Table 1.

List of H. pylori J99 genes and corresponding 26695 orthologs with putative functional assignmentsa

Gene no. in:Gene nameFunction
J9926695
Amino acid biosynthesis
 General
  2060220Aminotransferase
  5680624Aminotransferase
  6320696Hydantoin utilization
  6330695Hydantoin utilization
  6730736Aminotransferase
  9760405Aminotransferase
 Aromatic amino acid family
  1220134aroFPhospho-2-dehydro-3-deoxyheptonate aldolase
  1450157aroKShikamate kinase I
  2680283aroB3-Dehydroquinate synthase
  3861038aroD3-Dehydroquinate dehydratase
  6080663aroCChorismate synthase
  9800401aroA3-Phosphoshikimate 1-carboxyvinyl transferase
  11701249aroEShikimate 5-dehydrogenase
  11981277trpATryptophan synthase alpha chain
  11991278trpBTryptophan synthase beta chain
  12001279trpCIndole-3-glycerol phosphate synthase
  12011280trpDAnthranilate phosphoribosyltransferase
  12021281trpGAnthranilate synthase component II
  12031282trpEAnthranilate synthase component I
  12941380tyrAPrephenate dehydrogenase
 Aspartate family
  900098thrCThreonine synthase
  980106metBCystathionine gamma-synthase
  1980212dapESuccinyl-diaminopimelate desuccinylase
  2750290lysADiaminopimelate decarboxylase
  3751050thrBHomoserine kinase
  4101013dapADihydrodipicolinate synthase
  4600510dapBDihydrodipicolinate reductase
  5130566dapFDiaminopimelate epimerase
  5700626dapD2,3,4,5-Tetrahydropyridine-2-carboxylate-N-succinyltransferase
  5940649aspAAspartate ammonia-lyase
  6150672aspBAspartate aminotransferase
  7610822homHomoserine dehydrogenase
  11141189asdAspartate-semialdehyde dehydrogenase
  11501229lysCAspartokinase 2 alpha and beta subunits
 Glutamate family
  4610512glnAGlutamine synthetase
  10010380gdhAGlutamate dehydrogenase
  10851158proCPyrroline-5-carboxylate reductase
 Pyruvate family
  3130330ilvCKetol-acid reductoisomerase
  13611468ilvEBranched-chain amino acid aminotransferase
 Serine family
  990107cysKCysteine synthase
  1710183glyASerine hydroxymethyltransferase
  5970652serBPhosphoserine phosphatase
  9840397serAPhosphoglycerate dehydrogenase
  11331210cysESerine acetyltransferase
Biosynthesis of cofactors, prosthetic groups, and carriers
 Biotin
  250029bioDDethiobiotin synthetase
  5450598bioF8-Amino-7-oxononanoate synthase
  9100976bioAAdenosylmethionine-8-amino-7-oxononanoate aminotransferase
  10681140Biotin activation protein
  12981406bioBBiotin synthetase
 Folic acid
  2780293pabBp-Aminobenzoate synthetase
  3881036folK7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase
  5240577folDMethylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase
  8620928folEGTP cyclohydrolase I
  8630928folEGTP cyclohydrolase I
  11531232folPDihydropteroate synthase
  14031510folBDihydroneopterin aldolase
  14541545folCFolylpolyglutamate synthase
 Heme and porphyrin
  1500163hemBδ-Aminolevulinic acid dehydratase
  2220237hemCPorphobilinogen deaminase
  2240239hemAGlutamyl-tRNA reductase
  2910306hemLGlutamate-1-semialdehyde-2,1-aminomutase
  5510604hemEUroporphyrinogen decarboxylase
  6100665hemNOxygen-independent coproporphyrinogen III oxidase
  10000381hemGProtoporphyrinogen oxidase
  10050376hemHFerrochelatase
  11451224hemDUroporphyrinogen III synthase
  11471226hemNOxygen-independent coproporphyrinogen III oxidase
 Menaquinone and ubiquinone
  2250240ispBOctaprenyl-diphosphate synthase
  8640929ispAGeranyltransferase
  12781360ubiA4-Hydroxybenzoate octaprenyltransferase
  13691476ubiDOctaprenyl-4-hydroxybenzoate carboxy-lyase
  13761483ubiEUbiquinone/menaquinone biosynthesis methyltransferase
 Molybdopterin
  1580172moeAMolybdopterin biosynthesis protein
  7050768moaAMolybdopterin cofactor biosynthetic protein
  7060769mobAMolybdopterin-guanine dinucleotide biosynthesis protein A
  7340798moaCMolybdenum cofactor biosynthesis protein C
  7350799mogMolybdopterin biosynthesis protein
  7360800moaEMolybdopterin-converting factor, subunit 2
  7370801moaDMolybdopterin-converting factor, subunit 1
  7500814moeBMolybdopterin-synthase sulfurylase
 Pantothenate
  60006panCPantoate-β-alanine ligase
  300034panDAspartate-1-decarboxylase
  3671058panB3-Methyl-2-oxobutanoate hydroxymethyltransferase
  7790841dfpPantothenate metabolism flavoprotein
 Pyridoxine
  3280354dxs1-Deoxyxylulose-5-phosphate synthase
  14891582pdxJPyridoxal phosphate synthetase
  14901583pdxAPyridoxal phosphate biosynthetic protein A
 Riboflavin
  20002ribERiboflavin synthase beta chain
  3381087ribFRiboflavin kinase
  7380802ribAGTP cyclohydrolase II
  7400804ribBAGTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase
  13981505ribDRiboflavin-specific deaminase
  14821574ribCRiboflavin synthase alpha chain
 Thioredoxin, glutaredoxin, and glutathione
  7630824trxAThioredoxin
  7640825trxBThioredoxin reductase
  10461118ggtGamma-glutamyl transpeptidase
  10911164trxBThioredoxin reductase
  13511458Thioredoxin
 Thiamine
  7810843thiEThiamine phosphate pyrophosphorylase
  7820844thiDPhosphomethylpyrimidine kinase
  7830845thiMHydroxyethylthiazole kinase
 Pyridine nucleotides
  3120329nadENH3-dependent NAD+ synthetase
  12731355nadCNicotinate-nucleotide pyrophosphorylase
  12741356nadAQuinolinate synthetase
Cell envelope
 Membranes and porins
  70009Outer membrane protein
  210025Outer membrane protein
  730078Outer membrane protein
0079
  1170127Outer membrane protein
  1950209Outer membrane protein
  2120227Outer membrane protein
  2140229hopAOuter membrane protein—porin
  2370252Outer membrane protein
  2380253, 0254Outer membrane protein
  3070324Outer membrane protein
  3421083Outer membrane protein
  3591066Outer membrane protein
  4240472Outer membrane protein
  4290477Outer membrane protein
  4380486Outer membrane protein
  4390487Outer membrane protein
  4560506Outer membrane protein
  5140567Inner membrane protein
  5810638Outer membrane protein
  6000655Outer membrane protein
  6140671Outer membrane protein
  6340694Outer membrane protein
  6450706hopEOuter membrane protein—porin
  6490710Outer membrane protein
  6590722Outer membrane protein
  6620725Outer membrane protein
  6630726Outer membrane protein
  7190782Outer membrane protein
  7250788Outer membrane protein
  7320796Outer membrane protein
  7770839Outer membrane protein
  8100876frpBIron-regulated outer membrane protein
  8331243babBOuter membrane protein—adhesin
  8480912hopCOuter membrane protein—porin
  8490913hopBOuter membrane protein—porin
  8500914Outer membrane protein
  8510915, 0916frpBIron-regulated outer membrane protein
  8570923Outer membrane protein
  870Outer membrane protein
  10080373Outer membrane protein
  10220358Outer membrane protein
  10341107Outer membrane protein
  10401113Outer membrane protein
  10541125Outer membrane protein
  10831156Outer membrane protein
  10841157Outer membrane protein
  10941167Outer membrane protein
  11031177Outer membrane function
  11381215, 1216impRole in outer membrane permeability
  11640896babAOuter membrane protein—adhesin
  12611342Outer membrane protein
  13431450Inner membrane protein
  13461453Outer membrane protein
  13491456lpp20Conserved lipoprotein
  13601467Outer membrane protein
  13621469Outer membrane protein
  13941501Outer membrane protein
  14051512frpBIron-regulated outer membrane protein
  14321395Outer membrane protein
  14721564Outer membrane protein
  14791571Outer membrane protein
 Murein sacculus and peptidoglycan
  4450493mraYPhospho-N-acetylmuramoyl-pentapeptide-transferase
  4460494murDUDP-N-acetylmuramoylalanine-d-glutamate ligase
  4960549murIGlutamate racemase
  5440597Penicillin-binding protein
  5670623murCUDP-N-acetylmuramate-alanine ligase
  5900645Lytic murein transglycosylase
  5930648murAUDP-N-acetylglucosamine enolpyruvyltransferase
  6750738ddld-Alanine–d-alanine ligase
  6770740murFd-Alanyl–d-alanine-adding enzyme
  7090772amiAProbableN-acetylmuramoyl-l-alanine amidase
  8760941alrAlanine racemase, biosynthetic
  10821155murGUDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenoln-acetylglucosaminetransferase
  13131418murBUDP-N-acetylenolpyruvoyl glucosamine reductase
  13871494murEUDP-N-acetylmuramyl-tripeptide synthetase
  14641556Penicillin-binding protein
  14731565Penicillin-binding protein
 Surface polysaccharides, lipopolysaccharides, and antigens
  30003kdsA3-Deoxy-d-manno-octulosonic acid 8-phosphate synthase
  370043manA/manCPhosphomannose isomerase/GDP-mannose pyrophosphorylase
  380044GmdGDP-d-mannose dehydratase
  390045Sugar nucleotide biosynthesis
  700075glmMPhosphoglucosamine mutase
  860093, 0094α-(1,2)-Fucosyltransferase
  1470159Lipopolysaccharide biosynthesis protein
  1660178neuBSialic acid synthase
  1820196lpxDUDP-3-O-[3-hydroxymyristoyl] glucosamine N-acetyltransferase
  1940208Lipopolysaccharide biosynthesis protein
  2150230kdsB3-Deoxy-manno-octulosonate cytidylyltransferase
  2640279waaCLipopolysaccharide heptosyltransferase-1
  2650280waaMLipid A biosynthesis acyltransferase
  3090326neuAAcylneuraminate cytidylyltransferase
  3110328lpxKTetraacyldisaccharide-1-p 4′-kinase
  3731052lpxCUDP-3-O-[3-hydroxymyristoyl]-N-acetylglucosamine deacetylase
  562Lipopolysaccharide biosynthesis protein
  5630619Lipopolysaccharide biosynthesis protein
  5960651fucTα-(1,3)-Fucosyltransferase
  6200679Lipopolysaccharide biosynthesis protein
  7410805Lipopolysaccharide biosynthesis protein
  7650826Lipopolysaccharide biosynthesis protein
  7780840Sugar nucleotide biosynthesis protein
  7910857gmhAPhosphoheptose isomerase
  7920858waaEADP-d-glycero-d-mannoheptose synthase
  7930859gmhDADP-l-glycero-d-mannoheptose-6-epimerase
  8010867lpxBLipid-A-disaccharide synthase
  820Lipopolysaccharide biosynthesis protein
  8910957waaA3-Deoxy-d-manno-octulosonic-acid transferase
  9630421Polysaccharide biosynthesis protein
  10020379fucUα-(1,3)-Fucosyltransferase
  10150366Sugar nucleotide biosynthesis
  10200360galEUDP-glucose 4-epimerase
  10311105Lipopolysaccharide biosynthesis protein
  1032Lipopolysaccharide biosynthesis protein
  11161191waaFADP-heptose-lipopolysaccharide heptosyltransferase II
  11961275manBPhosphomannomutase
  12891375lpxAUDP-N-acetylglucosamine acyltransferase
  13111416Lipopolysaccharide biosynthesis protein
  13681475kdtBLipopolysaccharide core biosynthesis protein
  14881581wecAUndecaprenyl-phosphate-α-N-acetylglucosaminyltransferase
 Surface structures
  1070115flaBFlagellin B
  1590173fliRFlagellar biosynthesis protein
  2170232Motility protein
  2310246flgIFlagellar P-ring protein
  2800295flgLFlagellar hook-associated protein 3 (hap3)
  3080325flgHFlagellar L-ring protein precursor (basal body L-ring protein)
  3100327flaGFlagellar biosynthesis protein
  3250351fliFFlagellar M-ring protein
  3260352fliGFlagellar motor switch protein
  3270353fliHFlagellar export apparatus
  3331092flgGFlagellar basal-body rod protein
  3831041flhAFlagellar biosynthesis protein
  3891035flhFFlagellar biosynthesis protein
  3931031fliMFlagellar motor switch protein
  3941030Flagellar motor switch protein
  4440492Paralogue of hpaA
  5310584fliNFlagellar motor switch protein
  5480601flaAFlagellin A
  6250684, 0685fliPFlagellar biosynthesis protein
  6880751Flagellin protein
  6890752fliDFlagellar hook-associated protein 2 (hap2)
  6900753fliSFlagellar protein
  7070770flhBFlagellar biosynthesis protein
  7330797hpaANeuraminyllactose-binding hemagglutinin precursor
  7450809fliLFlagellar biosynthesis protein
  7510815motAChemotaxis protein (motility protein a)
  7520816motBFlagellar motor protein
  8040870flgEFlagellar hook protein
  8430907Flagellar biosynthesis protein
  8440908Flagellar basal-body/rod/hook protein
  9710410Paralogue of hpaA
  10471119flgKFlagellar hook-associated protein 1 (Hap1)
  11171192Motility protein
  11951274pflAFlagellar functional protein
  13141419fliQFlagellar biosynthesis protein
  13151420fliIFlagellum-specific ATP synthase
  13551462Motility protein
  14651557fliEFlagellar hook–basal-body complex protein
  14661558flgCFlagellar basal-body rod protein
  14671559flgBFlagellar basal-body rod protein
  14831575flhBFlagellar biosynthesis protein
  14921585flgGFlagellar basal-body rod protein (distal rod protein)
Cellular processes
 General
  40004icfACarbonic anhydrase
  1610175Peptidyl-prolyl cis-transisomerase
  1830197metKS-Adenosylmethionine synthetase
  2280243napANeutrophil-activating protein A
  4660517eraGTP-binding protein
  6780741HIT family protein
  8650930surEStationary-phase protein
  9770404HIT family protein
  11121186Carbonic anhydrase
 Cell division
  3140331minDCell division inhibitor
  3150332minECell division topological specificity factor
  3351090ftsKSeptum formation protein
  6800743rodARod shape-determining protein
  9120978ftsASeptum formation protein
  9130979ftsZGTPase in circumferential ring formation
  10861159ficcAMP-induced cell filamentation protein
  12871373mreBRod shape-determining protein
  14681560rodARod shape-determining protein
 Cell killing
  2740289Vacuolating cytotoxin (VacA) paralogue
  3391086hlyAHemolysin
  5560609, 0610Vacuolating cytotoxin (VacA) paralogue
  8190887vacAVacuolating cytotoxin
  8560922Vacuolating cytotoxin (VacA) paralog
 Cag island proteins and transposable elements
  150017virB4aDNA transfer protein
  360041, 0042virB10DNA transfer protein
  4690520orf6Cag island protein
  4700521orf7Cag island protein
  4710522orf8Cag island protein
  4720523orf9Cag island protein
  4730524virD4Cag island protein, DNA transfer protein
  4740525virB11aCag island protein, DNA transfer protein
  4750526orf12Cag island protein
  4760527orf13/14Cag island protein
  4770528orf15Cag island protein
  4780529orf16Cag island protein
  4790530orf17Cag island protein
  4800531orf18Cag island protein
  4810532cagTCag island protein
  4820534cagSCag island protein
  4830535cagQCag island protein
  4840536cagPCag island protein
  4850537cagMCag island protein
  4860538cagNCag island protein
  4870539cagLCag island protein
  4880540cagICag island protein
  4890541cagHCag island protein
  4900542cagGCag island protein
  4910543cagFCag island protein
  4920544cagEDNA transfer protein (Agrobacterium VirB4 homologue)
  4930545cagDCag island protein
  4940546cagCCag island protein
  4950547cagACag island protein, cytotoxicity-associated immunodominant antigen
  826tnpBIS606 transposase
  827tnpAIS606 transposase
  917virB4bDNA transfer protein
  918virB4cDNA transfer protein
  12791361comECDNA transfer protein
  13161421virB11bDNA transfer protein
 Chaperones
  80010groEL60-kDa chaperone
  90011groES10-kDa chaperone
  1010109dnaK70-kDa chaperone
  1020110grpE24-kDa chaperone
  1960210htpG90-kDa chaperone
  4001024dnaJ2Cochaperone with DnaK
  8610927htpXStress protein
  12521332dnaJ1Cochaperone with DnaK
 Detoxification
  8090875katACatalase
  9910390tpxThiol peroxidase
  9920389sodFIron-dependent superoxide dismutase
  14711563tsaAPeroxidase
 Protein and peptide secretion
  690074lspALipoprotein signal peptidase
  1680180lntApolipoproteinN-acyltransferase
  3290355lepAGTP-binding protein
  5230576lepBSignal peptidase I
  7000763ftsYFunctional homolog of srp receptor
  7230786secAPreprotein translocase subunit
  7310795tigTrigger factor
  8890955lgtProlipoprotein diacylglyceryl transferase
  10791152ffhSignal recognition particle protein
  1126A1203AsecEPreprotein translocase subunit
  11761255secGProtein export membrane protein
  12201300secYPreprotein translocase subunit
  14491550secDProtein export membrane protein
  14501549secFProtein export membrane protein
 Phosphorus compounds
  4131010ppkPolyphosphate kinase
  5640620ppaInorganic pyrophosphatase
 Polyamine biosynthesis
  180020nspCCarboxynorspermidine decarboxylase
  7710832speESpermidine synthase
  9620422speAArginine decarboxylase
 Urea
  620067ureHUrease accessory protein
  630068ureGUrease accessory protein
  640069ureFUrease accessory protein
  650070ureEUrease accessory protein
  670072ureBUrease beta subunit
  680073ureAUrease alpha subunit
DNA replication
  100012dnaGDNA primase
  1080116topADNA topoisomerase I
  1990213gidAGlucose-inhibited division protein A
  3621063gidBGlucose-inhibited division protein B
  4520500dnaNDNA polymerase III, beta chain
  4530501gyrBDNA gyrase subunit B
  5580615ligDNA ligase
  6410701gyrADNA gyrase subunit A
  6550717dnaXDNA polymerase III subunits gamma and tau
  8470911ATP-dependent helicase
  919topATopoisomerase I
  931topATopoisomerase I
  9940387priAPrimosomal protein n′ (replication factor y)
  11521231holBDNA polymerase III subunit delta′
  11661245ssbSingle-strand binding protein
  12801362dnaBReplicative DNA helicase
  13531460dnaEDNA polymerase III, alpha chain
  13631470polADNA polymerase I
  13711478repATP-dependent DNA helicase
  14121523recGATP-dependent DNA helicase
  14171529dnaAChromosomal replication initiator protein
  14381387DNA polymerase III
  14461553pcrAATP-dependent helicase
DNA restriction, modification, recombination, and repair
  430050Type II DNA modification enzyme (methyltransferase)
  44Type II DNA modification enzyme (methyltransferase)
  45Type II DNA modification enzyme (methyltransferase)
  46Type II restriction enzyme
  840091Type II restriction enzyme
  850092Type II DNA modification enzyme (methyltransferase)
  1300142mutYA/G-specific adenine glycosylase
  1410153recARecombination protein
  164Restriction enzyme
  2090223radADNA repair protein
  2430259xseAExodeoxyribonuclease large subunit
  2440260Type II DNA modification enzyme (methyltransferase)
  2480263Type II DNA modification enzyme (methyltransferase)
  3060323Endonuclease
  3220348recJSingle-stranded-DNA-specific exonuclease
  3661059ruvBHolliday junction DNA helicase
  414hsdS1Type I restriction enzyme (specificity subunit)
  4150463hsdM1Type I restriction enzyme (modification subunit)
  4160464hsdR1Type I restriction enzyme (restriction subunit)
  4300478Type II DNA modification enzyme (methyltransferase)
  4330481Type II DNA modification enzyme (methyltransferase)
  4350483Type II DNA modification enzyme (methyltransferase)
  5320585nthEndonuclease III
  5490602Endonuclease III
  5650621mutSDNA mismatch repair protein
  6060661rnhARNase HI
  6170675Integrase-recombinase protein (xerCD family)
  6180676ogtMethylated-DNA–protein-cysteine methyltransferase
  629Type II DNA modification enzyme (methyltransferase)
  630Type II restriction enzyme
  6440705uvrAExcinuclease ABC subunit A
  726hsdSType I restriction enzyme (specificity subunit)
  756Type II DNA modification enzyme (methyltransferase)
  7600821uvrCExcinuclease ABC subunit C
  7840846hsdR2Type I restriction enzyme (restriction subunit)
  7850848, 0849hsdS2Type I restriction enzyme (specificity subunit)
  7860850hsdM2Type I restriction enzyme (modification subunit)
  8110877ruvCCrossover junction endodeoxyribonuclease
  8150883ruvAHolliday junction DNA helicase
  8460910Type II DNA modification enzyme (methyltransferase)
  8590925recRRecombination protein
  9410995Integrase/recombinase (xerCD family)
  951Integrase/recombinase (xerCD family)
  10120369Type II DNA modification enzyme (methyltransferase)
  10411114uvrBExcinuclease ABC subunit B
  10501121Type II DNA modification enzyme (methyltransferase)
  11311208M.HpyIType II DNA modification enzyme (methyltransferase)
  11491228mutTdGTP pyrophosphohydrolase
  12431323rnhBRNase HII
  12661347ungUracil-DNA glycosylase
  12711352Type II DNA modification enzyme (methyltransferase)
  1284Type II DNA modification enzyme (methyltransferase)
  12951382Endonuclease
  1296mod1Type III DNA modification enzyme (methyltransferase)
  1297res1Type III restriction enzyme
  13641471Type II restriction enzyme
  13651472Type II DNA modification enzyme (methyltransferase)
  1409Type II DNA modification enzyme (methyltransferase)
  14101521res2Type III restriction enzyme
  14111522mod2Type III DNA modification enzyme (methyltransferase)
  14151526exoAExodeoxyribonuclease
  1422hsdS3Type I restriction enzyme (specificity subunit)
  14231403hsdM3Type I restriction enzyme (modification subunit)
  14241402hsdR3Type I restriction enzyme (restriction subunit)
  14341393recNDNA repair protein
  14421366Type II restriction enzyme
Energy metabolism
 Amino acids and amines
  1200132sdaBl-Serine/l-Threonine deaminase
  2790294aimEAliphatic amidase
  5853-Hydroxyacid dehydrogenase
  6610723ansBl-Asparaginase II
  11591238Aliphatic amidase
  14271399rocFArginase
  14281398aldl-Alanine dehydrogenase
 ATP-proton motive force interconversion
  7670828atpBATP synthase F0, subunit a
  10591131atpCATP synthase F1, subunit epsilon
  10601132atpDATP synthase F1, subunit beta
  10611133atpGATP synthase F1, subunit gamma
  10621134atpAATP synthase F1, subunit alpha
  10631135atpHATP synthase F1, subunit delta
  10641136atpFATP synthase F0, subunit b
  10651137atpXATP synthase B′
  11351212atpEATP synthase F0, subunit c
 Electron transport
  400047hypEHydrogenase expression/formation protein
  480056putAProline/pyrroline-5-carboxylate dehydrogenase
  1320144fixNCytochrome oxidase (CBB3-TYPE)
  1330145fixOCytochrome oxidase (CBB3-TYPE)
  1340146fixQCytochrome oxidase (CBB3-TYPE)
  1350147fixPCytochrome oxidase (CBB3-TYPE)
  1770191frdBFumarate reductase
  1780192frdAFumarate reductase
  1790193frdCFumarate reductase
  2500265ccdACytochromec biogenesis protein
  2620277Ferredoxin
  4590509glcDGlycolate oxidase
  5740631hyaAHydrogenase, small subunit
  5750632hyaBHydrogenase, large subunit
  5760633hyaCHydrogenase, cytochrome subunit
  5770634hyaDHydrogenase expression/formation protein
  6110666glpCGlycerol-3-phosphate dehydrogenase
  8030869hypAHydrogenase expression/formation protein
  8350898hypDHydrogenase expression/formation protein
  8360899hypCHydrogenase expression/formation protein
  8370900hypBHydrogenase expression/formation protein
  8780943dadAd-Amino acid dehydrogenase
  8950961gpsAGlycerol-3-phosphate dehydrogenase (NAD+)
  9740407S/N-oxide reductase
  10030378Cytochrome c biogenesis protein
  10351108porGPyruvate ferrodoxin oxidoreductase
  10361109porDPyruvate ferrodoxin oxidoreductase
  10371110porAPyruvate ferrodoxin oxidoreductase
  10381111porBPyruvate ferrodoxin oxidoreductase
  10881161fldAFlavodoxin
  10901163fixSComponent of cation transport for cbb3-type oxidase
  11431222dldd-Lactate dehydrogenase
  11481227Periplasmic cytochromec-553
  11811260nuoANADH oxidoreductase I
  11821261nuoBNADH oxidoreductase I
  11831262nuoCNADH oxidoreductase I
  11841263nuoDNADH oxidoreductase I
  11851264nuoENADH oxidoreductase I
  11861265nuoFNADH oxidoreductase I
  11871266nuoGNADH oxidoreductase I
  11881267nuoHNADH oxidoreductase I
  11891268nuoINADH oxidoreductase I
  11901269nuoJNADH oxidoreductase I
  11911270nuoKNADH oxidoreductase I
  11921271nuoLNADH oxidoreductase I
  11931272nuoMNADH oxidoreductase I
  11941273nuoNNADH oxidoreductase I
  13541461Cytochrome c peroxidase
  14011508fixGComponent of cation transport forcbb3-type oxidase
  14591540petAUbiquinol cytochrome c oxidoreductase, 2Fe-2S subunit
  14601539petBUbiquinol cytochrome coxidoreductase, cytochrome b subunit
  14611538petCUbiquinol cytochrome coxidoreductase, cytochrome c1 subunit
 Entner-Doudoroff pathway
  10251099eda2-Keto-3-deoxy-6-phosphogluconate aldolase
  10261100eddPhosphogluconate dehydratase
 Fermentation
  8400903ackAAcetate kinase
  8410904, 0905ptaPhosphotransacetylase
  10301104Zinc-dependent alcohol dehydrogenase
  1429Zinc-dependent alcohol dehydrogenase
 Gluconeogenesis
  1110121ppsAPhosphoenolpyruvate synthase
  1420154enoEnolase
  1620176fbaFructose-bisphosphate aldolase
  1800194tpiTriose-phosphate isomerase
  8550921gapGlyceraldehyde-3-phosphate dehydrogenase
  9080974pgm2,3-Bisphosphoglycerate-independent phosphoglycerate mutase
  10931166pgiGlucose-6-phosphate isomerase
  12641345pgkPhosphoglycerate kinase
  12651346gapGlyceraldehyde 3-phosphate dehydrogenase
  14401385fbpFructose-1,6-bisphosphatase
 Phosphopentose pathway
  3371088tktATransketolase
  5210574rpiRibose 5-phosphate isomerase
  10271101zwfGlucose-6-phosphate-1-dehydrogenase
  13881495talTransaldolase
  14391386rpeRibulose-phosphate-3-epimerase
 Sugars
  10291103glkGlucokinase
 Tricarboxylic acid cycle
  220026gltACitrate synthase
  230027icdIsocitrate dehydrogenase
  5360588oorDSubunit of 2-oxoglutarate oxidoreductase
  5370589oorASubunit of 2-oxoglutarate oxidoreductase
  5380590oorBSubunit of 2-oxoglutarate oxidoreductase
  5390591oorCSubunit of 2-oxoglutarate oxidoreductase
  7160779acnBAconitate hydratase
  12451325fumCFumarase
 Other
  880096Keto-acid dehydrogenase
  5860642Oxidoreductase
  8880954Aldehyde dehydrogenase
  10230357Oxidoreductase
  10281102Dehydrogenase
  13451452thdFThiophene/furan oxidation protein
Fatty acid and phospholipid metabolism
  830090fabDMalonyl-CoA-ACP transacylase
  1760190Cardiolipin synthase
  1810195fabIEnoyl-ACP reductase
  1870201plsXFatty acid/phospholipid synthesis protein
  1880202fabHβ-Ketoacyl-ACP synthase III
  2010215cdsACDP-diacylglycerol synthase
  3541071pssAPhosphatidylserine synthase
  4071016pgsAPhosphatidylglycerophosphate synthase
  4091014Short-chain dehydrogenase
  4510499pldAPhospholipase A1
  5040557accAAcetyl-CoAa carboxylase subunit A
  5050558fabBβ-Ketoacyl-ACP synthase I
  5060559acpPACP
  5080561fabGAcetyl-CoA carboxylase subunit A
  6360692scoB3-Oxoacid CoA-transferase, subunit B
  6370691scoA3-Oxoacid CoA-transferase, subunit A
  6380690thlAcetyl-CoA acetyltransferase
  6400700dgkADiacylglycerol kinase
  6740737pgpAPhosphatidylglycerophosphatase A
  7440808acpSHolo-ACP synthase
  8050871cdhCDP-diacylglycerol pyrophosphatase
  8840950accDAcetyl-CoA carboxylase subunit B
  9680416cfaCyclopocyclopropane fatty acid synthase
  10100371accBBiotin carboxyl carrier protein
  10110370accCBiotin carboxylase
  12671348plsC1-Acyl-SN-glycerol-3-phosphate acyltransferase
  12751357psdPhosphatidylserine decarboxylase
  12901376fabZHydroxymyristoyl-ACP dehydratase
Purines, pyrimidines, nucleosides and nucleotides
 2′-Deoxyribonucleotide metabolism
  6210680nrdARibonucleoside-diphosphate reductase 1 alpha chain
  7990865dutDeoxyuridine 5′-triphosphate nucleotidohydrolase
  10090372dcdDeoxycytidine triphosphate deaminase
  10160364nrdBRibonucleoside-diphosphate reductase 1 beta chain
 Purine ribonucleotide biosynthesis
  10391112purBAdenylosuccinate lyase
  11401218purDGlycinamide ribonucleotide synthetase
  13271434purUFormyltetrahydrofolate hydrolase
 Pyrimidine ribonucleotide biosynthesis
  50005pyrFOrotidine 5′-phosphate decarboxylase
  1840198ndkNucleoside diphosphate kinase
  2510266pyrC1Dihydroorotase
  3230349pyrGCTP synthase
  3411084pyrBAspartate carbamoyltransferase catalytic chain
  4121011pyrDDihydroorotate dehydrogenase
  5280581pyrC2Dihydroorotase
  7140777pyrHUridylate kinase
  8530919pyrA1Carbamoyl-phosphate synthase large chain
  11581237pyrA2Carbamoyl-phosphate synthase small chain
  11781257pyrEOrotate phosphoribosyltransferase
 Salvage and interconversion of nucleosides and nucleotides
  960104cpdB2′,3′-Cyclic nucleotide 2′-phosphodiesterase
  2390255purAAdenylosuccinate synthetase
  3040321gmkGuanylate kinase
  5190572aptAdenine phosphoribosyltransferase
  5610618adkAdenylate kinase
  6720735gptXanthine-guanine phosphoribosyltransferase
  6790742prsAPhosphoribosyl pyrophosphate synthetase
  7680829guaBInosine-5′-monophosphate dehydrogenase
  7900854guaCGMP reductase
  9720409guaAGMP synthetase
  11041178deoDPurine nucleoside phosphorylase
  11051179deoBPhosphopentomutase
  13671474tmkThymidylate kinase
 Sugar-nucleotide biosynthesis and conversions
  5910646galUUTP-glucose-1-phosphate uridylyltransferase
  6240683glmUUDP-N-acetylglucosamine pyrophosphorylase
  14201532glmSGlutamine fructose-6-phosphate minotransferase
Regulatory functions
 General
  410048Transcriptional regulator
  810088rpoDRNA polymerase sigma 70 factor
  1510164, 0165Histidine kinase sensor protein
  1520166Transcriptional regulator
  2290244Histidine kinase sensor protein
  2630278gppAGuanosine-5′-triphosphate,3′-diphosphate pyrophosphatase
  3811043Transcriptional regulator
  3921032fliARNA polymerase sigma 28 factor
  3971027furFerric uptake regulation protein
  3991025Transcriptional regulator
  4031021Transcriptional regulator
  6430703Transcriptional regulator
  6520714rpoNRNA polymerase sigma-54 factor
  6640727Transcriptional regulator
  7120775spoTGuanosine-3′,5′-bis(diphosphate)-3′-pyrophosphohydrolase
  9810400lytBLysis tolerance protein
  12071287Transcriptional regulator
  12821364Histidine kinase sensor protein
  12831365Transcriptional regulator
  13351442csrACarbon storage regulator
  14431365Transcriptional regulator
  14801572dniRRegulatory protein
 Chemotaxis and motility
  170019cheV1Chemotaxis protein
  750082MCP
  910099MCP
  950103MCP
  3581067cheYResponse regulator
  5460599MCP
  5590616cheV2Chemotaxis protein
  9880393cheV3Chemotaxis protein
  9890392cheAHistidine kinase
  9900391cheWHistidine kinase-MCP coupling protein
Transcription
 Degradation of RNA
  11361213pnpPolyribonucleotide nucleotidyltransferase
  11691248vacBRNase II family protein
  12991407rbnRNase N
 DNA-dependent RNA polymerase
  11211198rpoBDNA-directed RNA polymerase, beta subunit
  12131293rpoADNA-directed RNA polymerase, alpha subunit
  14581541mfdTranscription-repair coupling factor
 Transcription factors
  10001nusBTranscription termination
  4970550rhoTranscription termination factor
  8000866greATranscription elongation factor (transcript cleavage factor)
  11261203nusGTranscription antitermination protein
  14071514nusAN utilization substance protein A
 RNA processing
  5830640pcnBPolynucleotide adenylyltransferase
  6070662rncRNase III
Translation
 Aminoacyl-tRNA synthetases
  1130123thrSThreonyl-tRNA synthetase
  1700182lysSLysyl-tRNA synthetase
  2230238proSProlyl-tRNA synthetase
  3020319argSArginyl-tRNA synthetase
  4280476gltXGlutamyl-tRNA synthetase
  5600617aspSAspartyl-tRNA synthetase
  5880643gltXGlutamyl-tRNA synthetase
  7110774tyrSTyrosyl-tRNA synthetase
  8180886cysSCysteinyl-tRNA synthetase
  8940960glyQGlycyl-tRNA synthetase alpha chain
  9060972glySGlycyl-tRNA synthetase beta chain
  9670417metGMethionyl-tRNA synthetase
  9780403pheSPhenylalanyl-tRNA synthetase alpha chain
  9790402pheTPhenylalanyl-tRNA synthetase beta chain
  10801153valSValyl-tRNA synthetase
  11151190hisSHistidyl-tRNA synthetase
  11621241alaSAlanyl-tRNA synthetase
  11741253trpSTryptophanyl-tRNA synthetase
  13171422ileSIsoleucyl-tRNA synthetase
  13731480serSSeryl-tRNA synthetase
  14521547leuSLeucyl-tRNA synthetase
 Degradation of proteins, peptides and glycopeptides
  290033clpAATP-dependent protease, ATP-binding subunit
  1550169Protease
  2490264clpBHeat shock protein
  2710286ftsHATP-dependent Zn metallopeptidase
  3561069ftsHATP-dependent Zn metallopeptidase
  3871037pepQProline peptidase
  4051019htrAProtease DO
  4111012Zn protease
  4220470pepFOligopeptidase
  4640515hslVHeat shock protein
  4650516hslUHeat shock protein
  5170570pepAAminopeptidase
  6020657Processing protease
  6030658gatBGlu-tRNA amidotransferase, subunit B
  7300794clpPATP-dependent protease, proteolytic subunit
  7690830gatAGlu-tRNA amidotransferase, subunit A
  9090975gatCGlu-tRNA amidotransferase, subunit C
  9990382Zn-metallo protease
  12691350prcCarboxyl-terminal protease
  12881374clpXATP-dependent protease, ATP-binding subunit
  12931379lonATP-dependent protease 1a
  13281435sppAProtease
  14911584ydiEO-Sialoglycoprotein endopeptidase
 Nucleoproteins
  7740835DNA-binding protein HU
  10521123slyDFKBP-type peptidyl-prolylcis-trans isomerase
 Protein modification
  2100224Peptide methionine sulfoxide reductase
  7290793defPolypeptide deformylase
  10170363pcmProtein-l-isoaspartateO-methyltransferase
  12191299mapMethionine aminopeptidase
  13341441ppiAPeptidyl-prolyl cis-transisomerase
 Ribosomal proteins, synthesis and modification
  710076rpsT30S ribosomal protein S20
  760083rpsI30S ribosomal protein S9
  770084rplM50S ribosomal protein L13
  1150125rpmI50S ribosomal protein L35
  1160126rplT50S ribosomal protein L20
  1860200rpmF50S ribosomal protein L32
  2810296rplU50S ribosomal protein L21
  2820297rpmA50S ribosomal protein L27
  3571068prmARibosomal protein L11 methyltransferase
  3781047rbfARibosome-binding factor A
  3841040rpsO30S ribosomal protein S15
  4430491rpmB50S ribosomal protein L28
  4630514rplI50S ribosomal protein L9
  4980551rpmE50S ribosomal protein L31
  5090562rpsU30S ribosomal protein S21
  9820399rpsA30S ribosomal protein S1
  10741147rplS50S ribosomal protein L19
  10781151rpsP30S ribosomal protein S16
  11191196rpsG30S ribosomal protein S7
  11201197rpsL30S ribosomal protein S12
  11221199rplL50S ribosomal protein L7/L12
  11231200rplJ50S ribosomal protein L10
  11241201rplA50S ribosomal protein L1
  11251202rplK50S ribosomal protein L11
  11271204rpmG50S ribosomal protein L33
  11651244rpsR30S ribosomal protein S18
  11671246rpsF30S ribosomal protein S6
  12121292rplQ50S ribosomal protein L17
  12141294rpsD30S ribosomal protein S4
  12151295rpsK30S ribosomal protein S11
  12171296rpsM30S ribosomal protein S13
  12171297rpmJ50S ribosomal protein L36
  12211301rplO50S ribosomal protein L15
  12221302rpsE30S ribosomal protein S5
  12231303rplR50S ribosomal protein L18
  12241304rplF50S ribosomal protein L6
  12251305rpsH30S ribosomal protein S8
  12261306rpsN30S ribosomal protein S14
  12271307rplE50S ribosomal protein L5
  12281308rplX50S ribosomal protein L24
  12291309rplN50S ribosomal protein L14
  12301310rpsQ30S ribosomal protein S17
  12311311rpmC50S ribosomal protein L29
  12321312rplP50S ribosomal protein L16
  12331313rpsC30S ribosomal protein S3
  12341314rplV50S ribosomal protein L22
  12351315rpsS30S ribosomal protein S19
  12361316rplB50S ribosomal protein L2
  12371317rplW50S ribosomal protein L23
  12381318rplD50S ribosomal protein L4
  12391319rplC50S ribosomal protein L3
  12401320rpsJ30S ribosomal protein S10
  13401447rpmH50S ribosomal protein L34
  13891496rplY50S ribosomal protein L25
  14451554rpsB30S ribosomal protein S2
 tRNA modification
  2660281tgtQueuine-tRNA-ribosyltransferase
  3631062queAS-Adenosylmethionine tRNA ribosyltransferase-isomerase
  10190361truAPseudouridylate synthase I
  10691141fmtMethionyl-tRNA formyltransferase
  10751148trmDtRNA (guanine-n1)-methyltransferase
  12541335trmUtRNA(5-methylaminomethyl-2-thiouridylate)-methyltransferase
  13101415miaAtRNA delta(2)-isopentenylpyrophosphate transferase
  13411448rnpARNase protein component
  13901497pthPeptidyl-tRNA hydrolase
  14061513selAl-Seryl-tRNA selenium transferase
 Translation factors
  720077prfAPeptide chain release factor 1
  1140124infCTranslation initiation factor IF-3
  1570171prfBPeptide chain release factor 2 (RF-2)
  1630177efpElongation factor P (EF-P)
  2320247deaDATP-dependent RNA helicase dead
  3771048infBTranslation initiation factor IF-2
  11181195fusAElongation factor G (EF-G)
  11281205tufAElongation factor TU (EF-TU)
  11771256frrRibosome recycling factor (ribosome-releasing factor [RRF])
  12181298infATranslation initiation factor IF-1
  13221431ksgADimethyladenosine transferase
  14441555tfsElongation factor TS (EF-TS)
Transport and binding proteins
 General
  660071ureIUrea transporter
  1670179ABC transporter, ATP-binding protein
  2000214Transporter
  2350250ABC transporter, ATP-binding protein
  2360251ABC transporter, permease
  3000613ABC transporter, ATP-binding protein
  3431082msbAMultidrug resistance protein
  4490497Transporter
  4500498Transporter
  5470600Secretion/efflux ABC transporter, ATP-binding protein
  5530606Efflux transporter
  5540607Efflux transporter
  6530715ABC transporter, ATP-binding protein
  6850748ABC transporter, ATP-binding protein
  7540818Osmoprotection binding protein
  7570818Osmoprotection binding protein
  7580819Osmoprotection ATP-binding protein
  7890853ABC transporter, ATP-binding protein
  8060872phnAAlkylphosphonate uptake protein
  8710936proPProline/betaine transporter
  10551126tolBtonB-independent protein-uptake protein
  10571129exbD1Biopolymer transport protein
  10581130exbB1Biopolymer transport protein
  11071181Transporter
  11291206ABC transporter, ATP-binding protein
  11411220ABC transporter, ATP-binding protein
  13201427Histidine-rich metal-binding protein
  13211432Histidine- and glutamine-rich metal-binding protein
  13381445exbB3Biopolymer transport protein
  13391446exbD3Biopolymer transport protein
  14841576ABC transporter, ATP-binding protein
  14851577ABC transporter, permease
 Amino acids, peptides, and amines
  470055putPSodium/proline symporter
  1210133sdaCl-Serine transporter
  2830298dppAPeriplasmic dipeptide transport substrate-binding protein
  2840299dppBDipeptide transport system permease protein
  2850300dppCDipeptide transport system permease protein
  2860301dppDDipeptide transport system ATP-binding protein
  2870302dppFDipeptide transport system ATP-binding protein
  4061017Amino acid permease
  8740939Amino acid ABC transporter, permease protein
  8750940Amino acid ABC transporter, binding protein precursor
  8770942Sodium/alanine symporter
  10961169Amino acid ABC transporter, permease protein
  10971170Amino acid ABC transporter, permease protein
  10981171Amino acid ABC transporter, ATP-binding protein
  10991172Amino acid ABC transporter, binding protein precursor
  11721251Peptide ABC transporter, ATP-binding protein
  13581465Amino acid ABC transporter, ATP-binding protein
  13991506gltSSodium/glutamate symporter
 Anions
  4250473modAMolybdenum ABC transporter, periplasmic binding protein
  4260474modBMolybdenum ABC transporter, permease
  4270475modCMolybdenum ABC transporter, ATP-binding protein
  13841491Phosphate permease
 Carbohydrates, organic alcohols, and acids
  1280140lldPl-Lactate permease
  1290141lldPl-Lactate permease
  3341091kgtPα-Ketoglutarate permease
  6350693atoEShort-chain fatty acids transporter
  6600724dcuAAnaerobic C4-dicarboxylate membrane transporter
  11011174gluPGlucose/galactose transporter
 Cations
  1240136bcpBacterioferritin comigratory protein
  3481077nixAHigh-affinity nickel transport protein
  3521073copPCopper-associated protein
  3531072copACopper-transporting P-type ATPase
  4230471kefBGlutathione-regulated potassium efflux system protein
  4420490Putative potassium channel protein
  5290582tonB1Siderophore-mediated iron transport protein
  5980653pfrNonheme iron-containing ferritin
  6260686fecA1Iron(III) dicitrate transport protein
  6270687feoBFerrous iron transport protein B
  7270791hmcTHeavy-metal cation-transporting P-type ATPase
  7430807fecA2Iron(III) dicitrate transport protein
  8210888fecEIron(III) dicitrate transport system ATP-binding protein
  8220889fecDIron(III) dicitrate transport system permease protein
  9030969czcA1Cation efflux system protein
  9040970czcB1Cation efflux system protein
  11091183Na+/H+ antiporter
  12481328czcB2Cation efflux system protein
  12491329czcA2Cation efflux system protein
  12581339exbB2Biopolymer transport protein
  12591340exbD2Biopolymer transport protein
  12601341tonB2Siderophore-mediated iron transport protein
  12631344corAMagnesium and cobalt transport protein
  13961503fixIComponent of cation transport for cbb3-type oxidase
  14261400fecA3Iron(III) dicitrate transport protein
  14471552nhaANa+/H+antiporter I
 Nucleosides, purines, and pyrimidines
  11061180Nucleoside transporter
  12101290pnuCNicotinamide mononucleotide transporter
  • a Gene numbers correspond to those in Fig. 1.