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 2,706 G→T 22.7% L790F (TTG→TTT)  thrA → Bifunctional aspartokinase/homoserine dehydrogenase 1
RA 5,144 G→A 68.9% intergenic (+124/‑90) thrC → / → yaaX L‑threonine synthase/DUF2502 family putative periplasmic protein
RA 7,905 A→C 19.9% Y19D (TAC→GAC)  yaaJ ← putative transporter
RA 10,444 G→T 68.2% F17L (TTC→TTA)  satP ← succinate‑acetate transporter
RA 21,046 G→T 17.2% A11A (GCC→GCA)  rpsT ← 30S ribosomal subunit protein S20
RA 25,546 G→T 52.2% D114Y (GAC→TAC)  lspA → prolipoprotein signal peptidase (signal peptidase II)
RA 29,139 G→T 53.9% G256C (GGT→TGT)  dapB → dihydrodipicolinate reductase
RA 37,692 G→T 9.6% Q45K (CAG→AAG)  caiC ← putative crotonobetaine/carnitine‑CoA ligase
RA 44,123 G→T 6.1% A312A (GCG→GCT)  fixB → putative electron transfer flavoprotein, NAD/FAD‑binding domain and ETFP adenine nucleotide‑binding domain‑like protein
RA 48,260 G→T 18.7% A164A (GCG→GCT)  kefC → potassium:proton antiporter
RA 49,840 G→T 65.4% A6A (GCG→GCT)  folA → dihydrofolate reductase
RA 54,203 T→G 23.3% Q167P (CAA→CCA)  surA ← peptidyl‑prolyl cis‑trans isomerase (PPIase)
RA 55,590 G→T 58.9% T507K (ACG→AAG)  lptD ← LPS assembly OM complex LptDE, beta‑barrel component
RA 56,677 G→T 64.9% R145S (CGC→AGC)  lptD ← LPS assembly OM complex LptDE, beta‑barrel component
RA 67,293 C→A 20.6% A140A (GCC→GCA)  araC → ara regulon transcriptional activator; autorepressor
RA 80,123 C→T 48.9% G25S (GGC→AGC)  leuL ← leu operon leader peptide
RA 81,562 C→A 66.7% I236I (ATC→ATA)  leuO → global transcription factor
RA 85,890 G→T 33.9% intergenic (+371/‑231) cra → / → mraZ transcriptional repressor‑activator for carbon metabolism/RsmH methytransferase inhibitor
RA 97,521 C→A 61.8% A90A (GCC→GCA)  murC → UDP‑N‑acetylmuramate:L‑alanine ligase
RA 100,166 C→A 17.7% R175R (CGC→CGA)  ftsQ → divisome assembly protein, membrane anchored protein involved in growth of wall at septum
RA 103,467 G→T 65.5% D142Y (GAT→TAT)  lpxC → UDP‑3‑O‑acyl N‑acetylglucosamine deacetylase
RA 104,561 G→T 63.0% A124S (GCG→TCG)  secM → regulator of secA translation
RA 112,609 T→A 22.1% V326V (GTA→GTT)  hofB ← T2SE secretion family protein; P‑loop ATPase superfamily protein
RA 118,828 G→T 23.6% D84Y (GAT→TAT)  pdhR → pyruvate dehydrogenase complex repressor; autorepressor
RA 118,873 G→T 66.1% D99Y (GAC→TAC)  pdhR → pyruvate dehydrogenase complex repressor; autorepressor
RA 121,438 C→T 25.9% H645H (CAC→CAT)  aceE → pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA 127,851 G→A 21.2% intergenic (‑104/‑251) yacH ← / → acnB uncharacterized protein/bifunctional aconitate hydratase 2/2‑methylisocitrate dehydratase
RA 140,496 A→T 14.3% H103L (CAC→CTC)  yadH → inner membrane putative ABC superfamily transporter permease
RA 142,460 T→A 65.1% F298Y (TTC→TAC)  yadE → putative polysaccharide deacetylase lipoprotein
RA 148,074 G→T 18.7% Q5K (CAA→AAA)  yadK ← putative fimbrial‑like adhesin protein
RA 149,044 A→T 23.3% C86S (TGC→AGC)  yadM ← putative fimbrial‑like adhesin protein
RA 153,472 G→T 65.4% intergenic (‑102/+268) yadN ← / ← folK putative fimbrial‑like adhesin protein/2‑amino‑4‑hydroxy‑6‑hydroxymethyldihyropteridine pyrophosphokinase
RA 154,689 C→A 18.5% D309Y (GAT→TAT)  pcnB ← poly(A) polymerase
RA 158,287 C→A 69.5% D78Y (GAC→TAC)  ligT ← 2'‑5' RNA ligase
RA 158,967 C→A 26.5% H126N (CAT→AAT)  hrpB → putative ATP‑dependent helicase
RA 166,356 C→A 31.3% S31* (TCG→TAG)  fhuC → iron‑hydroxamate transporter subunit
RA 168,383 G→T 18.7% T145T (ACG→ACT)  fhuB → fused iron‑hydroxamate transporter subunits of ABC superfamily: membrane components
RA 169,092 T→G 8.0% L382V (TTG→GTG)  fhuB → fused iron‑hydroxamate transporter subunits of ABC superfamily: membrane components
RA 169,937 C→A 26.0% intergenic (+6/+152) fhuB → / ← hemL fused iron‑hydroxamate transporter subunits of ABC superfamily: membrane components/glutamate‑1‑semialdehyde aminotransferase (aminomutase)
RA 169,940 T→A 11.2% intergenic (+9/+149) fhuB → / ← hemL fused iron‑hydroxamate transporter subunits of ABC superfamily: membrane components/glutamate‑1‑semialdehyde aminotransferase (aminomutase)
RA 169,942 T→A 9.7% intergenic (+11/+147) fhuB → / ← hemL fused iron‑hydroxamate transporter subunits of ABC superfamily: membrane components/glutamate‑1‑semialdehyde aminotransferase (aminomutase)
RA 186,279 A→T 39.2% noncoding (81/136 nt) tff → novel sRNA, function unknown
RA 187,241 A→T 21.9% intergenic (+155/‑103) rpsB → / → tsf 30S ribosomal subunit protein S2/translation elongation factor EF‑Ts
RA 188,863 T→A 22.4% D174E (GAT→GAA)  pyrH → uridylate kinase
RA 202,989 C→T 21.9% I459I (ATC→ATT)  dnaE → DNA polymerase III alpha subunit
RA 230,250 C→A 35.2% D65Y (GAC→TAC)  mltD ← putative membrane‑bound lytic murein transglycosylase D
RA 232,860 G→T 67.0% D103Y (GAT→TAT)  dnaQ → DNA polymerase III epsilon subunit
RA 233,053 A→C 24.0% D167A (GAT→GCT)  dnaQ → DNA polymerase III epsilon subunit
RA 233,931 G→A 35.0% S37N (AGT→AAT)  yafT → lipoprotein
RA 234,984 G→T 18.5% I80I (ATC→ATA) ‡ ykfM ← lethality reduction protein, putative inner membrane protein
RA 234,985 A→T 12.9% I80N (ATC→AAC) ‡ ykfM ← lethality reduction protein, putative inner membrane protein
RA 234,994 G→T 27.5% S77* (TCA→TAA)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,010 G→T 22.4% L72I (CTT→ATT)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,019 C→A 24.7% V69L (GTA→TTA)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,022 G→T 24.7% H68N (CAT→AAT)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 235,036 G→T 12.9% S63Y (TCC→TAC)  ykfM ← lethality reduction protein, putative inner membrane protein
RA 238,195 G→T 64.6% V532V (GTC→GTA)  fadE ← acyl coenzyme A dehydrogenase
RA 248,215 A→C 18.8% V277V (GTA→GTC)  dinB → DNA polymerase IV
RA 249,964 A→T 20.9% intergenic (+316/‑2) yafP → / → ykfJ putative acyl‑CoA transferase/pseudogene
RA 267,806 G→T 15.9% pseudogene (332/426 nt) insN → pseudogene, IS911 transposase A;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related
RA 268,570 G→T 22.1% pseudogene (13/1108 nt) ykfC → CP4‑6 prophage; conserved protein;Phage or Prophage Related
RA 274,735 A→T 56.7% pseudogene (138/348 nt) afuB ← pseudogene, CP4‑6 prophage; ABC transporter permease family;Phage or Prophage Related
RA 278,630 G→T 20.1% A214A (GCG→GCT)  yagE → 2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage
RA 280,145 G→A 21.5% E412K (GAG→AAG)  yagF → CP4‑6 prophage; dehydratase family protein
RA 283,602 A→T 7.8% Y368F (TAT→TTT)  yagH → CP4‑6 prophage; putative xylosidase/arabinosidase
RA 283,636 A→C 13.3% Q379H (CAA→CAC)  yagH → CP4‑6 prophage; putative xylosidase/arabinosidase
RA 301,675 G→T 20.0% S285* (TCG→TAG)  ecpD ← polymerized tip adhesin of ECP fibers
RA 306,510 G→A 22.7% R180W (CGG→TGG)  ecpR ← putative transcriptional regulator for the ecp operon
RA 308,879 G→A 13.6% Y25Y (TAC→TAT)  ykgR ← uncharacterized protein
RA 312,532 G→A 74.7% pseudogene (349/684 nt) ykgA ← pseudogene, AraC family;putative regulator; Not classified; putative ARAC‑type regulatory protein
RA 320,920 G→A 67.0% S52S (AGC→AGT)  ykgH ← putative inner membrane protein
RA 321,223 C→A 59.9% intergenic (‑148/+65) ykgH ← / ← betA putative inner membrane protein/choline dehydrogenase, a flavoprotein
RA 333,621 G→T 21.3% R378L (CGC→CTC)  yahF → putative NAD(P)‑binding succinyl‑CoA synthase
RA 341,704 T→A 16.8% T115T (ACA→ACT)  yahN ← amino acid exporter for proline, lysine, glutamate, homoserine
RA 344,800 G→T 48.5% E136D (GAG→GAT)  prpB → 2‑methylisocitrate lyase
RA 345,428 T→C 6.4% intergenic (+145/‑295) prpB → / → prpC 2‑methylisocitrate lyase/2‑methylcitrate synthase
RA 347,382 G→T 39.3% E153* (GAA→TAA)  prpD → 2‑methylcitrate dehydratase
RA 347,718 G→T 17.3% E265* (GAA→TAA)  prpD → 2‑methylcitrate dehydratase
RA 351,447 T→A 21.2% L272Q (CTG→CAG)  codB → cytosine transporter
RA 353,486 A→T 5.3% intergenic (+321/+16) codA → / ← cynR cytosine/isoguanine deaminase/transcriptional activator of cyn operon; autorepressor
RA 360,114 A→T 6.4% intergenic (‑48/+547) lacZ ← / ← lacI pseudogene, truncated/DNA‑binding transcriptional repressor
RA 360,157 T→G 8.1% intergenic (‑91/+504) lacZ ← / ← lacI pseudogene, truncated/DNA‑binding transcriptional repressor
RA 360,165 G→C 5.7% intergenic (‑99/+496) lacZ ← / ← lacI pseudogene, truncated/DNA‑binding transcriptional repressor
RA 360,173 C→A 5.4% intergenic (‑107/+488) lacZ ← / ← lacI pseudogene, truncated/DNA‑binding transcriptional repressor
RA 360,752 A→G 100% V331A (GTG→GCG)  lacI ← DNA‑binding transcriptional repressor
JC 361,139 +GCCA 9.2% 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 63.1% I165I (ATC→ATA)  mhpR ← mhp operon transcriptional activator
RA 369,273 G→T 25.5% A299A (GCG→GCT)  mhpF → acetaldehyde‑CoA dehydrogenase II, NAD‑binding
RA 382,882 G→A 19.2% A152A (GCG→GCA)  tauC → taurine transporter subunit
RA 395,611 C→A 21.6% D257Y (GAC→TAC)  ddlA ← D‑alanine‑D‑alanine ligase A
RA 396,883 A→G 59.2% Q14Q (CAA→CAG)  iraP → anti‑RssB factor, RpoS stabilzer during Pi starvation; anti‑adapter protein
RA 399,156 T→A 19.7% intergenic (+99/‑3) psiF → / → yaiC PsiF family protein/diguanylate cyclase, cellulose regualtor
RA 400,260 G→T 27.4% E368* (GAA→TAA)  yaiC → diguanylate cyclase, cellulose regualtor
RA 401,692 T→C 22.4% intergenic (+14/‑169) yaiI → / → aroL UPF0178 family protein/shikimate kinase II
RA 402,340 G→T 66.4% V160V (GTG→GTT)  aroL → shikimate kinase II
RA 406,075 C→A 69.4% P159Q (CCG→CAG)  mak → manno(fructo)kinase
RA 408,940 G→T 22.1% A757E (GCG→GAG)  sbcC ← exonuclease, dsDNA, ATP‑dependent
RA 411,027 G→T 67.4% L61L (CTC→CTA)  sbcC ← exonuclease, dsDNA, ATP‑dependent
RA 414,730 A→T 17.9% intergenic (+90/‑317) phoR → / → brnQ sensory histidine kinase in two‑component regulatory system with PhoB/branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val
RA 421,799 C→A 56.8% I69I (ATC→ATA)  tgt → tRNA‑guanine transglycosylase
RA 433,551 G→T 67.5% S14Y (TCC→TAC)  yajO ← 2‑carboxybenzaldehyde reductase
RA 434,663 A→C 65.9% I324S (ATC→AGC)  dxs ← 1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA 435,336 G→T 60.4% Q100K (CAG→AAG)  dxs ← 1‑deoxyxylulose‑5‑phosphate synthase, thiamine triphosphate‑binding, FAD‑requiring
RA 437,672 T→A 66.1% V223E (GTG→GAG)  thiI → tRNA s(4)U8 sulfurtransferase
RA 438,099 G→T 24.4% E365D (GAG→GAT)  thiI → tRNA s(4)U8 sulfurtransferase
RA 444,489 G→A 67.5% R537C (CGT→TGT)  cyoB ← cytochrome o ubiquinol oxidase subunit I
RA 451,853 C→A 33.7% T422N (ACC→AAC)  tig → peptidyl‑prolyl cis/trans isomerase (trigger factor)
RA 456,298 T→A 67.2% L652Q (CTG→CAG)  lon → DNA‑binding ATP‑dependent protease La
RA 456,588 G→T 63.5% D749Y (GAC→TAC)  lon → DNA‑binding ATP‑dependent protease La
RA 467,332 G→A 20.7% R414H (CGC→CAC)  mdlB → putative multidrug transporter subunit of ABC superfamily, ATP‑binding component
RA 474,138 G→T 72.6% intergenic (‑65/+99) ylaB ← / ← ylaC putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase/DUF1449 family inner membrane protein
RA 475,805 C→A 69.1% A120A (GCG→GCT)  tomB ← Hha toxicity attenuator; conjugation‑related protein
RA 479,244 C→A 65.0% A206S (GCC→TCC)  acrB ← multidrug efflux system protein
RA 480,820 C→T 64.4% D86N (GAC→AAC)  acrA ← multidrug efflux system
RA 481,667 G→A 58.9% A151T (GCG→ACG)  acrR → transcriptional repressor
RA 515,501 G→T 22.4% A105S (GCG→TCG)  ybbA → putative ABC superfamily transporter ATP‑binding subunit
RA 521,002 G→T 23.4% E762D (GAG→GAT)  rhsD → Rhs family putative polymorphic toxin
RA 529,771 C→T 25.0% R134C (CGT→TGT)  gcl → glyoxylate carboligase
RA 530,466 C→A 68.8% F365L (TTC→TTA)  gcl → glyoxylate carboligase
RA 542,200 Δ1 bp 72.1% coding (65/1668 nt) fdrA → putative NAD(P)‑binding acyl‑CoA synthetase
RA 545,522 C→A 27.4% A147E (GCG→GAG)  ylbF → putative anaerobic allantoin catabolic oxamate carbamoyltransferase; DUF2877 family protein
RA 546,491 G→T 64.2% V199V (GTG→GTT)  ybcF → putative carbonate kinase
RA 549,397 G→T 64.3% intergenic (‑1/+2) lpxH ← / ← ppiB UDP‑2,3‑diacylglucosamine pyrophosphohydrolase/peptidyl‑prolyl cis‑trans isomerase B (rotamase B)
RA 555,235 T→C 24.5% L28S (TTA→TCA)  sfmD → putative outer membrane export usher protein
RA 560,727 C→A 21.2% V236V (GTG→GTT)  intD ← DLP12 prophage; putative phage integrase
RA 565,475 C→T 25.5% A373V (GCT→GTT)  ybcK → DLP12 prophage; putative recombinase
RA 576,183 G→T 9.8% intergenic (‑282/‑107) ylcI ← / → nohD DUF3950 family protein, DLP12 prophage/DLP12 prophage; DNA packaging protein
RA 576,998 G→T 63.4% pseudogene (189/309 nt) aaaD → pseudogene; DLP12 prophage; tail fiber assembly protein family;Phage or Prophage Related
RA 579,565 A→G 23.6% G143G (GGA→GGG)  appY → global transcriptional activator; DLP12 prophage
RA 581,203 A→T 65.4% intergenic (‑114/‑310) ompT ← / → pauD DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)/tRNA‑OTHER
RA 583,341 T→G 73.7% S33R (AGT→CGT)  ybcH ← PRK09936 family protein
RA 595,957 T→G 19.4% I596M (ATT→ATG)  cusA → copper/silver efflux system, membrane component
RA 597,428 C→A 15.7% S5* (TCA→TAA)  pheP → phenylalanine transporter
RA 604,824 C→T 23.8% intergenic (+191/+91) insL1 → / ← entD IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex
RA 607,931 G→A 68.9% S7F (TCC→TTC)  fepA ← iron‑enterobactin outer membrane transporter
RA 625,364 G→T 67.5% G5G (GGG→GGT)  cstA → carbon starvation protein involved in peptide utilization; APC peptide transporter family protein
RA 631,333 G→A 21.6% N231N (AAC→AAT)  ybdN ← PAPS reductase‑like domain protein
RA 636,974 G→T 17.0% S117* (TCG→TAG)  uspG ← universal stress protein UP12
RA 637,005 C→A 20.5% D107Y (GAT→TAT)  uspG ← universal stress protein UP12
RA 639,231 G→A 70.9% L65F (CTT→TTT)  rnk ← regulator of nucleoside diphosphate kinase
RA 645,258 G→A 18.6% S230L (TCG→TTG)  citE ← citrate lyase, citryl‑ACP lyase (beta) subunit
RA 647,422 G→T 75.5% intergenic (‑110/‑269) citC ← / → citA [citrate [pro‑3S]‑lyase] ligase/sensory histidine kinase in two‑component regulatory system with CitB
RA 647,509 T→C 70.6% intergenic (‑197/‑182) citC ← / → citA [citrate [pro‑3S]‑lyase] ligase/sensory histidine kinase in two‑component regulatory system with CitB
RA 648,056 C→A 63.6% F122L (TTC→TTA)  citA → sensory histidine kinase in two‑component regulatory system with CitB
RA 652,680 Δ1 bp 18.2% intergenic (+107/‑68) pagP → / → cspE phospholipid:lipid A palmitoyltransferase/constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein
RA 652,865 Δ1 bp 72.1% coding (118/210 nt) cspE → constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein
RA 657,177 C→T 20.9% A186A (GCG→GCA)  lipB ← octanoyltransferase; octanoyl‑[ACP]:protein N‑octanoyltransferase
RA 662,108 A→T 64.5% V522V (GTT→GTA)  mrdA ← transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA 662,631 C→A 69.9% R348L (CGC→CTC)  mrdA ← transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA 691,170 A→T 16.9% Q205L (CAG→CTG)  ubiF → 2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase
RA 693,425 C→A 7.5% P403P (CCG→CCT)  asnB ← asparagine synthetase B
RA 705,588 C→A 64.1% intergenic (+16/+68) chiQ → / ← fur chitosugar‑induced verified lipoprotein/ferric iron uptake regulon transcriptional repressor; autorepressor
RA 715,664 A→T 20.2% C85S (TGC→AGC)  speF ← ornithine decarboxylase isozyme, inducible
RA 717,582 A→T 19.1% S763S (TCT→TCA)  kdpD ← fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein
RA 724,813 A→T 63.8% intergenic (+17/‑226) ybfA → / → rhsC DUF2517 family protein/Rhs family putative polymorphic toxin
RA 731,316 A→T 29.2% T71S (ACA→TCA)  ybfC → putative periplasmic protein
RA 733,047 G→A 22.9% pseudogene (767/1137 nt) ybfL → pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein
RA 734,414 C→A 22.9% intergenic (+105/‑43) ybfD → / → ybgA H repeat‑associated putative transposase/DUF1722 family protein
RA 742,332 G→T 21.0% G298G (GGC→GGA)  abrB ← regulator of aidB expression; inner membrane protein
RA 746,784 G→T 7.1% T281K (ACG→AAG)  ybgQ ← putative outer membrane protein
RA 754,572 G→T 69.5% E137D (GAG→GAT)  sucA → 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding
RA 759,000 C→A 69.0% F177L (TTC→TTA)  sucC → succinyl‑CoA synthetase, beta subunit
RA 766,563 G→A 26.0% intergenic (+496/‑351) mngB → / → cydA alpha‑mannosidase/cytochrome d terminal oxidase, subunit I
RA 772,664 A→C 11.5% K289N (AAA→AAC)  tolA → membrane anchored protein in TolA‑TolQ‑TolR complex
RA 776,389 G→C 6.4% intergenic (+15/‑135) lysW → / → valZ tRNA‑Lys/tRNA‑Val
RA 776,394 A→T 8.2% intergenic (+20/‑130) lysW → / → valZ tRNA‑Lys/tRNA‑Val
RA 788,902 G→T 63.0% R115S (CGT→AGT)  modF ← fused molybdate transporter subunits of ABC superfamily: ATP‑binding components
RA 800,488 G→T 59.0% V510V (GTG→GTT)  ybhJ → putative hydratase
RA 800,779 G→T 73.5% E607D (GAG→GAT)  ybhJ → putative hydratase
RA 828,374 G→T 61.7% V11V (GTC→GTA)  ybiA ← DUF1768 family protein
RA 832,445 G→T 59.5% P213P (CCG→CCT)  ybiC → putative dehydrogenase
RA 833,118 G→T 22.2% intergenic (+226/+3) ybiC → / ← ybiJ putative dehydrogenase/DUF1471 family putative periplasmic protein
RA 837,090 G→A 13.7% intergenic (‑103/+162) fiu ← / ← mcbA catecholate siderophore receptor Fiu/colanic acid mucoidy stimulation protein
RA 843,299 C→A 57.7% W54C (TGG→TGT)  glnH ← glutamine transporter subunit
RA 853,320 A→T 7.5% W400R (TGG→AGG)  ybiU ← DUF1479 family protein
RA 853,968 A→T 8.3% Y184N (TAC→AAC)  ybiU ← DUF1479 family protein
RA 873,699 G→T 13.4% intergenic (‑208/‑5) rimO ← / → bssR ribosomal protein S12 methylthiotransferase; radical SAM superfamily/repressor of biofilm formation by indole transport regulation
RA 876,447 G→A 61.0% D89N (GAT→AAT)  dacC → D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 6a)
RA 879,085 G→T 71.3% intergenic (‑241/‑44) ybjG ← / → mdfA undecaprenyl pyrophosphate phosphatase/multidrug efflux system protein
RA 915,267 G→A 21.1% E193K (GAA→AAA)  macA → macrolide transporter subunit, membrane fusion protein (MFP) component
RA 918,501 G→A 18.8% D45N (GAC→AAC)  clpS → regulatory protein for ClpA substrate specificity
RA 925,160 G→T 51.4% S420* (TCA→TAA)  cydD ← fused glutathione, cysteine exporter subunits of ABC superfamily: membrane component/ATP‑binding component
RA 932,915 C→A 28.3% R30S (CGC→AGC)  lolA → lipoprotein chaperone
RA 939,763 C→A 26.0% S92* (TCG→TAG)  dmsC → dimethyl sulfoxide reductase, anaerobic, subunit C
RA 943,573 G→T 51.6% A297S (GCC→TCC)  ycaM → putative transporter
RA 947,895 C→A 22.9% M372I (ATG→ATT)  pflB ← formate C‑acetyltransferase 1, anaerobic; pyruvate formate‑lyase 1
RA 948,015 C→A 24.4% P332P (CCG→CCT)  pflB ← formate C‑acetyltransferase 1, anaerobic; pyruvate formate‑lyase 1
RA 955,662 G→A 30.9% intergenic (+111/‑58) aroA → / → ycaL 5‑enolpyruvylshikimate‑3‑phosphate synthetase/putative peptidase‑related chaperone
RA 958,121 C→A 8.8% A224D (GCC→GAC)  rpsA → 30S ribosomal subunit protein S1
RA 961,946 T→A 26.5% F724Y (TTT→TAT)  ycaI → ComEC family inner membrane protein
RA 965,130 G→T 26.0% D96Y (GAC→TAC)  ycaQ → DUF1006 family protein with C‑terminal wHTH domain
RA 968,415 G→T 60.6% S148* (TCG→TAG)  ycbC ← DUF218 superfamily protein
RA 971,532 A→T 21.9% Q152L (CAG→CTG)  mukE → chromosome condensin MukBEF, MukE localization factor
RA 983,370 T→A 26.0% N358Y (AAC→TAC)  asnS ← asparaginyl tRNA synthetase
RA 984,870 T→A 8.2% N315Y (AAT→TAT)  pncB ← nicotinate phosphoribosyltransferase
RA 1,035,405 G→T 25.2% A218A (GCG→GCT)  cbdB → cytochrome bd‑II oxidase, subunit II
RA 1,039,635 C→T 14.2% G11D (GGC→GAC)  etk ← tyrosine‑protein kinase, role in O‑antigen capsule formation
RA 1,048,928 C→A 64.2% E903* (GAA→TAA)  torS ← hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA 1,049,407 G→T 57.0% T743K (ACG→AAG)  torS ← hybrid sensory histidine kinase in two‑component regulatory system with TorR
RA 1,060,633 A→G 31.2% N381S (AAC→AGC)  yccE → uncharacterized protein
RA 1,061,397 G→T 26.9% A119A (GCG→GCT)  agp → glucose‑1‑phosphatase/inositol phosphatase
RA 1,071,320 T→C 20.3% I1007V (ATC→GTC)  putA ← fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase
RA 1,077,911 A→C 71.8% K71N (AAA→AAC)  efeO → inactive ferrous ion transporter EfeUOB
RA 1,084,103 A→T 53.7% L404* (TTA→TAA)  pgaB ← poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein
RA 1,087,742 A→T 21.5% Y2N (TAT→AAT)  pgaA ← biofilm adhesin polysaccharide PGA secretin; OM porin; poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein
RA 1,102,255 G→T 25.3% G149C (GGT→TGT)  clsC → stationary phase cardiolipin synthase 3
RA 1,105,157 G→T 24.1% D123Y (GAT→TAT)  opgG → osmoregulated periplasmic glucan (OPG) biosynthesis periplasmic protein
RA 1,116,964 A→G 61.4% intergenic (‑21/+53) dinI ← / ← pyrC DNA damage‑inducible protein I/dihydro‑orotase
RA 1,118,506 A→T 10.1% L75Q (CTA→CAA)  yceB ← lipoprotein, DUF1439 family
RA 1,123,001 A→C 22.4% Q247P (CAG→CCG)  yceM → putative oxidoreductase
RA 1,151,711 C→A 22.3% A165E (GCG→GAG)  holB → DNA polymerase III, delta prime subunit
RA 1,151,750 G→T 64.6% R178L (CGC→CTC)  holB → DNA polymerase III, delta prime subunit
RA 1,152,062 C→A 19.0% S282Y (TCT→TAT)  holB → DNA polymerase III, delta prime subunit
RA 1,152,278 G→T 68.3% E16* (GAA→TAA)  ycfH → putative DNase
RA 1,186,393 G→A 23.3% I350I (ATC→ATT)  purB ← adenylosuccinate lyase
RA 1,192,525 C→T 19.8% S155N (AGC→AAC)  ymfD ← e14 prophage; putative SAM‑dependent methyltransferase
RA 1,193,873 G→T 65.6% intergenic (‑180/‑278) ymfE ← / → lit e14 prophage; putative inner membrane protein/e14 prophage; cell death peptidase, inhibitor of T4 late gene expression
RA 1,193,912 G→A 34.5% intergenic (‑219/‑239) ymfE ← / → lit e14 prophage; putative inner membrane protein/e14 prophage; cell death peptidase, inhibitor of T4 late gene expression
RA 1,197,734 C→T 14.4% R219K (AGA→AAA)  cohE ← e14 prophage; repressor protein phage e14
RA 1,210,957 C→A 25.5% 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 23.8% 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 1,211,169 C→A 54.3% intergenic (‑238/‑76) 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 1,219,533 A→G 64.1% intergenic (+170/+202) ycgI → / ← minE pseudogene/cell division topological specificity factor
RA 1,220,996 G→T 58.4% R181R (CGG→AGG)  minC ← cell division inhibitor
RA 1,221,492 T→C 17.9% L15L (TTA→TTG)  minC ← cell division inhibitor
RA 1,224,292 G→A 66.4% D8N (GAT→AAT)  ycgN → UPF0153 family cysteine cluster protein
RA 1,226,292 T→A 56.5% C24S (TGT→AGT)  umuD → DNA polymerase V, subunit D
RA 1,228,591 G→T 66.5% intergenic (‑105/+41) dsbB ← / ← nhaB oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I/sodium:proton antiporter
RA 1,232,548 C→A 20.1% V50V (GTG→GTT)  ycgB ← SpoVR family stationary phase protein
RA 1,246,190 G→A 22.9% V35V (GTC→GTT)  dhaK ← dihydroxyacetone kinase, PTS‑dependent, dihydroxyacetone‑binding subunit
RA 1,247,740 G→T 7.7% G407C (GGC→TGC)  dhaR → dhaKLM operon transcription activator
RA 1,253,559 G→T 21.3% I137I (ATC→ATA)  pth ← peptidyl‑tRNA hydrolase
RA 1,268,592 G→T 22.5% L210L (CTG→CTT)  chaC → cation transport regulator
RA 1,275,339 G→T 14.2% R7L (CGG→CTG)  narG → nitrate reductase 1, alpha subunit
RA 1,277,786 G→A 64.5% D823N (GAC→AAC)  narG → nitrate reductase 1, alpha subunit
RA 1,281,933 C→T 25.7% P210L (CCG→CTG)  narI → nitrate reductase 1, gamma (cytochrome b(NR)) subunit
RA 1,282,421 A→T 13.0% intergenic (+439/+101) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA 1,283,978 C→T 21.8% V35I (GTA→ATA)  purU ← formyltetrahydrofolate hydrolase
RA 1,292,363 G→A 23.8% I405I (ATC→ATT)  adhE ← fused acetaldehyde‑CoA dehydrogenase/iron‑dependent alcohol dehydrogenase/pyruvate‑formate lyase deactivase
RA 1,310,034 C→A 24.1% intergenic (‑7/+79) yciF ← / ← yciG putative rubrerythrin/ferritin‑like metal‑binding protein/KGG family protein
RA 1,322,140 T→A 67.9% T159S (ACG→TCG)  btuR ← cob(I)yrinic acid a,c‑diamide adenosyltransferase
RA 1,332,695 G→A 19.7% A870T (GCG→ACG)  acnA → aconitate hydratase 1
RA 1,337,533 G→T 62.2% A18E (GCA→GAA)  osmB ← lipoprotein
RA 1,338,978 G→A 21.6% intergenic (‑112/+36) yciZ ← / ← gmr uncharacterized protein/cyclic‑di‑GMP phosphodiesterase; csgD regulator; modulator of Rnase II stability
RA 1,345,657 C→A 18.8% intergenic (‑361/+7) fabI ← / ← ycjD enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein
RA 1,355,349 T→A 27.3% intergenic (‑184/‑28) puuA ← / → puuD glutamate‑‑putrescine ligase/gamma‑glutamyl‑gamma‑aminobutyrate hydrolase
RA 1,365,283 G→T 69.6% E271* (GAG→TAG)  ycjM → alpha amylase catalytic domain family protein
RA 1,368,566 T→G 25.6% F74V (TTC→GTC)  ycjP → inner membrane putative ABC superfamily sugar transporter permease
RA 1,374,303 T→C 16.4% R721R (CGT→CGC)  ycjT → putative family 65 glycosyl hydrolase
JC JC 1,376,043 IS5 (–) +4 bp 89.9% pseudogene (10‑13/126 nt) ycjV → pseudogene; putative ATP‑binding component of a transport system
RA 1,377,394 C→T 69.0% A275A (GCG→GCA)  ycjW ← LacI family putative transcriptional repressor
RA 1,385,964 T→G 15.9% Q49H (CAA→CAC)  ycjY ← S9 homolog non‑peptidase family protein
RA 1,386,008 G→T 68.5% Q35K (CAG→AAG)  ycjY ← S9 homolog non‑peptidase family protein
RA 1,388,406 G→T 63.8% R308L (CGC→CTC)  mppA → murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit
RA 1,395,312 A→T 24.5% L240* (TTA→TAA)  abgT ← p‑aminobenzoyl‑glutamate transporter; membrane protein
RA 1,401,206 G→T 18.7% Q283K (CAG→AAG)  ydaM ← diguanylate cyclase, csgD regulator
RA 1,408,561 C→A 21.5% E164* (GAA→TAA)  recT ← Rac prophage; recombination and repair protein
RA 1,413,956 G→T 24.2% intergenic (‑243/+66) ydaG ← / ← racR Rac prophage; uncharacterized protein/Rac prophage; putative DNA‑binding transcriptional regulator
RA 1,424,234 C→A 56.8% S310* (TCA→TAA)  stfR → Rac prophage; putative tail fiber protein
JC JC 1,428,894 IS2 (–) +5 bp 77.3% intergenic (‑413/+317) ynaE ← / ← ttcC cold shock protein, Rac prophage/pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
RA 1,434,444 G→T 6.3% R200S (CGC→AGC)  pfo ← pyruvate‑flavodoxin oxidoreductase
RA 1,439,234 G→T 36.1% D643Y (GAT→TAT)  ydbH → putative membrane‑anchored protein, function unknown
RA 1,439,518 C→A 48.1% S737S (TCC→TCA)  ydbH → putative membrane‑anchored protein, function unknown
RA 1,447,216 C→A 22.5% V228V (GTG→GTT)  paaZ ← fused oxepin‑CoA hydrolase/3‑oxo‑5,6‑dehydrosuberyl‑CoA semialdehyde dehydrogenase
RA 1,454,724 G→T 47.5% G472C (GGT→TGT)  paaH → 3‑hydroxyadipyl‑CoA dehydrogenase, NAD+‑dependent
RA 1,459,404 C→T 20.6% intergenic (+86/+18) paaY → / ← ynbG putative hexapeptide repeat acetyltransferase/uncharacterized protein
RA 1,459,405 G→A 20.2% intergenic (+87/+17) paaY → / ← ynbG putative hexapeptide repeat acetyltransferase/uncharacterized protein
RA 1,460,861 G→A 7.6% pseudogene (1213/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,499,789 C→A 8.0% A183A (GCG→GCT)  ydcO ← BenE family inner membrane putative transporter
RA 1,510,179 G→T 26.0% A115A (GCG→GCT)  patD → gamma‑aminobutyraldehyde dehydrogenase
RA 1,519,349 T→A 63.4% K297* (AAA→TAA)  ansP ← L‑asparagine transporter
RA 1,548,144 G→T 66.4% intergenic (‑49/+85) adhP ← / ← maeA ethanol‑active dehydrogenase/acetaldehyde‑active reductase/malate dehydrogenase, (decarboxylating, NAD‑requiring) (malic enzyme)
RA 1,555,079 C→T 20.8% P36P (CCG→CCA)  ddpB ← D‑ala‑D‑ala transporter subunit
RA 1,556,659 A→T 22.3% V27E (GTA→GAA)  ddpA ← D‑ala‑D‑a la transporter subunit
RA 1,563,276 G→T 66.1% H491N (CAC→AAC)  gadC ← glutamate:gamma‑aminobutyric acid antiporter
RA 1,565,497 G→A 70.6% S269L (TCG→TTG)  gadB ← glutamate decarboxylase B, PLP‑dependent
RA 1,575,339 G→T 69.1% F481L (TTC→TTA)  ydeN ← putative Ser‑type periplasmic non‑aryl sulfatase
RA 1,589,490 C→T 20.6% pseudogene (2755/5323 nt) yneO ← pseudogene, AidA homolog
RA 1,592,412 T→C 26.4% intergenic (‑168/+462) yneO ← / ← lsrK pseudogene, AidA homolog/autoinducer‑2 (AI‑2) kinase
RA 1,592,504 A→T 6.8% intergenic (‑260/+370) yneO ← / ← lsrK pseudogene, AidA homolog/autoinducer‑2 (AI‑2) kinase
RA 1,596,093 T→G 16.9% L116R (CTC→CGC)  lsrA → autoinducer 2 import ATP‑binding protein
RA 1,599,970 T→A 22.4% D221E (GAT→GAA)  lsrB → autoinducer 2‑binding protein
RA 1,603,440 G→A 64.8% intergenic (‑161/+46) yneE ← / ← uxaB bestrophin family putative inner membrane protein/altronate oxidoreductase, NAD‑dependent
RA 1,605,163 G→A 20.8% intergenic (‑226/+1) uxaB ← / ← yneF altronate oxidoreductase, NAD‑dependent/putative membrane‑bound diguanylate cyclase
RA 1,607,556 A→C 19.0% intergenic (‑48/+16) glsB ← / ← sad glutaminase 2/succinate semialdehyde dehydrogenase, NAD(P)+‑dependent
RA 1,612,820 T→A 13.5% S116C (AGT→TGT)  marC ← UPF0056 family inner membrane protein
RA 1,620,961 T→G 64.5% Q226P (CAA→CCA)  dcp ← dipeptidyl carboxypeptidase II
RA 1,627,174 C→A 26.8% intergenic (‑632/‑155) ydfJ ← / → ydfK pseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein/cold shock protein, function unknown, Qin prophage
RA 1,628,207 G→A 91.9% G110E (GGA→GAA)  pinQ → Qin prophage; putative site‑specific recombinase
RA 1,633,239 A→G 16.9% intergenic (‑315/+48) cspI ← / ← rzpQ Qin prophage; cold shock protein/Rz‑like protein, Qin prophage
RA 1,658,420 C→A 14.9% S185R (AGC→AGA)  ynfH → oxidoreductase, membrane subunit
RA 1,661,763 C→A 66.4% P353P (CCG→CCT)  mlc ← glucosamine anaerobic growth regulon transcriptional repressor; autorepressor
RA 1,663,893 C→T 27.5% intergenic (‑44/‑63) ynfL ← / → ynfM LysR family putative transcriptional regulator/putative arabinose efflux transporter
RA 1,673,381 C→A 7.0% S233* (TCA→TAA)  ydgH → DUF1471 family periplasmic protein
RA 1,679,816 C→A 21.9% D344Y (GAC→TAC)  fumC ← fumarate hydratase (fumarase C),aerobic Class II
RA 1,693,517 G→T 20.7% intergenic (‑80/‑95) malI ← / → malX transcriptional repressor of Mal regulon/fused maltose and glucose‑specific PTS enzymes: IIB component, IIC component
RA 1,696,612 A→T 70.5% E41D (GAA→GAT)  add → adenosine deaminase
RA 1,701,291 T→G 9.5% L39R (CTG→CGG)  rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,702,966 T→A 8.2% 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 11.8% 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 5.5% A632A (GCA→GCT)  rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
RA 1,706,734 C→T 20.7% intergenic (+319/‑292) nth → / → dtpA DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A
RA 1,711,397 C→T 70.4% R28Q (CGA→CAA)  tyrS ← tyrosyl‑tRNA synthetase
RA 1,754,950 T→A 51.7% I367F (ATT→TTT)  sufD ← component of SufBCD Fe‑S cluster assembly scaffold
RA 1,756,616 C→T 25.5% D52N (GAT→AAT)  sufC ← SufBCD Fe‑S cluster assembly scaffold protein, ATP‑binding protein
RA 1,758,835 T→A 9.8% intergenic (‑192/+135) sufA ← / ← rydB Fe‑S cluster assembly protein/novel sRNA, function unknown
RA 1,770,281 T→A 62.8% D146E (GAT→GAA)  ydiF → putative acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit/beta subunit
RA 1,783,665 A→C 22.8% D325A (GAC→GCC)  aroH → 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible
RA 1,796,428 C→A 9.9% V134F (GTC→TTC)  thrS ← threonyl‑tRNA synthetase
RA 1,798,001 T→A 18.4% pseudogene (227/1476 nt) arpB → pseudogene, ankyrin repeats
RA 1,802,047 G→A 74.5% intergenic (+100/‑6) ydiZ → / → yniA uncharacterized protein/fructosamine kinase family protein
RA 1,805,969 T→A 15.0% L260Q (CTG→CAG)  ydjN → putative transporter
RA 1,823,835 A→C 11.0% W53G (TGG→GGG)  astD ← succinylglutamic semialdehyde dehydrogenase
RA 1,825,763 C→A 53.1% A159A (GCG→GCT)  astC ← succinylornithine transaminase, PLP‑dependent
RA 1,832,413 C→A 63.4% L315L (CTC→CTA)  ynjC → inner membrane putative ABC superfamily transporter permease
RA 1,833,730 C→A 63.0% R3S (CGT→AGT)  ynjE → molybdopterin synthase sulfurtransferase
RA 1,842,161 Δ1 bp 26.6% coding (105/1044 nt) selD ← selenophosphate synthase
RA 1,853,948 C→A 24.3% W180L (TGG→TTG)  ydjK ← putative transporter
RA 1,864,971 G→T 9.5% M110I (ATG→ATT)  yeaI → putative membrane‑anchored diguanylate cyclase
RA 1,865,422 C→A 72.3% R261R (CGA→AGA)  yeaI → putative membrane‑anchored diguanylate cyclase
RA 1,872,520 G→T 64.5% P183P (CCG→CCT)  yeaP → diguanylate cyclase
RA 1,889,399 A→T 21.8% D113V (GAT→GTT)  pabB → aminodeoxychorismate synthase, subunit I
RA 1,894,629 A→T 8.6% V405E (GTA→GAA)  yoaE ← putative membrane protein/conserved protein
RA 1,897,318 T→A 22.2% intergenic (+42/‑21) manX → / → manY fused mannose‑specific PTS enzymes: IIA component/IIB component/mannose‑specific enzyme IIC component of PTS
RA 1,907,967 C→A 21.9% L369F (TTG→TTT)  prc ← carboxy‑terminal protease for penicillin‑binding protein 3
RA 1,909,342 T→A 59.4% E150D (GAA→GAT)  proQ ← RNA chaperone, putative ProP translation regulator
RA 1,917,059 A→T 23.1% D56E (GAT→GAA)  pphA ← serine/threonine‑specific protein phosphatase 1
RA 1,932,312 T→A 25.6% L136* (TTA→TAA)  pykA → pyruvate kinase II
RA 1,940,407 C→A 24.7% E11* (GAA→TAA)  yobI ← uncharacterized protein
RA 1,942,066 G→T 36.7% H115N (CAT→AAT)  yebC ← UPF0082 family protein
RA 1,944,177 C→A 72.5% L201L (CTG→CTT)  aspS ← aspartyl‑tRNA synthetase
RA 1,969,291 G→T 68.4% I97I (ATC→ATA)  cheA ← fused chemotactic sensory histidine kinase in two‑component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein
RA 1,973,063 T→C 22.5% intergenic (‑609/‑171) flhD ← / → uspC flagellar class II regulon transcriptional activator, with FlhC/universal stress protein
RA 1,973,164 G→A 28.6% intergenic (‑710/‑70) flhD ← / → uspC flagellar class II regulon transcriptional activator, with FlhC/universal stress protein
RA 1,978,217 C→T 22.4% G112S (GGC→AGC)  araG ← fused L‑arabinose transporter subunits of ABC superfamily: ATP‑binding components
RA 1,986,289 T→A 61.8% N4Y (AAT→TAT)  pgsA ← phosphatidylglycerophosphate synthetase
RA 1,986,398 G→A 30.6% S597L (TCG→TTG)  uvrC ← excinuclease UvrABC, endonuclease subunit
RA 1,997,314 G→T 46.2% intergenic (‑227/‑39) fliC ← / → fliD flagellar filament structural protein (flagellin)/flagellar filament capping protein
RA 1,999,632 G→T 52.7% intergenic (+73/‑5) fliT → / → amyA putative flagellar synthesis and assembly chaperone/cytoplasmic alpha‑amylase
RA 2,011,138 T→A 22.0% I368I (ATT→ATA)  fliI → flagellum‑specific ATP synthase
RA 2,020,166 C→A 65.7% D445Y (GAC→TAC)  yedQ ← putative membrane‑anchored diguanylate cyclase
RA 2,035,090 C→A 54.1% Q79K (CAG→AAG)  zinT → zinc and cadmium binding protein, periplasmic
RA 2,048,571 A→T 12.5% P10P (CCA→CCT)  amn → AMP nucleosidase
RA 2,051,654 C→T 16.1% intergenic (‑71/+30) asnW ← / ← yeeO tRNA‑Asn/putative multdrug exporter, MATE family
RA 2,056,652 C→A 6.3% E51D (GAG→GAT)  ldtA ← L,D‑transpeptidase linking Lpp to murein
RA 2,058,833 C→T 21.2% G138E (GGA→GAA)  cobU ← bifunctional cobinamide kinase/ cobinamide phosphate guanylyltransferase
RA 2,059,588 C→T 6.8% pseudogene (48/87 nt) yeeH ← pseudogene
RA 2,067,248 C→A 24.7% S743R (AGC→AGA)  flu → CP4‑44 prophage; antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
RA 2,074,680 A→T 63.2% W22R (TGG→AGG)  sbmC ← DNA gyrase inhibitor
RA 2,092,916 T→A 19.3% H60L (CAC→CTC)  ugd ← UDP‑glucose 6‑dehydrogenase
RA 2,098,995 C→A 65.3% G182* (GGA→TGA)  wbbI ← d‑Galf:alpha‑d‑Glc beta‑1,6‑galactofuranosyltransferase
RA 2,101,664 C→A 24.4% Q49H (CAG→CAT)  glf ← UDP‑galactopyranose mutase, FAD/NAD(P)‑binding
RA 2,105,545 C→A 28.5% W333L (TGG→TTG)  rfbB ← dTDP‑glucose 4,6 dehydratase, NAD(P)‑binding
RA 2,107,730 C→A 26.9% E27* (GAG→TAG)  wcaN ← putative regulatory subunit for GalU
RA 2,114,911 A→T 68.6% L42Q (CTG→CAG)  wcaJ ← colanic biosynthesis UDP‑glucose lipid carrier transferase
RA 2,123,274 G→A 27.3% R362R (CGC→CGT)  wcaD ← putative colanic acid polymerase
RA 2,139,910 G→T 66.6% R1055L (CGA→CTA)  yegE → putative diguanylate cyclase
RA 2,144,474 C→A 69.8% intergenic (‑8/‑192) yegI ← / → yegJ protein kinase‑related putative non‑specific DNA‑binding protein/uncharacterized protein
RA 2,144,521 A→G 23.3% intergenic (‑55/‑145) yegI ← / → yegJ protein kinase‑related putative non‑specific DNA‑binding protein/uncharacterized protein
RA 2,149,603 A→T 55.8% E287V (GAA→GTA)  mdtB → multidrug efflux system, subunit B
RA 2,152,042 T→A 5.9% M59K (ATG→AAG)  mdtC → multidrug efflux system, subunit C
RA 2,155,911 C→A 16.0% R323S (CGC→AGC)  mdtD → putative arabinose efflux transporter
RA 2,168,487 A→T 44.3% D14E (GAT→GAA)  gatA ← galactitol‑specific enzyme IIA component of PTS
RA 2,168,795 C→A 73.9% D336Y (GAT→TAT)  gatZ ← D‑tagatose 1,6‑bisphosphate aldolase 2, subunit
RA 2,169,719 C→A 18.2% E28* (GAA→TAA)  gatZ ← D‑tagatose 1,6‑bisphosphate aldolase 2, subunit
RA 2,170,285 C→T 24.2% A133A (GCG→GCA)  gatY ← D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit
RA 2,170,707 C→A 19.9% intergenic (‑24/+284) gatY ← / ← fbaB D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA 2,170,713 C→A 21.1% 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 19.6% 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 7.5% intergenic (‑74/+234) gatY ← / ← fbaB D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I
RA 2,176,513 C→T 25.7% A206A (GCG→GCA)  yegX ← putative family 25 glycosyl hydrolase
RA 2,179,205 G→T 66.3% A24E (GCG→GAG)  rcnR ← transcriptional repressor of rcnA
RA 2,181,645 A→G 61.2% N83N (AAT→AAC)  yehA ← putative fimbrial‑like adhesin protein
RA 2,193,243 C→A 16.4% pseudogene (443/948 nt) yehH → DUF4132 family pseudogene; defective yehI paralog; molybdate metabolism regulator, first fragment; molybdate metabolism regulator, second fragment 2; yehI' molR mutations have phenotypes and the N‑terminal molR fragment of yehI' may be expressed and may have retained or evolved MolR function
RA 2,194,695 T→A 68.9% L313Q (CTA→CAA)  yehI → DUF4132 domain‑containing protein
RA 2,195,449 A→T 66.9% E564D (GAA→GAT)  yehI → DUF4132 domain‑containing protein
RA 2,216,296 C→A 64.0% I211I (ATC→ATA)  dld → D‑lactate dehydrogenase, FAD‑binding, NADH independent
RA 2,221,768 T→A 24.0% pseudogene (321/1287 nt) mdtQ ← pseudogene; putative channel/filament proteins
RA 2,225,190 C→T 53.2% G231G (GGC→GGT)  yohK → LrgB family inner membrane protein
RA 2,237,098 G→T 62.0% H12N (CAT→AAT)  folE ← GTP cyclohydrolase I
RA 2,260,734 G→T 21.6% P337P (CCG→CCT)  yeiQ → putative NAD‑dependent D‑mannonate oxidoreductase
RA 2,263,281 C→T 13.3% intergenic (+235/‑177) lpxT → / → mepS lipid A 1‑diphosphate synthase; undecaprenyl pyrophosphate:lipid A 1‑phosphate phosphotransferase/murein DD‑endopeptidase, space‑maker hydrolase, mutational suppressor of prc thermosensitivity, outer membrane lipoprotein
RA 2,264,143 G→A 69.0% 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 2,289,092 A→T 23.1% S236R (AGT→AGA)  ccmC ← heme exporter subunit
RA 2,289,374 C→A 67.6% V142V (GTG→GTT)  ccmC ← heme exporter subunit
RA 2,292,972 C→A 23.4% R29L (CGC→CTC)  napH ← ferredoxin‑type protein essential for electron transfer from ubiquinol to periplasmic nitrate reductase (NapAB)
RA 2,298,393 A→G 5.2% intergenic (+521/+194) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,298,467 T→C 5.4% intergenic (+595/+120) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,302,650 C→A 18.9% M57I (ATG→ATT)  alkB ← oxidative demethylase of N1‑methyladenine or N3‑methylcytosine DNA lesions
RA 2,303,070 T→G 70.9% Q272P (CAG→CCG)  ada ← fused DNA‑binding transcriptional dual regulator/O6‑methylguanine‑DNA methyltransferase
RA 2,305,116 C→A 68.9% intergenic (‑103/+9) apbE ← / ← ompC putative thiamine‑synthetic flavin transferase lipoprotein/outer membrane porin protein C
RA 2,305,135 T→C 64.3% Y365C (TAC→TGC)  ompC ← outer membrane porin protein C
RA 2,319,958 T→A 14.6% L124* (TTA→TAA)  atoB → acetyl‑CoA acetyltransferase
RA 2,320,977 C→A 14.9% E216* (GAA→TAA)  yfaP ← DUF2135 family protein, putative host defense protein
RA 2,330,502 C→A 50.0% D800Y (GAT→TAT)  gyrA ← DNA gyrase (type II topoisomerase), subunit A
RA 2,343,941 C→A 27.7% D184Y (GAT→TAT)  glpQ ← periplasmic glycerophosphodiester phosphodiesterase
RA 2,352,573 C→A 67.9% P353P (CCG→CCT)  rhmT ← putative L‑rhamnonate transporter
RA 2,353,889 C→A 52.3% V335V (GTG→GTT)  rhmD ← L‑rhamnonate dehydratase
RA 2,359,673 G→T 58.7% M89I (ATG→ATT)  arnB → uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent
RA 2,359,866 G→A 25.1% D154N (GAT→AAT)  arnB → uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent
RA 2,362,338 T→A 65.6% L274Q (CTG→CAG)  arnA → fused UDP‑L‑Ara4N formyltransferase/UDP‑GlcA C‑4'‑decarboxylase
RA 2,364,946 C→A 24.4% P187Q (CCG→CAG)  arnT → 4‑amino‑4‑deoxy‑L‑arabinose transferase
RA 2,370,361:1 +G 68.8% coding (711/759 nt) menH ← 2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA 2,370,987 C→A 63.8% E29* (GAA→TAA)  menH ← 2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
RA 2,372,716 C→A 15.4% R8L (CGA→CTA)  menD ← 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase; SEPHCHC synthase
RA 2,376,806 C→A 9.0% D205E (GAC→GAA)  elaD → protease, capable of cleaving an AMC‑ubiquitin model substrate
RA 2,381,131 G→A 12.9% intergenic (+215/+58) yfbM → / ← yfbN DUF1877 family protein/uncharacterized protein
RA 2,381,961 C→A 26.5% intergenic (‑56/‑153) yfbN ← / → yfbO uncharacterized protein/uncharacterized protein
RA 2,385,845 C→T 5.4% G226S (GGC→AGC)  nuoM ← NADH:ubiquinone oxidoreductase, membrane subunit M
RA 2,398,704 C→T 16.9% intergenic (‑153/+478) nuoA ← / ← lrhA NADH:ubiquinone oxidoreductase, membrane subunit A/transcriptional repressor of flagellar, motility and chemotaxis genes
RA 2,399,210 G→T 58.8% S304* (TCA→TAA)  lrhA ← transcriptional repressor of flagellar, motility and chemotaxis genes
RA 2,405,946 T→G 62.5% Q43P (CAG→CCG)  yfbU ← UPF0304 family protein
RA 2,407,789 G→T 8.1% E281* (GAA→TAA)  ackA → acetate kinase A and propionate kinase 2
RA 2,407,990 A→T 17.5% K348* (AAA→TAA)  ackA → acetate kinase A and propionate kinase 2
RA 2,416,101 C→A 67.1% intergenic (+21/+27) yfcH → / ← yfcI putative NAD‑dependent nucleotide‑sugar epimerase/transposase_31 family protein
RA 2,422,841 C→A 62.3% D293Y (GAT→TAT)  purF ← amidophosphoribosyltransferase
RA 2,424,074 C→T 65.0% D57N (GAC→AAC)  cvpA ← colicin V production membrane protein
RA 2,429,812 A→T 20.7% V106E (GTA→GAA)  usg ← putative semialdehyde dehydrogenase
RA 2,447,977 G→T 24.7% pseudogene (504/2646 nt) yfcU ← pseudogene, FimD fimbrial export usher family;putative membrane; Not classified; putative outer membrane protein
RA 2,450,335 C→T 73.7% intergenic (‑44/+159) sixA ← / ← fadJ phosphohistidine phosphatase/fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA 2,450,346 G→T 70.2% intergenic (‑55/+148) sixA ← / ← fadJ phosphohistidine phosphatase/fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA 2,452,454 G→T 67.6% P62Q (CCG→CAG)  fadJ ← fused enoyl‑CoA hydratase and epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase
RA 2,454,297 T→G 60.2% E39D (GAA→GAC)  yfcZ ← UPF0381 family protein
RA 2,462,531 G→A 23.4% G280E (GGA→GAA)  gtrB → CPS‑53 (KpLE1) prophage; bactoprenol glucosyl transferase
RA 2,463,906 C→A 23.8% Q433K (CAA→AAA)  gtrS → serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA 2,463,910 G→T 24.8% R434I (AGA→ATA)  gtrS → serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA 2,463,915 C→A 19.1% Q436K (CAA→AAA)  gtrS → serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
RA 2,464,269 G→A 22.2% intergenic (+328/‑25) gtrS → / → tfaS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage/pseudogene, CPS‑53 (KpLE1) prophage; tail fiber assembly protein fragment;Phage or Prophage Related
RA 2,464,528 G→A 18.4% pseudogene (235/291 nt) tfaS → pseudogene, CPS‑53 (KpLE1) prophage; tail fiber assembly protein fragment;Phage or Prophage Related
RA 2,466,589 T→G 18.8% pseudogene (476/708 nt) oweS ← pseudogene, CPS‑53 (KpLE1) prophage; bacteriophage replication protein O family;Phage or Prophage Related
RA 2,469,418 C→A 17.2% R23R (CGA→AGA)  yfdT → CPS‑53 (KpLE1) prophage; uncharacterized protein
RA 2,474,418 G→T 73.1% S413* (TCA→TAA)  emrY ← putative multidrug efflux system
RA 2,495,786 C→T 25.0% D727N (GAT→AAT)  fryA ← putative PTS enzyme, Hpr component/enzyme I component/enzyme IIA component
RA 2,509,632 C→A 14.3% L560F (TTG→TTT)  yfeA ← putative diguanylate cyclase
RA 2,520,229 G→T 16.7% intergenic (‑14/‑76) yfeR ← / → yfeH transcriptional regulator of yefH/putative inorganic ion transporter
RA 2,520,652 C→A 67.6% I116I (ATC→ATA)  yfeH → putative inorganic ion transporter
RA 2,534,961 C→T 23.8% G26G (GGG→GGA)  cysW ← sulfate/thiosulfate ABC transporter subunit
RA 2,536,051 G→T 19.3% I279I (ATC→ATA)  cysP ← thiosulfate‑binding protein
RA 2,549,676 C→A 65.4% L28L (CTG→CTT)  eutL ← putative ethanol utilization carboxysome structural protein
RA 2,550,263 G→T 18.8% L132I (CTC→ATC)  eutC ← ethanolamine ammonia‑lyase, small subunit (light chain)
RA 2,556,774 G→A 19.9% intergenic (+298/‑177) yffP → / → yffQ CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
RA 2,568,720 C→T 64.9% A33T (GCC→ACC)  eutP ← putative P‑loop NTPase ethanolamine utilization protein
RA 2,569,336 C→A 22.0% intergenic (‑172/+121) eutS ← / ← maeB putative ethanol utilization carboxysome structural protein/malic enzyme: putative oxidoreductase/putative phosphotransacetylase
RA 2,576,325 C→A 66.3% E171D (GAG→GAT)  nudK ← GDP‑mannose pyrophosphatase
RA 2,580,597 C→A 18.9% T503K (ACG→AAG)  narQ → sensory histidine kinase in two‑component regulatory system with NarP (NarL)
RA 2,587,029:1 +G 66.6% coding (101/699 nt) ypfH ← palmitoyl‑CoA esterase activity, uncertain physiological substrate
RA 2,589,933 G→A 69.4% T55I (ACC→ATC)  ypfJ ← putative neutral zinc metallopeptidase
RA 2,591,933 G→T 19.8% Q98K (CAG→AAG)  bamC ← BamABCDE complex OM biogenesis lipoprotein
RA 2,606,516 G→T 66.9% D420Y (GAC→TAC)  hyfR → hydrogenase‑4 transcriptional activator
RA 2,610,919 C→A 62.1% intergenic (+3/‑18) bepA → / → yfgD periplasmic metalloprotease and chaperone for OM protein maintenance and assembly/putative oxidoreductase
RA 2,614,168 C→A 71.5% D22Y (GAT→TAT)  upp ← uracil phosphoribosyltransferase
RA 2,617,102 G→T 20.2% D234Y (GAT→TAT)  ppk → polyphosphate kinase, component of RNA degradosome
RA 2,618,284 C→T 22.3% L628L (CTG→TTG)  ppk → polyphosphate kinase, component of RNA degradosome
RA 2,619,125 G→T 37.8% G218C (GGT→TGT)  ppx → exopolyphosphatase
RA 2,619,383 G→T 19.9% E304* (GAA→TAA)  ppx → exopolyphosphatase
RA 2,621,410 G→T 30.3% T296T (ACC→ACA)  yfgF ← cyclic‑di‑GMP phosphodiesterase, anaerobic
RA 2,633,091 C→A 5.7% V282L (GTG→TTG)  hisS ← histidyl tRNA synthetase
RA 2,643,286 C→A 17.4% A787A (GCG→GCT)  yfhM ← bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
RA 2,645,252 T→A 19.4% K132I (AAA→ATA)  yfhM ← bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
RA 2,645,521 T→A 16.2% S42S (TCA→TCT)  yfhM ← bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein
RA 2,651,665 G→T 65.1% G210G (GGC→GGA)  hscA ← DnaK‑like molecular chaperone specific for IscU
RA 2,654,144 G→T 24.0% I249I (ATC→ATA)  iscS ← cysteine desulfurase (tRNA sulfurtransferase), PLP‑dependent
RA 2,671,274 C→A 63.5% T149T (ACG→ACT)  yphE ← putative sugar transporter subunit of ABC superfamily, ATP‑binding component
RA 2,681,873 T→A 67.9% Q97L (CAG→CTG)  glrR ← response regulator regulating glmY sRNA in two‑component system with sensor protein GlrK
RA 2,683,829 C→A 65.2% R210L (CGT→CTT)  glrK ← sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR
RA 2,702,530 G→T 5.9% A78A (GCC→GCA)  rseA ← anti‑sigma factor
RA 2,711,673 A→C 11.4% V72G (GTT→GGT)  yfiF ← putative methyltransferase
RA 2,715,643 G→T 62.6% E778* (GAA→TAA)  pka → protein lysine acetyltransferase
RA 2,715,659 C→A 22.7% A783E (GCG→GAG)  pka → protein lysine acetyltransferase
RA 2,719,426 T→C 100% intergenic (‑321/+2) kgtP ← / ← rrfG alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon
RA 2,726,786 C→A 75.1% A249A (GCG→GCT)  clpB ← protein disaggregation chaperone
RA 2,734,317 G→T 17.7% H65N (CAT→AAT)  aroF ← 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tyrosine‑repressible
RA 2,744,009 T→A 27.6% D20V (GAT→GTT)  grpE ← heat shock protein
RA 2,748,452 T→C 19.9% F66F (TTT→TTC)  smpB → trans‑translation protein
RA 2,752,711 T→C 20.6% L123P (CTT→CCT)  yfjI → CP4‑57 prophage; uncharacterized protein
RA 2,752,877 C→A 27.3% G178G (GGC→GGA)  yfjI → CP4‑57 prophage; uncharacterized protein
RA 2,759,556 C→T 17.9% P94S (CCT→TCT)  rnlA → CP4‑57 prophage; RNase LS
RA 2,759,757 C→A 25.8% L161I (CTC→ATC)  rnlA → CP4‑57 prophage; RNase LS
RA 2,761,759 C→A 14.8% R231R (CGA→AGA)  yfjP → CP4‑57 prophage; 50S ribosome‑binding GTPase family protein
RA 2,767,939 C→T 27.0% Y421Y (TAC→TAT)  yfjW → CP4‑57 prophage; putative inner membrane protein
RA 2,771,358 G→A 63.6% intergenic (+217/+147) ypjF → / ← ypjA CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter
RA 2,779,067 C→A 66.6% intergenic (‑697/+54) ypjC ← / ← ileY pseudogene/tRNA‑Ile
RA 2,788,163 C→A 5.5% S184R (AGC→AGA)  gabP → gamma‑aminobutyrate transporter
RA 2,792,473 G→A 11.8% intergenic (‑619/‑50) stpA ← / → alaE DNA binding protein, nucleoid‑associated/alanine exporter, alanine‑inducible, stress‑responsive
RA 2,793,412 G→T 31.4% intergenic (‑59/‑93) ygaC ← / → ygaM uncharacterized protein/DUF883 family protein, putative membrane‑anchored ribosome‑binding protein
JC 2,811,717 Δ134 bp 7.0% [argV] [argV]
RA 2,825,783 C→T 62.7% intergenic (‑135/‑52) norR ← / → norV anaerobic nitric oxide reductase DNA‑binding transcriptional activator/anaerobic nitric oxide reductase flavorubredoxin
RA 2,828,952 C→A 58.0% T611T (ACG→ACT)  hypF ← carbamoyl phosphate phosphatase and maturation protein for [NiFe] hydrogenases
RA 2,841,044 C→A 61.8% A519A (GCG→GCT)  hycC ← hydrogenase 3, membrane subunit
RA 2,850,790 C→A 67.9% I113I (ATC→ATA)  mutS → methyl‑directed mismatch repair protein
RA 2,873,087 G→T 65.3% V15V (GTC→GTA)  ygbT ← multifunctional endonuclease Cas1, CRISPR adaptation protein; DNA repair enzyme
RA 2,876,760 C→T 69.4% G246G (GGG→GGA)  casA ← CRISP RNA (crRNA) containing Cascade antiviral complex protein
RA 2,877,756 T→C 8.2% intergenic (‑259/+156) casA ← / ← ygcB CRISP RNA (crRNA) containing Cascade antiviral complex protein/R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA 2,878,668 G→T 65.2% V637V (GTC→GTA)  ygcB ← R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA 2,879,449 G→T 54.4% S377* (TCA→TAA)  ygcB ← R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
RA 2,888,584 G→T 64.2% I185I (ATC→ATA)  ygcQ ← putative flavoprotein
RA 2,893,420 C→A 19.9% M71I (ATG→ATT)  ygcW ← putative dehydrogenase
RA 2,902,413 G→A 22.1% P205S (CCT→TCT)  pyrG ← CTP synthetase
RA 2,905,077 C→A 21.3% R645L (CGC→CTC)  relA ← (p)ppGpp synthetase I/GTP pyrophosphokinase
RA 2,914,443 C→A 15.7% V339V (GTG→GTT)  gudP ← putative D‑glucarate transporter
RA 2,927,164 C→T 17.9% intergenic (‑117/‑430) fucA ← / → fucP L‑fuculose‑1‑phosphate aldolase/L‑fucose transporter
RA 2,931,717 C→A 63.9% N307K (AAC→AAA)  fucK → L‑fuculokinase
RA 2,934,843 G→T 69.4% H50N (CAT→AAT)  ygdD ← UPF0382 family inner membrane protein
RA 2,936,686 G→T 37.3% intergenic (‑182/‑10) ygdI ← / → csdA DUF903 family verified lipoprotein/cysteine sulfinate desulfinase
RA 2,940,829 A→T 9.2% intergenic (+7/‑27) metZ → / → metW tRNA‑Met/tRNA‑Met
RA 2,940,834 A→T 8.2% intergenic (+12/‑22) metZ → / → metW tRNA‑Met/tRNA‑Met
RA 2,950,690 C→A 24.7% K518N (AAG→AAT)  ptrA ← protease III
RA 2,959,004 G→A 64.4% I131I (ATC→ATT)  lgt ← phosphatidylglycerol‑prolipoprotein diacylglyceryl transferase
RA 2,962,643 A→C 20.8% intergenic (‑307/‑378) rppH ← / → mutH RNA pyrophosphohydrolase/methyl‑directed mismatch repair protein
RA 2,962,657 G→A 8.2% intergenic (‑321/‑364) rppH ← / → mutH RNA pyrophosphohydrolase/methyl‑directed mismatch repair protein
RA 2,970,289 T→G 22.3% L111R (CTG→CGG)  galR → galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor
RA 2,981,600 G→C 11.0% intergenic (+73/‑261) yqeH → / → yqeI putative LuxR family transcriptional regulator/putative transcriptional regulator
RA 2,986,781 T→A 27.9% I443I (ATT→ATA)  ygeH → putative transcriptional regulator
RA 2,989,295 C→A 69.9% pseudogene (85/261 nt) ygeN ← pseudogene
RA 2,989,350 T→C 7.7% pseudogene (30/261 nt)
pseudogene (370/399 nt)		 ygeN ←
ygeO ←		 pseudogene
pseudogene, orgA homolog, part of T3SS PAI ETT2 remnant
RA 2,993,211 C→A 72.3% V14L (GTG→TTG)  ygeR ← LysM domain‑containing M23 family putative peptidase; septation lipoprotein
RA 2,993,699 C→A 59.0% intergenic (‑449/‑5) ygeR ← / → xdhA LysM domain‑containing M23 family putative peptidase; septation lipoprotein/xanthine dehydrogenase, molybdenum binding subunit
RA 3,007,278 C→A 7.5% V107V (GTG→GTT)  yqeB ← XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold
RA 3,017,285 G→T 63.9% D871Y (GAC→TAC)  xdhD → putative hypoxanthine oxidase, molybdopterin‑binding/Fe‑S binding
RA 3,017,759 A→T 23.5% D17V (GAT→GTT)  xanQ → xanthine permease
RA 3,020,228 G→T 23.1% A368A (GCG→GCT)  guaD → guanine deaminase
RA 3,024,983 C→G 61.6% G86G (GGC→GGG)  uacT → uric acid permease
RA 3,025,678 A→T 32.2% Q318L (CAA→CTA)  uacT → uric acid permease
RA 3,025,954 A→T 7.0% H410L (CAC→CTC)  uacT → uric acid permease
RA 3,034,205 G→T 23.8% L75L (CTC→CTA)  sdhE ← flavinator of succinate dehydrogenase; antitoxin of CptAB toxin‑antitoxin pair
RA 3,039,409 T→G 15.1% 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 66.2% intergenic (‑438/+10) gcvT ← / ← ubiI aminomethyltransferase, tetrahydrofolate‑dependent, subunit (T protein) of glycine cleavage complex/2‑octaprenylphenol hydroxylase, FAD‑dependent
RA 3,056,703 C→A 28.5% R120S (CGC→AGC)  argK → membrane ATPase/protein kinase
RA 3,056,837 C→A 30.9% V164V (GTC→GTA)  argK → membrane ATPase/protein kinase
RA 3,060,957 C→A 26.6% A161A (GCG→GCT)  yggE ← oxidative stress defense protein
RA 3,064,914 G→T 50.5% I356I (ATC→ATA)  pgk ← phosphoglycerate kinase
RA 3,067,329 A→G 18.3% intergenic (‑279/+6) epd ← / ← yggC D‑erythrose 4‑phosphate dehydrogenase/putative PanK family P‑loop kinase
RA 3,067,371 C→A 24.5% E226D (GAG→GAT)  yggC ← putative PanK family P‑loop kinase
RA 3,075,114 C→A 67.2% 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 62.4% D211Y (GAC→TAC)  speB ← agmatinase
RA 3,080,330 C→T 26.1% S89F (TCC→TTC)  metK → S‑adenosylmethionine synthetase
RA 3,080,618 T→A 68.9% V185E (GTG→GAG)  metK → S‑adenosylmethionine synthetase
RA 3,088,517 C→A 11.2% R21S (CGT→AGT)  yggS → UPF0001 family protein, PLP‑binding
RA 3,088,780 C→A 6.2% I108I (ATC→ATA)  yggS → UPF0001 family protein, PLP‑binding
RA 3,103,319 C→T 27.5% I136I (ATC→ATT)  yqgA → DUF554 family putative inner membrane protein
RA 3,106,398 A→C 23.1% intergenic (‑98/+28) yghF ← / ← yghG pseudogene, secretion pathway protein, C‑type protein homology;putative transport; Not classified; putative general secretion pathway for protein export (GSP)/secretin (GspDbeta) OM localization lipoprotein pilotin
RA 3,110,751 C→A 66.5% R574L (CGT→CTT)  yghJ ← DUF4092 family putative lipoprotein peptidase
RA 3,111,434 C→A 53.5% A346A (GCG→GCT)  yghJ ← DUF4092 family putative lipoprotein peptidase
RA 3,119,047 C→A 7.4% D279Y (GAC→TAC)  glcE ← glycolate oxidase FAD binding subunit
RA 3,120,216 C→A 62.2% D389Y (GAT→TAT)  glcD ← glycolate oxidase subunit, FAD‑linked
RA 3,137,675 C→A 15.3% P275P (CCG→CCT)  hybA ← hydrogenase 2 4Fe‑4S ferredoxin‑type component
RA 3,144,158 C→A 49.3% intergenic (+253/+19) yghA → / ← exbD putative oxidoreductase/membrane spanning protein in TonB‑ExbB‑ExbD complex
RA 3,169,378 G→T 21.3% S272* (TCA→TAA)  cpdA ← 3',5' cAMP phosphodiesterase
RA 3,171,989 G→T 16.2% A172A (GCG→GCT)  tolC → transport channel
RA 3,173,669 G→T 66.2% A189A (GCG→GCT)  ygiB → DUF1190 family protein
RA 3,182,370 C→A 18.8% pseudogene (1591/2445 nt) yqiG → pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein
RA 3,185,705 G→T 15.4% D47Y (GAT→TAT)  yqiJ → DUF1449 family inner membrane protein
RA 3,190,143 C→A 15.0% intergenic (‑31/+17) hldE ← / ← glnE fused heptose 7‑phosphate kinase/heptose 1‑phosphate adenyltransferase/fused deadenylyltransferase/adenylyltransferase for glutamine synthetase
RA 3,193,298 C→A 17.2% D343Y (GAT→TAT)  ygiF ← inorganic triphosphatase
RA 3,201,824 G→T 5.2% E148* (GAG→TAG)  ttdT → L‑tartrate/succinate antiporte
RA 3,212,068 A→C 23.7% I123S (ATC→AGC)  aer ← fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component
RA 3,224,927 C→A 64.0% intergenic (+329/‑97) ygjK → / → fadH alpha‑glucosidase/2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked
RA 3,230,658 T→A 19.4% intergenic (+67/‑12) ygjQ → / → ygjR DUF218 superfamily protein/putative NAD(P)‑dependent dehydrogenase
RA 3,237,091 T→A 18.4% Q337L (CAG→CTG)  uxaC ← uronate isomerase
RA 3,245,848 G→T 65.8% L62L (CTG→CTT)  yhaH → DUF805 family inner membrane protein
RA 3,246,908 G→A 25.1% R222R (CGC→CGT)  yhaJ ← LysR family putative transcriptional regulator
RA 3,249,372 C→A 19.2% A213A (GCG→GCT)  yhaM ← putative L‑serine dehydratase alpha chain
RA 3,252,258 C→A 67.3% D251Y (GAT→TAT)  tdcG ← L‑serine dehydratase 3, anaerobic
RA 3,263,315 T→C 5.1% intergenic (+354/+260) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,263,460 C→A 10.5% intergenic (+499/+115) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,266,646 C→A 58.9% G91C (GGT→TGT)  garL ← alpha‑dehydro‑beta‑deoxy‑D‑glucarate aldolase
RA 3,272,159 T→C 26.1% intergenic (‑135/‑114) agaR ← / → kbaZ transcriptional repressor of the aga regulon/tagatose 6‑phosphate aldolase 1, kbaZ subunit
RA 3,279,240 T→G 5.4% I135S (ATT→AGT)  agaD → N‑acetylgalactosamine‑specific enzyme IID component of PTS
RA 3,283,448 G→T 18.2% A426S (GCA→TCA)  yraJ → putative outer membrane protein
RA 3,302,027 G→T 67.7% S86* (TCG→TAG)  nlpI ← lipoprotein involved in osmotic sensitivity and filamentation
RA 3,313,793 C→A 20.7% D394Y (GAC→TAC)  yhbX ← putative EptAB family phosphoethanolamine transferase, inner membrane protein
RA 3,314,870 C→A 62.3% A35S (GCG→TCG)  yhbX ← putative EptAB family phosphoethanolamine transferase, inner membrane protein
RA 3,324,218 G→T 22.6% A299E (GCG→GAG)  obgE ← GTPase involved in cell partioning and DNA repair
RA 3,324,553 C→A 27.4% A187A (GCG→GCT)  obgE ← GTPase involved in cell partioning and DNA repair
RA 3,347,778 G→A 62.6% intergenic (‑369/‑306) yhcC ← / → gltB putative Fe‑S oxidoreductase, Radical SAM superfamily protein/glutamate synthase, large subunit
RA 3,347,792 A→G 25.4% intergenic (‑383/‑292) yhcC ← / → gltB putative Fe‑S oxidoreductase, Radical SAM superfamily protein/glutamate synthase, large subunit
RA 3,354,405 C→T 58.7% intergenic (+430/‑130) gltD → / → gltF glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA 3,365,607 G→T 69.7% I109I (ATC→ATA)  nanT ← sialic acid transporter
RA 3,366,254 C→T 15.1% D228N (GAT→AAT)  nanA ← N‑acetylneuraminate lyase
RA 3,373,985 C→A 70.9% intergenic (+37/‑117) yhcB → / → degQ DUF1043 family inner membrane‑anchored protein/serine endoprotease, periplasmic
RA 3,375,260 G→T 68.9% D387Y (GAT→TAT)  degQ → serine endoprotease, periplasmic
RA 3,376,534 C→A 19.3% R326S (CGC→AGC)  degS → serine endoprotease, periplasmic
RA 3,379,204 C→T 16.6% intergenic (+44/+12) yhcN → / ← yhcO cadmium and peroxide resistance protein, stress‑induced/putative barnase inhibitor
RA 3,385,571 C→G 8.5% intergenic (‑184/+246) tldD ← / ← yhdP putative peptidase/DUF3971‑AsmA2 domains protein
RA 3,386,399 C→A 6.4% T1073T (ACG→ACT)  yhdP ← DUF3971‑AsmA2 domains protein
RA 3,389,233 T→G 17.6% S129R (AGT→CGT)  yhdP ← DUF3971‑AsmA2 domains protein
RA 3,389,910 T→A 22.1% K415N (AAA→AAT)  rng ← ribonuclease G
RA 3,396,082 G→T 63.8% R204S (CGT→AGT)  csrD ← targeting factor for csrBC sRNA degradation
RA 3,406,591 C→T 30.8% T78T (ACG→ACA)  acrS ← acrAB operon transcriptional repressor
RA 3,416,890 T→G 7.4% noncoding (12/120 nt) rrfF ← 5S ribosomal RNA of rrnD operon
RA 3,440,151 G→T 68.9% I31I (ATC→ATA)  rpsN ← 30S ribosomal subunit protein S14
RA 3,440,444 G→T 67.2% S118S (TCC→TCA)  rplE ← 50S ribosomal subunit protein L5
RA 3,440,832 T→C 62.8% N99D (AAC→GAC)  rplX ← 50S ribosomal subunit protein L24
RA 3,453,663 C→A 24.9% S163* (TCA→TAA)  gspF → general secretory pathway component, cryptic
RA 3,455,867 C→A 68.9% I55I (ATC→ATA)  gspJ → putative general secretory pathway component, cryptic
RA 3,465,121 C→A 20.4% D585Y (GAC→TAC)  fusA ← protein chain elongation factor EF‑G, GTP‑binding
RA 3,473,139 G→T 70.9% I276I (ATC→ATA)  kefB ← potassium:proton antiporter
RA 3,473,885 C→A 21.1% G28C (GGT→TGT)  kefB ← potassium:proton antiporter
RA 3,479,769 A→T 60.1% E97D (GAA→GAT)  crp → cAMP‑activated global transcription factor, mediator of catabolite repression
RA 3,488,966 G→C 59.0% A533P (GCC→CCC)  nirB → nitrite reductase, large subunit, NAD(P)H‑binding
RA 3,489,397 C→A 45.7% F676L (TTC→TTA)  nirB → nitrite reductase, large subunit, NAD(P)H‑binding
RA 3,501,571 C→A 54.7% G127C (GGC→TGC)  php ← phosphotriesterase homology protein
RA 3,504,362 A→G 25.8% intergenic (‑27/+57) yhfX ← / ← yhfY putative pyridoxal 5'‑phosphate binding protein/PRD domain protein
RA 3,507,749 G→T 48.8% H224N (CAT→AAT)  rpe ← D‑ribulose‑5‑phosphate 3‑epimerase
RA 3,512,114 C→A 9.3% E104* (GAA→TAA)  aroK ← shikimate kinase I
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 3,522,558 G→T 26.1% A177A (GCG→GCT)  yrfG → GMP/IMP nucleotidase
RA 3,543,959 G→T 63.7% A625E (GCG→GAG)  malP ← maltodextrin phosphorylase
RA 3,545,150 G→C 6.1% P228R (CCG→CGG)  malP ← maltodextrin phosphorylase
RA 3,546,300 G→T 16.8% intergenic (‑468/‑144) malP ← / → malT maltodextrin phosphorylase/mal regulon transcriptional activator
RA 3,549,415 T→G 30.3% Q265P (CAG→CCG)  rtcA ← RNA 3'‑terminal phosphate cyclase
RA 3,555,311 T→C 28.1% 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 30.4% 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 69.1% W372L (TGG→TTG)  glgC ← glucose‑1‑phosphate adenylyltransferase
RA 3,577,878 T→C 16.0% intergenic (+209/‑241) yrhA → / → yrhB pseudogene, interrupted by IS1E/stable heat shock chaperone
RA 3,609,368 T→A 27.7% F256L (TTT→TTA)  nikB → nickel transporter subunit
RA 3,630,907 G→A 26.0% intergenic (‑137/‑95) yhiN ← / → pitA putative oxidoreductase/phosphate transporter, low‑affinity; tellurite importer
RA 3,632,594 C→T 21.8% intergenic (+93/+151) pitA → / ← uspB phosphate transporter, low‑affinity; tellurite importer/universal stress (ethanol tolerance) protein B
RA 3,639,551 C→A 43.9% T269T (ACC→ACA)  rlmJ → 23S rRNA m(6)A2030 methyltransferase, SAM‑dependent
RA 3,642,278 T→C 13.0% intergenic (+37/‑17) arsR → / → arsB arsenical resistance operon transcriptional repressor; autorepressor/arsenite/antimonite transporter
RA 3,649,457 C→T 26.3% G66S (GGT→AGT)  hdeB ← acid‑resistance protein
RA 3,657,875 T→C 25.0% K35R (AAA→AGA)  gadW ← transcriptional activator of gadA and gadBC; repressor of gadX
RA 3,662,660 T→C 56.8% intergenic (‑112/‑292) yhjA ← / → treF putative cytochrome C peroxidase/cytoplasmic trehalase
RA 3,662,801 T→A 25.2% intergenic (‑253/‑151) yhjA ← / → treF putative cytochrome C peroxidase/cytoplasmic trehalase
RA 3,676,141 T→C 20.6% I223V (ATT→GTT)  dctA ← C4‑dicarboxylic acid, orotate and citrate transporter
RA 3,679,301 T→G 71.5% Q1078P (CAG→CCG)  bcsC ← cellulose synthase subunit
RA 3,679,324 C→A 72.3% M1070I (ATG→ATT)  bcsC ← cellulose synthase subunit
RA 3,680,910 G→T 66.1% H542N (CAT→AAT)  bcsC ← cellulose synthase subunit
RA 3,708,406 A→T 23.7% L450Q (CTG→CAG)  bisC ← biotin sulfoxide reductase
RA 3,717,788 C→A 70.3% P297P (CCG→CCT)  glyQ ← glycine tRNA synthetase, alpha subunit
RA 3,721,469 A→C 6.2% D421E (GAT→GAG)  xylB ← xylulokinase
RA 3,721,485 T→G 7.5% Y416S (TAC→TCC)  xylB ← xylulokinase
RA 3,738,431 C→A 62.6% P90T (CCA→ACA)  yiaN → 2,3‑diketo‑L‑gulonate TRAP transporter large permease protein
RA 3,774,382 T→G 11.6% intergenic (+5/‑193) lldD → / → trmL L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
RA 3,779,281 C→G 5.9% A221G (GCT→GGT)  gpmM → phosphoglycero mutase III, cofactor‑independent
RA 3,785,915 G→T 72.1% intergenic (‑4/+271) kbl ← / ← yibB glycine C‑acetyltransferase/YibB family protein, function unknown
JC JC 3,795,902 IS5 (+) +4 bp 6.4% coding (514‑517/1020 nt) waaR ← UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑ alpha‑1,3‑D‑galactosyltransferase
RA 3,810,195 C→A 70.5% R54S (CGT→AGT)  yicC → UPF0701 family protein
RA 3,814,302 T→A 37.4% S77C (AGC→TGC)  ligB ← DNA ligase, NAD(+)‑dependent
RA 3,816,601 A→T 92.0% H281L (CAC→CTC)  spoT → bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA 3,818,010 C→A 68.8% H46N (CAT→AAT)  trmH → tRNA mG18‑2'‑O‑methyltransferase, SAM‑dependent
RA 3,822,340 A→C 14.3% Q12H (CAA→CAC)  xanP → xanthine permease
RA 3,825,702 C→A 70.6% K732N (AAG→AAT)  yicI ← putative alpha‑glucosidase
RA 3,830,134 A→G 19.2% intergenic (+218/‑179) yicT → / → setC pseudogene/putative arabinose efflux transporter
RA 3,830,197 C→A 72.0% intergenic (+281/‑116) yicT → / → setC pseudogene/putative arabinose efflux transporter
RA 3,830,311 G→T 69.5% intergenic (+395/‑2) yicT → / → setC pseudogene/putative arabinose efflux transporter
RA 3,833,272 T→G 24.1% S28R (AGC→CGC)  nlpA ← cytoplasmic membrane lipoprotein‑28
RA 3,834,271 T→A 23.4% K277* (AAA→TAA)  nepI ← putative transporter
RA 3,841,586 G→A 24.3% G133G (GGC→GGT)  uhpC ← membrane protein regulates uhpT expression
RA 3,860,159 C→A 64.8% P33P (CCG→CCT)  ibpB ← heat shock chaperone
RA 3,869,881 T→A 18.4% K144N (AAA→AAT)  yidA ← sugar phosphate phosphatase; substrates include erythrose 4‑P and mannose 1‑P phosphatase
RA 3,870,295 A→T 23.6% I6I (ATT→ATA)  yidA ← sugar phosphate phosphatase; substrates include erythrose 4‑P and mannose 1‑P phosphatase
RA 3,870,977 T→A 5.1% intergenic (‑152/+88) yidB ← / ← gyrB DUF937 family protein/DNA gyrase, subunit B
RA 3,871,570 A→C 25.1% L637R (CTG→CGG)  gyrB ← DNA gyrase, subunit B
RA 3,894,935 T→A 5.1% T216S (ACC→TCC)  bglH ← carbohydrate‑specific outer membrane porin, cryptic
RA 3,895,954 C→A 16.2% V370F (GTT→TTT)  bglB ← cryptic phospho‑beta‑glucosidase B
RA 3,897,492 G→T 21.5% P489Q (CCG→CAG)  bglF ← fused beta‑glucoside‑specific PTS enzymes: IIA component/IIB component/IIC component
RA 3,899,662 T→A 16.3% K89I (AAA→ATA)  bglG ← transcriptional antiterminator of the bgl operon
RA 3,901,867 T→G 6.5% intergenic (‑141/+42) pstB ← / ← pstA phosphate transporter subunit/phosphate transporter subunit
RA 3,902,982 C→A 23.0% S259S (TCG→TCT)  pstC ← phosphate transporter subunit
RA 3,905,246 C→A 16.6% D595Y (GAC→TAC)  glmS ← L‑glutamine:D‑fructose‑6‑phosphate aminotransferase
RA 3,908,261 T→A 20.2% L100F (TTA→TTT)  glmU ← fused N‑acetyl glucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyl transferase
RA 3,910,894 C→A 65.8% M244I (ATG→ATT)  atpG ← F1 sector of membrane‑bound ATP synthase, gamma subunit
RA 3,915,397 A→C 27.4% N5K (AAT→AAG)  atpB ← F0 sector of membrane‑bound ATP synthase, subunit a
RA 3,916,052 C→A 39.1% intergenic (‑252/+365) atpI ← / ← rsmG ATP synthase, membrane‑bound accessory factor/16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein
RA 3,916,494 C→A 24.4% E183* (GAA→TAA)  rsmG ← 16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein
RA 3,916,830 C→A 69.9% D71Y (GAT→TAT)  rsmG ← 16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein
RA 3,923,700 G→T 19.7% R252S (CGC→AGC)  ravA ← hexameric AAA+ MoxR family ATPase, putative molecular chaperone
RA 3,925,986 G→T 6.5% M437I (ATG→ATT)  kup → potassium transporter
RA 3,926,496 A→C 28.0% E607D (GAA→GAC)  kup → potassium transporter
RA 3,926,831 G→T 58.2% D41Y (GAT→TAT)  rbsD → putative cytoplasmic sugar‑binding protein
RA 3,931,245 C→A 15.7% R198S (CGT→AGT)  rbsK → ribokinase
RA 3,933,817 G→T 18.2% I52I (ATC→ATA)  hsrA ← putative multidrug or homocysteine efflux system
RA 3,946,683 G→T 5.9% P280P (CCG→CCT)  ilvE → branched‑chain amino‑acid aminotransferase
RA 3,954,751 G→T 21.6% V239L (GTG→TTG)  rep → DNA helicase and single‑stranded DNA‑dependent ATPase
RA 3,958,333 C→A 18.2% E220* (GAA→TAA)  rhlB ← ATP‑dependent RNA helicase
RA 3,960,036 G→A 92.7% R87H (CGC→CAC)  rho → transcription termination factor
RA 3,960,100 A→T 8.0% E108D (GAA→GAT)  rho → transcription termination factor
RA 3,964,617 A→T 27.9% S375S (TCA→TCT)  wecB → UDP‑N‑acetyl glucosamine‑2‑epimerase
RA 3,966,854 C→A 61.9% R325S (CGT→AGT)  rffG → dTDP‑glucose 4,6‑dehydratase
RA 3,969,710 G→T 55.6% G25C (GGT→TGT)  wzxE → O‑antigen translocase
RA 3,971,254 C→T 18.8% L124F (CTT→TTT)  wecF → TDP‑Fuc4NAc:lipidIIFuc4NAc transferase
RA 3,988,075 T→A 62.7% V65E (GTG→GAG)  yifL → putative lipoprotein
RA 3,994,076 A→T 67.0% L114* (TTA→TAA)  yigE ← DUF2233 family protein
RA 3,994,247 A→T 70.1% V57E (GTG→GAG)  yigE ← DUF2233 family protein
RA 3,995,906 G→T 23.5% S85Y (TCT→TAT)  yigF ← putative inner membrane protein
RA 4,005,640 A→C 22.7% I179M (ATT→ATG)  metR ← methionine biosynthesis regulon transcriptional regulator
RA 4,006,260 G→A 18.9% intergenic (‑84/‑153) metR ← / → metE methionine biosynthesis regulon transcriptional regulator/5‑methyltetrahydropteroyltriglutamate‑ homocysteine S‑methyltransferase
RA 4,006,954 T→A 13.3% L181Q (CTG→CAG)  metE → 5‑methyltetrahydropteroyltriglutamate‑ homocysteine S‑methyltransferase
RA 4,009,705 G→A 68.0% intergenic (‑176/‑86) ysgA ← / → udp putative carboxymethylenebutenolidase/uridine phosphorylase
RA 4,032,011 A→C 23.9% noncoding (1133/2905 nt) rrlA → 23S ribosomal RNA of rrnA operon
RA 4,042,128 A→C 13.1% K601N (AAA→AAC)  polA → fused DNA polymerase I 5'‑>3' polymerase/3'‑>5' exonuclease/5'‑>3' exonuclease
RA 4,056,018 T→A 73.6% F138I (TTC→ATC)  yihN → MFS transporter family protein
RA 4,062,424 G→T 65.0% I71I (ATC→ATA)  yihQ ← alpha‑glucosidase
RA 4,063,530 A→C 31.5% C78G (TGT→GGT)  yihR ← mutarotase superfamily protein, YihR family
RA 4,066,133 T→G 71.9% S267R (AGC→CGC)  yihU ← gamma‑hydroxybutyrate dehydrogenase, NADH‑dependent
RA 4,068,208 C→A 67.3% G60G (GGC→GGA)  yihW → DeoR family putative transcriptional regulator
RA 4,076,055 T→G 12.1% Q22P (CAG→CCG)  fdoH ← formate dehydrogenase‑O, Fe‑S subunit
RA 4,076,068 T→G 6.1% T18P (ACC→CCC)  fdoH ← formate dehydrogenase‑O, Fe‑S subunit
RA 4,094,362 C→A 64.3% W181L (TGG→TTG)  cpxA ← sensory histidine kinase in two‑component regulatory system with CpxR
RA 4,096,163 G→T 33.2% R139L (CGA→CTA)  cpxP → inhibitor of the cpx response; periplasmic adaptor protein
RA 4,097,822 G→T 68.5% E115* (GAA→TAA)  pfkA → 6‑phosphofructokinase I
RA 4,127,022 T→G 67.4% E188D (GAA→GAC)  yijF ← DUF1287 family protein
RA 4,143,375 A→G 5.3% intergenic (‑349/+249) ppc ← / ← argE phosphoenolpyruvate carboxylase/acetylornithine deacetylase
RA 4,148,380 C→T 25.8% intergenic (‑58/‑38) oxyS ← / → oxyR sRNA antisense regulator activates genes that detoxify oxidative damage, Hfq‑dependent/oxidative and nitrosative stress transcriptional regulator
RA 4,148,403 G→A 27.2% intergenic (‑81/‑15) oxyS ← / → oxyR sRNA antisense regulator activates genes that detoxify oxidative damage, Hfq‑dependent/oxidative and nitrosative stress transcriptional regulator
RA 4,158,250 A→C 13.6% intergenic (+122/‑50) rrsB → / → gltT 16S ribosomal RNA of rrnB operon/tRNA‑Glu
RA 4,176,823 G→T 68.3% D516Y (GAC→TAC)  rpoC → RNA polymerase, beta prime subunit
RA 4,178,758 G→T 35.7% G1161C (GGT→TGT)  rpoC → RNA polymerase, beta prime subunit
RA 4,194,324 T→A 5.8% R359R (CGT→CGA)  zraR → fused DNA‑binding response regulator in two‑component regulatory system with ZraS: response regulator/sigma54 interaction protein
RA 4,208,127 A→T 22.7% D364V (GAC→GTC)  aceA → isocitrate lyase
RA 4,211,576 G→T 65.3% S280R (AGC→AGA)  arpA ← ankyrin repeat protein
RA 4,211,803 G→A 64.8% P205S (CCT→TCT)  arpA ← ankyrin repeat protein
RA 4,213,602 T→C 25.1% intergenic (‑46/‑154) iclR ← / → metH transcriptional repressor/homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA 4,230,913 A→T 61.9% W424R (TGG→AGG)  xylE ← D‑xylose transporter
RA 4,236,535 T→A 8.1% intergenic (‑188/‑177) malE ← / → malK maltose transporter subunit/fused maltose transport subunit, ATP‑binding component of ABC superfamily/regulatory protein
RA 4,265,064 C→A 57.6% intergenic (‑95/‑335) yjcB ← / → yjcC putative inner membrane protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA 4,269,857 C→A 27.5% intergenic (+101/‑51) yjcD → / → yjcE inner membrane putative guanine permease/putative cation/proton antiporter
RA 4,273,868 C→A 20.7% M321I (ATG→ATT)  actP ← acetate transporter
RA 4,274,926 A→C 64.5% I72M (ATT→ATG)  yjcH ← DUF485 family inner membrane protein
RA 4,277,897 T→A 5.1% L69Q (CTG→CAG)  nrfA → nitrite reductase, formate‑dependent, cytochrome
RA 4,285,892 A→G 7.4% intergenic (+170/+361) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,285,893 A→C 7.0% intergenic (+171/+360) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,286,083 T→C 5.9% intergenic (+361/+170) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,286,717 T→A 8.1% I76F (ATC→TTC)  yjcO ← Sel1 family TPR‑like repeat protein
RA 4,290,080 G→T 68.7% I256I (ATC→ATA)  mdtP ← outer membrane factor of efflux pump
RA 4,294,402 C→T 16.8% intergenic (‑182/+27) ytcA ← / ← yjcS putative inner membrane DUF1656 family protein; efflux pump associated/metallo‑beta‑lactamase superfamily protein
RA 4,297,846 C→A 91.9% M150I (ATG→ATT)  alsE ← allulose‑6‑phosphate 3‑epimerase
RA 4,299,960 G→A 19.7% R280W (CGG→TGG)  alsA ← fused D‑allose transporter subunits of ABC superfamily: ATP‑binding components
RA 4,300,732 C→T 23.5% K22K (AAG→AAA)  alsA ← fused D‑allose transporter subunits of ABC superfamily: ATP‑binding components
RA 4,303,614 T→A 70.4% *150R (TGA→AGA)  rpiB → ribose 5‑phosphate isomerase B/allose 6‑phosphate isomerase
RA 4,308,595 C→A 17.6% E277* (GAG→TAG)  phnJ ← carbon‑phosphorus lyase, SAM‑dependent
RA 4,317,035 A→T 22.9% E28D (GAA→GAT)  crfC → clamp‑binding sister replication fork colocalization protein, dynamin‑related
RA 4,323,686 C→A 21.6% D28Y (GAT→TAT)  basR ← response regulator in two‑component regulatory system with BasS
RA 4,341,023 A→T 47.6% Y153N (TAC→AAC)  dcuS ← sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration
RA 4,348,101 C→A 24.6% D112Y (GAT→TAT)  cadA ← lysine decarboxylase, acid‑inducible
RA 4,354,610 A→T 36.3% W84R (TGG→AGG)  dsbD ← fused thiol:disulfide interchange protein: activator of DsbC/conserved protein
RA 4,381,381 T→A 24.8% intergenic (‑55/‑40) rsgA ← / → orn ribosome small subunit‑dependent GTPase A/oligoribonuclease
RA 4,382,270 C→A 5.7% intergenic (+18/‑19) glyV → / → glyX tRNA‑Gly/tRNA‑Gly
RA 4,382,314 A→T 18.2% noncoding (26/76 nt) glyX → tRNA‑Gly
RA 4,383,389 G→T 19.5% R166S (CGC→AGC)  queG ← epoxyqueuosine reductase, cobalamine‑stimulated; queosine biosynthesis
RA 4,388,902 G→T 71.7% A558A (GCG→GCT)  mutL → methyl‑directed mismatch repair protein
RA 4,396,598 A→T 63.2% E43V (GAA→GTA)  rnr → exoribonuclease R, RNase R
RA 4,396,975 G→T 19.7% D169Y (GAC→TAC)  rnr → exoribonuclease R, RNase R
RA 4,400,254 C→A 19.7% S102* (TCG→TAG)  yjfI → DUF2170 family protein
RA 4,417,551 A→C 66.2% pseudogene (41/402 nt) ytfA → pseudogene, related to transcriptional regulators
RA 4,424,241 T→G 23.3% A104A (GCT→GCG)  ytfH → DUF24 family HxlR‑type putative transcriptional regulator
RA 4,458,254 T→A 70.6% V271V (GTT→GTA)  mgtA → magnesium transporter
RA 4,458,609 G→T 71.9% D390Y (GAT→TAT)  mgtA → magnesium transporter
RA 4,458,688 T→A 18.9% L416Q (CTG→CAG)  mgtA → magnesium transporter
RA 4,466,283 A→T 28.1% N344Y (AAC→TAC)  yjgL → uncharacterized protein
RA 4,468,165 A→G 70.7% intergenic (‑37/‑125) argI ← / → rraB ornithine carbamoyltransferase 1/protein inhibitor of RNase E
RA 4,469,550 G→A 70.8% A2T (GCT→ACT)  yjgN → DUF898 family inner membrane protein
RA 4,470,017 G→A 65.6% M157I (ATG→ATA)  yjgN → DUF898 family inner membrane protein
RA 4,475,053 A→T 5.5% V239D (GTC→GAC)  pepA ← multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor
RA 4,481,566 G→T 8.7% V259V (GTC→GTA)  idnT ← L‑idonate and D‑gluconate transporter
RA 4,487,951 C→A 23.7% intergenic (+194/‑138) intB → / → insC1 pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase/IS2 repressor TnpA
RA 4,495,560 A→T 50.0% N153Y (AAC→TAC)  yjhC → putative oxidoreductase
RA 4,500,728 C→A 23.8% E183* (GAA→TAA)  fecE ← iron‑dicitrate transporter subunit
RA 4,506,430 A→T 19.0% L22Q (CTG→CAG)  fecA ← ferric citrate outer membrane transporter
RA 4,510,428 G→T 20.4% intergenic (‑287/+60) yjhU ← / ← yjhF putative DNA‑binding transcriptional regulator; KpLE2 phage‑like element/putative transporter
RA 4,512,693 T→A 80.2% K407* (AAG→TAG)  yjhG ← putative dehydratase
RA 4,512,731 A→C 6.4% L394R (CTC→CGC)  yjhG ← putative dehydratase
RA 4,520,215 T→A 33.2% N46Y (AAC→TAC)  sgcB ← putative enzyme IIB component of PTS
RA 4,524,046 C→A 27.5% intergenic (‑176/+201) yjhX ← / ← yjhZ UPF0386 family protein/pseudogene, rimK paralog, C‑terminal fragment
RA 4,524,111 A→T 26.9% intergenic (‑241/+136) yjhX ← / ← yjhZ UPF0386 family protein/pseudogene, rimK paralog, C‑terminal fragment
RA 4,525,234 G→A 72.5% pseudogene (415/1029 nt) yjhR → pseudogene, helicase family; putative frameshift suppressor
RA 4,526,511 G→A 21.6% H301Y (CAT→TAT)  nanS ← 9‑O‑acetyl N‑acetylneuraminic acid esterase
RA 4,529,829 T→C 22.0% intergenic (‑511/‑945) nanC ← / → fimB N‑acetylnuraminic acid outer membrane channel protein/tyrosine recombinase/inversion of on/off regulator of fimA
RA 4,531,143 A→T 68.5% I124F (ATT→TTT)  fimB → tyrosine recombinase/inversion of on/off regulator of fimA
RA 4,555,156 G→T 60.0% A171E (GCG→GAG)  yjiM ← putative 2‑hydroxyglutaryl‑CoA dehydratase
RA 4,562,043 C→A 73.8% intergenic (+311/‑188) yjiS → / → yjiT DUF1127 family protein/pseudogene
RA 4,562,157 C→T 6.4% intergenic (+425/‑74) yjiS → / → yjiT DUF1127 family protein/pseudogene
RA 4,577,795 C→A 18.4% T296T (ACG→ACT)  yjiA ← GTP‑binding protein, putative GTPase
RA 4,579,917 C→A 21.6% A394S (GCG→TCG)  yjiY ← putative transporter
RA 4,584,381 G→T 64.6% I53I (ATC→ATA)  yjjL ← L‑galactonate transporter
RA 4,584,388 G→A 22.1% A51V (GCG→GTG)  yjjL ← L‑galactonate transporter
RA 4,585,338 A→T 56.0% S111T (TCT→ACT)  yjjM ← yjjMN operon transcriptional activator
RA 4,595,116 G→T 28.2% P122Q (CCG→CAG)  fhuF ← ferric iron reductase involved in ferric hydroximate transport
RA 4,603,125 A→C 8.9% T300P (ACG→CCG)  yjjU → putative patatin‑like family phospholipase
RA 4,604,195 A→G 5.5% intergenic (+118/+302) yjjV → / ← yjjW putative DNase/putative pyruvate formate lyase activating enzyme
RA 4,617,129 G→T 18.0% intergenic (+18/‑3) radA → / → nadR DNA repair protein/trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor
RA 4,625,288 T→C 59.3% intergenic (‑161/‑50) rob ← / → creA right oriC‑binding transcriptional activator, AraC family/putative periplasmic protein
RA 4,626,111 T→A 20.7% I96I (ATT→ATA)  creB → response regulator in two‑component regulatory system with CreC
RA 4,629,622 C→A 18.0% A168S (GCC→TCC)  arcA ← response regulator in two‑component regulatory system with ArcB or CpxA
RA 4,629,649 A→T 42.7% Y159N (TAC→AAC)  arcA ← response regulator in two‑component regulatory system with ArcB or CpxA
RA 4,631,331 A→T 19.4% A191A (GCA→GCT)  yjtD → putative methyltransferase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP009273 373877 375076 1200 113 [112] [109] 116 frmA–[frmR] frmA,[frmR]
* * ÷ CP009273 4100635 4101493 859 119 [112] [111] 114 tpiA tpiA

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 360104 =220 (0.820)163 (0.610) 98/278 NT 42.6% 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)11006 (43.600)
+TTAATTAA		 195/262 NT 97.3% intergenic (‑212/+383) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 361823 319 (1.190)coding (831/834 nt) mhpR mhp operon transcriptional activator
* ? CP009273 360652 =331 (1.240)10435 (58.410)
+46 bp		 186/186 NT 98.3% intergenic (‑586/+9) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 1317577 201 (0.750)coding (101/882 nt) yciV PHP domain protein
* ? CP009273 376716 =NA (NA)218 (0.810) 121/278 NT 89.7% intergenic (‑1/‑91) yaiX/insC1 pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase/IS2 repressor TnpA
?CP009273 566411 = 25 (0.090)coding (63/552 nt) ybcL inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
* ? CP009273 = 378046NA (NA)207 (0.770) 97/278 NT 89.2% intergenic (+11/+1) insD1/yaiX IS2 transposase TnpB/pseudogene, interrupted by IS2A, acetyltransferase homolog; nonfunctional; interruped by IS2; putative transferase
?CP009273 = 566415 25 (0.090)coding (67/552 nt) ybcL inactive polymorphonuclear leukocyte migration suppressor; DLP12 prophage; secreted protein, UPF0098 family
* ? CP009273 776825 =170 (0.630)21 (0.080)
+G		 11/276 NT 10.8% noncoding (1/76 nt) lysZ tRNA‑Lys
?CP009273 = 2514488 181 (0.680)noncoding (216/1345 nt) IS186 repeat region
* ? CP009273 1203246 =76 (0.280)124 (0.520) 72/246 NT 67.7% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 1205075 = 51 (0.220)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 120326178 (0.290)236 (1.000) 115/246 NT 79.7% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 = 1205058 51 (0.220)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 1635219 =50 (0.190)140 (0.530) 91/274 NT 73.7% 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 = 163522348 (0.180)133 (0.500) 87/278 NT 73.5% 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 2989720 =NA (NA)11 (0.040) 10/276 NT 5.2% noncoding (1331/1331 nt) IS2 repeat region
?CP009273 3271002 = 202 (0.760)coding (307/465 nt) yhaV toxin of the SohB(PrlF)‑YhaV toxin‑antitoxin system
* ? CP009273 3179455 =NA (NA)15 (0.060) 12/278 NT 6.9% intergenic (+7/‑91) yqiG/insC1 pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein/IS2 repressor TnpA
?CP009273 = 3271006 203 (0.760)coding (311/465 nt) yhaV toxin of the SohB(PrlF)‑YhaV toxin‑antitoxin system
* ? CP009273 3904961 =200 (0.750)18 (0.070) 11/276 NT 8.3% intergenic (‑76/+238) pstS/glmS periplasmic phosphate binding protein, high‑affinity/L‑glutamine:D‑fructose‑6‑phosphate aminotransferase
?CP009273 = 4489327 NA (NA)intergenic (+10/+83) insD1/yjgX IS2 transposase TnpB/pseudogene fragment
* ? CP009273 = 3904966200 (0.750)13 (0.050) 10/278 NT 6.1% intergenic (‑81/+233) pstS/glmS periplasmic phosphate binding protein, high‑affinity/L‑glutamine:D‑fructose‑6‑phosphate aminotransferase
?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