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
  1220134 aroF Phospho-2-dehydro-3-deoxyheptonate aldolase
  1450157 aroK Shikamate kinase I
  2680283 aroB 3-Dehydroquinate synthase
  3861038 aroD 3-Dehydroquinate dehydratase
  6080663 aroC Chorismate synthase
  9800401 aroA 3-Phosphoshikimate 1-carboxyvinyl transferase
  11701249 aroE Shikimate 5-dehydrogenase
  11981277 trpA Tryptophan synthase alpha chain
  11991278 trpB Tryptophan synthase beta chain
  12001279 trpC Indole-3-glycerol phosphate synthase
  12011280 trpD Anthranilate phosphoribosyltransferase
  12021281 trpG Anthranilate synthase component II
  12031282 trpE Anthranilate synthase component I
  12941380 tyrA Prephenate dehydrogenase
 Aspartate family
  900098 thrC Threonine synthase
  980106 metB Cystathionine gamma-synthase
  1980212 dapE Succinyl-diaminopimelate desuccinylase
  2750290 lysA Diaminopimelate decarboxylase
  3751050 thrB Homoserine kinase
  4101013 dapA Dihydrodipicolinate synthase
  4600510 dapB Dihydrodipicolinate reductase
  5130566 dapF Diaminopimelate epimerase
  5700626 dapD 2,3,4,5-Tetrahydropyridine-2-carboxylate-N-succinyltransferase
  5940649 aspA Aspartate ammonia-lyase
  6150672 aspB Aspartate aminotransferase
  7610822 hom Homoserine dehydrogenase
  11141189 asd Aspartate-semialdehyde dehydrogenase
  11501229 lysC Aspartokinase 2 alpha and beta subunits
 Glutamate family
  4610512 glnA Glutamine synthetase
  10010380 gdhA Glutamate dehydrogenase
  10851158 proC Pyrroline-5-carboxylate reductase
 Pyruvate family
  3130330 ilvC Ketol-acid reductoisomerase
  13611468 ilvE Branched-chain amino acid aminotransferase
 Serine family
  990107 cysK Cysteine synthase
  1710183 glyA Serine hydroxymethyltransferase
  5970652 serB Phosphoserine phosphatase
  9840397 serA Phosphoglycerate dehydrogenase
  11331210 cysE Serine acetyltransferase
Biosynthesis of cofactors, prosthetic groups, and carriers
 Biotin
  250029 bioD Dethiobiotin synthetase
  5450598 bioF 8-Amino-7-oxononanoate synthase
  9100976 bioA Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
  10681140Biotin activation protein
  12981406 bioB Biotin synthetase
 Folic acid
  2780293 pabB p-Aminobenzoate synthetase
  3881036 folK 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase
  5240577 folD Methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase
  8620928 folE GTP cyclohydrolase I
  8630928 folE GTP cyclohydrolase I
  11531232 folP Dihydropteroate synthase
  14031510 folB Dihydroneopterin aldolase
  14541545 folC Folylpolyglutamate synthase
 Heme and porphyrin
  1500163 hemB δ-Aminolevulinic acid dehydratase
  2220237 hemC Porphobilinogen deaminase
  2240239 hemA Glutamyl-tRNA reductase
  2910306 hemL Glutamate-1-semialdehyde-2,1-aminomutase
  5510604 hemE Uroporphyrinogen decarboxylase
  6100665 hemN Oxygen-independent coproporphyrinogen III oxidase
  10000381 hemG Protoporphyrinogen oxidase
  10050376 hemH Ferrochelatase
  11451224 hemD Uroporphyrinogen III synthase
  11471226 hemN Oxygen-independent coproporphyrinogen III oxidase
 Menaquinone and ubiquinone
  2250240 ispB Octaprenyl-diphosphate synthase
  8640929 ispA Geranyltransferase
  12781360 ubiA 4-Hydroxybenzoate octaprenyltransferase
  13691476 ubiD Octaprenyl-4-hydroxybenzoate carboxy-lyase
  13761483 ubiE Ubiquinone/menaquinone biosynthesis methyltransferase
 Molybdopterin
  1580172 moeA Molybdopterin biosynthesis protein
  7050768 moaA Molybdopterin cofactor biosynthetic protein
  7060769 mobA Molybdopterin-guanine dinucleotide biosynthesis protein A
  7340798 moaC Molybdenum cofactor biosynthesis protein C
  7350799 mog Molybdopterin biosynthesis protein
  7360800 moaE Molybdopterin-converting factor, subunit 2
  7370801 moaD Molybdopterin-converting factor, subunit 1
  7500814 moeB Molybdopterin-synthase sulfurylase
 Pantothenate
  60006 panC Pantoate-β-alanine ligase
  300034 panD Aspartate-1-decarboxylase
  3671058 panB 3-Methyl-2-oxobutanoate hydroxymethyltransferase
  7790841 dfp Pantothenate metabolism flavoprotein
 Pyridoxine
  3280354 dxs 1-Deoxyxylulose-5-phosphate synthase
  14891582 pdxJ Pyridoxal phosphate synthetase
  14901583 pdxA Pyridoxal phosphate biosynthetic protein A
 Riboflavin
  20002 ribE Riboflavin synthase beta chain
  3381087 ribF Riboflavin kinase
  7380802 ribA GTP cyclohydrolase II
  7400804 ribBA GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase
  13981505 ribD Riboflavin-specific deaminase
  14821574 ribC Riboflavin synthase alpha chain
 Thioredoxin, glutaredoxin, and glutathione
  7630824 trxA Thioredoxin
  7640825 trxB Thioredoxin reductase
  10461118 ggt Gamma-glutamyl transpeptidase
  10911164 trxB Thioredoxin reductase
  13511458Thioredoxin
 Thiamine
  7810843 thiE Thiamine phosphate pyrophosphorylase
  7820844 thiD Phosphomethylpyrimidine kinase
  7830845 thiM Hydroxyethylthiazole kinase
 Pyridine nucleotides
  3120329 nadE NH3-dependent NAD+ synthetase
  12731355 nadC Nicotinate-nucleotide pyrophosphorylase
  12741356 nadA Quinolinate 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
  2140229 hopA Outer 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
  6450706 hopE Outer 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
  8100876 frpB Iron-regulated outer membrane protein
  8331243 babB Outer membrane protein—adhesin
  8480912 hopC Outer membrane protein—porin
  8490913 hopB Outer membrane protein—porin
  8500914Outer membrane protein
  8510915, 0916 frpB Iron-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, 1216 imp Role in outer membrane permeability
  11640896 babA Outer membrane protein—adhesin
  12611342Outer membrane protein
  13431450Inner membrane protein
  13461453Outer membrane protein
  13491456 lpp20 Conserved lipoprotein
  13601467Outer membrane protein
  13621469Outer membrane protein
  13941501Outer membrane protein
  14051512 frpB Iron-regulated outer membrane protein
  14321395Outer membrane protein
  14721564Outer membrane protein
  14791571Outer membrane protein
 Murein sacculus and peptidoglycan
  4450493 mraY Phospho-N-acetylmuramoyl-pentapeptide-transferase
  4460494 murD UDP-N-acetylmuramoylalanine-d-glutamate ligase
  4960549 murI Glutamate racemase
  5440597Penicillin-binding protein
  5670623 murC UDP-N-acetylmuramate-alanine ligase
  5900645Lytic murein transglycosylase
  5930648 murA UDP-N-acetylglucosamine enolpyruvyltransferase
  6750738 ddl d-Alanine–d-alanine ligase
  6770740 murF d-Alanyl–d-alanine-adding enzyme
  7090772 amiA ProbableN-acetylmuramoyl-l-alanine amidase
  8760941 alr Alanine racemase, biosynthetic
  10821155 murG UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenoln-acetylglucosaminetransferase
  13131418 murB UDP-N-acetylenolpyruvoyl glucosamine reductase
  13871494 murE UDP-N-acetylmuramyl-tripeptide synthetase
  14641556Penicillin-binding protein
  14731565Penicillin-binding protein
 Surface polysaccharides, lipopolysaccharides, and antigens
  30003 kdsA 3-Deoxy-d-manno-octulosonic acid 8-phosphate synthase
  370043 manA/manC Phosphomannose isomerase/GDP-mannose pyrophosphorylase
  380044 Gmd GDP-d-mannose dehydratase
  390045Sugar nucleotide biosynthesis
  700075 glmM Phosphoglucosamine mutase
  860093, 0094α-(1,2)-Fucosyltransferase
  1470159Lipopolysaccharide biosynthesis protein
  1660178 neuB Sialic acid synthase
  1820196 lpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acetyltransferase
  1940208Lipopolysaccharide biosynthesis protein
  2150230 kdsB 3-Deoxy-manno-octulosonate cytidylyltransferase
  2640279 waaC Lipopolysaccharide heptosyltransferase-1
  2650280 waaM Lipid A biosynthesis acyltransferase
  3090326 neuA Acylneuraminate cytidylyltransferase
  3110328 lpxK Tetraacyldisaccharide-1-p 4′-kinase
  3731052 lpxC UDP-3-O-[3-hydroxymyristoyl]-N-acetylglucosamine deacetylase
  562Lipopolysaccharide biosynthesis protein
  5630619Lipopolysaccharide biosynthesis protein
  5960651 fucT α-(1,3)-Fucosyltransferase
  6200679Lipopolysaccharide biosynthesis protein
  7410805Lipopolysaccharide biosynthesis protein
  7650826Lipopolysaccharide biosynthesis protein
  7780840Sugar nucleotide biosynthesis protein
  7910857 gmhA Phosphoheptose isomerase
  7920858 waaE ADP-d-glycero-d-mannoheptose synthase
  7930859 gmhD ADP-l-glycero-d-mannoheptose-6-epimerase
  8010867 lpxB Lipid-A-disaccharide synthase
  820Lipopolysaccharide biosynthesis protein
  8910957 waaA 3-Deoxy-d-manno-octulosonic-acid transferase
  9630421Polysaccharide biosynthesis protein
  10020379 fucU α-(1,3)-Fucosyltransferase
  10150366Sugar nucleotide biosynthesis
  10200360 galE UDP-glucose 4-epimerase
  10311105Lipopolysaccharide biosynthesis protein
  1032Lipopolysaccharide biosynthesis protein
  11161191 waaF ADP-heptose-lipopolysaccharide heptosyltransferase II
  11961275 manB Phosphomannomutase
  12891375 lpxA UDP-N-acetylglucosamine acyltransferase
  13111416Lipopolysaccharide biosynthesis protein
  13681475 kdtB Lipopolysaccharide core biosynthesis protein
  14881581 wecA Undecaprenyl-phosphate-α-N-acetylglucosaminyltransferase
 Surface structures
  1070115 flaB Flagellin B
  1590173 fliR Flagellar biosynthesis protein
  2170232Motility protein
  2310246 flgI Flagellar P-ring protein
  2800295 flgL Flagellar hook-associated protein 3 (hap3)
  3080325 flgH Flagellar L-ring protein precursor (basal body L-ring protein)
  3100327 flaG Flagellar biosynthesis protein
  3250351 fliF Flagellar M-ring protein
  3260352 fliG Flagellar motor switch protein
  3270353 fliH Flagellar export apparatus
  3331092 flgG Flagellar basal-body rod protein
  3831041 flhA Flagellar biosynthesis protein
  3891035 flhF Flagellar biosynthesis protein
  3931031 fliM Flagellar motor switch protein
  3941030Flagellar motor switch protein
  4440492Paralogue of hpaA
  5310584 fliN Flagellar motor switch protein
  5480601 flaA Flagellin A
  6250684, 0685 fliP Flagellar biosynthesis protein
  6880751Flagellin protein
  6890752 fliD Flagellar hook-associated protein 2 (hap2)
  6900753 fliS Flagellar protein
  7070770 flhB Flagellar biosynthesis protein
  7330797 hpaA Neuraminyllactose-binding hemagglutinin precursor
  7450809 fliL Flagellar biosynthesis protein
  7510815 motA Chemotaxis protein (motility protein a)
  7520816 motB Flagellar motor protein
  8040870 flgE Flagellar hook protein
  8430907Flagellar biosynthesis protein
  8440908Flagellar basal-body/rod/hook protein
  9710410Paralogue of hpaA
  10471119 flgK Flagellar hook-associated protein 1 (Hap1)
  11171192Motility protein
  11951274 pflA Flagellar functional protein
  13141419 fliQ Flagellar biosynthesis protein
  13151420 fliI Flagellum-specific ATP synthase
  13551462Motility protein
  14651557 fliE Flagellar hook–basal-body complex protein
  14661558 flgC Flagellar basal-body rod protein
  14671559 flgB Flagellar basal-body rod protein
  14831575 flhB Flagellar biosynthesis protein
  14921585 flgG Flagellar basal-body rod protein (distal rod protein)
Cellular processes
 General
  40004 icfA Carbonic anhydrase
  1610175Peptidyl-prolyl cis-transisomerase
  1830197 metK S-Adenosylmethionine synthetase
  2280243 napA Neutrophil-activating protein A
  4660517 era GTP-binding protein
  6780741HIT family protein
  8650930 surE Stationary-phase protein
  9770404HIT family protein
  11121186Carbonic anhydrase
 Cell division
  3140331 minD Cell division inhibitor
  3150332 minE Cell division topological specificity factor
  3351090 ftsK Septum formation protein
  6800743 rodA Rod shape-determining protein
  9120978 ftsA Septum formation protein
  9130979 ftsZ GTPase in circumferential ring formation
  10861159 fic cAMP-induced cell filamentation protein
  12871373 mreB Rod shape-determining protein
  14681560 rodA Rod shape-determining protein
 Cell killing
  2740289Vacuolating cytotoxin (VacA) paralogue
  3391086 hlyA Hemolysin
  5560609, 0610Vacuolating cytotoxin (VacA) paralogue
  8190887 vacA Vacuolating cytotoxin
  8560922Vacuolating cytotoxin (VacA) paralog
 Cag island proteins and transposable elements
  150017 virB4a DNA transfer protein
  360041, 0042 virB10 DNA transfer protein
  4690520 orf6 Cag island protein
  4700521 orf7 Cag island protein
  4710522 orf8 Cag island protein
  4720523 orf9 Cag island protein
  4730524 virD4 Cag island protein, DNA transfer protein
  4740525 virB11a Cag island protein, DNA transfer protein
  4750526 orf12 Cag island protein
  4760527 orf13/14 Cag island protein
  4770528 orf15 Cag island protein
  4780529 orf16 Cag island protein
  4790530 orf17 Cag island protein
  4800531 orf18 Cag island protein
  4810532 cagT Cag island protein
  4820534 cagS Cag island protein
  4830535 cagQ Cag island protein
  4840536 cagP Cag island protein
  4850537 cagM Cag island protein
  4860538 cagN Cag island protein
  4870539 cagL Cag island protein
  4880540 cagI Cag island protein
  4890541 cagH Cag island protein
  4900542 cagG Cag island protein
  4910543 cagF Cag island protein
  4920544 cagE DNA transfer protein (Agrobacterium VirB4 homologue)
  4930545 cagD Cag island protein
  4940546 cagC Cag island protein
  4950547 cagA Cag island protein, cytotoxicity-associated immunodominant antigen
  826 tnpB IS606 transposase
  827 tnpA IS606 transposase
  917 virB4b DNA transfer protein
  918 virB4c DNA transfer protein
  12791361 comEC DNA transfer protein
  13161421 virB11b DNA transfer protein
 Chaperones
  80010 groEL 60-kDa chaperone
  90011 groES 10-kDa chaperone
  1010109 dnaK 70-kDa chaperone
  1020110 grpE 24-kDa chaperone
  1960210 htpG 90-kDa chaperone
  4001024 dnaJ2 Cochaperone with DnaK
  8610927 htpX Stress protein
  12521332 dnaJ1 Cochaperone with DnaK
 Detoxification
  8090875 katA Catalase
  9910390 tpx Thiol peroxidase
  9920389 sodF Iron-dependent superoxide dismutase
  14711563 tsaA Peroxidase
 Protein and peptide secretion
  690074 lspA Lipoprotein signal peptidase
  1680180 lnt ApolipoproteinN-acyltransferase
  3290355 lepA GTP-binding protein
  5230576 lepB Signal peptidase I
  7000763 ftsY Functional homolog of srp receptor
  7230786 secA Preprotein translocase subunit
  7310795 tig Trigger factor
  8890955 lgt Prolipoprotein diacylglyceryl transferase
  10791152 ffh Signal recognition particle protein
  1126A1203A secE Preprotein translocase subunit
  11761255 secG Protein export membrane protein
  12201300 secY Preprotein translocase subunit
  14491550 secD Protein export membrane protein
  14501549 secF Protein export membrane protein
 Phosphorus compounds
  4131010 ppk Polyphosphate kinase
  5640620 ppa Inorganic pyrophosphatase
 Polyamine biosynthesis
  180020 nspC Carboxynorspermidine decarboxylase
  7710832 speE Spermidine synthase
  9620422 speA Arginine decarboxylase
 Urea
  620067 ureH Urease accessory protein
  630068 ureG Urease accessory protein
  640069 ureF Urease accessory protein
  650070 ureE Urease accessory protein
  670072 ureB Urease beta subunit
  680073 ureA Urease alpha subunit
DNA replication
  100012 dnaG DNA primase
  1080116 topA DNA topoisomerase I
  1990213 gidA Glucose-inhibited division protein A
  3621063 gidB Glucose-inhibited division protein B
  4520500 dnaN DNA polymerase III, beta chain
  4530501 gyrB DNA gyrase subunit B
  5580615 lig DNA ligase
  6410701 gyrA DNA gyrase subunit A
  6550717 dnaX DNA polymerase III subunits gamma and tau
  8470911ATP-dependent helicase
  919 topA Topoisomerase I
  931 topA Topoisomerase I
  9940387 priA Primosomal protein n′ (replication factor y)
  11521231 holB DNA polymerase III subunit delta′
  11661245 ssb Single-strand binding protein
  12801362 dnaB Replicative DNA helicase
  13531460 dnaE DNA polymerase III, alpha chain
  13631470 polA DNA polymerase I
  13711478 rep ATP-dependent DNA helicase
  14121523 recG ATP-dependent DNA helicase
  14171529 dnaA Chromosomal replication initiator protein
  14381387DNA polymerase III
  14461553 pcrA ATP-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)
  1300142 mutY A/G-specific adenine glycosylase
  1410153 recA Recombination protein
  164Restriction enzyme
  2090223 radA DNA repair protein
  2430259 xseA Exodeoxyribonuclease large subunit
  2440260Type II DNA modification enzyme (methyltransferase)
  2480263Type II DNA modification enzyme (methyltransferase)
  3060323Endonuclease
  3220348 recJ Single-stranded-DNA-specific exonuclease
  3661059 ruvB Holliday junction DNA helicase
  414 hsdS1 Type I restriction enzyme (specificity subunit)
  4150463 hsdM1 Type I restriction enzyme (modification subunit)
  4160464 hsdR1 Type I restriction enzyme (restriction subunit)
  4300478Type II DNA modification enzyme (methyltransferase)
  4330481Type II DNA modification enzyme (methyltransferase)
  4350483Type II DNA modification enzyme (methyltransferase)
  5320585 nth Endonuclease III
  5490602Endonuclease III
  5650621 mutS DNA mismatch repair protein
  6060661 rnhA RNase HI
  6170675Integrase-recombinase protein (xerCD family)
  6180676 ogt Methylated-DNA–protein-cysteine methyltransferase
  629Type II DNA modification enzyme (methyltransferase)
  630Type II restriction enzyme
  6440705 uvrA Excinuclease ABC subunit A
  726 hsdS Type I restriction enzyme (specificity subunit)
  756Type II DNA modification enzyme (methyltransferase)
  7600821 uvrC Excinuclease ABC subunit C
  7840846 hsdR2 Type I restriction enzyme (restriction subunit)
  7850848, 0849 hsdS2 Type I restriction enzyme (specificity subunit)
  7860850 hsdM2 Type I restriction enzyme (modification subunit)
  8110877 ruvC Crossover junction endodeoxyribonuclease
  8150883 ruvA Holliday junction DNA helicase
  8460910Type II DNA modification enzyme (methyltransferase)
  8590925 recR Recombination protein
  9410995Integrase/recombinase (xerCD family)
  951Integrase/recombinase (xerCD family)
  10120369Type II DNA modification enzyme (methyltransferase)
  10411114 uvrB Excinuclease ABC subunit B
  10501121Type II DNA modification enzyme (methyltransferase)
  11311208 M.HpyIType II DNA modification enzyme (methyltransferase)
  11491228 mutT dGTP pyrophosphohydrolase
  12431323 rnhB RNase HII
  12661347 ung Uracil-DNA glycosylase
  12711352Type II DNA modification enzyme (methyltransferase)
  1284Type II DNA modification enzyme (methyltransferase)
  12951382Endonuclease
  1296 mod1 Type III DNA modification enzyme (methyltransferase)
  1297 res1 Type III restriction enzyme
  13641471Type II restriction enzyme
  13651472Type II DNA modification enzyme (methyltransferase)
  1409Type II DNA modification enzyme (methyltransferase)
  14101521 res2 Type III restriction enzyme
  14111522 mod2 Type III DNA modification enzyme (methyltransferase)
  14151526 exoA Exodeoxyribonuclease
  1422 hsdS3 Type I restriction enzyme (specificity subunit)
  14231403 hsdM3 Type I restriction enzyme (modification subunit)
  14241402 hsdR3 Type I restriction enzyme (restriction subunit)
  14341393 recN DNA repair protein
  14421366Type II restriction enzyme
Energy metabolism
 Amino acids and amines
  1200132 sdaB l-Serine/l-Threonine deaminase
  2790294 aimE Aliphatic amidase
  5853-Hydroxyacid dehydrogenase
  6610723 ansB l-Asparaginase II
  11591238Aliphatic amidase
  14271399 rocF Arginase
  14281398 ald l-Alanine dehydrogenase
 ATP-proton motive force interconversion
  7670828 atpB ATP synthase F0, subunit a
  10591131 atpC ATP synthase F1, subunit epsilon
  10601132 atpD ATP synthase F1, subunit beta
  10611133 atpG ATP synthase F1, subunit gamma
  10621134 atpA ATP synthase F1, subunit alpha
  10631135 atpH ATP synthase F1, subunit delta
  10641136 atpF ATP synthase F0, subunit b
  10651137 atpX ATP synthase B′
  11351212 atpE ATP synthase F0, subunit c
 Electron transport
  400047 hypE Hydrogenase expression/formation protein
  480056 putA Proline/pyrroline-5-carboxylate dehydrogenase
  1320144 fixN Cytochrome oxidase (CBB3-TYPE)
  1330145 fixO Cytochrome oxidase (CBB3-TYPE)
  1340146 fixQ Cytochrome oxidase (CBB3-TYPE)
  1350147 fixP Cytochrome oxidase (CBB3-TYPE)
  1770191 frdB Fumarate reductase
  1780192 frdA Fumarate reductase
  1790193 frdC Fumarate reductase
  2500265 ccdA Cytochromec biogenesis protein
  2620277Ferredoxin
  4590509 glcD Glycolate oxidase
  5740631 hyaA Hydrogenase, small subunit
  5750632 hyaB Hydrogenase, large subunit
  5760633 hyaC Hydrogenase, cytochrome subunit
  5770634 hyaD Hydrogenase expression/formation protein
  6110666 glpC Glycerol-3-phosphate dehydrogenase
  8030869 hypA Hydrogenase expression/formation protein
  8350898 hypD Hydrogenase expression/formation protein
  8360899 hypC Hydrogenase expression/formation protein
  8370900 hypB Hydrogenase expression/formation protein
  8780943 dadA d-Amino acid dehydrogenase
  8950961 gpsA Glycerol-3-phosphate dehydrogenase (NAD+)
  9740407S/N-oxide reductase
  10030378Cytochrome c biogenesis protein
  10351108 porG Pyruvate ferrodoxin oxidoreductase
  10361109 porD Pyruvate ferrodoxin oxidoreductase
  10371110 porA Pyruvate ferrodoxin oxidoreductase
  10381111 porB Pyruvate ferrodoxin oxidoreductase
  10881161 fldA Flavodoxin
  10901163 fixS Component of cation transport for cbb3-type oxidase
  11431222 dld d-Lactate dehydrogenase
  11481227Periplasmic cytochromec-553
  11811260 nuoA NADH oxidoreductase I
  11821261 nuoB NADH oxidoreductase I
  11831262 nuoC NADH oxidoreductase I
  11841263 nuoD NADH oxidoreductase I
  11851264 nuoE NADH oxidoreductase I
  11861265 nuoF NADH oxidoreductase I
  11871266 nuoG NADH oxidoreductase I
  11881267 nuoH NADH oxidoreductase I
  11891268 nuoI NADH oxidoreductase I
  11901269 nuoJ NADH oxidoreductase I
  11911270 nuoK NADH oxidoreductase I
  11921271 nuoL NADH oxidoreductase I
  11931272 nuoM NADH oxidoreductase I
  11941273 nuoN NADH oxidoreductase I
  13541461Cytochrome c peroxidase
  14011508 fixG Component of cation transport forcbb3-type oxidase
  14591540 petA Ubiquinol cytochrome c oxidoreductase, 2Fe-2S subunit
  14601539 petB Ubiquinol cytochrome coxidoreductase, cytochrome b subunit
  14611538 petC Ubiquinol cytochrome coxidoreductase, cytochrome c1 subunit
 Entner-Doudoroff pathway
  10251099 eda 2-Keto-3-deoxy-6-phosphogluconate aldolase
  10261100 edd Phosphogluconate dehydratase
 Fermentation
  8400903 ackA Acetate kinase
  8410904, 0905 pta Phosphotransacetylase
  10301104Zinc-dependent alcohol dehydrogenase
  1429Zinc-dependent alcohol dehydrogenase
 Gluconeogenesis
  1110121 ppsA Phosphoenolpyruvate synthase
  1420154 eno Enolase
  1620176 fba Fructose-bisphosphate aldolase
  1800194 tpi Triose-phosphate isomerase
  8550921 gap Glyceraldehyde-3-phosphate dehydrogenase
  9080974 pgm 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase
  10931166 pgi Glucose-6-phosphate isomerase
  12641345 pgk Phosphoglycerate kinase
  12651346 gap Glyceraldehyde 3-phosphate dehydrogenase
  14401385 fbp Fructose-1,6-bisphosphatase
 Phosphopentose pathway
  3371088 tktA Transketolase
  5210574 rpi Ribose 5-phosphate isomerase
  10271101 zwf Glucose-6-phosphate-1-dehydrogenase
  13881495 tal Transaldolase
  14391386 rpe Ribulose-phosphate-3-epimerase
 Sugars
  10291103 glk Glucokinase
 Tricarboxylic acid cycle
  220026 gltA Citrate synthase
  230027 icd Isocitrate dehydrogenase
  5360588 oorD Subunit of 2-oxoglutarate oxidoreductase
  5370589 oorA Subunit of 2-oxoglutarate oxidoreductase
  5380590 oorB Subunit of 2-oxoglutarate oxidoreductase
  5390591 oorC Subunit of 2-oxoglutarate oxidoreductase
  7160779 acnB Aconitate hydratase
  12451325 fumC Fumarase
 Other
  880096Keto-acid dehydrogenase
  5860642Oxidoreductase
  8880954Aldehyde dehydrogenase
  10230357Oxidoreductase
  10281102Dehydrogenase
  13451452 thdF Thiophene/furan oxidation protein
Fatty acid and phospholipid metabolism
  830090 fabD Malonyl-CoA-ACP transacylase
  1760190Cardiolipin synthase
  1810195 fabI Enoyl-ACP reductase
  1870201 plsX Fatty acid/phospholipid synthesis protein
  1880202 fabH β-Ketoacyl-ACP synthase III
  2010215 cdsA CDP-diacylglycerol synthase
  3541071 pssA Phosphatidylserine synthase
  4071016 pgsA Phosphatidylglycerophosphate synthase
  4091014Short-chain dehydrogenase
  4510499 pldA Phospholipase A1
  5040557 accA Acetyl-CoAa carboxylase subunit A
  5050558 fabB β-Ketoacyl-ACP synthase I
  5060559 acpP ACP
  5080561 fabG Acetyl-CoA carboxylase subunit A
  6360692 scoB 3-Oxoacid CoA-transferase, subunit B
  6370691 scoA 3-Oxoacid CoA-transferase, subunit A
  6380690 thl Acetyl-CoA acetyltransferase
  6400700 dgkA Diacylglycerol kinase
  6740737 pgpA Phosphatidylglycerophosphatase A
  7440808 acpS Holo-ACP synthase
  8050871 cdh CDP-diacylglycerol pyrophosphatase
  8840950 accD Acetyl-CoA carboxylase subunit B
  9680416 cfa Cyclopocyclopropane fatty acid synthase
  10100371 accB Biotin carboxyl carrier protein
  10110370 accC Biotin carboxylase
  12671348 plsC 1-Acyl-SN-glycerol-3-phosphate acyltransferase
  12751357 psd Phosphatidylserine decarboxylase
  12901376 fabZ Hydroxymyristoyl-ACP dehydratase
Purines, pyrimidines, nucleosides and nucleotides
 2′-Deoxyribonucleotide metabolism
  6210680 nrdA Ribonucleoside-diphosphate reductase 1 alpha chain
  7990865 dut Deoxyuridine 5′-triphosphate nucleotidohydrolase
  10090372 dcd Deoxycytidine triphosphate deaminase
  10160364 nrdB Ribonucleoside-diphosphate reductase 1 beta chain
 Purine ribonucleotide biosynthesis
  10391112 purB Adenylosuccinate lyase
  11401218 purD Glycinamide ribonucleotide synthetase
  13271434 purU Formyltetrahydrofolate hydrolase
 Pyrimidine ribonucleotide biosynthesis
  50005 pyrF Orotidine 5′-phosphate decarboxylase
  1840198 ndk Nucleoside diphosphate kinase
  2510266 pyrC1 Dihydroorotase
  3230349 pyrG CTP synthase
  3411084 pyrB Aspartate carbamoyltransferase catalytic chain
  4121011 pyrD Dihydroorotate dehydrogenase
  5280581 pyrC2 Dihydroorotase
  7140777 pyrH Uridylate kinase
  8530919 pyrA1 Carbamoyl-phosphate synthase large chain
  11581237 pyrA2 Carbamoyl-phosphate synthase small chain
  11781257 pyrE Orotate phosphoribosyltransferase
 Salvage and interconversion of nucleosides and nucleotides
  960104 cpdB 2′,3′-Cyclic nucleotide 2′-phosphodiesterase
  2390255 purA Adenylosuccinate synthetase
  3040321 gmk Guanylate kinase
  5190572 apt Adenine phosphoribosyltransferase
  5610618 adk Adenylate kinase
  6720735 gpt Xanthine-guanine phosphoribosyltransferase
  6790742 prsA Phosphoribosyl pyrophosphate synthetase
  7680829 guaB Inosine-5′-monophosphate dehydrogenase
  7900854 guaC GMP reductase
  9720409 guaA GMP synthetase
  11041178 deoD Purine nucleoside phosphorylase
  11051179 deoB Phosphopentomutase
  13671474 tmk Thymidylate kinase
 Sugar-nucleotide biosynthesis and conversions
  5910646 galU UTP-glucose-1-phosphate uridylyltransferase
  6240683 glmU UDP-N-acetylglucosamine pyrophosphorylase
  14201532 glmS Glutamine fructose-6-phosphate minotransferase
Regulatory functions
 General
  410048Transcriptional regulator
  810088 rpoD RNA polymerase sigma 70 factor
  1510164, 0165Histidine kinase sensor protein
  1520166Transcriptional regulator
  2290244Histidine kinase sensor protein
  2630278 gppA Guanosine-5′-triphosphate,3′-diphosphate pyrophosphatase
  3811043Transcriptional regulator
  3921032 fliA RNA polymerase sigma 28 factor
  3971027 fur Ferric uptake regulation protein
  3991025Transcriptional regulator
  4031021Transcriptional regulator
  6430703Transcriptional regulator
  6520714 rpoN RNA polymerase sigma-54 factor
  6640727Transcriptional regulator
  7120775 spoT Guanosine-3′,5′-bis(diphosphate)-3′-pyrophosphohydrolase
  9810400 lytB Lysis tolerance protein
  12071287Transcriptional regulator
  12821364Histidine kinase sensor protein
  12831365Transcriptional regulator
  13351442 csrA Carbon storage regulator
  14431365Transcriptional regulator
  14801572 dniR Regulatory protein
 Chemotaxis and motility
  170019 cheV1 Chemotaxis protein
  750082MCP
  910099MCP
  950103MCP
  3581067 cheY Response regulator
  5460599MCP
  5590616 cheV2 Chemotaxis protein
  9880393 cheV3 Chemotaxis protein
  9890392 cheA Histidine kinase
  9900391 cheW Histidine kinase-MCP coupling protein
Transcription
 Degradation of RNA
  11361213 pnp Polyribonucleotide nucleotidyltransferase
  11691248 vacB RNase II family protein
  12991407 rbn RNase N
 DNA-dependent RNA polymerase
  11211198 rpoB DNA-directed RNA polymerase, beta subunit
  12131293 rpoA DNA-directed RNA polymerase, alpha subunit
  14581541 mfd Transcription-repair coupling factor
 Transcription factors
  10001 nusB Transcription termination
  4970550 rho Transcription termination factor
  8000866 greA Transcription elongation factor (transcript cleavage factor)
  11261203 nusG Transcription antitermination protein
  14071514 nusA N utilization substance protein A
 RNA processing
  5830640 pcnB Polynucleotide adenylyltransferase
  6070662 rnc RNase III
Translation
 Aminoacyl-tRNA synthetases
  1130123 thrS Threonyl-tRNA synthetase
  1700182 lysS Lysyl-tRNA synthetase
  2230238 proS Prolyl-tRNA synthetase
  3020319 argS Arginyl-tRNA synthetase
  4280476 gltX Glutamyl-tRNA synthetase
  5600617 aspS Aspartyl-tRNA synthetase
  5880643 gltX Glutamyl-tRNA synthetase
  7110774 tyrS Tyrosyl-tRNA synthetase
  8180886 cysS Cysteinyl-tRNA synthetase
  8940960 glyQ Glycyl-tRNA synthetase alpha chain
  9060972 glyS Glycyl-tRNA synthetase beta chain
  9670417 metG Methionyl-tRNA synthetase
  9780403 pheS Phenylalanyl-tRNA synthetase alpha chain
  9790402 pheT Phenylalanyl-tRNA synthetase beta chain
  10801153 valS Valyl-tRNA synthetase
  11151190 hisS Histidyl-tRNA synthetase
  11621241 alaS Alanyl-tRNA synthetase
  11741253 trpS Tryptophanyl-tRNA synthetase
  13171422 ileS Isoleucyl-tRNA synthetase
  13731480 serS Seryl-tRNA synthetase
  14521547 leuS Leucyl-tRNA synthetase
 Degradation of proteins, peptides and glycopeptides
  290033 clpA ATP-dependent protease, ATP-binding subunit
  1550169Protease
  2490264 clpB Heat shock protein
  2710286 ftsH ATP-dependent Zn metallopeptidase
  3561069 ftsH ATP-dependent Zn metallopeptidase
  3871037 pepQ Proline peptidase
  4051019 htrA Protease DO
  4111012Zn protease
  4220470 pepF Oligopeptidase
  4640515 hslV Heat shock protein
  4650516 hslU Heat shock protein
  5170570 pepA Aminopeptidase
  6020657Processing protease
  6030658 gatB Glu-tRNA amidotransferase, subunit B
  7300794 clpP ATP-dependent protease, proteolytic subunit
  7690830 gatA Glu-tRNA amidotransferase, subunit A
  9090975 gatC Glu-tRNA amidotransferase, subunit C
  9990382Zn-metallo protease
  12691350 prc Carboxyl-terminal protease
  12881374 clpX ATP-dependent protease, ATP-binding subunit
  12931379 lon ATP-dependent protease 1a
  13281435 sppA Protease
  14911584 ydiE O-Sialoglycoprotein endopeptidase
 Nucleoproteins
  7740835DNA-binding protein HU
  10521123 slyD FKBP-type peptidyl-prolylcis-trans isomerase
 Protein modification
  2100224Peptide methionine sulfoxide reductase
  7290793 def Polypeptide deformylase
  10170363 pcm Protein-l-isoaspartateO-methyltransferase
  12191299 map Methionine aminopeptidase
  13341441 ppiA Peptidyl-prolyl cis-transisomerase
 Ribosomal proteins, synthesis and modification
  710076 rpsT 30S ribosomal protein S20
  760083 rpsI 30S ribosomal protein S9
  770084 rplM 50S ribosomal protein L13
  1150125 rpmI 50S ribosomal protein L35
  1160126 rplT 50S ribosomal protein L20
  1860200 rpmF 50S ribosomal protein L32
  2810296 rplU 50S ribosomal protein L21
  2820297 rpmA 50S ribosomal protein L27
  3571068 prmA Ribosomal protein L11 methyltransferase
  3781047 rbfA Ribosome-binding factor A
  3841040 rpsO 30S ribosomal protein S15
  4430491 rpmB 50S ribosomal protein L28
  4630514 rplI 50S ribosomal protein L9
  4980551 rpmE 50S ribosomal protein L31
  5090562 rpsU 30S ribosomal protein S21
  9820399 rpsA 30S ribosomal protein S1
  10741147 rplS 50S ribosomal protein L19
  10781151 rpsP 30S ribosomal protein S16
  11191196 rpsG 30S ribosomal protein S7
  11201197 rpsL 30S ribosomal protein S12
  11221199 rplL 50S ribosomal protein L7/L12
  11231200 rplJ 50S ribosomal protein L10
  11241201 rplA 50S ribosomal protein L1
  11251202 rplK 50S ribosomal protein L11
  11271204 rpmG 50S ribosomal protein L33
  11651244 rpsR 30S ribosomal protein S18
  11671246 rpsF 30S ribosomal protein S6
  12121292 rplQ 50S ribosomal protein L17
  12141294 rpsD 30S ribosomal protein S4
  12151295 rpsK 30S ribosomal protein S11
  12171296 rpsM 30S ribosomal protein S13
  12171297 rpmJ 50S ribosomal protein L36
  12211301 rplO 50S ribosomal protein L15
  12221302 rpsE 30S ribosomal protein S5
  12231303 rplR 50S ribosomal protein L18
  12241304 rplF 50S ribosomal protein L6
  12251305 rpsH 30S ribosomal protein S8
  12261306 rpsN 30S ribosomal protein S14
  12271307 rplE 50S ribosomal protein L5
  12281308 rplX 50S ribosomal protein L24
  12291309 rplN 50S ribosomal protein L14
  12301310 rpsQ 30S ribosomal protein S17
  12311311 rpmC 50S ribosomal protein L29
  12321312 rplP 50S ribosomal protein L16
  12331313 rpsC 30S ribosomal protein S3
  12341314 rplV 50S ribosomal protein L22
  12351315 rpsS 30S ribosomal protein S19
  12361316 rplB 50S ribosomal protein L2
  12371317 rplW 50S ribosomal protein L23
  12381318 rplD 50S ribosomal protein L4
  12391319 rplC 50S ribosomal protein L3
  12401320 rpsJ 30S ribosomal protein S10
  13401447 rpmH 50S ribosomal protein L34
  13891496 rplY 50S ribosomal protein L25
  14451554 rpsB 30S ribosomal protein S2
 tRNA modification
  2660281 tgt Queuine-tRNA-ribosyltransferase
  3631062 queA S-Adenosylmethionine tRNA ribosyltransferase-isomerase
  10190361 truA Pseudouridylate synthase I
  10691141 fmt Methionyl-tRNA formyltransferase
  10751148 trmD tRNA (guanine-n1)-methyltransferase
  12541335 trmU tRNA(5-methylaminomethyl-2-thiouridylate)-methyltransferase
  13101415 miaA tRNA delta(2)-isopentenylpyrophosphate transferase
  13411448 rnpA RNase protein component
  13901497 pth Peptidyl-tRNA hydrolase
  14061513 selA l-Seryl-tRNA selenium transferase
 Translation factors
  720077 prfA Peptide chain release factor 1
  1140124 infC Translation initiation factor IF-3
  1570171 prfB Peptide chain release factor 2 (RF-2)
  1630177 efp Elongation factor P (EF-P)
  2320247 deaD ATP-dependent RNA helicase dead
  3771048 infB Translation initiation factor IF-2
  11181195 fusA Elongation factor G (EF-G)
  11281205 tufA Elongation factor TU (EF-TU)
  11771256 frr Ribosome recycling factor (ribosome-releasing factor [RRF])
  12181298 infA Translation initiation factor IF-1
  13221431 ksgA Dimethyladenosine transferase
  14441555 tfs Elongation factor TS (EF-TS)
Transport and binding proteins
 General
  660071 ureI Urea transporter
  1670179ABC transporter, ATP-binding protein
  2000214Transporter
  2350250ABC transporter, ATP-binding protein
  2360251ABC transporter, permease
  3000613ABC transporter, ATP-binding protein
  3431082 msbA Multidrug 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
  8060872 phnA Alkylphosphonate uptake protein
  8710936 proP Proline/betaine transporter
  10551126 tolB tonB-independent protein-uptake protein
  10571129 exbD1 Biopolymer transport protein
  10581130 exbB1 Biopolymer 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
  13381445 exbB3 Biopolymer transport protein
  13391446 exbD3 Biopolymer transport protein
  14841576ABC transporter, ATP-binding protein
  14851577ABC transporter, permease
 Amino acids, peptides, and amines
  470055 putP Sodium/proline symporter
  1210133 sdaC l-Serine transporter
  2830298 dppA Periplasmic dipeptide transport substrate-binding protein
  2840299 dppB Dipeptide transport system permease protein
  2850300 dppC Dipeptide transport system permease protein
  2860301 dppD Dipeptide transport system ATP-binding protein
  2870302 dppF Dipeptide 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
  13991506 gltS Sodium/glutamate symporter
 Anions
  4250473 modA Molybdenum ABC transporter, periplasmic binding protein
  4260474 modB Molybdenum ABC transporter, permease
  4270475 modC Molybdenum ABC transporter, ATP-binding protein
  13841491Phosphate permease
 Carbohydrates, organic alcohols, and acids
  1280140 lldP l-Lactate permease
  1290141 lldP l-Lactate permease
  3341091 kgtP α-Ketoglutarate permease
  6350693 atoE Short-chain fatty acids transporter
  6600724 dcuA Anaerobic C4-dicarboxylate membrane transporter
  11011174 gluP Glucose/galactose transporter
 Cations
  1240136 bcp Bacterioferritin comigratory protein
  3481077 nixA High-affinity nickel transport protein
  3521073 copP Copper-associated protein
  3531072 copA Copper-transporting P-type ATPase
  4230471 kefB Glutathione-regulated potassium efflux system protein
  4420490Putative potassium channel protein
  5290582 tonB1 Siderophore-mediated iron transport protein
  5980653 pfr Nonheme iron-containing ferritin
  6260686 fecA1 Iron(III) dicitrate transport protein
  6270687 feoB Ferrous iron transport protein B
  7270791 hmcT Heavy-metal cation-transporting P-type ATPase
  7430807 fecA2 Iron(III) dicitrate transport protein
  8210888 fecE Iron(III) dicitrate transport system ATP-binding protein
  8220889 fecD Iron(III) dicitrate transport system permease protein
  9030969 czcA1 Cation efflux system protein
  9040970 czcB1 Cation efflux system protein
  11091183Na+/H+ antiporter
  12481328 czcB2 Cation efflux system protein
  12491329 czcA2 Cation efflux system protein
  12581339 exbB2 Biopolymer transport protein
  12591340 exbD2 Biopolymer transport protein
  12601341 tonB2 Siderophore-mediated iron transport protein
  12631344 corA Magnesium and cobalt transport protein
  13961503 fixI Component of cation transport for cbb3-type oxidase
  14261400 fecA3 Iron(III) dicitrate transport protein
  14471552 nhaA Na+/H+antiporter I
 Nucleosides, purines, and pyrimidines
  11061180Nucleoside transporter
  12101290 pnuC Nicotinamide mononucleotide transporter
  • a Gene numbers correspond to those in Fig. 1.