-- dump date   	20140619_021925
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_002343473.1	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.
YP_002343474.1	binds the polymerase to DNA and acts as a sliding clamp
YP_002343475.1	negatively supercoils closed circular double-stranded DNA
YP_002343476.1	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
YP_002343477.1	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
YP_002343478.1	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
YP_002343479.1	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
YP_002343480.1	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
YP_002343481.1	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
YP_002343482.1	RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids
YP_002343483.1	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
YP_002343484.1	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
YP_002343485.1	catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis
YP_002343486.1	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
YP_002343487.1	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
YP_002343488.1	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
YP_002343489.1	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
YP_002343490.1	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
YP_002343491.1	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
YP_002343492.1	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
YP_002343493.1	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
YP_002343494.1	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
YP_002343495.1	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide
YP_002343496.1	Catalyzes the rate-limiting step in dNTP synthesis
YP_002343497.1	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
YP_002343498.1	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
YP_002343499.1	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
YP_002343500.1	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
YP_002343501.1	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
YP_002343502.1	Original (2000) note: Cj0030, unknown, len: 465 aa. No Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown
YP_002343503.1	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
YP_002343504.1	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
YP_002343505.1	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
YP_002343506.1	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
YP_002343507.1	Original (2000) note: Cj0036, unknown, len: 449 aa; 37.8% identity to HP1143 hypothetical protein. Functional classification - Conserved hypothetical proteins
YP_002343508.1	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
YP_002343509.1	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
YP_002343510.1	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
YP_002343511.1	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
YP_002343512.1	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
YP_002343513.1	acts as a scaffold for the assembly of hook proteins onto the flagellar basal body rod
YP_002343514.1	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
YP_002343515.1	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
YP_002343516.1	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
YP_002343517.1	catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs
YP_002343518.1	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
YP_002343519.1	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
YP_002343521.1	Original (2000) note: Cj0057, possible periplasmic protein, len: 284 aa; no Hp match. Contains possible N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins
YP_002343522.1	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
YP_002343523.1	One of three proteins involved in switching the direction of the flagellar rotation
YP_002343524.1	with FliG and FliN makes up the switch complex which is involved in switching the direction of the flagella rotation
YP_002343525.1	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
YP_002343526.1	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
YP_002343527.1	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
YP_002343528.1	positive regulator of class III flagellar genes
YP_002343529.1	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
YP_002343530.1	catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis
YP_002343531.1	Catalyzes the hydrolytic cleavage of a carbon-halogen bond in N-ethylammeline
YP_002343532.1	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
YP_002343533.1	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
YP_002343535.1	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
YP_002343536.1	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
YP_002343537.1	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
YP_002343538.1	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
YP_002343539.1	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
YP_002343540.1	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
YP_002343541.1	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
YP_002343542.1	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
YP_002343543.1	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
YP_002343544.1	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
YP_002343545.1	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
YP_002343546.1	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
YP_002343547.1	catalyzes the formation of fumarate from aspartate
YP_002343548.1	functions in anaerobic transport of C4-dicarboxylate compounds such as fumarate; similar to dcuB
YP_002343549.1	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
YP_002343550.1	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
YP_002343551.1	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
YP_002343552.1	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
YP_002343553.1	Original (2000) note: Cj0093, probable periplasmic protein, len: 400 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins
YP_002343554.1	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
YP_002343555.1	involved in the peptidyltransferase reaction during translation
YP_002343556.1	essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication
YP_002343557.1	catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis
YP_002343558.1	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
YP_002343559.1	catalyzes the formation of biotinyl-5'-AMP, also acts as a transcriptional repressor of the biotin operon
YP_002343560.1	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
YP_002343561.1	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
YP_002343562.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B' is part of the membrane proton channel.
YP_002343563.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel.
YP_002343564.1	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
YP_002343565.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit
YP_002343566.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit
YP_002343567.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit
YP_002343568.1	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
YP_002343569.1	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
YP_002343570.1	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
YP_002343571.1	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
YP_002343572.1	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
YP_002343573.1	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
YP_002343574.1	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
YP_002343575.1	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
YP_002343576.1	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
YP_002343577.1	enables the cleavage of the glycosidic bond in both 5'-methylthioadenosine and S-adenosylhomocysteine
YP_002343578.1	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
YP_002343579.1	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
YP_002343580.1	Original (2000) note: Cj0120, unknown, len: 204 aa; 41.7% identity to HP0951. Functional classification -Conserved hypothetical proteins
YP_002343581.1	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
YP_002343582.1	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
YP_002343583.1	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
YP_002343584.1	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
YP_002343585.1	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
YP_002343586.1	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
YP_002343587.1	catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer of AccA2D2 subunits
YP_002343588.1	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
YP_002343589.1	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
YP_002343590.1	catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate
YP_002343591.1	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
YP_002343592.1	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
YP_002343593.1	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
YP_002343594.1	catalyzes the formation of O-phospho-L-homoserine from L-homoserine in threonine biosynthesis from asparate
YP_002343595.1	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
YP_002343596.1	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
YP_002343597.1	associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock
YP_002343598.1	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
YP_002343599.1	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
YP_002343600.1	Original (2000) note: Cj0140, unknown, len: 443 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown
YP_002343601.1	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
YP_002343602.1	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
YP_002343603.1	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
YP_002343604.1	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
YP_002343605.1	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
YP_002343606.1	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
YP_002343607.1	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
YP_002343608.1	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
YP_002343609.1	catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine
YP_002343610.1	catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate
YP_002343611.1	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
YP_002343612.1	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
YP_002343613.1	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
YP_002343614.1	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
YP_002343615.1	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
YP_002343616.1	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
YP_002343617.1	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
YP_002343618.1	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
YP_002343619.1	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
YP_002343620.1	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
YP_002343621.1	together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z
YP_002343622.1	Original (2000) note: Cj0162c, probable periplasmic protein, len: 171 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins
YP_002343623.1	Original (2000) note: Cj0163c, unknown, len: 165 aa; no Hp match. Functional classification - Unknown
YP_002343624.1	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
YP_002343625.1	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
YP_002343626.1	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
YP_002343627.1	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
YP_002343628.1	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
YP_002343629.1	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
YP_002343630.1	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
YP_002343631.1	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
YP_002343632.1	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
YP_002343633.1	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
YP_002343634.1	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
YP_002343635.1	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
YP_002343636.1	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
YP_002343637.1	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
YP_002343638.1	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
YP_002343639.1	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
YP_002343640.1	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
YP_002343641.1	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
YP_002343642.1	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
YP_002343644.1	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
YP_002343645.1	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
YP_002343646.1	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
YP_002343647.1	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
YP_002343648.1	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
YP_002343649.1	cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+)
YP_002343650.1	hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates
YP_002343651.1	Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer
YP_002343652.1	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
YP_002343653.1	involved in type III protein export during flagellum assembly
YP_002343654.1	Catalyzes first step of the de novo purine nucleotide biosynthetic pathway
YP_002343655.1	catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis
YP_002343656.1	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
YP_002343657.1	Original (2000) note: Cj0199c, probable periplasmic protein, len: 373 aa; no Hp match. Contains N-terminal signal sequence. Functional classification - Miscellaneous periplasmic proteins
YP_002343658.1	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
YP_002343659.1	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
YP_002343661.1	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
YP_002343662.1	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
YP_002343663.1	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
YP_002343664.1	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
YP_002343665.1	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
YP_002343666.1	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
YP_002343667.1	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
YP_002343668.1	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
YP_002343669.1	catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate
YP_002343670.1	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
YP_002343671.1	catalyzes the methyl esterification of L-isoaspartyl residues that are formed in damaged proteins
YP_002343672.1	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
YP_002343673.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate
YP_002343674.1	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
YP_002343675.1	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
YP_002343676.1	involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_002343677.1	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
YP_002343678.1	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
YP_002343679.1	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
YP_002343680.1	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
YP_002343681.1	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
YP_002343682.1	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
YP_002343683.1	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
YP_002343684.1	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
YP_002343685.1	Original (2000) note: Cj0243c, unknown, len: 388 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown
YP_002343686.1	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
YP_002343687.1	binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit
YP_002343690.1	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
YP_002343691.1	Original (2000) note: Cj0249, unknown, len: 159 aa; no Hp match. Functional classification - Unknown
YP_002343692.1	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
YP_002343693.1	Original (2000) note: Cj0251c, highly acidic protein, len: 51 aa; 47.9% identity to HP0756. Functional classification - Conserved hypothetical proteins
YP_002343694.1	MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis
YP_002343695.1	Original (2000) note: Cj0253, unknown, len: 87 aa; 33.8% identity to HP0495. Functional classification -Conserved hypothetical proteins
YP_002343696.1	Original (2000) note: Cj0254, unknown, len: 386 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown
YP_002343697.1	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
YP_002343698.1	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
YP_002343699.1	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
YP_002343700.1	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
YP_002343701.1	catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis
YP_002343702.1	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
YP_002343703.1	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
YP_002343704.1	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
YP_002343705.1	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
YP_002343706.1	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
YP_002343707.1	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
YP_002343708.1	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
YP_002343709.1	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
YP_002343710.1	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
YP_002343711.1	catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids
YP_002343712.1	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
YP_002343713.1	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
YP_002343714.1	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
YP_002343715.1	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
YP_002343716.1	catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis
YP_002343717.1	binds and unfolds substrates as part of the ClpXP protease
YP_002343718.1	functions in MreBCD complex in some organisms
YP_002343719.1	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
YP_002343720.1	four CarB-CarA dimers form the carbamoyl phosphate synthetase holoenzyme that catalyzes the production of carbamoyl phosphate; CarB is responsible for the amidotransferase activity
YP_002343721.1	Original (2000) note: Cj0280, unknown, len: 140 aa; 52.8% identity to HP0918. Functional classification -Conserved hypothetical proteins
YP_002343722.1	Important for the balance of metabolites in the pentose-phosphate pathway
YP_002343723.1	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
YP_002343724.1	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
YP_002343725.1	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
YP_002343726.1	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
YP_002343727.1	Original (2000) note: Cj0286c, unknown, len: 205 aa; 28.4% identity to HP0394 (252 aa). Functional classification - Conserved hypothetical proteins
YP_002343728.1	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
YP_002343729.1	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
YP_002343730.1	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
YP_002343731.1	catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate
YP_002343732.1	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
YP_002343733.1	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
YP_002343734.1	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)
YP_002343735.1	catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine
YP_002343736.1	catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate
YP_002343737.1	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
YP_002343738.1	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
YP_002343739.1	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
YP_002343740.1	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
YP_002343741.1	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
YP_002343742.1	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
YP_002343743.1	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
YP_002343744.1	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
YP_002343745.1	catalyzes the formation of S-adenosyl-4-methylthionine-2-oxobutanoate and 7,8-diaminononanoate from S-adenosyl-L-methionine and 8-amino-7-oxononanoate
YP_002343746.1	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
YP_002343747.1	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
YP_002343748.1	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
YP_002343749.1	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
YP_002343750.1	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_002343751.1	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
YP_002343752.1	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
YP_002343753.1	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
YP_002343754.1	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
YP_002343755.1	catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis
YP_002343756.1	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
YP_002343757.1	One of three proteins involved in switching the direction of the flagellar rotation
YP_002343758.1	binds to and inhibits the function of flagella specific ATPase FliI
YP_002343759.1	catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate
YP_002343760.1	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
YP_002343761.1	Original (2000) note: Cj0323, unknown, len: 398 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown
YP_002343762.1	Catalyzes the carbon methylation reaction in the biosynthesis of ubiquinone
YP_002343763.1	bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides
YP_002343764.1	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
YP_002343765.1	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
YP_002343766.1	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
YP_002343767.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY
YP_002343768.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_002343769.1	Original (2000) note: Cj0331c, unknown, len: 117 aa; 34.7% identity to HP0199. Functional classification -Conserved hypothetical proteins
YP_002343770.1	catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate
YP_002343771.1	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
YP_002343772.1	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
YP_002343773.1	membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export
YP_002343774.1	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
YP_002343775.1	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
YP_002343776.1	has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair
YP_002343777.1	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
YP_002343778.1	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
YP_002343779.1	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
YP_002343780.1	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
YP_002343781.1	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
YP_002343782.1	Original (2000) note: Cj0344, unknown, len: 41 aa; no Hp match. Functional classification - Unknown
YP_002343783.1	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
YP_002343784.1	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
YP_002343785.1	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
YP_002343786.1	catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate
YP_002343787.1	catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis
YP_002343788.1	Original (2000) note: Cj0350, unknown, len: 140 aa; no Hp match. . Functional classification - Unknown
YP_002343789.1	One of three proteins involved in switching the direction of the flagellar rotation
YP_002343790.1	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
YP_002343791.1	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
YP_002343792.1	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
YP_002343793.1	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
YP_002343794.1	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
YP_002343795.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsX
YP_002343796.1	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
YP_002343797.1	catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
YP_002343798.1	lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis
YP_002343799.1	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
YP_002343800.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_002343801.1	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
YP_002343802.1	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
YP_002343803.1	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
YP_002343804.1	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
YP_002343805.1	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
YP_002343806.1	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
YP_002343807.1	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
YP_002343808.1	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
YP_002343809.1	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
YP_002343810.1	Involved in the metabolism of aromatic amino acids
YP_002343811.1	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
YP_002343812.1	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
YP_002343813.1	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
YP_002343814.1	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
YP_002343815.1	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
YP_002343816.1	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
YP_002343817.1	Original (2000) note: Cj0380c, unknonw, len: 261 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown
YP_002343818.1	type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase
YP_002343819.1	Regulates rRNA biosynthesis by transcriptional antitermination
YP_002343820.1	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
YP_002343821.1	catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis
YP_002343822.1	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
YP_002343823.1	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
YP_002343824.1	catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis
YP_002343825.1	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
YP_002343826.1	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
YP_002343827.1	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
YP_002343828.1	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
YP_002343829.1	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
YP_002343830.1	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
YP_002343831.1	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
YP_002343832.1	Original (2000) note: Cj0395c, unknown, len: 96 aa; no Hp match. Functional classification - Unknown
YP_002343833.1	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
YP_002343834.1	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
YP_002343835.1	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
YP_002343836.1	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
YP_002343837.1	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
YP_002343838.1	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
YP_002343839.1	catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate
YP_002343840.1	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
YP_002343841.1	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
YP_002343842.1	AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate
YP_002343843.1	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
YP_002343844.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_002343845.1	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
YP_002343846.1	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
YP_002343847.1	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
YP_002343848.1	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
YP_002343849.1	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
YP_002343850.1	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
YP_002343851.1	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
YP_002343852.1	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
YP_002343853.1	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
YP_002343854.1	Original (2000) note: Cj0417, unknown, len: 48 aa; no Hp match. Functional classification - Unknown
YP_002343855.1	Original (2000) note: Cj0418c, unknown, len: 234 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown
YP_002343856.1	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
YP_002343857.1	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
YP_002343858.1	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
YP_002343859.1	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
YP_002343860.1	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
YP_002343861.1	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
YP_002343862.1	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
YP_002343863.1	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
YP_002343864.1	Original (2000) note: Cj0427, unknown, len: 111 aa; no Hp match. Functional classification - Unknown
YP_002343865.1	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
YP_002343866.1	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
YP_002343867.1	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
YP_002343868.1	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
YP_002343869.1	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
YP_002343870.1	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
YP_002343871.1	catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
YP_002343872.1	Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis
YP_002343873.1	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
YP_002343874.1	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
YP_002343875.1	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
YP_002343876.1	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
YP_002343877.1	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
YP_002343878.1	carries the fatty acid chain in fatty acid biosynthesis
YP_002343879.1	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
YP_002343880.1	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
YP_002343881.1	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
YP_002343882.1	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
YP_002343883.1	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
YP_002343884.1	required for 70S ribosome assembly
YP_002343885.1	catalyzes the interconversion of D-ribulose 5-phosphate to xylulose 5-phosphate
YP_002343886.1	3'-5' exonuclease of DNA polymerase III
YP_002343887.1	required for the synthesis of the hydromethylpyrimidine moiety of thiamine
YP_002343888.1	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
YP_002343890.1	Original (2000) note: Cj0456c, unknown, len: 319 aa; no Hp match. Functional classification - Unknown
YP_002343891.1	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
YP_002343892.1	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)
YP_002343893.1	Original (2000) note: Cj0459c, unknown, len: 88 aa; 32.5% identical to HP0268. Functional classification -Conserved hypothetical proteins
YP_002343894.1	modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination
YP_002343895.1	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
YP_002343896.1	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
YP_002343897.1	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
YP_002343898.1	catalyzes branch migration in Holliday junction intermediates
YP_002343899.1	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
YP_002343900.1	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
YP_002343901.1	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
YP_002343902.1	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
YP_002343903.1	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
YP_002343904.1	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
YP_002343905.1	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
YP_002343906.1	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
YP_002343907.1	Modulates Rho-dependent transcription termination
YP_002343908.1	binds directly to 23S ribosomal RNA
YP_002343909.1	in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA
YP_002343910.1	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_002343911.1	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
YP_002343912.1	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
YP_002343913.1	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
YP_002343914.1	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
YP_002343915.1	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
YP_002343916.1	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
YP_002343917.1	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
YP_002343919.1	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
YP_002343920.1	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
YP_002343921.1	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
YP_002343922.1	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
YP_002343925.1	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
YP_002343926.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_002343927.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_002343928.1	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
YP_002343929.1	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
YP_002343930.1	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
YP_002343931.1	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
YP_002343932.1	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
YP_002343933.1	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
YP_002343934.1	catalyzes the selenophosphate-dependent transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA
YP_002343935.1	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
YP_002343936.1	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
YP_002343937.1	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
YP_002343938.1	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
YP_002343939.1	Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell
YP_002343940.1	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
YP_002343941.1	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
YP_002343942.1	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
YP_002343943.1	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
YP_002343944.1	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
YP_002343945.1	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
YP_002343946.1	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
YP_002343947.1	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
YP_002343948.1	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
YP_002343949.1	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
YP_002343950.1	molecular chaperone
YP_002343951.1	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
YP_002343952.1	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
YP_002343956.1	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
YP_002343957.1	forms a junction between the M-ring and FlgB during flagella biosynthesis
YP_002343958.1	with FlgF and B makes up the proximal portion of the flagellar basal body rod
YP_002343959.1	with FlgF and C makes up the proximal portion of the flagellar basal body rod; Vibrio parahaemolyticus protein is associated with the polar flagella
YP_002343960.1	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
YP_002343961.1	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
YP_002343962.1	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
YP_002343963.1	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
YP_002343964.1	catalyzes the interconversion of succinyl-CoA and succinate
YP_002343965.1	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
YP_002343966.1	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
YP_002343967.1	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
YP_002343968.1	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
YP_002343969.1	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
YP_002343970.1	Original (2000) note: Cj0539, unknown, len: 87 aa; no Hp match. Functional classification - Unknown
YP_002343971.1	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
YP_002343972.1	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
YP_002343973.1	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
YP_002343974.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_002343975.1	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
YP_002343976.1	transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis
YP_002343977.1	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
YP_002343978.1	possibly involved in flagella export
YP_002343979.1	Also called hook-associated protein 2; involved in flagellin assembly
YP_002343980.1	flagellin specific chaperone
YP_002343981.1	Original (2000) note: Cj0550, unknown, len: 91 aa; no Hp match. Functional classification - Unknown
YP_002343982.1	Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA
YP_002343983.1	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
YP_002343984.1	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
YP_002343985.1	Original (2000) note: Cj0554, unknown, len: 334 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown
YP_002343986.1	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
YP_002343987.1	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
YP_002343988.1	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
YP_002343989.1	Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway
YP_002343990.1	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
YP_002343991.1	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
YP_002343992.1	Original (2000) note: Cj0561c, possible periplasmic protein, len: 309 aa; no Hp match; Updated (2006) note: possible changed to . Functional classification - Miscellaneous periplasmic proteins
YP_002343993.1	unwinds double stranded DNA
YP_002343994.1	Original (2000) note: Cj0563, unknown, len: 200 aa; no Hp match. Functional classification - Unknown
YP_002343995.1	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
YP_002343996.1	Original (2000) note: Cj0566, unknown, len: 488 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown
YP_002343997.1	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
YP_002344000.1	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
YP_002344001.1	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
YP_002344002.1	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
YP_002344003.1	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
YP_002344004.1	catalyzes the formation of 2-acetolactate from pyruvate, leucine resistant; also known as acetolactate synthase 3 large subunit
YP_002344005.1	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
YP_002344006.1	adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis
YP_002344007.1	Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step
YP_002344008.1	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
YP_002344009.1	mediates the export of protein precursors bearing twin-arginine signal peptides
YP_002344010.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_002344011.1	hydrolyzes diadenosine polyphosphate
YP_002344012.1	catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation.
YP_002344013.1	Original (2000) note: Cj0583, unknown, len: 178 aa; 30.8% identity to HP1230. Functional classification -Conserved hypothetical proteins
YP_002344014.1	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
YP_002344015.1	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
YP_002344016.1	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
YP_002344017.1	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
YP_002344018.1	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
YP_002344019.1	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
YP_002344020.1	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
YP_002344021.1	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
YP_002344022.1	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
YP_002344023.1	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
YP_002344024.1	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
YP_002344025.1	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
YP_002344026.1	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
YP_002344027.1	catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1,6, bisphosphate
YP_002344028.1	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
YP_002344029.1	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
YP_002344030.1	Original (2000) note: Cj0600, unknown, len: 291 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown
YP_002344031.1	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
YP_002344032.1	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
YP_002344033.1	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
YP_002344034.1	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
YP_002344035.1	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
YP_002344036.1	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
YP_002344037.1	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
YP_002344038.1	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
YP_002344039.1	Original (2000) note: Cj0609c, possible periplasmic protein, len: 392 aa; no Hp match. Contains possible N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins
YP_002344040.1	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
YP_002344041.1	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
YP_002344042.1	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
YP_002344043.1	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
YP_002344044.1	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
YP_002344045.1	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
YP_002344046.1	ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation
YP_002344049.1	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
YP_002344050.1	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
YP_002344051.1	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
YP_002344052.1	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
YP_002344053.1	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
YP_002344054.1	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
YP_002344055.1	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
YP_002344056.1	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
YP_002344057.1	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
YP_002344058.1	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
YP_002344059.1	required for the assembly and function of the DNAX complex which is required for the assembly of the beta subunit onto primed DNA
YP_002344060.1	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
YP_002344061.1	catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis
YP_002344062.1	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
YP_002344063.1	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
YP_002344064.1	similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function
YP_002344065.1	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
YP_002344066.1	this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; provides protection against oxidative stress
YP_002344067.1	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
YP_002344068.1	essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP
YP_002344069.1	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
YP_002344070.1	catalyzes the phosphorylation of NAD to NADP
YP_002344071.1	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
YP_002344072.1	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
YP_002344073.1	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
YP_002344074.1	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
YP_002344075.1	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
YP_002344076.1	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
YP_002344077.1	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
YP_002344078.1	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
YP_002344079.1	binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential
YP_002344080.1	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
YP_002344081.1	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
YP_002344082.1	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
YP_002344083.1	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
YP_002344084.1	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
YP_002344085.1	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
YP_002344086.1	heat shock protein involved in degradation of misfolded proteins
YP_002344087.1	heat shock protein involved in degradation of misfolded proteins
YP_002344088.1	in Escherichia coli this protein is wrapped around the base of the L1 stalk
YP_002344089.1	catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming
YP_002344090.1	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
YP_002344091.1	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
YP_002344092.1	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
YP_002344093.1	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
YP_002344094.1	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
YP_002344095.1	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
YP_002344096.1	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
YP_002344098.1	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
YP_002344099.1	Original (2000) note: Cj0681, unknown, len: 76 aa; 36.2% identity to HP0385. Functional classification -Conserved hypothetical proteins
YP_002344100.1	Original (2000) note: Cj0682, unknown, len: 80 aa; no Hp match. Functional classification - Unknown
YP_002344101.1	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
YP_002344102.1	binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity
YP_002344103.1	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
YP_002344104.1	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
YP_002344105.1	part of the flagellar basal body which consists of four rings L,P, S and M mounted on a central rod
YP_002344106.1	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
YP_002344107.1	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
YP_002344108.1	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
YP_002344109.1	Original (2000) note: Cj0691, possible membrane protein, len: 163 aa; no Hp match. Contains two possible transmembrane domains. Functional classification -Membranes, lipoproteins and porins
YP_002344110.1	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
YP_002344111.1	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
YP_002344112.1	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
YP_002344113.1	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
YP_002344114.1	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
YP_002344115.1	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
YP_002344116.1	makes up the distal portion of the flagellar basal body rod
YP_002344117.1	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
YP_002344118.1	Original (2000) note: Cj0700, unknown, len: 231 aa; 49.4% identity to HP0170. Functional classification -Conserved hypothetical proteins
YP_002344119.1	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
YP_002344120.1	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
YP_002344121.1	Original (2000) note: Cj0703, unknown, len: 178 aa; 51.0% identity to HP0406. Functional classification -Conserved hypothetical proteins
YP_002344122.1	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
YP_002344123.1	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
YP_002344124.1	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
YP_002344125.1	catalyzes the transfer of 2-keto-3-deoxy-D-manno-octulosonic acid to lipid A
YP_002344126.1	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
YP_002344127.1	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
YP_002344128.1	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
YP_002344129.1	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
YP_002344130.1	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
YP_002344131.1	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA
YP_002344132.1	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
YP_002344133.1	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
YP_002344134.1	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
YP_002344135.1	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
YP_002344136.1	catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase
YP_002344137.1	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
YP_002344138.1	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
YP_002344139.1	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
YP_002344140.1	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
YP_002344141.1	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
YP_002344142.1	Original (2000) note: Cj0724, unknown, len: 61 aa; no Hp match. Functional classification - Unknown
YP_002344143.1	forms a trimer; related to eukaryotic protein gephyrin; functions during molybdenum cofactor biosynthesis
YP_002344144.1	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
YP_002344145.1	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
YP_002344146.1	Original (2000) note: Cj0728, probable periplasmic protein, len: 441 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins
YP_002344147.1	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
YP_002344148.1	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
YP_002344149.1	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
YP_002344150.1	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
YP_002344151.1	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
YP_002344152.1	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
YP_002344153.1	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
YP_002344154.1	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
YP_002344160.1	Original (2000) note: Cj0747, unknown, len: 35 aa; no Hp match. Functional classification - Unknown
YP_002344161.1	Original (2000) note: Cj0748, unknown, len: 30 aa; no Hp match. Functional classification - Unknown
YP_002344162.1	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
YP_002344163.1	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
YP_002344164.1	Acts as a negative regulator of the grpE-dnaK-dnaJ and groELS class I heat shock operons by preventing heat-shock induction
YP_002344165.1	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
YP_002344166.1	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
YP_002344167.1	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
YP_002344168.1	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
YP_002344169.1	catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate
YP_002344170.1	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
YP_002344171.1	catalyzes the formation of agmatine from arginine in putrescine and spermidine biosynthesis
YP_002344172.1	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
YP_002344173.1	catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP)
YP_002344174.1	Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA
YP_002344175.1	catalyzes the formation of 2-octaprenylphenol from 3-octaprenyl-4-hydroxybenzoate
YP_002344176.1	required for the assembly of the flagellar basal body P-ring
YP_002344177.1	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
YP_002344178.1	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
YP_002344179.1	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
YP_002344180.1	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
YP_002344181.1	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
YP_002344182.1	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
YP_002344183.1	Original (2000) note: Cj0776c, probable periplasmic protein, len: 340 aa; no Hp match. Contains N-terminal signal sequence. Functional classification - Miscellaneous periplasmic proteins
YP_002344184.1	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
YP_002344185.1	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
YP_002344186.1	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
YP_002344187.1	periplasmic; catalytic subunit; with NapBC catalyzes the reduction of nitrate to nitrite; NapAB receives electrons from NapC
YP_002344188.1	part of NapHG quinol dehydrogenase; couples electron transfer from ubiquinone-ubiquinol couple via NapC/B to NapA; secreted by twin arginine translocation pathway
YP_002344189.1	part of NapHG quinol dehydrogenase; couples electron transfer from ubiquinone-ubiquinol couple via NapC/B to NapA
YP_002344190.1	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
YP_002344191.1	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
YP_002344192.1	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
YP_002344193.1	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
YP_002344194.1	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
YP_002344195.1	Original (2000) note: Cj0788, unknown, len: 163 aa; 30.8% identity to HP0167. Functional classification -Conserved hypothetical proteins
YP_002344196.1	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
YP_002344197.1	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
YP_002344198.1	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
YP_002344199.1	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
YP_002344200.1	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
YP_002344201.1	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
YP_002344202.1	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
YP_002344203.1	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
YP_002344204.1	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
YP_002344205.1	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
YP_002344206.1	plays an essential role in ATP-dependent branch migration of the Holliday junction
YP_002344207.1	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
YP_002344208.1	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
YP_002344209.1	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
YP_002344210.1	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
YP_002344211.1	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
YP_002344212.1	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
YP_002344213.1	catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis
YP_002344214.1	Acts on the hydroxyl group at position 7 of the steroid frame
YP_002344215.1	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
YP_002344216.1	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
YP_002344217.1	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
YP_002344218.1	transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate
YP_002344219.1	catalyzes the formation of L-threonine from O-phospho-L-homoserine
YP_002344220.1	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
YP_002344224.1	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
YP_002344225.1	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
YP_002344226.1	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
YP_002344227.1	FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus
YP_002344228.1	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
YP_002344229.1	catalyzes the conjugation of cysteine to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, which is then decarboxylated to form 4'-phosphopantotheine
YP_002344230.1	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
YP_002344231.1	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
YP_002344232.1	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
YP_002344233.1	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
YP_002344234.1	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability
YP_002344235.1	catalyzes the formation of 2-oxobutanoate from L-threonine
YP_002344236.1	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
YP_002344237.1	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
YP_002344238.1	catalyzes the formation of 5-methyl-uridine at position 54 in all tRNAs
YP_002344239.1	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
YP_002344240.1	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
YP_002344241.1	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
YP_002344242.1	catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate
YP_002344243.1	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
YP_002344244.1	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
YP_002344245.1	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
YP_002344246.1	Original (2000) note: Cj0839c, unknown, len: 65 aa; 43.1% identity to HP1384. Functional classification -Conserved hypothetical proteins
YP_002344247.1	catalyzes the formation of D-fructose 6-phosphate from fructose-1,6-bisphosphate
YP_002344248.1	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
YP_002344249.1	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
YP_002344250.1	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
YP_002344251.1	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
YP_002344252.1	charges one glutamine molecule and pairs it with tRNA(Gln)
YP_002344253.1	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
YP_002344254.1	catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine
YP_002344255.1	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
YP_002344256.1	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
YP_002344257.1	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
YP_002344258.1	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
YP_002344259.1	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
YP_002344260.1	Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway
YP_002344261.1	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
YP_002344262.1	catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate
YP_002344263.1	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
YP_002344264.1	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
YP_002344265.1	adds enolpyruvyl to UDP-N-acetylglucosamine as a component of cell wall formation; gram-positive bacteria have 2 copies of MurA which are active
YP_002344266.1	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
YP_002344267.1	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
YP_002344268.1	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
YP_002344269.1	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
YP_002344270.1	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
YP_002344271.1	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
YP_002344272.1	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
YP_002344273.1	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
YP_002344277.1	Original (2000) note: Cj0877c, questionable ORF,len: 30 aa; no Hp match. Functional classification -Unknown
YP_002344278.1	Original (2000) note: Cj0878, unknown, len: 48 aa; no Hp match. Functional classification - Unknown
YP_002344279.1	Original (2000) note: Cj0879c, probable periplasmic protein, len: 210 aa; no Hp match. Functional classification - Miscellaneous periplasmic proteins
YP_002344280.1	Original (2000) note: Cj0880c, unknown, len: 240 aa; no Hp match. Functional classification - Unknown
YP_002344281.1	Original (2000) note: Cj0881c, unknown, len: 348 aa; 40.6% identity to HP1042. Functional classification -Conserved hypothetical proteins
YP_002344282.1	membrane protein involved in the flagellar export apparatus
YP_002344283.1	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
YP_002344284.1	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
YP_002344285.1	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
YP_002344286.1	with FlgK acts as a hook filament junction protein to join the flagellar filament to the hook
YP_002344287.1	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
YP_002344288.1	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
YP_002344289.1	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
YP_002344290.1	catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate
YP_002344291.1	Original (2000) note: Cj0892c, probable periplasmic protein, len: 162 aa; no Hp match. Functional classification - Miscellaneous periplasmic proteins
YP_002344292.1	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
YP_002344293.1	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
YP_002344294.1	catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis
YP_002344295.1	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
YP_002344296.1	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
YP_002344297.1	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
YP_002344298.1	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
YP_002344299.1	Original (2000) note: Cj0900c, small hydrophobic protein, len: 59 aa; 29.8% identity to HP0085. Functional classification - Conserved hypothetical proteins
YP_002344300.1	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
YP_002344301.1	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
YP_002344302.1	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
YP_002344303.1	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
YP_002344304.1	converts L-alanine to D-alanine which is used in cell wall biosynthesis; binds one pyridoxal phosphate per monomer; forms a homodimer
YP_002344305.1	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
YP_002344306.1	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
YP_002344307.1	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
YP_002344308.1	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
YP_002344309.1	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
YP_002344310.1	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
YP_002344311.1	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
YP_002344312.1	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
YP_002344313.1	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
YP_002344314.1	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
YP_002344315.1	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
YP_002344316.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP
YP_002344317.1	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
YP_002344318.1	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
YP_002344319.1	PEB1
YP_002344320.1	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
YP_002344321.1	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
YP_002344322.1	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
YP_002344323.1	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
YP_002344324.1	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
YP_002344325.1	catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis
YP_002344326.1	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
YP_002344327.1	catalyzes the removal of N-terminal amino acids preferably leucine from various peptides
YP_002344328.1	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
YP_002344329.1	catalyzes the formation of arginine from (N-L-arginino)succinate
YP_002344330.1	PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP
YP_002344331.1	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
YP_002344332.1	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
YP_002344333.1	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
YP_002344334.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit C is part of the membrane proton channel F0
YP_002344335.1	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
YP_002344336.1	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
YP_002344337.1	Original (2000) note: Cj0939c, unknown, len: 126 aa; 29.5% identity to HP1065. Functional classification -Conserved hypothetical proteins
YP_002344338.1	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
YP_002344339.1	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
YP_002344340.1	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
YP_002344341.1	participates with LolB in the incorporation of lipoprotein into the outer membrane
YP_002344342.1	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
YP_002344343.1	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
YP_002344344.1	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
YP_002344345.1	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
YP_002344346.1	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
YP_002344347.1	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
YP_002344348.1	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
YP_002344351.1	involved in de novo purine biosynthesis
YP_002344352.1	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
YP_002344353.1	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
YP_002344354.1	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
YP_002344355.1	Original (2000) note: Cj0957c, unknown, len: 272 aa; 42.5% identity to HP1451. Functional classification -Conserved hypothetical proteins
YP_002344356.1	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
YP_002344357.1	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
YP_002344358.1	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
YP_002344359.1	in Escherichia coli transcription of this gene is enhanced by polyamines
YP_002344360.1	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
YP_002344361.1	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
YP_002344362.1	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
YP_002344363.1	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
YP_002344364.1	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
YP_002344365.1	Original (2000) note: Cj0970, unknown, len: 100 aa; no Hp match. Functional classification - Unknown
YP_002344366.1	Original (2000) note: Cj0971, unknown, len: 130 aa; no Hp match. Functional classification - Unknown
YP_002344367.1	Original (2000) note: Cj0972, unknown, len: 107 aa; no Hp match. Functional classification - Unknown
YP_002344369.1	Original (2000) note: Cj0974, questionable CDS, len 46 aa; no Hp match. Functional classification - Unknown
YP_002344370.1	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
YP_002344371.1	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
YP_002344372.1	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
YP_002344373.1	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
YP_002344374.1	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
YP_002344375.1	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
YP_002344376.1	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
YP_002344377.1	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
YP_002344378.1	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
YP_002344379.1	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
YP_002344380.1	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
YP_002344383.1	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
YP_002344384.1	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
YP_002344385.1	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
YP_002344386.1	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
YP_002344387.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_002344388.1	Original (2000) note: Cj0993c, unknown, len: 163 aa; 30.1% identity to HP0664. Functional classification -Conserved hypothetical proteins
YP_002344389.1	catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation
YP_002344390.1	catalyzes the formation of porphobilinogen from 5-aminolevulinate
YP_002344391.1	catalyzes the conversion of GTP to formate and 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine and diphosphate
YP_002344392.1	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
YP_002344393.1	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
YP_002344394.1	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
YP_002344395.1	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
YP_002344396.1	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
YP_002344397.1	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
YP_002344398.1	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
YP_002344399.1	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
YP_002344400.1	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
YP_002344401.1	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
YP_002344402.1	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
YP_002344403.1	catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis
YP_002344404.1	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
YP_002344405.1	Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr)
YP_002344406.1	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
YP_002344407.1	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
YP_002344408.1	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
YP_002344409.1	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
YP_002344410.1	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
YP_002344411.1	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
YP_002344412.1	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
YP_002344413.1	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
YP_002344414.1	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
YP_002344415.1	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
YP_002344416.1	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
YP_002344417.1	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
YP_002344418.1	catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde
YP_002344419.1	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
YP_002344420.1	Original (2000) note: Cj1025c, unknown, len: 149 aa; no Hp match. Functional classification - Unknown
YP_002344421.1	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
YP_002344422.1	negatively supercoils closed circular double-stranded DNA
YP_002344423.1	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
YP_002344424.1	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
YP_002344425.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_002344426.1	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
YP_002344427.1	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
YP_002344428.1	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
YP_002344429.1	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide
YP_002344430.1	Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate
YP_002344431.1	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
YP_002344432.1	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
YP_002344433.1	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
YP_002344434.1	UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase; involved in cell wall formation; inner membrane-associated; last step of peptidoglycan synthesis
YP_002344435.1	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
YP_002344436.1	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
YP_002344437.1	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
YP_002344438.1	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
YP_002344439.1	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
YP_002344440.1	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
YP_002344441.1	catalyzes the adenylation of ThiS which is involved in the formation of 5-methyl-4-(beta-hydroxyethyl)thiazole phosphate
YP_002344442.1	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
YP_002344443.1	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.
YP_002344444.1	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
YP_002344445.1	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
YP_002344446.1	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
YP_002344447.1	MutS2; MutS-II; involved in blocking homologous and homeologous recombination; has ATPase activity stimulated by recombination intermediates; inhibits DNA strand exchange
YP_002344448.1	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
YP_002344449.1	Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis
YP_002344450.1	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
YP_002344451.1	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
YP_002344452.1	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
YP_002344453.1	catalyzes the synthesis of xanthosine monophosphate by the NAD+ dependent oxidation of inosine monophosphate
YP_002344454.1	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
YP_002344455.1	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
YP_002344456.1	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
YP_002344457.1	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
YP_002344458.1	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
YP_002344459.1	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
YP_002344460.1	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
YP_002344461.1	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
YP_002344462.1	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
YP_002344463.1	binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21
YP_002344464.1	binds to single stranded DNA and may facilitate the binding and interaction of other proteins to DNA
YP_002344465.1	binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit
YP_002344466.1	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
YP_002344467.1	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
YP_002344468.1	binds to flagellin and appears to stabilize flagellin during flagella assembly
YP_002344469.1	catalyzes the formation of L-proline from pyrroline-5-carboxylate
YP_002344470.1	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
YP_002344471.1	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
YP_002344472.1	Original (2000) note: Cj1079, probable periplasmic protein, len: 150 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins
YP_002344473.1	catalyzes the formation of uroporphyrinogen-III from hydroxymethylbilane; functions in tetrapyrrole and heme biosynthesis
YP_002344474.1	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
YP_002344475.1	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
YP_002344476.1	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
YP_002344477.1	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
YP_002344478.1	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
YP_002344479.1	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
YP_002344480.1	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
YP_002344481.1	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
YP_002344482.1	Original (2000) note: Cj1089c, unknown, len: 65 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown
YP_002344483.1	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
YP_002344484.1	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
YP_002344485.1	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
YP_002344486.1	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
YP_002344487.1	member of preprotein translocase; forms a heterotrimer with SecD and SecF; links the SecD/SecF/YajC/YidC complex with the SecY/SecE/SecG complex
YP_002344488.1	Transfers the fatty acyl group on membrane lipoproteins
YP_002344489.1	catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase
YP_002344490.1	involved in the import of serine and threonine coupled with the import of sodium
YP_002344491.1	catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis
YP_002344492.1	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
YP_002344493.1	Original (2000) note: Cj1100, unknown, len: 145 aa; 34.7% identity to HP0469. Functional classification -Conserved hypothetical proteins
YP_002344494.1	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
YP_002344495.1	catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs
YP_002344496.1	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
YP_002344497.1	catalyzes the phosphorylation of 4-diphosphocytidyl-2-C-methyl-D-erythritol in the nonmevalonate pathway of isoprenoid biosynthesis
YP_002344498.1	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
YP_002344499.1	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
YP_002344500.1	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
YP_002344501.1	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
YP_002344502.1	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
YP_002344503.1	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
YP_002344504.1	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
YP_002344505.1	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
YP_002344506.1	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
YP_002344507.1	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
YP_002344508.1	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
YP_002344509.1	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
YP_002344510.1	methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype
YP_002344511.1	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
YP_002344512.1	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
YP_002344513.1	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
YP_002344514.1	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
YP_002344515.1	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
YP_002344516.1	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
YP_002344517.1	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
YP_002344518.1	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
YP_002344519.1	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
YP_002344520.1	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
YP_002344521.1	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
YP_002344522.1	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
YP_002344523.1	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
YP_002344524.1	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
YP_002344525.1	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
YP_002344526.1	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
YP_002344527.1	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
YP_002344528.1	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
YP_002344529.1	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
YP_002344530.1	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
YP_002344531.1	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
YP_002344532.1	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
YP_002344533.1	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
YP_002344534.1	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
YP_002344535.1	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
YP_002344536.1	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
YP_002344537.1	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
YP_002344538.1	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
YP_002344539.1	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
YP_002344540.1	catalyzes the isomerization of sedoheptulose 7-phosphate to D-glycero-D-manno-heptose 7-phosphate
YP_002344541.1	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
YP_002344542.1	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
YP_002344543.1	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
YP_002344544.1	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
YP_002344545.1	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
YP_002344546.1	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
YP_002344547.1	An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes
YP_002344548.1	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
YP_002344549.1	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
YP_002344550.1	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
YP_002344551.1	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
YP_002344552.1	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
YP_002344553.1	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
YP_002344554.1	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
YP_002344555.1	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
YP_002344556.1	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
YP_002344557.1	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
YP_002344558.1	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
YP_002344559.1	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
YP_002344560.1	Original (2000) note: Cj1169c, probable periplasmic protein, len: 75 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins
YP_002344561.1	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
YP_002344562.1	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
YP_002344563.1	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
YP_002344564.1	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
YP_002344565.1	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
YP_002344566.1	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
YP_002344567.1	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
YP_002344568.1	Essential for recycling GMP and indirectly, cGMP
YP_002344569.1	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
YP_002344570.1	FliR, with proteins FliP and FliQ, forms the core of the central channel in the flagella export apparatus
YP_002344571.1	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
YP_002344572.1	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
YP_002344573.1	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
YP_002344574.1	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
YP_002344575.1	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
YP_002344576.1	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
YP_002344577.1	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
YP_002344578.1	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
YP_002344579.1	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
YP_002344580.1	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
YP_002344581.1	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
YP_002344582.1	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
YP_002344583.1	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
YP_002344584.1	Original (2000) note: Cj1193c, probable periplasmic protein, len: 268 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins
YP_002344585.1	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
YP_002344586.1	Catalyzes the reversible hydrolysis of the amide bond within dihydroorotate. This metabolic intermediate is required for the biosynthesis of pyrimidine nucleotides
YP_002344587.1	NAD(P)+; catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate
YP_002344588.1	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
YP_002344589.1	catalyzes the hydrolysis of S-ribosylhomocysteine to homocysteine and autoinducer-2
YP_002344590.1	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
YP_002344591.1	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
YP_002344592.1	catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine to form methionine
YP_002344593.1	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
YP_002344594.1	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
YP_002344595.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit A is part of the membrane proton channel F0
YP_002344596.1	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
YP_002344597.1	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
YP_002344598.1	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
YP_002344599.1	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
YP_002344600.1	protein from Staphylococcus aureus has phosphodiesterase activity against 2'-3'-cAMP and 2'-3'-cGMP
YP_002344601.1	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
YP_002344602.1	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
YP_002344603.1	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
YP_002344604.1	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
YP_002344605.1	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
YP_002344606.1	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
YP_002344607.1	Original (2000) note: Cj1216c, unknown, len: 67 aa; no Hp match. Functional classification - Unknown
YP_002344608.1	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
YP_002344609.1	catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine
YP_002344610.1	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
YP_002344611.1	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
YP_002344612.1	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
YP_002344613.1	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
YP_002344614.1	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
YP_002344615.1	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
YP_002344616.1	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
YP_002344617.1	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
YP_002344618.1	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
YP_002344619.1	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
YP_002344620.1	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
YP_002344621.1	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
YP_002344622.1	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
YP_002344623.1	Original (2000) note: Cj1232, unknown, len: 110 aa; no Hp match. Lys-rich. Functional classification -Unknown
YP_002344624.1	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
YP_002344625.1	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
YP_002344626.1	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
YP_002344627.1	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
YP_002344628.1	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
YP_002344629.1	involved in the de novo synthesis of pyridoxine (Vitamin B6)
YP_002344630.1	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)
YP_002344631.1	Original (2000) note: Cj1240c, probable periplasmic protein, len: 200 aa; no Hp match. Functional classification - Miscellaneous periplasmic proteins
YP_002344632.1	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
YP_002344633.1	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
YP_002344634.1	catalyzes the formation of coproporphyrinogen from uroporphyrinogen III
YP_002344635.1	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
YP_002344636.1	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
YP_002344637.1	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
YP_002344638.1	Original (2000) note: Cj1247c, unknown, len: 164 aa; 27.1% identity to HP0820. Functional classification -Conserved hypothetical proteins
YP_002344639.1	contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway
YP_002344640.1	Original (2000) note: Cj1249, unknown, len: 486 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown
YP_002344641.1	catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis
YP_002344642.1	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
YP_002344643.1	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
YP_002344644.1	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
YP_002344645.1	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
YP_002344646.1	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
YP_002344647.1	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
YP_002344648.1	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
YP_002344649.1	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
YP_002344650.1	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
YP_002344651.1	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
YP_002344652.1	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
YP_002344653.1	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
YP_002344654.1	involved in a recombinational process of DNA repair, independent of the recBC complex
YP_002344655.1	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
YP_002344656.1	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
YP_002344657.1	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
YP_002344658.1	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
YP_002344659.1	catalyzes the formation of 5-methylaminomethyl-2-thiouridine in position 34 of the anticodon of tRNA molecules
YP_002344660.1	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
YP_002344661.1	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
YP_002344662.1	catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr)
YP_002344663.1	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
YP_002344664.1	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
YP_002344665.1	Catalyzes the phosphorylation of UMP to UDP
YP_002344666.1	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
YP_002344667.1	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
YP_002344668.1	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
YP_002344669.1	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
YP_002344670.1	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
YP_002344671.1	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
YP_002344672.1	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
YP_002344673.1	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
YP_002344674.1	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
YP_002344675.1	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
YP_002344676.1	Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate
YP_002344677.1	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
YP_002344678.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_002344679.1	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
YP_002344680.1	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
YP_002344681.1	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
YP_002344682.1	Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis
YP_002344683.1	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
YP_002344684.1	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
YP_002344685.1	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
YP_002344688.1	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
YP_002344689.1	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
YP_002344690.1	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
YP_002344691.1	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
YP_002344692.1	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
YP_002344693.1	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
YP_002344694.1	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
YP_002344695.1	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
YP_002344696.1	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
YP_002344697.1	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
YP_002344698.1	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
YP_002344699.1	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
YP_002344700.1	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
YP_002344701.1	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
YP_002344702.1	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
YP_002344703.1	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
YP_002344704.1	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
YP_002344705.1	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
YP_002344706.1	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
YP_002344707.1	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
YP_002344708.1	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
YP_002344709.1	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
YP_002344710.1	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
YP_002344714.1	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
YP_002344715.1	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
YP_002344716.1	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
YP_002344717.1	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
YP_002344718.1	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
YP_002344719.1	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
YP_002344720.1	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
YP_002344721.1	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
YP_002344722.1	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
YP_002344723.1	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
YP_002344724.1	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
YP_002344725.1	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
YP_002344726.1	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
YP_002344727.1	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
YP_002344728.1	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
YP_002344729.1	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
YP_002344730.1	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
YP_002344731.1	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
YP_002344732.1	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
YP_002344733.1	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
YP_002344734.1	catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate
YP_002344735.1	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
YP_002344736.1	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
YP_002344737.1	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
YP_002344738.1	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
YP_002344739.1	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
YP_002344740.1	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
YP_002344741.1	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
YP_002344742.1	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
YP_002344743.1	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
YP_002344744.1	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
YP_002344745.1	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
YP_002344746.1	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
YP_002344747.1	catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate
YP_002344749.1	Original (2000) note: Cj1361c, unknown, len: 150 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown
YP_002344750.1	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
YP_002344751.1	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
YP_002344752.1	class II family (does not require metal); tetrameric enzyme; fumarase C; reversibly converts (S)-malate to fumarate and water; functions in the TCA cycle
YP_002344753.1	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
YP_002344754.1	Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source
YP_002344755.1	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
YP_002344756.1	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
YP_002344757.1	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
YP_002344758.1	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
YP_002344759.1	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
YP_002344760.1	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
YP_002344761.1	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
YP_002344762.1	HAM1-like protein; Rec-dependent growth; RgdB; yggV; it is suspected that this protein functions to remove misincorporated bases such as xanthine or hypoxanthine
YP_002344763.1	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
YP_002344764.1	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
YP_002344765.1	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
YP_002344766.1	catalyzes the formation of selenocysteinyl-tRNA(Sec) from seryl-tRNA(Sec) and L-selenophosphate in selenoprotein biosynthesis
YP_002344767.1	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
YP_002344768.1	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
YP_002344769.1	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
YP_002344770.1	An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group
YP_002344771.1	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
YP_002344772.1	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
YP_002344773.1	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
YP_002344774.1	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
YP_002344775.1	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
YP_002344776.1	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
YP_002344777.1	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
YP_002344778.1	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
YP_002344779.1	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide
YP_002344780.1	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
YP_002344781.1	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
YP_002344782.1	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
YP_002344783.1	NADH; Catalyzes a key regulatory step in fatty acid biosynthesis
YP_002344784.1	Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate
YP_002344785.1	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway
YP_002344786.1	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
YP_002344787.1	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
YP_002344788.1	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
YP_002344789.1	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
YP_002344790.1	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
YP_002344791.1	interacts with the cytoplasmic MS ring of the basal body and may act to stabilize the MotAB complexes which surround the MS ring
YP_002344792.1	Catalyzes the formation of holo-ACP, which mediates the essential transfer of acyl fatty acid intermediates during the biosynthesis of fatty acids and lipids
YP_002344793.1	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
YP_002344794.1	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
YP_002344795.1	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
YP_002344796.1	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
YP_002344797.1	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
YP_002344798.1	converts ATP and adenylyl sulfate to ADP and 3'-phosphoadenylyl sulfate; in Escherichia coli this enzyme functions in cysteine biosynthesis
YP_002344799.1	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
YP_002344800.1	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
YP_002344801.1	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
YP_002344802.1	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
YP_002344803.1	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
YP_002344804.1	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
YP_002344805.1	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
YP_002344806.1	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
YP_002344807.1	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
YP_002344808.1	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
YP_002344809.1	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
YP_002344810.1	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
YP_002344811.1	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
YP_002344812.1	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
YP_002344813.1	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
YP_002344814.1	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
YP_002344815.1	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
YP_002344816.1	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
YP_002344817.1	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
YP_002344818.1	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
YP_002344819.1	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
YP_002344820.1	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
YP_002344821.1	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
YP_002344822.1	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
YP_002344823.1	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
YP_002344824.1	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
YP_002344825.1	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
YP_002344826.1	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
YP_002344827.1	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
YP_002344828.1	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
YP_002344829.1	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
YP_002344830.1	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
YP_002344831.1	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
YP_002344832.1	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
YP_002344833.1	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
YP_002344834.1	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
YP_002344835.1	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
YP_002344836.1	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
YP_002344837.1	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
YP_002344838.1	Original (2000) note: Cj1456c, probable periplasmic protein, len: 104 aa; no Hp match. Contains possible N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins
YP_002344839.1	catalyzes the modification of U13 in tRNA(Glu)
YP_002344840.1	catalyzes the formation of thiamine diphosphate from thiamine phosphate ant ATP
YP_002344841.1	Original (2000) note: Cj1459, unknown, len: 357 aa; 24.8% identity to HP0468. Functional classification -Conserved hypothetical proteins
YP_002344842.1	Original (2000) note: Cj1460, unknown, len: 127 aa; 41.0% identity to HP0811. Functional classification -Conserved hypothetical proteins
YP_002344843.1	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
YP_002344844.1	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
YP_002344845.1	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
YP_002344846.1	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
YP_002344847.1	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
YP_002344848.1	with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook
YP_002344849.1	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
YP_002344850.1	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
YP_002344851.1	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
YP_002344852.1	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
YP_002344853.1	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
YP_002344854.1	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
YP_002344855.1	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
YP_002344856.1	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
YP_002344857.1	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
YP_002344858.1	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
YP_002344859.1	forms a direct contact with the tRNA during translation
YP_002344860.1	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit
YP_002344861.1	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
YP_002344862.1	Original (2000) note: Cj1482c, unknown, len: 788 aa; 29.5% identity to HP1089. Functional classification -Conserved hypothetical proteins
YP_002344863.1	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
YP_002344864.1	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
YP_002344865.1	Original (2000) note: Cj1485c, probable periplasmic protein, len: 33 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins
YP_002344866.1	Original (2000) note: Cj1486c, probable periplasmic protein, len: 73 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins
YP_002344867.1	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
YP_002344868.1	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
YP_002344869.1	CcoO; FixO
YP_002344870.1	CcoN; FixN
YP_002344871.1	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
YP_002344872.1	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
YP_002344873.1	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
YP_002344874.1	catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers
YP_002344875.1	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
YP_002344876.1	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
YP_002344877.1	Original (2000) note: Cj1497c, unknown, len: 142 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown
YP_002344878.1	catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis
YP_002344879.1	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
YP_002344880.1	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
YP_002344881.1	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
YP_002344882.1	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
YP_002344883.1	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
YP_002344884.1	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
YP_002344885.1	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
YP_002344886.1	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
YP_002344887.1	involved in the production or activity of formate dehydrogenase-H which is active when nitrate is not present during anaerobic growth
YP_002344888.1	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
YP_002344889.1	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
YP_002344890.1	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
YP_002344891.1	Original (2000) note: Cj1513c, possible periplasmic protein, len: 63 aa; no Hp match. Contains possible N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins
YP_002344892.1	Original (2000) note: Cj1514c, unknown, len: 237 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown
YP_002344893.1	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
YP_002344894.1	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
YP_002344895.1	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
YP_002344896.1	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
YP_002344897.1	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
YP_002344898.1	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
YP_002344899.1	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
YP_002344900.1	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
YP_002344901.1	catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis
YP_002344902.1	catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis
YP_002344903.1	involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate
YP_002344904.1	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
YP_002344905.1	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
YP_002344906.1	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
YP_002344907.1	catalyzes the formation of D-fructose 6-phosphate from D-glucose 6-phosphate
YP_002344908.1	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
YP_002344909.1	Acs; catalyzes the conversion of acetate and CoA to acetyl-CoA
YP_002344910.1	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
YP_002344911.1	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
YP_002344912.1	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
YP_002344913.1	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
YP_002344914.1	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
YP_002344915.1	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
YP_002344916.1	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
YP_002344917.1	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
YP_002344918.1	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
YP_002344919.1	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
YP_002344920.1	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
YP_002344921.1	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
YP_002344922.1	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
YP_002344923.1	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
YP_002344924.1	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
YP_002344925.1	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
YP_002344926.1	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
YP_002344927.1	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
YP_002344932.1	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
YP_002344933.1	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
YP_002344934.1	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
YP_002344935.1	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
YP_002344936.1	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
YP_002344937.1	Catalyzes the transfer of electrons from NADH to ubiquinone
YP_002344938.1	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
YP_002344939.1	Catalyzes the transfer of electrons from NADH to quinone
YP_002344940.1	Catalyzes the transfer of electrons from NADH to quinone
YP_002344941.1	Catalyzes the transfer of electrons from NADH to quinone
YP_002344942.1	Catalyzes the transfer of electrons from NADH to ubiquinone
YP_002344943.1	Original (2000) note: Cj1574c, unknown, len: 230 aa; 26.5% identity to HP1265. Functional classification -Conserved hypothetical proteins
YP_002344944.1	Original (2000) note: Cj1575c, unknown, len: 75 aa; 52.0% identity to HP1264. Functional classification -Conserved hypothetical proteins
YP_002344945.1	Catalyzes the transfer of electrons from NADH to quinone
YP_002344946.1	Catalyzes the transfer of electrons from NADH to ubiquinone
YP_002344947.1	The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen
YP_002344948.1	Catalyzes the transfer of electrons from NADH to ubiquinone
YP_002344949.1	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
YP_002344950.1	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
YP_002344951.1	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
YP_002344952.1	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
YP_002344953.1	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
YP_002344954.1	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
YP_002344955.1	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
YP_002344956.1	efflux pump for the antibacterial peptide microcin J25
YP_002344957.1	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
YP_002344958.1	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
YP_002344959.1	stimulates the activities of the other two initiation factors, IF-2 and IF-3
YP_002344960.1	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
YP_002344961.1	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
YP_002344962.1	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
YP_002344963.1	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
YP_002344964.1	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
YP_002344965.1	is a component of the macrolide binding site in the peptidyl transferase center
YP_002344966.1	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
YP_002344967.1	catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer
YP_002344968.1	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
YP_002344969.1	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
YP_002344970.1	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
YP_002344971.1	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
YP_002344972.1	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
YP_002344973.1	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
YP_002344974.1	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
YP_002344975.1	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
YP_002344976.1	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
YP_002344977.1	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
YP_002344978.1	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
YP_002344979.1	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
YP_002344980.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase
YP_002344981.1	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
YP_002344982.1	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
YP_002344983.1	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
YP_002344984.1	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
YP_002344985.1	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
YP_002344986.1	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
YP_002344987.1	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
YP_002344988.1	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
YP_002344989.1	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
YP_002344990.1	Original (2000) note: Cj1621, possible periplasmic protein, len: 250 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins
YP_002344991.1	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
YP_002344992.1	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
YP_002344993.1	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
YP_002344994.1	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
YP_002344995.1	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
YP_002344996.1	Original (2000) note: Cj1627c, unknown, len: 247 aa; no Hp match; Updated (2006) note: Similar to hypothetical proteins from other bacteria. Functional classification -Unknown
YP_002344997.1	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
YP_002344998.1	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
YP_002344999.1	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
YP_002345000.1	Original (2000) note: Cj1631c, unknown, len: 289 aa; no Hp match. Contains PS00018 EF-hand calcium-binding domain. Functional classification - Unknown
YP_002345001.1	Original (2000) note: Cj1632c, possible periplasmic protein, len: 53 aa; no Hp match. Contains possible N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins
YP_002345002.1	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
YP_002345003.1	catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis
YP_002345004.1	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
YP_002345005.1	An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids
YP_002345006.1	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
YP_002345007.1	synthesizes RNA primers at the replication forks
YP_002345008.1	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
YP_002345009.1	Original (2000) note: Cj1640, unknown, len: 183 aa; 27.7% identity to HP1493. Functional classification -Conserved hypothetical proteins
YP_002345010.1	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
YP_002345011.1	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
YP_002345012.1	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
YP_002345013.1	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
YP_002345014.1	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
YP_002345015.1	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
YP_002345016.1	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
YP_002345017.1	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
YP_002345018.1	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
YP_002345019.1	Original (2000) note: Cj1650, unknown, len: 166 aa; 30.7% identity to HP1076. Functional classification -Conserved hypothetical proteins
YP_002345020.1	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
YP_002345021.1	converts L-glutamate to D-glutamate, a component of peptidoglycan
YP_002345022.1	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
YP_002345023.1	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
YP_002345024.1	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
YP_002345025.1	Original (2000) note: Cj1656c, unknown, len: 180 aa; no Hp match. Functional classification - Unknown
YP_002345026.1	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
YP_002345027.1	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
YP_002345028.1	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
YP_002345029.1	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
YP_002345030.1	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
YP_002345031.1	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
YP_002345032.1	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
YP_002345033.1	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
YP_002345034.1	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
YP_002345036.1	Original (2000) note: Cj1668c, probable periplasmic protein, len: 138 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins
YP_002345037.1	catalyzes the formation of a phosphodiester at the site of a single-strand break in duplex DNA
YP_002345038.1	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
YP_002345039.1	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
YP_002345040.1	enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis
YP_002345041.1	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
YP_002345042.1	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
YP_002345043.1	with proteins FliP and FliR forms the core of the central channel in the flagella export apparatus
YP_002345044.1	catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis
YP_002345045.1	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
YP_002345046.1	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
YP_002345047.1	Original (2000) note: Cj1680c, probable periplasmic protein, len: 255 aa; no Hp match. Contains probable N-terminal signal sequence. Functional classification -Miscellaneous periplasmic proteins
YP_002345048.1	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
YP_002345049.1	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
YP_002345050.1	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
YP_002345051.1	catalyzes the formation of biotin from dethiobiotin and sulfur
YP_002345052.1	catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity
YP_002345053.1	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
YP_002345054.1	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
YP_002345055.1	late assembly protein
YP_002345056.1	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
YP_002345057.1	binds 5S rRNA along with protein L5 and L25
YP_002345058.1	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
YP_002345059.1	binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YP_002345060.1	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
YP_002345061.1	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
YP_002345062.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_002345063.1	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase
YP_002345064.1	primary binding protein; helps mediate assembly; involved in translation fidelity
YP_002345065.1	one of the stabilizing components for the large ribosomal subunit
YP_002345066.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_002345067.1	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
YP_002345068.1	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
YP_002345069.1	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_002345070.1	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
YP_002345071.1	binds third domain of 23S rRNA and protein L29; part of exit tunnel
YP_002345072.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_002345073.1	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
YP_002345074.1	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
YP_002345075.1	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
YP_002345076.1	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
YP_002345077.1	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
YP_002345078.1	Original (2000) note: Cj1712, unknown, len: 178 aa; 40.9% identity to HP1530 (called purine nucleoside phosphorylase (punB). Functional classification -Conserved hypothetical proteins
YP_002345079.1	23S rRNA m2A2503 methyltransferase; methylates the C2 position of the A2530 nucleotide in 23S rRNA; may be involved in antibiotic resistance
YP_002345080.1	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
YP_002345081.1	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
YP_002345082.1	catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D
YP_002345083.1	dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate
YP_002345084.1	catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis
YP_002345085.1	catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis
YP_002345086.1	Original (2000) note: Cj1720, unknown, len: 209 aa; no Hp match. Functional classification - Unknown
YP_002345087.1	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
YP_002345090.1	NADPH-dependent; catalyzes the reduction of 7-cyano-7-deazaguanine to 7-aminomethyl-7-deazaguanine in queuosine biosynthesis
YP_002345091.1	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
YP_002345092.1	catalyzes the formation of O-succinyl-L-homoserine from succinyl-CoA and L-homoserine in methionine biosynthesis
YP_002345093.1	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
YP_002345095.1	the hook connects flagellar basal body to the flagellar filament
YP_002345096.1	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