel-dependent hydrogenases b-type cytochrome subunit signature 2, and fam match to entry PF01292 Ni_hydr_CYTB, Nickel-dependent hydrogenases b-type cytochrome subunit; Updated (2006) note: Four probable transmembrane helices predicted by TMHMM2.0. Characterised within Wolinella succinogenes with acceptable identity score, so not added to product function. Functional classification - Energy metabolism - Respiration; PMID:10525739, PMID:1587288, PMID:2180913; Ni/Fe-hydrogenase B-type cytochrome subunit complement(1194793..1195485) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905556 YP_002344657.1 CDS hydB NC_002163.1 1195496 1197211 R Original (2000) note: Cj1266c, hydB, probable Ni/Fe-hydrogenase large subunit, len: 571 aa; similar to e.g. MBHL_WOLSU quinone-reactive Ni/Fe-hydrogenase large chain (575 aa), fasta scores; opt: 2619 z-score: 3068.8 E(): 0, 65.3% identity in 567 aa overlap, and MBHM_ECOLI hydrogenase-2 large chain (567 aa), fasta scores; opt: 1355 z-score: 1587.5 E(): 0, 42.1% identity in 589 aa overlap. 64.7% identity to HP0632. Contains PS00507 and PS00508 Nickel-dependent hydrogenases large subunit signatures 1 and 2, and Pfam match to entry PF00374 NiFeSe_Hases, Nickel-dependent hydrogenases; Updated (2006) note: Characterised within Wolinella succinogenes, so not added to product function. Functional classification - Energy metabolism -Respiration; PMID:10525739, PMID:1587288, PMID:2180913; Ni/Fe-hydrogenase large subunit complement(1195496..1197211) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905557 YP_002344658.1 CDS hydA NC_002163.1 1197214 1198353 R Original (2000) note: Cj1267c, hydA, probable Ni/Fe-hydrogenase small subunit, len: 379 aa; similar to e.g. MBHS_WOLSU quinone-reactive Ni/Fe-hydrogenase small chain precursor (354 aa), fasta scores; opt: 1968 z-score: 2288.8 E(): 0, 78.1% identity in 351 aa overlap, and MBHS_ECOLI hydrogenase-1 small chain precursor (372 aa),fasta scores; opt: 1058 z-score: 1232.4 E(): 0, 44.0% identity in 361 aa overlap. 68.2% identity to HP0631. Also similar to Cj1399c (50.8% identity in 329 aa overlap); Updated (2006) note: Pfam domain PF01058 NADH ubiquinone oxidoreductase, 20 Kd subunit identified within CDS. Further support given to product function. Characterised within Wolinella succinogenes, so not added to product function. Functional classification -Energy metabolism - Respiration; PMID:10525739, PMID:1587288, PMID:2180913; Ni/Fe-hydrogenase small chain complement(1197214..1198353) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905558 YP_002344659.1 CDS mnmC NC_002163.1 1198474 1200315 R catalyzes the formation of 5-methylaminomethyl-2-thiouridine in position 34 of the anticodon of tRNA molecules; 5-methylaminomethyl-2-thiouridine methyltransferase complement(1198474..1200315) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905559 YP_002344660.1 CDS amiA NC_002163.1 1200312 1202291 R Original (2000) note: Cj1269c, amiA, probable N-acetylmuramoyl-L-alanine amidase, len: 659 aa; similar in N-terminus to many e.g. AMIA_ECOLI probable N-acetylmuramoyl-L-alanine amidase AMIA precursor (EC 3.5.1.28) (289 aa), fasta scores; opt: 393 z-score: 409.5 E(): 1.6e-15, 32.2% identity in 264 aa overlap, and CWLB_BACSU N-acetylmuramoyl-L-alanine amidase CWLB precursor (496 aa), fasta scores; opt: 250 z-score: 260.4 E(): 3.3e-07, 24.9% identity in 365 aa overlap. Similar in N-term to HP0772 (51.8% identity in 253 aa overlap). C-term approx 400 aa appear to be unique. Contains probable N-terminal signal sequence; Updated (2006) 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; PMID:12787347, PMID:6137479, PMID:11454209,PMID:12787347; N-acetylmuramoyl-L-alanine amidase complement(1200312..1202291) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905560 YP_002344661.1 CDS Cj1270c NC_002163.1 1202291 1203382 R Original (2000) note: Cj1270c, unknown, len: 363 aa; similar to hypothetical proteins e.g. TR:O66549 (EMBL:AE000676) Aquifex aeolicus AQ_159 (182 aa), fasta scores; opt: 550 z-score: 647.2 E(): 9.5e-29, 52.2% identity in 161 aa overlap. 61.1% identity to HP0773; Updated (2006) 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, so kept within product function. Functional classification - Misc; 2-nitropropane dioxygenase,oxidoreductase complement(1202291..1203382) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905561 YP_002344662.1 CDS tyrS NC_002163.1 1203379 1204584 R catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr); tyrosyl-tRNA synthetase complement(1203379..1204584) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905562 YP_002344663.1 CDS spoT NC_002163.1 1204596 1206791 R Original (2000) note: Cj1272c, spoT, probable guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase,len: 731 aa; similar to e.g. SPOT_ECOLI guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (EC 3.1.7.2) (702 aa), fasta scores; opt: 1208 z-score: 1408.2 E(): 0, 32.8% identity in 677 aa overlap. 40.7% identity to HP0775. Also similar to e.g. RELA_ECOLI GTP pyrophosphokinase (744 aa), fasta scores; opt: 855 z-score: 995.9 E(): 0, 28.3% identity in 668 aa overlap. There appears to be no distinct relA homolog in Cj or Hp; Updated (2006) note: Pfam domains PF01842 ACT domain, PF02824 TGS domain, PF04607 Region found in RelA / 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, so kept within product function. Literature search identified paper giving further clues to product function. Functional classification - Broad regulatory functions; PMID:15773975, PMID:2549050; guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase complement(1204596..1206791) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905563 YP_002344664.1 CDS rpoZ NC_002163.1 1206775 1206999 R Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits; DNA-directed RNA polymerase subunit omega complement(1206775..1206999) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905564 YP_002344665.1 CDS pyrH NC_002163.1 1207010 1207729 R Catalyzes the phosphorylation of UMP to UDP; uridylate kinase complement(1207010..1207729) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905565 YP_002344666.1 CDS Cj1275c NC_002163.1 1207781 1208974 R Original (2000) note: Cj1275c, probable periplasmic protein, len: 397 aa; weak similarity to hypothetical proteins e.g. YIBP_ECOLI (419 aa), fasta scores; opt: 203 z-score: 198.7 E(): 0.0009, 21.5% identity in 396 aa overlap. 36.4% identity to HP0750. Contains probable N-terminal signal sequence and coiled-coil regions between approx. aa 30-100 and 165-230; Updated (2006) note: Pfam domain PF01551 Peptidase family M23 identified within CDS. Also, 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, so kept within product function. Functional classification - Degradation of macromolecules - Proteins,peptides and glycopeptides. Functional classification -Degradation of macromolecules - Proteins, peptides and glycopeptides; peptidase M23 family protein complement(1207781..1208974) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905566 YP_002344667.1 CDS Cj1276c NC_002163.1 1208971 1209777 R Original (2000) note: Cj1276c, probable integral membrane protein, len: 268 aa; 32.1% identity to HP0749; Updated (2006) 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, lipoproteins and porins; integral membrane protein complement(1208971..1209777) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905567 YP_002344668.1 CDS Cj1277c NC_002163.1 1209764 1210429 R Original (2000) note: Cj1277c, probable ABC transporter ATP-binding protein, len: 221 aa; similar to many e.g. YCFV_ECOLI hypothetical ABC transporter ATP-binding protein (233 aa), fast scores; opt: 464 z-score: 566.5 E(): 2.9e-24, 38.2% identity in 220 aa overlap, and FTSE_ECOLI cell division ATP-binding protein FTSE (222 aa), fasta scores; opt: 455 z-score: 556.0 E(): 1.1e-23, 38.5% identity in 213 aa overlap. 54.8% identity to HP0748. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00211 ABC transporters family signature, and Pfam match to entry PF00005 ABC_tran, ABC transporters; Updated (2006) note: Similar to more than one characterised strain/genus. Literature search added for further information. kept within product function. Functional classification - Transport/binding proteins - Other; PMID:11844772, PMID:10783239, PMID:12823819; ABC transporter ATP-binding protein complement(1209764..1210429) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905568 YP_002344669.1 CDS trmB NC_002163.1 1210499 1211677 R tRNA (guanine-N(7)-)-methyltransferase; catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA by transferring the methyl residue from S-adenosyl-L-methionine; tRNA (guanine-N(7)-)-methyltransferase complement(1210499..1211677) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905569 YP_002344670.1 CDS Cj1279c NC_002163.1 1211677 1212912 R Original (2000) note: Cj1279c, probable fibronectin domain-containing lipoprotein, len: 411 aa; 31.1% 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, Fibronectin type III domain; Updated (2006) note: Specific characterisation with acceptable identity score has not been carried out yet, so kept within product function. Functional classification - Pathogenicity; fibronectin domain-containing lipoprotein complement(1211677..1212912) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905570 YP_002344671.1 CDS Cj1280c NC_002163.1 1212857 1213825 R Original (2000) note: Cj1280c, probable ribosomal pseudouridine synthase, len: 322 aa; similar to e.g. RLUD_ZYMMO ribosomal large subunit pseudouridine synthase D (EC 4.2.1.70) (317 aa), fasta scores; opt: 508 z-score: 590.1 E(): 1.4e-25, 33.5% identity in 310 aa overlap. 51.4% identity to HP0745. Also similar to Cj0708 (26.9% identity in 223 aa overlap), and Cj0022c (31.7% identity in 246 aa overlap). Contains PS01129 Hypothetical yabO/yceC/sfhB family signature, and Pfam match to entry PF00849 YABO, Hypothetical yabO/yceC/sfhB family; Updated (2006) note: No specific characterisation with acceptable identity score carried out yet, so kept within product function. Functional classification - Ribosomal protein synthesis and modification; ribosomal pseudouridine synthase complement(1212857..1213825) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905571 YP_002344672.1 CDS mrdB NC_002163.1 1213903 1215003 D Original (2000) note: Cj1282, mrdB, probable RodA protein homolog, len: 366 aa; similar to e.g. RODA_ECOLI rod shape-determining protein RODA (370 aa), fasta scores; opt: 699 z-score: 837.9 E(): 0, 35.8% identity in 355 aa overlap, and SP5E_BACSU stage V sporulation protein E (366 aa), fasta scores; opt: 526 z-score: 632.0 E(): 6.6e-28,30.3% identity in 337 aa overlap. 52.8% identity to HP0743. Contains Pfam match to entry PF01098 FTSW_RODA_SPOVE, Cell cycle protein; Updated (2006) note: Nine probable transmembrane helices predicted by TMHMM2.0. Homolog designation kept within product function. Functional classification -Murein sacculus and peptidoglycan; PMID:6243629; RodA protein 1213903..1215003 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905572 YP_002344673.1 CDS ktrB NC_002163.1 1215456 1216799 D Original (2000) note: Cj1283, ktrB, probable K+ uptake protein, len: 447 aa; similar to e.g. TR:O87953 (EMBL:D89592) Vibrio alginolyticus K+-uptake system KTRB protein (455 aa), fasta scores; opt: 844 z-score: 981.2 E(): 0, 33.8% identity in 438 aa overlap. Also similar to NTPJ_ENTHR V-type sodium ATP synthase subunit J (451 aa),fasta scores; opt: 853 z-score: 991.7 E(): 0, 33.3% identity in 447 aa overlap, and TRKH_ECOLI TRK system potassium uptake protein TRKH (483 aa), fasta scores; opt: 210 z-score: 247.5 E(): 1.7e-06, 26.8% identity in 426 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF02386 Cation transport protein domain identified within CDS. Also,eleven probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. No specific characterisation with acceptable identity score yet, so kept within product function. Functional classification - Transport/binding proteins - Cations; PMID:16210320, PMID:12562800, PMID:9642210; K+ uptake protein 1215456..1216799 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905575 YP_002344674.1 CDS ktrA NC_002163.1 1216810 1217460 D Original (2000) note: Cj1284, ktrA, probable K+ uptake protein, len: 216 aa; similar to e.g. TR:O87952 (EMBL:D89592) Vibrio alginolyticus K+-uptake system KTRA protein (220 aa), fasta scores; opt: 316 z-score: 371.1 E(): 2.3e-13, 29.2% identity in 212 aa overlap. No Hp match; Updated (2006) 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, so kept within product function. Functional classification - Transport/binding proteins - Cations; PMID:16210320, PMID:12562800, PMID:9642210; K+ uptake protein 1216810..1217460 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905576 YP_002344675.1 CDS Cj1285c NC_002163.1 1217457 1218128 R Original (2000) note: Cj1285c, unknown, len: 223 aa; similar to hypothetical proteins e.g. TR:O29858 (EMBL:AE001077) Archaeoglobus fulgidus AF0389 (249 aa),fasta scores; opt: 120 z-score: 148.0 E(): 0.61, 23.7% identity in 257 aa overlap. 46.8% identity to HP0778; Updated (2006) note: Pfam domains PF02621 Uncharacterized ACR, COG1427 identified within CDS. Conserved added to product funtion. Functional classification - Conserved hypothetical proteins; hypothetical protein complement(1217457..1218128) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905577 YP_002344676.1 CDS upp NC_002163.1 1218134 1218760 R Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate; uracil phosphoribosyltransferase complement(1218134..1218760) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905578 YP_002344677.1 CDS Cj1287c NC_002163.1 1218757 1219992 R Original (2000) note: Cj1287c, probable malate oxidoreductase, len: 411 aa; highly similar to many e.g. MAOX_BACST malate oxidoreductase (NAD) (EC 1.1.1.38) (478 aa), fasta scores; opt: 1193 z-score: 1304.5 E(): 0, 49.9% identity in 411 aa overlap. No Hp match. Contains Pfam match to entry PF00390 malic, Malic enzymes; Updated (2006) note: Characterised in more than one genus with acceptable identity scores, so not added to product function. Functional classification -Central intermediary metabolism - Gluconeogenesis; PMID:1371255, PMID:7798145, PMID:9535928,PMID:36376; malate oxidoreductase complement(1218757..1219992) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905579 YP_002344678.1 CDS gltX NC_002163.1 1219994 1221385 R Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation; glutamyl-tRNA synthetase complement(1219994..1221385) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905580 YP_002344679.1 CDS Cj1289 NC_002163.1 1221450 1222265 D Original (2000) note: Cj1289, possible periplasmic protein, len: 271 aa; 25.8% identity to C-terminus of HP0659. Contains possible N-terminal signal sequence. Functional classification - Miscellaneous periplasmic proteins; periplasmic protein 1221450..1222265 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905581 YP_002344680.1 CDS accC NC_002163.1 1222303 1223634 R biotin carboxylase; biotin carboxylase catalyzes the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-CoA; catalyzes the formation of malonyl-CoA, which in turn controls the rate of fatty acid metabolism; biotin carboxylase complement(1222303..1223634) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905582 YP_002344681.1 CDS accB NC_002163.1 1223636 1224091 R Original (2000) note: Cj1291c, accB, probable biotin carboxyl carrier protein of acetyl-CoA carboxylase,len: 151 aa; similar to e.g. BCCP_ECOLI biotin carboxyl carrier protein of acetyl-CoA carboxylase (EC 6.4.1.2) (156 aa), fasta scores; opt: 307 z-score: 329.6 E(): 4.6e-11, 38.9% identity in 162 aa overlap. 41.4% identity to HP0371. Contains Pfam match to entry PF00364 biotin_req_enzy, Biotin-requiring enzymes; Updated (2006) note: Some characterisation work carried out within Bacillus subtilis. kept within product function. Functional classification - Fatty acid biosynthesis; PMID:7592499, PMID:1358874; biotin carboxyl carrier protein of acetyl-CoA carboxylase complement(1223636..1224091) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905583 YP_002344682.1 CDS dcd NC_002163.1 1224239 1224799 D Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis; deoxycytidine triphosphate deaminase 1224239..1224799 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905584 YP_002344683.1 CDS pseB NC_002163.1 1224849 1225853 D Original (2000) note: Cj1293, possible sugar nucleotide epimerase/dehydratase, len: 334 aa; similar to many e..g TR:Q45984 (EMBL:U27301) Caulobacter crescentus FLAA1 protein (331 aa), fasta scores; opt: 1240 z-score: 1410.9 E(): 0, 57.8% identity in 329 aa overlap,CAPD_STAAU CAPD protein (599 aa), fasta scores; opt: 529 z-score: 602.6 E(): 2.9e-26, 33.9% identity in 319 aa overlap, and TR:O69130 (EMBL:AF064070) Burkholderia pseudomallei epimerase/dehydratase WBII (637 aa),fasta scores; opt: 433 z-score: 493.6 E(): 3.4e-20, 30.5% identity in 282 aa overlap. 64.6% identity to HP0840. Contains PS00017 ATP/GTP-binding site motif A (P-loop; Updated (2006) 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(6) dehydratase activity. This enzyme catalyzes the first step in the biosynthesis of bacillosamine, a sugar found in Campylobacter jejuni glycosylation motifs (PMID:14960321). Recently, 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-2,6-dideoxy-beta-L-arabino-4-hexulose and UDP-2-acetamido-2,6-dideoxy-alpha-D-xylo-4-hexulose (PMID:16286454). Plays a direct role in CMP-Pse5NAc7NAc or CMP-Pse5NAc7Am pathyways. Logan (Susan.Logan@nrc-cnrc.gc.ca) personal communication. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Surface structures; PMID:16421095, PMID:16286454, PMID:14960321,PMID:14617187, PMID:16573682, PMID:12781527; UDP-GlcNAc-specific C4,6 dehydratase/C5 epimerase 1224849..1225853 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905585 YP_002344684.1 CDS pseC NC_002163.1 1225855 1226985 D Original (2000) note: Cj1294, probable aminotransferase, len: 376 aa; similar to many members of the degT family e.g. SPSC_BACSU spore coat polysaccharide biosynthesis protein (389 aa), fasta scores; opt: 586 z-score: 676.7 E(): 2.1e-30, 35.3% identity in 385 aa overlap, and TR:O88001 (EMBL:AJ007747) Bordetella bronchiseptica amino-sugar biosynthesis protein WLBC (366 aa), fasta scores; opt: 482 z-score: 558.1 E(): 8.7e-24, 28.8% identity in 330 aa overlap. 44.8% identity to HP0366 . Contains Pfam match to entry PF01041 DegT_DnrJ_EryC1, DegT/DnrJ/EryC1/StrS family; Updated (2006) note: Specific characterisation with acceptable identity scores has been carried out in Campylobacter jejuni, 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, a C4 epimer of diacetamidobacillosamine not yet described in C. jejuni proteoglycans, suggesting that the composition of C. jejuni proteoglycans is more variable than anticipated (PMID:15790564). Recent work has demonstrated that Cj1294 utilize only UDP-2-acetamido-2,6-dideoxy-beta-L-arabino-4-hexulose as substrate producing UDP-4-amino-4,6-dideoxy-beta-L-AltNAc,a precursor in the pseudaminic acid biosynthetic pathway (PMID:16286454). Plays a direct role in CMP-Pse5NAc7NAc or CMP-Pse5NAc7Am pathyways. Logan (Susan.Logan@nrc-cnrc.gc.ca) personal communication. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Surface structures; PMID:16421095, PMID:15790564, PMID:16286454,PMID:14960321, PMID:14617187, PMID:12704196,PMID:16573682, PMID:12781527; C4 aminotransferase 1225855..1226985 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905586 YP_002344685.1 CDS Cj1295 NC_002163.1 1226978 1228285 D Original (2000) note: Cj1295, unknown, len: 435 aa; no Hp match; Updated (2006) note: PIR (Protein Information Resource) database has a match with IPR012353 Uncharacterised conserved protein, PIRSF01524 polysaccharide biosynthesis aminopeptidase-like protein. Members of this group from Streptomyces sp. and Brucella melitensis are encoded by polysaccharide biosynthesis gene clusters, and are believed to be involved in polysaccharide biosynthesis (PMID:12644223). Members of this group exhibit distant sequence similarity to aminopeptidases. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Unknown; PMID:12644223, PMID:16573682, PMID:12781527; hypothetical protein 1226978..1228285 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905587 YP_002344686.1 CDS Cj1296 NC_002163.1 1228282 1228641 D Original (2000) note: Cj1296, unknown, len: 119 aa; weak similarity to aminoglycoside N3'-acetyltransferases e.g. AAC3_PSEAE aminoglycoside N3'-acetyltransferase III (271 aa), fasta scores; opt: 102 z-score: 144.2 E(): 1,31.7% identity in 60 aa overlap. No Hp match. Similar to N-terminus of Cj1298 (65.7% identity in 105 aa overlap). Similarity continues in downstream ORF Cj1297. There is a G(9) tract at aa 104 that, if variable, would allow translation to continue into Cj1297; Updated (2006) note: Literature search identified paper linking product function of Cj1296/Cj1297/Cj1298 to antimicrobial efflux pumps. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Antibiotic resistance; PMID:16573682, PMID:12781527; hypothetical protein 1228282..1228641 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905588 YP_002344687.1 CDS Cj1297 NC_002163.1 1228638 1229075 D Original (2000) note: Cj1297, unknown, len: 145 aa; no Hp match. Similar to C-terminus of Cj1298 (44.7% identity in 141 aa overlap). Similarity continues from upstream gene Cj1296. There is a G(9) tract upstream of this start that, if variable, would allow translation from Cj1296; Updated (2006) note: Literature search identified paper linking product function of Cj1296/Cj1297/Cj1298 to antimicrobial efflux pumps. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Antibiotic resistance; PMID:16573682, PMID:12781527; hypothetical protein 1228638..1229075 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905589 YP_002344688.1 CDS Cj1298 NC_002163.1 1229096 1229887 D Original (2000) note: Cj1298, unknown, len: 263 aa; weak similarity to aminoglycoside N3'-acetyltransferases e.g. AAC4_SALSP aminoglycoside N3'-acetyltransferase IV (261 aa), fasta scores; opt: 139 z-score: 177.8 E(): 0.014, 25.7% identity in 175 aa overlap. Similar in N- and C-terminus to upstream ORFs Cj1296 (65.7% identity in 105 aa overlap), and Cj1297 (44.7% identity in 141 aa overlap). No Hp match. There is a G(9) tract that, if variable, would allow fusion of Cj1296 and Cj1297. There is no equivalent repetitive tract in this CDS; Updated (2006) note: Literature search identified paper linking product function of Cj1296/Cj1297/Cj1298 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 (Cj1293 - Cj1342). Functional classification - Surface structures; PMID:15790564, PMID:16573682, PMID:12781527; N-acetyltransferase 1229096..1229887 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905590 YP_002344689.1 CDS acpP2 NC_002163.1 1229918 1230148 D Original (2000) note: Cj1299, acpP2, probable acyl carrier protein, len: 76 aa; similar to many e.g. ACPH_MYCGE acyl carrier protein homolog (84 aa), fasta scores; opt: 111 z-score: 172.6 E(): 0.026, 35.8% identity in 81 aa overlap. No Hp match. Also similar to acpP Cj0441 (34.1% identity in 41 aa overlap); Updated (2006) 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 (Cj1293 - Cj1342). Functional classification - Fatty acid biosynthesis; PMID:16573682, PMID:12781527; acyl carrier protein 1229918..1230148 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905591 YP_002344690.1 CDS Cj1300 NC_002163.1 1230145 1231038 D Original (2000) note: Cj1300, unknown, len: 297 aa; no Hp match; Updated (2006) note: Prosite domains PS50193 SAM_BIND, SAM (and some other nucleotide) binding motif and PS50124 MET_TRANS, 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 (Cj1293 - Cj1342). Functional classification - Misc; PMID:16573682, PMID:12781527; SAM domain containing methyltransferase 1230145..1231038 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905592 YP_002344691.1 CDS Cj1301 NC_002163.1 1231031 1231447 D Original (2000) note: Cj1301, unknown, len: 138 aa; similar to a hypothetical protein from Pyrococcus horikoshii TR:O58010 (EMBL:AP000001) PH0272 (136 aa),fasta scores; opt: 137 z-score: 188.8 E(): 0.0032, 32.8% identity in 137 aa overlap. No Hp match; Updated (2006) note: Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Conserved hypothetical proteins; PMID:16573682, PMID:12781527; hypothetical protein 1231031..1231447 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905593 YP_002344692.1 CDS Cj1302 NC_002163.1 1231444 1233006 D Original (2000) note: Cj1302, unknown, len: 520 aa; no Hp match; Updated (2006) note: TIGRFAM domain TIGR01681 HAD-SF-IIIC, 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, so kept within product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Misc; PMID:16573682, PMID:12781527; HAD-superfamily hydrolase 1231444..1233006 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905594 YP_002344693.1 CDS fabH2 NC_002163.1 1232996 1234057 D FabH; beta-ketoacyl-acyl carrier protein synthase III; catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation; differs from 3-oxoacyl-(acyl carrier protein) synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs; paralogs which do not contain the N-X-R ACP-binding site motif; 3-oxoacyl-ACP synthase 1232996..1234057 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905595 YP_002344694.1 CDS acpP3 NC_002163.1 1234057 1234278 D Original (2000) note: Cj1304, acpP3, probable acyl carrier protein, len: 73 aa; similar to e.g. CP_MYXXA acyl carrier protein (78 aa), fasta scores; opt: 101 z-score: 157.0 E(): 0.19, 28.4% identity in 74 aa overlap. No Hp match. Also similar to acpP2 Cj1299 (25.4% identity in 63 aa overlap); Updated (2006) note: No specific charactersiation with acceptable identity score has been carried out yet,so kept within product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Fatty acid biosynthesis; PMID:16573682, PMID:12781527; acyl carrier protein 1234057..1234278 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905596 YP_002344695.1 CDS Cj1305c NC_002163.1 1234292 1235509 R Original (2000) note: Cj1305c, unknown, len: 405 aa; no Hp match. A member of the 617 family of C.j. proteins containing homopolymeric tracts; similar to Cj0617/Cj0618 (38.9% identity in 180 aa overlap/37.1% identity in 221 aa overlap), Cj1306c (78.1% identity in 407 aa overlap), Cj1310c (63.7% identity in 402 aa overlap), Cj1342c (38.0% identity in 426 aa overlap). Contains a variable polyG-tract at aa 194; G(9) (consensus) gives this ORF, G(10) would cause truncation after 22 aa; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Unknown; PMID:16573682, PMID:12781527; hypothetical protein complement(1234292..1235509) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905597 YP_002344696.1 CDS Cj1306c NC_002163.1 1235522 1236748 R Original (2000) note: Cj1306c, unknown, len: 405 aa; no Hp match. A member of the 617 family of C.j. proteins containing homopolymeric tracts; similar to Cj1310c (59.8% identity in 410 aa overlap), Cj1305c (78.1% identity in 407 aa overlap), Cj1342c (38.5% identity in 426 aa overlap) and Cj0617/Cj0618 (39.2% identity in 181 aa overlap/39.5% identity in 220 aa overlap). Contains a variable polyG-tract at aa 194; G(9) (consensus) gives this ORF, G(8) would cause truncation after 5 aa; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Unknown; PMID:16573682, PMID:12781527; hypothetical protein complement(1235522..1236748) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905598 YP_002344697.1 CDS Cj1307 NC_002163.1 1236809 1238317 D Original (2000) note: Cj1307, possible amino acid activating enzyme, len: 502 aa; similar to e.g. DLTA_BACSU D-alanine-activating enzyme (EC 6.3.2.-) (503 aa), fasta scores; opt: 726 z-score: 837.7 E(): 0, 30.3% identity in 495 aa overlap, and to parts of ENTF_ECOLI enterobactin synthetase component F (1293 aa), fasta scores; opt: 549 z-score: 627.8 E(): 1.1e-27, 27.4% identity in 460 aa overlap, and GRSB_BACBR gramicidin S synthetase II (4451 aa), fasta scores; opt: 571 z-score: 644.7 E(): 1.3e-28,29.9% identity in 508 aa overlap. No Hp match. Contains PS00455 AMP-binding domain signature, and Pfam match to entry PF00501 AMP-binding, AMP-binding enzyme; Updated (2006) note: Similar to many different designations, however, no specific characterisation with acceptable identity score carried out yet. kept within product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Cell envelope; PMID:7797557, PMID:16573682, PMID:12781527; amino acid activating enzyme 1236809..1238317 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905599 YP_002344698.1 CDS Cj1308 NC_002163.1 1238357 1238584 D Original (2000) note: Cj1308, acpP4, possible acyl carrier protein, len: 75 aa; some similartiy to e.g. ACP_CYAPA acyl carrier protein (103 aa), fasta scores; opt: 84 z-score: 126.5 E(): 9.5, 31.3% identity in 64 aa overlap. No Hp match; Updated (2006) 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 (Cj1293 - Cj1342). Functional classification - Fatty acid biosynthesis; PMID:7797557, PMID:16573682, PMID:12781527; acyl carrier protein 1238357..1238584 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905600 YP_002344699.1 CDS Cj1309c NC_002163.1 1238581 1239651 R Original (2000) note: Cj1309c, unknown, len 356 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Unknown; PMID:16573682, PMID:12781527; hypothetical protein complement(1238581..1239651) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905601 YP_002344700.1 CDS Cj1310c NC_002163.1 1239673 1240887 R Original (2000) note: Cj1310c, unknown, len: 404 aa; no Hp match. A member of the 617 family of C.j. proteins containing homopolymeric tracts; similar to Cj1305c (63.7% identity in 402 aa overlap), Cj1306c (59.8% identity in 410 aa overlap), Cj1342c (37.1% identity in 426 aa overlap) and Cj0617/Cj0618 (37.4% identity in 182 aa overlap/34.1% identity in 220 aa overlap). Contains a variable polyG-tract at aa 194; G(9) (consensus) gives this ORF, G(10) would cause truncation after 22 aa; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Unknown; PMID:16573682, PMID:12781527; hypothetical protein complement(1239673..1240887) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905602 YP_002344701.1 CDS pseF NC_002163.1 1240966 1241664 D Original (2000) note: Cj1311, neuA2, probable acylneuraminate cytidylyltransferase (CMP-N-acetylneuraminic acid synthetase), len: 232 aa; simlar to e.g. NEUA_ECOLI acylneuraminate cytidylyltransferase (EC 2.7.7.43) (CMP-N-acetylneuraminic acid synthetase) (419 aa), fasta scores; opt: 316 z-score: 379.1 E(): 8.2e-14, 29.0% identity in 231 aa overlap. 39.6% identity to HP0326. Also similar to Cj1143 (31.6% identity in 215 aa overlap), and Cj1331 (32.9% identity in 234 aa overlap); Updated (2006) 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 (Cj1293 - Cj1342). Functional classification - Surface polysaccharides, lipopolysaccharides and antigens; PMID:2549035, PMID:16573682, PMID:12781527; acylneuraminate cytidylyltransferase 1240966..1241664 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905603 YP_002344702.1 CDS pseG NC_002163.1 1241648 1242472 D Original (2000) note: Cj1312, possible flagellar protein, len: 274 aa; similar to e.g. SPSG_BACSU spore coat polysaccharide biosynthesis protein SPSG (222 aa),fasta scores; opt: 166 z-score: 208.1 E(): 0.00028, 24.8% identity in 226 aa overlap, and TR:Q45987 (EMBL:U27302) Caulobacter crescentus FLAR (329 aa), fasta scores; opt: 234 z-score: 286.7 E(): 1.2e-08, 23.1% identity in 277 aa overlap; Updated (2006) note: Characterised in Campylobacter jejuni (PMID:16728396). Product function further updated. not added to product function. Plays a direct role in CMP-Pse5NAc7NAc or CMP-Pse5NAc7Am pathyways. Logan (Susan.Logan@nrc-cnrc.gc.ca) personal communication. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Surface structures; PMID:16728396, PMID:16751642, PMID:16573682,PMID:12781527, PMID:16684771, PMID:16728396; nucleotidase specific for PseC product,UDP-4-amino-4,6-dideoxy-beta-L-AltNAc 1241648..1242472 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905604 YP_002344703.1 CDS pseH NC_002163.1 1242469 1242942 D Original (2000) note: Cj1313, possible flagellar protein, len: 157 aa; similar to e.g. TR:Q45990 (EMBL:U28867) Caulobacter crescentus FLAG. 31.9% identity to HP0327; Updated (2006) note: Pfam domain PF00583 Acetyltransferase (GNAT) 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, 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 (Susan.Logan@nrc-cnrc.gc.ca) personal communication. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Surface structures; PMID:16684771, PMID:16751642, PMID:9748431,PMID:16573682, PMID:12781527; N-acetyltransferase specific for PseC product,UDP-4-amino-4,6-dideoxy-beta-L-AltNAc 1242469..1242942 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905605 YP_002344704.1 CDS hisF NC_002163.1 1242907 1243653 R catalyzes the conversion of 5-[(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino]- 1-(5-phosphoribosyl)imidazole-4-carboxamide and glutamine to imidazole-glycerolphosphate, 5-aminoimidazol-4-carboxamideribonucleotide and glutamate; the HisF subunit acts as a cyclase; imidazole glycerol phosphate synthase subunit HisF complement(1242907..1243653) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905606 YP_002344705.1 CDS hisH NC_002163.1 1243654 1244259 R with HisF IGPS catalyzes the conversion of phosphoribulosyl-formimino-5-aminoimidazole-4-carboxamide ribonucleotide phosphate and glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamide ribonucleotide, and glutamate in histidine biosynthesis; 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; imidazole glycerol phosphate synthase subunit HisH complement(1243654..1244259) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905607 YP_002344706.1 CDS pseA NC_002163.1 1244256 1245392 R Original (2000) note: Cj1316c, unknown, len: 378 aa; similar to e.g. TR:P72140 (EMBL:U50396) Pseudomonas aeruginosa WBPG (lipopolysaccharide gene cluster) (376 aa), fasta scores; opt: 257 z-score: 302.0 E(): 1.6e-09,23.5% identity in 366 aa overlap. No Hp match. Also similar to Cj1324 (33.2% identity in 373 aa overlap); Updated (2006) note: Prosite domain PS00761 SPASE_I_3, Peptidase S26A, 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 (PseAm) directly from PseAc by transfer of an acetamidino group (PMID:11461915). Plays a direct role in CMP-Pse5NAc7NAc or CMP-Pse5NAc7Am biosynthesis or transfer. Logan (Susan.Logan@nrc-cnrc.gc.ca) personal communication. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Surface structures; PMID:16573682, PMID:12781527, PMID:16684771; pseudaminic acid biosynthesis PseA protein complement(1244256..1245392) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905608 YP_002344707.1 CDS pseI NC_002163.1 1245650 1246681 D Original (2000) note: Cj1317, neuB3,N-acetylneuraminic acid synthetase, len: 343 aa; 97.6% identical to TR:O52907 (EMBL:AJ000855) C. jejuni neuB, and similar to e.g. TR:Q57265 (EMBL:U40740) Neisseria meningitidis N-acetylneuraminic acid synthetase (EC 4.1.3.-) (349 aa), fasta scores; opt: 584 z-score: 664.1 E(): 1.1e-29, 35.1% identity in 350 aa overlap. 49.5% identity to HP0178. Also similar to Cj1327 (36.3% identity in 336 aa overlap), and Cj1141 (34.7% identity in 340 aa overlap); Updated (2006) 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 (Susan.Logan@nrc-cnrc.gc.ca) personal communication. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Surface structures; PMID:11461915, PMID:16120604, PMID:10712693,PMID:11832511, PMID:16421095; Pse synthetase 1245650..1246681 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905609 YP_002344708.1 CDS maf1 NC_002163.1 1246678 1248627 D Original (2000) note: Cj1318, unknown, len: 649 aa; no Hp ortholog, but 33.9% identity to HP0114. A member of the 1318 family of proteins. Similar to Cj1335/Cj1336 (100.0% identity in 59 aa overlap/100.0% identity in 592 aa overlap), Cj1333 (72.5% identity in 658 aa overlap),Cj1334 (41.5% identity in 648 aa overlap), Cj1337 (48.1% identity in 643 aa overlap), Cj1341c (30.2% identity in 640 aa overlap), Cj1340c (31.4% identity in 641 aa overlap). Contains G(10-11) polymorphic tract at aa 57. G(11) (consensus) gives this ORF, G(10) causes truncation after 1 aa; Updated (2006) note: Pfam domain PF01973 Protein of unknown function DUF115 identified within CDS. Characterisation work has been carried out within Campylobacter jejuni (PMID:11895937). Product function modified to more specific family member. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Misc; PMID:11895937, PMID:16573682, PMID:12781527; motility accessory factor 1246678..1248627 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905610 YP_002344709.1 CDS Cj1319 NC_002163.1 1248624 1249595 D Original (2000) note: Cj1319, probable nucleotide sugar dehydratase, len: 323 aa; similar to e.g. TR:Q54116 (EMBL:L37354) thymidine diphosphoglucose 4,6-dehydratase (329 aa), fasta scores; opt: 526 z-score: 600.3 E(): 3.9e-26, 29.5% identity in 315 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00106 adh_short,Alcohol/other dehydrogenases, short chain type; Updated (2006) note: Pfam domain now altered to PF01370 NAD dependent epimerase/dehydratase 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 (Cj1293 - Cj1342). Functional classification -Surface polysaccharides, lipopolysaccharides and antigens; PMID:16573682, PMID:12781527; nucleotide sugar dehydratase 1248624..1249595 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905611 YP_002344710.1 CDS Cj1320 NC_002163.1 1249588 1250742 D Original (2000) note: Cj1320, probable aminotransferase, len: 384 aa; similar to members of the degT family e.g. TR:Q06953 (EMBL:X59554) Vibrio cholerae RFBE protein (367 aa), fasta scores; opt: 315 z-score: 377.4 E(): 1e-13, 32.7% identity in 361 aa overlap. No Hp ortholog. Contains Pfam match to entry PF01041 DegT_DnrJ_EryC1, DegT/DnrJ/EryC1/StrS family; Updated (2006) 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 (Cj1293 - Cj1342). Functional classification - Surface polysaccharides, lipopolysaccharides and antigens; PMID:16573682, PMID:12781527; DegT family aminotransferase 1249588..1250742 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905612 YP_002344711.1 CDS Cj1321 NC_002163.1 1250852 1251394 D Original (2000) note: Cj1321, probable transferase,len: 180 aa; similar to TR:Q46674 (EMBL:U05248) E. coli polysialic acid gene cluster region 2 neuD (207 aa), fasta scores; opt: 267 z-score: 337.2 E(): 1.8e-11, 29.6% identity in 162 aa overlap, some simialrity to e.g. LPXA_BRUAB acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase (283 aa), fasta scores; opt: 134 z-score: 173.4 E(): 0.025, 31.6% identity in 95 aa overlap. No Hp match. Also similar to Cj1123c wlaI (30.2% identity in 179 aa overlap). Contains 2x Pfam match to entry PF00132 hexapep, Bacterial transferase hexapeptide (four repeats). Upstream region contains a G(10-11) hypervariable tract; Updated (2006) 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 (Cj1293 - Cj1342). Literature search identified paper linking Cj1321-Cj1326 as being a glycosylation islet (PMID:16230626). Functional classification - Surface polysaccharides, lipopolysaccharides and antigens; PMID:16230626, PMID:11832511, PMID:16573682,PMID:12781527; transferase 1250852..1251394 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905613 YP_002344712.1 CDS Cj1322 NC_002163.1 1251467 1251787 D Original (2000) note: Cj1322, unknown, len: 106 aa; no Hp match; Updated (2006) note: Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Literature search identified paper linking Cj1321-Cj1326 as being a glycosylation islet (PMID:16230626). Functional classification - Unknown; PMID:16230626, PMID:12586395, PMID:16573682,PMID:12781527; hypothetical protein 1251467..1251787 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905614 YP_002344713.1 CDS Cj1323 NC_002163.1 1251775 1252161 D Original (2000) note: Cj1323, unknown, len: 128 aa; no Hp match; Updated (2006) note: Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Literature search identified paper linking Cj1321-Cj1326 as being a glycosylation islet (PMID:16230626). Functional classification - Unknown; PMID:16230626, PMID:16573682, PMID:12781527; hypothetical protein 1251775..1252161 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905615 YP_002344714.1 CDS Cj1324 NC_002163.1 1252278 1253399 D Original (2000) note: Cj1324, unknown, len: 373 aa; some similarity to TR:P72140 (EMBL:U50396) Pseudomonas aeruginosa WBPG (lipopolysaccharide gene cluster) (376 aa), fasta scores; opt: 166 z-score: 199.7 E(): 0.0008,20.1% identity in 378 aa overlap. No Hp match. Also similar to Cj1316c; Updated (2006) note: Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Literature search identified paper linking Cj1321-Cj1326 as being a glycosylation islet (PMID:16230626). Also shows some similarity to Cj1316 pseudaminic acid biosynthesis PseA protein. Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:16230626, PMID:16573682, PMID:12781527; hypothetical protein 1252278..1253399 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905616 YP_002344715.1 CDS Cj1325 NC_002163.1 1253417 1254092 D Original (2000) note: Cj1326, unknown, len: 140 aa; no Hp match. Contains polyporphic sequence G(9-10) at N-terminus; G(9) allows translation from the upstream CDS Cj1325, G(10) (consensus) would only allow this CDS to start at aa 22. Similar to Cj0171 (51.9% identity in 135 aa overlap), which also contains a polymorphic sequence allowing possible translation from Cj0170; Original (2000) note: Cj1325, unknown, len: 89 aa; no Hp match. Contains polyporphic sequence G(9-10) at C-terminus; G(10) (consensus) gives this translation stop,G(9) allows translation into the downstream CDS Cj1326. Similar to Cj0170 (73.8% identity in 61 aa overlap), which also contains a polymorphic sequence allowing possible translation into Cj0171; Updated (2006) 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 (Cj1293 - Cj1342). Literature search identified paper linking Cj1321-Cj1326 as being a glycosylation islet (PMID:16230626). 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; PMID:16230626, PMID:14985343; methyltransferase join(1253417..1253671,1253673..1254092) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905617 YP_002344716.1 CDS neuB2 NC_002163.1 1254132 1255136 D Original (2000) note: Cj1327, neuB2,N-acetylneuraminic acid synthetase, len: 334 aa; similar to e.g. TR:Q46675 (EMBL:U05248) E.coli polysialic acid gene cluster region 2 neuB (346 aa), fasta scores; opt: 1112 z-score: 1285.6 E(): 0, 51.5% identity in 336 aa overlap, and TR:Q57265 (EMBL:U40740) Neisseria meningitidis N-acetylneuraminic acid synthetase (EC 4.1.3.-) (349 aa), fasta scores; opt: 624 z-score: 724.6 E(): 4.6e-33, 34.5% identity in 333 aa overlap; Updated (2006) note: Pfam domains PF03102 NeuB family was identified within CDS. Prosite domains PS00141 ASP_PROTEASE, Peptidase aspartic, active site and PS00867 CPSASE_2, Carbamoyl-phosphate synthase L chain,ATP-binding were both identified within CDS. Further support given to product function. Characterised within Campylobacter jejuni (PMID:10712693). not added to product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:10712693, PMID:16573682, PMID:12781527; N-acetylneuraminic acid synthetase 1254132..1255136 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905619 YP_002344717.1 CDS neuC2 NC_002163.1 1255129 1256283 D Original (2000) note: Cj1328, neuC2, probable N-acetylglucosamine-6-phosphate 2-epimerase/N-acetylglucosamine-6-phosphatase, len: 371 aa; similar to e.g. TR:Q47400 (EMBL:M84026) E. coli neuC (391 aa), fasta scores; opt: 779 z-score: 889.7 E(): 0,36.1% identity in 388 aa overlap, and TR:Q57141 (EMBL:X78068) Neisseria meningitidis N-acetylglucosamine-6-phosphate 2-epimerase (EC 5.1.3.-) / N-acetylglucosamine-6-phosphatase (EC 3.1.3.-) (377 aa),fatsta scores; opt: 561 z-score: 642.7 E(): 1.7e-28, 33.5% identity in 391 aa overlap. No Hp match. Also similar to Cj1142 (34.6% identity in 384 aa overlap); Updated (2006) note: Some characterisation work within Campylobacter coli (PMID:8825781, PMID:12406231). Product function updated and kept within product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Surface structures; PMID:10712693, PMID:16573682, PMID:12781527,PMID:16481326, PMID:12406231, PMID:8825781; UDP-N-acetylglucosamine 2-epimerase 1255129..1256283 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905620 YP_002344718.1 CDS Cj1329 NC_002163.1 1256292 1257317 D Original (2000) note: Cj1329, probable sugar-phosphate nucleotide transferase, len: 341 aa; similar in C-term (120 aa - end) to many predicted transferases, and to MPG1_YEAST mannose-1-phosphate guanyltransferase (361 aa), fasta scores; opt: 304 z-score: 343.2 E(): 8.1e-12, 28.9% identity in 225 aa overlap. N-term has some similarity to CBS domains in nucleotide dehydrogenases e.g. IMDH_BACSU inosine-5'-monophosphate dehydrogenase (513 aa), blastp scores; E=0.00034, 30% identity in 116 overlap. N-term contains 2x Pfam match to entry PF00571 CBS, CBS domain,C-term contains Pfam match to entry PF00483 NTP_transferase, Nucleotidyl transferase. No Hp match. Also similar in C-terminus to Cj1423c (35.6% identity in 216 aa overlap); Updated (2006) note: Some characterisation work carried out in Campylobacter coli (PMID:12406231). Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:16573682, PMID:12781527, PMID:12406231; sugar-phosphate nucleotide transferase 1256292..1257317 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905621 YP_002344719.1 CDS Cj1330 NC_002163.1 1257314 1258219 D Original (2000) note: Cj1330, unknown, len: 301 aa; some similarity to predicted oxidoreductases e.g. TR:O26961 (EMBL:AE000863) Methanobacterium thermoautotrophicum MTH875 (predicted 3-chlorobenzoate-3,4-dioxygenase dyhydrogenase related protein) (318 aa), fasta scores; opt: 199 z-score: 244.0 E(): 2.7e-06, 24.7% identity in 267 aa overlap, and TR:Q53739 (EMBL:X92429) Streptomyces alboniger predicted oxido-reductase (338 aa), fasta scores; opt: 135 z-score: 167.8 E(): 0.048, 27.0% identity in 196 aa overlap. No Hp match; Updated (2006) note: Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Conserved hypothetical proteins; PMID:16573682, PMID:12781527; hypothetical protein 1257314..1258219 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905622 YP_002344720.1 CDS ptmB NC_002163.1 1258212 1258919 D Original (2000) note: Cj1331, ptmB, neuA3, probable acylneuraminate cytidylyltransferase (CMP-N-acetylneuraminic acid synthetase), len: 235 aa; 83.8% identical to PTMB_CAMCO posttranslational flagellin modification protein B (235 aa), and simlar to e.g. NEUA_NEIME acylneuraminate cytidylyltransferase (EC 2.7.7.43) (228 aa), fasta scores; opt: 357 z-score: 438.8 E(): 3.8e-17, 30.1% identity in 226 aa overlap. No Hp ortholog. Also similar to e.g. Cj1311 neuA2 (32.9% identity in 234 aa overlap) and Cj1143 neuA (34.7% identity in 219 aa overlap); Updated (2006) note: Pfam domain PF02348 Cytidylyltransferase identified within CDS. Further support given to product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Surface structures; PMID:16573682, PMID:12781527, PMID:8825781; acylneuraminate cytidylyltransferase 1258212..1258919 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905623 YP_002344721.1 CDS ptmA NC_002163.1 1258919 1259689 D Original (2000) note: Cj1332, ptmA, probable oxidoreductase, len: 256 aa; 79.3% identical to PTMA_CAMCO posttranslational flagellin modification protein A (256 aa), and similar to e.g. DHG2_BACME glucose 1-dehydrogenase II (261 aa), fasta scores; opt: 236 z-score: 281.8 E(): 2.1e-08, 24.1% identity in 261 aa overlap. No Hp ortholog. Contains fam match to entry PF00106 adh_short, Alcohol/other dehydrogenases, short chain type, and Pfam match to entry PF00678 adh_short_C2,Short chain dehydrogenase/reductase C-terminus; Updated (2006) note: kept within product function. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Surface structures; PMID:16573682, PMID:12781527, PMID:8825781; flagellin modification protein A 1258919..1259689 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905624 YP_002344722.1 CDS pseD NC_002163.1 1259677 1261638 D Original (2000) note: Cj1333, unknown, len: 653 aa; no Hp ortholog, but 34.6% identity to HP0114. A member of the 1318 family of proteins. Similar to Cj1318 (72.5% identity in 658 aa overlap), Cj1337 (48.6% identity in 636 aa overlap), Cj1334 (41.8% identity in 644 aa overlap),Cj1340c (30.4% identity in 615 aa overlap), Cj1341c (31.2% identity in 616 aa overlap) and Cj1335/Cj1336 (94.2% identity in 52 aa overlap/71.7% identity in 597 aa overlap); Updated (2006) note: Pfam domain PF01973 Protein of unknown function DUF115 identified within CDS. Characterised work has been carried out within Campylobacter jejuni (PMID:16573682) and noted to play a role in attachment of pseudaminic acid. Previously designated at Maf2 (motility accessory protein). Recently shown to play no part in CMP-Pse5NAc7NAc or CMP-Pse5NAc7Am pathyways. Logan (Susan.Logan@nrc-cnrc.gc.ca) personal communication. Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Misc; PMID:11832511, PMID:11895937, PMID:16573682,PMID:12781527, PMID:11895937, PMID:16573682; PseD protein 1259677..1261638 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905625 YP_002344723.1 CDS maf3 NC_002163.1 1261635 1263494 D Original (2000) note: Cj1334, unknown, len: 619 aa; no Hp ortholog, but 34.8% identity to HP0114. A member of the 1318 family of proteins. Similar to Cj1333 (41.9% identity in 645 aa overlap), Cj1318 (41.0% identity in 647 aa overlap), Cj1336 (41.9% identity in 590 aa overlap),Cj1337 (43.8% identity in 628 aa overlap), Cj1341c (34.3% identity in 621 aa overlap), and Cj1340c (34.0% identity in 618 aa overlap); Updated (2006) 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 (Cj1293 - Cj1342). Functional classification - Misc; PMID:11832511, PMID:16573682, PMID:12781527,PMID:16573682; motility accessory factor 1261635..1263494 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905626 YP_002344724.1 CDS maf4 NC_002163.1 1263507 1265454 D Original (2000) note: Cj1335, unknown, len: 60 aa; no Hp match. A member of the 1318 family of proteins. Identical to the N-terminus of Cj1318 (100.0% identity in 59 aa overlap) and similar to Cj1333 (94.2% identity in 52 aa overlap). Contains a G(9-10) polymorphic region at aa 57. G(9) (consensus) gives this ORF, G(10) would extend the ORF by 18 aa. G(8) or G(11) (not seen in shotgun) would allow translation into the downstream ORF Cj1336,giving a protein similar to other members of the 1318 family; Original (2000) note: Cj1336, unknown, len: 593 aa; no Hp ortholog, but 34.0% identity to HP0114. A member of the 1318 family of proteins. Identical to Cj1318 (except the C-term, 100.0% identity in 592 aa overlap), ands similar to Cj1333 (71.7% identity in 597 aa overlap),Cj1334 (42.3% identity in 591 aa overlap), Cj1337 (48.6% identity in 586 aa overlap), Cj1341c (30.8% identity in 578 aa overlap) and Cj1340c (32.0% identity in 579 aa overlap). Contains a G(9-10) polymorphic region at aa 2. G(9) (consensus) gives this ORF, G(10) would allow translation to start at aa 21. G(8) or G(11) (not seen in shotgun) would allow translation from the upstream ORF Cj1335, giving a protein similar to other members of the 1318 family; Updated (2006) 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 (Cj1293 - Cj1342). 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; PMID:11832511, PMID:16573682, PMID:12781527; motility accessory factor join(1263507..1263677,1263676..1265454) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905627 YP_002344725.1 CDS pseE NC_002163.1 1265451 1267337 D Original (2000) note: Cj1337, unknown, len: 628 aa; 35.0% identity to HP0114. A member of the 1318 family of proteins. Simlar to Cj1333 (48.6% identity in 636 aa overlap), Cj1318 (48.1% identity in 643 aa overlap),Cj1336 (48.6% identity in 586 aa overlap), Cj1334 (43.6% identity in 628 aa overlap), Cj1340c (32.2% identity in 624 aa overlap), Cj1341c (31.9% identity in 627 aa overlap); Updated (2006) 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, however, may be involved in glycan transfer to flagellin (PMID:16684771). Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Misc; PMID:16684771, PMID:16573682, PMID:12781527,PMID:11461915; PseE protein 1265451..1267337 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905629 YP_002344726.1 CDS flaB NC_002163.1 1267368 1269086 R FlaB; structural flagella protein; in Helicobacter the flagella are composed of flagellin A and flagellin B; the amounts of each seem to be controlled by environmental conditions; flagellin complement(1267368..1269086) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905630 YP_002344727.1 CDS flaA NC_002163.1 1269232 1270950 R FlaA; structural flagella protein; in Helicobacter the flagella are composed of flagellin A and flagellin B; the amounts of each seem to be controlled by environmental conditions; flagellin complement(1269232..1270950) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905631 YP_002344728.1 CDS Cj1340c NC_002163.1 1271047 1272864 R Original (2000) note: Cj1340c, unknown, len: 605 aa; no Hp ortholog, but 28.5% identity to HP0114. A member of the 1318 family of proteins. Similar to Cj1341c (83.4% identity in 598 aa overlap), Cj1337 (32.5% identity in 625 aa overlap), Cj1333 (30.4% identity in 615 aa overlap),Cj1336 (32.0% identity in 579 aa overlap), Cj1318 (31.4% identity in 641 aa overlap), and Cj1334 (34.1% identity in 618 aa overlap); Updated (2006) 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 (PMID:11895937). Identifed as part of Campylobacter jejuni O-linked glycosylation locus (Cj1293 - Cj1342). Functional classification - Conserved hypothetical proteins; PMID:11895937, PMID:16573682, PMID:12781527; hypothetical protein complement(1271047..1272864) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905632 YP_002344729.1 CDS maf6 NC_002163.1 1272861 1274684 R Original (2000) note: Cj1341c, unknown, len: 607 aa; no Hp ortholog, but 28.4% identity to HP0114. A member of the 1318 family of proteins. Similar to Cj1340c (83.4% identity in 598 aa overlap), Cj1334 (34.6% identity in 622 aa overlap), Cj1336 (30.8% identity in 578 aa overlap),Cj1333 (31.2% identity in 616 aa overlap), Cj1318 (30.2% identity in 640 aa overlap), and Cj1337 (32.0% identity in 628 aa overlap); Updated (2006) 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 (Cj1293 - Cj1342). Functional classification - Misc; PMID:11832511, PMID:16573682, PMID:12781527,PMID:16573682; motility accessory factor complement(1272861..1274684) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905633 YP_002344730.1 CDS maf7 NC_002163.1 1274694 1275935 R Original (2000) note: Cj1342c, unknown, len: 413 aa; no Hp match. A member of the 617 family of C.j. proteins containing homopolymeric tracts; similar to Cj1310c (37.3% identity in 424 aa overlap), Cj1305c (38.5% identity in 423 aa overlap), Cj0617/Cj0618 (49.7% identity in 191 aa overlap/43.4% identity in 221 aa overlap),Cj1306c (38.3% identity in 426 aa overlap). Contains C(9-10) polymorphic region at aa 188. C(9) consensus gives this ORF, C(10) gives truncation after a further 19 aa; Updated (2006) 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 (Cj1293 - Cj1342). Functional classification - Misc; PMID:11832511, PMID:16573682, PMID:12781527,PMID:16573682; motility accessory factor complement(1274694..1275935) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905634 YP_002344731.1 CDS Cj1343c NC_002163.1 1275935 1276450 R Original (2000) note: Cj1343c, probable periplasmic protein, len: 171 aa; no Hp match. Some similarity to N-terminus of secretion proteins e.g. GSPG_ECOLI general secretion pathway protein (145 aa), fasta scores; opt: 153 z-score: 192.8 E(): 0.0019, 35.6% identity in 59 aa overlap. Contains probable N-terminal signal sequence; Updated (2006) 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; PMID:12949093; periplasmic protein complement(1275935..1276450) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905635 YP_002344732.1 CDS Cj1344c NC_002163.1 1276451 1277458 R in most organisms, only the N-terminal domain is present in a single polypeptide; in some archaea this domain is fused to a kinase domain; this gene is essential for growth in Escherichia coli and Bacillus subtilis; the secreted glycoprotease from Pasteurella haemolytica showed specificity for O-sialoglycosylated proteins; the Pyrococcus structure shows DNA-binding properties, iron-binding, ATP-binding, and AP endonuclease activity; DNA-binding/iron metalloprotein/AP endonuclease complement(1276451..1277458) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905636 YP_002344733.1 CDS Cj1345c NC_002163.1 1277455 1278849 R Original (2000) note: Cj1345c, probable periplasmic protein, len: 464 aa; 41.2% identity to HP1075. Contains probable N-terminal signal sequence; Updated (2006) note: Paper identified linking protein to glycoprotein. Functional classification -Miscellaneous periplasmic proteins; PMID:12186869; periplasmic protein complement(1277455..1278849) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905637 YP_002344734.1 CDS dxr NC_002163.1 1278851 1279921 R catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate; 1-deoxy-D-xylulose 5-phosphate reductoisomerase complement(1278851..1279921) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905638 YP_002344735.1 CDS cdsA NC_002163.1 1279918 1280643 R Original (2000) note: Cj1347c, cdsA, probable phosphatidate cytidylyltransferase, len: 241 aa; similar to e.g. CDSA_ECOLI phosphatidate cytidylyltransferase (EC 2.7.7.41) (249 aa), fasta scores; opt: 381 z-score: 465.5 E(): 1.2e-18, 40.7% identity in 182 aa overlap. 39.3% identity to HP0215. Contains PS01315 Phosphatidate cytidylyltransferase signature, and Pfam match to entry PF01148 Cytidylyltrans, Phosphatidate cytidylyltransferase; Updated (2006) 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; PMID:9083091, PMID:2995359; phosphatidate cytidylyltransferase complement(1279918..1280643) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905639 YP_002344736.1 CDS Cj1348c NC_002163.1 1280652 1280990 R Original (2000) note: Cj1348c, probable coiled-coil protein, len: 112 aa; Lys-, Glu-rich, highly hydrophilic,contains probable coiled-coil from approx aa 50-80. No Hp match. Functional classification - Unknown; coiled-coil protein complement(1280652..1280990) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905640 YP_002344737.1 CDS Cj1349c NC_002163.1 1280992 1282299 R Original (2000) note: Cj1349c, possible fibronectin/fibrinogen-binding protein, len: aa; similar to TR:Q54858 (EMBL:L28919) Streptococcus pyogenes fibronectin/fibrinogen-binding protein FBP54 (474 aa),fasta scores; opt: 213 z-score: 230.0 E(): 1.7e-05, 23.2% identity in 466 aa overlap. 30.6% identity to HP1392; Updated (2006) note: Pfam domain PF05670 Domain of unknown function (DUF814) identified within CDS. No specific characterisation with acceptable identity score carried out yet, so kept within product function. Functional classification - Pathogenicity; fibronectin/fibrinogen-binding protein complement(1280992..1282299) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905641 YP_002344738.1 CDS mobA NC_002163.1 1282361 1282936 D Original (2000) note: Cj1350, mobA, probable molybdopterin-guanine dinucleotide biosynthesis protein,len: 191 aa; similar to e.g. MOBA_ECOLI molybdopterin-guanine dinucleotide biosynthesis protein A (194 aa), fasta scores; opt: 194 z-score: 249.0 E(): 1.5e-06, 22.9% identity in 192 aa overlap. 26.6% identity to HP0769; Updated (2006) note: Some characterisation in Escherichia coli, however, identity score was unacceptable. Thus, kept within product function. Functional classification - Biosynthesis of cofactors,prosthetic groups and carriers - Molybdopterin; PMID:10978347; molybdopterin-guanine dinucleotide biosynthesis protein 1282361..1282936 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905642 YP_002344739.1 CDS pldA NC_002163.1 1282933 1283922 D Original (2000) note: Cj1351, pldA, probable phospholipase A, len: 329 aa; highly similar to TR:O32349 (EMBL:Y11031) Campylobacter coli phospholipase A (297 aa),fasta scores; opt: 1544 z-score: 1835.1 E(): 0, 75.2% identity in 298 aa overlap, and similar to e.g. PA1_ECOLI phospholipase A1 precursor (EC 3.1.1.32) (289 aa), fasta scores; opt: 467 z-score: 560.5 E(): 6.4e-24, 34.7% identity in 262 aa overlap. 25.5% identity to HP0499. Contains probable N-terminal signal sequence; Updated (2006) note: Pfam domain PF02253 Phospholipase A1 identified within CDS. Further support given to product function. Characterised within Campylobacter coli, so not added to product function (PMID:9119448). Functional classification -Pathogenicity; PMID:9119448, PMID:8300539; phospholipase A 1282933..1283922 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905643 YP_002344740.1 CDS ceuB NC_002163.1 1284008 1284976 D Original (2000) note: Cj1352, ceuB, probable enterochelin uptake permease, len: 322 aa; highly similar to TR:Q46003 (EMBL:X88849) Campylobacter coli ceuB (322 aa), fasta scores; opt: 1839 z-score: 2038.7 E(): 0, 89.1% identity in 322 aa overlap, and similar to e.g. FATD_VIBAN ferric anguibactin transport system permease FATD (314 aa), fasta scores; opt: 921 z-score: 1026.8 E(): 0,43.3% identity in 305 aa overlap. Also similar to Cj1615 (31.0% identity in 326 aa overlap), and Cj1353 (27.2% identity in 316 aa overlap). Contains Pfam match to entry PF01032 FecCD_family, FecCD transport family; Updated (2006) note: Nine probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Campylobacter coli,so not added to product function. Functional classification - Transport/binding proteins - Cations; PMID:8574410; enterochelin uptake permease 1284008..1284976 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905644 YP_002344741.1 CDS ceuC NC_002163.1 1284969 1285907 D Original (2000) note: Cj1353, ceuC, probable enterochelin uptake permease, len: 312 aa; highly similar to TR:Q46004 (EMBL:X88849) Campylobacter coli ceuC (312 aa), fasta scores; opt: 1784 z-score: 2112.8 E(): 0, 88.8% identity in 312 aa overlap, and similar to e.g. FATC_VIBAN ferric anguibactin transport system permease FATC (317 aa), fasta scores; opt: 593 z-score: 708.6 E(): 3.6e-32, 31.7% identity in 306 aa overlap. No Hp ortholog. Also similar to e.g. Cj1352 (27.2% identity in 316 aa overlap), and Cj1615 (27.5% identity in 298 aa overlap). Contains Pfam match to entry PF01032 FecCD_family, FecCD transport family; Updated (2006) note: Nine probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Characterised within Campylobacter coli,so not added to product function. Functional classification - Transport/binding proteins - Cations; PMID:8574410; enterochelin uptake permease 1284969..1285907 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905645 YP_002344742.1 CDS ceuD NC_002163.1 1285904 1286659 D Original (2000) note: Cj1354, ceuD, probable enterochelin uptake ATP-binding protein, len: 251 aa; highly similar to TR:Q46005 (EMBL:X88849) Campylobacter coli ceuD (251 aa), fasta scores; opt: 1258 z-score: 1347.9 E(): 0, 82.5% identity in 246 aa overlap, and similar to e.g. FHUC_BACSU ferrichrome transport ATP-binding protein (269 aa), fasta scores; opt: 613 z-score: 663.4 E(): 1.2e-29, 38.0% identity in 245 aa overlap. No Hp ortholog. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00211 ABC transporters family signature, and Pfam match to entry PF00005 ABC_tran, ABC transporters; Updated (2006) note: Characterised within Campylobacter coli, so not added to product function. Functional classification - Transport/binding proteins - Cations; PMID:8574410; enterochelin uptake ATP-binding protein 1285904..1286659 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905646 YP_002344743.1 CDS ceuE NC_002163.1 1286672 1287664 D Original (2000) note: Cj1355, ceuE, probable enterochelin uptake periplasmic binding protein, len: 330 aa; highly similar to TR:Q46006 (EMBL:X88849) Campylobacter coli ceuE (328 aa), fasta scores; opt: 1903 z-score: 2111.3 E(): 0, 90.6% identity in 330 aa overlap,and similar to e.g. FATB_VIBAN ferric anguibactin-binding protein precursor (322 aa), fasta scores; opt: 540 z-score: 605.4 E(): 2e-26, 30.1% identity in 279 aa overlap. No Hp match. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site; Updated (2006) note: Characterised within Campylobacter coli, so not added to product function. Pfam domain PF01497 Periplasmic binding protein identified within CDS. Further support given to product function. Functional classification - Transport/binding proteins - Cations; PMID:8574410; enterochelin uptake periplasmic binding protein 1286672..1287664 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905647 YP_002344744.1 CDS Cj1356c NC_002163.1 1287890 1288444 R Original (2000) note: Cj1356c, probable integral membrane protein, len: 184 aa; highly similar to TR:Q46007 (EMBL:X88849) Campylobacter coli ORF (210 aa), fasta scores; opt: 545 z-score: 652.8 E(): 4.6e-29, 67.1% identity in 210 aa overlap. 31.8% identity to HP0234; Updated (2006) note: Three probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; integral membrane protein complement(1287890..1288444) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905649 YP_002344745.1 CDS nrfA NC_002163.1 1288580 1290412 R Original (2000) note: Cj1357c, probable periplasmic cytochrome C, len: 610 aa; similar to e.g. NRFA_ECOLI cytochrome C552 precursor (478 aa), fasta scores; opt: 298 z-score: 333.9 E(): 2.7e-11, 31.0% identity in 455 aa overlap. No Hp match. Contains probable N-terminal signal sequence and 5x PS00190 Cytochrome c family heme-binding site signature; Updated (2006) note: Pfam domain PF02335 Cytochrome c552 was identified within CDS. Further support given to product function. Characterisation work carried out within Wolinella succinogenes (PMID:10672190, PMID:10984487). Identity score was marginal. kept within product function. Functional classification - Energy metabolism -Electron transport; PMID:10672190, PMID:10984487, PMID:12095623,PMID:12618466; periplasmic cytochrome C complement(1288580..1290412) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905650 YP_002344746.1 CDS nrfH NC_002163.1 1290427 1290942 R Original (2000) note: Cj1358c, probable periplasmic cytochrome C, len: 171 aa; similar to e.g. NAPC_ECOLI cytochrome C-type protein NAPC (200 aa), fasta scores opt: 201 z-score: 242.9 E(): 3.1e-06, 34.5% identity in 165 aa overlap. No Hp match. Contains probable N-terminal signal sequence and 3x PS00190 Cytochrome c family heme-binding site signature; Updated (2006) note: Pfam domain PF03264 NapC/NirT cytochrome c family, N-terminal was identified within CDS. Further support given to product function. Characterisation work carried out within Wolinella succinogenes (PMID:10672190). Identity score was marginal. was kept within product function. Functional classification - Energy metabolism - Electron transport; PMID:10672190, PMID:12095623, PMID:12618466; periplasmic cytochrome C complement(1290427..1290942) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905651 YP_002344747.1 CDS ppk NC_002163.1 1291131 1293215 D catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate; polyphosphate kinase 1291131..1293215 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905652 YP_002344748.1 CDS Cj1360c NC_002163.1 1293527 >1293571 R Original (2000) note: Cj1360c, probable proteolysis tag for 10Sa_RNA ((A)ANNVKFAPAYAKAA), len: 14 aa; similar to TR:P96347 (EMBL:U68082) H. pylori coded portion of proteolysis tag (fragment) (14 aa), fasta scores; opt: 66 z-score: 192.9 E(): 0.0019, 76.9% identity in 13 aa overlap. Corresponds to c(838688..838726) in Hp seq. Functional classification - Degradation of macromolecules - Proteins, peptides and glycopeptides; proteolysis tag for 10Sa_RNA complement(1293527..>1293571) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905653 YP_002344749.1 CDS Cj1361c NC_002163.1 1293659 1294111 R Original (2000) note: Cj1361c, unknown, len: 150 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein complement(1293659..1294111) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905654 YP_002344750.1 CDS ruvB NC_002163.1 1294160 1295167 D promotes strand exchange during homologous recombination; RuvAB complex promotes branch migration; RuvABC complex scans the DNA during branch migration and resolves Holliday junctions at consensus sequences; forms hexameric rings around opposite DNA arms; requires ATP for branch migration and orientation of RuvAB complex determines direction of migration; Holliday junction DNA helicase RuvB 1294160..1295167 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905655 YP_002344751.1 CDS amaA NC_002163.1 1295171 1296214 D Original (2000) note: Cj1363, amaA, acid membrane antigen A, len: 347 aa; similar to many hypothetical membrane proteins e.g. TR:O66948 (EMBL:AE000705) Aquifex aeolicus AQ_740 (353 aa), fasta scores; opt: 268 z-score: 311.7 E(): 4.6e-10, 24.1% identity in 352 aa overlap. 32.2% identity to HP0567. Identical in part to TR:O69293 (EMBL:Y16882) C. jejuni predicted outer membrane protein from rearranged lambda clone (364 aa). (Phillippa Connerton(p.connerton@ic.ac.uk) pers. comm.); Updated (2006) note: Seven probable transmembrane helices predicted by TMHMM2.0. Pfam domain PF01594 Domain of unknown function DUF20 also identified within CDS. Functional classification - Membranes, lipoproteins and porins; acid membrane antigen A 1295171..1296214 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905656 YP_002344752.1 CDS fumC NC_002163.1 1296244 1297635 R class II family (does not require metal); tetrameric enzyme; fumarase C; reversibly converts (S)-malate to fumarate and water; functions in the TCA cycle; fumarate hydratase complement(1296244..1297635) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905657 YP_002344753.1 CDS Cj1365c NC_002163.1 1297691 1300816 R Original (2000) note: Cj1365c, probable secreted serine protease, len: 1041 aa; similar to e.g. TR:Q54484 (EMBL:D78380) Serratia marcescens serine protease homologue SSP-H2 (1034 aa), fasta scores; opt: 245 z-score: 257.1 E(): 5.1e-07, 23.5% identity in 591 aa overlap, and PRTS_SERMA extracellular serine protease precursor (EC 3.4.21.-) (1045 aa), fasta scores; opt: 205 z-score: 214.6 E(): 0.00012, 23.7% identity in 615 aa overlap. No Hp match. Contains PS00137 Serine proteases,subtilase family, histidine active site, PS00138 Serine proteases, subtilase family, serine active site, Pfam match to entry PF00082 subtilase, Subtilase family of serine proteases, and probable N-terminal signal sequence; Updated (2006) note: Specific characterisation with acceptable identity scores not carried out yet, so kept within product function. Functional classification - Degradation of macromolecules - Proteins,peptides and glycopeptides; secreted serine protease complement(1297691..1300816) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905658 YP_002344754.1 CDS glmS NC_002163.1 1300819 1302615 R Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source; glucosamine--fructose-6-phosphate aminotransferase complement(1300819..1302615) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905659 YP_002344755.1 CDS Cj1367c NC_002163.1 1302620 1304968 R Original (2000) note: Cj1367c, possible nucleotidyltransferase, len: 782 aa; weak similarity to TR:Q53245 (EMBL:U47030) Rhizobium tropici uridylyltransferase/uridylyl-removing enzyme (971 aa),fasta scores; opt: 202 z-score: 226.1 E(): 2.7e-05, 19.7% identity in 857 aa overlap, and GLND_HAEIN [protein-PII] uridylyltransferase (863 aa), fasta scores; opt: 119 z-score: 133.2 E(): 4, 19.5% identity in 822 aa overlap,(blastp score; E=4.3e-07). No Hp match. Contains C(1-2) polymorphic region at aa 148; C(2) (consensus) gives this ORF, C(1) gives truncation after +8 aa; Updated (2006) note: No specific characterisation with acceptable identity score carried out yet, so kept within product funciton. Functional classification - Misc; nucleotidyltransferase complement(1302620..1304968) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905660 YP_002344756.1 CDS Cj1368 NC_002163.1 1305112 1306176 D Original (2000) note: Cj1368, unknown, len: 354 aa; similar to hypothetical proteins e.g. TR:O66888 (EMBL:AE000700) Aquifex aeolicus AQ_648 (371 aa), fasta scores; opt: 956 z-score: 1117.5 E(): 0, 44.1% identity in 349 aa overlap. 57.4% identity to HP0654. Also similar to Cj0462 (35.5% identity in 349 aa overlap); Updated (2006) 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, so kept within product function. Functional classification -Misc; hypothetical protein 1305112..1306176 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905661 YP_002344757.1 CDS Cj1369 NC_002163.1 1306186 1307505 D Original (2000) note: Cj1369, probable transmembrane transport protein, len: 439 aa; similar to many hypothetical membrane proteins e.g. YJCD_ECOLI (449 aa), fasta scores; opt: 897 z-score: 1039.1 E(): 0, 34.7% identity in 429 aa overlap. 50.7% identity to HP1175. Contains Pfam match to entry PF00860 xan_ur_permease,Xanthine/uracil permeases family; Updated (2006) note: Pfam domain PF00860 Permease family protein identified within CDS. Also, 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, so kept within product function. Functional classification - Transport/binding proteins -Other; permease 1306186..1307505 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905662 YP_002344758.1 CDS Cj1370 NC_002163.1 1307519 1307962 D Original (2000) note: Cj1370, possible nucleotide phosphoribosyltransferase, len: 147 aa; similar to e.g. TR:O50284 (EMBL:AF035967) hypoxanthine ribosyl transferase (176 aa), fasta scores; opt: 158 z-score: 205.5 E(): 0.00038, 26.2% identity in 145 aa overlap, and XGPT_ECOLI xanthine-guanine phosphoribosyltransferase (152 aa), fasta scores; opt: 128 z-score: 170.3 E(): 0.035, 24.6% identity in 142 aa overlap. 39.5% identity to HP0735. Contains PS00103 Purine/pyrimidine phosphoribosyl transferases signature; Updated (2006) 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, so kept within product function. Functional classification - Salvage of nucleosides and nucleotides; nucleotide phosphoribosyltransferase 1307519..1307962 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905663 YP_002344759.1 CDS Cj1371 NC_002163.1 1308007 1308705 D Original (2000) note: Cj1371, probable periplasmic protein (vacJ homolog), len: 232 aa; similar to e.g. VACJ_SHIFL VACJ lipoprotein precursor (required for intercellular spreading of Shigella flexneri) (251 aa),fasta scores; opt: 310 z-score: 377.2 E(): 1e-13, 32.5% identity in 197 aa overlap. No Hp match. Contains probable N-terminal signal sequence; Updated (2006) note: Pfam domain PF04333 VacJ like lipoprotein identitied within CDS. Further support given to product function. kept within product function. Functional classification - Pathogenicity; PMID:8145644; periplasmic protein 1308007..1308705 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905664 YP_002344760.1 CDS Cj1372 NC_002163.1 1308715 1309284 D Original (2000) note: Cj1372, probable periplasmic protein, len: 189 aa; similar to e.g. YRBC_ECOLI (211 aa),fasta scores; opt: 189 z-score: 222.3 E(): 4.4e-05, 22.5% identity in 200 aa overlap. No Hp match. Contains probable N-terminal signal sequence; Updated (2006) note: Pfam domain PF05494 Toluene tolerance, 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, so kept within product function. Functional classification - Miscellaneous periplasmic proteins; PMID:9658016; periplasmic protein 1308715..1309284 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905665 YP_002344761.1 CDS Cj1373 NC_002163.1 1309284 1311755 D Original (2000) note: Cj1373, probable integral membrane protein, len: 823 aa; similar to hypothetical membrane proteins e.g. TR:O51268 (EMBL:AE001135) Borrelia burgdorferi conserved hypothetical integral membrane protein (767 aa), fasta scores; opt: 331 z-score: 348.2 E(): 4.2e-12, 24.8% identity in 840 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF02460 Patched family protein identified within CDS. Prosite domain PS50156 SSD x2, Sterol-sensing 5TM box was also identified within CDS. Also, thirteen probable transmembrane helices predicted by TMHMM2.0. No specific characterisation carried out yet, so kept within product function. Functional classification - Membranes, lipoproteins and porins; integral membrane protein 1309284..1311755 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905666 YP_002344762.1 CDS Cj1374c NC_002163.1 1311786 1312388 R HAM1-like protein; Rec-dependent growth; RgdB; yggV; it is suspected that this protein functions to remove misincorporated bases such as xanthine or hypoxanthine; deoxyribonucleotide triphosphate pyrophosphatase complement(1311786..1312388) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905667 YP_002344763.1 CDS Cj1375 NC_002163.1 1312555 1313850 D Original (2000) note: Cj1375, probable efflux protein, len: 431 aa; similar to members of the major facilitator family e.g. BMR1_BACSU multidrug resistance protein 1 (multidrug-efflux transporter 1) (389 aa), fasta scores; opt: 364 z-score: 415.1 E(): 8e-16, 27.1% identity in 384 aa overlap, and NORA_STAAU quinolone resistance NORA protein (388 aa), fasta scores; opt: 353 z-score: 402.8 E(): 3.9e-15, 26.7% identity in 375 aa overlap. 41.9% identity to HP1181. Also similar to Cj0035c (24.7% identity in 372 aa overlap). Contains Pfam match to entry PF00083 sugar_tr, Sugar (and other) transporters; Updated (2006) note: Pfam domain PF07690 Major Facilitator Superfamily identified within CDS. Prints motif also identified TCRTETA domain, Tetracycline resistance protein signature IPR001958. Also, 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, so kept within product function. Functional classification - Drug/analogue sensitivity; PMID:7961792; multidrug efflux transporter 1312555..1313850 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905668 YP_002344764.1 CDS Cj1376 NC_002163.1 1313847 1314656 D Original (2000) note: Cj1376, probable periplasmic protein, len: 269 aa; similar to TR:O32102 (EMBL:Z99120) B. subtilis YUII protein (314 aa), fasta scores; opt: 209 z-score: 257.4 E(): 4.9e-07, 30.6% identity in 242 aa overlap, and TR:O54506 (EMBL:U97227) Salmonella enterica IROE (305 aa), fasta scores; opt: 195 z-score: 240.9 E(): 4.1e-06, 26.4% identity in 277 aa overlap. No Hp match. Contains probable N-terminal signal sequence. Functional classification - Miscellaneous periplasmic proteins; periplasmic protein 1313847..1314656 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905669 YP_002344765.1 CDS Cj1377c NC_002163.1 1314649 1316310 R Original (2000) note: Cj1377c, probable ferredoxin,len: 553 aa; limited similarity to e.g. HYCF_ECOLI formate hydrogenlyase subunit 6 (180 aa), fasta scores; opt: 212 z-score: 241.0 E(): 4e-06, 30.6% identity in 134 aa overlap. No Hp match. Contains PS00198 4Fe-4S ferredoxins,iron-sulfur binding region signature, and 2x Pfam match to entry PF00037 fer4, 4Fe-4S ferredoxins and related iron-sulfur cluster binding domains; Updated (2006) note: No specific characterisation with acceptable identity score carried out yet, so kept within product function. Functional classification - Energy metabolism - Electron transport; ferredoxin complement(1314649..1316310) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905670 YP_002344766.1 CDS selA NC_002163.1 1316388 1317710 D catalyzes the formation of selenocysteinyl-tRNA(Sec) from seryl-tRNA(Sec) and L-selenophosphate in selenoprotein biosynthesis; selenocysteine synthase 1316388..1317710 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905671 YP_002344767.1 CDS selB NC_002163.1 1317707 1319512 D Original (2000) note: Cj1379, selB, probable selenocysteine-specific elongation factor, len: 601 aa; similar to e.g. SELB_ECOLI selenocysteine-specific elongation factor (614 aa), fasta scores; opt: 479 z-score: 491.6 E(): 4.4e-20, 26.2% identity in 362 aa overlap. No Hp ortholog. Contains PS00017 ATP/GTP-binding site motif A (P-loop), and Pfam match to entry PF00009 GTP_EFTU, Elongation factor Tu family; Updated (2006) note: kept within product function as no characterisation with acceptable identity score has been carried out yet. Functional classification - Protein translation and modification; PMID:2140572, PMID:16511023; selenocysteine-specific elongation factor 1317707..1319512 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905672 YP_002344768.1 CDS Cj1380 NC_002163.1 1319561 1320271 D Original (2000) note: Cj1380, probable periplasmic protein, len: 236 aa; some similarity to e.g. DSBG_ECOLI thiol:disulfide interchange protein DSBG precursor (248 aa), fasta scores; opt: 138 z-score: 165.8 E(): 0.062,26.8% identity in 164 aa overlap (the active site is conserved). 34.1% identity to HP0231. Contains probable N-terminal signal sequence; Updated (2006) note: Paper identified linking protein to glycoprotein. Functional classification -Miscellaneous periplasmic proteins; PMID:12186869; periplasmic protein 1319561..1320271 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905673 YP_002344769.1 CDS Cj1381 NC_002163.1 1320277 1320807 D Original (2000) note: Cj1381, probable lipoprotein,len: 176 aa; no Hp match. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes, lipoproteins and porins; lipoprotein 1320277..1320807 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905674 YP_002344770.1 CDS fldA NC_002163.1 1320852 1321343 R An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group; flavodoxin FldA complement(1320852..1321343) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905675 YP_002344771.1 CDS Cj1383c NC_002163.1 1321343 1322038 R Original (2000) note: Cj1383c, unknown, len: 231 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Literature search identified paper giving further clues to product function. Functional classification - Unknown; PMID:15231804; hypothetical protein complement(1321343..1322038) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905676 YP_002344772.1 CDS Cj1384c NC_002163.1 1322041 1322355 R Original (2000) note: Cj1384c, unknown, len: 104 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Literature search identified paper giving further clues to product function. Functional classification - Unknown; PMID:15231804; hypothetical protein complement(1322041..1322355) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905677 YP_002344773.1 CDS katA NC_002163.1 1322526 1323950 D Original (2000) note: Cj1385, katA, catalase, len: 474 aa; 98.5% identical to TR:Q59296 (EMBL:X85130) C. jejuni catalase (EC 1.11.1.6) (507 aa), and similar to e.g. CATA_BRUAB catalase (498 aa), fasta scores; opt: 2093 z-score: 2432.5 E(): 0, 65.6% identity in 474 aa overlap. 56.1% identity to HP0875. Contains PS00437 Catalase proximal heme-ligand signature, and Pfam match to entry PF00199 catalase; Updated (2006) note: Characterised within Campylobacter jejuni, so not added to product function. Functional classification - Detoxification; PMID:7670638; catalase 1322526..1323950 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905678 YP_002344774.1 CDS Cj1386 NC_002163.1 1324007 1324477 D Original (2000) note: Cj1386, ankyrin-repeat containing protein, len: 412 aa; similar to proteins downstream of catalase in Pseudomonads e.g. TR:P95546 (EMBL:U16026) Pseudomonas syringae ANKF precursor (183 aa), fasta scores; opt: 217 z-score: 286.8 E(): 1.2e-08,31.3% identity in 134 aa overlap, and to eukaryotic ankyrin proteins e.g. ANK1_MOUSE ankyrin (1862 aa), fasta scores; opt: 181 z-score: 226.3 E(): 2.8e-05, 29.1% identity in 117 aa overlap. No Hp match. Also similar to Cj0834c (29.3% identity in 99 aa overlap). Contains 2x Pfam match to entry PF00023 ank, Ank repeat; Updated (2006) note: Literature search identified paper giving further clues to product function. Functional classification - Misc; PMID:15632442; ankyrin-repeat containing protein 1324007..1324477 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905679 YP_002344775.1 CDS Cj1387c NC_002163.1 1324478 1325134 R Original (2000) note: Cj1387c, unknown, len: 218 aa; similar to hypothetical proteins e.g. YHEO_ECOLI (240 aa), fasta scores; opt: 164 z-score: 202.0 E(): 0.00063,29.4% identity in 204 aa overlap. No Hp match. Contains probable helix-turn-helix motif at aa 194-215 (Score 1100,+2.93 SD). Functional classification - Broad regulatory functions; hypothetical protein complement(1324478..1325134) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905680 YP_002344776.1 CDS Cj1388 NC_002163.1 1325302 1325664 D Original (2000) note: Cj1388, unknown, len: 120 aa; similar to prokaryotic hypothetical proteins e.g. YA28_PYRHO Pyrococcus horikoshii PHAL028 (137 aa), fasta scores; opt: 399 z-score: 503.4 E(): 1e-20, 53.8% identity in 117 aa overlap, and to e.g. UK14_HUMAN 14.5 KD translational inhibitor protein (137 aa), fasta scores; opt: 384 z-score: 485.1 E(): 1.1e-19, 48.3% identity in 116 aa overlap. 53.0% identity to HP0944. Also similar to Cj0327 (34.4% identity in 96 aa overlap). Contains Pfam match to entry PF01042 DUF10, Domain of unknown function; Updated (2006) note: Pfam domain PF01042 Endoribonuclease L-PSP identified within CDS. This domain is found in endoribonucleases, 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, so kept within product function. Functional classification -DNA replication, restriction/modification, recombination and repair; endoribonuclease L-PSP 1325302..1325664 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905681 YP_002344777.1 CDS metC' NC_002163.1 1327120 1327257 D Original (2000) note: Cj1392, metC', probable cystathionine beta-lyase, N-terminus, len: 348 aa; similar to many e.g. METC_HAEIN cystathionine beta-lyase (EC 4.4.1.8) (396 aa), fasta scores; opt: 88 z-score: 151.7 E(): 0.4, 45.2% 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, or possibly programmed ribosomal frameshifting; Updated (2006) note: Gene names for Cj1392 and Cj1393 are identical with a ' denoting two separate terminals for the same CDS. May well be a pseudogene. kept within product function. Functional classification - Amino acid biosynthesis - Aspartate family; PMID:8831789; cystathionine beta-lyase, N-terminus 1327120..1327257 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 5066043 YP_002344778.1 CDS metC' NC_002163.1 1327236 1328282 D Original (2000) note: Cj1393, metC', probable cystathionine beta-lyase, len: 348 aa; similar to many e.g. METC_ECOLI cystathionine beta-lyase (EC 4.4.1.8) (395 aa), fasta scores; opt: 802 z-score: 979.2 E(): 0, 35.6% identity in 354 aa overlap. 36.2% identity to HP0106. Also similar to Cj1727c, 30.0% identity in 363 aa overlap. Contains PS00868 Cys/Met metabolism enzymes pyridoxal-phosphate attachment site, and Pfam match to entry PF01053 Cys_Met_Meta_PP, 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, or possibly programmed ribosomal frameshifting; Updated (2006) note: Gene names for Cj1392 and Cj1393 are identical with a ' denoting two separate terminals for the same CDS. May well be a pseudogene. kept in product function. Functional classification - Amino acid biosynthesis - Aspartate family; PMID:8831789; cystathionine beta-lyase 1327236..1328282 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905683 YP_002344779.1 CDS Cj1394 NC_002163.1 1328292 1329659 D Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide; adenylosuccinate lyase 1328292..1329659 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905684 YP_002344780.1 CDS Cj1397 NC_002163.1 1331090 1331314 D Original (2000) note: Cj1397, unknown, len: 74 aa; similar to hypothetical proteins e.g. TR:AAD06110 (EMBL:AE001486) H. pylori J99 JHP0533 (78 aa), fasta scores; opt: 143 z-score: 219.1 E(): 6.9e-05, 41.2% identity in 68 aa overlap, and TR:P73181 (EMBL:D90904) Synechocystis sp. ssr2333 (79 aa), fasta scores; opt: 94 z-score: 151.5 E(): 0.41, 28.6% identity in 77 aa overlap. Not predicted in TIGR Hp, but 38.8% identity to c(615977..616192); Updated (2006) note: Pfam domain PF04023 FeoA domain identified within CDS. This family of protein is thought to be involved in Fe2+ transport. Product modified to more specific family member based on motif search result. No characterisation has been carried out yet, so kept in product function. Functional classification - Transport/binding proteins - Cations; PMID:8407793; ferrous iron transport protein 1331090..1331314 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905686 YP_002344781.1 CDS feoB NC_002163.1 1331311 1333152 D Original (2000) note: Cj1398, feoB, probable ferrous iron transport protein, len: 613 aa; similar to many e.g. FEOB_ECOLI ferrous iron transport protein B (773 aa), fasta scores; opt: 726 z-score: 805.2 E(): 0, 29.3% identity in 726 aa overlap. 50.5% identity to HP0687. Contains PS00017 ATP/GTP-binding site motif A (P-loop); Updated (2006) note: Pfam domains PF01926 GTPase of unknown function, PF02421 Ferrous iron transport protein B, PF07670 Nucleoside recognition, PF07664 Ferrous iron transport protein B C terminus and PF07670 Nucleoside recognition were all identified within CDS. Also, 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/binding proteins - Cations; PMID:14735223, PMID:12446835; ferrous iron transport protein 1331311..1333152 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905687 YP_002344782.1 CDS hydA2 NC_002163.1 1333149 1334642 R Original (2000) note: Cj1399c, hydA2, probable Ni/Fe-hydrogenase small subunit, len: 497 aa; similar to e.g. MBHS_WOLSU quinone-reactive Ni/Fe-hydrogenase small chain (354 aa), fasta scores; opt: 1122 z-score: 1317.8 E(): 0, 52.6% identity in 285 aa overlap. No Hp ortholog. Also similar to Cj1267c (51.5% identity in 330 aa overlap). Contains C-terminal extension not present in other hydrogenase small subunits; Updated (2006) note: Pfam domain PF01058 NADH ubiquinone oxidoreductase, 20 Kd subunit identified within CDS. Further support given to product function. Characterised within Wolinella succinogenes, however,sequence alignment was only partial. Thus, kept within product function. Functional classification -Energy metabolism - Respiration; PMID:1587288; Ni/Fe-hydrogenase small subunit complement(1333149..1334642) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905688 YP_002344783.1 CDS fabI NC_002163.1 1334646 1335470 R NADH; Catalyzes a key regulatory step in fatty acid biosynthesis; enoyl-(acyl carrier protein) reductase complement(1334646..1335470) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905689 YP_002344784.1 CDS tpiA NC_002163.1 1335474 1336145 R Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate; triosephosphate isomerase complement(1335474..1336145) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905690 YP_002344785.1 CDS pgk NC_002163.1 1336142 1337344 R Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway; phosphoglycerate kinase complement(1336142..1337344) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905691 YP_002344786.1 CDS gapA NC_002163.1 1337347 1338345 R Original (2000) note: Cj1403c, gapA, glyceraldehyde 3-phosphate dehydrogenase, len: 332 aa; similar to e.g. G3P1_BACSU glyceraldehyde 3-phosphate dehydrogenase 1 (334 aa), fasta scores; opt: 1070 z-score: 1216.4 E(): 0, 50.3% identity in 332 aa overlap. 45.6% identity to HP1346 and 46.7% identity to HP0921. Contains Pfam match to entry PF00044 gpdh, glyceraldehyde 3-phosphate dehydrogenases,and PS00071 Glyceraldehyde 3-phosphate dehydrogenase active site; Updated (2006) note: Pfam domains PF02800 and PF00044 Glyceraldehyde 3-phosphate dehydrogenase,C-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; PMID:10799476; glyceraldehyde 3-phosphate dehydrogenase complement(1337347..1338345) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905692 YP_002344787.1 CDS nadD NC_002163.1 1338404 1338949 D Original (2000) note: Cj1404, unknown, len: 181 aa; similar to hypothetical proteins e.g. YQEJ_BACSU (189 aa),fasta scores; opt: 305 z-score: 391.3 E(): 1.8e-14, 30.2% identity in 182 aa overlap. 40.4% identity to HP1337; Updated (2006) note: Pfam domain PF01467 Cytidylyltransferase identified within CDS. Product modified to more specific family member based on motif match. Characterised within Bacillus subtilis, however,identity scores were marginal. Thus, kept within product function. Functional classification - Misc; PMID:11704676, PMID:16153292; nicotinate-nucleotide adenylyltransferase 1338404..1338949 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905693 YP_002344788.1 CDS Cj1405 NC_002163.1 1338977 1339303 D Original (2000) note: Cj1405, unknown, len: 108 aa; similar to hypothetical proteins e.g. YBEB_ECOLI (105 aa),fasta scores; opt: 185 z-score: 245.5 E(): 2.4e-06, 28.1% identity in 96 aa overlap. 51.4% identity to HP1414; Updated (2006) note: Pfam domain PF02410 Domain of unknown function DUF143 identified within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins; hypothetical protein 1338977..1339303 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905694 YP_002344789.1 CDS Cj1406c NC_002163.1 1339362 1339712 R Original (2000) note: Cj1406c, probable periplasmic protein, len: 116 aa; similar to YQJC_ECOLI (predicted periplasmic protein) (127 aa), fasta scores; opt: 160 z-score: 185.2 E(): 0.0054 32.4% identity in 111 aa overlap. No Hp match. Contains probable N-terminal signal sequence; Updated (2006) note: Pfam domain PF06476 Protein of unknown function (DUF1090) identified within CDS. Functional classification - Miscellaneous periplasmic proteins; periplasmic protein complement(1339362..1339712) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905695 YP_002344790.1 CDS Cj1407c NC_002163.1 1339759 1341147 R Original (2000) note: Cj1407c, probable phospho-sugar mutase, len: 462 aa; simial to e.g. ALGC_PSEAE phosphomannomutase (462 aa), fasta scores; opt: 1037 z-score: 1216.2 E(): 0, 40.7% identity in 457 aa overlap, and PGMU_NEIGO phosphoglucomutase (460 aa), fasta scores; opt: 884 z-score: 1037.2 E(): 0, 35.4% identity in 435 aa overlap. 44.7% identity to HP1275. Contains Pfam match to entry PF00408 PGM_PMM, Phosphoglucomutase and phosphomannomutase, and PS00017 ATP/GTP-binding site motif A (P-loop). Also similar to Cj0360 (28.8% identity in 386 aa overlap); Updated (2006) note: No specific characterisation with acceptable identity score identified. kept within product function. Functional classification -Central intermediary metabolism - General; PMID:11839312, PMID:8050998; phospho-sugar mutase complement(1339759..1341147) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905696 YP_002344791.1 CDS fliL NC_002163.1 1341250 1341786 D interacts with the cytoplasmic MS ring of the basal body and may act to stabilize the MotAB complexes which surround the MS ring; flagellar basal body-associated protein FliL 1341250..1341786 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905697 YP_002344792.1 CDS acpS NC_002163.1 1341786 1342133 D Catalyzes the formation of holo-ACP, which mediates the essential transfer of acyl fatty acid intermediates during the biosynthesis of fatty acids and lipids; 4'-phosphopantetheinyl transferase 1341786..1342133 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905698 YP_002344793.1 CDS Cj1410c NC_002163.1 1342134 1342553 R Original (2000) note: Cj1410c, possible membrane protein, len: 139 aa; no Hp match. Contains hydrophobic domain and PS00041 Bacterial regulatory proteins, araC family signature. Functional classification - Membranes,lipoproteins and porins; hypothetical protein complement(1342134..1342553) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905699 YP_002344794.1 CDS Cj1411c NC_002163.1 1342550 1343911 R Original (2000) note: Cj1411c, probable cytochrome P450, len: 453 aa; similar to many e.g. cytochrome P450 domain of CPXB_BACME cytochrome P450/NADPH-cytochrome P450 reductase (1048 aa), fasta scores; opt: 505 z-score: 578.8 E(): 6.4e-25, 28.3% identity in 407 aa overlap. No Hp match. Contains PS00086 Cytochrome P450 cysteine heme-iron ligand signature, and Pfam match to entry PF00067 p450,Cytochrome P450; Updated (2006) note: No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification -Energy metabolism - Electron transport; PMID:9308178; cytochrome P450 complement(1342550..1343911) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905700 YP_002344795.1 CDS Cj1412c NC_002163.1 1343908 1345029 R Original (2000) note: Cj1412c, probable integral membrane protein, len: 373 aa; no Hp match; Updated (2006) note: Three probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; integral membrane protein complement(1343908..1345029) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905701 YP_002344796.1 CDS kpsS NC_002163.1 1345102 1346286 R Original (2000) note: Cj1413c, possible polysaccharide modification protein, len: 394 aa; similar to e.g. LIPB_NEIME capsule polysaccharide modification protein (419 aa), fasta scores; opt: 744 z-score: 897.9 E(): 0, 38.5% identity in 395 aa overlap, and KSS5_ECOLI capsule polysaccharide export protein KPSS (389 aa), fasta scores; opt: 919 z-score: 1108.7 E(): 0, 40.2% identity in 383 aa overlap. No Hp match; Updated (2006) 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 (Cj1413c -Cj1448c). Functional classification - Surface polysaccharides, lipopolysaccharides and antigens; PMID:8326861, PMID:8397187, PMID:10672176; capsule polysaccharide modification protein complement(1345102..1346286) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905702 YP_002344797.1 CDS kpsC NC_002163.1 1346283 1348352 R Original (2000) note: Cj1414c, possible polysaccharide modification protein, len: 689 aa; similar to e.g. LIPA_NEIME capsule polysaccharide modification protein (400 aa), fasta scores; opt: 927 z-score: 1062.5 E(): 0, 39.6% identity in 394 aa overlap, and KSC5_ECOLI capsule polysaccharide export protein KPSC (675 aa), fasta scores; opt: 724 z-score: 827.0 E(): 0, 38.5% identity in 655 aa overlap. No Hp match; Updated (2006) 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 (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:8326861, PMID:8397187, PMID:15612919,PMID:10672176; capsule polysaccharide modification protein complement(1346283..1348352) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905703 YP_002344798.1 CDS cysC NC_002163.1 1348349 1348861 R converts ATP and adenylyl sulfate to ADP and 3'-phosphoadenylyl sulfate; in Escherichia coli this enzyme functions in cysteine biosynthesis; adenylylsulfate kinase complement(1348349..1348861) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905704 YP_002344799.1 CDS Cj1416c NC_002163.1 1348851 1349612 R Original (2000) note: Cj1416c, probable sugar nucleotidyltransferase, len: 253 aa; similar to predicted nucleotidyltransferases e.g. TR:O29123 (EMBL:AE001025) Archaeoglobus fulgidus predicted glucose-1-phosphate cytidylyltransferase AF1142 (241 aa), fasta scores; opt: 252 z-score: 309.2 E(): 6.7e-10, 26.7% identity in 251 aa overlap. Also similar in part to LICC_HAEIN LICC protein (involved in LPS synthesis) (198 aa), fasta scores; opt: 209 z-score: 259.6 E(): 3.9e-07, 32.7% identity in 107 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00483 NTP_transferase, Nucleotidyl transferase; Updated (2006) note: Specific characterisation still required, so kept within product function. Identifed as part of Campylobacter jejuni capsule locus (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides, lipopolysaccharides and antigens; PMID:15612919, PMID:10672176; sugar nucleotidyltransferase complement(1348851..1349612) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905705 YP_002344800.1 CDS Cj1417c NC_002163.1 1349614 1350216 R Original (2000) note: Cj1417c, unknown, len: 200 aa; some similarity to the C-terminus of carbamoyl-phosphate synthase small subunitss e.g. CARX_BACSU carbamoyl-phosphate synthase,arginine-specific, small chain (353 aa), fasta scores; opt: 134 z-score: 174.1 E(): 0.022, 27.3% identity in 99 aa overlap. No Hp ortholog; Updated (2006) note: Pfam domain PF00117, 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 (Cj1413c - Cj1448c). Functional classification - Misc; PMID:15612919, PMID:10672176; amidotransferase complement(1349614..1350216) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905706 YP_002344801.1 CDS Cj1418c NC_002163.1 1350207 1352546 R Original (2000) note: Cj1418c, unknown, len: 779 aa; weak similarity in part to several phosphoenolpyruvate synthases e.g. PPSA_STAMA probable phosphoenolpyruvate synthase (834 aa), fasta scores; opt: 166 z-score: 182.8 E(): 0.0074, 23.9% identity in 226 aa overlap. No Hp ortholog; Updated (2006) note: Interpro IPR008279,PEP-utilising enzyme, 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 (Cj1413c - Cj1448c). Functional classification - Misc; PMID:15612919, PMID:10672176, PMID:2176881; hypothetical protein complement(1350207..1352546) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905707 YP_002344802.1 CDS Cj1419c NC_002163.1 1352561 1353322 R Original (2000) note: Cj1419c, possible methyltransferase, len: 253 aa; similar to hypothetical proteins e.g. TR:O53392 (EMBL:AL021841) Mycobacterium tuberculosis Rv3342 (MTV016.42) (243 aa), fasta scores; opt: 210 z-score: 250.1 E(): 1.3e-06, 32.0% identity in 122 aa overlap. Also contains weak similarity in part to several methyltransferases e.g. UBIE_ECOLI ubiquinone/menaquinone biosynthesis methyltransferase (251 aa), fasta scores; opt: 141 z-score: 171.3 E(): 0.032,24.2% identity in 132 aa overlap. No Hp match. Also similar to Cj1420c (33.7% identity in 255 aa overlap); Updated (2006) 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 (Cj1413c - Cj1448c). Functional classification - Misc; PMID:15612919, PMID:10672176; methyltransferase complement(1352561..1353322) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905708 YP_002344803.1 CDS Cj1420c NC_002163.1 1353375 1354148 R Original (2000) note: Cj1420c, unknown, len: 258 aa; similar to hypothetical proteins e.g. TR:O53392 (EMBL:AL021841) Mycobacterium tuberculosis Rv3342 (MTV016.42) (243 aa), fasta scores; opt: 219 z-score: 263.3 E(): 2.4e-07, 30.7% identity in 137 aa overlap. Also similar to Cj1419c (34.1% identity in 255 aa overlap). Contains C(9-10) polymorphic region at aa 132. C9 (consensus) gives this ORF, C10 would give truncation after a further 19 aa; Updated (2006) note: Prostie domain PS00213 LIPOCALIN, 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, so kept within product function. Literature search identified paper giving further clues to product function. Identifed as part of Campylobacter jejuni capsule locus (Cj1413c - Cj1448c). Functional classification - Misc; PMID:15612919, PMID:10672176; methyltransferase complement(1353375..1354148) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905709 YP_002344804.1 CDS Cj1421c NC_002163.1 1354215 1356053 R Original (2000) note: Cj1421c, possible sugar transferase, len: 612 aa; no Hp match. Similar to polymorphic tract-containing genes Cj1422c (overall 58.2% identity in 636 aa overlap, but N- and C-terminal 250 and 40 aa are identical), Cj0685c (28.0% identity in 404 aa overlap). N-terminus is simlar to parts of Cj1431c (38.6% identity in 114 aa overlap), and sugar transferases Cj1434c (39.6% identity in 111 aa overlap),and Cj1438c (34.6% identity in 127 aa overlap). Contains C(8-10) polymorphic tract at aa 30. C9 (consensus) gives this ORF, C8 gives truncation after +1 aa, C10 gives truncation after +5 aa. functional assignment is based on family clustering (BLASTP) with other C. jejuni predicted sugar transferases e.g. Cj1434c, and Cj1438c; Updated (2006) note: Identified within the Campylobacter jejuni Capsule locus (Cj1413c - Cj1448c). No specific characterisation has been carried out yet. kept within product function. Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:15612919, PMID:10672176; sugar transferase complement(1354215..1356053) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905710 YP_002344805.1 CDS Cj1422c NC_002163.1 1356108 1357985 R Original (2000) note: Cj1422c, possible sugar transferase, len: 625 aa; no Hp match. Similar to polymorphic tract-containing genes Cj1421c (overall 58.2% identity in 636 aa overlap, but N- and C-terminal 250 and 40 aa are identical), Cj0685c (25.6% identity in 442 aa overlap). N-terminus is simlar to parts of Cj1431c (38.6% identity in 114 aa overlap), and sugar transferases Cj1434c (39.6% identity in 111 aa overlap),and Cj1438c (23.5% identity in 452 aa overlap). Contains C(9-10) polymorphic tract at aa 30. C9 (consensus) gives this ORF, C10 gives truncation after +5 aa. functional assignment is based on family clustering (BLASTP) with other C. jejuni predicted sugar transferases e.g. Cj1434c, and Cj1438c; Updated (2006) 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 (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:15612919, PMID:10672176; sugar transferase complement(1356108..1357985) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905711 YP_002344806.1 CDS hddC NC_002163.1 1358036 1358701 R Original (2000) note: Cj1423c, possible sugar-phosphate nucleotidyltransferase, len: 221 aa; similar to many predicted nucleotidyltransferases, e.g. TR:O58775 (EMBL:AP000004) Pyrococcus horikoshii hypothetical sugar-phosphate nucleotydyl transferase PH1022 (416 aa), fasta scores; opt: 413 z-score: 496.0 E(): 2.6e-20, 34.3% identity in 230 aa overlap, and MPG1_YEAST mannose-1-phosphate guanyltransferase (361 aa),fasta scores; opt: 258 z-score: 313.4 E(): 3.9e-10, 28.9% identity in 232 aa overlap. Contains Pfam match to entry PF00483 NTP_transferase, Nucleotidyl transferase. No Hp ortholog. Also similar to Cj1329 (35.6% identity in 216 aa overlap); Updated (2006) 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 (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:15612919, PMID:10672176; D-glycero-D-manno-heptose 1-phosphate guanosyltransferase complement(1358036..1358701) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905712 YP_002344807.1 CDS gmhA2 NC_002163.1 1358689 1359294 R Original (2000) note: Cj1424c, gmhA2, probable phosphoheptose isomerase, len: 201 aa; similar to many e.g. LPCA_ECOLI phosphoheptose isomerase (EC 5.-.-.-) (192 aa), fasta scores; opt: 453 z-score: 548.7 E(): 3.1e-23,39.2% identity in 186 aa overlap. No Hp ortholog. Also similar to Cj1149c gmhA (57.8% identity in 147 aa overlap); Updated (2006) 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, so removed from product function. Identifed as part of Campylobacter jejuni capsule locus (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:15612919, PMID:10672176, PMID:12101286; phosphoheptose isomerase complement(1358689..1359294) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905713 YP_002344808.1 CDS hddA NC_002163.1 1359282 1360301 R Original (2000) note: Cj1425c, possible sugar kinase, len: 339 aa; similar to e.g. GAL1_LACHE galactokinase (388 aa), fasta scores; opt: 186 z-score: 227.6 E(): 2.4e-05, 24.3% identity in 371 aa overlap. Contains PS00012 Phosphopantetheine attachment site. No Hp match; Updated (2006) 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, so kept within product function. Identifed as part of Campylobacter jejuni capsule locus (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:15612919, PMID:10672176; D-glycero-D-manno-heptose 7-phosphate kinase complement(1359282..1360301) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905714 YP_002344809.1 CDS Cj1426c NC_002163.1 1360321 1361172 R Original (2000) note: Cj1426c, unknown, len: 283 aa; no Hp match. Contains C(10-11) polymorphic region at aa 99. C10 (consensus) gives this ORF, C11 gives truncation after +8 aa; Updated (2006) note: TIGRFAM motif TIGR01444 Methyltransferase FkbM, identified within CDS. Product modified to more specific family member based on motif match. No specific characterisation has been carried out yet, so kept within product function. Identifed as part of Campylobacter jejuni capsule locus (Cj1413c -Cj1448c). Functional classification - Misc; PMID:15612919, PMID:10672176; methyltransferase family protein complement(1360321..1361172) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905715 YP_002344810.1 CDS Cj1427c NC_002163.1 1361191 1362132 R Original (2000) note: Cj1427c, probable sugar-nucleotide epimerase/dehydratease, len: 313 aa; similar to many predicted epimerases/dehydrateases e.g. TR:Q25130 (EMBL:D25537) HALOCYNTHIA RORETZI (SEA SQUIRT) gene with similarity to UDPglucose4-epimerases and 3beta-hydroxysteroid dehydrogenase/isomerases HREPIB (241 aa), fasta scores; opt: 585 z-score: 691.2 E(): 3.5e-31,44.2% identity in 208 aa overlap, and TR:O73960 (EMBL:AP000002) Pyrococcus horikoshii hypothetical UDP-glucose 4-epimerase (318 aa), fasta scores; opt: 304 z-score: 361.7 E(): 7.9e-13, 26.4% identity in 326 aa overlap. No Hp ortholog; Updated (2006) note: Pfam domain PF01370 NAD dependent epimerase/dehydratase 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 (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides, lipopolysaccharides and antigens; PMID:15612919, PMID:10672176, PMID:9708982; sugar-nucleotide epimerase/dehydratease complement(1361191..1362132) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905716 YP_002344811.1 CDS fcl NC_002163.1 1362156 1363196 R Original (2000) note: Cj1428c, fcl, probable fucose synthetase, len: 346 aa; similar to e.g. FCL_ECOLI fucose synthetase (321 aa), fasta scores; opt: 562 z-score: 690.0 E(): 4.1e-31, 39.0% identity in 341 aa overlap. 29.6% identity to HP0045. Contains PS00017 ATP/GTP-binding site motif A (P-loop); Updated (2006) note: Pfam domain PF01370 NAD dependent epimerase/dehydratase 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 (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:15612919, PMID:10672176, PMID:11021971,PMID:9862812; GDP-L-fucose synthetase complement(1362156..1363196) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905717 YP_002344812.1 CDS Cj1429c NC_002163.1 1363196 1364122 R Original (2000) note: Cj1429c, unknown, len: 308 aa; no Hp match. Contains C(9-10) polymorphic region at aa 98. C10 (consensus) gives this ORF, C9 would give truncation after +1 aa; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Identifed as part of Campylobacter jejuni capsule locus (Cj1413c - Cj1448c). Functional classification - Unknown; PMID:15612919, PMID:10672176; hypothetical protein complement(1363196..1364122) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905718 YP_002344813.1 CDS rfbC NC_002163.1 1364126 1364671 R Original (2000) note: Cj1430c, probable nucleotide-sugar epimerase/dehydratase, len: 181 aa; similar to e.g. RFBC_ECOLI DTDP-4-dehydrorhamnose 3,5-epimerase (185 aa), fasta scores; opt: 303 z-score: 386.2 E(): 3.4e-14, 33.9% identity in 165 aa overlap, and TR:Q46770 (EMBL:U23775) E. coli rmlC DTDP-6-deoxy-l-lyxo-4-hexulose reductase (183 aa), fasta scores; opt: 306 z-score: 390.0 E(): 2.1e-14, 33.5% identity in 164 aa overlap. No Hp match. Contains Pfam match to entry PF00908 dTDP_sugar_isom,dTDP-4-dehydrorhamnose 3,5-epimerase; Updated (2006) note: Pfam domain PF00908 dTDP-4-dehydrorhamnose 3,5-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 (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:15612919, PMID:10672176, PMID:7517390; dTDP-4-dehydrorhamnose 3,5-epimerase complement(1364126..1364671) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905719 YP_002344814.1 CDS hddC NC_002163.1 1364671 1366419 R Original (2000) note: Cj1431c, unknown, len: 582 aa; no Hp match. Similar in part to N-termini of Cj1421c (38.6% identity in 114 aa overlap), and Cj1422c (38.6% identity in 114 aa overlap). Contains PS00455 AMP-binding domain signature; Updated (2006) 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 (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides, lipopolysaccharides and antigens; PMID:15612919; capsular polysaccharide heptosyltransferase complement(1364671..1366419) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905720 YP_002344815.1 CDS Cj1432c NC_002163.1 1366422 1369517 R Original (2000) note: Cj1432c, possible sugar transferase, len: 1031 aa; weakly similar to e.g. TR:Q48232 (EMBL:X78559) Haemophilus influenzae orf3 in DNA for serotypE B capsulation locus (1215 aa), fasta scores; opt: 361 z-score: 398.4 E(): 7.2e-15, 22.8% identity in 1029 aa overlap, and TR:O84910 (EMBL:AF010183) glycosyltransferase WBPZ (381 aa), fasta scores; opt: 161 z-score: 182.7 E(): 0.0074, 23.1% identity in 251 aa overlap. Contains Pfam match to entry PF00534 Glycos_transf_1, Glycosyl transferases group 1. Also similar to Cj1434c (23.1% identity in 424 aa overlap); Updated (2006) note: Literature search identified papers giving further clues about product function. Identifed as part of Campylobacter jejuni capsule locus (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides, lipopolysaccharides and antigens; PMID:15612919, PMID:10672176; sugar transferase complement(1366422..1369517) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905721 YP_002344816.1 CDS Cj1433c NC_002163.1 1369527 1370633 R Original (2000) note: Cj1433c, unknown, len: 368 aa; no Hp match. Contains 9 repeats of the aa sequence KIDLNNT near the N-terminus; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Identifed as part of Campylobacter jejuni capsule locus (Cj1413c - Cj1448c). Functional classification - Unknown; PMID:15612919, PMID:10672176; hypothetical protein complement(1369527..1370633) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905722 YP_002344817.1 CDS Cj1434c NC_002163.1 1370667 1372004 R Original (2000) note: Cj1434c, probable sugar transferase, len: 445 aa; similar in N-terminus to e.g. TR:O07340 (EMBL:O07340) Streptococcus pneumoniae SS-1,4-galactosyltransferase (318 aa), fasta scores; opt: 344 z-score: 405.7 E(): 2.8e-15, 27.3% identity in 326 aa overlap. No Hp ortholog. Highly similar to Cj1438c (72.4% identity in 456 aa overlap). Contains Pfam match to entry PF00535 Glycos_transf_2, Glycosyl transferases; Updated (2006) note: No specific characterisation has been carried out yet, so kept within product function. Literature search identified papers giving further clues to product funciton. Identifed as part of Campylobacter jejuni capsule locus (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:15612919, PMID:10672176; sugar transferase complement(1370667..1372004) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905723 YP_002344818.1 CDS Cj1435c NC_002163.1 1372056 1372691 R Original (2000) note: Cj1435c, unknown, len: 211 aa; similar to TR:Q58989 (EMBL:U67599) Methanococcus jannaschii hypothetical protein MJ1594 (211 aa), fasta scores; opt: 177 z-score: 228.6 E(): 2.1e-05, 23.5% identity in 196 aa overlap. No Hp match; Updated (2006) 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, so kept within product function. Identifed as part of Campylobacter jejuni capsule locus (Cj1413c - Cj1448c). Functional classification - Misc; PMID:15612919, PMID:10672176; phosphatase complement(1372056..1372691) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905724 YP_002344819.1 CDS Cj1436c NC_002163.1 1372695 1373867 R Original (2000) note: Cj1436c, probable aminotransferase, len: 390 aa; weakly similar to e.g. HIS8_BACSU histidinol-phosphate aminotransferase (360 aa),fasta scores; opt: 304 z-score: 351.9 E(): 2.8e-12, 25.5% identity in 318 aa overlap. No Hp match. Also similar to Cj0317 (hisC) (25.7% identity in 304 aa overlap), and Cj1437c (23.1% identity in 347 aa overlap). Contains PS00105 Aminotransferases class-I pyridoxal-phosphate attachment site; Updated (2006) 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 (Cj1413c - Cj1448c). Functional classification - Misc; PMID:15612919, PMID:10672176; aminotransferase complement(1372695..1373867) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905725 YP_002344820.1 CDS Cj1437c NC_002163.1 1373917 1375020 R Original (2000) note: Cj1437c, probable aminotransferase, len: 367 aa; similar to e.g. HIS8_BACSU histidinol-phosphate aminotransferase (360 aa), fasta scores; opt: 408 z-score: 478.1 E(): 2.6e-19, 28.6% identity in 360 aa overlap. No Hp match. Also similar to Cj0317 (hisC) (29.9% identity in 344 aa overlap), and Cj1436c (23.3% identity in 347 aa overlap). Contains Pfam match to entry PF00222 aminotran_2, Aminotransferases class-II, and PS00599 Aminotransferases class-II pyridoxal-phosphate attachment site; Updated (2006) 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 (Cj1413c - Cj1448c). Functional classification - Misc; PMID:15612919, PMID:10672176; aminotransferase complement(1373917..1375020) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905726 YP_002344821.1 CDS Cj1438c NC_002163.1 1375007 1377337 R Original (2000) note: Cj1438c, probable sugar transferase, len: 776 aa; similar in N-terminus to e.g. TR:O07340 (EMBL:O07340) Streptococcus pneumoniae SS-1,4-galactosyltransferase (318 aa), fasta scores; opt: 325 z-score: 375.2 E(): 1.4e-13, 26.9% identity in 316 aa overlap. Similar in C-terminus to TR:O31348 (EMBL:Y11138) Bacillus cereus hypothetical protein (ORF2) (300 aa),fasta scores; opt: 355 z-score: 409.9 E(): 1.7e-15, 31.2% identity in 340 aa overlap. 27.7% identity in 260 aa overlap to HP0102. Also highly similar to Cj1434c (72.9% identity in 457 aa overlap) in N-term, and similar to Cj1421c (34.6% identity in 127 aa overlap) and Cj1422c (23.5% identity in 452 aa overlap) in C-term. Contains Pfam match to entry PF00535 Glycos_transf_2, Glycosyl transferases; Updated (2006) note: Literature search identified paper giving further information on product function. Specific characterisation still required, so kept within product function. Identifed as part of Campylobacter jejuni capsule locus (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:15612919, PMID:10672176; sugar transferase complement(1375007..1377337) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905727 YP_002344822.1 CDS glf NC_002163.1 1377339 1378445 R Original (2000) note: Cj1439c, glf, probable UDP-galactopyranose mutase, len: aa; highly simiar to e.g. TR:O86897 (EMBL:AJ006986) Streptococcus pneumoniae polysaccharide capsule bisynthesis cluster UDP-galactopyranose mutase (EC 5.4.99.9) (369 aa), fasta scores; opt: 1546 z-score: 1775.3 E(): 0, 59.9% identity in 364 aa overlap, and GLF_ECOLI UDP-galactopyranose mutase (EC 5.4.99.9) (367 aa), fasta scores; opt: 1545 z-score: 1774.2 E(): 0, 60.8% identity in 362 aa overlap. No Hp match; Updated (2006) 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 (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:8576037, PMID:15947206, PMID:10672176; UDP-galactopyranose mutase complement(1377339..1378445) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905728 YP_002344823.1 CDS Cj1440c NC_002163.1 1378483 1379706 R Original (2000) note: Cj1440c, probable sugar transferase, len: 407 aa; similar in N-terminus to e.g. TR:O07340 (EMBL:O07340) Streptococcus pneumoniae SS-1,4-galactosyltransferase (318 aa), fasta scores; opt: 280 z-score: 326.2 E(): 7.5e-11, 26.7% identity in 374 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00535 Glycos_transf_2, Glycosyl transferases; Updated (2006) note: Literature search identified papers giving further information towards product function. Specific characterisation still required, so kept within product function. Identifed as part of Campylobacter jejuni capsule locus (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:15612919, PMID:10672176, PMID:11422559; sugar transferase complement(1378483..1379706) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905729 YP_002344824.1 CDS kfiD NC_002163.1 1379716 1380897 R Original (2000) note: Cj1441c, kfiD, probable UDP-glucose 6-dehydrogenase, len: 393 aa; similar to many e.g. UDG5_ECOLI UDP-glucose 6-dehydrogenase (EC 1.1.1.22) (392 aa), fasta scores; opt: 1386 z-score: 1511.4 E(): 0,52.3% identity in 392 aa overlap. No Hp match. Contains Pfam match to entry PF00984 UDPG_MGDP_dh,UDP-glucose/GDP-mannose dehydrogenase family; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. removed from product function. Identifed as part of Campylobacter jejuni capsule locus (Cj1413c - Cj1448c). Functional classification - Central intermediary metabolism - Sugar nucleotides; PMID:12851388, PMID:9383197, PMID:7635844,PMID:12392544; UDP-glucose 6-dehydrogenase complement(1379716..1380897) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905730 YP_002344825.1 CDS Cj1442c NC_002163.1 1380894 1382528 R Original (2000) note: Cj1442c, unknown, len: 544 aa; no Hp match; Updated (2006) note: Literature search identified papers giving further information about product function. Specific characterisation still required, so kept within product function. Identifed as part of Campylobacter jejuni capsule locus (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:15612919, PMID:10672176, PMID:11422559; sugar transferase complement(1380894..1382528) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905731 YP_002344826.1 CDS kpsF NC_002163.1 1382528 1383475 R Original (2000) note: Cj1443c, kpsF, unknown, len: 315 aa; similar to hypothetical proteins belonging to the kpsF/gutQ family e.g. KSF1_ECOLI KPSF protein (317 aa),fasta scores; opt: 849 z-score: 979.3 E(): 0, 46.5% identity in 297 aa overlap. 38.7% identity to HP1429. Contains 2x Pfam match to entry PF00571 CBS, CBS domain; Updated (2006) 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 (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:16390329, PMID:11956197, PMID:10672176; D-arabinose 5-phosphate isomerase complement(1382528..1383475) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905732 YP_002344827.1 CDS kpsD NC_002163.1 1383486 1385144 R Original (2000) note: Cj1444c, kpsD, probable capsule polysaccharide export system periplasmic protein,len: aa; similar to e.g. KSD1_ECOLI polysialic acid transport protein KPSD PREC (558 aa), fasta scores; opt: 1187 z-score: 1306.9 E(): 0, 36.1% identity in 560 aa overlap. Contains probable N-terminal signal sequence. No Hp match; Updated (2006) note: Pfam domain PF02563 Polysaccharide biosynthesis/export protein identified within CDS. Paper identified linking protein to glycoprotein (PMID:Cj12186869). Characterised within Escherichia coli with acceptable identity score. removed from product function. Identifed as part of Campylobacter jejuni capsule locus (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:12186869, PMID:8021185, PMID:16420360,PMID:10672176; capsule polysaccharide export system periplasmic protein complement(1383486..1385144) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905733 YP_002344828.1 CDS kpsE NC_002163.1 1385146 1386264 R Original (2000) note: Cj1445c, kpsE, probable capsule polysaccharide export system inner membrane protein, len: 372 aa; similar to e.g. KSE1_ECOLI capsule polysaccharide export inner-membrane protein (382 aa),fasta scores; opt: 752 z-score: 755.4 E(): 0, 34.2% identity in 351 aa overlap. No Hp match; Updated (2006) 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 (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:8253690, PMID:7868584, PMID:11467848,PMID:10672176; capsule polysaccharide export system inner membrane protein complement(1385146..1386264) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905734 YP_002344829.1 CDS kpsT NC_002163.1 1386264 1386926 R Original (2000) note: Cj1447c, kpsT, probable capsule polysaccharide export ATP-binding protein, len: 220 aa; identical to TR:O69286 (EMBL:AJ000856) C. jejuni ABC transporter protein (220 aa), and highly similar to e.g. KST1_ECOLI polysialic acid transport ATP-binding protein (219 aa), fasta scores; opt: 810 z-score: 945.3 E(): 0, 58.7% identity in 218 aa overlap. No Hp ortholog. Contains PS00017 ATP/GTP-binding site motif A (P-loop),PS00211 ABC transporters family signature, and Pfam match to entry PF00005 ABC_tran, ABC transporters; Updated (2006) note: Characterised within Campylobacter jejuni. removed from product function. Identifed as part of Campylobacter jejuni capsule locus (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides,lipopolysaccharides and antigens; PMID:12855177, PMID:9802032, PMID:10672176,PMID:11359581; capsule polysaccharide export ATP-binding protein complement(1386264..1386926) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905735 YP_002344830.1 CDS kpsM NC_002163.1 1386923 1387705 R Original (2000) note: Cj1448c, kpsM, probable capsule polysaccharide export system inner membrane protein, len: 260 aa; identical to TR:O69285 (EMBL:AJ000856) C. jejuni ABC transporter protein (260 aa), and highly similar to e.g. KPM1_ECOLI polysialic acid transport protein KPSM (258 aa), fasta scores; opt: 488 z-score: 558.3 E(): 8.9e-24, 34.3% identity in 254 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF01061 ABC-2 type transporter identified within CDS. Further support given to product function. Also, 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 (Cj1413c - Cj1448c). Functional classification - Surface polysaccharides, lipopolysaccharides and antigens; PMID:7715449, PMID:12855177, PMID:11500474,PMID:11359581, PMID:10672176, PMID:16436427; capsule polysaccharide export system inner membrane protein complement(1386923..1387705) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905736 YP_002344831.1 CDS Cj1449c NC_002163.1 1387777 1388184 R Original (2000) note: Cj1449c, unknown, len: 135 aa; similar to YHBP_ECOLI hypothetical protein (147 aa),fasta scores; opt: 236 z-score: 315.0 E(): 3.2e-10, 30.5% identity in 131 aa overlap. No Hp match. Functional classification - Conserved hypothetical proteins; hypothetical protein complement(1387777..1388184) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905737 YP_002344832.1 CDS Cj1450 NC_002163.1 1388259 1388822 D Original (2000) note: Cj1450, probable ATP/GTP-binding protein, len: 187 aa; no Hp match. Contains PS00017 ATP/GTP-binding site motif A (P-loop),and probable coiled-coil domain at C-terminus (aa 150-175); Updated (2006) note: Literature search identified paper giving further clues to product function. Functional classification - Unknown; PMID:16740937; ATP/GTP-binding protein 1388259..1388822 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905738 YP_002344833.1 CDS dut NC_002163.1 1388859 1389548 D Original (2000) note: Cj1451, dut, possible dUTPase, len: 229 aa; similar to two enzymes of eukaryotic origin e.g. TR:O15826 (EMBL:L76742) Leishmania major characterised dUTPase (EC 3.6.1.23) (dUTP pyrophosphatase) (268 aa), fasta scores; opt: 311 z-score: 382.3 E(): 5.7e-14, 33.6% identity in 226 aa overlap, and TR:O15923 (EMBL:U93211) Trypanosoma cruzi deoxyuridine triphosphatase (283 aa), fasta scores; opt: 198 z-score: 246.6 E(): 2.1e-06, 32.9% 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; Updated (2006) note: Characterisation work carried out within Campylobacter jejuni. removed from product function. Functional classification -2'-deoxyribonucleotide biosynthesis; PMID:15364583; dUTPase 1388859..1389548 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905739 YP_002344834.1 CDS Cj1452 NC_002163.1 1389550 1390263 D Original (2000) note: Cj1452, possible integral membrane protein, len: 237 aa; 29.7% identity to HP0174. Contains four large hydrophobic domains; Updated (2006) note: Pfam domain PF04401 Protein of unknown function (DUF540) identified within CDS. Functional classification - Membranes, lipoproteins and porins; integral membrane protein 1389550..1390263 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905740 YP_002344835.1 CDS tilS NC_002163.1 1390246 1391211 R Original (2000) note: Cj1453c, unknown, len: 321 aa; similar to hypothetical proteins e.g. YACA_BACSU (486 aa), fasta scores; opt: 290 z-score: 342.2 E(): 9.7e-12,26.8% identity in 257 aa overlap. 40.7% identity to HP0728; Updated (2006) 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(Ile)-lysidine synthase. Product modified to more specific famlily member. Identity scores were marginal, so kept within product function. Functional classification -Aminoacyl tRNA synthetases and their modification; PMID:14527414, PMID:15894617, PMID:16039592; tRNA(Ile)-lysidine synthase complement(1390246..1391211) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905741 YP_002344836.1 CDS Cj1454c NC_002163.1 1391201 1392520 R Original (2000) note: Cj1454c, unknown, len: 439 aa; similar to hypothetical proteins e.g. YLIG_ECOLI (441 aa), fasta scores; opt: 671 z-score: 748.3 E(): 0, 34.2% identity in 433 aa overlap. 52.1% identity to HP0734. Also similar to Cj1006c (28.6% identity in 419 aa overlap), and Cj0458c (26.7% identity in 371 aa overlap). Contains PS01278 Uncharacterized protein family UPF0004 signature,and Pfam match to entry PF00919 UPF0004, Uncharacterized protein family UPF0004; Updated (2006) 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, so kept within product function. Functional classification - Misc; radical SAM domain family protein complement(1391201..1392520) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905742 YP_002344837.1 CDS prfB NC_002163.1 1392594 1393691 D 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; in some organisms control of PrfB protein levels is maintained through a +1 ribosomal frameshifting mechanism; this protein is similar to release factor 1; peptide chain release factor 2 1392594..1393691 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905743 YP_002344838.1 CDS Cj1456c NC_002163.1 1393849 1394163 R Original (2000) note: Cj1456c, probable periplasmic protein, len: 104 aa; no Hp match. Contains possible N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein complement(1393849..1394163) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905744 YP_002344839.1 CDS truD NC_002163.1 1394285 1395403 R catalyzes the modification of U13 in tRNA(Glu); tRNA pseudouridine synthase D complement(1394285..1395403) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905745 YP_002344840.1 CDS thiL NC_002163.1 1395372 1396193 R catalyzes the formation of thiamine diphosphate from thiamine phosphate ant ATP; thiamine monophosphate kinase complement(1395372..1396193) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905746 YP_002344841.1 CDS Cj1459 NC_002163.1 1396280 1397353 D Original (2000) note: Cj1459, unknown, len: 357 aa; 24.8% identity to HP0468. Functional classification -Conserved hypothetical proteins; hypothetical protein 1396280..1397353 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905747 YP_002344842.1 CDS Cj1460 NC_002163.1 1397350 1397733 D Original (2000) note: Cj1460, unknown, len: 127 aa; 41.0% identity to HP0811. Functional classification -Conserved hypothetical proteins; hypothetical protein 1397350..1397733 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905748 YP_002344843.1 CDS Cj1461 NC_002163.1 1397726 1398409 D Original (2000) note: Cj1461, possible DNA methylase, len: 227 aa; similar to hypothetical proteins e.g. YHHF_ECOLI (198 aa), fasta scores; opt: 186 z-score: 224.4 E(): 3.5e-05, 27.1% identity in 181 aa overlap. 37.2% identity to HP0810. Contains PS00092 N-6 Adenine-specific DNA methylases signature; Updated (2006) note: Pfam domain PF03602 Conserved hypothetical protein identified within CDS. Specific characterisation with acceptable identity score has not been carried out yet, so kept within product function. Functional classification - DNA replication,restriction/modification, recombination and repair; DNA methylase 1397726..1398409 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905749 YP_002344844.1 CDS flgI NC_002163.1 1398468 1399514 D part of the basal body which consists of four rings L, P, S, and M mounted on a central rod; Vibrio parahaemolyticus, Yersinia, Bradyrhizobium and other bacteria have two copies of this and other flagellar genes; the V. parahaemolyticus protein is associated with the polar flagella and the Bradyrhizobium protein is associated with the thick flagellum; flagellar basal body P-ring protein 1398468..1399514 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905750 YP_002344845.1 CDS flgJ NC_002163.1 1399514 1399855 D Original (2000) note: Cj1463, unknown, len: 113 aa; 46.0% identity to HP0245; Updated (2006) note: Literature search identified papers giving clues to product function. C.Penn unpublished observation has predicted to be FlgJ. Functional classification - Conserved hypothetical proteins; PMID:14617189, PMID:14960570, PMID:15812042; hypothetical protein 1399514..1399855 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905751 YP_002344846.1 CDS flgM NC_002163.1 1399918 1400115 D Original (2000) note: Cj1464, unknown, len: 65 aa; no Hp match; Updated (2006) note: Literature search identified papers giving further clues to product function. Has been linked to flagellar anti FliA (sigma 28) factor FlgM protein. Functional classification - Unknown; PMID:14617189, PMID:14702320, PMID:14985343; hypothetical protein 1399918..1400115 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905752 YP_002344847.1 CDS Cj1465 NC_002163.1 1400158 1400592 D Original (2000) note: Cj1465, unknown, len: 144 aa; 31.9% identity to HP1120; Updated (2006) 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; PMID:14702320; hypothetical protein 1400158..1400592 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905753 YP_002344848.1 CDS flgK NC_002163.1 1400602 1402428 D with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook; flagellar hook-associated protein FlgK 1400602..1402428 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905754 YP_002344849.1 CDS Cj1467 NC_002163.1 1402445 1403209 D Original (2000) note: Cj1467, unknown, len: 254 aa; some similarity to TR:O51480 (EMBL:AE001154) Borrelia burgdorferi BB0530 (217 aa), fasta scores; opt: 331 z-score: 404.6 E(): 3.2e-15, 32.8% identity in 189 aa overlap. No Hp match. Functional classification -Conserved hypothetical proteins; hypothetical protein 1402445..1403209 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905755 YP_002344850.1 CDS Cj1468 NC_002163.1 1403213 1403977 D Original (2000) note: Cj1468, probable integral membrane protein, len: 254 aa; similar to hypothetical membrane proteins e.g. YFCA_ECOLI (269 aa), fasta scores; opt: 612 z-score: 731.5 E(): 0, 43.4% identity in 242 aa overlap. No Hp ortholog; Updated (2006) note: Pfam domain PF01925 Domain of unknown function DUF81 identified within CDS. Also, seven probable transmembrane helices predicted by TMHMM2.0. Furhter support given to product function. Functional classification - Membranes, lipoproteins and porins; integral membrane protein 1403213..1403977 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905756 YP_002344851.1 CDS ctsE NC_002163.1 1405147 1406706 R Original (2000) note: Cj1471c, probable type II protein secretion system E protein, len: 519 aa; similar to e.g. GSPE_ERWCA general secretion pathway protein E (498 aa), fasta scores; opt: 993 z-score: 1102.0 E(): 0,38.2% identity in 487 aa overlap, and HOFB_ECOLI protein transport protein HOFB (461 aa), fasta scores; opt: 925 z-score: 1027.3 E(): 0, 37.7% identity in 453 aa overlap. No Hp match. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00662 Bacterial type II secretion system protein E signature, and Pfam match to entry PF00437 GSPII_E, Bacterial type II secretion system protein; Updated (2006) 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; PMID:12949093, PMID:1971619; type II protein secretion system E protein complement(1405147..1406706) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905758 YP_002344852.1 CDS Cj1472c NC_002163.1 1406696 1407283 R Original (2000) note: Cj1472c, probable membrane protein, len: 195 aa; no Hp match; Updated (2006) note: One probable transmembrane helix predicted by TMHMM2.0. Literature search identified paper giving further clues to product function. Functional classification - Membranes, lipoproteins and porins; PMID:12949093; hypothetical protein complement(1406696..1407283) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905759 YP_002344853.1 CDS ctsP NC_002163.1 1407287 1407895 R Original (2000) note: Cj1473c, probable ATP/GTP-binding protein, len: 202 aa; no Hp match. Contains PS00017 ATP/GTP-binding site motif A (P-loop); Updated (2006) note: Literature search identified paper giving further clues to product function. Functional classification - Unknown; PMID:12949093; ATP/GTP-binding protein complement(1407287..1407895) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905760 YP_002344854.1 CDS ctsD NC_002163.1 1407888 1409306 R Original (2000) note: Cj1474c, probable type II protein secretion system D protein, len: 472 aa; similar to e.g. GSPD_PSEAE general secretion pathway protein D precursor (658 aa), fasta scores; opt: 305 z-score: 332.5 E(): 3.4e-11, 26.5% identity in 268 aa overlap. No Hp match. Contains Pfam match to entry PF00263 Bac_GSPproteins, Bacterial type II secretion system protein, and probable N-terminal signal sequence; Updated (2006) 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; PMID:12949093; type II protein secretion system D protein complement(1407888..1409306) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905761 YP_002344855.1 CDS ctsR NC_002163.1 1409278 1409595 R Original (2000) note: Cj1475c, unknown, len: 105 aa; no Hp match; Updated (2006) note: Literature search identified paper giving further clues to product function. Functional classification - Unknown; PMID:12949093; hypothetical protein complement(1409278..1409595) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905762 YP_002344856.1 CDS Cj1476c NC_002163.1 1409619 1413179 R Original (2000) note: Cj1476c, probable pyruvate-flavodoxin oxidoreductase, len: 1186 aa; highly similar to many e.g. NIFJ_ECOLI probable pyruvate-flavodoxin oxidoreductase (1174 aa), fasta scores; opt: 3586 z-score: 3799.5 E(): 0, 47.2% identity in 1193 aa overlap. N-term has 28.6% identity to HP1110,C-term has 29.7% identity to HP1111. Contains 2x PS00198 4Fe-4S ferredoxins, iron-sulfur binding region signature,and Pfam match to entry PF00037 fer4, 4Fe-4S ferredoxins and related iron-sulfur cluster binding domains; Updated (2006) note: Pfam domains PF02775 Thiamine pyrophosphate enzyme, C-terminal, PF01558 Pyruvate ferredoxin/flavodoxin oxidoreductase and PF01855 Pyruvate flavodoxin/ferredoxin 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; pyruvate-flavodoxin oxidoreductase complement(1409619..1413179) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905763 YP_002344857.1 CDS Cj1477c NC_002163.1 1413272 1413913 R Original (2000) note: Cj1477c, probable hydrolase,len: 206 aa; similar to e.g. GPH_ECOLI phosphoglycolate phosphatase (252 aa), fasta scores; opt: 209 z-score: 257.5 E(): 5.1e-07, 27.5% identity in 222 aa overlap. Contains Pfam match to entry PF00702 Hydrolase, haloacid dehalogenase-like hydrolase. Also similar to Cj1233 (27.3% identity in 205 aa overlap). No Hp match; Updated (2006) note: Similar to different types of hydrolases. kept within product function. Functional classification - Misc; PMID:12576589; hydrolase complement(1413272..1413913) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905764 YP_002344858.1 CDS cadF NC_002163.1 1413913 1414872 R Original (2000) note: Cj1478c, cadF, outer membrane fibronectin-binding protein, len: 319 aa; 82.8% identical to TR:O06895 (EMBL:U87559) C. jejuni CADF precursor (fibronectin-binding protein) (326 aa), and similar to many oprF proteins e.g. PORF_PSEFL outer membrane porin F precursor (root adhesin) (326 aa), fasta scores; opt: 401 z-score: 458.6 E(): 3.2e-18, 29.1% identity in 316 aa overlap. No Hp match. Contains PS01068 OmpA-like domain,and Pfam match to entry PF00691 OmpA, OmpA family; Updated (2006) note: Characterised within Campylobacter jejuni, so not added to product function. Functional classification - Pathogenicity; PMID:9220003, PMID:9435102, PMID:16091041; outer membrane fibronectin-binding protein complement(1413913..1414872) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905765 YP_002344859.1 CDS rpsI NC_002163.1 1414997 1415386 R forms a direct contact with the tRNA during translation; 30S ribosomal protein S9 complement(1414997..1415386) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905766 YP_002344860.1 CDS rplM NC_002163.1 1415389 1415814 R in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit; 50S ribosomal protein L13 complement(1415389..1415814) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905767 YP_002344861.1 CDS Cj1481c NC_002163.1 1415898 1418663 R Original (2000) note: Cj1481c, possible helicase,len: 921 aa; weak similarity to several predicted helicases e.g. UVRD_MYCGE DNA helicase II homolog (703 aa), fasta scores; opt: 220 z-score: 237.1 E(): 7e-06, 24.5% identity in 715 aa overlap, and to e.g. ADDA_BACSU ATP-dependent nuclease subunit A (contains helicase activity) (1232 aa), fasta scores; opt: 204 z-score: 216.2 E(): 0.0001, 23.0% identity in 868 aa overlap. 30.5% identity to HP1553. Also similar to predicted helicases Cj1101 (23.9% identity in 532 aa overlap), and Cj0777 (24.1% identity in 673 aa overlap). Contains PS00017 ATP/GTP-binding site motif A (P-loop); Updated (2006) note: Pfam domain PF00580 UvrD/REP helicase identified within CDS. Further support given to product function. Not yet specifically characterised within related bacteria with acceptable identity score. Thus, kept within product function. Functional classification - DNA replication,restriction/modification, recombination and repair; recombination protein RecB complement(1415898..1418663) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905768 YP_002344862.1 CDS Cj1482c NC_002163.1 1418660 1421026 R Original (2000) note: Cj1482c, unknown, len: 788 aa; 29.5% identity to HP1089. Functional classification -Conserved hypothetical proteins; hypothetical protein complement(1418660..1421026) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905769 YP_002344863.1 CDS Cj1483c NC_002163.1 1421023 1421544 R Original (2000) note: Cj1483c, probable lipoprotein, len: 173 aa; 30.8% identity (in N-term) to HP0150. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. Functional classification - Membranes, lipoproteins and porins; lipoprotein complement(1421023..1421544) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905770 YP_002344864.1 CDS Cj1484c NC_002163.1 1421531 1422133 R Original (2000) note: Cj1484c, probable membrane protein, len: 200 aa; no Hp match. Contains probable N-terminal signal sequence and probable C-terminal transmembrane domain. Functional classification -Membranes, lipoproteins and porins; hypothetical protein complement(1421531..1422133) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905771 YP_002344865.1 CDS Cj1485c NC_002163.1 1422130 1422231 R Original (2000) note: Cj1485c, probable periplasmic protein, len: 33 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein complement(1422130..1422231) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905772 YP_002344866.1 CDS Cj1486c NC_002163.1 1422228 1422449 R Original (2000) note: Cj1486c, probable periplasmic protein, len: 73 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein complement(1422228..1422449) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905773 YP_002344867.1 CDS ccoP NC_002163.1 1422446 1423309 R Original (2000) note: Cj1487c, ccoP, cb-type cytochrome C oxidase subunit III, len: 287 aa; simlar to TR:O87196 (EMBL:AB018105) H. pylori characterised cb-type cytochrome C oxidase subunit III (EC 1.9.3.1) (292 aa),fasta scores; opt: 952 z-score: 1043.8 E(): 0, 51.0% identity in 292 aa overlap (=HP0147, 51.2% identity). Contains 2x Pfam match to entry PF00034 cytochrome_c, and 2x PS00190 Cytochrome c family heme-binding site signature; Updated (2006) note: Characterised in Helicobacter pylori with acceptable identity score. not added to product function. Functional classification - Energy metabolism - Electron transport; PMID:9880817; cb-type cytochrome C oxidase subunit III complement(1422446..1423309) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905774 YP_002344868.1 CDS ccoQ NC_002163.1 1423309 1423572 R Original (2000) note: Cj1488c, ccoQ, cb-type cytochrome C oxidase subunit IV, len: 87 aa; similar to TR:O87195 (EMBL:AB018105) H. pylori characterised cb-type cytochrome C oxidase subunit IV (EC 1.9.3.1) (72 aa),fasta scores; opt: 143 z-score: 226.7 E(): 2.6e-05, 35.1% identity in 57 aa overlap (=HP0146); Updated (2006) note: Characterised in Helicobacter pylori with acceptable identity score. not added to product function. Functional classification - Energy metabolism - Electron transport; PMID:9880817; cb-type cytochrome C oxidase subunit IV complement(1423309..1423572) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905775 YP_002344869.1 CDS ccoO NC_002163.1 1423577 1424242 R CcoO; FixO; cbb3-type cytochrome c oxidase subunit II complement(1423577..1424242) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905776 YP_002344870.1 CDS ccoN NC_002163.1 1424255 1425721 R CcoN; FixN; cbb3-type cytochrome c oxidase subunit I complement(1424255..1425721) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905777 YP_002344871.1 CDS Cj1491c NC_002163.1 1425847 1426527 R Original (2000) note: Cj1491c, probable two-component regulator, len: 226 aa; similar to many e.g. VANR_ENTFA regulatory protein VANRB (220 aa), fasta scores; opt: 322 z-score: 369.3 E(): 3e-13, 29.9% identity in 214 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00072 response_reg, Response regulator receiver domain; Updated (2006) note: Pfam domain PF00486 Transcriptional regulatory protein, C terminal identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score has been carried out yet, so kept within product function. Functional classification - Signal transduction; two-component regulator complement(1425847..1426527) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905778 YP_002344872.1 CDS Cj1492c NC_002163.1 1426530 1427741 R Original (2000) note: Cj1492c, probable two-component sensor, len: 403 aa; similar to many e.g. KINC_BACSU sporulation kinase C (428 aa), fasta scores; opt: 281 z-score: 301.1 E(): 1.9e-09, 29.3% identity in 242 aa overlap. No Hp ortholog. Contains Pfam match to entry PF00512 signal, Signal carboxyl-terminal domain; Updated (2006) note: No specific characterisation with acceptable identity score has been carried out yet,so kept within product function. Functional classification - Signal transduction; two-component sensor complement(1426530..1427741) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905779 YP_002344873.1 CDS Cj1493c NC_002163.1 1427738 1428397 R Original (2000) note: Cj1493c, probable integral membrane protein, len: 219 aa; 33.9% identity to HP0861; Updated (2006) note: Six probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; integral membrane protein complement(1427738..1428397) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905783 YP_002344874.1 CDS carA NC_002163.1 1428394 1429512 R catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers; carbamoyl phosphate synthase small subunit complement(1428394..1429512) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905785 YP_002344875.1 CDS Cj1495c NC_002163.1 1429512 1430063 R Original (2000) note: Cj1495c, unknown, len: 183 aa; similar to hypothetical proteins e.g. TR:O67633 (EMBL:AE000754) Aquifex aeolicus AQ_1752 (183 aa), fasta scores; opt: 268 z-score: 310.8 E(): 5.4e-10, 24.6% identity in 183 aa overlap. 45.4% identity to HP1236; Updated (2006) note: Pfam domain PF04368 Protein of unknown function (DUF507) identified within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins; hypothetical protein complement(1429512..1430063) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905784 YP_002344876.1 CDS Cj1496c NC_002163.1 1430156 1430674 R Original (2000) note: Cj1496c, probable periplasmic protein, len: 172 aa; similar to TR:O30719 (EMBL:AF016039) H. pylori PDP protein (HP0257) (223 aa), fasta scores; opt: 232 z-score: 243.0 E(): 3.3e-06, 33.3% identity in 177 aa overlap. Contains probable N-terminal signal sequence; Updated (2006) note: Paper identified linking protein to glycoprotein. Functional classification -Miscellaneous periplasmic proteins; PMID:12186869; periplasmic protein complement(1430156..1430674) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 906007 YP_002344877.1 CDS Cj1497c NC_002163.1 1430667 1431095 R Original (2000) note: Cj1497c, unknown, len: 142 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein complement(1430667..1431095) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905781 YP_002344878.1 CDS purA NC_002163.1 1431092 1432342 R catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis; adenylosuccinate synthetase complement(1431092..1432342) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905786 YP_002344879.1 CDS Cj1500 NC_002163.1 1432607 1433815 D Original (2000) note: Cj1500, probable integral membrane protein, len: 402 aa; similar to hypothetical membrane protens e.g. YEDE_ECOLI (401 aa), fasta scores; opt: 722 z-score: 819.1 E(): 0, 44.3% identity in 395 aa overlap. No Hp match; Updated (2006) note: Pfam domain x2 PF04143 YeeE/YedE family (DUF395) identified within CDS. Also, ten probable transmembrane helices predicted by TMHMM2.0. Further support given to product function. Functional classification - Membranes, lipoproteins and porins; inner membrane protein 1432607..1433815 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905787 YP_002344880.1 CDS Cj1501 NC_002163.1 1433819 1434046 D Updated (2006) note: Conserved added to product function due to present motif within CDS; Original (2000) note: Cj1501, unknown, len: 85 aa; similar to hypothetical proteins e.g. YEDF_ECOLI (77 aa),fasta scores; opt: 341 z-score: 453.8 E(): 5.9e-18, 65.7% identity in 70 aa overlap. No Hp match. Contains PS01148 Uncharacterized protein family UPF0033 signature, and Pfam match to entry PF01206 UPF0033, Uncharacterized protein family UPF0033; hypothetical protein 1433819..1434046 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905791 YP_002344881.1 CDS putP NC_002163.1 1434062 1435549 R Original (2000) note: Cj1502c, putP, probable sodium/proline symporter, len: 495 aa; similar to many e.g. PUTP_ECOLI sodium/proline symporter (proline permease) (502 aa), fatsa scores; opt: 1695 z-score: 1986.4 E(): 0, 51.7% identity in 487 aa overlap. 74.9% identity to HP0055. Contains Pfam match to entry PF00474 SSF, Sodium:solute symporter family; Updated (2006) 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/binding proteins - Amino acids and amines; PMID:1567896, PMID:3302614; sodium/proline symporter complement(1434062..1435549) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905789 YP_002344882.1 CDS putA NC_002163.1 1435549 1439037 R Original (2000) note: Cj1503c, putA, possible proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase, len: 1162 aa; similar to e.g. PUTA_ECOLI bifunctional PUTA protein [includes: proline dehydrogenase (EC 1.5.99.8); delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12) (1320 aa), fasta scores; opt: 611 z-score: 639.8 E(): 2.6e-28, 26.9% identity in 892 aa overlap. 65.0% identity to HP0056. Contains Pfam match to entry PF00171 aldedh, Aldehyde dehydrogenase, PS00017 ATP/GTP-binding site motif A (P-loop), PS00687 Aldehyde dehydrogenases glutamic acid active site, and PS00070 Aldehyde dehydrogenases cysteine active site; Updated (2006) note: Pfam domain PF01619 Proline dehydrogenase also identified within CDS. Further support given to product function. Characterised within Escherichia coli, however, identity score was not acceptable. kept within product function. Functional classification - Degradation - Amino acids; PMID:15449943, PMID:7966312, PMID:12009917; proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase complement(1435549..1439037) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905792 YP_002344883.1 CDS selD NC_002163.1 1439168 1440094 R Original (2000) note: Cj1504c, selD, probable selenide,water dikinase, len: 308 aa; similar to e.g. SELD_ECOLI selenide,water dikinase (selenophosphate synthetase) (EC 2.7.9.3) (347 aa), fasta scores; opt: 638 z-score: 720.3 E(): 8.4e-33, 37.2% identity in 298 aa overlap. No Hp match. Contains Pfam match to entry PF00586 AIRS, AIR synthase related proteins; Updated (2006) note: Characterised wihtin Escherichia coli with acceptable identity score. kept within product function. Functional classification -Aminoacyl tRNA synthetases and their modification; PMID:2405383, PMID:1527085; selenide,water dikinase complement(1439168..1440094) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905797 YP_002344884.1 CDS Cj1505c NC_002163.1 1440200 1440772 R Original (2000) note: Cj1505c, unknown, len: 190 aa; similar in N-term to hypothetical proteins e.g. Y990_METJA (75 aa), fasta scores; opt: 121 z-score: 164.1 E(): 0.081, 33.3% identity in 69 aa overlap. No Hp match. Some simlarity to Cj1492c (21.1% identity in 190 aa overlap). Contains Pfam match to entry PF01206 UPF0033,Uncharacterized protein family UPF0033; Updated (2006) 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, so kept within product function. Functional classification - Signal transduction; PMID:14645287; two-component response regulator complement(1440200..1440772) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905793 YP_002344885.1 CDS Cj1506c NC_002163.1 1440883 1442985 R Original (2000) note: Cj1506c, probable MCP-type signal transduction protein, len: 700 aa; similar to many e.g. TR:CAB38318 (EMBL:AJ132321) Halobacterium salinarium arginine chemotaxis CAR protein (452 aa), fasta scores; opt: 382 z-score: 382.7 E(): 5.4e-14, 29.9% identity in 281 aa overlap. Contains two possible transmembrane domains and Pfam match to entry PF00015 MCPsignal,Methyl-accepting chemotaxis protein (MCP) signaling domain. 35.3% identity to HP0099; Updated (2006) note: No specific characterisation with acceptable identity score carried out yet. kept in product function. Functional classification -Signal transduction; PMID:9750306; MCP-type signal transduction protein complement(1440883..1442985) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905796 YP_002344886.1 CDS Cj1507c NC_002163.1 1443095 1443832 R Original (2000) note: Cj1507c, unknown, len: 245 aa; no Hp match; Updated (2006) note: Pfam domain PF00126 Bacterial regulatory helix-turn-helix protein, lysR family identified within CDS. Product modified to more specific family based on motif match. No specific characterisation has been carried out yet, so kept within product function. Literature search identified paper giving further clues to product function. Functional classification - Broad regulatory functions; PMID:14641908; regulatory protein complement(1443095..1443832) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905800 YP_002344887.1 CDS fdhD NC_002163.1 1443825 1444607 R involved in the production or activity of formate dehydrogenase-H which is active when nitrate is not present during anaerobic growth; formate dehydrogenase accessory protein complement(1443825..1444607) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905799 YP_002344888.1 CDS fdhC NC_002163.1 1444774 1445706 R Original (2000) note: Cj1509c, fdhC, probable formate dehydrogenase, cytochrome B subunit, len: 310 aa; similar to e.g. TR:P28180 (EMBL:X54057) Wolinella succinogenes formate dehydrogenase C precursor (306 aa),fasta scores; opt: 634 z-score: 759.3 E(): 0, 42.8% identity in 318 aa overlap, and FDNI_ECOLI formate dehydrogenase, nitrate-inducible, cytochrome B556(fdn) subunit (217 aa), fasta scores; opt: 189 z-score: 234.3 E(): 9.9e-06, 25.5% identity in 212 aa overlap. No Hp ortholog; Updated (2006) 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; PMID:9006048, PMID:1781728; formate dehydrogenase, cytochrom B subunit complement(1444774..1445706) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905794 YP_002344889.1 CDS fdhB NC_002163.1 1445703 1446344 R Original (2000) note: Cj1510c, fdhB, probable formate dehydrogenase iron-sulfur subunit, len: 213 aa; similar to e.g. FDHB_WOLSU formate dehydrogenase iron-sulfur subunit (EC 1.2.1.2) (200 aa), fasta scores; opt: 1025 z-score: 1153.1 E(): 0, 69.5% identity in 197 aa overlap. No Hp ortholog. Contains PS00198 4Fe-4S ferredoxins, iron-sulfur binding region signature, and Pfam match to entry PF00037 fer4, 4Fe-4S ferredoxins and related iron-sulfur cluster binding domains; Updated (2006) note: Some characterisation in Wolinella succinogenes with acceptable identity score. kept within product function. Functional classification - Energy metabolism - Respiration -Anaerobic; PMID:1781728, PMID:9006048; formate dehydrogenase iron-sulfur subunit complement(1445703..1446344) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905790 YP_002344890.1 CDS fdhA NC_002163.1 1446341 1449145 R Original (2000) note: Cj1511c, fdhA, probable formate dehydrogenase large subunit, len: 934 aa; similar to e.g. TR:P28179 (EMBL:X54057) Wolinella succinogenes formate dehydrogenase large subunit precursor (EC 1.2.1.2)(939 aa), fasta scores; opt: 3368 z-score: 3913.9 E(): 7.3e-211, 52.8% identity in 930 aa overlap, and FDHF_ECOLI formate dehydrogenase H (EC 1.2.1.2) (formate-hydrogen-lyase-linked, selenocysteine-containing polypeptide) (715 aa), fasta scores; opt: 813 z-score: 943.1 E(): 2.2e-45, 30.9% identity in 696 aa overlap. No Hp match. Contains Pfam match to entry PF00384 molybdopterin, Prokaryotic molybdopterin oxidoreductases,and PS00551 Prokaryotic molybdopterin oxidoreductases signature 1. Note that TGA codes for Selenocysteine at codon 181 complement(1448602..1448604); Updated (2006) 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; PMID:2941757, PMID:9036855, PMID:9006048; formate dehydrogenase large subunit complement(1446341..1449145) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905795 YP_002344891.1 CDS Cj1513c NC_002163.1 1449145 1449336 R Original (2000) note: Cj1513c, possible periplasmic protein, len: 63 aa; no Hp match. Contains possible N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein complement(1449145..1449336) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905788 YP_002344892.1 CDS Cj1514c NC_002163.1 1449311 1450024 R Original (2000) note: Cj1514c, unknown, len: 237 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein complement(1449311..1450024) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905802 YP_002344893.1 CDS Cj1515c NC_002163.1 1450328 1451476 R Original (2000) note: Cj1515c, probable decarboxylase, len: 382 aa; similar to TR:Q56575 (EMBL:D31783) Vibrio alginolyticus carboxynorspermidine decarboxylase (377 aa), fasta scores; opt: 667 z-score: 807.5 E(): 0, 36.6% identity in 380 aa overlap. 45.8% identity to HP0020; Updated (2006) note: Pfam domain PF00278 Pyridoxal-dependent decarboxylase, C-terminal identified within CDS. Further support given to product function. No specific characterisation with acceptable identity score carried out yet, so kept within product function. Functional classification - Misc; decarboxylase complement(1450328..1451476) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905798 YP_002344894.1 CDS Cj1516 NC_002163.1 1451600 1453141 D Original (2000) note: Cj1516, probable periplasmic oxidoreductase, len: 1539 aa; similar to members of the multicoper oxidase family e.g. YACK_ECOLI probable blue-copper protein yack precursor (516 aa), fasta scores; opt: 376 z-score: 429.0 E(): 1.4e-16, 28.7% identity in 460 aa overlap, and BLRO_MYRVE bilirubin oxidase precursor (572 aa), fasta scores; opt: 309 z-score: 352.2 E(): 2.7e-12, 24.8% identity in 499 aa overlap. No Hp match. Contains possible N-terminal signal sequence, Pfam match to entry PF00394 Cu-oxidase, Multicopper oxidase, and PS00080 Multicopper oxidases signature 2; Updated (2006) note: No specific characterisation with acceptable identity score carried out yet, so kept within product function. Functional classification - Misc; periplasmic oxidoreductase 1451600..1453141 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905803 YP_002344895.1 CDS moaD NC_002163.1 1453143 1453364 D Original (2000) note: Cj1517, moaD, possible molybdopterin converting factor, subunit 1, len: 73 aa; similar to many predicted moaD genes, e.g. TR:O31706 (EMBL:AF012285) Bacillus subtilis molybdopterin converting factor (subunit 1) (77 aa), fasta scores; opt: 111 z-score: 167.7 E(): 0.051, 30.5% identity in 59 aa overlap, and weakly similar to MOAD_ECOLI molybdopterin [mpt] converting factor, subunit 1 (81 aa), fasta scores; opt: 81 z-score: 127.5 E(): 8.8, 38.5% identity in 26 aa overlap. 61.6% identity to HP0801; Updated (2006) 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,so kept within product function. Functional classification - Biosynthesis of cofactors, prosthetic groups and carriers - Molybdopterin; molybdopterin converting factor subunit 1 1453143..1453364 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905801 YP_002344896.1 CDS moaE NC_002163.1 1453365 1453811 D Original (2000) note: Cj1518, moaE, possible molybdopterin converting factor, subunit 2, len: 148 aa; similar to many predicted moaE genes, e.g. TR:O31705 (EMBL:AF012285) Bacillus subtilis molybdopterin converting factor (subunit 2) (157 aa), fasta scores; opt: 134 z-score: 182.4 E(): 0.0078, 25.2% identity in 131 aa overlap, and to MOAE_ECOLI molybdopterin [mpt] converting factor, subunit 2 (149 aa), fasta scores opt: 133 z-score: 181.4 E(): 0.0087, 26.0% identity in 123 aa overlap. 50.4% identity to HP0800; Updated (2006) 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,so kept within product function. Functional classification - Biosynthesis of cofactors, prosthetic groups and carriers - Molybdopterin; molybdopterin converting factor subunit 2 1453365..1453811 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905805 YP_002344897.1 CDS moeA2 NC_002163.1 1453815 1455005 D Original (2000) note: Cj1519, moeA2, probable molybdopterin biosynthesis protein, len: 396 aa; similar to e.g. MOEA_ECOLI molybdopterin biosynthesis MOEA protein (411 aa), fasta scores; opt: 541 z-score: 624.0 E(): 1.9e-27, 29.2% identity in 366 aa overlap. No Hp ortholog,but 37.3% identity to HP0172. Also similar to Cj0857c moeA (33.3% identity in 378 aa overlap). Contains Pfam match to entry PF00994 MoCF_biosynth, Molybdenum cofactor biosynthesis protein; Updated (2006) note: Pfam domains PF03453 MoeA N-terminal region (domain I and II), PF00994 Probable molybdopterin binding domain and PF03454 MoeA C-terminal region (domain IV) were all identified within CDS. Further support given to product function. Specific characterisation with acceptable similairty score has not been carried out yet, so kept within product function. Functional classification - Biosynthesis of cofactors, prosthetic groups and carriers - Molybdopterin; molybdopterin biosynthesis protein 1453815..1455005 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905804 YP_002344898.1 CDS Cj1521c NC_002163.1 1455569 1456000 R Original (2000) note: Cj1521c, unknown, len: 143 aa; no Hp match; Updated (2006) note: Cj1521c,CJ1522c and Cj1523c are believed to be CRISPR-associated proteins that contribute to the CRISPR repeat region formation. Functional classification - Misc; PMID:11952905, PMID:16612537, PMID:16545108; CRISPR-associated protein complement(1455569..1456000) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905810 YP_002344899.1 CDS Cj1522c NC_002163.1 1455993 1456883 R Original (2000) note: Cj1522c, unknown, len: 296 aa; very weak simlarity to TR:O28401 (EMBL:AE000973) Archaeoglobus fulgidus AF1878 (345 aa), fasta scores; opt: 156 z-score: 198.5 E(): 0.00099, 25.3% identity in 281 aa overlap. No Hp match; Updated (2006) note: Cj1521c,CJ1522c and Cj1523c are believed to be CRISPR-associated proteins that contribute to the CRISPR repeat region formation. Functional classification - Misc; PMID:11952905, PMID:16612537, PMID:16545108; CRISPR-associated protein complement(1455993..1456883) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905808 YP_002344900.1 CDS Cj1523c NC_002163.1 1456880 1459834 R Original (2000) note: Cj1523c, unknown, len: 984 aa; no Hp match; Updated (2006) note: Cj1521c,CJ1522c and Cj1523c are believed to be CRISPR-associated proteins that contribute to the CRISPR repeat region formation. Functional classification - Misc; PMID:11952905, PMID:16612537, PMID:16545108; CRISPR-associated protein complement(1456880..1459834) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905809 YP_002344901.1 CDS purM NC_002163.1 1461504 1462493 R catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis; phosphoribosylaminoimidazole synthetase complement(1461504..1462493) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905806 YP_002344902.1 CDS coaE NC_002163.1 1462554 1463159 D catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis; dephospho-CoA kinase 1462554..1463159 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905813 YP_002344903.1 CDS dapF NC_002163.1 1463156 1463905 D involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate; diaminopimelate epimerase 1463156..1463905 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905812 YP_002344904.1 CDS Cj1532 NC_002163.1 1463880 1464611 D Original (2000) note: Cj1532, possible periplasmic protein, len: 243 aa; some similarity to N-terminus of BAX_ECOLI BAX protein (274 aa), fasta scores; opt: 240 z-score: 286.1 E(): 1.3e-08, 38.3% identity in 120 aa overlap. No Hp match. Contains possible N-terminal signal sequence; Updated (2006) note: Pfam domain PF01832 Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase (Glucosaminidase) identified within CDS. No specific characterisation carried out yet, so kept within product function. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein 1463880..1464611 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905246 YP_002344905.1 CDS Cj1533c NC_002163.1 1464608 1465645 R Original (2000) note: Cj1533c, unknown, len: 345 aa; 27.9% identity to HP1321. Contains possible helix-turn-helix motif at aa 191-212 (Score 1065, +2.81 SD). Functional classification - Broad regulatory functions; hypothetical protein complement(1464608..1465645) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905815 YP_002344906.1 CDS Cj1534c NC_002163.1 1465710 1466159 R Original (2000) note: Cj1534c, possible bacterioferritin, len: 149 aa; similar to many members of the DPS family e.g. NAPA_HELPY neutrophil-activating protein A (=HP0243) (bacterioferritin)(144 aa), fasta scores; opt: 397 z-score: 495.1 E(): 3e-20, 41.3% identity in 143 aa overlap, TPF1_TREPA antigen TPF1 (176 aa), fasta scores; opt: 296 z-score: 372.0 E(): 2.1e-13, 33.3% identity in 144 aa overlap, MRGA_BACSU metalloregulation DNA-binding stress protein (153 aa), fasta scores; opt: 234 z-score: 298.1 E(): 2.8e-09, 33.1% identity in 127 aa overlap, and FRI_LISIN non-heme iron-containing ferritin (156 aa), fasta scores; opt: 226 z-score: 288.3 E(): 9.8e-09, 31.8% identity in 148 aa overlap; Updated (2006) 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 (PMID:12186869). Functional classification -Transport/binding proteins - Cations; PMID:7883175, PMID:8709848, PMID:12186869; bacterioferritin complement(1465710..1466159) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905816 YP_002344907.1 CDS pgi NC_002163.1 1466289 1467509 R catalyzes the formation of D-fructose 6-phosphate from D-glucose 6-phosphate; glucose-6-phosphate isomerase complement(1466289..1467509) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905817 YP_002344908.1 CDS galU NC_002163.1 1467503 1468327 R Original (2000) note: Cj1536c, galU, probable UTP--glucose-1-phosphate uridylyltransferase, len: 274 aa; highly similar to many e.g. GALU_PSEAE UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (279 aa), fasta scores; opt: 1245 z-score: 1547.3 E(): 0,65.9% identity in 270 aa overlap. 61.3% identity to HP0646. Contains Pfam match to entry PF00483 NTP_transferase, Nucleotidyl transferase; Updated (2006) note: Characterised in Pseudomonas aeruginosa with acceptable identity score. Thus, was not added to product function. Functional classification - Degradation - Carbon compounds; PMID:8169209; UTP-glucose-1-phosphate uridylyltransferase complement(1467503..1468327) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905818 YP_002344909.1 CDS acs NC_002163.1 1468409 1470382 R Acs; catalyzes the conversion of acetate and CoA to acetyl-CoA; acetyl-CoA synthetase complement(1468409..1470382) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905819 YP_002344910.1 CDS Cj1538c NC_002163.1 1470520 1471515 R Original (2000) note: Cj1538c, possible anion-uptake ABC-transport system ATP-binding protein,len: 331 aa; similar to many e.g. LACK_AGRRD lactose transport ATP-binding protein LACK (363 aa), fasta scores; opt: 319 z-score: 386.4 E(): 3.3e-14, 28.8% identity in 208 aa overlap, and UGPC_ECOLI SN-glycerol-3-phosphate transport ATP-binding protein (356 aa), fasta scores; opt: 298 z-score: 361.6 E(): 8.1e-13, 32.1% identity in 196 aa overlap. No Hp ortholog. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00211 ABC transporters family signature, and Pfam match to entry PF00005 ABC_tran, ABC transporters. identification as anion-uptake is due to similarities of associated permease Cj1539c; Updated (2006) note: No specific characterisation with acceptable identity score carried out yet. kept in product function. Functional classification -Transport/binding proteins - Anions; anion-uptake ABC-transport system ATP-binding protein complement(1470520..1471515) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905820 YP_002344911.1 CDS Cj1539c NC_002163.1 1471517 1472236 R Original (2000) note: Cj1539c, possible anion-uptake ABC-transport system permease, len: 239 aa; similar to many involved in anion uptake e.g. CYST_ECOLI sulfate transport system permease (277 aa), fasta scores; opt: 235 z-score: 293.7 E(): 4.9e-09,23.6% identity in 220 aa overlap, and MODB_ECOLI molybdenum transport system permease proteim (229 aa),fasta scores; opt: 201 z-score: 253.9 E(): 8.1e-07, 25.2% identity in 214 aa overlap. No Hp otholog; Updated (2006) note: Pfam domain PF00528 Binding-protein-dependent transport system inner membrane component identified within CDS. Also, five probable transmembrane helices predicted by TMHMM2.0. No specific characterisation with acceptable identity score, so kept within product function. Functional classification - Transport/binding proteins - Anions; anion-uptake ABC-transport system permease complement(1471517..1472236) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905821 YP_002344912.1 CDS Cj1540 NC_002163.1 1472282 1473091 D Original (2000) note: Cj1540, probable periplasmic protein, len: 269 aa; similar to TR:O26579 (EMBL:AE000832) Methanobacterium thermoautotrophicum MTH479 (293 aa),fasta scores; opt: 416 z-score: 475.8 E(): 3.5e-19, 37.0% identity in 273 aa overlap. No Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein 1472282..1473091 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905822 YP_002344913.1 CDS Cj1541 NC_002163.1 1473233 1474000 D Original (2000) note: Cj1541, unknown, len: 255 aa; similar to hypothetical proteins e.g. YCSF_BACSU (211 aa),fasta scores; opt: 736 z-score: 875.7 E(): 0, 59.9% identity in 177 aa overlap, and to LAMB_EMENI Aspergillus nidulans lactam utilization protein LAMB (262 aa), fasta scores; opt: 405 z-score: 485.4 E(): 1e-19, 44.9% identity in 127 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF03746 LamB/YcsF family identified within CDS. No specific characterisation has been carried out yet, so kept within product function. Functional classification - Conserved hypothetical proteins; LamB/YcsF family protein 1473233..1474000 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905823 YP_002344914.1 CDS Cj1542 NC_002163.1 1474010 1474750 D Original (2000) note: Cj1542, unknown, len: 246 aa; similar to hypothetical proteins e.g. YCSJ_BACSU (578 aa),fasta scores; opt: 569 z-score: 690.1 E(): 4.1e-31, 41.8% identity in 237 aa overlap. No Hp match; Updated (2006) 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, so kept within product function. Also,similarity to Bacillus subtilis kinase a inhibitor (sporulation inhibitor kipi) (PMID:9334321). Functional classification - Degradation - Carbon compounds; PMID:9334321; allophanate hydrolase subunit 1 1474010..1474750 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905826 YP_002344915.1 CDS Cj1543 NC_002163.1 1474731 1475696 D Original (2000) note: Cj1543, unknown, len: 321 aa; similar to hypothetical proteins e.g. YBGK_ECOLI (310 aa),fasta scores; opt: 553 z-score: 652.4 E(): 5.1e-29, 32.7% identity in 312 aa overlap. Also similar to part of DUR1_YEAST urea amidolyase [includes: urea carboxylase; allophanate hydrolase] (1835 aa), fasta scores; opt: 307 z-score: 353.8 E(): 2.2e-12, 28.5% identity in 333 aa overlap. No Hp match; Updated (2006) 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, so kept within product function. Functional classification - Degradation - Carbon compounds; allophanate hydrolase subunit 2 1474731..1475696 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905824 YP_002344916.1 CDS Cj1544c NC_002163.1 1475693 1476589 R Original (2000) note: Cj1544c, probable integral membrane protein, len: 298 aa; simlar to hypothetical membrane proteins e.g. YYAM_BACSU (305 aa), fasta scores; opt: 244 z-score: 300.4 E(): 2.1e-09, 22.3% identity in 300 aa overlap. No Hp match. Contains Pfam match to entry PF00892 DUF6, Integral membrane protein; Updated (2006) note: Ten probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; integral membrane protein complement(1475693..1476589) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905162 YP_002344917.1 CDS Cj1545c NC_002163.1 1476622 1477200 R Original (2000) note: Cj1545c, unknown, len: 192 aa; similar to e.g. MDAB_ECOLI modulator of drug activity B (193 aa), fasta scores; opt: 777 z-score: 934.0 E(): 0,57.8% identity in 192 aa overlap. Also weak simlarity to many boxidoreductases e.g. YCAK_ECOLI NAD(P)H oxidoreductase YCAK (196 aa), fasta scores; opt: 124 z-score: 159.3 E(): 0.15, 24.7% identity in 174 aa overlap. 65.1% identity to HP0630; Updated (2006) 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; MdaB protein complement(1476622..1477200) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904498 YP_002344918.1 CDS Cj1546 NC_002163.1 1477300 1477647 D Original (2000) note: Cj1546, unknown, len: 115 aa; similar to hypothetical proteins e.g. YYBR_BACSU (125 aa),fasta scores; opt: 278 z-score: 389.5 E(): 2.3e-14, 42.5% identity in 106 aa overlap. No Hp match. Also similar to Cj1556 (43.6% identity in 101 aa overlap); Updated (2006) 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; transcriptional regulator 1477300..1477647 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905827 YP_002344919.1 CDS Cj1547 NC_002163.1 1477635 1478084 D Original (2000) note: Cj1547, unknown, len: 149 aa; similar to e.g. BLC_ECOLI outer membrane lipoprotein BLC precursor (177 aa), fasta scores; opt: 230 z-score: 307.6 E(): 8.2e-10, 27.6% identity in 145 aa overlap, and APD_MOUSE apolipoprotein D precursor (189 aa), fasta scores; opt: 151 z-score: 206.3 E(): 0.00036, 30.3% identity in 145 aa overlap. No Hp match. Contains PS00213 Lipocalin signature, but no N-terminal signal sequence. Functional classification - Conserved hypothetical proteins; Blc protein 1477635..1478084 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904541 YP_002344920.1 CDS Cj1548c NC_002163.1 1478086 1479162 R Original (2000) note: Cj1548c, probable NADP-dependent alcohol dehydrogenase, len: 358 aa; similar to e.g. ADH_MYCTU NADP-dependent alcohol dehydrogenase (EC 1.1.1.2) (346 aa), fasta scores; opt: 997 z-score: 1095.7 E(): 0, 43.9% identity in 344 aa overlap. Also similar to plant lignin production alcohol dehydrogenases e.g. CAD3_ARATH cinnamyl-alcohol dehydrogenase ELI3-2 (359 aa),fasta scores; opt: 949 z-score: 1043.1 E(): 0, 40.9% identity in 352 aa overlap. 65.8% identity to HP1104. Contains PS00059 Zinc-containing alcohol dehydrogenases signature, and Pfam match to entry PF00107 adh_zinc,Zinc-binding dehydrogenases; Updated (2006) note: kept within product function as acceptable identity score to more than one characterised bacteria. Functional classification - Misc; PMID:1427101; NADP-dependent alcohol dehydrogenase complement(1478086..1479162) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904495 YP_002344921.1 CDS hsdR NC_002163.1 1479390 1482485 R Original (2000) note: Cj1549c, probable type I restriction enzyme R protein, len: 1031 aa; similar to many e.g. T1R1_ECOLI type I restriction enzyme EcoR124II R protein (EC 3.1.21.3) (1033 aa), fasta scores; opt: 353 z-score: 372.8 E(): 1.9e-13, 23.5% identity in 1047 aa overlap. 26.4% identity to HP1402; Updated (2006) note: Pfam domains PF04851 Type III restriction enzyme, 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 (genes Cj1549-Cj1553). Some characterisation work within Escherichia coli, however, kept within product function as identity score was unnacceptable. Functional classification - DNA replication, restriction/modification, recombination and repair; PMID:15699185, PMID:9016588; type I restriction enzyme R protein complement(1479390..1482485) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905828 YP_002344922.1 CDS rloH NC_002163.1 1482488 1484254 R Original (2000) note: Cj1550c, probable ATP/GTP-binding protein, len: 588 aa; some similarity to hypothetical proteins e.g. TR:O50349 Lactobacillus helveticus plasmid plh1 hypothetical protein (495 aa),fasta scores; opt: 209 z-score: 231.6 E(): 1.4e-05, 22.6% identity in 412 aa overlap. No Hp match. Contains PS00017 ATP/GTP-binding site motif A (P-loop); Updated (2006) note: Prosite domain PS50893 ABC_TRANSPORTER_2, ATP-binding cassette, 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 (genes Cj1549-Cj1553). kept within product function. Functional classification - Conserved hypothetical proteins; PMID:15699185; ATP/GTP-binding protein complement(1482488..1484254) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905829 YP_002344923.1 CDS hsdS NC_002163.1 1484265 1485407 R Original (2000) note: Cj1551c, probable type I restriction enzyme S protein, len: 588 aa; simlar to many e.g. T1S_SALTY type I restriction enzymE StySJI specificity protein (S protein) (469 aa), fasta scores; opt: 173 z-score: 199.9 E(): 0.00082, 25.6% identity in 301 aa overlap. 24.1% identity to HP0462; Updated (2006) note: Literature search identified work carried out within Helicobacter pylori and Campylobacter jejuni. This CDS is within a type I locus (genes Cj1549-Cj1553). Some characterisation work within Escherichia coli, however, kept within product function as identity scores were unnacceptable. Functional classification - DNA replication,restriction/modification, recombination and repair; PMID:15699185, PMID:3025838, PMID:1453962; type I restriction enzyme S protein complement(1484265..1485407) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905830 YP_002344924.1 CDS mloB NC_002163.1 1485626 1487092 R Original (2000) note: Cj1552c, unknown, len: 488 aa; no Hp match; Updated (2006) 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 (genes Cj1549-Cj1553). Functional classification - Unknown; PMID:15699185; hypothetical protein complement(1485626..1487092) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905831 YP_002344925.1 CDS hsdM NC_002163.1 1487089 1488591 R Original (2000) note: Cj1553c, probable type I restriction enzyme M protein, len: 500 aa; simlar to many e.g. T1M1_ECOLI type I restriction enzyme EcoR124II M protein (EC 2.1.1.72) (520 aa), fasta scores; opt: 447 z-score: 527.4 E(): 4.7e-22, 25.9% identity in 521 aa overlap. 30.2% identity to HP0850. Contains PS00092 N-6 Adenine-specific DNA methylases signature; Updated (2006) 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 (genes Cj1549-Cj1553). Some characterisation work within Escherichia coli, however, kept within product function as identity scores were unnacceptable. Functional classification - DNA replication,restriction/modification, recombination and repair; PMID:15699185, PMID:8145241, PMID:9016588; type I restriction enzyme M protein complement(1487089..1488591) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905832 YP_002344926.1 CDS Cj1555c NC_002163.1 1488961 1489596 R Original (2000) note: Cj1555c, unknown, len: 211 aa; similar to TR:P71037 Bacillus subtilis YWNB (213 aa),fasta scores; opt: 519 z-score: 635.5 E(): 4.5e-28, 42.9% identity in 212 aa overlap. No Hp match. Functional classification - Conserved hypothetical proteins; hypothetical protein complement(1488961..1489596) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905833 YP_002344927.1 CDS Cj1556 NC_002163.1 1489789 1490121 D Original (2000) note: Cj1556, unknown, len: 110 aa; similar to hypothetical proteins e.g. YYBR_BACSU (125 aa),fasta scores; opt: 307 z-score: 402.3 E(): 4.3e-15, 43.7% identity in 103 aa overlap. No Hp match. Also similar to Cj1546 (43.6% identity in 101 aa overlap); Updated (2006) 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, so kept within product function. Functional classification - Broad regulatory functions; transcriptional regulator 1489789..1490121 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905834 YP_002344928.1 CDS Cj1558 NC_002163.1 1490206 1490379 D Original (2000) note: Cj1558, probable membrane protein, len: 57 aa; no Hp match. May constitute the 5' end of Cj1560, which may be a pseudogene; Updated (2006) note: One probable transmembrane helix predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; hypothetical protein 1490206..1490379 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905835 YP_002344930.1 CDS Cj1561 NC_002163.1 1491162 1491341 D Original (2000) note: Cj1561, probable transcriptional regulator, len: 59 aa; similar to N-terminus of e.g. ARR1_ECOLI arsenical resistance operon repressor (117 aa), fasta scores; opt: 142 z-score: 236.5 E(): 7.4e-06, 38.2% identity in 55 aa overlap, and CADC_LISMO cadmium efflux system accessory protein (119 aa), fasta scores; opt: 134 z-score: 224.1 E(): 3.7e-05,42.0% identity in 50 aa overlap. No Hp match. Contains helix-turn-helix motif at aa 30-51 (Score 1478, +4.22 SD); Updated (2006) note: Similar to more than one characterised bacteria. designation kept within product function. Functional classification - Broad regulatory functions; transcriptional regulator 1491162..1491341 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905837 YP_002344931.1 CDS Cj1562 NC_002163.1 1491332 1491484 D Original (2000) note: Cj1562, unknown, len: 50 aa; no Hp match. Functional classification - Unknown; hypothetical protein 1491332..1491484 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905838 YP_002344932.1 CDS Cj1563c NC_002163.1 1491492 1491923 R Original (2000) note: Cj1563c, probable transcriptional regulator, len: 143 aa; similar to members of the MerR family e.g. Y186_HAEIN hypothetical transcriptional regulator HI0186 (135 aa), fasta scores; opt: 241 z-score: 290.6 E(): 7.3e-09, 31.9% identity in 119 aa overlap, and BLTR_BACSU multidrug-efflux transporter 2 regulator (273 aa), fasta scores; opt: 149 z-score: 182.1 E(): 0.008, 24.4% identity in 127 aa overlap. No Hp match. Contains helix-turn-helix motif at aa 4-25 (Score 1172, +3.18 SD); Updated (2006) 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, so kept within product function. Functional classification - Broad regulatory functions; transcriptional regulator complement(1491492..1491923) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904355 YP_002344933.1 CDS Cj1564 NC_002163.1 1492003 1493991 D Original (2000) note: Cj1564, probable methyl-accepting chemotaxis signal transduction protein,len: 662 aa; similar to many e.g. TLPC_BACSU methyl-accepting chemotaxis protein TLPC (573 aa), fasta scores; opt: 351 z-score: 363.6 E(): 6.2e-13, 26.2% identity in 553 aa overlap. No Hp ortholog. C-terminus contains repeat1, 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,Methyl-accepting chemotaxis protein (MCP) signaling domain; Updated (2006) note: Two probable transmembrane helices predicted by TMHMM2.0. Characterisation work carried out within Bacillus subtilis, however, identity scores were marginal. kept within product function. Functional classification - Chemotaxis and mobility; PMID:6213619, PMID:7921238; methyl-accepting chemotaxis signal transduction protein 1492003..1493991 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904333 YP_002344934.1 CDS pflA NC_002163.1 1494034 1496400 R Original (2000) note: Cj1565c, pflA, required for flagellar function, len: 788 aa; identical to TR:Q46092 (EMBL:U09019) C. jejuni pflA (788 aa). 22.7% identity to HP1274. Contains probable N-terminal signal sequence; Updated (2006) 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; PMID:7715450, PMID:12186869; paralysed flagellum protein complement(1494034..1496400) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905864 YP_002344935.1 CDS nuoN NC_002163.1 1496422 1497810 R Original (2000) note: Cj1566c, nuoN, probable NADH dehydrogenase I chain N, len: 462 aa; similar to many e.g. NUON_ECOLI NADH dehydrogenase I chain N (EC 1.6.5.3) (425 aa), fasta scores; opt: 592 z-score: 716.4 E(): 1.4e-32,32.3% identity in 402 aa overlap. 35.3% identity to HP1273. Contains Pfam match to entry PF00361 oxidored_q1,NADH-Ubiquinone/plastoquinone (complex I), various chains; Updated (2006) note: Characterised operon within Escherichia coli. Appropriate motifs also present. Identity score was acceptable, so not added to product function. Twelve probable transmembrane helices predicted by TMHMM2.0. Functional classification - Energy metabolism - Respiration - Aerobic; PMID:7565112, PMID:7730262, PMID:15368583,PMID:12718520; NADH dehydrogenase I chain N complement(1496422..1497810) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905839 YP_002344936.1 CDS nuoM NC_002163.1 1497800 1499287 R Original (2000) note: Cj1567c, nuoM, probable NADH dehydrogenase I chain M, len: 495 aa; similar to many e.g. NU4M_CHOCR NADH-ubiquinone oxidoreductase chain 4 (EC 1.6.5.3) (492 aa), fasta scores; opt: 1055 z-score: 1213.7 E(): 0, 36.4% identity in 495 aa overlap, and NUOM_ECOLI NADH dehydrogenase I chain M(EC 1.6.5.3) (509 aa), blastp scores; E= 1.5e-58, 32% identity in 419 aa overlap. 40.1% identity to HP1272. Contains Pfam match to entry PF00361 oxidored_q1, NADH-Ubiquinone/plastoquinone (complex I),various chains; Updated (2006) note: Characterised operon within Escherichia coli. Appropriate motifs present. Identity score was acceptable, so not added to product function. Fourteen probable transmembrane helices predicted by TMHMM2.0. Functional classification - Energy metabolism - Respiration - Aerobic; PMID:7565112, PMID:7730262, PMID:15368583,PMID:12923180; NADH dehydrogenase I chain M complement(1497800..1499287) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905840 YP_002344937.1 CDS nuoL NC_002163.1 1499289 1501079 R Catalyzes the transfer of electrons from NADH to ubiquinone; NADH dehydrogenase subunit L complement(1499289..1501079) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905250 YP_002344938.1 CDS nuoK NC_002163.1 1501081 1501377 R Original (2000) note: Cj1569c, nuoK, probable NADH dehydrogenase I chain K, len: 98 aa; similar to many e.g. NUOK_ECOLI NADH dehydrogenase I chain K (EC 1.6.5.3) (100 aa), fasta scores; opt: 212 z-score: 302.0 E(): 1.7e-09,32.6% identity in 95 aa overlap. 45.8% identity to HP1270. Contains Pfam match to entry PF00420 oxidored_q2,NADH-ubiquinone/plastoquinone oxidoreductase chain 4L; Updated (2006) note: Characterised operon within Escherichia coli. Appropriate motifs present. Identity score was acceptable, so not added to product function. Three probable transmembrane helices predicted by TMHMM2.0. Functional classification - Energy metabolism - Respiration - Aerobic; PMID:7565112, PMID:7730262, PMID:15368583,PMID:15996109; NADH dehydrogenase I chain K complement(1501081..1501377) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904491 YP_002344939.1 CDS nuoJ NC_002163.1 1501374 1501892 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit J complement(1501374..1501892) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905841 YP_002344940.1 CDS nuoI NC_002163.1 1501889 1502530 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit I complement(1501889..1502530) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905842 YP_002344941.1 CDS nuoH NC_002163.1 1502540 1503538 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit H complement(1502540..1503538) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905843 YP_002344942.1 CDS nuoG NC_002163.1 1503531 1505993 R Catalyzes the transfer of electrons from NADH to ubiquinone; NADH dehydrogenase subunit G complement(1503531..1505993) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905177 YP_002344943.1 CDS Cj1574c NC_002163.1 1505990 1506682 R Original (2000) note: Cj1574c, unknown, len: 230 aa; 26.5% identity to HP1265. Functional classification -Conserved hypothetical proteins; hypothetical protein complement(1505990..1506682) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905844 YP_002344944.1 CDS Cj1575c NC_002163.1 1506679 1506906 R Original (2000) note: Cj1575c, unknown, len: 75 aa; 52.0% identity to HP1264. Functional classification -Conserved hypothetical proteins; hypothetical protein complement(1506679..1506906) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905845 YP_002344945.1 CDS nuoD NC_002163.1 1506903 1508129 R Catalyzes the transfer of electrons from NADH to quinone; NADH dehydrogenase subunit D complement(1506903..1508129) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905846 YP_002344946.1 CDS nuoC NC_002163.1 1508131 1508925 R Catalyzes the transfer of electrons from NADH to ubiquinone; NADH dehydrogenase subunit C complement(1508131..1508925) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905847 YP_002344947.1 CDS nuoB NC_002163.1 1508922 1509425 R The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen; NADH dehydrogenase subunit B complement(1508922..1509425) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905848 YP_002344948.1 CDS nuoA NC_002163.1 1509407 1509796 R Catalyzes the transfer of electrons from NADH to ubiquinone; NADH dehydrogenase subunit A complement(1509407..1509796) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905849 YP_002344949.1 CDS Cj1580c NC_002163.1 1509909 1510574 R Original (2000) note: Cj1580c, probable peptide ABC-transport system ATP-binding protein, len: 221 aa; similar to e.g. DPPF_ECOLI dipeptide transport ATP-binding protein (334 aa), fasta scores; opt: 436 z-score: 498.1 E(): 2e-20, 34.8% identity in 210 aa overlap, and APPF_BACSU oligopeptide transport ATP-binding protein (329 aa), fasta scores; opt: 419 z-score: 479.2 E(): 2.3e-19,30.8% identity in 211 aa overlap. 30.6% identity to HP0302. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00211 ABC transporters family signature, and Pfam match to entry PF00005 ABC_tran, ABC transporters; Updated (2006) note: Similar to different transport systems with acceptable identity scores. kept within product function. Functional classification -Transport/binding proteins - Other; peptide ABC transporter ATP-binding protein complement(1509909..1510574) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905850 YP_002344950.1 CDS Cj1581c NC_002163.1 1510567 1511277 R Original (2000) note: Cj1581c, probable peptide ABC-transport system ATP-binding protein, len: 236 aa; similar to e.g. OPPD_ECOLI oligopeptide transport ATP-binding protein (337 aa), fasta scores opt: 385 z-score: 442.8 E(): 2.4e-17, 31.5% identity in 232 aa overlap. 29.8% identity to HP0301. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00211 ABC transporters family signature, and Pfam match to entry PF00005 ABC_tran, ABC transporters; Updated (2006) note: Similar to different transport systems with acceptable identity scores. kept within product function. Functional classification -Transport/binding proteins - Other; peptide ABC transporter ATP-binding protein complement(1510567..1511277) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905851 YP_002344951.1 CDS Cj1582c NC_002163.1 1511274 1512068 R Original (2000) note: Cj1582c, probable peptide ABC-transport system permease, len: 264 aa; similar to e.g. PPC_BACSU oligopeptide transport permease (303 aa), fasta scores; opt: 397 z-score: 467.3 E(): 1e-18, 29.1% identity in 261 aa overlap. 26.3% identity to HP0300. Contains Pfam match to entry PF00528 BPD_transp, Binding-protein-dependent transport systems inner membrane component; Updated (2006) 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/binding proteins - Other; PMID:16045618; peptide ABC transporter permease complement(1511274..1512068) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905852 YP_002344952.1 CDS Cj1583c NC_002163.1 1512055 1512999 R Original (2000) note: Cj1583c, probable peptide ABC-transport system permease, len: 314 aa; similar to e.g. OPPB_LACLC oligopeptide transport system permease (319 aa), fasta scores; opt: 476 z-score: 540.7 E(): 8.5e-23, 28.4% identity in 317 aa overlap. 24.1% identity to HP0299; Updated (2006) 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/binding proteins - Other; peptide ABC transporter permease complement(1512055..1512999) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905853 YP_002344953.1 CDS Cj1584c NC_002163.1 1512999 1514534 R Original (2000) note: Cj1584c, probable peptide ABC-transport system periplasmic peptide-binding protein,len: 511 aa; similar to e.g. APPA_BACSU oligopeptide-binding protein APPA precursor (543 aa),fasta scores; opt: 700 z-score: 791.8 E(): 0, 30.5% identity in 509 aa overlap. 26.7% identity to HP0298. Contains probable N-terminal signal sequence and Pfam match to entry PF00496 SBP_bac_5, Bacterial extracellular solute-binding proteins, family 5; Updated (2006) note: Prosite domain PS00092 N6_MTASE, 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/binding proteins - Other; peptide ABC transporter periplasmic peptide-binding protein complement(1512999..1514534) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905854 YP_002344954.1 CDS Cj1585c NC_002163.1 1514644 1517415 R Original (2000) note: Cj1585c, probable oxidoreductase, len: 923 aa; similar to e.g. YDIJ_ECOLI (1018 aa), fasta scores; opt: 299 z-score: 326.0 E(): 7.7e-11, 24.0% identity in 668 aa overlap, and GLCD_ECOLI glycolate oxidase subunit GLCD (499 aa), fasta scores; opt: 258 z-score: 285.3 E(): 1.4e-08, 23.4% identity in 483 aa overlap. 49.2% identity to HP1222 (misannotated as D-lactate dehydrogenase). Contains PS00551 Prokaryotic molybdopterin oxidoreductases signature 1, ands 2x PS00198 4Fe-4S ferredoxins, iron-sulfur binding region signature; Updated (2006) note: Pfam domains PF02913 FAD linked oxidases, C-terminal domain and PF01565 FAD binding domain were identified within CDS. Not specifically characterised with acceptable identity score. Thus, kept within product function. Literature search identified paper giving further support to product function. Functional classification - Misc; PMID:15292134; oxidoreductase complement(1514644..1517415) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905855 YP_002344955.1 CDS cgb NC_002163.1 1517567 1517989 D Original (2000) note: Cj1586, probable bacterial haemoglobin, len: 140 aa; similar to e.g. BAHG_VITST bacterial hemoglobin (soluble cytochrome O) (146 aa),fasta scores; opt: 417 z-score: 527.0 E(): 4.9e-22, 49.6% identity in 141 aa overlap. No Hp match. Contains Pfam match to entry PF00042 globin; Updated (2006) note: Characterised within Campylobacter jejuni. Cgb protein plays a role in detoxification of NO and related compounds. NssR (Nitrosative stress sensing Regulator - Cj0466) controls the expression of a nitrosative stress-responsive regulon in Campylobacter jejuni which includes ctb (Cj0465c) and cgb (Cj1586). not added to product function. Functional classification - Energy metabolism - Electron transport; PMID:16045618, PMID:15292134, PMID:16339953,PMID:16681372; single domain haemoglobin 1517567..1517989 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905856 YP_002344956.1 CDS Cj1587c NC_002163.1 1518009 1519640 R efflux pump for the antibacterial peptide microcin J25; multidrug transporter membrane component/ATP-binding component complement(1518009..1519640) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905857 YP_002344957.1 CDS Cj1588c NC_002163.1 1519690 1520985 R Original (2000) note: Cj1588c, probable transmembrane transport protein, len: 431 aa; similar to e.g. YHJE_ECOLI hypothetical metabolite transport protein (440 aa), fasta scores; opt: 682 z-score: 771.4 E(): 0,28.9% identity in 422 aa overlap, and PROP_ECOLI proline/betaine transporter (proline porter II) (500 aa),fasta scores; opt: 655 z-score: 740.4 E(): 0, 30.1% identity in 415 aa overlap. No Hp ortholog. Contains PS00217 Sugar transport proteins signature 2, and Pfam match to entry PF00083 sugar_tr, Sugar (and other) transporters; Updated (2006) note: Pfam domain PF07690 Major Facilitator Superfamily identified within CDS. Also,twelve 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/binding proteins -Other; MFS transport protein complement(1519690..1520985) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905858 YP_002344958.1 CDS Cj1589 NC_002163.1 1521072 1521869 D Original (2000) note: Cj1589, unknown, len: 265 aa; some similarity to TR:O34910 (EMBL:AF027868) Bacillus subtilis YOBT (233 aa), fasta scores; opt: 178 z-score: 211.5 E(): 0.00019, 27.6% identity in 203 aa overlap. No Hp match. Contains Pfam match to entry PF00753 lactamase_B, Metallo-beta-lactamase superfamily. Functional classification - Conserved hypothetical proteins; hypothetical protein 1521072..1521869 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905859 YP_002344959.1 CDS infA NC_002163.1 1521957 1522175 D stimulates the activities of the other two initiation factors, IF-2 and IF-3; translation initiation factor IF-1 1521957..1522175 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905860 YP_002344960.1 CDS rpmJ NC_002163.1 1522347 1522460 D smallest protein in the large subunit; similar to what is found with protein L31 and L33 several bacterial genomes contain paralogs which may be regulated by zinc; the protein from Thermus thermophilus has a zinc-binding motif and contains a bound zinc ion; the proteins in this group have the motif; 50S ribosomal protein L36 1522347..1522460 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905861 YP_002344961.1 CDS rpsM NC_002163.1 1522463 1522828 D located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA; makes contact with the large subunit via RNA-protein interactions and via protein-protein interactions with L5; contacts P-site tRNA; 30S ribosomal protein S13 1522463..1522828 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905825 YP_002344962.1 CDS rpsK NC_002163.1 1522838 1523230 D located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA; forms part of the Shine-Dalgarno cleft in the 70S ribosome; interacts with S7 and S18 and IF-3; 30S ribosomal protein S11 1522838..1523230 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905862 YP_002344963.1 CDS rpsD NC_002163.1 1523258 1523884 D primary rRNA binding protein; nucleates 30S assembly; involved in translational accuracy with proteins S5 and S12; interacts with protein S5; involved in autogeneously regulating ribosomal proteins by binding to pseudoknot structures in the polycistronic mRNA; interacts with transcription complex and functions similar to protein NusA in antitermination; 30S ribosomal protein S4 1523258..1523884 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905863 YP_002344964.1 CDS rpoA NC_002163.1 1523897 1524910 D 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; DNA-directed RNA polymerase subunit alpha 1523897..1524910 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905865 YP_002344965.1 CDS rplQ NC_002163.1 1524914 1525267 D is a component of the macrolide binding site in the peptidyl transferase center; 50S ribosomal protein L17 1524914..1525267 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905866 YP_002344966.1 CDS hisG NC_002163.1 1525440 1526339 D long form of enzyme; catalyzes the formation of N'-5'-phosphoribosyl-ATP from phosphoribosyl pyrophosphate; crucial role in histidine biosynthesis; forms active dimers and inactive hexamers which is dependent on concentration of substrates and inhibitors; ATP phosphoribosyltransferase 1525440..1526339 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905867 YP_002344967.1 CDS hisD NC_002163.1 1526347 1527633 D catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer; histidinol dehydrogenase 1526347..1527633 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905868 YP_002344968.1 CDS hisB NC_002163.1 1527630 1528688 D catalyzes the formation of 3-(imidazol-4-yl)-2-oxopropyl phosphate from D-ethythro-1-(imidazol-4-yl)glycerol 3-phosphate and histidinol from histidinol phosphate; imidazole glycerol-phosphate dehydratase/histidinol phosphatase 1527630..1528688 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905869 YP_002344969.1 CDS hisH NC_002163.1 1528685 1529272 D with HisF IGPS catalyzes the conversion of phosphoribulosyl-formimino-5-aminoimidazole-4-carboxamide ribonucleotide phosphate and glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamide ribonucleotide, and glutamate in histidine biosynthesis; 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; imidazole glycerol phosphate synthase subunit HisH 1528685..1529272 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904385 YP_002344970.1 CDS hisA NC_002163.1 1529269 1530000 D catalyzes the formation of 5-(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino-l- (5-phosphoribosyl)imidazole-4-carboxamide from 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide; 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase 1529269..1530000 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904505 YP_002344971.1 CDS Cj1602 NC_002163.1 1529985 1530941 D Original (2000) note: Cj1602, unknown, len: 318 aa; 35.8% identity to HP0852; Updated (2006) note: Pfam domain PF04373 Protein of unknown function (DUF511) identified within CDS. Conserved added to product function. Functional classification -Conserved hypothetical proteins; PMID:11956101, PMID:15901688; hypothetical protein 1529985..1530941 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905870 YP_002344972.1 CDS hisF NC_002163.1 1530942 1531709 D catalyzes the conversion of 5-[(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino]- 1-(5-phosphoribosyl)imidazole-4-carboxamideand glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamideribonucleotide and glutamate; the HisF subunit acts as a cyclase; imidazole glycerol phosphate synthase subunit HisF 1530942..1531709 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905871 YP_002344973.1 CDS hisI NC_002163.1 1531711 1532334 D catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribosyl)-ATP and the subsequent formation of 1-(5-phosphoribosyl)-5-((5- phosphoribosylamino)methylideneamino)imidazole-4- carboxamide from 1-(5-phosphoribosyl)-AMP in histidine biosynthesis; bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase 1531711..1532334 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905159 YP_002344974.1 CDS dapD NC_002163.1 1532359 1533519 R Updated (2006) note: Identity score with Escherichia coli was marginal. kept within product function as sequence alignment was partial; Original (2000) note: Cj1605c, dapD, possible 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase, len: 386 aa; simlar in N-terminus to e.g. TR:O69283 (EMBL:AJ004934) Corynebacterium glutamicum tetrahydrodipicolinate succinylase (EC 2.3.1.117) (230 aa), fasta scores; opt: 587 z-score: 643.6 E(): 1.6e-28, 47.3% identity in 245 aa overlap, and weakly similar to DAPD_ECOLI 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (EC 2.3.1.117) (274 aa), fasta scores; opt: 190 z-score: 214.3 E(): 0.00013, 27.3% identity in 143 aa overlap. 48.5% identity to HP0626. Functional classification - Amino acid biosynthesis -Aspartate family; 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase complement(1532359..1533519) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905872 YP_002344975.1 CDS mrp NC_002163.1 1533545 1534651 R Original (2000) note: Cj1606c, mrp, probable ATP/GTP-binding protein (mrp protein homolog), len: 368 aa; similar to many members of the MRP family e.g. MRP_ECOLI MRP protein (379 aa), fasta scores; opt: 839 z-score: 921.1 E(): 0, 37.1% identity in 340 aa overlap. 50.1% identity to HP0207. Also similar to Cj0063c (31.4% identity in 159 aa overlap). Contains PS00017 ATP/GTP-binding site motif A (P-loop); Updated (2006) note: Pfam domain PF01883 Domain of unknown function DUF59 identified within CDS. Functional classification - Conserved hypothetical proteins; ATP/GTP-binding protein complement(1533545..1534651) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905873 YP_002344976.1 CDS ispDF NC_002163.1 1534774 1535889 D 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 2,4-cyclodiphosphate and CMP from 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate; involved in isoprenoid and isopentenyl-PP biosynthesis; binds divalent cations; bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase 1534774..1535889 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905874 YP_002344977.1 CDS Cj1608 NC_002163.1 1535886 1536773 D Original (2000) note: Cj1608, possible two-component regulator, len: 295 aa, some similarity to regulatory components of tw-component systems e.g. TR:O87527 (EMBL:AF082668) Streptococcus pyogenes capsule synthesis regulator CSRR (228 aa), fasta scores; opt: 170 z-score: 203.9 E(): 0.00049, 35.0% identity in 123 aa overlap, and BASR_ECOLI transcriptional regulatory protein (222 aa), blastp scores; E = 1.6e-06 29% identity in 113 aa overlap. 33.8% identity to HP1021. Contains helix-turn-helix motif at aa 271-292 (Score 997, +2.58 SD). Also some similarity to Cj1024c (22.0% identity in 341 aa overlap); Updated (2006) note: PMID:15901688; Updated (2006) 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; PMID:15901688; two-component regulator 1535886..1536773 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905875 YP_002344978.1 CDS Cj1609 NC_002163.1 1536751 1537911 D Original (2000) note: Cj1609, possible sulfate adenylyltransferase, len: 386 aa; similar to e.g. TR:O34764 (EMBL:) BAcillus subtilis sulfate adenylyltransferase (382 aa), fasta scores; opt: 360 z-score: 414.1 E(): 9.6e-16, 23.4% identity in 351 aa overlap, and TR:O66036 (EMBL:U84759) Chromatium vinosum sulfate adenylyltransferase (EC 2.7.7.4) (397 aa), fasta scores; opt: 273 z-score: 315.2 E(): 3.1e-10, 21.8% identity in 357 aa overlap. No Hp match; Updated (2006) note: No specific characterisation with acceptable identity score carried out yet. kept within product function. Functional classification -Central intermediary metabolism - Sulphur metabolism; sulfate adenylyltransferase 1536751..1537911 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905876 YP_002344979.1 CDS pgpA NC_002163.1 1537916 1538416 D Original (2000) note: Cj1610, pgpA, probable phosphatidylglycerophosphatase, len: 166 aa; simlar to e.g. PGPA_ECOLI phosphatidylglycerophosphatase A (EC 3.1.3.27) (172 aa), fasta scores; opt: 238 z-score: 319.5 E(): 1.8e-10, 33.3% identity in 135 aa overlap. 47.1% identity to HP0737; Updated (2006) note: Three probable transmembrane helices predicted by TMHMM2.0. Some characterisation work carried out within Escherichia coli, however, identity score was marginal. Sequence alignment was only partial. kept within product function. Functional classification - Synthesis and modification of macromolecules - Phospholipids; PMID:2846510, PMID:1309518; phosphatidylglycerophosphatase 1537916..1538416 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905877 YP_002344980.1 CDS rpsT NC_002163.1 1538495 1538758 D binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase; 30S ribosomal protein S20 1538495..1538758 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905878 YP_002344981.1 CDS prfA NC_002163.1 1538777 1539844 D 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; this protein is similar to release factor 2; peptide chain release factor 1 1538777..1539844 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905879 YP_002344982.1 CDS Cj1613c NC_002163.1 1539858 1540613 R Original (2000) note: Cj1613c, unknown, len: 251 aa; similar to hypothetical proteins e.g. Y854_HAEIN hypothetical protein HI0854 (253 aa), fasta scores; opt: 827 z-score: 991.6 E(): 0, 48.4% identity in 248 aa overlap. 56.1% identity to HP0318; Updated (2006) note: Pfam domain PF01243 Pyridoxamine 5'-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 (PMID:15632442) giving further clues to product function. Functional classification - Biosynthesis of cofactors, prosthetic groups and carriers - Pyridoxine; PMID:15632442, PMID:12686112; pyridoxamine 5'-phosphate oxidase complement(1539858..1540613) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905880 YP_002344983.1 CDS chuA NC_002163.1 1540807 1542936 D Original (2000) note: Cj1614, chuA, haemin uptake system outer membrane receptor, len: 709 aa; mutants are unable to grow on haemin - see van Vliet et al, J. Bact 180, 5921-5298 (1998). Similar to TR:O85161 (EMBL:AF047484) Vibrio vulnificus heme receptor (712 aa),fasta scores; opt: 270 z-score: 302.6 E(): 1.6e-09, 22.9% identity in 750 aa overlap, and TR:Q56644 (EMBL:L27149) Vibrio cholerae heme receptor (693 aa), fast scores; opt: 242 z-score: 271.3 E(): 8.6e-08, 23.0% identity in 744 aa overlap. 21.6% identity to HP0807. Also similar to Cj0755 (23.6% identity in 770 aa overlap), and Cj0444 (32.1% identity in 190 aa overlap). Contains Pfam match to entry PF00593 TonB_boxC, TonB dependant receptor C-terminal region; Updated (2006) note: Characterisation work within Campylobacter jejuni. not added to product function. Functional classification - Transport/binding proteins - Cations; PMID:9157252, PMID:9765558; haemin uptake system outer membrane receptor 1540807..1542936 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905881 YP_002344984.1 CDS chuB NC_002163.1 1542911 1543897 D Original (2000) note: Cj1615, chuB, probable haemin uptake system permease, len: 328 aa; similar to e.g. FHUB_BACSU ferrichrome transport permease FHUB (384 aa), fasta scores; opt: 505 z-score: 606.7 E(): 1.8e-26, 29.5% identity in 336 aa overlap. 31.2% identity to HP0889. Contains Pfam match to entry PF01032 FecCD_family, FecCD transport family. Predicted function is based on apparent co-transcription with Cj1614 chuA; Updated (2006) 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/binding proteins - Cations; PMID:9765558; hemin uptake system permease 1542911..1543897 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905882 YP_002344985.1 CDS chuC NC_002163.1 1543897 1544673 D Original (2000) note: Cj1616, chuC, probable haemin uptake system ATP-binding protein, len: 258 aa; similar to e.g. FEPC_ECOLI ferric enterobactin transport ATP-binding protein (271 aa), fasta scores; opt: 477 z-score: 544.5 E(): 5.2e-23, 32.6% identity in 242 aa overlap. 32.9% identity to HP0888. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00211 ABC transporters family signature, and Pfam match to entry PF00005 ABC_tran, ABC transporters. Predicted function is based on apparent co-transcription with Cj1614 chuA; Updated (2006) note: Yet to be specifically characterised with acceptable identity score. kept within product function. Functional classification -Transport/binding proteins - Cations; PMID:9765558; hemin uptake system ATP-binding protein 1543897..1544673 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905883 YP_002344986.1 CDS chuD NC_002163.1 1544670 1545476 D Original (2000) note: Cj1617, chuD, probable haemin uptake system periplasmic haemin-binding protein, len: 268 aa; similar to e.g. HMUT_YERPE hemin-binding periplasmic protein HMUT precursor (278 aa), fasta scores; opt: 189 z-score: 223.7 E(): 3.9e-05, 23.9% 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; Updated (2006) 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/binding proteins - Cations; PMID:9765558; hemin uptake system periplasmic hemin-binding protein 1544670..1545476 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905884 YP_002344987.1 CDS Cj1618c NC_002163.1 1545473 1546390 R Original (2000) note: Cj1618c, unknown, len: 305 aa; weak similarity to hypothetical proteins e.g. TR:Q59026 (EMBL:U67603) Methanococcus jannaschii hypothetical protein MJ1632 (255 aa), fasta scores; opt: 138 z-score: 169.9 E(): 0.038, 25.8% identity in 256 aa overlap (contains predicted iron-sulfur cluster which is conserved in Cj1618c). 34.5% identity to HP0568; Updated (2006) 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; radical SAM domain protein complement(1545473..1546390) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905885 YP_002344988.1 CDS kgtP NC_002163.1 1546496 1547755 D Original (2000) note: Cj1619, kgtP, probable alpha-ketoglutarate permease, len: 419 aa; similar to KGTP_ECOLI alpha-ketoglutarate permease (432 aa), fasta scores; opt: 1348 z-score: 1575.2 E(): 0, 49.0% identity in 414 aa overlap. 49.9% identity to HP1091. Contains PS00217 Sugar transport proteins signature 2, and Pfam match to entry PF00083 sugar_tr, Sugar (and other) transporters; Updated (2006) note: PMID:2053984; Updated (2006) 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/binding proteins - Carbohydrates, organic acids and alcohols; PMID:2053984; alpha-ketoglutarate permease 1546496..1547755 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905886 YP_002344989.1 CDS mutY NC_002163.1 1547741 1548760 R Original (2000) note: Cj1620c, mutY, probable A/G-specific adenine glycosylase, len: 339 aa; similar to e.g. MUTY_ECOLI A/G-specific adenine glycosylase (EC 3.2.2.-) (350 aa), blastp scores; E= 1.0e-41, 39% identity in 271 aa overlap. 47.6% identity to HP0142. Contains Pfam match to entry PF00730 Endonuclease_3, Endonuclease III; Updated (2006) 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, restriction/modification, recombination and repair; PMID:2197596, PMID:9846876, PMID:15456766; A/G-specific adenine glycosylase complement(1547741..1548760) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905887 YP_002344990.1 CDS Cj1621 NC_002163.1 1548833 1549585 D Original (2000) note: Cj1621, possible periplasmic protein, len: 250 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein 1548833..1549585 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905888 YP_002344991.1 CDS ribD NC_002163.1 1550235 1551245 D Original (2000) note: Cj1622, ribD, probable riboflavin-specific deaminase, len: 336 aa; similar to e.g. RIBD_ACTPL riboflavin-specific deaminase (EC 3.5.4.-) (410 aa), fasta scores; opt: 320 z-score: 381.1 E(): 6.6e-14, 35.7% identity in 235 aa overlap, and RIBD_ECOLI riboflavin-specific deaminase (EC 3.5.4.-). (367 aa), opt: 249 z-score: 298.4 E(): 2.7e-09, 28.4% identity in 282 aa overlap. 37.9% identity to ; HP1505. Contains Pfam match to entry PF00383 dCMP_cyt_deam, Cytidine and deoxycytidylate deaminases zinc-binding region; Updated (2006) 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, prosthetic groups and carriers - Riboflavin; PMID:11024263, PMID:9068650; riboflavin-specific deaminase/reductase 1550235..1551245 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905894 YP_002344992.1 CDS Cj1623 NC_002163.1 1551226 1551747 D Original (2000) note: Cj1623, probable membrane protein, len: 173 aa; no Hp match; Updated (2006) note: Two probable transmembrane helices predicted by TMHMM2.0. Functional classification -Membranes, lipoproteins and porins; hypothetical protein 1551226..1551747 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905895 YP_002344993.1 CDS sdaA NC_002163.1 1551755 1553119 R Original (2000) note: Cj1624c, sdaA, probable L-serine dehydratase, len: 454 aa; similar to many e.g. SDHL_ECOLI L-serine dehydratase 1 (EC 4.2.1.13) (454 aa),fasta scores; opt: 1316 z-score: 1553.3 E(): 0, 46.0% identity in 465 aa overlap. 53.4% identity to HP0132; Updated (2006) 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; PMID:8436113, PMID:14688104; L-serine dehydratase complement(1551755..1553119) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905896 YP_002344994.1 CDS sdaC NC_002163.1 1553134 1554384 R Original (2000) note: Cj1625c, sdaC, probable serine transporter, len: 416 aa; similar to e.g. SDAC_ECOLI serine transporter (429 aa), fasta scores; opt: 1392 z-score: 1574.7 E(): 0, 50.1% identity in 417 aa overlap, and TDCC_ECOLI threonine/serine transporter (443 aa), fasta scores; opt: 848 z-score: 961.6 E(): 0, 43.8% identity in 432 aa overlap. 42.0% identity to HP0133; Updated (2006) note: Prosite domains PS50286 AROMATIC_AA_PERM_2, Amino acid/polyamine transporter II and PS50285 AMINO_ACID_PERMEASE_2, Amino acid/polyamine 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/binding proteins -Amino acids and amines; PMID:8026499, PMID:15743941, PMID:14688104; amino acid transporter complement(1553134..1554384) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905897 YP_002344995.1 CDS Cj1626c NC_002163.1 1554644 1555060 R Original (2000) note: Cj1626c, probable periplasmic protein, len: 138 aa; no Hp match. Also similar to Cj1004 (38.6% identity in 140 aa overlap), and in N-terminus to Cj1722c (53.1% identity in 32 aa overlap); Updated (2006) note: Literature search identified paper giving further clues to product function. Functional classification - Miscellaneous periplasmic proteins; PMID:15554967; periplasmic protein complement(1554644..1555060) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905898 YP_002344996.1 CDS Cj1627c NC_002163.1 1555124 1555867 R Original (2000) note: Cj1627c, unknown, len: 247 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown; hypothetical protein complement(1555124..1555867) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905899 YP_002344997.1 CDS exbB2 NC_002163.1 1556025 1556450 D Original (2000) note: Cj1628, exbB2, probable exbB/tolQ family transport protein, len: 141 aa; similar to many e.g. EXBB_HAEDU biopolymer transport EXBB protein (150 aa), fasta scores; opt: 426 z-score: 531.7 E(): 2.7e-22, 51.2% identity in 129 aa overlap. 54.4% identity to HP1339. Also similar to Cj0179 exbB (31.3% identity in 150 aa overlap), and Cj0109 exbB2 (44.4% identity in 81 aa overlap); Updated (2006) note: Pfam domain PF01618 MotA/TolQ/ExbB 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, so kept within product function. Functional classification - Transport/binding proteins - Other; PMID:9781885; exbB/tolQ family transport protein 1556025..1556450 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905901 YP_002344998.1 CDS exbD2 NC_002163.1 1556443 1556832 D Original (2000) note: Cj1629, exbD2, probable exbD/tolR family transport protein, len: 129 aa; similar to many e.g. EXBD_HAEDU biopolymer transport EXBD protein (129 aa), fasta scores; opt: 337 z-score: 414.6 E(): 9e-16, 44.8% identity in 125 aa overlap. 49.6% identity to HP1340. Also similar to Cj0180 exbD (31.1% identity in 122 aa overlap) and Cj0110 exbD2 (26.4% identity in 121 aa overlap); Updated (2006) note: Pfam domain PF02472 Biopolymer transport protein ExbD/TolR 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, so kept within product function. Functional classification - Transport/binding proteins -Other; PMID:9781885; exbD/tolR family transport protein 1556443..1556832 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905902 YP_002344999.1 CDS tonB2 NC_002163.1 1556829 1557512 D Original (2000) note: Cj1630, tonB2, probable tonB transport protein, len: 227 aa; similar to many e.g. TONB_CAMCO TONB protein (232 aa), fasta scores; opt: 412 z-score: 428.1 E(): 1.6e-16, 41.9% identity in 236 aa overlap. 25.9% identity to HP0582. Also similar to Cj0753c tonB (41.7% identity in 230 aa overlap); Updated (2006) note: Pfam domain PF03544 Gram-negative bacterial tonB protein identified within CDS. Further support given to product function. Also, 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, however, identity score was unnacceptable. kept within product function. Functional classification - Transport/binding proteins - Other; PMID:9190817, PMID:10689178, PMID:15557661; TonB transport protein 1556829..1557512 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905903 YP_002345000.1 CDS Cj1631c NC_002163.1 1557525 1558394 R Original (2000) note: Cj1631c, unknown, len: 289 aa; no Hp match. Contains PS00018 EF-hand calcium-binding domain. Functional classification - Unknown; hypothetical protein complement(1557525..1558394) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905904 YP_002345001.1 CDS Cj1632c NC_002163.1 1558398 1558559 R Original (2000) note: Cj1632c, possible periplasmic protein, len: 53 aa; no Hp match. Contains possible N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein complement(1558398..1558559) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905905 YP_002345002.1 CDS Cj1633 NC_002163.1 1558654 1559637 D Original (2000) note: Cj1633, unknown, len: 327 aa; similar to hypothetical proteins e.g. TR:O67046 (EMBL:AE000713) Aquifex aeolicus AQ_898 (251 aa), fasta scores; opt: 544 z-score: 648.2 E(): 8.8e-29, 50.2% identity in 221 aa overlap. 44.7% identity to HP0013. Contains HP0013; Updated (2006) 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; ATP-binding protein 1558654..1559637 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905906 YP_002345003.1 CDS aroC NC_002163.1 1559723 1560811 R catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis; chorismate synthase complement(1559723..1560811) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905907 YP_002345004.1 CDS rnc NC_002163.1 1560811 1561485 R cytoplasmic enzyme involved in processing rRNA and some mRNAs; substrates typically have dsRNA regions; forms a homodimer; have N-terminal nuclease and C-terminal RNA-binding domains; requires magnesium as preferred ion for activity; ribonuclease III complement(1560811..1561485) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905908 YP_002345005.1 CDS rnhA NC_002163.1 1561472 1561912 R An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids; ribonuclease H complement(1561472..1561912) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905909 YP_002345006.1 CDS Cj1637c NC_002163.1 1561899 1562885 R Original (2000) note: Cj1637c, probable periplasmic protein, len: 328 aa; 26.1% identity to HP0660. Contains possible N-terminal signal sequence; Updated (2006) note: Pfam domain PF07719 Tetratricopeptide repeat identified within CDS. Functional classification - Miscellaneous periplasmic proteins; periplasmic protein complement(1561899..1562885) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905910 YP_002345007.1 CDS dnaG NC_002163.1 1562955 1564772 D synthesizes RNA primers at the replication forks; DNA primase 1562955..1564772 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905911 YP_002345008.1 CDS Cj1639 NC_002163.1 1564854 1565126 D Original (2000) note: Cj1639, unknown, len: 90 aa; similar to members of the NIFU family of hypothetical poteins e.g. NIU1_RHOCA NIFU protein 1 (135 aa), fasta scores; opt: 158 z-score: 219.3 E(): 6.8e-05 36.5% identity in 63 aa overlap. Identical to TR:O69292 (EMBL:Y16882) C. jejuni NIFU-like protein. 52.2% identity to HP1492. Contains Pfam match to entry PF01106 NifU-like,NifU-like domain. Also similar to N-terminus of Cj0239c (38.2% identity in 76 aa overlap). Functional classification - Conserved hypothetical proteins; NifU protein 1564854..1565126 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905912 YP_002345009.1 CDS Cj1640 NC_002163.1 1565113 1565664 D Original (2000) note: Cj1640, unknown, len: 183 aa; 27.7% identity to HP1493. Functional classification -Conserved hypothetical proteins; hypothetical protein 1565113..1565664 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905913 YP_002345010.1 CDS murE NC_002163.1 1565648 1566931 D involved in cell wall formation; peptidoglycan synthesis; cytoplasmic enzyme; catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-aceylmuramoyl-l-alanyl-d-glutamate; UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase 1565648..1566931 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905914 YP_002345011.1 CDS Cj1642 NC_002163.1 1566935 1567246 D Original (2000) note: Cj1642, unknown, len: 309 aa; similar to hypothetical proteins e.g. TR:O34247 (EMBL:AJ003049) Wolinella succinogenes ORF102 (102 aa),fasta scores; opt: 351 z-score: 446.1 E(): 1.6e-17, 62.5% identity in 96 aa overlap, and YBAB_ECOLI (109 aa), fast scores; opt: 182 z-score: 240.6 E(): 4.4e-06, 36.7% identity in 98 aa overlap. 45.4% identity to HP0035; Updated (2006) note: Pfam domain PF02575 Uncharacterised BCR, YbaB family COG0718 identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins; hypothetical protein 1566935..1567246 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905915 YP_002345012.1 CDS Cj1643 NC_002163.1 1567243 1568337 D Original (2000) note: Cj1643, probable periplasmic protein, len: 364 aa; similar to hypothetical proteins e.g. TR:O34248 (EMBL:AJ003049) Wolinella succinogenes ORF341 protein (341 aa), fasta scores; opt: 238 z-score: 283.8 E(): 1.7e-08, 23.6% identity in 314 aa overlap. 25.5% identity to HP0036. Contains probable N-terminal signal sequence, and Pfam match to entry PF00595 PDZ, PDZ domain (Also known as DHR or GLGF); Updated (2006) note: Paper identified linking protein to glycoprotein. Functional classification -Miscellaneous periplasmic proteins; PMID:12186869; periplasmic protein 1567243..1568337 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905916 YP_002345013.1 CDS ispA NC_002163.1 1568334 1569179 D Original (2000) note: Cj1644, ispA, probable geranyltranstransferase, len: 281 aa; similar to many e.g. ISPA_ECOLI geranyltranstransferase (EC 2.5.1.10) (FARN (299 aa), fast scores; opt: 520 z-score: 633.4 E(): 5.8e-28, 37.5% identity in 275 aa overlap. 48.0% identity to HP0929. Alos similar to Cj0541 (27.6% identity in 268 aa overlap). Contains PS00723 and PS00444 Polyprenyl synthetases signatures 1 and 2, and Pfam match to entry PF00348 polyprenyl_synt, Polyprenyl synthetases; Updated (2006) note: Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification -Biosynthesis of cofactors, prosthetic groups and carriers - Menaquinone and ubiquinine; PMID:2089044; geranyltranstransferase 1568334..1569179 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905917 YP_002345014.1 CDS tkt NC_002163.1 1569190 1571088 D catalyzes the formation of ribose 5-phosphate and xylulose 5-phosphate from sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate; can transfer ketol groups between several groups; in Escherichia coli there are two tkt genes, tktA expressed during exponential growth and the tktB during stationary phase; transketolase 1569190..1571088 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905918 YP_002345015.1 CDS iamB NC_002163.1 1571090 1572199 D Original (2000) note: Cj1646, iamB, possible ABC transport system permease, len: 369 aa; 91.6% identity to TR:O68254 (EMBL:AF023133) C. jejuni iamB gene fragment (133 aa). Similar to hypothetical proteins e.g. YRBE_ECOLI (260 aa), fast scores; opt: 363 z-score: 423.9 E(): 2.7e-16, 28.1% identity in 256 aa overlap, and to TR:AAD17958 (EMBL:AF106002) Pseudomonas putida toluene tolerance protein TTG2B (265 aa), fast scores; opt: 381 z-score: 444.3 E(): 2e-17, 30.0% identity in 203 aa overlap. 41.1% identity to HP1466; Updated (2006) 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/binding proteins -Other; PMID:11283056, PMID:12694614; ABC transporter permease 1571090..1572199 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905919 YP_002345016.1 CDS iamA NC_002163.1 1572200 1572922 D Original (2000) note: Cj1647, iamA, probable ABC transport system ATP-binding protein, len: 240 aa; 89.5% identity to TR:O68255(EMBL:AF023133) C. jejuni iamA ABC-transporter. Similar to hypothetical proteins e.g. YRBF_ECOLI HYPOTHETICAL ABC transporter ATP-binding protein (269 aa), fasta scores; opt: 453 z-score: 533.0 E(): 2.3e-22, 31.8% identity in 239 aa overlap, and to TR:AAD17957 (EMBL:AF106002) Pseudomonas putida toluene tolerance protein TTG2A (269 aa), fasta scores; opt: 491 z-score: 576.9 E(): 8.2e-25, 34.5% identity in 238 aa overlap. 40.5% identity to HP1465. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00211 ABC transporters family signature, and fam match to entry PF00005 ABC_tran, ABC transporters; Updated (2006) note: Specific characterisation with acceptable identity score has not been carried out yet. Thus, kept within product function. Some work carried out within Campylobacter spp. Functional classification - Transport/binding proteins - Other; PMID:11283056, PMID:16300911; ABC transporter ATP-binding protein 1572200..1572922 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905920 YP_002345017.1 CDS Cj1648 NC_002163.1 1572925 1573815 D Original (2000) note: Cj1648, possible ABC transport system periplasmic substrate-binding protein,len: 296 aa; similar to hypothetical proteins e.g. TR:O67491 (EMBL:AE000744) Aquifex aeolicus AQ_1533 (300 aa), fasta scores; opt: 362 z-score: 406.8 E(): 2.4e-15,29.7% identity in 303 aa overlap, and, weakly, to TR:AAD17959 (EMBL:AF106002) Pseudomonas putida toluene tolerance protein TTG2C (161 aa), fasta scores; opt: 161 z-score: 190.8 E(): 0.0026, 28.7% identity in 122 aa overlap. 24.0% identity to HP1464. Contains probable N-terminal signal sequence; Updated (2006) 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/binding proteins - Other; ABC transporter substrate-binding protein 1572925..1573815 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905921 YP_002345018.1 CDS Cj1649 NC_002163.1 1573815 1574414 D Original (2000) note: Cj1649, probable lipoprotein,len: 199 aa; some similarity to YFXK_BRAJA hypothetical protein in (fragment) (180 aa), fast scores; opt: 184 z-score: 235.4 E(): 8.6e-06, 24.5% 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, lipoproteins and porins; lipoprotein 1573815..1574414 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905922 YP_002345019.1 CDS Cj1650 NC_002163.1 1574470 1574970 D Original (2000) note: Cj1650, unknown, len: 166 aa; 30.7% identity to HP1076. Functional classification -Conserved hypothetical proteins; hypothetical protein 1574470..1574970 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905923 YP_002345020.1 CDS map NC_002163.1 1575339 1576097 R catalyzes the removal of N-terminal amino acids from peptides and arylamides; generally Co(II) however activity has been shown for some methionine aminopeptidases with Zn, Fe, or Mn; methionine aminopeptidase complement(1575339..1576097) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905924 YP_002345021.1 CDS murI NC_002163.1 1576099 1576851 R converts L-glutamate to D-glutamate, a component of peptidoglycan; glutamate racemase complement(1576099..1576851) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905925 YP_002345022.1 CDS Cj1653c NC_002163.1 1576853 1577311 R Original (2000) note: Cj1653c, probable lipoprotein, len: 152 aa; similar to hypothetical proteins e.g. NLPC_ECOLI probable lipoprotein NLPC precursor (154 aa), fasta scores; opt: 381 z-score: 485.2 E(): 1e-19,40.3% identity in 154 aa overlap, and SPR_ECOLI lipoprotein SPR precursor (188 aa), fasta scores; opt: 355 z-score: 451.8 E(): 7.6e-18, 44.7% identity in 123 aa overlap. No Hp match. Contains probable N-terminal signal sequence with appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site, and Pfam match to entry PF00877 NLPC_P60, NLP/P60 family. Functional classification - Membranes, lipoproteins and porins; lipoprotein complement(1576853..1577311) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905926 YP_002345023.1 CDS nhaA NC_002163.1 1577320 1578489 R exports sodium by using the electrochemical proton gradient to allow protons into the cell; functions in adaptation to high salinity and alkaline pH; activity increases at higher pH; downregulated at acidic pH; pH-dependent sodium/proton antiporter complement(1577320..1578489) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905927 YP_002345024.1 CDS nhaA1 NC_002163.1 1578486 1579634 R Original (2000) note: Cj1655c, nhaA1, probable Na(+)/H(+) antiporter, len: 382 aa; similar to e.g. NHAA_ECOLI Na(+)/H(+) antiporter 1 (388 aa), fasta scores; opt: 1165 z-score: 1343.6 E(): 0, 47.3% identity in 383 aa overlap. 41.0% identity to HP1552. Also similar to Cj1654c nhaA2 (56.3% identity in 378 aa overlap); Updated (2006) note: Pfam domain PF06965 Na+/H+ antiporter identified within CDS. Further support given to product function. Also, ten probable transmembrane helices predicted by TMHMM2.0. Characterised within Escherichia coli with acceptable identity score. not added to product function. Functional classification - Transport/binding proteins - Cations; PMID:1645730, PMID:1657980, PMID:9507001; Na(+)/H(+) antiporter complement(1578486..1579634) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905928 YP_002345025.1 CDS Cj1656c NC_002163.1 1579777 1579959 R Original (2000) note: Cj1656c, unknown, len: 180 aa; no Hp match. Functional classification - Unknown; hypothetical protein complement(1579777..1579959) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905929 YP_002345026.1 CDS Cj1658 NC_002163.1 1580836 1582926 D Original (2000) note: Cj1658, probable integral membrane protein, len: 696 aa; similar to TR:CAA21360 (EMBL:AL031866) Yersinia pestis ORF37 upstream of p19 homolog in 102 kbases unstable region (639 aa), fasta scores; opt: 1055 z-score: 1112.1 E(): 0, 31.6% identity in 706 aa overlap. Contains possible N-terminal signal sequence, followed by non-membrane domain with three coiled-coil regions to aa 440. C-terminal domain contains six possible membrane spanning sequences, and is similar to hypothetical membrane proteins e.g. YWBL_BACSU (481 aa), fasta scores; opt: 439 z-score: 466.4 E(): 1.2e-18,26.5% identity in 449 aa overlap. No Hp match; Updated (2006) note: Pfam domain PF03239 Iron permease FTR1 family identified within CDS. Also, 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, so kept within product function. Literature search identified paper giving further clues to product function. Functional classification -Transport/binding proteins - Cations; PMID:15632442; iron permease 1580836..1582926 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905930 YP_002345027.1 CDS p19 NC_002163.1 1582923 1583462 D Original (2000) note: Cj1659, p19, periplasmic protein, len: 179 aa; identical to TR:O07089 (EMBL:Y13641) C. jejuni 19 kDa periplamic protein (fragment) (152 aa),and similar to TR:CAA21359 (EMBL:AL031866) Yersinia pestis ORF36 in 102 kbases unstable region (175 aa), fasta scores; opt: 677 z-score: 805.8 E(): 0, 57.9% identity in 178 aa overlap, and TA34_TREPA 34 kD membrane antigen precursor (pathogen-specific membrane antigen) (204 aa),fasta scores; opt: 353 z-score: 425.6 E(): 2.2e-16, 35.8% identity in 159 aa overlap. No Hp match. Contains probable N-terminal signal sequence; Updated (2006) note: One probable transmembrane helix predicted by TMHMM2.0. Characterised within Campylobacter jejuni, so not added to product function. Paper identified linking protein to glycoprotein. Functional classification - Miscellaneous periplasmic proteins; PMID:12186869, PMID:9766213; periplasmic protein p19 1582923..1583462 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905931 YP_002345028.1 CDS Cj1660 NC_002163.1 1583545 1584948 D Original (2000) note: Cj1660, probable integral membrane protein, len: 467 aa; 97.3% identity to TR:O07090 (EMBL:Y13641) C. jejuni hypothetical protein (fragment) (73 aa), and similar to TR:CAA21358 (EMBL:AL031866) Yersinia pestis ORF35 in 102 kbases unstable region (469 aa), fasta scores; opt: 687 z-score: 761.3 E(): 0, 27.5% identity in 465 aa overlap. No Hp match; Updated (2006) 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, so kept within product function. Literature search identified paper giving further clues to product function. Functional classification - Membranes, lipoproteins and porins; PMID:15632442; integral membrane protein 1583545..1584948 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905932 YP_002345029.1 CDS Cj1661 NC_002163.1 1584935 1586227 D Original (2000) note: Cj1661, possible ABC transport system permease, len: 430 aa; similar to hypothetical membrane proteins e.g. TR:CAA21357 (EMBL:AL031866) Yersinia pestis ORF34 in 102 kbases unstable region (430 aa), fasta scores; opt: 929 z-score: 1043.7 E(): 0, 36.1% identity in 435 aa overlap, and to the membrane domain of hypothetical ACB-transporters e.g. YBJZ_ECOLI hypothetical ABC transporter ATP-binding protein (648 aa), fasta scores; opt: 189 z-score: 214.0 E(): 0.00014, 22.0% identity in 241 aa overlap. No Hp match. Also similar to Cj1662 (28.1% identity in 437 aa overlap); Updated (2006) 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,so kept within product function. Functional classification - Transport/binding proteins - Other; ABC transporter permease 1584935..1586227 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905933 YP_002345030.1 CDS Cj1662 NC_002163.1 1586217 1587335 D Original (2000) note: Cj1662, probable integral membrane protein, len: 372 aa; similar to hypothetical membrane proteins e.g. TR:CAA21356 (EMBL:AL031866) Yersinia pestis ORF33 in 102 kbases unstable region (387 aa), fasta scores; opt: 637 z-score: 710.8 E(): 2.9e-32,32.5% identity in 375 aa overlap. No Hp match. Also similar to Cj1661 (28.1% identity in 437 aa overlap). Possibly a permease for an ABC transport system; ABC-binding protein is downstream; Updated (2006) 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,so kept within product function. Functional classification - Transport/binding proteins - Other; integral membrane protein 1586217..1587335 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905934 YP_002345031.1 CDS Cj1663 NC_002163.1 1587332 1587985 D Original (2000) note: Cj1663, probable ABC transport system ATP-binding protein, len: 217 aa; similar to many e.g. TR:CAA21355(EMBL:AL031866) Yersinia pestis ORF32 in 102 kbases unstable region (237 aa), fasta scores; opt: 859 z-score: 985.9 E(): 0, 60.8% identity in 209 aa overlap, and GLNQ_ECOLI glutamine transport ATP-binding protein (240 aa), fasta scores; opt: 555 z-score: 641.1 E(): 2.2e-28, 43.5% identity in 214 aa overlap. No Hp ortholog. Contains PS00017 ATP/GTP-binding site motif A (P-loop), PS00211 ABC transporters family signature, and Pfam match to entry PF00005 ABC_tran, ABC transporters; Updated (2006) note: kept within product function as similar to more than one transport system. Functional classification - Transport/binding proteins -Other; ABC transporter ATP-binding protein 1587332..1587985 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905935 YP_002345032.1 CDS Cj1664 NC_002163.1 1587982 1588470 D Original (2000) note: Cj1664, possible periplasmic thiredoxin, len: 162 aa; similar to e.g. TR:CAA21354 (EMBL:AL031866) Yersinia pestis ORF31 in 102 kbases unstable region (165 aa), fast scores; opt: 225 z-score: 278.4 E(): 3.5e-08, 33.3% identity in 141 aa overlap, and weakly to RESA_BACSU RESA protein (contains thiredoxin domain) (181 aa), fasta scores; opt: 124 z-score: 159.5 E(): 0.15, 25.0% identity in 112 aa overlap. No Hp match. Contains PS00194 Thioredoxin family active site and probable N-terminal signal sequence; Updated (2006) 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 (PMID:15632442). Functional classification - Energy metabolism - Respiration - Electron transport; PMID:15322369, PMID:15632442; periplasmic thiredoxin 1587982..1588470 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905936 YP_002345033.1 CDS Cj1665 NC_002163.1 1588431 1588934 D Original (2000) note: Cj1665, possible lipoprotein thiredoxin, len: 167 aa; similar to TR:O33920 (EMBL:U75949) Salmonella typhimurium suppressor for copper-sensitivity D (168 aa), fasta scores; opt: 121 z-score: 163.1 E(): 0.093, 27.5% identity in 153 aa overlap, and weakly to many thiredoxins, e.g. THIO_BUCAP thioredoxin (108 aa), fasta scores; opt: 108 z-score: 149.9 E(): 0.5, 28.6% identity in 112 aa overlap. Contains probable N-terminal signal sequence and appropriately positioned PS00013 Prokaryotic membrane lipoprotein lipid attachment site. No Hp match; Updated (2006) 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 (PMID:15632442). Functional classification - Energy metabolism - Respiration - Electron transport; PMID:15632442; lipoprotein thiredoxin 1588431..1588934 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905937 YP_002345034.1 CDS Cj1666c NC_002163.1 1588944 1589381 R Original (2000) note: Cj1666c, probable periplasmic protein, len: 145 aa; similar to TR:AAD11752 (EMBL:AF067954) Salmonella typhimurium ORF105 in silver resistance cluster (105 aa), fasta scores; opt: 244 z-score: 293.2 E(): 5.2e-09, 39.2% identity in 102 aa overlap, and TR:O67205 (EMBL:AE000724) Aquifex aeolicus AQ_1129 (122 aa), fats scores; opt: 231 z-score: 277.7 E(): 3.8e-08, 33.3% identity in 117 aa overlap. No Hp match. Contains probable N-terminal signal sequence; Updated (2006) note: Pfam domain PF04214 Protein of unknown function, DUF identified within CDS. Functional classification - Miscellaneous periplasmic proteins; periplasmic protein complement(1588944..1589381) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905938 YP_002345035.1 CDS Cj1667c NC_002163.1 1589462 1589614 R Original (2000) note: Cj1667c, repA protein homolog, len: 50 aa; highly similar to TR:Q46016 (EMBL:X82080) Campylobacter coli plasmid PCCT2 repA protein (26 aa), fast scores; opt: 93 z-score: 179.3 E(): 0.011, 57.7% identity in 26 aa overlap. No Hp match. This gene sequence is < 19% G+C and has an atypical positional base preference. Functional classification - Plasmid related functions; RepA protein complement(1589462..1589614) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905939 YP_002345036.1 CDS Cj1668c NC_002163.1 1589680 1590096 R Original (2000) note: Cj1668c, probable periplasmic protein, len: 138 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein complement(1589680..1590096) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905940 YP_002345037.1 CDS Cj1669c NC_002163.1 1590752 1591600 R catalyzes the formation of a phosphodiester at the site of a single-strand break in duplex DNA; DNA ligase complement(1590752..1591600) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905944 YP_002345038.1 CDS cgpA NC_002163.1 1591600 1592262 R Original (2000) note: Cj1670c, probable periplasmic protein, len: 220 aa; 27.3% identity to HP0156. Contains probable N-terminal signal sequence; Updated (2006) note: Characterisation paper within Campylobacter jejuni identified new gene name. Papers identified linking protein to glycoprotein (PMID:12186869). Functional classification - Miscellaneous periplasmic proteins; PMID:12186869, PMID:11985725; periplasmic protein complement(1591600..1592262) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905945 YP_002345039.1 CDS Cj1671c NC_002163.1 1592252 1592455 R Original (2000) note: Cj1671c, unknown, len: 67 aa; 38.7% identity to HP0155; Updated (2006) note: One probable transmembrane helix predicted by TMHMM2.0. Functional classification -Conserved hypothetical proteins; hypothetical protein complement(1592252..1592455) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905946 YP_002345040.1 CDS eno NC_002163.1 1592521 1593765 R enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis; phosphopyruvate hydratase complement(1592521..1593765) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905947 YP_002345041.1 CDS recA NC_002163.1 1593765 1594796 R catalyzes the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs; recombinase A complement(1593765..1594796) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905948 YP_002345042.1 CDS Cj1674 NC_002163.1 1594902 1595762 D Original (2000) note: Cj1674, unknown, len: 286 aa; similar to hypothetical proteins e.g. TR:AE000683 (EMBL:AE000683) (279 aa), fasta scores; opt: 489 z-score: 599.3 E(): 4.7e-26, 35.4% identity in 260 aa overlap. 58.7% identity to HP0152; Updated (2006) note: Pfam domain PF02642 Uncharacterized ACR, COG2107 identified within CDS. Conserved added to product function. Functional classification - Conserved hypothetical proteins; hypothetical protein 1594902..1595762 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905949 YP_002345043.1 CDS fliQ NC_002163.1 1595774 1596043 D with proteins FliP and FliR forms the core of the central channel in the flagella export apparatus; flagellar biosynthesis protein FliQ 1595774..1596043 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905950 YP_002345044.1 CDS murB NC_002163.1 1596040 1596816 D catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis; UDP-N-acetylenolpyruvoylglucosamine reductase 1596040..1596816 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905951 YP_002345045.1 CDS Cj1677 NC_002163.1 1597008 1600372 D Original (2000) note: Cj1678, possible lipoprotein,len: 928 aa; no Hp match. Contains a poly-T tract at aa 1 which, if variable, would allow translation from Cj1677 (which contains a signal sequence and lipid attachment site). Otherwise translation could start at aa 46. Highly similar to Cj0629 (90.7% identity in 901 aa overlap). Cj0629 has a non-variable poly-T tract in an quivalent position, which could allow translation from Cj0628 (similar to Cj1677); Original (2000) note: Cj1677, probable lipoprotein,len: 216 aa; 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 (aa 194) which, if variable, 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 (highly similar to Cj1678); Updated (2006) 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, lipoproteins and porins; lipoprotein join(1597008..1597589,1597592..1600372) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905952 YP_002345046.1 CDS Cj1679 NC_002163.1 1600574 1602328 D Original (2000) note: Cj1679, unknown, len: 584 aa; no Hp match; Updated (2006) note: Pfam domain x2 PF07719 Tetratricopeptide repeat identified within CDS. Functional classification - Unknown; hypothetical protein 1600574..1602328 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905954 YP_002345047.1 CDS Cj1680c NC_002163.1 1602332 1603099 R Original (2000) note: Cj1680c, probable periplasmic protein, len: 255 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein complement(1602332..1603099) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905955 YP_002345048.1 CDS cysQ NC_002163.1 1603139 1603903 R Original (2000) note: Cj1681c, cysQ, probable cysQ protein homolog, len: 254 aa; similar to e.g. CYSQ_ECOLI CYSQ protein (246 aa), fasta scores; opt: 421 z-score: 500.9 E(): 1.4e-20, 32.4% identity in 247 aa overlap. No Hp match. Contains Pfam match to entry PF00459 inositol_P,Inositol monophosphatase family, and PS00629 Inositol monophosphatase family signature 1. Functional classification - Central intermediary metabolism - Sulphur metabolism; PMID:1729235, PMID:7493934; CysQ protein complement(1603139..1603903) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905956 YP_002345049.1 CDS gltA NC_002163.1 1603983 1605251 R Original (2000) note: Cj1682c, gltA, probable citrate synthase, len: 422 aa; similar to many e.g. CISY_PSEAE citrate synthase (EC 4.1.3.7) (428 aa), fasta scores; opt: 1520 z-score: 1734.6 E(): 0, 53.8% identity in 405 aa overlap. 52.8% identity to HP0026. Contains PS00480 Citrate synthase signature, and Pfam match to entry PF00285 citrate_synt, Citrate synthase; Updated (2006) 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; PMID:2507528; citrate synthase complement(1603983..1605251) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905957 YP_002345050.1 CDS Cj1684c NC_002163.1 1605366 1606541 R Original (2000) note: Cj1684c, probable transmembrane transport protein, len: 391 aa; simlar to many predicted Na+/H+ antiporters, and to KEFB_ECOLI Glutathione-regulated potassium-efflux system protein (601 aa), fasta scores; opt: 197 z-score: 237.9 E(): 6.2e-06,21.9% identity in 324 aa overlap, and NAPA_ENTHR Na(+)/H(+) antiporter (383 aa), blastp scores; E= 3.1e-10,22% identity in 372 aa overlap. 35.9% identity to HP1183 (called NA+/H+ antiporter (napA) on basis of match to NAPA_ENTHR); Updated (2006) 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/binding proteins - Other; transmembrane transport protein complement(1605366..1606541) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905958 YP_002345051.1 CDS bioB NC_002163.1 1606522 1607358 R catalyzes the formation of biotin from dethiobiotin and sulfur; biotin synthase complement(1606522..1607358) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905959 YP_002345052.1 CDS topA NC_002163.1 1607360 1609462 R catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity; DNA topoisomerase I complement(1607360..1609462) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905960 YP_002345053.1 CDS Cj1687 NC_002163.1 1609657 1610928 D Original (2000) note: Cj1687, possible efflux protein, len: 423 aa; similar to members of the major facilitator family e.g. NORA_STAAU quinolone resistance NORA protein (388 aa), fasta scores; opt: 333 z-score: 386.0 E(): 3.5e-14, 23.1% identity in 350 aa overlap, and BMR1_BACSU multidrug resistance protein 1 (389 aa), fasta scores; opt: 282 z-score: 327.8 E(): 6.1e-11, 24.6% identity in 305 aa overlap. No Hp match. Contains Pfam match to entry PF00083 sugar_tr, Sugar (and other) transporters; Updated (2006) note: Pfam domain PF07690 Major Facilitator Superfamily identified within CDS. Also,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. Literature search identified paper giving further clues to product function. Functional classification - Antibiotic resistance; PMID:16048946; efflux protein 1609657..1610928 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905961 YP_002345054.1 CDS secY NC_002163.1 1610956 1612221 R forms heterotrimeric complex in the membrane; in bacteria the complex consists of SecY which forms the channel pore and SecE and SecG; the SecG subunit is not essential; in bacteria translocation is driven via the SecA ATPase; preprotein translocase subunit SecY complement(1610956..1612221) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905962 YP_002345055.1 CDS rplO NC_002163.1 1612221 1612613 R late assembly protein; 50S ribosomal protein L15 complement(1612221..1612613) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905963 YP_002345056.1 CDS rpsE NC_002163.1 1612618 1613061 R located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body; contacts S4 and S8; with S4 and S12 plays a role in translational accuracy; mutations in this gene result in spectinomycin resistance; 30S ribosomal protein S5 complement(1612618..1613061) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905964 YP_002345057.1 CDS rplR NC_002163.1 1613073 1613429 R binds 5S rRNA along with protein L5 and L25; 50S ribosomal protein L18 complement(1613073..1613429) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905965 YP_002345058.1 CDS rplF NC_002163.1 1613439 1613975 R 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; RNA-binding appears to be in the C-terminal domain; mutations in the L6 gene confer resistance to aminoglycoside antibiotics such as gentamicin and these occur in truncations of the C-terminal domain; it has been localized to a region between the base of the L7/L12 stalk and the central protuberance; 50S ribosomal protein L6 complement(1613439..1613975) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905966 YP_002345059.1 CDS rpsH NC_002163.1 1614054 1614449 R binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit; 30S ribosomal protein S8 complement(1614054..1614449) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905967 YP_002345060.1 CDS rpsN NC_002163.1 1614459 1614644 R located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit; similar to what is observed with proteins L31 and L33, some proteins in this family contain CXXC motifs that are involved in zinc binding; if two copies are present in a genome, then the duplicated copy appears to have lost the zinc-binding motif and is instead regulated by zinc; the proteins in this group appear to contain the zinc-binding motif; 30S ribosomal protein S14 complement(1614459..1614644) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905968 YP_002345061.1 CDS rplE NC_002163.1 1614646 1615191 R part of 50S and 5S/L5/L18/L25 subcomplex; contacts 5S rRNA and P site tRNA; forms a bridge to the 30S subunit in the ribosome by binding to S13; 50S ribosomal protein L5 complement(1614646..1615191) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905969 YP_002345062.1 CDS rplX NC_002163.1 1615195 1615428 R assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel; 50S ribosomal protein L24 complement(1615195..1615428) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905970 YP_002345063.1 CDS rplN NC_002163.1 1615428 1615796 R binds to the 23S rRNA between the centers for peptidyl transferase and GTPase; 50S ribosomal protein L14 complement(1615428..1615796) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905971 YP_002345064.1 CDS rpsQ NC_002163.1 1615796 1616047 R primary binding protein; helps mediate assembly; involved in translation fidelity; 30S ribosomal protein S17 complement(1615796..1616047) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905972 YP_002345065.1 CDS rpmC NC_002163.1 1616057 1616242 R one of the stabilizing components for the large ribosomal subunit; 50S ribosomal protein L29 complement(1616057..1616242) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905973 YP_002345066.1 CDS rplP NC_002163.1 1616229 1616654 R located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e; 50S ribosomal protein L16 complement(1616229..1616654) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905974 YP_002345067.1 CDS rpsC NC_002163.1 1616657 1617358 R forms a complex with S10 and S14; binds the lower part of the 30S subunit head and the mRNA in the complete ribosome to position it for translation; 30S ribosomal protein S3 complement(1616657..1617358) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905975 YP_002345068.1 CDS rplV NC_002163.1 1617358 1617783 R binds specifically to 23S rRNA during the early stages of 50S assembly; makes contact with all 6 domains of the 23S rRNA in the assembled 50S subunit and ribosome; mutations in this gene result in erythromycin resistance; located near peptidyl-transferase center; 50S ribosomal protein L22 complement(1617358..1617783) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905976 YP_002345069.1 CDS rpsS NC_002163.1 1617794 1618075 R protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA; 30S ribosomal protein S19 complement(1617794..1618075) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905977 YP_002345070.1 CDS rplB NC_002163.1 1618077 1618907 R one of the primary rRNA-binding proteins; required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation; 50S ribosomal protein L2 complement(1618077..1618907) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905978 YP_002345071.1 CDS rplW NC_002163.1 1618909 1619190 R binds third domain of 23S rRNA and protein L29; part of exit tunnel; 50S ribosomal protein L23 complement(1618909..1619190) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905979 YP_002345072.1 CDS rplD NC_002163.1 1619193 1619807 R L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA; 50S ribosomal protein L4 complement(1619193..1619807) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905980 YP_002345073.1 CDS rplC NC_002163.1 1619804 1620379 R binds directly near the 3' end of the 23S rRNA, where it nucleates assembly of the 50S subunit; essential for peptidyltransferase activity; mutations in this gene confer resistance to tiamulin; 50S ribosomal protein L3 complement(1619804..1620379) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905981 YP_002345074.1 CDS rpsJ NC_002163.1 1620389 1620700 R NusE; involved in assembly of the 30S subunit; in the ribosome, this protein is involved in the binding of tRNA; in Escherichia coli this protein was also found to be involved in transcription antitermination; NusB/S10 heterodimers bind boxA sequences in the leader RNA of rrn operons which is required for antitermination; binding of NusB/S10 to boxA nucleates assembly of the antitermination complex; 30S ribosomal protein S10 complement(1620389..1620700) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905982 YP_002345075.1 CDS Cj1709c NC_002163.1 1620899 1621660 R Original (2000) note: Cj1709c, probable ribosomal pseudouridine synthase, len: 253 aa; similar to e.g. RLUB_BACSU ribosomal large subunit pseudouridine synthase B (EC 4.2.1.70) (229 aa), fasta scores; opt: 338 z-score: 414.2 E(): 9.5e-16, 33.9% identity in 236 aa overlap. 50.4% identity to HP1459. Contains PS01149 RsuA family of pseudouridine synthase signature; Updated (2006) 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; PMID:9888802; ribosomal pseudouridine synthase complement(1620899..1621660) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905983 YP_002345076.1 CDS Cj1710c NC_002163.1 1621696 1623690 R Original (2000) note: Cj1710c, unknown, len: 664 aa; similar to hypothetical proteins e.g. YKQC_BACSU (555 aa), fasta scores; opt: 1429 z-score: 1605.6 E(): 0, 39.5% identity in 544 aa overlap. N-terminal 100 aa is evry hydrophilic, and is conserved only with the Hp homolog and YOR4_CORGL (645 aa), fasta scores; opt: 1223 z-score: 1373.2 E(): 0, 34.4% identity in 613 aa overlap. 55.3% identity to HP1430. Contains S01292 Uncharacterized protein family UPF0036 signature, and fam match to entry PF00753 lactamase_B, Metallo-beta-lactamase superfamily; Updated (2006) 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, kept within product function. Functional classification -Misc; metallo-beta-lactamase family protein complement(1621696..1623690) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905984 YP_002345077.1 CDS ksgA NC_002163.1 1623659 1624459 R catalyzes the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases A1518 and A1519 in 16S rRNA; mutations in ksgA causes resistance to the translation initiation inhibitor kasugamycin; dimethyladenosine transferase complement(1623659..1624459) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905985 YP_002345078.1 CDS Cj1712 NC_002163.1 1624541 1625077 D Original (2000) note: Cj1712, unknown, len: 178 aa; 40.9% identity to HP1530 (called purine nucleoside phosphorylase (punB). Functional classification -Conserved hypothetical proteins; hypothetical protein 1624541..1625077 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905986 YP_002345079.1 CDS Cj1713 NC_002163.1 1625100 1626170 D 23S rRNA m2A2503 methyltransferase; methylates the C2 position of the A2530 nucleotide in 23S rRNA; may be involved in antibiotic resistance; ribosomal RNA large subunit methyltransferase N 1625100..1626170 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905987 YP_002345080.1 CDS Cj1714 NC_002163.1 1626167 1626265 D Original (2000) note: Cj1714, small hydrophobic protein, len: 32 aa; no Hp match; Updated (2006) note: One probable transmembrane helix predicted by TMHMM2.0. Functional classification -Unknown; hypothetical protein 1626167..1626265 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905988 YP_002345081.1 CDS Cj1715 NC_002163.1 1626807 1627337 D Original (2000) note: Cj1715, possible acetyltransferase, len: 176 aa; similar to several plasmid- or integron-encoded genes e.g. STA_ECOLI streptothricin acetyltransferase (174 aa), fasta scores; opt: 149 z-score: 192.6 E(): 0.0021, 21.7% identity in 161 aa overlap, and TR:P75025 (EMBL:P75025) plasmid PVS1 hypothetical protein (166 aa), fasta scores; opt: 201 z-score: 255.1 E(): 6.9e-07, 26.1% identity in 161 aa overlap. Also simlilar to TR:O31513 (EMBL:Z99107) Bacillus subtilis chromosomal YESJ protein (180 aa), fasta scores; opt: 157 z-score: 202.0 E(): 0.00063, 20.6% identity in 155 aa overlap. No Hp match. Contains Pfam match to entry PF00583 Acetyltransf, Acetyltransferase (GNAT) family; Updated (2006) note: Specific characterisation with acceptable identity score has not been carried out yet. Thus, kept within product function. Functional classification - Antibiotic resistance; acetyltransferase 1626807..1627337 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905992 YP_002345082.1 CDS leuD NC_002163.1 1627317 1627919 R catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D; isopropylmalate isomerase small subunit complement(1627317..1627919) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905993 YP_002345083.1 CDS leuC NC_002163.1 1627921 1629333 R dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate; isopropylmalate isomerase large subunit complement(1627921..1629333) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905994 YP_002345084.1 CDS leuB NC_002163.1 1629320 1630396 R catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis; 3-isopropylmalate dehydrogenase complement(1629320..1630396) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905995 YP_002345085.1 CDS leuA NC_002163.1 1630393 1631928 R catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis; 2-isopropylmalate synthase complement(1630393..1631928) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905996 YP_002345086.1 CDS Cj1720 NC_002163.1 1632248 1632877 D Original (2000) note: Cj1720, unknown, len: 209 aa; no Hp match. Functional classification - Unknown; hypothetical protein 1632248..1632877 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905997 YP_002345087.1 CDS Cj1721c NC_002163.1 1632901 1633545 R Original (2000) note: Cj1721c, possible outer membrane protein, len: 214 aa; very weak similarity to several e.g. TR:P95343 (EMBL:U52069) Neisseria gonorrhoeae outer membrane protein precursor (174 aa), blastp scores; E= 0.0043, 29% identity in 176 aa overlap. Contains probable N-terminal signal sequence. 22.3% identity to HP0706 (outer membrane protein (omp15)). Functional classification - Membranes, lipoproteins and porins; outer membrane protein complement(1632901..1633545) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905998 YP_002345088.1 CDS Cj1722c NC_002163.1 1633791 1633892 R Original (2000) note: Cj1722c, unknown, len: 33 aa; no Hp match. Similar to the N-termini of predicted periplasmic proteins Cj1626c (53.1% identity in 32 aa overlap), and Cj1004 (46.2% identity in 26 aa overlap). Functional classification - Unknown; hypothetical protein complement(1633791..1633892) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905999 YP_002345089.1 CDS Cj1723c NC_002163.1 1633895 1634119 R Original (2000) note: Cj1723c, probable periplasmic protein, len: 74 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein complement(1633895..1634119) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 906000 YP_002345090.1 CDS Cj1724c NC_002163.1 1634296 1634679 R NADPH-dependent; catalyzes the reduction of 7-cyano-7-deazaguanine to 7-aminomethyl-7-deazaguanine in queuosine biosynthesis; 7-cyano-7-deazaguanine reductase complement(1634296..1634679) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905900 YP_002345091.1 CDS Cj1725 NC_002163.1 1634839 1635438 D Original (2000) note: Cj1725, probable periplasmic protein, len: 199 aa; similar to TR:O66724 (EMBL:AE000688) Aquifex aeolicus AQ_407 (203 aa), fasta scores; opt: 411 z-score: 483.0 E(): 1.4e-19, 34.0% identity in 203 aa overlap. No Hp match. Functional classification -Miscellaneous periplasmic proteins; periplasmic protein 1634839..1635438 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905202 YP_002345092.1 CDS metA NC_002163.1 1635443 1636324 R catalyzes the formation of O-succinyl-L-homoserine from succinyl-CoA and L-homoserine in methionine biosynthesis; homoserine O-succinyltransferase complement(1635443..1636324) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 906001 YP_002345093.1 CDS metB NC_002163.1 1636407 1637678 R Original (2000) note: Cj1727c, metY, possible O-acetylhomoserine (thiol)-lyase, len: 423 aa; TR:P94890 (EMBL:Y10744) Leptospira meyeri O-acetylhomoserine sulfhydrylase (metY) (442 aa), fasta scores; opt: 1198 z-score: 1372.4 E(): 0, 43.0% identity in 433 aa overlap,and CYSD_EMENI O-acetylhomoserine (thiol)-lyase (EC 4.2.99.10) (437 aa), fasta scores; opt: 1001 z-score: 1147.5 E(): 0, 39.4% identity in 419 aa overlap. No Hp ortholog. Also similar to Cj1393 metC (30.0% identity in 363 aa overlap). Contains Pfam match to entry PF01053 Cys_Met_Meta_PP, Gamma-family of PLP-dependent enzymes; Updated (2006) note: No specific characterisation in related bacteria with acceptable identity score. kept within product function. Functional classification - Amino acid biosynthesis - Aspartate family; O-acetylhomoserine (thiol)-lyase complement(1636407..1637678) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 906002 YP_002345094.1 CDS Cj1728c NC_002163.1 1637923 1638078 R Original (2000) note: Cj1728c, small hydrophobic protein, len: 51 aa; no Hp match. Some similarity to Cj1203c (33.3% identity in 42 aa overlap); Updated (2006) note: One probable transmembrane helix predicted by TMHMM2.0. Functional classification -Unknown; hypothetical protein complement(1637923..1638078) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 906003 YP_002345095.1 CDS flgE NC_002163.1 1638104 1640701 R the hook connects flagellar basal body to the flagellar filament; flagellar hook protein FlgE complement(1638104..1640701) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 906004 YP_002345096.1 CDS ruvC NC_002163.1 1640904 1641386 R endonuclease; resolves Holliday structures; forms a complex of RuvABC; the junction binding protein RuvA forms a hexameric ring along with the RuvB helicase and catalyzes branch migration; RuvC then interacts with RuvAB to resolve the Holliday junction by nicking DNA strands of like polarity; Holliday junction resolvase complement(1640904..1641386) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 906005 Cjp01 tRNA tRNAAla NC_002163.1 40866 40941 D tRNA-Ala 40866..40941 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904368 Cjp02 tRNA tRNAIle NC_002163.1 40950 41026 D tRNA-Ile 40950..41026 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904458 Cjp03 tRNA tRNAGlu NC_002163.1 165728 165802 D tRNA-Glu 165728..165802 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904506 Cjp04 tRNA tRNAAla NC_002163.1 395747 395822 D tRNA-Ala 395747..395822 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904755 Cjp05 tRNA tRNAIle NC_002163.1 395831 395907 D tRNA-Ile 395831..395907 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904756 Cjp06 tRNA tRNAThr NC_002163.1 433867 433942 D tRNA-Thr 433867..433942 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904793 Cjp07 tRNA tRNATyr NC_002163.1 433992 434077 D tRNA-Tyr 433992..434077 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904794 Cjp08 tRNA tRNAGly NC_002163.1 434084 434160 D tRNA-Gly 434084..434160 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904795 Cjt1 tRNA tRNAThr NC_002163.1 434265 434339 D tRNA-Thr 434265..434339 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 3245039 Cjp09 tRNA tRNATrp NC_002163.1 435831 435906 D tRNA-Trp 435831..435906 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904798 Cjp10 tRNA tRNAArg NC_002163.1 460270 460346 D tRNA-Arg 460270..460346 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904823 Cjp12 tRNA tRNAMet NC_002163.1 533097 533172 R tRNA-Met complement(533097..533172) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904895 Cjp13 tRNA tRNAGln NC_002163.1 533206 533280 R tRNA-Gln complement(533206..533280) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904896 Cjp14 tRNA tRNAAla NC_002163.1 698041 698116 D tRNA-Ala 698041..698116 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905060 Cjp15 tRNA tRNAIle NC_002163.1 698125 698201 D tRNA-Ile 698125..698201 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905061 Cjp16 tRNA tRNALeu NC_002163.1 826066 826152 D tRNA-Leu 826066..826152 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905179 Cjp17 tRNA tRNAGly NC_002163.1 826163 826237 D tRNA-Gly 826163..826237 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 904415 Cjt01 tRNA tRNALeu NC_002163.1 872889 872974 D tRNA-Leu 872889..872974 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 3245043 Cjt02 tRNA tRNAAsp NC_002163.1 878095 878171 R tRNA-Asp complement(878095..878171) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 3245040 Cjp19 tRNA tRNAVal NC_002163.1 878223 878298 R tRNA-Val complement(878223..878298) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905029 Cjp20 tRNA tRNALys NC_002163.1 878400 878475 R tRNA-Lys complement(878400..878475) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905235 Cjt2 tRNA tRNAAsp NC_002163.1 878480 878556 R tRNA-Asp complement(878480..878556) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 3245055 Cjt03 tRNA tRNAVal NC_002163.1 878608 878683 R tRNA-Val complement(878608..878683) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 3245044 Cjt04 tRNA tRNALys NC_002163.1 878691 878766 R tRNA-Lys complement(878691..878766) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 3245048 Cjp21 tRNA tRNAArg NC_002163.1 943535 943611 D tRNA-Arg 943535..943611 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905303 Cjp22 tRNA tRNAAsn NC_002163.1 1154100 1154174 R tRNA-Asn complement(1154100..1154174) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905516 Cjp23 tRNA tRNAMet NC_002163.1 1215057 1215133 D tRNA-Met 1215057..1215133 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905573 Cjp24 tRNA tRNAPhe NC_002163.1 1215241 1215316 R tRNA-Phe complement(1215241..1215316) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905574 Cjp25 tRNA tRNASer NC_002163.1 1287737 1287826 R tRNA-Ser complement(1287737..1287826) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905648 Cjp26 tRNA tRNASeC NC_002163.1 1432370 1432467 R tRNA-Sec complement(1432370..1432467) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905782 Cjp27 tRNA tRNAGly NC_002163.1 1549657 1549731 D tRNA-Gly 1549657..1549731 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905889 Cjp28 tRNA tRNALeu NC_002163.1 1549741 1549829 D tRNA-Leu 1549741..1549829 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905890 Cjp29 tRNA tRNACys NC_002163.1 1549848 1549921 D tRNA-Cys 1549848..1549921 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905892 Cjp30 tRNA tRNASer NC_002163.1 1549943 1550030 D tRNA-Ser 1549943..1550030 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905893 Cjt05 tRNA tRNALeu NC_002163.1 1590271 1590355 R tRNA-Leu complement(1590271..1590355) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 3245052 Cjt3 tRNA tRNAArg NC_002163.1 1590360 1590436 R tRNA-Arg complement(1590360..1590436) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 3245047 Cjt4 tRNA tRNAArg NC_002163.1 1590451 1590527 R tRNA-Arg complement(1590451..1590527) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 3245057 Cjp32 tRNA tRNAHis NC_002163.1 1590531 1590607 R tRNA-His complement(1590531..1590607) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905942 Cjp33 tRNA tRNAPro NC_002163.1 1590632 1590709 R tRNA-Pro complement(1590632..1590709) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905943 Cjp34 tRNA tRNAMet NC_002163.1 1626279 1626355 R tRNA-Met complement(1626279..1626355) Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905989 Cjt06 tRNA tRNASer NC_002163.1 1626491 1626578 D tRNA-Ser 1626491..1626578 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 3245049 Cjp35 tRNA tRNAAla NC_002163.1 1626625 1626700 D tRNA-Ala 1626625..1626700 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905990 Cjp36 tRNA tRNAVal NC_002163.1 1626704 1626779 D tRNA-Val 1626704..1626779 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 905991 Cjr01 rRNA Cjr01 NC_002163.1 39249 40761 D 16S ribosomal RNA 39249..40761 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 3245054 Cjr02 rRNA Cjr02 NC_002163.1 41568 44457 D 23S ribosomal RNA 41568..44457 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 3245050 Cjr03 rRNA Cjr03 NC_002163.1 44741 44860 D 5S ribosomal RNA 44741..44860 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 3245045 Cjr04 rRNA Cjr04 NC_002163.1 394130 395642 D 16S ribosomal RNA 394130..395642 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 3245051 Cjr05 rRNA Cjr05 NC_002163.1 396449 399360 D 23S ribosomal RNA 396449..399360 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 3245053 Cjr06 rRNA Cjr06 NC_002163.1 399644 399763 D 5S ribosomal RNA 399644..399763 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 3245056 Cjr07 rRNA Cjr07 NC_002163.1 696424 697936 D 16S ribosomal RNA 696424..697936 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 3245041 Cjr08 rRNA Cjr08 NC_002163.1 698743 701654 D 23S ribosomal RNA 698743..701654 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 3245038 Cjr09 rRNA Cjr09 NC_002163.1 701939 702058 D 5S ribosomal RNA 701939..702058 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819 3245042