breseq  version 0.32.1  revision aa8f2595a244
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
RA 7,925 +A coding (35/1431 nt) yaaJ ← putative transporter
RA 10,647 A→G V237A (GTC→GCC)  yaaW ← UPF0174 family protein
RA 14,301 C→T A45V (GCG→GTG)  dnaJ → chaperone Hsp40, DnaK co‑chaperone
RA 28,269 C→T intergenic (+62/‑105) rihC → / → dapB ribonucleoside hydrolase 3/dihydrodipicolinate reductase
RA 30,616 T→C P322P (CCT→CCC)  carA → carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
RA 35,373 G→C intergenic (‑2/+4) caiE ← / ← caiD stimulator of CaiD and CaiB enzyme activities/carnitinyl‑CoA dehydratase
RA 37,903 C→T D405N (GAC→AAC)  caiB ← crotonobetainyl CoA:carnitine CoA transferase
RA 47,776 G→A *177* (TAG→TAA) 
S3N (AGC→AAC) 		 kefF →
kefC →		 potassium‑efflux system ancillary protein for KefC, glutathione‑regulated, quinone oxidoreductase, FMN‑dependent
potassium:proton antiporter
RA 49,765 C→T intergenic (+134/‑58) kefC → / → folA potassium:proton antiporter/dihydrofolate reductase
RA 49,831 T→C S3S (AGT→AGC)  folA → dihydrofolate reductase
RA 66,447 T→C E35G (GAG→GGG)  araD ← L‑ribulose‑5‑phosphate 4‑epimerase
RA 72,115 G→A *255* (TAG→TAA)  yabI → DedA family inner membrane protein
RA 72,229 C→T *233* (TAG→TAA)  thiQ ← thiamine/thiamine pyrophosphate ABC transporter ATPase
RA 75,447 A→G C12R (TGC→CGC)  thiB ← thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein
RA 96,008 G→A *453* (TAG→TAA) 
V3I (GTT→ATT) 		 murF →
mraY →		 UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase
phospho‑N‑acetylmuramoyl‑pentapeptide transferase
RA 104,352 A→G E124G (GAG→GGG)  ftsA → ATP‑binding cell division FtsK recruitment protein
RA 111,433 G→A *130* (TAG→TAA)  mutT → dGTP‑preferring nucleoside triphosphate pyrophosphohydrolase
RA 115,661 T→C M22V (ATG→GTG)  hofC ← assembly protein in type IV pilin biogenesis, transmembrane protein
RA 117,798 A→G L283P (CTA→CCA)  nadC ← quinolinate phosphoribosyltransferase
RA 122,856 G→A *255* (TAG→TAA)  pdhR → pyruvate dehydrogenase complex repressor, autorepressor
RA 125,227 T→C R737R (CGT→CGC)  aceE → pyruvate dehydrogenase, decarboxylase component E1, thiamine triphosphate‑binding
RA 150,947 T→C T3A (ACT→GCT)  yadC ← putative fimbrial‑like adhesin protein
RA 152,036 C→T V66I (GTA→ATA)  yadL ← putative fimbrial‑like adhesin protein
RA 155,935 T→C K89K (AAA→AAG)  yadV ← putative periplasmic pilin chaperone
RA 160,782 C→T *235* (TAG→TAA)  sfsA ← sugar fermentation stimulation protein A
RA 162,927 G→A A275T (GCT→ACT)  hrpB → putative ATP‑dependent helicase
RA 167,743 C→T T87I (ACC→ATC)  fhuA → ferrichrome outer membrane transporter
RA 169,645 A→G Y721C (TAC→TGC)  fhuA → ferrichrome outer membrane transporter
RA 177,662 C→T *267* (TAG→TAA)  btuF ← vitamin B12 ABC transporter periplasmic binding protein
RA 183,215 C→T G251G (GGC→GGT)  cdaR → carbohydrate diacid regulon transcriptional regulator, autoregulator
RA 183,607 Δ1 bp coding (1145/1158 nt) cdaR → carbohydrate diacid regulon transcriptional regulator, autoregulator
RA 183,620 G→A *386* (TAG→TAA)  cdaR → carbohydrate diacid regulon transcriptional regulator, autoregulator
RA 184,257 C→T *271* (TAG→TAA)  yaeI ← phosphodiesterase with model substrate bis‑pNPP
RA 185,465 G→A G161G (GGC→GGT)  dapD ← 2,3,4,5‑tetrahydropyridine‑2‑carboxylate N‑succinyltransferase
RA 197,574 T→C S343S (AGT→AGC)  rseP → inner membrane zinc RIP metalloprotease, RpoE activator, by degrading RseA, cleaved signal peptide endoprotease
RA 200,214 C→T P763S (CCA→TCA)  bamA → BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor
RA 219,364 T→C P77P (CCA→CCG)  tsaA ← tRNA‑Thr(GGU) m(6)t(6)A37 methyltransferase, SAM‑dependent
RA 220,239 C→T L230L (CTG→CTA)  metQ ← DL‑methionine transporter subunit
RA 239,378 G→A pseudogene (273/273 nt) yafF → pseudogene, H repeat‑associated protein
RA 247,461 G→A *250* (TAG→TAA)  yafL → putative lipoprotein and C40 family peptidase
RA 247,466 Δ1 bp intergenic (+5/‑171) yafL → / → rayT putative lipoprotein and C40 family peptidase/RAYT REP element‑mobilizing transposase, TnpA(REP)
RA 253,084 A→G T126A (ACA→GCA)  yafP → GNAT family putative N‑acetyltransferase
RA 255,659 A→G C20R (TGT→CGT)  pepD ← aminoacyl‑histidine dipeptidase (peptidase D)
MC JC 257,908 Δ776 bp [crl] [crl]
RA 262,563 G→A R354H (CGT→CAT)  proA → gamma‑glutamylphosphate reductase
RA 280,024 C→T pseudogene (94/174 nt) insI1 → IS30 transposase,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related
RA 281,662 Δ1 bp coding (322/1155 nt) yagA ← CP4‑6 prophage, putative DNA‑binding transcriptional regulator
RA 284,869 C→T P557S (CCG→TCG)  yagF → CP4‑6 prophage, dehydratase family protein
RA 287,977 A→G M397V (ATG→GTG)  yagH → CP4‑6 prophage, putative xylosidase/arabinosidase
RA 291,324 C→T C8Y (TGT→TAT)  insA ← IS1 repressor TnpA
RA 309,358 C→T *223* (TAG→TAA)  ecpB ← ECP production pilus chaperone
RA 312,189 C→T G26G (GGC→GGT)  ykgL → uncharacterized protein
RA 315,244 G→A intergenic (+16/‑47) eaeH → / → insE1 pseudogene, attaching and effacing protein homology,factor, Not classified/IS3 transposase A
RA 316,453 G→A *289* (TAG→TAA)  insF1 → IS3 transposase B
RA 321,564 (G)7→6 intergenic (+483/‑44) rclR → / → ykgE reactive chlorine species (RCS)‑specific activator of the rcl genes/cysteine‑rich LutA family protein, putative electron transport chain YkgEFG component
RA 323,355 C→T P340S (CCA→TCA)  ykgF → ferridoxin‑like LutB family protein, putative electron transport chain YkgEFG component
RA 335,970 C→T Q16* (CAA→TAA)  yahE → DUF2877 family protein
RA 340,089 G→A intergenic (+346/‑76) yahG → / → yahI DUF1116 family protein/carbamate kinase‑like protein
RA 344,674 T→C Y167H (TAC→CAC)  yahL → uncharacterized protein
RA 344,991 G→A *272* (TAG→TAA)  yahL → uncharacterized protein
RA 345,649 G→A *82* (TAG→TAA)  yahM → uncharacterized protein
RA 349,847 T→C intergenic (+275/‑165) prpB → / → prpC 2‑methylisocitrate lyase/2‑methylcitrate synthase
RA 354,592 G→A *629* (TAG→TAA)  prpE → propionate‑‑CoA ligase
RA 357,591 C→T intergenic (+137/+200) codA → / ← cynR cytosine/isoguanine deaminase/transcriptional activator of cyn operon, autorepressor
RA 357,606 C→T intergenic (+152/+185) codA → / ← cynR cytosine/isoguanine deaminase/transcriptional activator of cyn operon, autorepressor
RA 357,626 2 bp→TA intergenic (+172/+164) codA → / ← cynR cytosine/isoguanine deaminase/transcriptional activator of cyn operon, autorepressor
RA 357,791 C→T *300* (TAG→TAA)  cynR ← transcriptional activator of cyn operon, autorepressor
RA 371,542 C→T Q102* (CAA→TAA)  mhpC → 2‑hydroxy‑6‑ketonona‑2,4‑dienedioic acid hydrolase
RA 372,966 A→G T16A (ACC→GCC)  mhpF → acetaldehyde‑CoA dehydrogenase II, NAD‑binding
RA 375,067 A→G intergenic (+186/‑392) mhpE → / → mhpT 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter
RA 375,307 C→T intergenic (+426/‑152) mhpE → / → mhpT 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter
RA 379,606 C→T *92* (TAG→TAA)  frmR ← regulator protein that represses frmRAB operon
RA 380,022 (G)10→9 intergenic (‑141/+47) frmR ← / ← yaiO regulator protein that represses frmRAB operon/outer membrane protein
RA 382,579 G→A *302* (TAG→TAA)  insD1 → IS2 transposase TnpB
RA 383,259 C→T R226Q (CGG→CAG)  yaiP ← putative family 2 glycosyltransferase
RA 384,059 C→T *186* (TAG→TAA)  yaiS ← putative PIG‑L family deacetylase
RA 385,737 A→G D169G (GAT→GGT)  tauA → taurine ABC transporter periplasmic binding protein
RA 391,739 C→T *289* (TAG→TAA)  insF1 ← IS3 transposase B
RA 401,548 (G)5→4 coding (163/261 nt) iraP → anti‑RssB factor, RpoS stabilzer during Pi starvation, anti‑adapter protein
RA 411,297 C→T *395* (TAG→TAA)  araJ ← L‑arabinose‑inducible putative transporter, MFS family
RA 427,675 A→G Y10C (TAC→TGC)  secD → SecYEG protein translocase auxillary subunit
RA 437,107 G→A *173* (TAG→TAA)  pgpA → phosphatidylglycerophosphatase A
RA 443,051 C→T *197* (TAG→TAA)  yajL ← oxidative‑stress‑resistance chaperone
RA 443,604 C→T S13N (AGT→AAT) 
*304* (TAG→TAA) 		 yajL ←
panE ←		 oxidative‑stress‑resistance chaperone
2‑dehydropantoate reductase, NADPH‑specific
RA 444,641 C→T intergenic (‑126/‑42) panE ← / → yajQ 2‑dehydropantoate reductase, NADPH‑specific/phage Phi6 host factor, ATP/GTP binding protein
RA 450,764 C→T A283T (GCT→ACT)  cyoA ← cytochrome o ubiquinol oxidase subunit II
RA 461,242 G→A *785* (TAG→TAA)  lon → DNA‑binding ATP‑dependent protease La
RA 468,510 A→G E43G (GAG→GGG)  ybaO → putative DNA‑binding transcriptional regulator
RA 469,429 A→G K187E (AAG→GAG)  mdlA → putative multidrug ABC transporter ATPase
RA 470,643 G→A *591* (TAG→TAA) 
S3N (AGT→AAT) 		 mdlA →
mdlB →		 putative multidrug ABC transporter ATPase
putative multidrug ABC transporter ATPase
RA 475,667 T→C S97P (TCA→CCA)  ybaY → outer membrane lipoprotein
RA 477,025 G→A *118* (TAG→TAA)  ybaA → DUF1428 family protein
RA 477,435 T→C T395A (ACT→GCT)  ylaB ← putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA 478,533 C→T A29T (GCC→ACC)  ylaB ← putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA 480,334 C→T *125* (TAG→TAA)  tomB ← Hha toxicity attenuator, conjugation‑related protein
RA 486,641 T→C S36P (TCA→CCA)  mscK → mechanosensitive channel protein, intermediate conductance, K+ regulated
RA 490,285 C→T *176* (TAG→TAA)  priC ← primosomal replication protein N''
RA 491,776 T→C V122A (GTT→GCT)  apt → adenine phosphoribosyltransferase
RA 499,014 C→T R320R (CGC→CGT) 
*320* (TAG→TAA) 		 hemH →
aes ←		 ferrochelatase
acetyl esterase
RA 515,808 C→T intergenic (‑35/‑111) qmcA ← / → fetA PHB domain membrane‑anchored putative protease/iron export ABC transporter ATPase, peroxide resistance protein
RA 518,721 C→A M143I (ATG→ATT)  ybbO ← putative oxidoreductase
RA 522,463 T→C V683A (GTG→GCG)  ybbP → putative ABC transporter permease
RA 524,158 C→T L300L (CTG→TTG)  rhsD → Rhs protein with DUF4329 family putative toxin domain, putative neighboring cell growth inhibitor
RA 540,515 C→T intergenic (+7/‑50) allB → / → ybbY allantoinase/putative uracil/xanthine transporter
RA 542,530 A→G T215A (ACG→GCG)  glxK → glycerate kinase II
RA 544,754 C→T R180H (CGT→CAT)  allC ← allantoate amidohydrolase
RA 551,332 G→A *298* (TAG→TAA)  ybcF → putative carbonate kinase
RA 568,004 G→A *289* (TAG→TAA)  insF1 → IS3 transposase B
RA 571,444 G→A *184* (TAG→TAA)  ybcL → inactive polymorphonuclear leukocyte migration suppressor, DLP12 prophage, UPF0098 family secreted protein
RA 572,454 C→T C29C (TGC→TGT)  ylcH → uncharacterized protein, DLP12 prophage
RA 578,568 G→A *154* (TAG→TAA)  rzpD → DLP12 prophage, putative murein endopeptidase
RA 582,148 Δ1 bp intergenic (+51/+4) tfaD → / ← ybcY pseudogene, DLP12 prophage, tail fiber assembly protein family,Phage or Prophage Related/pseudogene, DLP12 prophage, methyltransferase homology,Phage or Prophage Related
RA 582,152 C→T pseudogene (653/653 nt) ybcY ← pseudogene, DLP12 prophage, methyltransferase homology,Phage or Prophage Related
RA 586,280 T→C N210S (AAC→AGC)  envY ← porin thermoregulatory transcriptional activator
RA 607,988 G→A *51* (TAG→TAA)  hokE → toxic polypeptide, small
RA 631,812 T→C F640S (TTC→TCC)  cstA → carbon starvation protein involved in peptide utilization, APC peptide transporter family protein
RA 634,746 2 bp→AT [ybdL]–[ybdM] [ybdL], [ybdM]
RA 649,372 A→G F67S (TTC→TCC)  citF ← citrate lyase, citrate‑ACP transferase (alpha) subunit
RA 649,648 A→G G281G (GGT→GGC)  citE ← citrate lyase, citryl‑ACP lyase (beta) subunit
RA 662,153 C→A E42D (GAG→GAT)  lipB ← octanoyltransferase, octanoyl‑[ACP]:protein N‑octanoyltransferase
RA 664,102 C→T *363* (TAG→TAA)  rlpA ← septal ring protein, suppressor of prc, minor lipoprotein
RA 672,947 C→A V613F (GTT→TTT)  leuS ← leucyl‑tRNA synthetase
RA 675,570 C→T *326* (TAG→TAA)  ybeQ ← Sel1 family TPR‑like repeat protein
RA 675,601 Δ1 bp coding (947/978 nt) ybeQ ← Sel1 family TPR‑like repeat protein
RA 677,889 G→A A159T (GCC→ACC)  djlB → putative HscC co‑chaperone, uncharacterized J domain‑containing protein
RA 679,874 G→A G123R (GGG→AGG)  ybeU → DUF1266 family protein
RA 696,276 G→A *392* (TAG→TAA)  ubiF → 2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase
RA 711,724 C→T A59T (GCG→ACG)  ybfE ← LexA‑regulated protein, CopB family
RA 716,388 C→T pseudogene (210/651 nt) ybfG ← pseudogene
RA 723,528 (T)8→9 coding (887/2685 nt) kdpD ← fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein
RA 738,853 G→A *254* (TAG→TAA)  ybfD → H repeat‑associated putative transposase
RA 746,723 C→T H263H (CAC→CAT) 
*349* (TAG→TAA) 		 nei →
abrB ←		 endonuclease VIII and 5‑formyluracil/5‑hydroxymethyluracil DNA glycosylase
regulator of aidB expression, inner membrane protein
RA 746,726 G→A *264* (TAG→TAA) 
A348A (GCC→GCT) 		 nei →
abrB ←		 endonuclease VIII and 5‑formyluracil/5‑hydroxymethyluracil DNA glycosylase
regulator of aidB expression, inner membrane protein
RA 762,739 G→A *406* (TAG→TAA)  sucB → dihydrolipoyltranssuccinase
RA 775,120 G→A A123A (GCG→GCA)  ybgC → acyl‑CoA thioester hydrolase
RA 789,464 G→A I172I (ATC→ATT)  galK ← galactokinase
RA 812,947 G→A *226* (TAG→TAA)  bioD → dethiobiotin synthetase
RA 819,747 G→A *151* (TAG→TAA)  moaE → molybdopterin synthase, large subunit
RA 821,506 G→A *238* (TAG→TAA)  ybhM → BAX Inhibitor‑1 family inner membrane protein
RA 825,102 G→A A336V (GCG→GTG)  ybhR ← putative ABC transporter permease
RA 826,119 C→T *378* (TAG→TAA)  ybhS ← putative ABC transporter permease
RA 829,972 C→T M1M (GTG→ATG) †
*224* (TAG→TAA) 		 ybhG ←
ybiH ←		 putative membrane fusion protein (MFP) component of efflux pump, membrane anchor
DUF1956 domain‑containing tetR family putative transcriptional regulator
RA 850,389 T→C intergenic (‑292/‑61) rhtA ← / → ompX threonine and homoserine efflux system/outer membrane protein X
RA 852,869 C→T *43* (TAG→TAA)  mntS ← Mn(2)‑response protein, MntR‑repressed
RA 854,765 G→A *373* (TAG→TAA)  ybiR → putative transporter
RA 855,796 A→G intergenic (‑52/‑167) ldtB ← / → ybiT L,D‑transpeptidase linking Lpp to murein/ABC‑F family putative regulatory ATPase
RA 860,638 A→G Y657H (TAT→CAT)  ybiW ← putative pyruvate formate lyase
RA 872,801 G→A *304* (TAG→TAA)  gsiD → glutathione ABC transporter permease
RA 875,327 G→A *783* (TAG→TAA)  yliE → putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA 879,857 G→A *372* (TAG→TAA) 
S208S (AGC→AGT) 		 yliI →
gstB ←		 soluble aldose sugar dehydrogenase
glutathione S‑transferase
JC JC 883,665 IS1 (–) +9 bp [mdfA] [mdfA]
RA 887,959 G→A *179* (TAG→TAA)  rcdA → transcriptional regulator of csgD and ybiJI, autoregulator
RA 892,869 G→A *301* (TAG→TAA)  rimK → ribosomal protein S6 modification protein
RA 905,743 G→A *277* (TAG→TAA) 
R337R (CGC→CGT) 		 amiD →
ybjS ←		 1,6‑anhydro‑N‑acetylmuramyl‑L‑alanine amidase, Zn‑dependent, OM lipoprotein
putative NAD(P)H‑dependent oxidoreductase
RA 911,132 A→G intergenic (‑83/+50) poxB ← / ← hcr pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding/HCP oxidoreductase, NADH‑dependent
RA 913,349 G→A L156L (CTG→TTG)  hcp ← hybrid‑cluster [4Fe‑2S‑2O] subunit of anaerobic terminal reductases
RA 915,730 T→C K106K (AAA→AAG)  aqpZ ← aquaporin Z
RA 922,366 C→T *75* (TAG→TAA)  cspD ← inhibitor of DNA replication, cold shock protein homolog
RA 927,205 A→G R76R (CGT→CGC)  aat ← leucyl/phenylalanyl‑tRNA‑protein transferase
RA 932,340 (A)8→7 intergenic (‑290/‑255) trxB ← / → lrp thioredoxin reductase, FAD/NAD(P)‑binding/leucine‑responsive global transcriptional regulator
RA 937,983 G→A *204* (TAG→TAA)  lolA → lipoprotein chaperone
RA 966,584 G→A *755* (TAG→TAA)  ycaI → ComEC family inner membrane protein
RA 967,118 A→G Q166Q (CAA→CAG)  msbA → lipid ABC transporter permease/ATPase
RA 969,352 G→A *329* (TAG→TAA)  lpxK → lipid A 4'kinase
RA 983,623 G→A *183* (TAG→TAA)  ycbK → M15A protease‑related family periplasmic protein
RA 986,671 A→G R104R (CGT→CGC)  ompF ← outer membrane porin 1a (Ia,b,F)
RA 1,006,415 Δ1 bp coding (464/543 nt) zapC → FtsZ stabilizer
RA 1,006,491 C→T V180V (GTC→GTT) 
*370* (TAG→TAA) 		 zapC →
ycbX ←		 FtsZ stabilizer
6‑N‑hydroxylaminopurine detoxification oxidoreductase
RA 1,050,350 C→A S108S (TCC→TCA)  insB1 → IS1 transposase B
RA 1,068,254 G→A *58* (TAG→TAA)  ymdF → KGG family protein
RA 1,068,276 Δ1 bp intergenic (+22/+235) ymdF → / ← rutG KGG family protein/pyrimidine permease
RA 1,068,285 Δ1 bp intergenic (+31/+226) ymdF → / ← rutG KGG family protein/pyrimidine permease
RA 1,072,060 G→A L34L (CTG→TTG)  rutC ← putative aminoacrylate deaminase, reactive intermediate detoxification, weak enamine/imine deaminase activity
RA 1,073,732 C→T A94T (GCG→ACG)  rutA ← pyrimidine oxygenase, FMN‑dependent
RA 1,082,060 A→G pseudogene (601/726 nt) efeU → ferrous iron permease (pseudogene)
RA 1,082,896 T→A R218R (CGT→CGA)  efeO → inactive ferrous ion transporter EfeUOB
RA 1,089,570 T→C E96E (GAA→GAG)  pgaB ← poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein
RA 1,094,275 C→T *289* (TAG→TAA)  insF1 ← IS3 transposase B
RA 1,102,221 T→C E107E (GAA→GAG)  csgE ← curlin secretion specificity factor
RA 1,119,307 C→T *47* (TAG→TAA)  yceO ← uncharacterized protein
RA 1,125,011 A→G C106R (TGC→CGC)  mdtH ← multidrug resistance efflux transporter conferring overexpression resistance to norfloxacin and enoxacin
RA 1,139,406 Δ1 bp coding (1029/1644 nt) flgK → flagellar hook‑filament junction protein 1
RA 1,146,011 C→T *195* (TAG→TAA)  yceF ← m(7)GTP pyrophosphatase
RA 1,148,691 G→A *357* (TAG→TAA)  plsX → putative phosphate acyltransferase
RA 1,149,712 G→A *318* (TAG→TAA)  fabH → 3‑oxoacyl‑[acyl‑carrier‑protein] synthase III
RA 1,153,047 A→G D370G (GAT→GGT)  fabF → 3‑oxoacyl‑[acyl‑carrier‑protein] synthase II
RA 1,154,109 G→A *270* (TAG→TAA)  pabC → 4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex
RA 1,168,350 Δ1 bp coding (483/633 nt) ycfQ ← repressor for bhsA(ycfR)
RA 1,190,061 (G)6→7 coding (387/672 nt) phoP ← response regulator in two‑component regulatory system with PhoQ
RA 1,200,881 G→A A51V (GCC→GTC)  xisE ← e14 prophage, putative excisionase
RA 1,203,224 G→A *67* (TAG→TAA)  croE → e14 prophage, putative DNA‑binding transcriptional regulator
RA 1,204,160 G→A *113* (TAG→TAA)  ymfM → e14 prophage, uncharacterized protein
RA 1,205,731 G→A *61* (TAG→TAA) 
pseudogene (1/412 nt)		 ymfR →
beeE →		 e14 prophage, uncharacterized protein
pseudogene, portal protein family, e14 prophage,Phage or Prophage Related
RA 1,208,517 C→T P129L (CCT→CTT) 
*201* (TAG→TAA) 		 tfaP →
tfaE ←		 e14 prophage, uncharacterized protein
e14 prophage, putative tail fiber assembly protein
RA 1,208,534 Δ1 bp coding (403/414 nt);coding (586/603 nt) tfaP →
tfaE ←		 e14 prophage, uncharacterized protein
e14 prophage, putative tail fiber assembly protein
RA 1,211,652 C→T intergenic (+75/+28) icdC → / ← iraM pseudogene, isocitrate dehydrogenase C‑terminal gene fragment, idcC' is a 54 codon 3' gene fragment created during e14 prophage insertion/RpoS stabilzer during Mg starvation, anti‑RssB factor
RA 1,212,233 A→G intergenic (‑230/+470) iraM ← / ← ycgX RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein
RA 1,212,703 C→T *135* (TAG→TAA)  ycgX ← DUF1398 family protein
RA 1,216,996 Δ2 bp [ymgC] [ymgC]
RA 1,228,724 A→G T216A (ACT→GCT)  ycgM → putative isomerase/hydrolase
RA 1,245,600 G→A *147* (TAG→TAA)  ycgY → uncharacterized protein
RA 1,250,629 (C)5→6 coding (210/1071 nt) dhaK ← dihydroxyacetone kinase, PTS‑dependent, dihydroxyacetone‑binding subunit
RA 1,252,038 G→A A325T (GCT→ACT)  dhaR → dhaKLM operon transcription activator
RA 1,252,961 A→G A632A (GCA→GCG)  dhaR → dhaKLM operon transcription activator
RA 1,260,528 A→G I92I (ATT→ATC)  dauA ← C4‑dicarboxylic acid transporter
RA 1,264,919 C→T D402D (GAC→GAT)  hemA → glutamyl tRNA reductase
RA 1,264,970 G→A *419* (TAG→TAA)  hemA → glutamyl tRNA reductase
MC JC 1,265,001 1086 bp→GAGG [prfA] [prfA]
RA 1,271,455 G→A T132I (ACC→ATC)  chaA ← calcium/sodium:proton antiporter
RA 1,275,815 T→C E5E (GAA→GAG)  narL ← response regulator in two‑component regulatory system with NarX
RA 1,286,793 A→G intergenic (+267/+273) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA 1,286,796 T→C intergenic (+270/+270) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA 1,286,805 2 bp→AA intergenic (+279/+260) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA 1,286,831 T→A intergenic (+305/+235) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA 1,286,859 T→C intergenic (+333/+207) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA 1,286,984 G→A intergenic (+458/+82) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA 1,287,152 T→C noncoding (85/171 nt)
T9A (ACT→GCT) 		 rttR ←
tpr ←		 rtT sRNA, processed from tyrT transcript
protamine‑like protein
RA 1,287,161 2 bp→AA noncoding (75‑76/171 nt)
coding (15‑16/90 nt)		 rttR ←
tpr ←		 rtT sRNA, processed from tyrT transcript
protamine‑like protein
JC JC 1,293,006 IS5 (+) +4 bp intergenic (‑84/‑518) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
MC JC 1,299,499 Δ1,199 bp intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
RA 1,309,016 C→T *418* (TAG→TAA)  kch ← voltage‑gated potassium channel
RA 1,354,505 C→T S5N (AGC→AAC) 
*322* (TAG→TAA) 		 sapC ←
sapB ←		 antimicrobial peptide transport ABC transporter permease
antimicrobial peptide transport ABC transporter permease
RA 1,366,935 C→T *326* (TAG→TAA)  pspF ← psp operon transcriptional activator
RA 1,370,044 (T)9→8 intergenic (+41/‑172) pspE → / → ycjM thiosulfate:cyanide sulfurtransferase (rhodanese)/alpha amylase catalytic domain family protein
RA 1,380,807 G→A *220* (TAG→TAA)  ycjU → beta‑phosphoglucomutase
RA 1,381,789 G→A pseudogene (13/126 nt) ycjV → pseudogene, putative ATP‑binding component of a transport system
RA 1,387,095 G→A A126T (GCA→ACA)  tyrR → aromatic amino acid biosynthesis and transport regulon transcriptional regulator, autorepressor, ATPase, phosphatase
RA 1,389,242 C→T Q105* (CAA→TAA)  ycjG → L‑Ala‑D/L‑Glu epimerase
RA 1,389,499 C→T C190C (TGC→TGT)  ycjG → L‑Ala‑D/L‑Glu epimerase
RA 1,389,895 G→A *322* (TAG→TAA) 
P235L (CCT→CTT) 		 ycjG →
mpaA ←		 L‑Ala‑D/L‑Glu epimerase
murein peptide amidase A
RA 1,392,890 G→A *300* (TAG→TAA)  pgrR → murein peptide degradation regulator
RA 1,399,985 (C)7→8 coding (252/516 nt) ogt ← O‑6‑alkylguanine‑DNA:cysteine‑protein methyltransferase
RA 1,412,000 C→T *412* (TAG→TAA)  intR ← Rac prophage, integrase
RA 1,418,386 G→A intergenic (‑157/‑285) kilR ← / → sieB killing protein, Rac prophage, FtsZ inhibitor protein/phage superinfection exclusion protein, Rac prophage
RA 1,419,159 G→A *163* (TAG→TAA) 
S51S (AGC→AGT) 		 sieB →
ydaF ←		 phage superinfection exclusion protein, Rac prophage
uncharacterized protein, Rac prophage
RA 1,419,344 G→A A38V (GCT→GTT)  ydaG ← Rac prophage, uncharacterized protein
RA 1,419,721 (G)7→8 intergenic (‑265/+44) ydaG ← / ← racR Rac prophage, uncharacterized protein/Rac prophage, putative DNA‑binding transcriptional regulator
RA 1,425,980 G→A pseudogene (351/453 nt) ydaY → pseudogene, Rac prophage,Phage or Prophage Related
RA 1,426,023 A→G pseudogene (394/453 nt) ydaY → pseudogene, Rac prophage,Phage or Prophage Related
RA 1,426,288 G→A intergenic (+206/‑166) ydaY → / → tmpR pseudogene, Rac prophage,Phage or Prophage Related/Rac prophage, pseudogene, tail protein family,Phage or Prophage Related, putative alpha helix protein
RA 1,431,882 T→C V945A (GTG→GCG)  stfR → Rac prophage, putative tail fiber protein
RA 1,432,273 G→A A1075A (GCG→GCA)  stfR → Rac prophage, putative tail fiber protein
RA 1,450,392 C→T A320T (GCA→ACA)  tynA ← tyramine oxidase, copper‑requiring
RA 1,454,292 C→A G122G (GGC→GGA)  paaA → ring 1,2‑phenylacetyl‑CoA epoxidase subunit
RA 1,458,617 A→G A118A (GCA→GCG)  paaG → 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming
RA 1,459,052 G→A *263* (TAG→TAA)  paaG → 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming
RA 1,464,489 G→A *317* (TAG→TAA) 
D7N (GAC→AAC) 		 paaX →
paaY →		 transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer
thioesterase required for phenylacetic acid degradation, trimeric, phenylacetate regulatory and detoxification protein, hexapeptide repeat protein
RA 1,466,996 T→C pseudogene (1605/2513 nt) ydbA → pseudogene, autotransporter homolog, interrupted by IS2 and IS30
RA 1,467,921 C→T *302* (TAG→TAA)  insD1 ← IS2 transposase TnpB
RA 1,472,037 A→G pseudogene (1521/3497 nt) ydbA → pseudogene, autotransporter homolog, interrupted by IS2 and IS30
RA 1,491,389 A→G K163R (AAG→AGG)  cybB → cytochrome b561
RA 1,493,219 A→G E250E (GAA→GAG)  trg → methyl‑accepting chemotaxis protein III, ribose and galactose sensor receptor
RA 1,497,308 A→G E151E (GAA→GAG)  opgD → OPG biosynthetic periplasmic protein
RA 1,503,125 G→A *223* (TAG→TAA)  ydcL → lipoprotein
RA 1,513,468 T→C S218P (TCC→CCC)  ydcT → putative ABC transporter ATPase
RA 1,529,938 G→A pseudogene (2037/2037 nt)
R6K (AGA→AAA) 		 rhsE →
ydcD →		 pseudogene, Rhs family
putative immunity protein for RhsE
RA 1,533,045 C→T intergenic (+93/‑7) ydcC → / → pptA H repeat‑associated putative transposase/4‑oxalocrotonate tautomerase
RA 1,542,804 C→T P419P (CCG→CCA)  narU ← nitrate/nitrite transporter
RA 1,544,384 C→T pseudogene (381/381 nt) yddK ← pseudogene, leucine‑rich protein, putative glycoportein
RA 1,548,360 C→T D320D (GAC→GAT)  fdnG → formate dehydrogenase‑N, alpha subunit, nitrate‑inducible
RA 1,557,112 C→T *309* (TAG→TAA)  ddpF ← D,D‑dipeptide ABC transporter ATPase
RA 1,559,680 G→A G77G (GGC→GGT)  ddpC ← D,D‑dipeptide ABC transporter permease
RA 1,565,758 C→T *461* (TAG→TAA)  dosC ← diguanylate cyclase, cold‑ and stationary phase‑induced oxygen‑dependent biofilm regulator
RA 1,571,332 G→T I238I (ATC→ATA)  gadB ← glutamate decarboxylase B, PLP‑dependent
RA 1,571,902 G→A D48D (GAC→GAT)  gadB ← glutamate decarboxylase B, PLP‑dependent
RA 1,571,917 G→A F43F (TTC→TTT)  gadB ← glutamate decarboxylase B, PLP‑dependent
RA 1,598,617 C→T *531* (TAG→TAA)  lsrK ← autoinducer‑2 (AI‑2) kinase
RA 1,614,789 C→T intergenic (‑86/‑15) sad ← / → yneJ succinate semialdehyde dehydrogenase, NAD(P)+‑dependent/putative DNA‑binding transcriptional regulator
RA 1,618,218 G→A *397* (TAG→TAA)  ydeA → arabinose efflux transporter, arabinose‑inducible
RA 1,619,957 G→A *128* (TAG→TAA)  marA → multiple antibiotic resistance transcriptional regulator
RA 1,620,207 G→A *73* (TAG→TAA)  marB → periplasmic mar operon regulator
RA 1,621,542 G→A D71N (GAC→AAC)  ydeE → putative transporter
RA 1,624,357 (T)8→7 coding (141/393 nt) ydeI ← hydrogen peroxide resistance OB fold protein, putative periplasmic protein
RA 1,626,825 C→T V186I (GTT→ATT)  dcp ← dipeptidyl carboxypeptidase II
RA 1,627,625 T→C L37L (TTG→CTG)  ydfG → NADP‑dependent 3‑hydroxy acid dehydrogenase, malonic semialdehyde reductase
RA 1,630,986 A→G intergenic (‑73/+16) ydfI ← / ← ydfJ putative NAD‑dependent D‑mannonate oxidoreductase/pseudogene, MFS transporter family, interrupted by Qin prophage,Phage or Prophage Related, putative transport protein
RA 1,639,030 C→T *166* (TAG→TAA)  rzpQ ← Rz‑like protein, Qin prophage
RA 1,649,041 G→A *73* (TAG→TAA)  ydfC → uncharacterized protein, Qin prophage
RA 1,651,537 G→A pseudogene (693/693 nt) insD1 → IS2 transposase TnpB,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related
RA 1,655,057 T→C T29A (ACG→GCG)  rspA ← bifunctional D‑altronate/D‑mannonate dehydratase
RA 1,655,347 C→T *109* (TAG→TAA)  ynfA ← UPF0060 family inner membrane protein
RA 1,655,360 (C)5→4 coding (314/327 nt) ynfA ← UPF0060 family inner membrane protein
RA 1,656,744 G→A *187* (TAG→TAA)  speG → spermidine N(1)‑acetyltransferase
RA 1,664,096 T→C I163T (ATA→ACA)  ynfH → oxidoreductase, membrane subunit
RA 1,665,120 G→A *205* (TAG→TAA)  dmsD → twin‑argninine leader‑binding protein for DmsA and TorA
RA 1,670,581 G→A G295R (GGA→AGA)  ynfM → putative arabinose efflux transporter
RA 1,685,542 (C)6→5 coding (1047/1404 nt) fumC ← fumarate hydratase (fumarase C),aerobic Class II
RA 1,691,192 G→A Q447Q (CAG→CAA)  ydgA → DUF945 family protein
RA 1,696,452 (A)5→4 intergenic (‑381/+10) uidA ← / ← uidR beta‑D‑glucuronidase/transcriptional repressor
RA 1,700,201 (T)5→6 coding (847/1593 nt) malX → maltose and glucose‑specific PTS enzyme IIB component and IIC component
RA 1,709,163 T→C S8P (TCC→CCC)  rsxD → SoxR iron‑sulfur cluster reduction factor component, putative membrane protein of electron transport complex
RA 1,712,518 (C)6→7 intergenic (+360/‑251) nth → / → dtpA DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A
RA 1,719,058 G→A P182L (CCG→CTG)  anmK ← anhydro‑N‑acetylmuramic acid kinase
RA 1,726,622 G→A *200* (TAG→TAA)  nemR → transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated
RA 1,733,703 G→A *1539* (TAG→TAA)  lhr → putative ATP‑dependent helicase
RA 1,735,484 T→C V36A (GTC→GCC)  sodB → superoxide dismutase, Fe
RA 1,742,575 G→A intergenic (+14/+26) cfa → / ← ribC cyclopropane fatty acyl phospholipid synthase, SAM‑dependent/riboflavin synthase, alpha subunit
RA 1,744,740 C→T G428G (GGC→GGT)  mdtK → multidrug efflux system transporter
RA 1,757,006 G→A A437T (GCT→ACT)  pykF → pyruvate kinase I
RA 1,757,721 C→T *335* (TAG→TAA)  ldtE ← murein L,D‑transpeptidase
MC JC 1,757,753 Δ5 bp coding (969‑973/1005 nt) ldtE ← murein L,D‑transpeptidase
RA 1,759,680 (C)5→6 coding (844/1221 nt) sufS ← cysteine desulfurase, stimulated by SufE, selenocysteine lyase, PLP‑dependent
RA 1,761,518 G→A R92C (CGT→TGT)  sufD ← component of SufBCD Fe‑S cluster assembly scaffold
RA 1,763,987 Δ1 bp coding (23/1488 nt) sufB ← component of SufBCD Fe‑S cluster assembly scaffold
RA 1,764,018 C→T *123* (TAG→TAA)  sufA ← Fe‑S cluster assembly protein
RA 1,769,478 (G)7→8 coding (405/1113 nt) ydiK → UPF0118 family inner membrane protein
RA 1,781,964 C→G G190G (GGC→GGG)  ydiS → putative oxidoreductase
RA 1,788,278 G→A *278* (TAG→TAA)  ppsR → PEP synthase kinase and PEP synthase pyrophosphorylase
RA 1,788,844 T→C V137A (GTC→GCC)  aroH → 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible
RA 1,789,804 G→A *64* (TAG→TAA)  ydiE → hemin uptake protein HemP homolog
RA 1,792,267 C→T *155* (TAG→TAA)  nlpC ← putative C40 clan peptidase lipoprotein
RA 1,794,172 C→T *327* (TAG→TAA)  btuC ← vitamin B12 ABC transporter permease
RA 1,799,883 T→C K39K (AAA→AAG)  rpmI ← 50S ribosomal subunit protein L35
RA 1,803,567 G→A pseudogene (50/1476 nt) arpB → pseudogene, ankyrin repeats
RA 1,819,569 A→G G79G (GGT→GGC)  chbA ← N,N'‑diacetylchitobiose‑specific enzyme IIA component of PTS
RA 1,821,867 (A)8→7 intergenic (‑248/+51) chbB ← / ← osmE N,N'‑diacetylchitobiose‑specific enzyme IIB component of PTS/osmotically‑inducible lipoprotein
RA 1,826,546 T→C E126E (GAA→GAG)  astE ← succinylglutamate desuccinylase
RA 1,834,111 G→A *237* (TAG→TAA)  ydjX → TVP38/TMEM64 family inner membrane protein
RA 1,835,944 G→A A144T (GCT→ACT)  ynjA → carboxymuconolactone decarboxylase family protein
RA 1,841,897 G→A *136* (TAG→TAA) 
T80I (ACT→ATT) 		 nudG →
ynjH ←		 CTP pyrophosphohydrolase, also hydrolyzes 2‑hydroxy‑dATP, 8‑hydroxy‑dGTP, 5‑hydroxy‑CTP, dCTP and 5‑methyl‑dCTP
DUF1496 family protein
RA 1,850,810 (C)5→4 intergenic (+117/‑50) sppA → / → ansA protease IV (signal peptide peptidase)/cytoplasmic L‑asparaginase 1
RA 1,862,634 A→G intergenic (‑205/‑137) msrB ← / → gapA methionine sulfoxide reductase B/glyceraldehyde‑3‑phosphate dehydrogenase A
RA 1,863,004 T→C R78R (CGT→CGC)  gapA → glyceraldehyde‑3‑phosphate dehydrogenase A
RA 1,869,022 (T)6→5 coding (68/1284 nt) yeaH → UPF0229 family protein
RA 1,874,078 C→T *35* (TAG→TAA)  yoaI ← uncharacterized protein
RA 1,874,798 G→A *149* (TAG→TAA) 
T260I (ACT→ATT) 		 yeaL →
yeaM ←		 UPF0756 family putative inner membrane protein
putative DNA‑binding transcriptional regulator
RA 1,875,056 (C)6→5 coding (521/822 nt) yeaM ← putative DNA‑binding transcriptional regulator
RA 1,881,463 G→A A116V (GCG→GTG)  dmlR ← transcriptional activator of dmlA
RA 1,886,810 G→A *322* (TAG→TAA)  yeaX → putative YeaWX dioxygenase beta subunit, reductase component
RA 1,892,402 A→G S278S (AGT→AGC)  yoaA ← putative ATP‑dependent helicase, DinG family
RA 1,905,805 G→A G40S (GGC→AGC)  mntP → putative Mn(2+) efflux pump, mntR‑regulated
RA 1,906,662 (A)5→4 coding (399/810 nt) rlmA ← 23S rRNA m(1)G745 methyltransferase, SAM‑dependent
RA 1,909,123 C→T P67S (CCG→TCG)  yobH → uncharacterized protein
RA 1,910,474 T→C S67P (TCC→CCC)  yebQ → putative transporter
RA 1,920,205 (T)7→8 intergenic (+62/‑18) yebT → / → rsmF MCE domain protein/16S rRNA m(5)C1407 methyltransferase, SAM‑dependent
RA 1,926,096 G→A *219* (TAG→TAA)  yobB → C‑N hydrolase family protein
RA 1,926,782 G→A *221* (TAG→TAA) 
D686D (GAC→GAT) 		 exoX →
ptrB ←		 exodeoxyribonuclease 10, DNA exonuclease X
protease II
RA 1,934,874 T→C T481A (ACC→GCC)  zwf ← glucose‑6‑phosphate 1‑dehydrogenase
RA 1,939,673 T→C N174S (AAC→AGC)  lpxM ← myristoyl‑acyl carrier protein (ACP)‑dependent acyltransferase
RA 1,942,993 G→A G111E (GGG→GAG)  znuC → zinc ABC transporter ATPase
RA 1,950,559 (C)5→6 intergenic (‑37/‑273) aspS ← / → yecD aspartyl‑tRNA synthetase/isochorismatase family protein
RA 1,952,661 G→A *132* (TAG→TAA)  yecN → MAPEG family inner membrane protein
RA 1,964,697 G→A L118L (CTC→CTT)  flhA ← putative flagellar export pore protein
MC JC 1,978,503 Δ776 bp insB1–insA insB1, insA
RA 1,980,188 C→T *475* (TAG→TAA)  otsA ← trehalose‑6‑phosphate synthase
RA 1,998,494 C→T *329* (TAG→TAA)  dcyD ← D‑cysteine desulfhydrase, PLP‑dependent
RA 2,012,001 C→T pseudogene (40/678 nt) yedN ← pseudogene, IpaH/YopM family
RA 2,012,700 C→T *105* (TAG→TAA)  fliE ← flagellar basal‑body component
RA 2,016,095 G→A L76L (CTG→CTA)  fliH → negative regulator of FliI ATPase activity
RA 2,021,501 G→A *138* (TAG→TAA)  fliN → flagellar motor switching and energizing component
RA 2,022,606 G→A *246* (TAG→TAA)  fliP → flagellar biosynthesis protein
RA 2,022,885 G→A *90* (TAG→TAA)  fliQ → flagellar biosynthesis protein
RA 2,029,729 (C)6→5 coding (191/921 nt) yedA → amino acid exporter for phenylalanine, threonine
RA 2,034,536 G→A pseudogene (486/663 nt) yedS → pseudogene, outer membrane protein homology, putative outer membrane protein
RA 2,049,336 C→T P1467S (CCG→TCG)  yeeJ → putative adhesin
RA 2,059,964 C→T *317* (TAG→TAA)  cbl ← ssuEADCB/tauABCD operon transcriptional activator
RA 2,068,952 C→T *302* (TAG→TAA)  insD1 ← IS2 transposase TnpB
RA 2,073,151 T→C L538P (CTG→CCG)  flu → CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
RA 2,084,773 G→A G251G (GGC→GGT)  yeeE ← UPF0394 family inner membrane protein
RA 2,085,831 A→G L411P (CTG→CCG)  plaP ← putrescine importer, low affinity
RA 2,090,046 G→A *17* (TAG→TAA)  hisL → his operon leader peptide
RA 2,099,237 G→A A126V (GCG→GTG)  ugd ← UDP‑glucose 6‑dehydrogenase
RA 2,104,494 C→T V6I (GTC→ATC) 
*197* (TAG→TAA) 		 wbbK ←
wbbJ ←		 lipopolysaccharide biosynthesis protein
putative lipopolysaccharide biosynthesis O‑acetyl transferase
RA 2,114,502 C→T *465* (TAG→TAA)  wcaM ← colanic acid biosynthesis protein
RA 2,115,907 C→T *407* (TAG→TAA)  wcaL ← putative glycosyl transferase
RA 2,118,164 G→A R81C (CGT→TGT)  wcaK ← colanic acid biosynthesis protein
RA 2,130,853 C→T S9N (AGC→AAC) 
*406* (TAG→TAA) 		 wcaD ←
wcaC ←		 putative colanic acid polymerase
putative glycosyl transferase
RA 2,131,667 T→C D135G (GAC→GGC)  wcaC ← putative glycosyl transferase
RA 2,139,759 C→T *618* (TAG→TAA)  asmA ← suppressor of OmpF assembly mutants, putative outer membrane protein assembly factor, inner membrane‑anchored periplasmic protein
RA 2,149,963 G→T G341G (GGC→GGA)  yegI ← protein kinase‑related putative non‑specific DNA‑binding protein
RA 2,164,998 G→A *241* (TAG→TAA)  baeR → response regulator in two‑component regulatory system with BaeS
RA 2,169,693 C→T pseudogene (475/475 nt) gatR ← pseudogene, repressor for gat operon, interrupted by IS3, split galactitol utilization operon repressor, fragment 2, split galactitol utilization operon repressor, interrupted
RA 2,171,398 G→A *289* (TAG→TAA)  insF1 → IS3 transposase B
RA 2,173,363 Δ2 bp intergenic (‑1/+1) gatC ← / ← gatC pseudogene, galactitol‑specific enzyme IIC component of PTS,transport, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS,transport, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system galactitol‑specific enzyme IIC
RA 2,179,330 T→C S170S (AGT→AGC)  yegT → nucleoside transporter, low affinity
RA 2,182,035 C→T L314L (CTA→TTA) 
*249* (TAG→TAA) 		 yegV →
yegW ←		 putative kinase
putative DNA‑binding transcriptional regulator
RA 2,182,061 G→A *322* (TAG→TAA) 
L241L (CTA→TTA) 		 yegV →
yegW ←		 putative kinase
putative DNA‑binding transcriptional regulator
RA 2,189,594 C→T A439A (GCG→GCA)  yehB ← putative outer membrane protein
RA 2,199,998 A→G pseudogene (677/948 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 2,200,454 (A)8→7 coding (176/3633 nt) yehI → DUF4132 domain‑containing protein
RA 2,210,944 G→A pseudogene (1845/2001 nt) yehQ → pseudogene
RA 2,214,339 (C)6→5 coding (306/1686 nt) yehU ← inner membrane putative sensory kinase in two‑component system with YehT
RA 2,218,207 C→T A117A (GCG→GCA)  yehY ← putative ABC transporter permease
RA 2,220,789 G→A R401C (CGT→TGT)  bglX ← beta‑D‑glucoside glucohydrolase, periplasmic
RA 2,225,044 C→T *196* (TAG→TAA)  yohC ← Yip1 family inner membrane protein
RA 2,226,509 C→T *254* (TAG→TAA)  yohF ← putative oxidoreductase
RA 2,233,597 G→A *240* (TAG→TAA)  sanA → DUF218 superfamily vancomycin high temperature exclusion protein
RA 2,240,754 (C)5→6 coding (915/1041 nt) galS ← galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor, mgl operon transcriptional repressor, autorepressor
RA 2,263,478 T→C V6V (GTA→GTG)  fruB ← fused fructose‑specific PTS enzymes: IIA component/HPr component
RA 2,266,013 T→C R188R (CGT→CGC)  yeiP → elongation factor P‑like protein
RA 2,274,166 A→G K601K (AAA→AAG)  yejA → microcin C ABC transporter periplasmic binding protein
RA 2,274,178 G→A *605* (TAG→TAA)  yejA → microcin C ABC transporter periplasmic binding protein
RA 2,276,298 G→A *342* (TAG→TAA)  yejE → microcin C ABC transporter permease
RA 2,288,561 (C)7→6 pseudogene (354/2525 nt) yejO ← pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system
RA 2,289,027 G→A intergenic (‑113/+38) yejO ← / ← insH1 pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system/IS5 transposase and trans‑activator
RA 2,291,973 T→C G146G (GGA→GGG)  ccmH ← heme lyase, CcmH subunit
RA 2,297,114 (C)7→8 coding (531/624 nt) ccmA ← heme export ABC transporter ATPase
RA 2,316,160 G→A *891* (TAG→TAA)  rcsD → phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
RA 2,317,027 C→T *950* (TAG→TAA)  rcsC ← hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA 2,318,019 G→A R620C (CGT→TGT)  rcsC ← hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA 2,334,336 C→T pseudogene (67/4605 nt)
*208* (TAG→TAA) 		 yfaS ←
yfaT ←		 pseudogene, bacterial alpha2‑macroglobulin YfaS variant family, putative membrane protein
DUF1175 family protein, putative host defense protein
RA 2,350,162 A→G L284L (TTG→CTG)  glpQ ← periplasmic glycerophosphodiester phosphodiesterase
RA 2,358,163 G→A A228V (GCG→GTG)  rhmA ← 2‑keto‑3‑deoxy‑L‑rhamnonate aldolase
RA 2,370,019 T→C *661R (TGA→CGA) 
M1T (ATG→ACG) †		 arnA →
arnD →		 fused UDP‑L‑Ara4N formyltransferase/UDP‑GlcA C‑4'‑decarboxylase
undecaprenyl phosphate‑alpha‑L‑ara4FN deformylase
RA 2,379,348 C→T *432* (TAG→TAA)  menF ← isochorismate synthase 2
RA 2,414,699 T→C intergenic (+27/‑48) ackA → / → pta acetate kinase A and propionate kinase 2/phosphate acetyltransferase
RA 2,416,763 2 bp→TC coding (2017‑2018/2145 nt) pta → phosphate acetyltransferase
RA 2,438,548 T→C V200A (GTG→GCG)  flk → putative flagella assembly protein
RA 2,441,742 G→A intergenic (‑137/‑22) fabB ← / → mnmC 3‑oxoacyl‑[acyl‑carrier‑protein] synthase I/fused 5‑methylaminomethyl‑2‑thiouridine‑forming enzyme methyltransferase and FAD‑dependent demodification enzyme
RA 2,449,228 C→T *274* (TAG→TAA)  yfcO ← DUF2544 family putative outer membrane protein
RA 2,453,265 C→T pseudogene (1737/2646 nt) yfcU ← pseudogene, FimD fimbrial export usher family,putative membrane, Not classified, putative outer membrane protein
RA 2,462,889 (C)9→8 intergenic (+243/‑123) fadL → / → yfdF long‑chain fatty acid outer membrane transporter/uncharacterized protein
RA 2,468,106 T→C A84A (GCT→GCC)  gtrA → CPS‑53 (KpLE1) prophage, bactoprenol‑linked glucose translocase/flippase
RA 2,471,105 G→A pseudogene (291/291 nt)
P138L (CCT→CTT) 		 tfaS →
yfdK ←		 pseudogene, CPS‑53 (KpLE1) prophage, tail fiber assembly protein fragment,Phage or Prophage Related
CPS‑53 (KpLE1) prophage, conserved protein
RA 2,478,092 A→G V82V (GTA→GTG)  dsdX → D‑serine transporter
RA 2,484,897 (C)6→7 coding (524/3594 nt) evgS → hybrid sensory histidine kinase in two‑component regulatory system with EvgA
RA 2,494,694 T→C intergenic (‑292/‑4) yfdX ← / → ypdI uncharacterized protein/putative lipoprotein involved in colanic acid biosynthesis
RA 2,494,950 T→C Y85H (TAT→CAT)  ypdI → putative lipoprotein involved in colanic acid biosynthesis
RA 2,494,973 G→A *92* (TAG→TAA)  ypdI → putative lipoprotein involved in colanic acid biosynthesis
RA 2,495,050 C→T *81* (TAG→TAA)  yfdY ← DUF2545 family putative inner membrane protein
RA 2,510,886 G→A *419* (TAG→TAA)  yfeO → putative ion channel protein
RA 2,511,468 C→T *413* (TAG→TAA)  mntH ← manganese/divalent cation transporter
RA 2,521,593 C→T *295* (TAG→TAA)  xapR ← transcriptional activator of xapAB
RA 2,521,852 T→C D209G (GAT→GGT)  xapR ← transcriptional activator of xapAB
MC JC 2,525,917 Δ9 bp intergenic (+26/+5) yfeN → / ← yfeR putative outer membrane protein/transcriptional regulator of yefH
RA 2,525,930 C→T *309* (TAG→TAA)  yfeR ← transcriptional regulator of yefH
RA 2,534,031 T→C intergenic (+10/‑35) ptsH → / → ptsI phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr)/PEP‑protein phosphotransferase of PTS system (enzyme I)
RA 2,552,094 G→A I15I (ATC→ATT)  ypeA ← GNAT family putative N‑acetyltransferase
RA 2,574,135 G→A D57D (GAC→GAT)  eutT ← cobalamin adenosyltransferase involved in ethanolamine utilization
RA 2,589,535 C→T I647I (ATC→ATT)  acrD → aminoglycoside/multidrug efflux system
RA 2,591,603 G→A *119* (TAG→TAA)  yffB → putative ArsC family reductase
RA 2,595,227 T→C Q211Q (CAA→CAG)  tmcA ← elongator methionine tRNA (ac4C34) acetyltransferase
RA 2,600,609 (C)5→6 coding (132/471 nt) bcp → peroxiredoxin, thiol peroxidase, thioredoxin‑dependent
MC JC 2,614,614 Δ3 bp coding (681‑683/849 nt) focB → putative formate transporter
RA 2,618,075 C→T *234* (TAG→TAA)  hda ← ATPase regulatory factor involved in DnaA inactivation
RA 2,621,307 A→G E37E (GAA→GAG)  purM → phosphoribosylaminoimidazole synthetase
RA 2,629,481 G→A *64* (TAG→TAA)  yfgG → uncharacterized protein
RA 2,637,295 C→T R21H (CGT→CAT)  der ← GTPase, multicopy suppressor of ftsJ
RA 2,645,013 C→T *771* (TAG→TAA)  pbpC ← penicillin‑insensitive murein repair transglycosylase, inactive transpeptidase domain protein
RA 2,655,767 T→C T198A (ACT→GCT)  pepB ← aminopeptidase B
RA 2,658,145 T→C Q264R (CAG→CGG)  hscA ← DnaK‑like molecular chaperone specific for IscU
RA 2,673,768 G→A *141* (TAG→TAA)  yphA → DoxX family inner membrane protein
RA 2,684,971 G→A G179G (GGC→GGT)  glyA ← serine hydroxymethyltransferase
RA 2,685,561 T→C intergenic (‑54/‑274) glyA ← / → hmp serine hydroxymethyltransferase/fused nitric oxide dioxygenase/dihydropteridine reductase 2
RA 2,685,910 G→A A26T (GCC→ACC)  hmp → fused nitric oxide dioxygenase/dihydropteridine reductase 2
RA 2,697,915 C→T *212* (TAG→TAA)  pgpC ← phosphatidylglycerophosphatase C, membrane bound
RA 2,713,568 T→C W225R (TGG→CGG)  srmB → ATP‑dependent RNA helicase
RA 2,723,065 G→A A113A (GCG→GCA)  pssA → phosphatidylserine synthase, CDP‑diacylglycerol‑serine O‑phosphatidyltransferase
RA 2,724,448 C→T H107H (CAC→CAT) 
*433* (TAG→TAA) 		 yfiM →
kgtP ←		 putative lipoprotein
alpha‑ketoglutarate transporter
RA 2,737,495 G→A *114* (TAG→TAA)  raiA → cold shock protein associated with 30S ribosomal subunit
RA 2,742,962 G→A D194N (GAT→AAT)  yfiN → putative membrane‑anchored diguanylate cyclase
RA 2,758,359 C→T S81N (AGC→AAC)  yfjH ← CP4‑57 prophage, uncharacterized protein
RA 2,765,829 (C)5→4 intergenic (‑53/‑89) yfjM ← / → rnlA CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, RNase LS
RA 2,767,445 (C)7→9 intergenic (+90/‑265) rnlB → / → yfjP CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, 50S ribosome‑binding GTPase family protein
RA 2,769,486 G→A *274* (TAG→TAA)  yfjQ → CP4‑57 prophage, uncharacterized protein
RA 2,769,648 (C)6→5 intergenic (+162/‑55) yfjQ → / → yfjR CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, putative DNA‑binding transcriptional regulator
RA 2,770,404 G→A *234* (TAG→TAA)  yfjR → CP4‑57 prophage, putative DNA‑binding transcriptional regulator
RA 2,781,132 T→C D532G (GAC→GGC)  ypjA ← adhesin‑like autotransporter
RA 2,782,393 (C)5→4 coding (334/4581 nt) ypjA ← adhesin‑like autotransporter
RA 2,784,529 C→T pseudogene (483/1374 nt) ypjC ← pseudogene
RA 2,786,729 G→A pseudogene (333/2253 nt) ygaQ → uncharacterized protein, putative enzyme
RA 2,786,746 Δ1 bp pseudogene (350/2253 nt) ygaQ → uncharacterized protein, putative enzyme
RA 2,787,434 G→A pseudogene (1038/2253 nt) ygaQ → uncharacterized protein, putative enzyme
RA 2,788,238 G→A pseudogene (1842/2253 nt) ygaQ → uncharacterized protein, putative enzyme
RA 2,794,015 G→A *427* (TAG→TAA)  gabT → 4‑aminobutyrate aminotransferase, PLP‑dependent
RA 2,796,146 C→T A158V (GCG→GTG)  csiR → transcriptional repressor of csiD
RA 2,796,337 C→T *150* (TAG→TAA)  ygaU ← uncharacterized protein
RA 2,796,916 T→C Y38C (TAT→TGT)  yqaE ← cyaR sRNA‑regulated protein
RA 2,800,475 G→A *110* (TAG→TAA)  ygaM → putative membrane‑anchored DUF883 family ribosome‑binding protein
RA 2,814,218 C→T *172* (TAG→TAA)  luxS ← S‑ribosylhomocysteine lyase
RA 2,824,491 C→T *362* (TAG→TAA)  mltB ← membrane‑bound lytic murein transglycosylase B
RA 2,824,496 Δ1 bp coding (1081/1086 nt) mltB ← membrane‑bound lytic murein transglycosylase B
RA 2,827,351 G→A *320* (TAG→TAA)  srlE → glucitol/sorbitol‑specific enzyme IIB component of PTS
RA 2,835,045 G→A *378* (TAG→TAA)  norW → NADH:flavorubredoxin oxidoreductase
RA 2,839,384 T→A intergenic (‑120/‑140) ascG ← / → ascF asc operon transcriptional repressor, prpBC operon repressor/cellobiose/arbutin/salicin‑specific PTS enzymes, IIB and IC components
RA 2,842,414 G→A *475* (TAG→TAA)  ascB → cryptic 6‑phospho‑beta‑glucosidase
RA 2,842,573 C→T *157* (TAG→TAA)  hycI ← protease involved in processing C‑terminal end of HycE
RA 2,851,873 G→A *291* (TAG→TAA) 
G4S (GGC→AGC) 		 hypB →
hypC →		 GTP hydrolase involved in nickel liganding into hydrogenases
hydrogenase maturation protein
RA 2,856,453 C→T *118* (TAG→TAA)  ygbA ← uncharacterized protein
RA 2,859,538 C→T L816L (CTG→TTG)  mutS → methyl‑directed mismatch repair protein
RA 2,860,416 G→A *219* (TAG→TAA)  pphB → serine/threonine‑specific protein phosphatase 2
RA 2,860,426 Δ1 bp intergenic (+10/+41) pphB → / ← ygbI serine/threonine‑specific protein phosphatase 2/DeoR family putative transcriptional regulator
RA 2,876,944 G→A A122T (GCC→ACC)  iap → aminopeptidase in alkaline phosphatase isozyme conversion
RA 2,893,928 G→A *424* (TAG→TAA) 
A4T (GCC→ACC) 		 ygcN →
ygcO →		 putative oxidoreductase
putative 4Fe‑4S cluster‑containing protein
MC JC 2,893,961 Δ3 bp coding (43‑45/261 nt) ygcO → putative 4Fe‑4S cluster‑containing protein
RA 2,902,543 G→A G216G (GGG→GGA)  ygcE → putative kinase
RA 2,905,532 T→C intergenic (‑114/‑25) queE ← / → yqcG 7‑carboxy‑7‑deazaguanine synthase, queosine biosynthesis/membrane stress resistance protein
RA 2,910,756 C→T *112* (TAG→TAA)  mazF ← mRNA interferase toxin, antitoxin is MazE
RA 2,911,417 C→T *745* (TAG→TAA)  relA ← (p)ppGpp synthetase I/GTP pyrophosphokinase
RA 2,913,699 C→T *434* (TAG→TAA)  rlmD ← 23S rRNA m(5)U1939 methyltransferase, SAM‑dependent
RA 2,915,105 C→T P17S (CCG→TCG)  barA → hybrid sensory histidine kinase, in two‑component regulatory system with UvrY
RA 2,935,917 G→A G112S (GGC→AGC)  fucI → L‑fucose isomerase
RA 2,936,931 T→C F450L (TTC→CTC)  fucI → L‑fucose isomerase
RA 2,937,802 A→G D112G (GAC→GGC)  fucK → L‑fuculokinase
RA 2,962,441 C→T *108* (TAG→TAA)  ppdC ← putative prepilin peptidase‑dependent protein
RA 2,966,188 C→T *749* (TAG→TAA)  ptsP ← PEP‑protein phosphotransferase enzyme I, GAF domain containing protein
RA 2,970,351 G→A *230* (TAG→TAA)  mutH → methyl‑directed mismatch repair protein
RA 2,979,943 C→T A308V (GCT→GTT) 
*231* (TAG→TAA) 		 lysR →
ygeA ←		 transcriptional activator of lysA, autorepressor
Asp/Glu_racemase family protein
RA 2,983,288 C→T *279* (TAG→TAA)  kduI ← hexuronate isomerase
RA 2,984,411 C→T *394* (TAG→TAA)  yqeF ← short chain acyltransferase
RA 2,993,856 G→A *73* (TAG→TAA)  ygeI → uncharacterized protein
RA 2,994,415 G→A pseudogene (34/60 nt) pbl → pseudogene, peptidoglycan‑binding enzyme family
RA 2,995,231 (A)7→8 intergenic (‑139/+83) ygeK ← / ← ygeN pseudogene, response regulator family, part of T3SS PAI ETT2 remnant, putative 2‑component transcriptional regulator/pseudogene, orgB family, part of T3SS PAI ETT2 remnant
RA 2,995,314 C→T pseudogene (447/447 nt) ygeN ← pseudogene, orgB family, part of T3SS PAI ETT2 remnant
RA 2,996,372 C→T *302* (TAG→TAA)  insD1 ← IS2 transposase TnpB
RA 2,997,689 C→T intergenic (‑89/+3) insC1 ← / ← ygeQ IS2 repressor TnpA/pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant
RA 3,012,553 Δ1 bp intergenic (+160/+61) yqeA → / ← yqeB putative amino acid kinase/XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold
RA 3,014,259 Δ1 bp intergenic (‑20/+28) yqeB ← / ← yqeC XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold/putative selenium‑dependent hydroxylase accessory protein
RA 3,014,287 C→T *257* (TAG→TAA)  yqeC ← putative selenium‑dependent hydroxylase accessory protein
RA 3,015,738 G→A *193* (TAG→TAA)  mocA → CTP:molybdopterin cytidylyltransferase
RA 3,032,032 G→A S222S (TCG→TCA)  uacT → uric acid permease
RA 3,035,546 T→C T246A (ACG→GCG)  prfB ← peptide chain release factor RF‑2
RA 3,036,373 C→T *578* (TAG→TAA)  recJ ← ssDNA exonuclease, 5' ‑‑> 3'‑specific
RA 3,056,273 G→A P11P (CCG→CCA)  fau → 5‑formyltetrahydrofolate cyclo‑ligase family protein
RA 3,059,293 T→C G11G (GGA→GGG)  rpiA ← ribose 5‑phosphate isomerase, constitutive
RA 3,061,202 A→G N118S (AAC→AGC)  scpA → methylmalonyl‑CoA mutase
RA 3,068,173 C→T *212* (TAG→TAA)  argO ← arginine transporter
RA 3,078,852 T→C N3S (AAC→AGC)  cmtA ← putative mannitol‑specific PTS IIB and IIC components
RA 3,082,038 T→C D42D (GAT→GAC)  loiP → Phe‑Phe periplasmic metalloprotease, OM lipoprotein, low salt‑inducible, Era‑binding heat shock protein
RA 3,083,620 G→A R60C (CGT→TGT)  speB ← agmatinase
RA 3,085,461 A→G S151P (TCC→CCC)  speA ← biosynthetic arginine decarboxylase, PLP‑binding
RA 3,094,234 T→C T283A (ACA→GCA)  yggR ← putative PilT family AAA+ ATPase
RA 3,096,673 G→A *97* (TAG→TAA)  yggU → UPF0235 family protein
RA 3,101,039 (C)7→8 coding (585/720 nt) yggN ← DUF2884 family putative periplasmic protein
RA 3,104,065 G→A *351* (TAG→TAA)  mutY → adenine DNA glycosylase
RA 3,129,036 G→A *255* (TAG→TAA)  glcC → glycolate‑inducible glc operon transcriptional repressor, autorepressor
MC JC 3,129,500 Δ646 bp IS5‑mediated [yghO] [yghO]
RA 3,131,341 C→T *356* (TAG→TAA)  yghQ ← putative inner membrane polysaccharide flippase
RA 3,134,811 Δ1 bp coding (681/693 nt) yghT → putative ATP‑binding protein
RA 3,134,823 G→A *231* (TAG→TAA)  yghT → putative ATP‑binding protein
RA 3,140,294 T→C S9G (AGC→GGC)  hybF ← protein involved with the maturation of hydrogenases 1 and 2
RA 3,162,308 G→A S121L (TCG→TTG)  ftsP ← septal ring component that protects the divisome from stress, multicopy suppressor of ftsI(Ts)
RA 3,171,879 C→T *111* (TAG→TAA)  ygiZ ← inner membrane protein
RA 3,176,721 G→A T38I (ACC→ATC)  cpdA ← 3',5' cAMP phosphodiesterase
RA 3,176,858 C→T *141* (TAG→TAA)  yqiB ← DUF1249 protein YqiB
RA 3,178,015 G→A intergenic (‑105/‑100) nudF ← / → tolC ADP‑ribose pyrophosphatase/transport channel
RA 3,183,006 G→A G153S (GGT→AGT)  zupT → zinc transporter
RA 3,187,415 G→A *302* (TAG→TAA)  insD1 → IS2 transposase TnpB
RA 3,187,588 G→A pseudogene (162/2439 nt) yqiG → pseudogene, fimbrial export usher family,putative membrane, Not classified, putative membrane protein
RA 3,191,696 G→A *355* (TAG→TAA)  yqiI → fimbrial protein
RA 3,199,429 T→C A71A (GCA→GCG)  glnE ← fused deadenylyltransferase/adenylyltransferase for glutamine synthetase
RA 3,205,324 C→T *311* (TAG→TAA)  ttdR ← transcriptional activator of ttdABT
RA 3,218,365 C→T E238K (GAG→AAG)  aer ← fused signal transducer for aerotaxis sensory component/methyl accepting chemotaxis component
RA 3,220,190 G→A A233T (GCT→ACT)  patA → putrescine:2‑oxoglutaric acid aminotransferase, PLP‑dependent
RA 3,238,562 (T)7→6 intergenic (+265/‑18) ygjR → / → alx putative NAD(P)‑dependent dehydrogenase/putative membrane‑bound redox modulator
JC 3,240,984 (G)7→10 coding (1041/1245 nt) sstT → sodium:serine/threonine symporter
RA 3,248,939 T→C intergenic (+117/‑30) mzrA → / → yqjC modulator of EnvZ/OmpR regulon/DUF1090 family putative periplasmic protein
RA 3,255,020 G→A *234* (TAG→TAA)  yhaK → redox‑sensitive bicupin
RA 3,257,675 G→A G112G (GGC→GGT)  yhaO ← putative transporter
RA 3,266,127 C→T *313* (TAG→TAA)  tdcA ← tdc operon transcriptional activator
RA 3,269,012 A→G S200G (AGT→GGT)  yhaC → pentapetide repeats‑related protein
RA 3,269,602 G→A *396* (TAG→TAA)  yhaC → pentapetide repeats‑related protein
RA 3,271,932 T→C T274A (ACG→GCG)  garR ← tartronate semialdehyde reductase
RA 3,277,726 C→T F130F (TTC→TTT)  yhaV → toxin of the SohB(PrlF)‑YhaV toxin‑antitoxin system
RA 3,277,867 C→T V267I (GTC→ATC)  agaR ← transcriptional repressor of the aga regulon
RA 3,296,984 G→A *192* (TAG→TAA)  yraP → outer membrane lipoprotein
RA 3,298,035 T→C E35G (GAA→GGA)  yraQ ← putative inner membrane permease
RA 3,299,438 A→G T155T (ACA→ACG)  yhbO → stress‑resistance protein
RA 3,299,999 G→A A12T (GCC→ACC)  yhbQ → GIY‑YIG nuclease superfamily protein
RA 3,301,599 G→A G39S (GGC→AGC)  yhbU → U32 peptidase family protein
RA 3,304,455 G→A *336* (TAG→TAA)  yhbW → putative luciferase‑like monooxygenase
RA 3,308,040 C→T *295* (TAG→TAA)  nlpI ← lipoprotein involved in osmotic sensitivity and filamentation
RA 3,308,868 G→A C19C (TGC→TGT)  nlpI ← lipoprotein involved in osmotic sensitivity and filamentation
RA 3,309,006 (C)6→5 intergenic (‑82/+27) nlpI ← / ← pnp lipoprotein involved in osmotic sensitivity and filamentation/polynucleotide phosphorylase/polyadenylase
RA 3,309,007 G→A intergenic (‑83/+26) nlpI ← / ← pnp lipoprotein involved in osmotic sensitivity and filamentation/polynucleotide phosphorylase/polyadenylase
RA 3,320,333 T→C E427E (GAA→GAG)  yhbX ← putative EptAB family phosphoethanolamine transferase, inner membrane protein
RA 3,330,357 +T coding (1395/1434 nt) dacB → D‑alanyl‑D‑alanine carboxypeptidase
RA 3,330,396 G→A *478* (TAG→TAA)  dacB → D‑alanyl‑D‑alanine carboxypeptidase
RA 3,340,588 T→C L105S (TTA→TCA)  yrbG → putative calcium/sodium:proton antiporter
RA 3,347,069 G→A *164* (TAG→TAA)  ptsN → sugar‑specific enzyme IIA component of PTS
RA 3,353,121 C→T *310* (TAG→TAA)  yhcC ← putative Fe‑S oxidoreductase, Radical SAM superfamily protein
RA 3,360,769 G→A intergenic (+153/‑407) gltD → / → gltF glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
RA 3,361,329 G→A G52S (GGC→AGC)  gltF → periplasmic protein
RA 3,365,664 G→A intergenic (+113/+38) yhcE → / ← insH1 pseudogene fragment, interrupted by IS5/IS5 transposase and trans‑activator
RA 3,366,953 G→A G10R (GGA→AGA)  yhcF → putative transcriptional regulator
RA 3,372,254 G→A G107G (GGC→GGT)  nanT ← sialic acid transporter
RA 3,385,857 C→T *91* (TAG→TAA)  yhcO ← putative barnase inhibitor
RA 3,398,875 C→T M1M (GTG→ATG) †
*368* (TAG→TAA) 		 mreD ←
mreC ←		 cell wall structural complex MreBCD transmembrane component MreD
cell wall structural complex MreBCD transmembrane component MreC
RA 3,400,773 A→G R105R (CGT→CGC)  mreB ← cell wall structural complex MreBCD, actin‑like component MreB
RA 3,410,406 T→C S43P (TCT→CCT)  dusB → tRNA‑dihydrouridine synthase B
RA 3,432,994 (C)6→8 coding (567/1125 nt) smf ← DNA recombination‑mediator A family protein
RA 3,434,577 G→A A122T (GCA→ACA)  fmt → 10‑formyltetrahydrofolate:L‑methionyl‑tRNA(fMet) N‑formyltransferase
RA 3,439,141 C→T *123* (TAG→TAA)  yhdN ← DUF1992 family protein
RA 3,440,950 G→A T27I (ACC→ATC)  rpoA ← RNA polymerase, alpha subunit
RA 3,457,616 G→A A414T (GCC→ACC)  gspD → general secretory pathway component, cryptic
RA 3,466,313 A→G L138P (CTT→CCT)  bfr ← bacterioferritin, iron storage and detoxification protein
RA 3,478,592 C→T *67* (TAG→TAA)  yheV ← DUF2387 family putative metal‑binding protein
RA 3,478,802 C→T *602* (TAG→TAA)  kefB ← potassium:proton antiporter
RA 3,482,967 T→C L560P (CTG→CCG)  yheS → ABC‑F family protein predicted regulatory ATPase
RA 3,503,952 G→A *262* (TAG→TAA)  frlD → fructoselysine 6‑kinase
RA 3,507,942 A→G Y217H (TAC→CAC)  php ← phosphotriesterase homology protein
RA 3,508,454 Δ1 bp coding (137/879 nt) php ← phosphotriesterase homology protein
RA 3,511,746 (A)8→9 coding (599/906 nt) yhfZ ← putative DNA‑binding transcriptional regulator
RA 3,515,726 T→C Y63C (TAT→TGT)  dam ← DNA adenine methyltransferase
RA 3,516,104 T→C K401K (AAA→AAG)  damX ← cell division protein that binds to the septal ring
RA 3,531,605 T→C T279A (ACA→GCA)  yhgE ← DUF4153 family putative inner membrane protein
RA 3,534,656 C→T G405R (GGG→AGG)  envZ ← sensory histidine kinase in two‑component regulatory system with OmpR
RA 3,544,074 C→T *257* (TAG→TAA)  bioH ← pimeloyl‑ACP methyl ester carboxylesterase
RA 3,545,565 G→A *228* (TAG→TAA)  gntX → DNA catabolic protein
RA 3,547,986 C→T *695* (TAG→TAA)  malQ ← 4‑alpha‑glucanotransferase (amylomaltase)
RA 3,556,033 A→G Y273H (TAC→CAC)  rtcA ← RNA 3'‑terminal phosphate cyclase
RA 3,560,455 +G intergenic (‑2/+1) glpR ← / ← glpR pseudogene, DNA‑binding transcriptional repressor,regulator, Energy metabolism, carbon: Anaerobic respiration, repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor,regulator, Energy metabolism, carbon: Anaerobic respiration, repressor of the glp operon
RA 3,566,600 C→T *478* (TAG→TAA)  glgA ← glycogen synthase
RA 3,567,251 C→T L261L (TTG→TTA)  glgA ← glycogen synthase
RA 3,583,454 G→A intergenic (+36/‑29) yrhA → / → insA pseudogene, interrupted by IS1E/IS1 repressor TnpA
RA 3,587,370 C→T T143I (ACT→ATT) 
*248* (TAG→TAA) 		 yhhA →
ugpQ ←		 DUF2756 family protein
glycerophosphodiester phosphodiesterase, cytosolic
RA 3,589,820 T→C S70G (AGC→GGC)  ugpE ← sn‑glycerol‑3‑phosphate ABC transporter permease
RA 3,598,557 A→G *368Q (TAA→CAA)  livJ ← branched‑chain amino acid ABC transporter periplasmic binding protein
RA 3,614,092 T→C I142I (ATT→ATC)  nikA → nickel/heme ABC transporter periplasmic binding protein
RA 3,643,899 G→A G428G (GGC→GGT)  prlC ← oligopeptidase A
RA 3,652,144 G→A intergenic (+113/+38) yhiS → / ← insH1 pseudogene/IS5 transposase and trans‑activator
RA 3,658,893 G→A *176* (TAG→TAA)  gadE → gad regulon transcriptional activator
RA 3,664,363 (G)6→7 coding (256/729 nt) gadW ← transcriptional activator of gadA and gadBC, repressor of gadX
RA 3,664,986 C→T *275* (TAG→TAA)  gadX ← acid resistance regulon transcriptional activator, autoactivator
RA 3,683,630 C→T *663* (TAG→TAA)  yhjK ← cyclic‑di‑GMP phosphodiesterase
RA 3,694,840 G→A H133Y (CAT→TAT)  bcsA ← cellulose synthase, catalytic subunit
RA 3,695,997 C→T *63* (TAG→TAA)  yhjR ← DUF2629 family protein
RA 3,706,174 G→A P511L (CCG→CTG)  dppA ← dipeptide/heme ABC transporter periplasmic binding protein, dipeptide chemotaxis receptor
RA 3,709,561 (C)6→7 coding (915/1692 nt) eptB ← KDO phosphoethanolamine transferase, Ca(2+)‑inducible
RA 3,719,768 G→A *97* (TAG→TAA)  yiaG → HTH_CROC1 family putative transcriptional regulator
JC 3,728,118 (C)8→11 coding (1254/1455 nt) xylB ← xylulokinase
RA 3,731,980 G→A G284S (GGT→AGT)  xylF → D‑xylose transporter subunit
RA 3,732,319 G→A G40E (GGG→GAG)  xylG → D‑xylose ABC transporter dual domain ATPase
RA 3,736,157 G→A *393* (TAG→TAA)  xylR → xylose divergent operon transcriptional activator
RA 3,736,160 +A intergenic (+3/+193) xylR → / ← bax xylose divergent operon transcriptional activator/putative glucosaminidase
RA 3,750,092 G→A *287* (TAG→TAA) 
E3K (GAG→AAG) 		 sgbU →
sgbE →		 putative L‑xylulose 5‑phosphate 3‑epimerase
L‑ribulose‑5‑phosphate 4‑epimerase
RA 3,761,850 C→T A36T (GCG→ACG)  yibF ← glutathione S‑transferase homolog
RA 3,766,316 G→A *1378* (TAG→TAA)  rhsA → Rhs protein with putative toxin 55 domain, putative polysaccharide synthesis/export protein, putative neighboring cell growth inhibitor
RA 3,767,179 G→A *281* (TAG→TAA)  yibA → putative immunity protein for polymorphic toxin RhsA, HEAT‑domain protein, lethality reduction protein
RA 3,773,602 T→C V441A (GTT→GCT)  mtlA → mannitol‑specific PTS enzyme: IIA, IIB and IIC components
RA 3,781,017 G→A *397* (TAG→TAA)  lldD → L‑lactate dehydrogenase, FMN‑linked
RA 3,781,688 G→A *158* (TAG→TAA)  trmL → tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
RA 3,785,051 (A)7→6 intergenic (‑36/‑209) yibN ← / → gpmM putative rhodanese‑related sulfurtransferase/phosphoglycero mutase III, cofactor‑independent
RA 3,789,047 C→T A316V (GCT→GTT) 
*345* (TAG→TAA) 		 yibQ →
waaH ←		 putative polysaccharide deacetylase
LPS(HepIII)‑glucuronic acid glycosyltransferase
RA 3,789,352 G→A R244C (CGC→TGC)  waaH ← LPS(HepIII)‑glucuronic acid glycosyltransferase
RA 3,792,826 C→T *286* (TAG→TAA)  yibB ← YibB family protein, function unknown
RA 3,810,304 G→A *160* (TAG→TAA)  coaD → pantetheine‑phosphate adenylyltransferase
RA 3,815,863 C→T pseudogene (19/48 nt) rph ← ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH
RA 3,815,908 Δ1 bp pseudogene (642/669 nt) rph ← ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH
RA 3,818,584 G→A *275* (TAG→TAA)  dinD → DNA damage‑inducible protein
RA 3,819,488 C→T H205H (CAC→CAT) 
*561* (TAG→TAA) 		 yicG →
ligB ←		 UPF0126 family inner membrane protein
DNA ligase, NAD(+)‑dependent
RA 3,838,137 G→A *395* (TAG→TAA)  setC → putative arabinose efflux transporter
RA 3,842,455 C→T *445* (TAG→TAA)  adeQ ← adenine permease, high affinity, adenine:H+ symporter
RA 3,852,890 C→T *33* (TAG→TAA)  ivbL ← ilvB operon leader peptide
RA 3,855,960 C→T S4N (AGC→AAC) 
*116* (TAG→TAA) 		 yidG ←
yidH ←		 inner membrane protein
DUF202 family inner membrane protein
RA 3,862,497 C→T pseudogene (1107/1617 nt) glvC ← pseudogene, arbutin specific enzyme IIC component of PTS,enzyme, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system, arbutin‑like IIB component, PTS system, arbutin‑like IIC component
RA 3,862,518 Δ1 bp pseudogene (1086/1617 nt) glvC ← pseudogene, arbutin specific enzyme IIC component of PTS,enzyme, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system, arbutin‑like IIB component, PTS system, arbutin‑like IIC component
JC 3,862,524 Δ3 bp pseudogene (1078‑1080/1617 nt) glvC ← pseudogene, arbutin specific enzyme IIC component of PTS,enzyme, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system, arbutin‑like IIB component, PTS system, arbutin‑like IIC component
RA 3,870,441 G→A *355* (TAG→TAA) 
G430G (GGC→GGT) 		 cbrA →
dgoT ←		 colicin M resistance protein, FAD‑binding protein, putative oxidoreductase
D‑galactonate transporter
RA 3,892,455 G→A A281T (GCG→ACG)  mdtL → multidrug efflux system protein
RA 3,897,050 +G coding (277/666 nt) yieH → phosphoenolpyruvate and 6‑phosphogluconate phosphatase
RA 3,897,439 G→A *222* (TAG→TAA)  yieH → phosphoenolpyruvate and 6‑phosphogluconate phosphatase
RA 3,898,609 G→A *196* (TAG→TAA)  cbrC → UPF0167 family protein
RA 3,908,514 A→G intergenic (‑148/+35) pstB ← / ← pstA phosphate ABC transporter ATPase/phosphate ABC transporter permease
RA 3,920,950 C→T *80* (TAG→TAA)  atpE ← F0 sector of membrane‑bound ATP synthase, subunit c
RA 3,921,515 C→T T179T (ACG→ACA)  atpB ← F0 sector of membrane‑bound ATP synthase, subunit a
RA 3,931,183 (G)7→8 intergenic (‑90/‑133) ravA ← / → kup hexameric AAA+ MoxR family ATPase, putative molecular chaperone/potassium transporter
RA 3,937,168 G→A *297* (TAG→TAA)  rbsB → D‑ribose ABC transporter periplasmic binding protein, ribose chemotaxis receptor
RA 3,939,219 G→A *331* (TAG→TAA) 
S465F (TCT→TTT) 		 rbsR →
hsrA ←		 transcriptional repressor of ribose metabolism
putative multidrug or homocysteine efflux system
RA 3,950,420 G→A *33* (TAG→TAA)  ilvL → ilvG operon leader peptide
RA 3,956,875 G→A *515* (TAG→TAA)  ilvA → l‑threonine dehydratase, biosynthetic, also known as threonine deaminase
RA 3,963,829 C→T R134H (CGC→CAC)  gpp ← guanosine pentaphosphatase/exopolyphosphatase
RA 3,970,015 T→C W329R (TGG→CGG)  wzzE → Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein
RA 3,970,032 (G)6→7 coding (1002/1047 nt) wzzE → Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein
RA 3,970,077 G→A *349* (TAG→TAA)  wzzE → Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein
RA 3,976,605 T→C F110L (TTT→CTT)  wzxE → O‑antigen translocase
RA 3,980,957 (G)6→7 coding (71/1386 nt) yifK → putative APC family amino acid transporter
RA 3,984,193 G→A *412* (TAG→TAA)  aslB → putative AslA‑specific sulfatase‑maturating enzyme
RA 3,986,686 C→T *399* (TAG→TAA)  hemY ← putative protoheme IX synthesis protein
RA 3,991,148 A→G intergenic (‑382/‑5) hemC ← / → cyaA hydroxymethylbilane synthase/adenylate cyclase
RA 3,992,054 C→T P301L (CCA→CTA)  cyaA → adenylate cyclase
RA 3,992,898 C→T S582S (AGC→AGT)  cyaA → adenylate cyclase
RA 4,002,813 C→T *127* (TAG→TAA)  yigG ← PRK11371 family inner membrane protein
RA 4,007,693 G→A *610* (TAG→TAA)  recQ → ATP‑dependent DNA helicase
RA 4,018,760 G→A *476* (TAG→TAA)  rmuC → DNA recombination protein
RA 4,024,336 G→A *261* (TAG→TAA) 
L162L (CTC→CTT) 		 tatD →
rfaH ←		 quality control of Tat‑exported FeS proteins, Mg‑dependent cytoplasmic DNase
transcription antitermination protein
RA 4,054,439 A→G T280T (ACT→ACC)  glnG ← fused DNA‑binding response regulator in two‑component regulatory system with GlnL: response regulator/sigma54 interaction protein
RA 4,061,157 G→A *237* (TAG→TAA)  yihL → putative DNA‑binding transcriptional regulator
RA 4,075,454 G→A *262* (TAG→TAA)  yihW → putative transcriptional regulator for sulphoquinovose utilization
RA 4,076,627 G→C S161T (AGT→ACT)  yihY → BrkB family putative transporter, inner membrane protein
RA 4,077,469 G→A L7L (TTG→TTA)  yiiD → GNAT family putative N‑acetyltransferase
RA 4,078,438 G→A *330* (TAG→TAA)  yiiD → GNAT family putative N‑acetyltransferase
RA 4,106,320 G→A *167* (TAG→TAA)  cpxP → inhibitor of the cpx response, periplasmic adaptor protein
RA 4,117,123 G→A R34C (CGC→TGC)  glpK ← glycerol kinase
RA 4,136,603 (G)6→7 coding (496/906 nt) yijE → EamA‑like transporter family protein
RA 4,137,229 A→G S143S (AGT→AGC)  yijF ← DUF1287 family protein
RA 4,147,479 G→A *114* (TAG→TAA) 
T280I (ACT→ATT) 		 frwD →
yijO ←		 putative enzyme IIB component of PTS
AraC family putative transcriptional activator
RA 4,148,681 C→T G529S (GGC→AGC)  eptC ← LPS heptose I phosphoethanolamine transferase
RA 4,158,575 A→G Q29R (CAG→CGG)  oxyR → oxidative and nitrosative stress transcriptional regulator
RA 4,204,645 G→A *442* (TAG→TAA) 
N429N (AAC→AAT) 		 zraR →
purD ←		 fused DNA‑binding response regulator in two‑component regulatory system with ZraS: response regulator/sigma54 interaction protein
phosphoribosylglycinamide synthetase phosphoribosylamine‑glycine ligase
RA 4,213,680 C→T *148* (TAG→TAA)  yjaB ← GNAT‑family putative N‑acetyltransferase, acetyl coenzyme A‑binding protein
RA 4,218,815 A→G T74A (ACG→GCG)  aceK → isocitrate dehydrogenase kinase/phosphatase
RA 4,232,752 G→A A161V (GCG→GTG)  lysC ← lysine‑sensitive aspartokinase 3
RA 4,268,487 (T)7→8 intergenic (+180/+322) tyrB → / ← yjbS tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent/uncharacterized protein
RA 4,268,809 C→T *68* (TAG→TAA)  yjbS ← uncharacterized protein
RA 4,279,849 A→G intergenic (+21/‑131) ghxP → / → yjcE guanine/hypoxanthine permease, high affinity, guanine/hypoxanthine:H+ symporter/putative cation/proton antiporter
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,297,668 C→T D567N (GAC→AAC)  fdhF ← formate dehydrogenase‑H, selenopolypeptide subunit
RA 4,302,240 A→G I280T (ATC→ACC)  mdtO ← membrane translocase (MDR) of MdtNOP efflux pump, PET family
RA 4,317,409 C→T G163S (GGC→AGC)  phnL ← ribophosphonate triphosphate synthase subunit, putative ABC transporter‑related ATPase
RA 4,324,876 A→G L97P (CTG→CCG)  phnC ← phosphonate ABC transporter ATPase
RA 4,325,152 A→G I5T (ATC→ACC)  phnC ← phosphonate ABC transporter ATPase
RA 4,331,634 C→T A378V (GCG→GTG)  proP → proline/glycine betaine transporter
RA 4,332,869 C→T R135H (CGC→CAC)  basS ← sensory histidine kinase in two‑component regulatory system with BasR
RA 4,336,405 A→G S209S (AGT→AGC)  adiC ← arginine:agmatine antiporter
RA 4,346,086 A→G I414T (ATC→ACC)  fumB ← anaerobic class I fumarate hydratase (fumarase B)
RA 4,352,880 G→A *99* (TAG→TAA)  ghoS → antitoxin of GhoTS toxin‑antitoxin pair, endonuclease for ghoT mRNA
RA 4,353,081 G→A *58* (TAG→TAA)  ghoT → toxin of GhoTS toxin‑antitoxin pair, membrane‑lytic protein, stimulator of persister cell formation
RA 4,377,189 C→T H105H (CAC→CAT) 
*178* (TAG→TAA) 		 sugE →
blc ←		 multidrug efflux system protein
outer membrane lipoprotein cell division and growth lipocalin
RA 4,386,872 C→T A833A (GCG→GCA)  mscM ← mechanosensitive channel protein, miniconductance
RA 4,389,934 A→G Y143H (TAC→CAC)  psd ← phosphatidylserine decarboxylase
RA 4,395,058 C→T G331G (GGC→GGT)  nnr → bifunctional NAD(P)H‑hydrate repair enzyme, C‑terminal domain ADP‑dependent (S)‑NAD(P)H‑hydrate dehydratase and N‑terminal domain NAD(P)H‑hydrate epimerase
RA 4,422,793 C→T A203V (GCC→GTC)  ulaD → 3‑keto‑L‑gulonate 6‑phosphate decarboxylase
RA 4,424,386 G→A *229* (TAG→TAA)  ulaF → L‑ribulose 5‑phosphate 4‑epimerase
RA 4,424,516 C→T *92* (TAG→TAA)  yjfY ← YhcN family protein, periplasmic
RA 4,424,543 Δ1 bp coding (249/276 nt) yjfY ← YhcN family protein, periplasmic
RA 4,425,834 G→A *105* (TAG→TAA)  priB → primosomal protein N
RA 4,428,079 C→T pseudogene (386/402 nt)
*213* (TAG→TAA) 		 ytfA →
ytfB ←		 pseudogene, related to transcriptional regulators
OapA family protein
RA 4,433,164 C→T *287* (TAG→TAA)  qorB ← NAD(P)H:quinone oxidoreductase
RA 4,441,538 C→T *213* (TAG→TAA)  msrA ← methionine sulfoxide reductase A
RA 4,442,007 T→C E57G (GAG→GGG)  msrA ← methionine sulfoxide reductase A
RA 4,447,869 Δ1 bp coding (3758/3780 nt) tamB → translocation and assembly module for autotransporter export, inner membrane subunit
RA 4,447,891 G→A *1260* (TAG→TAA)  tamB → translocation and assembly module for autotransporter export, inner membrane subunit
RA 4,474,138 (A)6→7 coding (15/594 nt) bdcR → transcriptional repressor for divergent bdcA
RA 4,474,391 G→A G90S (GGC→AGC)  bdcR → transcriptional repressor for divergent bdcA
RA 4,475,562 (G)6→7 coding (126/1815 nt) yjgL → SopA‑central‑domain‑like hexapeptide repeat protein
MC JC 4,490,116 Δ11 bp intergenic (‑53/+15) yjgR ← / ← idnR DUF853 family protein with NTPase fold/transcriptional repressor, 5‑gluconate‑binding
RA 4,490,141 C→T *333* (TAG→TAA)  idnR ← transcriptional repressor, 5‑gluconate‑binding
RA 4,490,375 C→T A255A (GCG→GCA)  idnR ← transcriptional repressor, 5‑gluconate‑binding
RA 4,495,332 A→G L293P (CTG→CCG)  ahr ← broad specificity NADPH‑dependent aldehyde reductase, Zn‑containing
RA 4,499,500 G→A *302* (TAG→TAA)  insD1 → IS2 transposase TnpB
RA 4,500,043 C→T pseudogene (492/942 nt) yjgX ← pseudogene fragment
RA 4,500,060 C→T pseudogene (475/942 nt) yjgX ← pseudogene fragment
RA 4,504,006 G→A intergenic (‑575/‑52) insG ← / → yjhB IS4 transposase/putative MFS transporter, membrane protein
RA 4,507,463 G→A intergenic (+12/+3) insO → / ← insI1 pseudogene, IS911 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related/IS30 transposase
RA 4,510,188 A→G intergenic (+55/+502) yjhV → / ← fecE pseudogene, KpLE2 phage‑like element/ferric citrate ABC transporter ATPase
RA 4,510,690 C→T *256* (TAG→TAA)  fecE ← ferric citrate ABC transporter ATPase
RA 4,511,146 C→T W104* (TGG→TGA)  fecE ← ferric citrate ABC transporter ATPase
RA 4,515,284 C→T G465D (GGC→GAC)  fecA ← TonB‑dependent outer membrane ferric citrate transporter and signal transducer, ferric citrate extracelluar receptor, FecR‑interacting protein
RA 4,519,014 G→A pseudogene (294/504 nt) insB1 → IS1 transposase B,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related
RA 4,535,441 C→T pseudogene (439/1029 nt) yjhR → pseudogene, helicase family, putative frameshift suppressor
RA 4,538,785 C→T *239* (TAG→TAA)  nanC ← N‑acetylnuraminic acid outer membrane channel protein
RA 4,541,559 G→A *201* (TAG→TAA)  fimB → tyrosine recombinase/inversion of on/off regulator of fimA
RA 4,549,001 G→A C65Y (TGC→TAC)  fimH → minor component of type 1 fimbriae
RA 4,565,464 C→A L129F (TTG→TTT)  yjiM ← putative 2‑hydroxyglutaryl‑CoA dehydratase
RA 4,565,966 C→T *427* (TAG→TAA)  yjiN ← zinc‑type alcohol dehydrogenase‑like protein
RA 4,569,309 G→A pseudogene (312/921 nt) yjiP → pseudogene, transposase_31 family protein
RA 4,577,958 C→T M1M (GTG→ATG) †
*460* (TAG→TAA) 		 mcrC ←
mcrB ←		 5‑methylcytosine‑specific restriction enzyme McrBC, subunit McrC
5‑methylcytosine‑specific restriction enzyme McrBC, subunit McrB
RA 4,581,621 G→A A476A (GCC→GCT)  hsdM ← DNA methyltransferase M
RA 4,604,202 G→A *242* (TAG→TAA) 
E15K (GAA→AAA) 		 yjjQ →
bglJ →		 putative transcriptional regulator
bgl operon transcriptional activator
RA 4,606,215 (G)8→9 noncoding (72/87 nt) leuP ← tRNA‑Leu
RA 4,606,239 A→G noncoding (48/87 nt) leuP ← tRNA‑Leu
RA 4,609,336 (C)7→8 intergenic (+13/‑78) yjjG → / → prfC dUMP phosphatase/peptide chain release factor RF‑3
RA 4,612,289 G→A *54* (TAG→TAA)  ytjA → uncharacterized protein
RA 4,614,260 G→A *260* (TAG→TAA)  yjjV → putative DNase
MC JC 4,619,478 Δ9 bp coding (1250‑1258/1323 nt) deoA → thymidine phosphorylase
RA 4,619,913 A→G E104G (GAA→GGA)  deoB → phosphopentomutase
RA 4,623,101 C→T *339* (TAG→TAA)  lplA ← lipoate‑protein ligase A
RA 4,638,120 G→A *475* (TAG→TAA)  creC → sensory histidine kinase in two‑component regulatory system with CreB or PhoB

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 66608 66738 131 22 [17] [11] 19 araD/araA L‑ribulose‑5‑phosphate 4‑epimerase/L‑arabinose isomerase
* * ÷ NC_000913 225830–226603 226861–226607 5–1032 20 [18] [18] 19 rrlH 23S ribosomal RNA of rrnH operon
* * ÷ NC_000913 789973 789980 8 22 [17] [0] 73 [galK] [galK]
* * ÷ NC_000913 807336 810369 3034 19 [18] [18] 19 ybhB–[bioB] ybhB, bioA, [bioB]
* * ÷ NC_000913 1427872–1427959 1428195–1427996 38–324 20 [18] [18] 20 insH1 IS5 transposase and trans‑activator
* * ÷ NC_000913 1432743–1433666 1433996–1433672 7–1254 19 [18] [15] 19 [tfaR]–[ynaE] [tfaR], pinR, [ynaE]
* * ÷ NC_000913 2629625 2629722 98 19 [15] [17] 22 yfgG/yfgH uncharacterized protein/outer membrane integrity lipoprotein
* * ÷ NC_000913 3423732–3424233 3424558–3424240 8–827 21 [17] [16] 22 [rrfD]–[rrlD] [rrfD], [rrlD]
* * ÷ NC_000913 3762351–3764072 3765223–3764077 6–2873 20 [17] [18] 19 rhsA Rhs protein with putative toxin 55 domain, putative polysaccharide synthesis/export protein, putative neighboring cell growth inhibitor
* * ÷ NC_000913 4037941–4038687 4039299–4038729 43–1359 20 [16] [18] 20 rrlA 23S ribosomal RNA of rrnA operon

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 7888310 (0.000)73 (1.020) 49/204 0.2 100% coding (7/1041 nt)
coding (1149/1149 nt)		 galM
galK		 aldose 1‑epimerase, type‑1 mutarotase, galactose mutarotase
galactokinase
?NC_000913 789981 = 0 (0.000)intergenic (‑2/+2) galK/galT galactokinase/galactose‑1‑phosphate uridylyltransferase
* ? NC_000913 788831 =0 (0.000)109 (1.500) 58/208 0.1 99.1% coding (7/1041 nt)
coding (1149/1149 nt)		 galM
galK		 aldose 1‑epimerase, type‑1 mutarotase, galactose mutarotase
galactokinase
?NC_000913 3742633 = 2 (0.030)intergenic (‑101/‑100) yiaJ/yiaK transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon/2,3‑diketo‑L‑gulonate reductase, NADH‑dependent
* ? NC_000913 1207790 =16 (0.220)60 (0.970) 35/176 0.5 82.5% coding (290/630 nt) stfP e14 prophage, uncharacterized protein
?NC_000913 1209619 = 12 (0.190)pseudogene (1/501 nt) stfE pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
* ? NC_000913 = 120780515 (0.210)37 (0.600) 30/176 0.8 75.0% coding (305/630 nt) stfP e14 prophage, uncharacterized protein
?NC_000913 = 1209602 12 (0.190)pseudogene (18/501 nt) stfE pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related
* ? NC_000913 = 128708425 (0.340)32 (0.540) 22/168 1.3 50.7% noncoding (153/171 nt) rttR rtT sRNA, processed from tyrT transcript
?NC_000913 1287557 = 42 (0.720)noncoding (66/85 nt) tyrT tRNA‑Tyr
* ? NC_000913 = 132314770 (0.960)41 (0.560) 19/208 2.4 53.6% intergenic (‑65/‑73) trpL/yciV trp operon leader peptide/PHP domain protein
?NC_000913 = 3742633 1 (0.010)intergenic (‑101/‑100) yiaJ/yiaK transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon/2,3‑diketo‑L‑gulonate reductase, NADH‑dependent