breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 5,144 G→A 34.1% intergenic (+124/‑90) thrC → / → yaaX L‑threonine synthase/DUF2502 family putative periplasmic protein
RA 7,905 A→C 20.5% Y19D (TAC→GAC)  yaaJ ← putative transporter
RA 8,137 G→T 10.0% intergenic (‑178/‑101) yaaJ ← / → talB putative transporter/transaldolase B
RA 10,444 G→T 49.2% F17L (TTC→TTA satP ← succinate‑acetate transporter
RA 11,676 G→T 6.1% N37K (AAC→AAA yaaI ← UPF0412 family protein
RA 13,308 G→T 5.3% L382L (CTG→CTT dnaK → chaperone Hsp70, with co‑chaperone DnaJ
RA 29,139 G→T 25.4% G256C (GGT→TGT)  dapB → dihydrodipicolinate reductase
RA 34,496 T→A 12.4% L66Q (CTG→CAG)  caiF → cai operon transcriptional activator
RA 43,364 G→T 10.9% P59P (CCG→CCT fixB → putative electron transfer flavoprotein, NAD/FAD‑binding domain and ETFP adenine nucleotide‑binding domain‑like protein
RA 47,560 G→T 6.4% T105T (ACG→ACT kefF → potassium‑efflux system ancillary protein for KefC, glutathione‑regulated; quinone oxidoreductase, FMN‑dependent
RA 47,837 G→T 8.7% A23A (GCG→GCT kefC → potassium:proton antiporter
RA 56,677 G→T 32.8% R145S (CGC→AGC)  lptD ← LPS assembly OM complex LptDE, beta‑barrel component
RA 66,606:1 +T 6.0% intergenic (‑74/‑268) araD ← / → araC pseudogene, truncated/ara regulon transcriptional activator; autorepressor
RA 72,392 G→T 11.0% F465L (TTC→TTA sgrR ← transcriptional DNA‑binding transcriptional activator of sgrS sRNA
RA 87,619 G→A 5.8% R34Q (CGA→CAA)  ftsL → membrane bound cell division protein at septum containing leucine zipper motif
RA 101,236 G→T 6.8% A256A (GCG→GCT ftsA → ATP‑binding cell division protein involved in recruitment of FtsK to Z ring
RA 104,042 A→T 5.7% intergenic (+81/‑150) lpxC → / → secM UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase/regulator of secA translation
RA 104,948 A→T 32.4% E61D (GAA→GAT secA → preprotein translocase subunit, ATPase
RA 105,563 C→A 13.4% D266E (GAC→GAA secA → preprotein translocase subunit, ATPase
RA 118,828 G→T 20.9% D84Y (GAT→TAT)  pdhR → pyruvate dehydrogenase complex repressor; autorepressor
RA 118,873 G→T 61.7% D99Y (GAC→TAC)  pdhR → pyruvate dehydrogenase complex repressor; autorepressor
RA 119,002 G→T 12.1% D142Y (GAT→TAT)  pdhR → pyruvate dehydrogenase complex repressor; autorepressor
RA 123,870 G→T 23.6% P563P (CCG→CCT aceF → pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2
RA 127,629 G→T 5.3% P40Q (CCG→CAG)  yacH ← uncharacterized protein
RA 142,460 T→A 55.1% F298Y (TTC→TAC)  yadE → putative polysaccharide deacetylase lipoprotein
RA 147,946 G→T 14.3% I47I (ATC→ATA yadK ← putative fimbrial‑like adhesin protein
RA 149,502 G→T 5.2% V804V (GTC→GTA htrE ← putative outer membrane usher protein
RA 153,472 G→T 28.9% intergenic (‑102/+268) yadN ← / ← folK putative fimbrial‑like adhesin protein/2‑amino‑4‑hydroxy‑6‑hydroxymethyldihyropteridine pyrophosphokinase
RA 157,178 C→A 20.8% intergenic (‑87/+91) dksA ← / ← sfsA transcriptional regulator of rRNA transcription, DnaK suppressor protein/sugar fermentation stimulation protein A
RA 158,287 C→A 52.1% D78Y (GAC→TAC)  ligT ← 2'‑5' RNA ligase
RA 158,967 C→A 19.1% H126N (CAT→AAT)  hrpB → putative ATP‑dependent helicase
RA 161,068 A→C 30.9% intergenic (+47/‑149) hrpB → / → mrcB putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA 161,171 G→T 14.4% intergenic (+150/‑46) hrpB → / → mrcB putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
RA 177,994 C→T 8.3% V208V (GTC→GTT degP → serine endoprotease (protease Do), membrane‑associated
RA 188,863 T→A 9.2% D174E (GAT→GAA pyrH → uridylate kinase
RA 198,022 C→A 21.5% R189S (CGT→AGT)  lpxD → UDP‑3‑O‑(3‑hydroxymyristoyl)‑glucosamine N‑acyltransferase
RA 214,044 G→T 7.6% R407S (CGT→AGT)  proS ← prolyl‑tRNA synthetase
JC 216,968 Δ3 bp 15.3% coding (446‑448/816 nt) metQ ← DL‑methionine transporter subunit
RA 230,561 G→A 5.3% P237S (CCT→TCT)  gloB ← hydroxyacylglutathione hydrolase
RA 232,860 G→T 67.1% D103Y (GAT→TAT)  dnaQ → DNA polymerase III epsilon subunit
RA 233,053 A→C 18.9% D167A (GAT→GCT)  dnaQ → DNA polymerase III epsilon subunit
RA 234,984 G→T 13.6% I80I (ATC→ATA ykfM ← lethality reduction protein, putative inner membrane protein
RA 234,990 G→T 16.8% F78L (TTC→TTA ykfM ← lethality reduction protein, putative inner membrane protein
RA 234,994 G→T 26.1% S77* (TCA→TAA)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,005 C→A 12.2% T73T (ACG→ACT ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,010 G→T 26.8% L72I (CTT→ATT)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,019 C→A 26.5% V69L (GTA→TTA)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,022 G→T 27.2% H68N (CAT→AAT)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,036 G→T 16.6% S63Y (TCC→TAC)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 238,195 G→T 38.7% V532V (GTC→GTA fadE ← acyl coenzyme A dehydrogenase
RA 241,630 G→T 7.9% Y221* (TAC→TAA yafK ← L,D‑transpeptidase‑related protein
RA 241,773 A→T 11.0% Y174N (TAC→AAC)  yafK ← L,D‑transpeptidase‑related protein
RA 248,470 A→C 13.6% intergenic (+30/‑22) dinB → / → yafN DNA polymerase IV/antitoxin of the YafO‑YafN toxin‑antitoxin system
RA 249,629 G→A 9.9% R145Q (CGA→CAA)  yafP → putative acyl‑CoA transferase
RA 281,469 A→T 8.6% T122S (ACC→TCC)  yagG → CP4‑6 prophage; putative sugar transporter
RA 295,695 T→G 15.8% E317D (GAA→GAC paoC ← PaoABC aldehyde oxidoreductase, Moco‑containing subunit
RA 301,808 C→A 5.0% E241* (GAA→TAA)  ecpD ← polymerized tip adhesin of ECP fibers
RA 306,510 G→A 14.2% R180W (CGG→TGG)  ecpR ← putative transcriptional regulator for the ecp operon
RA 307,398 G→A 6.1% intergenic (‑351/‑425) ecpR ← / → ykgL putative transcriptional regulator for the ecp operon/uncharacterized protein
RA 312,532 G→A 53.3% pseudogene (349/684 nt) ykgA ← pseudogene, AraC family;putative regulator; Not classified; putative ARAC‑type regulatory protein
JC JC 312,806 IS2 (+) +5 bp 14.0% pseudogene (71‑75/684 nt) ykgA ← pseudogene, AraC family;putative regulator; Not classified; putative ARAC‑type regulatory protein
RA 320,920 G→A 33.6% S52S (AGC→AGT ykgH ← putative inner membrane protein
RA 325,936 A→T 7.3% K255* (AAG→TAG)  betT → choline transporter of high affinity
RA 334,250 G→T 15.9% R72L (CGT→CTT)  yahG → DUF1116 family protein
RA 341,060 C→A 11.0% intergenic (+358/‑55) yahL → / → yahM uncharacterized protein/uncharacterized protein
RA 345,353 A→G 5.4% intergenic (+70/‑370) prpB → / → prpC 2‑methylisocitrate lyase/2‑methylcitrate synthase
RA 351,359 G→T 16.0% G243C (GGT→TGT)  codB → cytosine transporter
RA 351,447 T→A 18.2% L272Q (CTG→CAG)  codB → cytosine transporter
RA 353,357 A→T 5.7% intergenic (+192/+145) codA → / ← cynR cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor
RA 353,486 A→T 9.5% intergenic (+321/+16) codA → / ← cynR cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor
RA 353,489 C→T 8.9% intergenic (+324/+13) codA → / ← cynR cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor
RA 353,517 T→C 5.4% G295G (GGA→GGG cynR ← transcriptional activator of cyn operon; autorepressor
RA 359,028 C→A 9.8% pseudogene (1039/1125 nt) lacZ ← pseudogene, truncated
RA 360,752 A→G 100% V331A (GTG→GCG)  lacI ← DNA‑binding transcriptional repressor
JC 361,139 +GCCA 11.3% coding (605/1083 nt) lacI ← DNA‑binding transcriptional repressor
RA 361,806 G→A 100% intergenic (‑63/+14) lacI ← / ← mhpR DNA‑binding transcriptional repressor/mhp operon transcriptional activator
RA 362,159 G→T 31.0% I165I (ATC→ATA mhpR ← mhp operon transcriptional activator
RA 372,966 G→T 6.9% intergenic (+199/+25) yaiL → / ← frmB DUF2058 family protein/S‑formylglutathione hydrolase
RA 376,532 C→A 18.5% pseudogene (184/416 nt) yaiX ← pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
RA 379,943 C→T 8.1% G44R (GGA→AGA)  yaiS ← putative PIG‑L family deacetylase
RA 379,966 G→A 12.6% S36L (TCG→TTG)  yaiS ← putative PIG‑L family deacetylase
RA 395,611 C→A 9.8% D257Y (GAC→TAC)  ddlA ← D‑alanine‑D‑alanine ligase A
RA 402,340 G→T 53.1% V160V (GTG→GTT aroL → shikimate kinase II
RA 404,844 T→G 7.9% K211T (AAA→ACA)  rdgC ← nucleoid‑associated ssDNA and dsDNA binding protein; competitive inhibitor of RecA function
RA 406,075 C→A 51.4% P159Q (CCG→CAG)  mak → manno(fructo)kinase
RA 411,027 G→T 54.4% L61L (CTC→CTA sbcC ← exonuclease, dsDNA, ATP‑dependent
RA 419,663 G→T 7.5% E564* (GAA→TAA)  malZ → maltodextrin glucosidase
RA 433,551 G→T 49.0% S14Y (TCC→TAC)  yajO ← 2‑carboxybenzaldehyde reductase
RA 434,663 A→C 48.9% I324S (ATC→AGC)  dxs ← 1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA 435,336 G→T 28.3% Q100K (CAG→AAG)  dxs ← 1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA 437,672 T→A 30.9% V223E (GTG→GAG)  thiI → tRNA s(4)U8 sulfurtransferase
RA 442,299 G→T 13.4% S288* (TCG→TAG)  cyoE ← protoheme IX farnesyltransferase
RA 443,933 C→T 6.9% D62N (GAC→AAC)  cyoC ← cytochrome o ubiquinol oxidase subunit III
RA 456,588 G→T 56.2% D749Y (GAC→TAC)  lon → DNA‑binding ATP‑dependent protease La
RA 461,641 G→A 11.1% V376V (GTC→GTT ybaE ← putative ABC superfamily transporter periplasmic‑binding protein
RA 473,180 T→A 11.3% K298N (AAA→AAT ylaB ← putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA 474,138 G→T 59.1% intergenic (‑65/+99) ylaB ← / ← ylaC putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase/DUF1449 family inner membrane protein
RA 479,244 C→A 32.5% A206S (GCC→TCC)  acrB ← multidrug efflux system protein
RA 480,820 C→T 52.7% D86N (GAC→AAC)  acrA ← multidrug efflux system
RA 488,062 A→C 5.9% Q172P (CAA→CCA)  dnaX → DNA polymerase III/DNA elongation factor III, tau and gamma subunits
RA 495,504 A→T 9.0% intergenic (‑75/‑77) aes ← / → gsk acetyl esterase/inosine/guanosine kinase
RA 505,336 C→T 12.1% E500E (GAG→GAA copA ← copper transporter
RA 511,415 G→A 8.0% G14E (GGA→GAA)  fetA → iron exporter, ATP‑binding subunit, ABC transporter FetAB subunit; peroxide resistance protein
RA 513,720 T→C 15.0% I6V (ATT→GTT)  ybbN ← DnaK co‑chaperone, thioredoxin‑like protein
RA 525,424 T→C 15.1% pseudogene (49/357 nt) ylbG ← pseudogene, DNA‑binding transcriptional regulator homology
RA 530,466 C→A 55.1% F365L (TTC→TTA gcl → glyoxylate carboligase
RA 542,200 Δ1 bp 27.4% coding (65/1668 nt) fdrA → putative NAD(P)‑binding acyl‑CoA synthetase
RA 546,491 G→T 55.1% V199V (GTG→GTT ybcF → putative carbonate kinase
RA 549,397 G→T 56.3% intergenic (‑1/+2) lpxH ← / ← ppiB UDP‑2,3‑diacylglucosamine pyrophosphohydrolase/peptidyl‑prolyl cis‑trans isomerase B (rotamase B)
RA 564,590 G→T 5.2% G78V (GGA→GTA)  ybcK → DLP12 prophage; putative recombinase
RA 565,317 G→A 5.4% A320A (GCG→GCA ybcK → DLP12 prophage; putative recombinase
RA 579,710 G→A 9.9% A192T (GCA→ACA)  appY → global transcriptional activator; DLP12 prophage
RA 581,203 A→T 8.3% intergenic (‑114/‑310) ompT ← / → pauD DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)/tRNA‑OTHER
RA 583,341 T→G 61.9% S33R (AGT→CGT)  ybcH ← PRK09936 family protein
RA 592,124 A→T 6.6% I357F (ATT→TTT)  cusC → copper/silver efflux system, outer membrane component
RA 595,736 C→A 9.3% R523S (CGT→AGT)  cusA → copper/silver efflux system, membrane component
RA 596,756 G→T 8.6% E863* (GAG→TAG)  cusA → copper/silver efflux system, membrane component
RA 599,256 C→T 5.4% A288A (GCG→GCA ybdG ← mechanosensitive channel protein, miniconductance
RA 601,154 T→A 11.4% L63F (TTA→TTT ybdF ← DUF419 family protein
RA 603,481 A→C 6.7% intergenic (+37/‑40) hokE → / → insL1 toxic polypeptide, small/IS186 transposase
RA 607,660 G→T 9.1% R97R (CGC→CGA fepA ← iron‑enterobactin outer membrane transporter
RA 607,931 G→A 58.1% S7F (TCC→TTC)  fepA ← iron‑enterobactin outer membrane transporter
RA 608,174 G→A 21.5% intergenic (‑224/‑19) fepA ← / → fes iron‑enterobactin outer membrane transporter/enterobactin/ferric enterobactin esterase
RA 620,885 A→T 5.4% H182L (CAT→CTT)  entC → isochorismate synthase 1
RA 625,362 G→T 6.5% G5W (GGG→TGG) ‡ cstA → carbon starvation protein involved in peptide utilization; APC peptide transporter family protein
RA 625,363 G→T 7.5% G5V (GGG→GTG) ‡ cstA → carbon starvation protein involved in peptide utilization; APC peptide transporter family protein
RA 625,364 G→A 22.7% G5G (GGG→GGA) ‡ cstA → carbon starvation protein involved in peptide utilization; APC peptide transporter family protein
RA 627,794 G→A 5.6% D53N (GAC→AAC)  ybdD → DUF466 family protein
RA 632,406 T→A 19.4% K223N (AAA→AAT ybdO ← putative DNA‑binding transcriptional regulator
RA 635,464 G→T 16.3% E86* (GAG→TAG)  ahpF → alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding
RA 639,231 G→A 47.1% L65F (CTT→TTT)  rnk ← regulator of nucleoside diphosphate kinase
RA 641,886 C→A 15.1% E51* (GAG→TAG)  citT ← citrate:succinate antiporter
RA 646,796 C→A 6.9% D173Y (GAC→TAC)  citC ← [citrate [pro‑3S]‑lyase] ligase
RA 647,422 G→T 32.1% intergenic (‑110/‑269) citC ← / → citA [citrate [pro‑3S]‑lyase] ligase/sensory histidine kinase in two‑component regulatory system with CitB
RA 648,056 C→A 50.3% F122L (TTC→TTA citA → sensory histidine kinase in two‑component regulatory system with CitB
RA 651,481 G→A 5.3% intergenic (‑57/‑532) dcuC ← / → pagP anaerobic C4‑dicarboxylate transport/phospholipid:lipid A palmitoyltransferase
RA 651,752 G→A 5.6% intergenic (‑328/‑261) dcuC ← / → pagP anaerobic C4‑dicarboxylate transport/phospholipid:lipid A palmitoyltransferase
RA 652,865 Δ1 bp 51.3% coding (118/210 nt) cspE → constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein
RA 660,816 G→A 16.2% V318V (GTC→GTT mrdB ← cell wall shape‑determining protein
RA 661,164 C→A 5.8% L202L (CTG→CTT mrdB ← cell wall shape‑determining protein
RA 662,631 C→A 27.6% R348L (CGC→CTC)  mrdA ← transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA 668,351 G→T 6.3% P630Q (CCG→CAG)  leuS ← leucyl‑tRNA synthetase
RA 672,092 C→T 7.6% intergenic (‑89/‑75) ybeQ ← / → ybeR Sel1 family TPR‑like repeat protein/uncharacterized protein
RA 685,713 G→T 5.5% R209S (CGT→AGT)  lnt ← apolipoprotein N‑acyltransferase
RA 693,065 A→T 10.8% C523* (TGT→TGA asnB ← asparagine synthetase B
RA 705,588 C→A 37.1% intergenic (+16/+68) chiQ → / ← fur chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA 706,766 C→T 5.7% L52L (CTG→CTA fldA ← flavodoxin 1
RA 707,409 C→A 20.5% intergenic (‑55/+85) ybfE ← / ← ybfF LexA‑regulated protein, CopB family/acyl‑CoA esterase
RA 708,018 C→A 6.6% D81Y (GAC→TAC)  ybfF ← acyl‑CoA esterase
RA 731,316 A→T 6.4% T71S (ACA→TCA)  ybfC → putative periplasmic protein
RA 738,149 G→A 5.1% intergenic (‑137/‑134) dtpD ← / → ybgI dipeptide and tripeptide permease D/NIF3 family metal‑binding protein
RA 754,572 G→T 58.3% E137D (GAG→GAT sucA → 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding
RA 757,524 C→A 9.7% R183S (CGC→AGC)  sucB → dihydrolipoyltranssuccinase
RA 759,000 C→A 58.4% F177L (TTC→TTA sucC → succinyl‑CoA synthetase, beta subunit
RA 760,181 G→T 16.0% P182P (CCG→CCT sucD → succinyl‑CoA synthetase, NAD(P)‑binding, alpha subunit
RA 775,513 C→T 7.1% Q154* (CAG→TAG)  ybgF → periplasmic TolA‑binding protein
RA 788,902 G→T 42.6% R115S (CGT→AGT)  modF ← fused molybdate transporter subunits of ABC superfamily: ATP‑binding components
RA 789,274 G→T 8.0% intergenic (‑30/+38) modF ← / ← modE fused molybdate transporter subunits of ABC superfamily: ATP‑binding components/transcriptional repressor for the molybdenum transport operon modABC
RA 800,779 G→T 52.7% E607D (GAG→GAT ybhJ → putative hydratase
RA 828,374 G→T 56.7% V11V (GTC→GTA ybiA ← DUF1768 family protein
RA 832,574 G→T 14.4% T256T (ACG→ACT ybiC → putative dehydrogenase
RA 839,518 A→T 7.9% I473I (ATT→ATA ybiO ← mechanosensitive channel protein, intermediate conductance
RA 864,209 G→A 6.4% A412T (GCT→ACT)  gsiA → glutathione transporter ATP‑binding protein, ABC superfamily
RA 874,768 G→T 11.6% E191* (GAA→TAA)  yliI → soluble aldose sugar dehydrogenase
RA 876,447 G→A 52.3% D89N (GAT→AAT)  dacC → D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 6a)
RA 879,085 G→T 49.4% intergenic (‑241/‑44) ybjG ← / → mdfA undecaprenyl pyrophosphate phosphatase/multidrug efflux system protein
RA 882,441 A→T 10.5% S119T (TCT→ACT)  ybjJ ← putative transporter
RA 889,030 A→T 7.5% intergenic (+141/‑210) ybjN → / → potF negative regulator of motility; multicopy suppressor of coaA(Ts)/putrescine transporter subunit: periplasmic‑binding component of ABC superfamily
RA 890,514 G→T 5.2% R23L (CGC→CTC)  potG → putrescine transporter subunit: ATP‑binding component of ABC superfamily
RA 909,274 C→A 6.5% intergenic (‑4/+140) hcp ← / ← ybjE hybrid‑cluster [4Fe‑2S‑2O] protein in anaerobic terminal reductases/putative transporter
RA 910,654 C→G 5.0% intergenic (‑341/+154) ybjE ← / ← aqpZ putative transporter/aquaporin Z
JC JC 919,057 IS5 (–) +4 bp 18.6% coding (338‑341/2277 nt) clpA → ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity
RA 920,469 G→T 11.9% G584C (GGT→TGT)  clpA → ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity
RA 922,710 G→A 5.1% S60L (TCG→TTG)  aat ← leucyl/phenylalanyl‑tRNA‑protein transferase
RA 923,312 G→T 9.3% S447* (TCG→TAG)  cydC ← fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA 924,521 G→T 5.9% S44* (TCG→TAG)  cydC ← fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA 930,998 G→A 7.7% A773A (GCG→GCA ftsK → DNA translocase at septal ring sorting daughter chromsomes
RA 932,915 C→A 7.8% R30S (CGC→AGC)  lolA → lipoprotein chaperone
RA 935,943 C→A 9.2% R354S (CGT→AGT)  serS → seryl‑tRNA synthetase, also charges selenocysteinyl‑tRNA with serine
RA 939,763 C→A 7.7% S92* (TCG→TAG)  dmsC → dimethyl sulfoxide reductase, anaerobic, subunit C
RA 947,211 C→A 15.9% P600P (CCG→CCT pflB ← formate C‑acetyltransferase 1, anaerobic; pyruvate formate‑lyase 1
RA 955,629 T→A 8.8% intergenic (+78/‑91) aroA → / → ycaL 5‑enolpyruvylshikimate‑3‑phosphate synthetase/putative peptidase‑related chaperone
RA 960,265 T→G 8.7% F164V (TTT→GTT)  ycaI → ComEC family inner membrane protein
RA 960,909 C→A 5.9% V378V (GTC→GTA ycaI → ComEC family inner membrane protein
RA 961,946 T→A 7.3% F724Y (TTT→TAT)  ycaI → ComEC family inner membrane protein
RA 968,415 G→T 55.2% S148* (TCG→TAG)  ycbC ← DUF218 superfamily protein
RA 971,532 A→T 17.6% Q152L (CAG→CTG)  mukE → chromosome condensin MukBEF, MukE localization factor
RA 982,037 G→T 6.1% T134T (ACC→ACA ompF ← outer membrane porin 1a (Ia;b;F)
RA 1,006,218 G→T 12.6% E267* (GAG→TAG)  uup → putative transporter subunit of ABC superfamily: ATP‑binding component
RA 1,011,972 A→T 15.6% intergenic (‑46/+23) fabA ← / ← ycbZ beta‑hydroxydecanoyl thioester dehydrase/putative peptidase
RA 1,028,922 C→A 6.7% F71L (TTC→TTA hyaB → hydrogenase 1, large subunit
RA 1,029,664 C→T 6.2% L319L (CTG→TTG)  hyaB → hydrogenase 1, large subunit
RA 1,050,246 G→T 20.2% L463L (CTC→CTA torS ← hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA 1,058,961 C→A 5.4% A91S (GCC→TCC)  cbpA ← DnaK co‑chaperone; curved DNA‑binding protein
RA 1,071,619 G→A 7.1% A907V (GCC→GTC)  putA ← fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase
RA 1,071,939 C→A 6.5% L800L (CTG→CTT putA ← fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase
RA 1,077,911 A→C 47.5% K71N (AAA→AAC efeO → inactive ferrous ion transporter EfeUOB
RA 1,087,844 G→A 8.8% intergenic (‑99/‑488) pgaA ← / → ycdT biofilm adhesin polysaccharide PGA secretin; OM porin; poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein/diguanylate cyclase, membrane‑anchored
RA 1,090,918 T→A 11.9% intergenic (‑25/‑43) insE1 ← / → ymdE IS3 transposase A/pseudogene
RA 1,116,964 A→G 54.8% intergenic (‑21/+53) dinI ← / ← pyrC DNA damage‑inducible protein I/dihydro‑orotase
RA 1,118,506 A→T 10.6% L75Q (CTA→CAA)  yceB ← lipoprotein, DUF1439 family
RA 1,121,966 C→T 6.2% R118R (CGC→CGT yceH → UPF0502 family protein
RA 1,122,159 G→T 12.2% A183S (GCG→TCG)  yceH → UPF0502 family protein
RA 1,123,001 A→C 5.5% Q247P (CAG→CCG)  yceM → putative oxidoreductase
RA 1,129,182 G→A 7.9% A385T (GCC→ACC)  flgE → flagellar hook protein
RA 1,129,363 G→A 14.4% A36T (GCG→ACG)  flgF → flagellar component of cell‑proximal portion of basal‑body rod
RA 1,141,912 C→A 6.4% R47L (CGA→CTA)  yceF ← Maf‑like protein
RA 1,151,750 G→T 31.2% R178L (CGC→CTC)  holB → DNA polymerase III, delta prime subunit
RA 1,152,278 G→T 43.1% E16* (GAA→TAA)  ycfH → putative DNase
RA 1,164,408 T→A 5.2% intergenic (‑120/‑121) ycfQ ← / → bhsA repressor for bhsA(ycfR)/biofilm, cell surface and signaling protein
RA 1,192,525 C→T 21.7% S155N (AGC→AAC)  ymfD ← e14 prophage; putative SAM‑dependent methyltransferase
RA 1,193,873 G→T 45.8% intergenic (‑180/‑278) ymfE ← / → lit e14 prophage; putative inner membrane protein/e14 prophage; cell death peptidase, inhibitor of T4 late gene expression
RA 1,194,365 G→T 14.7% W72L (TGG→TTG)  lit → e14 prophage; cell death peptidase, inhibitor of T4 late gene expression
RA 1,197,027 G→T 13.7% M25I (ATG→ATT ymfI → e14 prophage; uncharacterized protein
RA 1,197,734 C→T 6.3% R219K (AGA→AAA)  cohE ← e14 prophage; repressor protein phage e14
RA 1,206,219 A→G 5.4% I140V (ATA→GTA)  mcrA → putative 5‑methylcytosine/5‑hydroxymethylcytosine‑specific restriction nuclease; 5‑methylcytosine DNA binding protein; e14 prophage gene
RA 1,210,957 C→A 6.2% intergenic (‑26/‑288) bluF ← / → ycgZ anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP/RcsB connector protein for regulation of biofilm and acid‑resistance
RA 1,211,142 C→T 22.3% intergenic (‑211/‑103) bluF ← / → ycgZ anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP/RcsB connector protein for regulation of biofilm and acid‑resistance
RA 1,215,174 G→T 14.3% pseudogene (118/2648 nt) ycgH → pseudogene; putative ATP‑binding component of a transport system
RA 1,216,183 C→A 7.7% pseudogene (1127/2648 nt) ycgH → pseudogene; putative ATP‑binding component of a transport system
RA 1,217,884 A→T 15.3% I69I (ATT→ATA ymgD ← uncharacterized protein
RA 1,218,640 C→T 8.7% intergenic (‑21/‑80) ymgI ← / → ymgJ uncharacterized protein/uncharacterized protein
RA 1,220,996 G→T 49.4% R181R (CGG→AGG)  minC ← cell division inhibitor
RA 1,226,964 C→A 6.4% T108K (ACA→AAA)  umuC → DNA polymerase V, subunit C
RA 1,228,591 G→T 54.5% intergenic (‑105/+41) dsbB ← / ← nhaB oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I/sodium:proton antiporter
RA 1,228,879 A→C 16.8% L432R (CTG→CGG)  nhaB ← sodium:proton antiporter
RA 1,229,460 G→T 12.0% F238L (TTC→TTA nhaB ← sodium:proton antiporter
RA 1,232,720 C→A 5.7% intergenic (‑23/‑307) ycgB ← / → dadA SpoVR family stationary phase protein/D‑amino acid dehydrogenase
RA 1,234,574 A→T 6.8% E80D (GAA→GAT dadX → alanine racemase, catabolic, PLP‑binding
RA 1,243,278 G→A 14.1% S431S (AGC→AGT dhaM ← putative dihydroxyacetone‑specific PTS enzymes: HPr component/EI component
RA 1,247,376 G→T 15.8% V285V (GTG→GTT dhaR → dhaKLM operon transcription activator
RA 1,282,421 A→T 12.5% intergenic (+439/+101) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA 1,282,676 A→G 5.4% noncoding (17/171 nt) rttR ← rtT sRNA, processed from tyrT transcript
RA 1,283,124 G→A 12.8% intergenic (‑46/+114) tyrT ← / ← purU tRNA‑Tyr/formyltetrahydrofolate hydrolase
RA 1,306,564 A→T 6.2% intergenic (‑61/+44) yciA ← / ← yciB acyl‑CoA esterase/IspA family inner membrane protein
RA 1,308,862 A→C 5.6% S196R (AGC→CGC)  ompW → outer membrane protein W
RA 1,311,385 T→A 5.9% Q32L (CAG→CTG)  trpA ← tryptophan synthase, alpha subunit
RA 1,322,140 T→A 54.1% T159S (ACG→TCG)  btuR ← cob(I)yrinic acid a,c‑diamide adenosyltransferase
RA 1,326,970 C→A 5.5% H556N (CAC→AAC)  topA → DNA topoisomerase I, omega subunit
RA 1,342,794 C→T 5.9% D126N (GAC→AAC)  rnb ← ribonuclease II
RA 1,345,657 C→A 5.8% intergenic (‑361/+7) fabI ← / ← ycjD enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein
RA 1,350,335 G→T 5.2% R345S (CGC→AGC)  sapA ← antimicrobial peptide transport ABC transporter periplasmic binding protein
RA 1,352,314 C→A 5.6% V377V (GTG→GTT puuP ← putrescine importer
RA 1,353,519 A→C 8.7% intergenic (‑75/+228) puuP ← / ← puuA putrescine importer/glutamate‑‑putrescine ligase
RA 1,361,131 G→T 5.4% intergenic (+59/+61) puuE → / ← pspF 4‑aminobutyrate aminotransferase, PLP‑dependent/psp operon transcriptional activator
RA 1,361,433 G→T 12.7% P246Q (CCG→CAG)  pspF ← psp operon transcriptional activator
RA 1,365,202 C→A 13.6% H244N (CAT→AAT)  ycjM → alpha amylase catalytic domain family protein
RA 1,365,283 G→T 35.5% E271* (GAG→TAG)  ycjM → alpha amylase catalytic domain family protein
RA 1,368,566 T→G 19.0% F74V (TTC→GTC)  ycjP → inner membrane putative ABC superfamily sugar transporter permease
JC JC 1,376,043 IS5 (–) +4 bp 81.8% pseudogene (10‑13/126 nt) ycjV → pseudogene; putative ATP‑binding component of a transport system
RA 1,377,394 C→T 52.0% A275A (GCG→GCA ycjW ← LacI family putative transcriptional repressor
RA 1,385,315 C→A 5.3% A266S (GCA→TCA)  ycjY ← S9 homolog non‑peptidase family protein
RA 1,385,964 T→G 10.7% Q49H (CAA→CAC ycjY ← S9 homolog non‑peptidase family protein
RA 1,386,008 G→T 34.1% Q35K (CAG→AAG)  ycjY ← S9 homolog non‑peptidase family protein
RA 1,388,406 G→T 37.4% R308L (CGC→CTC)  mppA → murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit
RA 1,397,096 G→A 7.4% R139R (CGC→CGT abgB ← p‑aminobenzoyl‑glutamate hydrolase, B subunit
RA 1,397,506 C→T 5.5% E3K (GAA→AAA)  abgB ← p‑aminobenzoyl‑glutamate hydrolase, B subunit
RA 1,399,129 A→C 5.6% E44D (GAA→GAC abgR → putative DNA‑binding transcriptional regulator of abgABT operon
RA 1,402,363 G→A 6.7% M19I (ATG→ATA ydaN → putative Zn(II) transporter
RA 1,413,956 G→T 10.7% intergenic (‑243/+66) ydaG ← / ← racR Rac prophage; uncharacterized protein/Rac prophage; putative DNA‑binding transcriptional regulator
RA 1,418,325 A→T 5.6% E96V (GAA→GTA)  trkG → Rac prophage; potassium transporter subunit
RA 1,459,790 C→T 5.5% pseudogene (142/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,461,652 G→T 12.3% pseudogene (2004/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,471,707 A→T 23.2% *769C (TGA→TGT ydbD → PF10971 family putative periplasmic methylglyoxal resistance protein
RA 1,488,445 T→A 5.0% Q295L (CAG→CTG)  ydcI ← putative DNA‑binding transcriptional regulator
RA 1,497,653 A→T 5.6% pseudogene (254/432 nt) insP ← pseudogene, IS609 transposase A;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related
RA 1,503,048 G→T 6.3% intergenic (+49/+43) ydcP → / ← yncJ putative peptidase/uncharacterized protein
RA 1,506,689 A→T 6.2% Q260L (CAG→CTG)  ydcS → polyhydroxybutyrate (PHB) synthase, ABC transporter periplasmic binding protein homolog
RA 1,513,440 T→A 10.3% Y53N (TAT→AAT)  curA → curcumin/dihydrocurcumin reductase, NADPH‑dependent
RA 1,519,349 T→A 54.8% K297* (AAA→TAA)  ansP ← L‑asparagine transporter
RA 1,521,211 A→T 6.9% L5F (TTA→TTT yncH → IPR020099 family protein
RA 1,521,805 C→T 5.1% intergenic (+396/‑354) yncH → / → rhsE IPR020099 family protein/pseudogene, Rhs family protein
RA 1,524,654 G→T 12.0% W159L (TGG→TTG)  ydcD → uncharacterized protein
RA 1,538,906 G→A 16.9% pseudogene (116/381 nt) yddK ← pseudogene, leucine‑rich protein; putative glycoportein
RA 1,539,484 G→A 6.5% pseudogene (488/951 nt) yddK ← pseudogene, leucine‑rich protein; putative glycoportein
RA 1,548,144 G→T 50.2% intergenic (‑49/+85) adhP ← / ← maeA ethanol‑active dehydrogenase/acetaldehyde‑active reductase/malate dehydrogenase, (decarboxylating, NAD‑requiring) (malic enzyme)
RA 1,563,276 G→T 60.4% H491N (CAC→AAC)  gadC ← glutamate:gamma‑aminobutyric acid antiporter
RA 1,565,497 G→A 57.2% S269L (TCG→TTG)  gadB ← glutamate decarboxylase B, PLP‑dependent
RA 1,569,899 A→G 5.2% S660P (TCT→CCT)  yddB ← putative TonB‑dependent outer membrane receptor
RA 1,576,869 G→A 15.7% intergenic (‑88/+314) ydeN ← / ← ydeO putative Ser‑type periplasmic non‑aryl sulfatase/UV‑inducible global regulator, EvgA‑, GadE‑dependent
RA 1,582,413 G→T 6.1% N47K (AAC→AAA ydeR ← putative fimbrial‑like adhesin protein
RA 1,587,275 C→A 8.3% pseudogene (4970/5323 nt) yneO ← pseudogene, AidA homolog
RA 1,596,093 T→G 6.5% L116R (CTC→CGC)  lsrA → autoinducer 2 import ATP‑binding protein
RA 1,599,970 T→A 11.2% D221E (GAT→GAA lsrB → autoinducer 2‑binding protein
RA 1,604,068 G→T 13.2% T290T (ACC→ACA uxaB ← altronate oxidoreductase, NAD‑dependent
RA 1,607,556 A→C 20.7% intergenic (‑48/+16) glsB ← / ← sad glutaminase 2/succinate semialdehyde dehydrogenase, NAD(P)+‑dependent
RA 1,611,821 C→A 9.7% I179I (ATC→ATA ydeA → arabinose efflux transporter, arabinose‑inducible
RA 1,628,207 G→A 84.2% G110E (GGA→GAA)  pinQ → Qin prophage; putative site‑specific recombinase
RA 1,640,268 A→C 14.9% K39Q (AAG→CAG)  ydfV → Qin prophage; uncharacterized protein
RA 1,641,686 G→A 6.1% pseudogene (208/279 nt) ydfX ← pseudogene, Qin prophage;Phage or Prophage Related
RA 1,643,394 A→G 5.4% intergenic (+96/‑245) ydfC → / → dicF uncharacterized protein, Qin prophage/sRNA antisense regulator, inhibits ftsZ, Hfq‑dependent; Qin prophage
RA 1,649,456 C→T 13.4% intergenic (‑58/+148) rspA ← / ← ynfA bifunctional D‑altronate/D‑mannonate dehydratase/UPF0060 family inner membrane protein
RA 1,652,812 A→T 6.0% I163F (ATC→TTC)  ynfE → putative selenate reductase, periplasmic
RA 1,661,763 C→A 55.3% P353P (CCG→CCT mlc ← glucosamine anaerobic growth regulon transcriptional repressor; autorepressor
RA 1,673,381 C→A 7.7% S233* (TCA→TAA)  ydgH → DUF1471 family periplasmic protein
RA 1,700,047 T→C 9.4% F8F (TTT→TTC rsxA → SoxR iron‑sulfur cluster reduction factor component; inner membrane protein of electron transport complex
RA 1,702,966 T→A 6.5% R597R (CGT→CGA rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,703,062 T→A 12.7% R629R (CGT→CGA rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,703,071 A→T 8.4% A632A (GCA→GCT rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,703,101 C→G 7.7% A642A (GCC→GCG rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,704,060 A→T 8.5% Q221L (CAA→CTA)  rsxD → SoxR iron‑sulfur cluster reduction factor component; putative membrane protein of electron transport complex
RA 1,711,397 C→T 49.3% R28Q (CGA→CAA)  tyrS ← tyrosyl‑tRNA synthetase
RA 1,726,289 A→T 8.7% P982P (CCA→CCT lhr → putative ATP‑dependent helicase
RA 1,747,398 C→A 7.3% A230A (GCG→GCT ydhV ← putative oxidoreductase subunit
RA 1,748,094 T→A 5.8% intergenic (‑7/+14) ydhV ← / ← ydhY putative oxidoreductase subunit/putative 4Fe‑4S ferridoxin‑type protein; FNR, Nar, NarP‑regulated protein; putative subunit of YdhYVWXUT oxidoreductase complex
RA 1,749,729 T→C 5.5% intergenic (‑331/‑226) ydhZ ← / → pykF uncharacterized protein/pyruvate kinase I
RA 1,770,281 T→A 33.0% D146E (GAT→GAA ydiF → putative acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit/beta subunit
RA 1,772,512 G→A 5.9% D354N (GAT→AAT)  ydiO → putative acyl‑CoA dehydrogenase
RA 1,780,104 C→A 10.0% A422A (GCG→GCT ppsA ← phosphoenolpyruvate synthase
RA 1,784,723 A→C 8.1% F260C (TTT→TGT)  ydiU ← UPF0061 family protein
RA 1,784,836 A→T 5.0% V222V (GTT→GTA ydiU ← UPF0061 family protein
RA 1,784,952 A→G 14.9% F184L (TTT→CTT)  ydiU ← UPF0061 family protein
RA 1,788,683 C→T 11.5% V243I (GTT→ATT)  btuC ← vitamin B12 transporter subunit: membrane component of ABC superfamily
RA 1,795,380 A→T 8.4% V483E (GTA→GAA)  thrS ← threonyl‑tRNA synthetase
RA 1,802,047 G→A 47.2% intergenic (+100/‑6) ydiZ → / → yniA uncharacterized protein/fructosamine kinase family protein
RA 1,807,639 G→A 13.5% intergenic (‑250/+39) ydjO ← / ← cedA uncharacterized protein/cell division modulator
RA 1,824,998 G→T 11.0% R9R (CGA→AGA)  astA ← arginine succinyltransferase
RA 1,832,413 C→A 29.9% L315L (CTC→CTA ynjC → inner membrane putative ABC superfamily transporter permease
RA 1,833,730 C→A 49.0% R3S (CGT→AGT)  ynjE → molybdopterin synthase sulfurtransferase
RA 1,849,412 T→A 6.2% T273S (ACT→TCT)  ydjG ← alpha‑Keto reductase, NADH‑dependent; can use methylglyoxal as substrate
RA 1,850,966 G→A 8.5% L74F (CTC→TTC)  ydjH ← putative kinase
RA 1,865,422 C→A 53.8% R261R (CGA→AGA)  yeaI → putative membrane‑anchored diguanylate cyclase
RA 1,872,520 G→T 51.0% P183P (CCG→CCT yeaP → diguanylate cyclase
RA 1,884,059 G→A 6.0% intergenic (‑56/+149) fadD ← / ← yeaY acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase)/Slp family lipoprotein, RpoE‑regulated
RA 1,906,096 T→A 6.7% K246N (AAA→AAT htpX ← putative endopeptidase
RA 1,906,578 C→A 11.5% A86S (GCT→TCT)  htpX ← putative endopeptidase
RA 1,909,342 T→A 49.6% E150D (GAA→GAT proQ ← RNA chaperone, putative ProP translation regulator
RA 1,909,792 G→T 5.3% intergenic (‑1/+96) proQ ← / ← msrC RNA chaperone, putative ProP translation regulator/free methionine‑(R)‑sulfoxide reductase
RA 1,915,555 A→C 15.9% Q359P (CAG→CCG)  rsmF → 16S rRNA m(5)C1407 methyltransferase, SAM‑dependent
RA 1,930,013 G→A 5.9% L187L (CTG→TTG)  zwf ← glucose‑6‑phosphate 1‑dehydrogenase
RA 1,934,690 G→T 10.0% N401K (AAC→AAA mepM ← murein DD‑endopeptidase, space‑maker hydrolase, septation protein
RA 1,936,668 G→A 5.6% S58L (TCA→TTA)  znuA ← zinc transporter subunit: periplasmic‑binding component of ABC superfamily
RA 1,938,106 C→A 5.5% R146S (CGC→AGC)  znuB → zinc transporter subunit: membrane component of ABC superfamily
RA 1,940,407 C→A 6.3% E11* (GAA→TAA)  yobI ← uncharacterized protein
RA 1,944,177 C→A 31.7% L201L (CTG→CTT aspS ← aspartyl‑tRNA synthetase
RA 1,948,159 C→T 6.1% T154M (ACG→ATG)  cmoB → tRNA (cmo5U34)‑carboxymethyltransferase, carboxy‑SAM‑dependent
RA 1,949,009 T→A 5.9% P752P (CCA→CCT torZ ← trimethylamine N‑oxide reductase system III, catalytic subunit
RA 1,969,349 C→A 6.8% R78L (CGA→CTA)  cheA ← fused chemotactic sensory histidine kinase in two‑component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein
RA 1,984,340 G→A 11.5% L393L (TTG→TTA tyrP → tyrosine transporter
RA 1,999,220 C→A 10.2% F9L (TTC→TTA fliT → putative flagellar synthesis and assembly chaperone
RA 2,020,166 C→A 25.1% D445Y (GAC→TAC)  yedQ ← putative membrane‑anchored diguanylate cyclase
RA 2,039,761 C→A 9.3% S448* (TCA→TAA)  yeeJ → putative adhesin
RA 2,048,571 A→T 20.4% P10P (CCA→CCT amn → AMP nucleosidase
RA 2,056,803 A→T 8.0% M1K (ATG→AAG) † ldtA ← L,D‑transpeptidase linking Lpp to murein
RA 2,070,058 C→A 10.8% A90A (GCC→GCA yeeS → CP4‑44 prophage; putative DNA repair protein
RA 2,078,521 C→A 11.9% V162V (GTG→GTT yeeE ← UPF0394 family inner membrane protein
RA 2,084,482 C→T 5.2% S270S (AGC→AGT hisG → ATP phosphoribosyltransferase
RA 2,094,530 C→T 5.9% V74M (GTG→ATG)  gnd ← 6‑phosphogluconate dehydrogenase, decarboxylating
RA 2,098,995 C→A 53.7% G182* (GGA→TGA)  wbbI ← d‑Galf:alpha‑d‑Glc beta‑1,6‑galactofuranosyltransferase
RA 2,102,316 A→T 10.2% F250L (TTT→TTA wzxB ← putative polisoprenol‑linked O‑antigen transporter
RA 2,114,911 A→T 26.9% L42Q (CTG→CAG)  wcaJ ← colanic biosynthesis UDP‑glucose lipid carrier transferase
RA 2,120,334 T→C 5.8% K113R (AAA→AGA)  wcaG ← bifunctional GDP‑fucose synthetase: GDP‑4‑dehydro‑6‑deoxy‑D‑mannose epimerase/ GDP‑4‑dehydro‑6‑L‑deoxygalactose reductase
RA 2,121,548 A→T 5.9% V83E (GTG→GAG)  gmd ← GDP‑D‑mannose dehydratase, NAD(P)‑binding
RA 2,122,367 C→T 7.5% M1M (ATG→ATA) † wcaF ← putative acyl transferase
RA 2,139,910 G→T 51.0% R1055L (CGA→CTA)  yegE → putative diguanylate cyclase
RA 2,144,474 C→A 69.9% intergenic (‑8/‑192) yegI ← / → yegJ protein kinase‑related putative non‑specific DNA‑binding protein/uncharacterized protein
RA 2,166,765 C→T 5.5% P331P (CCG→CCA gatC ← galactitol PTS permease ‑ GatC subunit
RA 2,170,285 C→T 6.7% A133A (GCG→GCA gatY ← D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit
RA 2,170,708 G→T 8.3% intergenic (‑25/+283) gatY ← / ← fbaB D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA 2,170,713 C→A 24.8% intergenic (‑30/+278) gatY ← / ← fbaB D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA 2,170,724 G→T 25.0% intergenic (‑41/+267) gatY ← / ← fbaB D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA 2,170,757 T→A 5.6% intergenic (‑74/+234) gatY ← / ← fbaB D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA 2,178,915 C→G 8.5% intergenic (‑135/+88) thiM ← / ← rcnR hydoxyethylthiazole kinase/transcriptional repressor of rcnA
RA 2,195,449 A→T 49.3% E564D (GAA→GAT yehI → DUF4132 domain‑containing protein
RA 2,216,296 C→A 28.9% I211I (ATC→ATA dld → D‑lactate dehydrogenase, FAD‑binding, NADH independent
RA 2,237,098 G→T 33.8% H12N (CAT→AAT)  folE ← GTP cyclohydrolase I
RA 2,240,469 G→T 6.5% intergenic (‑221/+73) cirA ← / ← lysP colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter/lysine transporter
RA 2,242,501 C→A 13.2% E199D (GAG→GAT yeiE ← putative DNA‑binding transcriptional regulator
RA 2,243,053 C→A 7.0% L15F (TTG→TTT yeiE ← putative DNA‑binding transcriptional regulator
RA 2,249,281 C→A 5.5% Q150K (CAG→AAG)  yeiL → putative transcriptional regulator
RA 2,254,334 C→A 8.0% G186C (GGT→TGT)  fruA ← fused fructose‑specific PTS enzymes: IIBcomponent/IIC components
RA 2,254,517 C→T 15.0% A125T (GCC→ACC)  fruA ← fused fructose‑specific PTS enzymes: IIBcomponent/IIC components
RA 2,258,182 A→T 9.5% K281* (AAG→TAG)  setB → lactose/glucose efflux system
RA 2,259,989 A→G 5.6% N89S (AAT→AGT)  yeiQ → putative NAD‑dependent D‑mannonate oxidoreductase
RA 2,264,143 G→A 27.9% intergenic (+119/‑62) mepS → / → rtn murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein/resistance protein for phages lambda and N4, putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA 2,276,920 G→A 5.4% F169F (TTC→TTT yejK ← spermidine nucleoid‑associated protein
RA 2,289,287 C→A 11.6% P171P (CCG→CCT ccmC ← heme exporter subunit
RA 2,289,374 C→A 55.0% V142V (GTG→GTT ccmC ← heme exporter subunit
RA 2,293,295 C→T 9.2% V149I (GTT→ATT)  napG ← ferredoxin‑type protein essential for electron transfer from ubiquinol to periplasmic nitrate reductase (NapAB)
RA 2,295,611 C→T 6.5% A208T (GCG→ACG)  napA ← nitrate reductase, periplasmic, large subunit
RA 2,298,128 C→T 12.6% intergenic (+256/+459) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,298,354 C→T 6.5% intergenic (+482/+233) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,299,282 C→T 7.7% V318I (GTT→ATT)  mqo ← malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,302,650 C→A 19.8% M57I (ATG→ATT alkB ← oxidative demethylase of N1‑methyladenine or N3‑methylcytosine DNA lesions
RA 2,305,116 C→A 51.5% intergenic (‑103/+9) apbE ← / ← ompC putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C
RA 2,310,952 C→T 5.6% E802K (GAG→AAG)  rcsC ← hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA 2,321,444 T→A 5.2% D60V (GAT→GTT)  yfaP ← DUF2135 family protein, putative host defense protein
RA 2,328,078 A→T 6.3% Y121N (TAC→AAC)  yfaT ← DUF1175 family protein, putative host defense protein
RA 2,338,611 C→A 6.2% R90S (CGT→AGT)  nrdA → ribonucleoside‑diphosphate reductase 1, alpha subunit
RA 2,338,758 C→A 5.5% R139S (CGT→AGT)  nrdA → ribonucleoside‑diphosphate reductase 1, alpha subunit
RA 2,348,261 Δ1 bp 6.9% coding (518/1260 nt) glpB → sn‑glycerol‑3‑phosphate dehydrogenase (anaerobic), membrane anchor subunit
RA 2,352,573 C→A 54.4% P353P (CCG→CCT rhmT ← putative L‑rhamnonate transporter
RA 2,359,673 G→T 43.8% M89I (ATG→ATT arnB → uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent
RA 2,362,338 T→A 47.7% L274Q (CTG→CAG)  arnA → fused UDP‑L‑Ara4N formyltransferase/UDP‑GlcA C‑4'‑decarboxylase
RA 2,367,110 G→A 5.3% intergenic (‑93/+17) pmrD ← / ← menE inactive two‑component system connector protein/O‑succinylbenzoate‑CoA ligase
RA 2,370,361:1 +G 54.5% coding (711/759 nt) menH ← 2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA 2,370,841 G→A 5.5% I77I (ATC→ATT menH ← 2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA 2,370,987 C→A 57.9% E29* (GAA→TAA)  menH ← 2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA 2,390,862 C→A 15.2% V20V (GTG→GTT nuoH ← NADH:ubiquinone oxidoreductase, membrane subunit H
RA 2,400,871 T→C 6.1% intergenic (‑751/‑169) lrhA ← / → alaA transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2
RA 2,403,195 G→T 8.8% S546* (TCG→TAG)  yfbS ← putative transporter
RA 2,405,946 T→G 55.5% Q43P (CAG→CCG)  yfbU ← UPF0304 family protein
RA 2,407,141 G→T 10.3% E65* (GAA→TAA)  ackA → acetate kinase A and propionate kinase 2
RA 2,414,178 C→A 5.3% R27S (CGC→AGC)  yfcG → GSH‑dependent disulfide bond oxidoreductase
RA 2,420,367 T→A 5.4% intergenic (‑100/+121) hisJ ← / ← argT histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit
RA 2,422,841 C→A 44.3% D293Y (GAT→TAT)  purF ← amidophosphoribosyltransferase
RA 2,424,074 C→T 55.0% D57N (GAC→AAC)  cvpA ← colicin V production membrane protein
RA 2,431,731 G→T 11.6% A101A (GCG→GCT flk → putative flagella assembly protein
RA 2,443,111 C→T 9.8% G140S (GGC→AGC)  yfcO ← DUF2544 family putative outer membrane protein
RA 2,446,543 G→A 9.8% pseudogene (1938/2646 nt) yfcU ← pseudogene, FimD fimbrial export usher family;putative membrane; Not classified; putative outer membrane protein
RA 2,447,486 C→T 5.5% pseudogene (995/2646 nt) yfcU ← pseudogene, FimD fimbrial export usher family;putative membrane; Not classified; putative outer membrane protein
RA 2,450,335 C→T 55.3% intergenic (‑44/+159) sixA ← / ← fadJ phosphohistidine phosphatase/fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA 2,454,297 T→G 35.1% E39D (GAA→GAC yfcZ ← UPF0381 family protein
RA 2,463,037 C→T 5.1% A143V (GCA→GTA)  gtrS → serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA 2,463,906 C→A 15.8% Q433K (CAA→AAA)  gtrS → serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA 2,463,910 G→T 13.7% R434I (AGA→ATA)  gtrS → serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA 2,463,915 C→A 11.5% Q436K (CAA→AAA)  gtrS → serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA 2,474,418 G→T 52.0% S413* (TCA→TAA)  emrY ← putative multidrug efflux system
RA 2,477,974 C→A 5.2% P41Q (CCA→CAA)  evgS → hybrid sensory histidine kinase in two‑component regulatory system with EvgA
RA 2,478,274 T→A 6.9% L141* (TTG→TAG)  evgS → hybrid sensory histidine kinase in two‑component regulatory system with EvgA
RA 2,520,863 G→T 15.4% D187Y (GAC→TAC)  yfeH → putative inorganic ion transporter
RA 2,525,695 C→T 6.1% intergenic (+112/‑73) cysZ → / → cysK EI24 family inner membrane protein; putative sulfate transporter/cysteine synthase A, O‑acetylserine sulfhydrolase A subunit
RA 2,530,470 C→A 5.0% G43C (GGC→TGC)  pdxK ← pyridoxal‑pyridoxamine kinase/hydroxymethylpyrimidine kinase
RA 2,542,903 G→T 6.9% intergenic (+138/+102) yfeW → / ← yfeX penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity/porphyrinogen oxidase, cytoplasmic
RA 2,544,288 C→A 5.9% V96V (GTG→GTT yfeY ← RpoE‑regulated lipoprotein
RA 2,548,703 C→T 5.1% E129K (GAA→AAA)  eutK ← putative ethanol utilization carboxysome structural protein
RA 2,556,774 G→A 21.5% intergenic (+298/‑177) yffP → / → yffQ CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
RA 2,576,254 G→A 11.8% intergenic (‑118/+8) ypfG ← / ← nudK DUF1176 family protein/GDP‑mannose pyrophosphatase
RA 2,576,325 C→A 45.0% E171D (GAG→GAT nudK ← GDP‑mannose pyrophosphatase
RA 2,587,029:1 +G 40.2% coding (101/699 nt) ypfH ← palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA 2,589,257 G→T 5.1% C280* (TGC→TGA ypfJ ← putative neutral zinc metallopeptidase
RA 2,595,292 C→A 6.6% S39* (TCG→TAG)  hyfB → hydrogenase 4, membrane subunit
RA 2,598,122 T→G 7.1% L306R (CTT→CGT)  hyfC → hydrogenase 4, membrane subunit
RA 2,600,721 C→A 8.5% S149* (TCG→TAG)  hyfF → hydrogenase 4, membrane subunit
RA 2,606,516 G→T 54.3% D420Y (GAC→TAC)  hyfR → hydrogenase‑4 transcriptional activator
RA 2,609,187 C→A 25.6% A18A (GCG→GCT yfgO ← putative UPF0118 family inner membrane permease
RA 2,614,168 C→A 51.0% D22Y (GAT→TAT)  upp ← uracil phosphoribosyltransferase
RA 2,624,800 C→A 5.0% P365P (CCG→CCT guaA ← GMP synthetase (glutamine aminotransferase)
RA 2,631,037 G→T 6.4% R325R (CGC→CGA bamB ← BamABCDE complex OM biogenesis lipoprotein
RA 2,644,397 A→T 8.3% L417* (TTG→TAG)  yfhM ← bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
RA 2,647,653 C→A 7.4% D214Y (GAT→TAT)  sseB ← rhodanase‑like enzyme, sulfur transfer from thiosulfate
RA 2,651,665 G→T 46.1% G210G (GGC→GGA hscA ← DnaK‑like molecular chaperone specific for IscU
RA 2,654,099 C→A 18.9% A264A (GCG→GCT iscS ← cysteine desulfurase (tRNA sulfurtransferase), PLP‑dependent
RA 2,654,144 G→T 7.7% I249I (ATC→ATA iscS ← cysteine desulfurase (tRNA sulfurtransferase), PLP‑dependent
RA 2,660,189 G→T 6.1% I339I (ATC→ATA hcaT ← putative 3‑phenylpropionic transporter
RA 2,660,345 A→T 6.4% T287T (ACT→ACA hcaT ← putative 3‑phenylpropionic transporter
RA 2,665,296 C→T 5.4% S238L (TCG→TTG)  hcaB → 2,3‑dihydroxy‑2,3‑dihydrophenylpropionate dehydrogenase
RA 2,667,539 C→T 5.2% R170Q (CGG→CAG)  yphB ← mutarotase superfamily protein, YphB family
RA 2,670,769 C→A 5.1% E318* (GAA→TAA)  yphE ← putative sugar transporter subunit of ABC superfamily, ATP‑binding component
RA 2,671,274 C→A 48.0% T149T (ACG→ACT yphE ← putative sugar transporter subunit of ABC superfamily, ATP‑binding component
RA 2,672,639 C→A 6.5% E30* (GAA→TAA)  yphF ← putative ABC superfamily sugar transporter periplasmic‑binding protein
RA 2,674,941 G→T 10.7% I388I (ATC→ATA yphG ← DUF4380 domain‑containing TPR repeat protein
RA 2,678,300 G→A 5.7% I189I (ATC→ATT glyA ← serine hydroxymethyltransferase
RA 2,679,933 C→A 13.2% A247D (GCT→GAT)  hmp → fused nitric oxide dioxygenase/dihydropteridine reductase 2
RA 2,681,873 T→A 56.9% Q97L (CAG→CTG)  glrR ← response regulator regulating glmY sRNA in two‑component system with sensor protein GlrK
RA 2,684,388 G→A 5.9% L24L (CTG→TTG)  glrK ← sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR
RA 2,694,471 G→A 5.5% I206I (ATC→ATT pdxJ ← pyridoxine 5'‑phosphate synthase
RA 2,708,587 C→A 5.7% T31T (ACG→ACT yfiE ← putative DNA‑binding transcriptional regulator
RA 2,711,673 A→C 7.6% V72G (GTT→GGT)  yfiF ← putative methyltransferase
JC 2,713,645 +CCTGCGC 20.5% coding (334/2661 nt) pka → protein lysine acetyltransferase
RA 2,715,618 C→A 5.9% N769K (AAC→AAA pka → protein lysine acetyltransferase
RA 2,715,643 G→T 55.3% E778* (GAA→TAA)  pka → protein lysine acetyltransferase
RA 2,715,694 G→T 9.2% G795C (GGC→TGC)  pka → protein lysine acetyltransferase
RA 2,718,953 G→T 12.6% I51I (ATC→ATA kgtP ← alpha‑ketoglutarate transporter
RA 2,719,426 T→C 100% intergenic (‑321/+2) kgtP ← / ← rrfG alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon
RA 2,740,398 C→T 5.6% D253N (GAT→AAT)  ffh ← Signal Recognition Particle (SRP) component with 4.5S RNA (ffs)
RA 2,749,167 T→A 5.2% intergenic (+430/‑351) smpB → / → intA trans‑translation protein/CP4‑57 prophage; integrase
RA 2,753,064 G→A 6.4% D241N (GAC→AAC)  yfjI → CP4‑57 prophage; uncharacterized protein
RA 2,756,275 C→A 5.6% E209* (GAG→TAG)  yfjK ← DEAD/H helicase‑like protein, CP4‑57 putative defective prophage
RA 2,759,184 C→T 14.7% intergenic (‑49/‑93) yfjM ← / → rnlA CP4‑57 prophage; uncharacterized protein/CP4‑57 prophage; RNase LS
RA 2,763,361 G→T 6.3% V100V (GTG→GTT yfjR → CP4‑57 prophage; putative DNA‑binding transcriptional regulator
RA 2,766,832 T→A 6.6% N52K (AAT→AAA yfjW → CP4‑57 prophage; putative inner membrane protein
RA 2,767,403 G→A 10.7% D243N (GAT→AAT)  yfjW → CP4‑57 prophage; putative inner membrane protein
RA 2,767,939 C→T 5.3% Y421Y (TAC→TAT yfjW → CP4‑57 prophage; putative inner membrane protein
RA 2,771,358 G→A 34.9% intergenic (+217/+147) ypjF → / ← ypjA CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter
RA 2,771,400 C→T 6.7% intergenic (+259/+105) ypjF → / ← ypjA CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter
RA 2,775,830 C→T 11.0% D86N (GAT→AAT)  ypjA ← adhesin‑like autotransporter
RA 2,777,166 A→T 8.6% pseudogene (1205/1374 nt) ypjC ← pseudogene
RA 2,777,493 T→G 6.3% pseudogene (878/1374 nt) ypjC ← pseudogene
RA 2,778,307 C→T 9.4% pseudogene (64/1374 nt) ypjC ← pseudogene
RA 2,783,685 G→A 7.1% E115E (GAG→GAA lhgO → L‑2‑hydroxyglutarate oxidase
RA 2,793,020 C→T 6.1% E112K (GAA→AAA)  ygaC ← uncharacterized protein
RA 2,809,924 G→T 6.3% R126S (CGC→AGC)  yqaA ← COG1238 family inner membrane protein
RA 2,811,408 T→A 5.5% intergenic (‑189/+10) argQ ← / ← argZ tRNA‑Arg/tRNA‑Arg
RA 2,811,566 C→A 9.9% noncoding (68/77 nt) argY ← tRNA‑Arg
RA 2,813,717 C→A 5.9% V552F (GTT→TTT)  alaS ← alanyl‑tRNA synthetase
RA 2,820,083 C→A 7.1% G111G (GGC→GGA srlE → glucitol/sorbitol‑specific enzyme IIB component of PTS
RA 2,825,783 C→T 54.6% intergenic (‑135/‑52) norR ← / → norV anaerobic nitric oxide reductase DNA‑binding transcriptional activator/anaerobic nitric oxide reductase flavorubredoxin
RA 2,832,247 C→A 6.9% R126L (CGT→CTT)  ascG ← asc operon transcriptional repressor; prpBC operon repressor
RA 2,834,296 C→A 5.0% Q472K (CAG→AAG)  ascF → fused cellobiose/arbutin/salicin‑specific PTS enzymes: IIB component/IC component
RA 2,835,413 C→A 13.6% I355I (ATC→ATA ascB → cryptic 6‑phospho‑beta‑glucosidase
RA 2,850,790 C→A 47.3% I113I (ATC→ATA mutS → methyl‑directed mismatch repair protein
RA 2,869,269 C→A 7.1% E140D (GAG→GAT cysD ← sulfate adenylyltransferase, subunit 2
RA 2,873,087 G→T 55.3% V15V (GTC→GTA ygbT ← multifunctional endonuclease Cas1, CRISPR adaptation protein; DNA repair enzyme
RA 2,873,729 G→T 8.9% V6V (GTC→GTA casE ← CRISPR RNA precursor cleavage enzyme; CRISP RNA (crRNA) containing Cascade antiviral complex protein
RA 2,876,760 C→T 56.5% G246G (GGG→GGA casA ← CRISP RNA (crRNA) containing Cascade antiviral complex protein
RA 2,878,668 G→T 34.7% V637V (GTC→GTA ygcB ← R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA 2,890,873 A→T 10.9% I119I (ATT→ATA ygcS ← putative transporter
RA 2,891,523 T→A 5.1% N419Y (AAT→TAT)  ygcU ← putative FAD‑containing dehydrogenase
RA 2,916,403 C→T 5.4% E247E (GAG→GAA truC ← tRNA(Ile1,Asp) pseudouridine(65) synthase
RA 2,928,446 G→T 13.0% A285S (GCT→TCT)  fucP → L‑fucose transporter
RA 2,930,611 G→T 5.3% E557* (GAA→TAA)  fucI → L‑fucose isomerase
RA 2,930,943 C→A 6.5% I49I (ATC→ATA fucK → L‑fuculokinase
RA 2,931,717 C→A 48.8% N307K (AAC→AAA fucK → L‑fuculokinase
RA 2,932,934 C→A 5.3% H70N (CAC→AAC)  fucR → l‑fucose operon activator
RA 2,934,843 G→T 58.4% H50N (CAT→AAT)  ygdD ← UPF0382 family inner membrane protein
RA 2,953,398 C→A 11.3% G797V (GGC→GTC)  recC ← exonuclease V (RecBCD complex), gamma chain
RA 2,955,808 G→T 6.2% R106S (CGT→AGT)  ppdC ← putative prepilin peptidase‑dependent protein
RA 2,971,037 G→A 5.5% R408C (CGC→TGC)  lysA ← diaminopimelate decarboxylase, PLP‑binding
RA 2,975,754 T→A 6.8% intergenic (‑213/+102) araE ← / ← kduD arabinose transporter/hexuronate dehydrogenase; hexuronate utilization in high osmolarity
RA 2,978,108 C→A 7.7% G282C (GGT→TGT)  yqeF ← short chain acyltransferase
RA 2,979,880 C→A 6.0% H225Q (CAC→CAA yqeG → putative transporter
RA 2,982,873 G→T 10.4% G71* (GGA→TGA)  yqeJ → uncharacterized protein
RA 2,983,868 G→T 19.2% intergenic (‑149/‑45) yqeK ← / → ygeF uncharacterized protein/pseudogene
RA 2,984,780 G→A 8.6% E52K (GAA→AAA)  ygeG → SycD‑like chaperone family TPR‑repeat‑containing protein
RA 2,989,295 C→A 51.8% pseudogene (85/261 nt) ygeN ← pseudogene
RA 2,993,195 A→G 9.8% V19A (GTT→GCT)  ygeR ← LysM domain‑containing M23 family putative peptidase; septation lipoprotein
RA 2,993,211 C→A 50.8% V14L (GTG→TTG)  ygeR ← LysM domain‑containing M23 family putative peptidase; septation lipoprotein
RA 2,995,609 C→A 7.6% L636I (CTT→ATT)  xdhA → xanthine dehydrogenase, molybdenum binding subunit
RA 3,001,919 C→A 5.8% H351N (CAT→AAT)  ygeX → 2,3‑diaminopropionate ammonia lyase, PLP‑dependent
RA 3,009,563 G→T 6.5% E49* (GAA→TAA)  ygfK → putative Fe‑S subunit oxidoreductase subunit
RA 3,017,288 G→A 5.2% A872T (GCC→ACC)  xdhD → putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA 3,020,228 G→T 17.8% A368A (GCG→GCT guaD → guanine deaminase
RA 3,020,629 C→A 10.8% I50I (ATC→ATA ygfQ → putative purine permease
RA 3,024,983 C→G 30.9% G86G (GGC→GGG uacT → uric acid permease
RA 3,033,430 G→T 17.3% D73Y (GAC→TAC)  fldB → flavodoxin 2
RA 3,035,672 C→A 8.9% intergenic (+20/+176) ygfZ → / ← yqfA iron‑sulfur cluster repair protein, plumbagin resistance/hemolysin III family HylIII inner membrane protein
RA 3,039,409 T→G 16.4% intergenic (‑149/+118) ygfF ← / ← gcvP putative NAD(P)‑dependent oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex
RA 3,044,464 G→A 54.4% intergenic (‑438/+10) gcvT ← / ← ubiI aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent
RA 3,044,493 A→C 11.5% L395W (TTG→TGG)  ubiI ← 2‑octaprenylphenol hydroxylase, FAD‑dependent
RA 3,049,606 C→A 5.8% R3R (CGG→AGG)  fau → 5‑formyltetrahydrofolate cyclo‑ligase family protein
RA 3,050,166 C→A 14.5% intergenic (+18/‑42) fau → / → sibC 5‑formyltetrahydrofolate cyclo‑ligase family protein/sRNA antisense regulator of toxic IbsC protein
RA 3,056,703 C→A 6.5% R120S (CGC→AGC)  argK → membrane ATPase/protein kinase
RA 3,075,107 C→A 5.6% intergenic (‑113/‑165) tktA ← / → loiP transketolase 1, thiamine triphosphate‑binding/Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; heat shock protein that binds Era
RA 3,075,114 C→A 50.1% intergenic (‑120/‑158) tktA ← / → loiP transketolase 1, thiamine triphosphate‑binding/Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; heat shock protein that binds Era
RA 3,076,526 C→A 34.1% D211Y (GAC→TAC)  speB ← agmatinase
RA 3,079,934 T→C 5.5% intergenic (+173/‑131) yqgC → / → metK uncharacterized protein/S‑adenosylmethionine synthetase
RA 3,080,618 T→A 46.7% V185E (GTG→GAG)  metK → S‑adenosylmethionine synthetase
RA 3,080,755 T→G 21.0% F231V (TTC→GTC)  metK → S‑adenosylmethionine synthetase
RA 3,095,507 G→T 5.0% F235L (TTC→TTA trmI ← tRNA m(7)G46 methyltransferase, SAM‑dependent
RA 3,096,752 G→T 6.1% S127S (TCG→TCT mutY → adenine DNA glycosylase
RA 3,103,319 C→T 14.9% I136I (ATC→ATT yqgA → DUF554 family putative inner membrane protein
RA 3,110,066 A→C 5.6% V802V (GTT→GTG yghJ ← DUF4092 family putative lipoprotein peptidase
RA 3,111,434 C→A 62.3% A346A (GCG→GCT yghJ ← DUF4092 family putative lipoprotein peptidase
RA 3,116,892 C→A 5.5% L91L (CTG→CTT glcB ← malate synthase G
RA 3,120,216 C→A 58.5% D389Y (GAT→TAT)  glcD ← glycolate oxidase subunit, FAD‑linked
RA 3,126,414 C→A 5.4% R53L (CGG→CTG)  yghR ← putative ATP‑binding protein
RA 3,132,876 C→A 5.3% P264Q (CCG→CAG)  yghU → putative S‑transferase
RA 3,137,675 C→T 6.2% P275P (CCG→CCA hybA ← hydrogenase 2 4Fe‑4S ferredoxin‑type component
RA 3,151,657 G→T 9.3% D217Y (GAT→TAT)  yqhG → DUF3828 family putative periplasmic protein
RA 3,173,669 G→T 37.9% A189A (GCG→GCT ygiB → DUF1190 family protein
RA 3,181,300 C→T 5.7% pseudogene (521/2445 nt) yqiG → pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein
RA 3,182,319 G→T 11.0% pseudogene (1540/2445 nt) yqiG → pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein
RA 3,184,128 C→T 6.4% S46S (AGC→AGT yqiI → fimbrial protein
RA 3,192,913 C→A 5.5% A30S (GCA→TCA)  glnE ← fused deadenylyltransferase/adenylyltransferase for glutamine synthetase
RA 3,196,371 G→T 7.0% P374P (CCG→CCT cca → fused tRNA nucleotidyl transferase/2'3'‑cyclic phosphodiesterase/2'nucleotidase and phosphatase
RA 3,202,506 C→A 5.3% S375* (TCG→TAG)  ttdT → L‑tartrate/succinate antiporte
RA 3,209,857 C→A 6.4% intergenic (‑7/‑281) yqjH ← / → yqjI putative siderophore interacting protein/PadR family putative transcriptional regulator
RA 3,211,932 C→A 15.3% V168V (GTG→GTT aer ← fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component
RA 3,215,584 C→A 5.0% H254N (CAT→AAT)  ebgR → transcriptional repressor
RA 3,246,908 G→A 22.2% R222R (CGC→CGT yhaJ ← LysR family putative transcriptional regulator
RA 3,252,258 C→A 53.5% D251Y (GAT→TAT)  tdcG ← L‑serine dehydratase 3, anaerobic
RA 3,263,315 T→C 8.0% intergenic (+354/+260) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,263,460 C→A 7.3% intergenic (+499/+115) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,267,619 G→T 5.7% I216I (ATC→ATA garP ← putative (D)‑galactarate transporter
RA 3,278,427 C→A 17.8% C128* (TGC→TGA agaC → N‑acetylgalactosamine‑specific enzyme IIC component of PTS
RA 3,302,027 G→T 30.1% S86* (TCG→TAG)  nlpI ← lipoprotein involved in osmotic sensitivity and filamentation
RA 3,314,415 C→A 7.8% P186P (CCG→CCT yhbX ← putative EptAB family phosphoethanolamine transferase, inner membrane protein
RA 3,314,944 G→A 12.2% T10I (ACT→ATT)  yhbX ← putative EptAB family phosphoethanolamine transferase, inner membrane protein
RA 3,316,300 C→A 6.8% R377L (CGT→CTT)  glmM ← phosphoglucosamine mutase
RA 3,337,617 T→A 5.4% I105I (ATT→ATA lptB → lipopolysaccharide export ABC transporter ATP‑binding protein of the LptBFGC export complex
RA 3,346,662 G→T 9.3% R250S (CGC→AGC)  yhcC ← putative Fe‑S oxidoreductase, Radical SAM superfamily protein
RA 3,354,405 C→T 62.9% intergenic (+430/‑130) gltD → / → gltF glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA 3,365,797 A→T 5.1% V46E (GTA→GAA)  nanT ← sialic acid transporter
RA 3,371,372 G→T 12.7% I65I (ATC→ATA rpsI ← 30S ribosomal subunit protein S9
RA 3,373,985 C→A 59.5% intergenic (+37/‑117) yhcB → / → degQ DUF1043 family inner membrane‑anchored protein/serine endoprotease, periplasmic
RA 3,375,260 G→T 53.9% D387Y (GAT→TAT)  degQ → serine endoprotease, periplasmic
RA 3,378,352 G→T 8.1% V97V (GTG→GTT argR → l‑arginine‑responsive arginine metabolism regulon transcriptional regulator
RA 3,378,591 G→A 5.1% intergenic (+59/‑306) argR → / → yhcN l‑arginine‑responsive arginine metabolism regulon transcriptional regulator/cadmium and peroxide resistance protein, stress‑induced
RA 3,385,479 C→G 11.0% intergenic (‑92/+338) tldD ← / ← yhdP putative peptidase/DUF3971‑AsmA2 domains protein
RA 3,385,516 A→T 10.2% intergenic (‑129/+301) tldD ← / ← yhdP putative peptidase/DUF3971‑AsmA2 domains protein
RA 3,385,518 G→C 7.6% intergenic (‑131/+299) tldD ← / ← yhdP putative peptidase/DUF3971‑AsmA2 domains protein
RA 3,385,571 C→G 9.0% intergenic (‑184/+246) tldD ← / ← yhdP putative peptidase/DUF3971‑AsmA2 domains protein
RA 3,385,702 A→C 5.5% intergenic (‑315/+115) tldD ← / ← yhdP putative peptidase/DUF3971‑AsmA2 domains protein
RA 3,387,121 C→T 7.0% A833T (GCT→ACT)  yhdP ← DUF3971‑AsmA2 domains protein
RA 3,392,594 A→C 8.4% A248A (GCT→GCG mreC ← cell wall structural complex MreBCD transmembrane component MreC
RA 3,396,082 G→T 37.1% R204S (CGT→AGT)  csrD ← targeting factor for csrBC sRNA degradation
RA 3,400,220 C→A 9.9% I315I (ATC→ATA accC → acetyl‑CoA carboxylase, biotin carboxylase subunit
RA 3,416,666 T→G 11.4% intergenic (+113/+116) yhdZ → / ← rrfF putative amino‑acid transporter subunit/5S ribosomal RNA of rrnD operon
RA 3,440,151 G→T 38.2% I31I (ATC→ATA rpsN ← 30S ribosomal subunit protein S14
RA 3,440,444 G→T 55.0% S118S (TCC→TCA rplE ← 50S ribosomal subunit protein L5
RA 3,441,811 C→T 11.6% K39K (AAG→AAA rpsQ ← 30S ribosomal subunit protein S17
RA 3,455,867 C→A 57.5% I55I (ATC→ATA gspJ → putative general secretory pathway component, cryptic
RA 3,461,906 G→A 6.7% T436I (ACT→ATT)  chiA ← periplasmic endochitinase
RA 3,465,121 C→A 5.7% D585Y (GAC→TAC)  fusA ← protein chain elongation factor EF‑G, GTP‑binding
RA 3,469,871 T→A 5.0% intergenic (‑72/+95) yheO ← / ← fkpA putative PAS domain‑containing DNA‑binding transcriptional regulator/FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase)
RA 3,471,921 C→A 7.8% intergenic (‑65/+30) slyD ← / ← yheV FKBP‑type peptidyl prolyl cis‑trans isomerase (rotamase)/DUF2387 family putative metal‑binding protein
RA 3,473,139 G→T 57.7% I276I (ATC→ATA kefB ← potassium:proton antiporter
RA 3,476,265 G→A 5.2% A540T (GCC→ACC)  yheS → putative transporter subunit of ABC superfamily: ATP‑binding component
RA 3,477,579 G→T 8.7% C340F (TGT→TTT) 
M1M (ATG→ATT) †
yheT →
yheU →
UPF0017 family putative hydrolase
UPF0270 family protein
RA 3,495,992 G→A 10.2% M98I (ATG→ATA frlC → fructoselysine 3‑epimerase
RA 3,497,725 G→T 5.7% V105V (GTG→GTT frlR → putative DNA‑binding transcriptional regulator
RA 3,498,214 T→G 8.7% intergenic (+72/+80) frlR → / ← yhfS putative DNA‑binding transcriptional regulator/FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein
RA 3,501,910 G→A 11.3% H14Y (CAT→TAT)  php ← phosphotriesterase homology protein
RA 3,502,657 G→T 6.3% I172I (ATC→ATA yhfW ← phosphopentomutase‑related metalloenzyme superfamily protein
RA 3,504,812 C→T 12.5% E298K (GAA→AAA)  yhfZ ← putative DNA‑binding transcriptional regulator
RA 3,516,949 C→A 11.0% F240L (TTC→TTA mrcA → fused penicillin‑binding protein 1a: murein transglycosylase/murein transpeptidase
RA 3,519,657 G→T 100% intergenic (‑149/‑171) nudE ← / → yrfF adenosine nucleotide hydrolase; substrates include Ap3A, Ap2A, ADP‑ribose, NADH/inner membrane protein
RA 3,527,522 G→T 10.1% R449L (CGT→CTT)  pck → phosphoenolpyruvate carboxykinase
RA 3,529,524 G→T 13.6% F140L (TTC→TTA ompR ← response regulator in two‑component regulatory system with EnvZ
RA 3,530,481 G→T 17.2% R104L (CGT→CTT)  greB → transcript cleavage factor
RA 3,531,954 A→T 9.3% Q404L (CAG→CTG)  yhgF → putative transcriptional accessory protein
RA 3,539,825 G→T 5.0% intergenic (+267/‑93) nfuA → / → gntT Fe/S biogenesis protein; putative scaffold/chaperone for damaged Fe/S proteins/gluconate transporter, high‑affinity GNT I system
RA 3,543,959 G→T 55.0% A625E (GCG→GAG)  malP ← maltodextrin phosphorylase
RA 3,551,253 C→A 7.1% P62P (CCG→CCT rtcB ← RNA‑splicing ligase
RA 3,553,566 C→A 11.9% D134Y (GAT→TAT)  glpR ← GlpR DNA‑binding transcriptional repressor
RA 3,555,311 T→C 5.2% intergenic (‑128/‑62) glpE ← / → glpD thiosulfate:cyanide sulfurtransferase (rhodanese)/sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding
RA 3,555,325 T→C 21.7% intergenic (‑142/‑48) glpE ← / → glpD thiosulfate:cyanide sulfurtransferase (rhodanese)/sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding
RA 3,561,574 C→A 51.1% W372L (TGG→TTG)  glgC ← glucose‑1‑phosphate adenylyltransferase
RA 3,572,998 T→A 10.4% Y3F (TAC→TTC)  yhhW ← quercetinase activity in vitro
RA 3,574,166 G→T 6.0% intergenic (‑1/+121) yhhX ← / ← ryhB putative oxidoreductase/sRNA antisense regulator mediating positive Fur regulon response, Hfq‑dependent; global iron regulator
RA 3,575,020 G→A 9.0% intergenic (+34/‑203) yhhY → / → yhhZ putative acetyltransferase/putative Hcp1 family polymorphic toxin protein; putative colicin‑like DNase/tRNase activity
RA 3,575,575 T→A 5.6% I118N (ATC→AAC)  yhhZ → putative Hcp1 family polymorphic toxin protein; putative colicin‑like DNase/tRNase activity
RA 3,579,422 C→A 5.9% E254D (GAG→GAT ggt ← gamma‑glutamyltranspeptidase
RA 3,609,368 T→A 9.1% F256L (TTT→TTA nikB → nickel transporter subunit
RA 3,622,519 C→A 11.1% R127L (CGA→CTA)  rbbA ← ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein
RA 3,627,494 T→C 5.2% pseudogene (325/1194 nt) yhiL ← pseudogene, DUF4049 family protein
RA 3,631,222 A→G 6.9% Y74C (TAT→TGT)  pitA → phosphate transporter, low‑affinity; tellurite importer
RA 3,634,084 C→T 14.5% intergenic (+179/‑138) uspA → / → dtpB universal stress global response regulator/dipeptide and tripeptide permease B
RA 3,636,207 T→A 9.8% T96S (ACT→TCT)  rsmJ ← 16S rRNA m(2)G1516 methyltransferase, SAM‑dependent
RA 3,640,489 T→A 13.1% V277V (GTT→GTA gor → glutathione oxidoreductase
RA 3,646,542 C→A 11.3% S6I (AGC→ATC)  insH1 ← IS5 transposase and trans‑activator
RA 3,657,073 C→A 6.3% intergenic (+186/+177) mdtF → / ← gadW anaerobic multidrug efflux transporter, ArcA‑regulated/transcriptional activator of gadA and gadBC; repressor of gadX
RA 3,662,801 T→A 7.8% intergenic (‑253/‑151) yhjA ← / → treF putative cytochrome C peroxidase/cytoplasmic trehalase
RA 3,671,771 T→A 12.5% intergenic (‑61/+9) yhjG ← / ← yhjH putative inner membrane‑anchored periplasmic AsmA family protein/cyclic‑di‑GMP phosphodiesterase, FlhDC‑regulated
RA 3,679,301 T→G 37.5% Q1078P (CAG→CCG)  bcsC ← cellulose synthase subunit
RA 3,679,324 C→A 58.8% M1070I (ATG→ATT bcsC ← cellulose synthase subunit
RA 3,681,219 C→A 11.1% A439S (GCG→TCG)  bcsC ← cellulose synthase subunit
RA 3,698,074 C→A 9.3% M16I (ATG→ATT dppC ← dipeptide/heme transporter
RA 3,721,480 T→G 7.4% T418P (ACG→CCG)  xylB ← xylulokinase
RA 3,721,485 T→G 8.5% Y416S (TAC→TCC)  xylB ← xylulokinase
RA 3,727,917 C→A 5.7% L280I (CTC→ATC)  xylH → D‑xylose ABC transporter permease subunit
RA 3,731,688 C→T 8.3% Q278* (CAG→TAG)  malS → alpha‑amylase
RA 3,733,135 A→T 12.0% N24I (AAC→ATC)  avtA → valine‑pyruvate aminotransferase 1
RA 3,738,431 C→A 48.5% P90T (CCA→ACA)  yiaN → 2,3‑diketo‑L‑gulonate TRAP transporter large permease protein
RA 3,745,447 C→A 6.5% I32I (ATC→ATA yiaU → putative DNA‑binding transcriptional regulator
RA 3,751,414 T→G 13.2% H603P (CAT→CCT)  selB ← selenocysteinyl‑tRNA‑specific translation factor
RA 3,758,601 G→T 8.2% R1020L (CGG→CTG)  rhsA → Rhs family protein, putative polymorphic toxin; putative polysaccharide synthesis/export protein; putative neighboring cell growth inhibitor
RA 3,774,410 T→A 9.4% intergenic (+33/‑165) lldD → / → trmL L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
RA 3,780,155 C→A 5.3% I512I (ATC→ATA gpmM → phosphoglycero mutase III, cofactor‑independent
RA 3,785,915 G→T 48.4% intergenic (‑4/+271) kbl ← / ← yibB glycine C‑acetyltransferase/YibB family protein, function unknown
RA 3,786,687 C→A 6.4% L119F (TTG→TTT yibB ← YibB family protein, function unknown
RA 3,810,195 C→A 50.0% R54S (CGT→AGT)  yicC → UPF0701 family protein
RA 3,813,962 T→C 13.5% Q190R (CAA→CGA)  ligB ← DNA ligase, NAD(+)‑dependent
RA 3,816,601 A→T 81.4% H281L (CAC→CTC)  spoT → bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA 3,818,010 C→A 46.1% H46N (CAT→AAT)  trmH → tRNA mG18‑2'‑O‑methyltransferase, SAM‑dependent
RA 3,822,340 A→C 14.6% Q12H (CAA→CAC xanP → xanthine permease
RA 3,822,345 T→G 7.2% V14G (GTT→GGT)  xanP → xanthine permease
RA 3,825,702 C→A 57.2% K732N (AAG→AAT yicI ← putative alpha‑glucosidase
RA 3,830,311 G→T 29.4% intergenic (+395/‑2) yicT → / → setC pseudogene/putative arabinose efflux transporter
RA 3,837,177 C→T 24.9% intergenic (‑28/‑147) yicO ← / → ade putative adenine permease/cryptic adenine deaminase
RA 3,839,562 C→A 6.5% A322A (GCG→GCT uhpT ← hexose phosphate transporter
RA 3,844,801 C→A 6.2% M448I (ATG→ATT ilvB ← acetolactate synthase 2 large subunit
RA 3,846,882 T→G 5.5% intergenic (‑265/‑31) istR ← / → tisB sRNA antisense regulators IstR‑1 and IstR‑2, affectr tisB, Hfq‑dependent/toxic membrane persister formation peptide, LexA‑regulated
RA 3,850,839 G→T 20.9% P309Q (CCG→CAG)  yidJ ← sulfatase/phosphatase superfamily protein
RA 3,860,159 C→A 48.4% P33P (CCG→CCT ibpB ← heat shock chaperone
RA 3,868,359 C→A 11.9% A54A (GCG→GCT dgoR ← putative DNA‑binding transcriptional regulator
RA 3,888,527 G→T 13.4% L172L (CTG→CTT chrR → chromate reductase, Class I, flavoprotein
RA 3,895,371 C→A 11.8% T70T (ACG→ACT bglH ← carbohydrate‑specific outer membrane porin, cryptic
RA 3,897,492 G→T 8.4% P489Q (CCG→CAG)  bglF ← fused beta‑glucoside‑specific PTS enzymes: IIA component/IIB component/IIC component
RA 3,898,210 G→T 7.4% L250I (CTA→ATA)  bglF ← fused beta‑glucoside‑specific PTS enzymes: IIA component/IIB component/IIC component
RA 3,901,867 T→G 6.1% intergenic (‑141/+42) pstB ← / ← pstA phosphate transporter subunit/phosphate transporter subunit
RA 3,907,094 G→A 19.4% intergenic (‑66/+96) glmS ← / ← glmU L‑glutamine:D‑fructose‑6‑phosphate aminotransferase/fused N‑acetyl glucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyl transferase
RA 3,910,894 C→A 55.3% M244I (ATG→ATT atpG ← F1 sector of membrane‑bound ATP synthase, gamma subunit
RA 3,912,648 A→T 9.1% G190G (GGT→GGA atpA ← F1 sector of membrane‑bound ATP synthase, alpha subunit
RA 3,915,397 A→C 7.2% N5K (AAT→AAG atpB ← F0 sector of membrane‑bound ATP synthase, subunit a
RA 3,921,086 A→T 7.3% K191I (AAA→ATA)  asnA → asparagine synthetase A
RA 3,923,700 G→T 6.7% R252S (CGC→AGC)  ravA ← hexameric AAA+ MoxR family ATPase, putative molecular chaperone
RA 3,924,918 G→A 7.0% G81G (GGG→GGA kup → potassium transporter
RA 3,930,891 G→T 9.3% D80Y (GAT→TAT)  rbsK → ribokinase
RA 3,960,036 G→A 81.7% R87H (CGC→CAC)  rho → transcription termination factor
RA 3,964,617 A→T 8.7% S375S (TCA→TCT wecB → UDP‑N‑acetyl glucosamine‑2‑epimerase
RA 3,975,679 A→C 6.0% intergenic (+47/‑56) yifK → / → argX putative APC family amino acid transporter/tRNA‑Arg
RA 3,994,247 A→T 63.0% V57E (GTG→GAG)  yigE ← DUF2233 family protein
RA 3,999,888 A→G 6.2% K222R (AAA→AGA)  recQ → ATP‑dependent DNA helicase
RA 4,009,705 G→A 46.7% intergenic (‑176/‑86) ysgA ← / → udp putative carboxymethylenebutenolidase/uridine phosphorylase
RA 4,037,227 G→T 5.2% V150V (GTG→GTT dsbA → periplasmic protein disulfide isomerase I
RA 4,049,008 A→T 16.3% L231Q (CTG→CAG)  glnL ← sensory histidine kinase in two‑component regulatory system with GlnG
RA 4,056,018 T→A 58.2% F138I (TTC→ATC)  yihN → MFS transporter family protein
RA 4,062,424 G→T 49.0% I71I (ATC→ATA yihQ ← alpha‑glucosidase
RA 4,064,048 T→G 11.8% N357H (AAT→CAT)  yihS ← aldose‑ketose isomerase; D‑mannose isomerase
RA 4,066,133 T→G 54.3% S267R (AGC→CGC)  yihU ← gamma‑hydroxybutyrate dehydrogenase, NADH‑dependent
RA 4,068,208 C→A 57.1% G60G (GGC→GGA yihW → DeoR family putative transcriptional regulator
RA 4,080,364 G→T 9.2% M1M (ATG→ATT) † yiiG → DUF3829 family lipoprotein
RA 4,081,000 A→C 5.1% E213D (GAA→GAC yiiG → DUF3829 family lipoprotein
RA 4,094,362 C→A 59.2% W181L (TGG→TTG)  cpxA ← sensory histidine kinase in two‑component regulatory system with CpxR
RA 4,096,163 G→T 10.2% R139L (CGA→CTA)  cpxP → inhibitor of the cpx response; periplasmic adaptor protein
RA 4,097,822 G→T 35.6% E115* (GAA→TAA)  pfkA → 6‑phosphofructokinase I
RA 4,127,022 T→G 51.0% E188D (GAA→GAC yijF ← DUF1287 family protein
RA 4,142,369 A→T 10.1% Y220N (TAC→AAC)  ppc ← phosphoenolpyruvate carboxylase
RA 4,143,544 C→T 6.0% intergenic (‑518/+80) ppc ← / ← argE phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA 4,152,581 T→C 8.6% V206V (GTA→GTG trmA ← tRNA m(5)U54 methyltransferase, SAM‑dependent; tmRNA m(5)U341 methyltransferase
RA 4,158,250 A→C 9.9% intergenic (+122/‑50) rrsB → / → gltT 16S ribosomal RNA of rrnB operon/tRNA‑Glu
RA 4,164,396 C→A 6.0% D187Y (GAT→TAT)  coaA ← pantothenate kinase
RA 4,172,013 G→A 5.4% D281N (GAC→AAC)  rpoB → RNA polymerase, beta subunit
RA 4,175,869 T→A 13.2% C198S (TGC→AGC)  rpoC → RNA polymerase, beta prime subunit
RA 4,176,823 G→T 42.1% D516Y (GAC→TAC)  rpoC → RNA polymerase, beta prime subunit
RA 4,211,803 G→A 33.0% P205S (CCT→TCT)  arpA ← ankyrin repeat protein
RA 4,212,014 G→T 7.0% F134L (TTC→TTA arpA ← ankyrin repeat protein
RA 4,219,527 C→A 7.1% A182S (GCG→TCG)  pepE ← (alpha)‑aspartyl dipeptidase
RA 4,230,913 A→T 29.2% W424R (TGG→AGG)  xylE ← D‑xylose transporter
RA 4,246,967 G→T 6.3% intergenic (+34/‑76) dgkA → / → lexA diacylglycerol kinase/transcriptional repressor of SOS regulon
RA 4,250,821 C→A 5.9% Q99K (CAG→AAG)  yjbM → uncharacterized protein
RA 4,271,152 G→T 11.8% M415I (ATG→ATT yjcE → putative cation/proton antiporter
RA 4,273,077 C→A 6.5% intergenic (‑74/+104) yjcF ← / ← actP pentapeptide repeats protein/acetate transporter
RA 4,273,158 A→T 11.6% intergenic (‑155/+23) yjcF ← / ← actP pentapeptide repeats protein/acetate transporter
RA 4,274,926 A→C 5.0% I72M (ATT→ATG yjcH ← DUF485 family inner membrane protein
RA 4,280,478 T→G 5.4% I25M (ATT→ATG nrfD → formate‑dependent nitrite reductase, membrane subunit
RA 4,286,083 T→C 5.9% intergenic (+361/+170) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,290,080 G→T 35.5% I256I (ATC→ATA mdtP ← outer membrane factor of efflux pump
RA 4,291,537 G→T 13.3% I453I (ATC→ATA mdtO ← membrane translocase (MDR) of MdtNOP efflux pump, PET family
RA 4,294,039 A→G 6.7% I61T (ATT→ACT)  ytcA ← putative inner membrane DUF1656 family protein; efflux pump associated
RA 4,295,572 C→T 5.9% E281E (GAG→GAA yjcS ← metallo‑beta‑lactamase superfamily protein
RA 4,295,721 A→G 11.2% Y232H (TAC→CAC)  yjcS ← metallo‑beta‑lactamase superfamily protein
RA 4,297,846 C→A 79.1% M150I (ATG→ATT alsE ← allulose‑6‑phosphate 3‑epimerase
RA 4,302,249 T→A 6.3% Q187L (CAG→CTG)  alsR ← d‑allose‑inducible als operon transcriptional repressor; autorepressor; repressor of rpiR
RA 4,303,256 G→T 9.1% V30V (GTG→GTT rpiB → ribose 5‑phosphate isomerase B/allose 6‑phosphate isomerase
RA 4,303,614 T→A 29.9% *150R (TGA→AGA)  rpiB → ribose 5‑phosphate isomerase B/allose 6‑phosphate isomerase
RA 4,306,969 T→A 19.0% N23Y (AAC→TAC)  phnM ← ribophosphonate triphosphate hydrolase
RA 4,312,246 C→A 16.2% intergenic (‑7/+14) phnF ← / ← phnE putative DNA‑binding transcriptional regulator of phosphonate uptake and biodegradation/defective phosphonate ABC transporter permease;transport; Transport of small molecules: Anions; membrane channel protein component of Pn transporter; membrane component of ABC superfamily
RA 4,315,765 A→G 6.0% intergenic (‑207/+451) yjdN ← / ← yjdM metalloprotein superfamily protein/zinc‑ribbon family protein
RA 4,356,453 C→A 8.2% P46P (CCG→CCT dcuA ← C4‑dicarboxylate antiporter
RA 4,367,995 G→A 10.0% P256L (CCC→CTC)  ampC ← penicillin‑binding protein; beta‑lactamase, intrinsically weak
RA 4,380,814 C→A 5.5% A171A (GCG→GCT rsgA ← ribosome small subunit‑dependent GTPase A
RA 4,382,806 T→A 12.5% Q360L (CAA→CTA)  queG ← epoxyqueuosine reductase, cobalamine‑stimulated; queosine biosynthesis
RA 4,388,902 G→T 53.7% A558A (GCG→GCT mutL → methyl‑directed mismatch repair protein
RA 4,396,598 A→T 53.5% E43V (GAA→GTA)  rnr → exoribonuclease R, RNase R
RA 4,413,425 G→T 5.2% E255* (GAA→TAA)  ulaE → L‑xylulose 5‑phosphate 3‑epimerase
RA 4,431,847 C→T 5.4% A49A (GCG→GCA msrA ← methionine sulfoxide reductase A
RA 4,440,479 C→T 9.8% A234V (GCG→GTG)  ytfQ → galactofuranose binding proteint: periplasmic‑binding component of ABC superfamily
RA 4,450,473 C→A 6.3% D669Y (GAC→TAC)  nrdD ← anaerobic ribonucleoside‑triphosphate reductase
RA 4,458,254 T→A 48.9% V271V (GTT→GTA mgtA → magnesium transporter
RA 4,458,609 G→T 61.0% D390Y (GAT→TAT)  mgtA → magnesium transporter
RA 4,463,946 C→A 6.0% V2V (GTC→GTA bdcR → transcriptional repressor for divergent bdcA
RA 4,464,572 G→T 14.2% intergenic (+38/‑107) bdcR → / → tabA transcriptional repressor for divergent bdcA/biofilm modulator regulated by toxins; DUF386 family protein, cupin superfamily
RA 4,469,550 G→A 28.7% A2T (GCT→ACT)  yjgN → DUF898 family inner membrane protein
RA 4,470,017 G→A 49.5% M157I (ATG→ATA yjgN → DUF898 family inner membrane protein
RA 4,478,322 G→A 5.7% intergenic (+105/+56) lptG → / ← yjgR lipopolysaccharide export ABC permease of the LptBFGC export complex/DUF853 family protein with NTPase fold
RA 4,480,048 G→A 5.4% A303A (GCC→GCT idnR ← transcriptional repressor, 5‑gluconate‑binding
RA 4,489,542 A→T 10.2% pseudogene (810/942 nt) yjgX ← pseudogene fragment
RA 4,493,546 G→T 5.7% intergenic (‑298/‑329) insG ← / → yjhB IS4 transposase/putative transporter
RA 4,502,777 G→A 5.7% N150N (AAC→AAT fecC ← iron‑dicitrate transporter subunit
RA 4,505,471 C→T 6.6% D342N (GAC→AAC)  fecA ← ferric citrate outer membrane transporter
RA 4,510,428 G→T 21.7% intergenic (‑287/+60) yjhU ← / ← yjhF putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA 4,511,877 G→A 13.6% intergenic (‑40/+67) yjhF ← / ← yjhG putative transporter/putative dehydratase
RA 4,512,693 T→A 58.5% K407* (AAG→TAG)  yjhG ← putative dehydratase
RA 4,521,271 C→A 6.8% A66A (GCG→GCT sgcX ← putative endoglucanase with Zn‑dependent exopeptidase domain
RA 4,522,721 C→A 5.4% D94Y (GAT→TAT)  yjhP ← putative methyltransferase
RA 4,525,234 G→A 49.2% pseudogene (415/1029 nt) yjhR → pseudogene, helicase family; putative frameshift suppressor
RA 4,531,143 A→T 52.7% I124F (ATT→TTT)  fimB → tyrosine recombinase/inversion of on/off regulator of fimA
RA 4,540,328 G→T 5.1% I262I (ATC→ATA gntP ← fructuronate transporter
RA 4,556,296 C→T 21.7% Q256Q (CAG→CAA yjiN ← zinc‑type alcohol dehydrogenase‑like protein
RA 4,562,043 C→A 49.4% intergenic (+311/‑188) yjiS → / → yjiT DUF1127 family protein/pseudogene
RA 4,579,917 C→A 6.8% A394S (GCG→TCG)  yjiY ← putative transporter
RA 4,582,677 G→T 6.3% E402* (GAA→TAA)  tsr → methyl‑accepting chemotaxis protein I, serine sensor receptor
RA 4,584,381 G→T 57.8% I53I (ATC→ATA yjjL ← L‑galactonate transporter
RA 4,588,471 G→A 6.8% A263V (GCG→GTG)  opgB ← phosphoglycerol transferases I and II
RA 4,601,014 T→C 11.5% intergenic (+194/‑199) prfC → / → osmY peptide chain release factor RF‑3/periplasmic protein
RA 4,603,129 T→G 6.9% V301G (GTT→GGT)  yjjU → putative patatin‑like family phospholipase
RA 4,604,195 A→G 7.5% intergenic (+118/+302) yjjV → / ← yjjW putative DNase/putative pyruvate formate lyase activating enzyme
RA 4,604,616 C→A 6.1% G249C (GGC→TGC)  yjjW ← putative pyruvate formate lyase activating enzyme
JC 4,615,993 Δ3 bp 5.9% coding (265‑267/1383 nt) radA → DNA repair protein
RA 4,626,235 G→T 11.8% E138* (GAA→TAA)  creB → response regulator in two‑component regulatory system with CreC
RA 4,629,507 C→A 5.6% R206L (CGC→CTC)  arcA ← response regulator in two‑component regulatory system with ArcB or CpxA
RA 4,629,622 C→A 7.0% A168S (GCC→TCC)  arcA ← response regulator in two‑component regulatory system with ArcB or CpxA

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP009273 373836 375121 1286 206 [204] [203] 206 frmA–[frmR] frmA,[frmR]
* * ÷ CP009273 4100608 4101527 920 207 [202] [204] 206 [cdh]–tpiA [cdh],tpiA

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 = 289472223 (0.750)13 (0.040) 11/274 NT 5.5% coding (158/699 nt) yagL CP4‑6 prophage; DNA‑binding protein
?CP009273 = 1463497 NA (NA)noncoding (1/1331 nt) IS2 repeat region
* ? CP009273 360104 =235 (0.790)182 (0.610) 98/276 NT 43.6% intergenic (‑38/+557) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 360286 NA (NA)intergenic (‑220/+375) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
* ? CP009273 = 360278NA (NA)5597 (19.880)
+TTAATTAA
194/260 NT 95.7% intergenic (‑212/+383) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 361823 267 (0.890)coding (831/834 nt) mhpR mhp operon transcriptional activator
* ? CP009273 360652 =301 (1.010)5640 (28.400)
+46 bp
183/184 NT 96.8% intergenic (‑586/+9) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 1317577 253 (0.850)coding (101/882 nt) yciV PHP domain protein
* ? CP009273 376716 =NA (NA)29 (0.100) 21/276 NT 9.7% intergenic (‑1/‑91) yaiX/insC1 pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA
?CP009273 = 386403 271 (0.910)pseudogene (697/1458 nt) yaiT pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
* ? CP009273 376716 =NA (NA)225 (0.750) 130/276 NT 81.5% intergenic (‑1/‑91) yaiX/insC1 pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA
?CP009273 566411 = 51 (0.170)coding (63/552 nt) ybcL inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
* ? CP009273 = 378046NA (NA)47 (0.160) 30/276 NT 14.8% intergenic (+11/+1) insD1/yaiX IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
?CP009273 386399 = 271 (0.910)pseudogene (693/1458 nt) yaiT pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
* ? CP009273 = 378046NA (NA)235 (0.790) 132/276 NT 82.2% intergenic (+11/+1) insD1/yaiX IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
?CP009273 = 566415 51 (0.170)coding (67/552 nt) ybcL inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
* ? CP009273 777033 =147 (0.490)74 (0.250)
+G
6/274 NT 27.7% noncoding (1/76 nt) lysQ tRNA‑Lys
?CP009273 = 2514488 242 (0.810)noncoding (216/1345 nt) IS186 repeat region
* ? CP009273 1203246 =35 (0.120)211 (0.800) 116/244 NT 85.8% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 1205075 = 39 (0.150)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 120326135 (0.120)232 (0.880) 116/244 NT 86.9% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 = 1205058 39 (0.150)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 1635219 =145 (0.490)186 (0.630) 103/272 NT 56.2% intergenic (‑377/+377) essQ/cspB Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
?CP009273 = 2063752 NA (NA)noncoding (1/1331 nt) IS2 repeat region
* ? CP009273 = 1635223150 (0.500)145 (0.490) 88/276 NT 49.2% intergenic (‑381/+373) essQ/cspB Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
?CP009273 = 1645805 NA (NA)intergenic (+11/‑3) insD1/intQ IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related
* ? CP009273 = 3613151NA (NA)4 (0.010) 4/258 NT 100% coding (600/4236 nt) rhsB Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor
?CP009273 3613476 = 0 (0.000)coding (925/4236 nt) rhsB Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor
* ? CP009273 3904514 =239 (0.800)44 (0.150) 31/276 NT 15.5% coding (372/1041 nt) pstS periplasmic phosphate binding protein, high‑affinity
?CP009273 4487998 = NA (NA)intergenic (+241/‑91) intB/insC1 pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase/IS2 repressor TnpA
* ? CP009273 = 3904519257 (0.860)34 (0.110) 26/274 NT 11.8% coding (367/1041 nt) pstS periplasmic phosphate binding protein, high‑affinity
?CP009273 = 4489327 NA (NA)intergenic (+10/+83) insD1/yjgX IS2 transposase TnpB/pseudogene fragment
* ? CP009273 4532499 =210 (0.700)31 (0.110) 25/258 NT 11.2% intergenic (+49/‑433) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?CP009273 4532813 = 294 (1.050)intergenic (+363/‑119) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
* ? CP009273 = 4532507214 (0.720)39 (0.140) 29/258 NT 13.6% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?CP009273 = 4532803 294 (1.050)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)