mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 22,105 | T→G | G233G (GGT→GGG) | ribF → | bifunctional riboflavin kinase/FAD synthetase |
| RA | 46,040 | T→G | D78E (GAT→GAG) | yaaU → | putative MFS sugar transporter; membrane protein |
| RA | 46,153 | T→G | I116S (ATC→AGC) | yaaU → | putative MFS sugar transporter; membrane protein |
| RA | 46,879 | A→C | Y358S (TAT→TCT) | yaaU → | putative MFS sugar transporter; membrane protein |
| RA | 61,420 | T→G | K615N (AAA→AAC) | rapA ← | RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase |
| RA | 62,084 | T→G | E394A (GAA→GCA) | rapA ← | RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase |
| RA | 83,522 | T→G | Q3P (CAG→CCG) | leuA ← | 2‑isopropylmalate synthase |
| RA | 99,341 | G→T | V313V (GTG→GTT) | ftsW → | putative lipid II flippase; integral membrane protein; FtsZ ring stabilizer |
| RA | 111,305 | G→T | E88* (GAA→TAA) | mutT → | dGTP‑preferring nucleoside triphosphate pyrophosphohydrolase |
| RA | 126,032 | T→G | I113S (ATC→AGC) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| RA | 136,062 | T→G | K135Q (AAG→CAG) | speE ← | spermidine synthase (putrescine aminopropyltransferase) |
| RA | 141,194 | A→C | L11* (TTA→TGA) | gcd ← | glucose dehydrogenase |
| RA | 158,000 | A→C | L376W (TTG→TGG) | pcnB ← | poly(A) polymerase |
| RA | 163,110 | A→C | I336L (ATC→CTC) | hrpB → | putative ATP‑dependent helicase |
| RA | 184,410 | A→C | V220V (GTT→GTG) | yaeI ← | phosphodiesterase with model substrate bis‑pNPP |
| RA | 197,703 | T→G | I386M (ATT→ATG) | rseP → | inner membrane zinc RIP metalloprotease; RpoE activator, by degrading RseA; cleaved signal peptide endoprotease |
| RA | 204,870 | T→G | D126E (GAT→GAG) | rnhB → | ribonuclease HII, degrades RNA of DNA‑RNA hybrids |
| RA | 212,003 | T→G | S43A (TCA→GCA) | yaeR → | putative lyase |
| RA | 216,474 | A→C | F177C (TTC→TGC) | yaeF ← | putative lipoprotein |
| RA | 219,876 | T→G | K40N (AAA→AAC) | rcsF ← | putative outer membrane protein |
| RA | 235,475 | A→C | K220N (AAA→AAC) | yafS → | putative S‑adenosyl‑L‑methionine‑dependent methyltransferase |
| RA | 243,573 | A→C | N11H (AAC→CAC) | gmhA → | D‑sedoheptulose 7‑phosphate isomerase |
| RA | 256,342 | T→G | V122V (GTT→GTG) | gpt → | xanthine phosphoribosyltransferase; xanthine‑guanine phosphoribosyltransferase |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 266,989 | A→C | intergenic (‑22/+195) | ykfK ← / ← yafZ | CP4‑6 prophage; putative DNA‑binding transcriptional regulator;Phage or Prophage Related/CP4‑6 prophage; conserved protein |
| RA | 289,154 | A→C | I3M (ATT→ATG) | yagI ← | CP4‑6 prophage; putative DNA‑binding transcriptional regulator |
| RA | 353,745 | A→C | E347A (GAA→GCA) | prpE → | propionate‑‑CoA ligase |
| RA | 417,041 | T→G | intergenic (‑89/‑101) | sbcD ← / → phoB | exonuclease, dsDNA, ATP‑dependent/response regulator in two‑component regulatory system with PhoR |
| RA | 431,697 | A→C | F106C (TTC→TGC) | tsx ← | nucleoside channel, receptor of phage T6 and colicin K |
| RA | 435,380 | A→C | K82Q (AAA→CAA) | nusB → | transcription antitermination protein |
| RA | 468,115 | A→C | Q235P (CAA→CCA) | cof → | thiamine pyrimidine pyrophosphate hydrolase; HMP‑PP phosphatase |
| RA | 487,353 | T→G | V273G (GTC→GGC) | mscK → | mechanosensitive channel protein, intermediate conductance, K+ regulated |
| RA | 505,546 | T→G | I211M (ATT→ATG) | ushA → | bifunctional UDP‑sugar hydrolase/5'‑nucleotidase |
| RA | 544,671 | T→G | N208H (AAT→CAT) | allC ← | allantoate amidohydrolase |
| RA | 577,020 | A→C | intergenic (‑195/‑378) | nmpC ← / → essD | DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage/DLP12 prophage; putative phage lysis protein |
| RA | 600,653 | A→C | E647A (GAG→GCG) | cusA → | copper/silver efflux system, membrane component |
| RA | 634,387 | T→G | S268A (TCG→GCG) | ybdL → | methionine aminotransferase, PLP‑dependent |
| RA | 716,122 | T→G | pseudogene (476/651 nt) | ybfG ← | pseudogene |
| RA | 729,193 | T→G | V20V (GTT→GTG) | ybfA → | DUF2517 family protein |
| RA | 770,824 | T→G | intergenic (+213/‑634) | mngB → / → cydA | alpha‑mannosidase/cytochrome d terminal oxidase, subunit I |
| RA | 772,414 | T→G | R319R (CGT→CGG) | cydA → | cytochrome d terminal oxidase, subunit I |
| RA | 791,879 | A→C | I59M (ATT→ATG) | galE ← | UDP‑galactose‑4‑epimerase |
| RA | 808,046 | A→C | I404M (ATT→ATG) | bioA ← | 7,8‑diaminopelargonic acid synthase, PLP‑dependent |
| RA | 838,474 | A→C | intergenic (‑18/+56) | ybiI ← / ← ybiX | DksA‑type zinc finger protein/Fe(II)‑dependent oxygenase superfamily protein |
| RA | 888,480 | A→C | F447C (TTC→TGC) | ybjL ← | putative transporter |
| RA | 902,592 | T→G | N133H (AAC→CAC) | artI ← | arginine transporter subunit |
| RA | 914,569 | T→G | K97Q (AAA→CAA) | ybjE ← | putative transporter |
| RA | 936,254 | A→C | K1011Q (AAA→CAA) | ftsK → | DNA translocase at septal ring sorting daughter chromsomes |
| RA | 960,522 | A→C | N87H (AAT→CAT) | ycaL → | putative peptidase‑related chaperone |
| RA | 997,715 | A→C | intergenic (‑203/‑153) | ssuE ← / → elfA | NAD(P)H‑dependent FMN reductase/laminin‑binding fimbrin subunit |
| RA | 1,052,447 | T→G | K306Q (AAA→CAA) | yccM ← | putative 4Fe‑4S membrane protein |
| RA | 1,063,726 | T→G | D17A (GAT→GCT) | cbpA ← | DnaK co‑chaperone; curved DNA‑binding protein |
| RA | 1,133,140 | T→G | S189R (AGT→AGG) | flgE → | flagellar hook protein |
| RA | 1,157,282 | A→C | D169A (GAT→GCT) | ycfH → | putative DNase |
| RA | 1,194,916 | T→G | Q12H (CAA→CAC) | rluE ← | 23S rRNA pseudouridine(2457) synthase |
| RA | 1,196,616 | A→C | intergenic (+243/+251) | icd → / ← ymfD | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase/e14 prophage; putative SAM‑dependent methyltransferase |
| RA | 1,201,688 | A→C | T64T (ACA→ACC) | ymfI → | e14 prophage; uncharacterized protein |
| RA | 1,202,079 | A→C | N2K (AAT→AAG) | ymfJ ← | e14 prophage; uncharacterized protein |
| RA | 1,213,848 | T→G | E71A (GAA→GCA) | bluR ← | repressor of blue light‑responsive genes |
| RA | 1,217,327 | A→C | intergenic (+331/‑1) | ymgC → / → ycgG | Blue light, low temperature and stress induced protein/putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| RA | 1,217,877 | A→C | T184P (ACG→CCG) | ycgG → | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| RA | 1,253,248 | T→G | N902T (AAC→ACC) | ycgV ← | putative adhesin |
| RA | 1,263,618 | T→G | intergenic (‑118/‑96) | lolB ← / → hemA | lipoprotein localization factor/glutamyl tRNA reductase |
| RA | 1,265,930 | A→C | N307H (AAC→CAC) | prfA → | peptide chain release factor RF‑1 |
| RA | 1,277,396 | T→G | K75Q (AAA→CAA) | narX ← | sensory histidine kinase in two‑component regulatory system with NarL |
| RA | 1,317,315 | A→C | D367E (GAT→GAG) | trpB ← | tryptophan synthase, beta subunit |
| RA | 1,323,663 | T→G | L148L (CTT→CTG) | yciV → | PHP domain protein |
| RA | 1,334,673 | T→G | G273G (GGT→GGG) | cysB → | N‑acetylserine‑responsive cysteine regulon transcriptional activator; autorepressor |
| RA | 1,399,602 | T→G | intergenic (‑76/+119) | fnr ← / ← ogt | oxygen‑sensing anaerobic growth regulon transcriptional regulator FNR; autorepressor/O‑6‑alkylguanine‑DNA:cysteine‑protein methyltransferase |
| RA | 1,404,625 | A→C | intergenic (‑60/‑116) | abgA ← / → abgR | p‑aminobenzoyl‑glutamate hydrolase, A subunit/putative DNA‑binding transcriptional regulator of abgABT operon |
| RA | 1,406,711 | A→C | V362G (GTG→GGG) | ydaM ← | diguanylate cyclase, csgD regulator |
| RA | 1,412,371 | T→G | K289Q (AAA→CAA) | intR ← | Rac prophage; integrase |
| RA | 1,476,087 | A→C | E315A (GAG→GCG) | ydbD → | PF10971 family putative periplasmic methylglyoxal resistance protein |
| RA | 1,486,129 | T→G | G1023G (GGT→GGG) | hrpA → | putative ATP‑dependent helicase |
| RA | 1,498,172 | A→C | E439D (GAA→GAC) | opgD → | OPG biosynthetic periplasmic protein |
| RA | 1,508,711 | T→G | L644R (CTG→CGG) | ydcP → | putative peptidase |
| RA | 1,548,145 | A→C | N249H (AAC→CAC) | fdnG → | formate dehydrogenase‑N, alpha subunit, nitrate‑inducible |
| RA | 1,557,770 | A→C | L90R (CTC→CGC) | ddpF ← | D,D‑dipeptide ABC transporter ATPase |
| RA | 1,627,153 | A→C | F76L (TTT→TTG) | dcp ← | dipeptidyl carboxypeptidase II |
| RA | 1,638,290 | T→G | intergenic (‑181/+165) | ynfN ← / ← cspI | Qin prophage; cold shock‑induced protein/Qin prophage; cold shock protein |
| RA | 1,702,865 | T→G | I211M (ATT→ATG) | add → | adenosine deaminase |
| RA | 1,704,474 | T→G | intergenic (‑166/‑77) | ydgJ ← / → blr | putative oxidoreductase/beta‑lactam resistance membrane protein; divisome‑associated protein |
| RA | 1,736,170 | A→C | F374C (TTT→TGT) | ydhP ← | putative MFS transporter, inner membrane protein |
| RA | 1,740,207 | A→C | V99V (GTA→GTC) | ydhC → | putative arabinose efflux transporter |
| RA | 1,747,584 | A→C | S152R (AGC→CGC) | ydhS → | putative oxidoreductase |
| RA | 1,784,693 | A→C | intergenic (+16/+41) | fadK → / ← ppsA | short chain acyl‑CoA synthetase, anaerobic/phosphoenolpyruvate synthase |
| RA | 1,789,184 | T→G | D250E (GAT→GAG) | aroH → | 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible |
| RA | 1,804,145 | A→C | pseudogene (628/1476 nt) | arpB → | pseudogene, ankyrin repeats |
| RA | 1,804,989 | T→G | pseudogene (1472/1476 nt) | arpB → | pseudogene, ankyrin repeats |
| RA | 1,822,544 | T→G | F29L (TTT→TTG) | nadE → | NAD synthetase, NH3/glutamine‑dependent |
| RA | 1,823,935 | A→C | N141H (AAC→CAC) | cho → | endonuclease of nucleotide excision repair |
| RA | 1,837,673 | A→C | V154V (GTA→GTC) | ynjC → | putative ABC transporter permease |
| RA | 1,873,762 | A→C | V63V (GTA→GTC) | yeaK → | aminoacyl‑tRNA editing domain protein |
| RA | 1,880,386 | A→C | L125R (CTG→CGG) | leuE ← | leucine efflux protein |
| RA | 1,880,672 | A→C | F30V (TTT→GTT) | leuE ← | leucine efflux protein |
| RA | 1,898,641 | T→G | L72R (CTT→CGT) | yoaD → | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase, regulator of cellulose production |
| RA | 1,924,236 | A→C | L119R (CTG→CGG) | yebZ ← | inner membrane protein |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 1,980,663 | T→G | E317A (GAA→GCA) | otsA ← | trehalose‑6‑phosphate synthase |
| RA | 1,984,547 | A→C | S175A (TCT→GCT) | araG ← | L‑arabinose ABC transporter ATPase |
| RA | 1,988,111 | T→G | intergenic (‑152/‑111) | azuC ← / → yecR | acid‑inducible small membrane‑associated protein/lipoprotein, function unknown |
| RA | 1,998,061 | T→G | Q140P (CAG→CCG) | yecS ← | ABC family putative inner membrane permease |
| RA | 2,004,251 | A→C | K127T (AAA→ACA) | fliD → | flagellar filament capping protein |
| RA | 2,025,260 | T→G | intergenic (+47/‑251) | yodD → / → yedP | uncharacterized protein/putative mannosyl‑3‑phosphoglycerate phosphatase |
| RA | 2,049,519 | A→C | K1528Q (AAA→CAA) | yeeJ → | putative adhesin |
| RA | 2,056,488 | A→C | R476R (CGA→CGC) | amn → | AMP nucleosidase |
| RA | 2,059,927 | A→C | intergenic (+1/+37) | asnU → / ← cbl | tRNA‑Asn/ssuEADCB/tauABCD operon transcriptional activator |
| RA | 2,083,952 | T→G | V399V (GTT→GTG) | sbcB → | exodeoxyribonuclease I; exonuclease I |
| RA | 2,103,393 | A→C | *373G (TGA→GGA) | wbbK ← | lipopolysaccharide biosynthesis protein |
| RA | 2,107,808 | T→G | R174S (AGA→AGC) | glf ← | UDP‑galactopyranose mutase, FAD/NAD(P)‑binding |
| RA | 2,160,092 | T→G | S569R (AGT→AGG) | mdtC → | multidrug efflux system, subunit C |
| 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 | 2,176,270 | A→C | S18A (TCA→GCA) | gatZ ← | D‑tagatose 1,6‑bisphosphate aldolase 2, subunit |
| RA | 2,187,468 | A→C | I316R (ATA→AGA) | yehA ← | putative fimbrial‑like adhesin protein |
| RA | 2,214,569 | T→G | K26Q (AAA→CAA) | yehU ← | inner membrane putative sensory kinase in two‑component system with YehT |
| RA | 2,217,824 | A→C | L245R (CTG→CGG) | yehY ← | putative ABC transporter permease |
| RA | 2,246,382 | T→G | I130L (ATC→CTC) | cirA ← | colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter |
| RA | 2,266,579 | T→G | I112S (ATT→AGT) | yeiQ → | putative NAD‑dependent D‑mannonate oxidoreductase |
| RA | 2,283,668 | T→G | K94Q (AAA→CAA) | yejK ← | spermidine nucleoid‑associated protein |
| RA | 2,316,351 | A→C | M59L (ATG→CTG) | rcsB → | response regulator in two‑component regulatory system with RcsC and YojN |
| RA | 2,338,288 | T→G | H378P (CAT→CCT) | gyrA ← | DNA gyrase (type II topoisomerase), subunit A |
| RA | 2,343,779 | A→C | S131A (TCC→GCC) | yfaL ← | adhesin |
| RA | 2,372,999 | T→G | F36L (TTT→TTG) | arnF → | undecaprenyl phosphate‑alpha‑L‑ara4N exporter; flippase ArnEF subunit |
| RA | 2,422,240 | T→G | L178R (CTG→CGG) | yfcH → | putative NAD‑dependent nucleotide‑sugar epimerase |
| RA | 2,423,579 | T→G | intergenic (‑40/+157) | yfcI ← / ← hisP | transposase_31 family protein/histidine ABC transporter ATPase |
| RA | 2,438,570 | A→C | P207P (CCA→CCC) | flk → | putative flagella assembly protein |
| RA | 2,486,868 | T→G | V832G (GTC→GGC) | evgS → | hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
| RA | 2,493,412 | T→G | intergenic (‑158/+355) | frc ← / ← yfdX | formyl‑CoA transferase, NAD(P)‑binding/uncharacterized protein |
| RA | 2,554,262 | T→G | Q307H (CAA→CAC) | eutR ← | eut operon transcriptional activator, AraC family |
| RA | 2,560,597 | T→G | V114G (GTA→GGA) | yffL → | CPZ‑55 prophage; uncharacterized protein |
| RA | 2,578,624 | A→C | intergenic (‑247/‑42) | maeB ← / → talA | malic enzyme: putative oxidoreductase/phosphotransacetylase/transaldolase A |
| RA | 2,594,162 | A→C | D566E (GAT→GAG) | tmcA ← | elongator methionine tRNA (ac4C34) acetyltransferase |
| RA | 2,615,883 | A→C | intergenic (‑2/‑211) | yfgO ← / → bepA | putative UPF0118 family inner membrane permease/OM protein maintenance and assembly metalloprotease and chaperone, periplasmic |
| RA | 2,617,317 | T→G | D408E (GAT→GAG) | bepA → | OM protein maintenance and assembly metalloprotease and chaperone, periplasmic |
| RA | 2,626,437 | T→G | L441L (CTT→CTG) | ppx → | exopolyphosphatase |
| RA | 2,652,948 | A→C | E152A (GAA→GCA) | sseA → | 3‑mercaptopyruvate sulfurtransferase |
| RA | 2,657,657 | T→G | K427Q (AAA→CAA) | hscA ← | DnaK‑like molecular chaperone specific for IscU |
| RA | 2,683,710 | A→C | Q283P (CAA→CCA) | yphH → | putative DNA‑binding transcriptional regulator |
| RA | 2,690,978 | T→G | S41R (AGC→CGC) | glrK ← | sensor protein kinase regulating glmY sRNA in two‑component system with response regulator GlrR |
| RA | 2,724,576 | A→C | Y391D (TAC→GAC) | kgtP ← | alpha‑ketoglutarate transporter |
| RA | 2,731,287 | A→C | intergenic (‑130/+313) | rrsG ← / ← clpB | 16S ribosomal RNA of rrnG operon/protein disaggregation chaperone |
| RA | 2,776,304 | A→C | E129A (GAG→GCG) | yfjX → | CP4‑57 prophage; putative antirestriction protein |
| RA | 2,778,122 | A→C | intergenic (+340/+24) | ypjF → / ← ypjA | CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter |
| RA | 2,805,674 | T→G | L287* (TTA→TGA) | proV → | glycine betaine/proline ABC transporter periplasmic binding protein |
| RA | 2,814,754 | T→G | intergenic (‑21/+129) | luxS ← / ← gshA | S‑ribosylhomocysteine lyase/glutamate‑cysteine ligase |
| RA | 2,822,103 | A→C | intergenic (‑92/+36) | alaS ← / ← recX | alanyl‑tRNA synthetase/regulatory protein for RecA |
| RA | 2,849,435 | T→G | I139L (ATC→CTC) | hycB ← | hydrogenase 3, Fe‑S subunit |
| RA | 2,914,828 | T→G | K58T (AAA→ACA) | rlmD ← | 23S rRNA m(5)U1939 methyltransferase, SAM‑dependent |
| RA | 2,964,868 | T→G | K96N (AAA→AAC) | thyA ← | thymidylate synthetase |
| RA | 2,967,937 | A→C | Y166* (TAT→TAG) | ptsP ← | PEP‑protein phosphotransferase enzyme I; GAF domain containing protein |
| RA | 2,993,609 | T→G | intergenic (+139/‑29) | ygeH → / → ygeI | putative transcriptional regulator/uncharacterized protein |
| RA | 3,105,735 | A→C | K8Q (AAA→CAA) | nupG → | nucleoside transporter |
| RA | 3,107,858 | A→C | L433R (CTG→CGG) | speC ← | ornithine decarboxylase, constitutive |
| RA | 3,112,162 | A→C | pseudogene (780/849 nt) | yghF ← | pseudogene, secretion pathway protein, C‑type protein homology;putative transport; Not classified; putative general secretion pathway for protein export (GSP) |
| RA | 3,120,887 | T→G | G131G (GGA→GGC) | glcA ← | glycolate transporter |
| RA | 3,140,222 | T→G | I33L (ATT→CTT) | hybF ← | protein involved with the maturation of hydrogenases 1 and 2 |
| RA | 3,149,618 | A→C | intergenic (‑147/‑44) | yqhA ← / → yghA | UPF0114 family putative inner membrane protein/putative oxidoreductase |
| RA | 3,186,190 | A→C | I2L (ATT→CTT) | insC1 → | IS2 repressor TnpA |
| RA | 3,204,192 | T→G | intergenic (‑61/+29) | bacA ← / ← folB | undecaprenyl pyrophosphate phosphatase/dihydroneopterin aldolase and dihydroneopterin triphosphate 2'‑epimerase |
| RA | 3,263,574 | T→G | V29V (GTA→GTC) | tdcD ← | propionate kinase/acetate kinase C, anaerobic |
| RA | 3,286,411 | A→C | N48H (AAT→CAT) | agaI → | galactosamine‑6‑phosphate isomerase |
| RA | 3,286,675 | A→C | N136H (AAC→CAC) | agaI → | galactosamine‑6‑phosphate isomerase |
| RA | 3,308,757 | T→G | L56F (TTA→TTC) | nlpI ← | lipoprotein involved in osmotic sensitivity and filamentation |
| RA | 3,317,296 | A→C | L77L (CTT→CTG) | nusA ← | transcription termination/antitermination L factor |
| RA | 3,334,208 | A→C | I167L (ATC→CTC) | ispB → | octaprenyl diphosphate synthase |
| RA | 3,343,061 | T→G | S76A (TCG→GCG) | lptC → | periplasmic membrane‑anchored LPS‑binding protein; LPS export protein |
| RA | 3,362,192 | A→C | S27S (TCA→TCC) | yhcA → | putative periplasmic chaperone protein |
| RA | 3,365,608 | T→G | intergenic (+57/+94) | yhcE → / ← insH1 | pseudogene fragment; interrupted by IS5/IS5 transposase and trans‑activator |
| RA | 3,372,680 | A→C | intergenic (‑106/+3) | nanT ← / ← nanA | sialic acid transporter/N‑acetylneuraminate lyase |
| RA | 3,373,852 | T→G | E213A (GAA→GCA) | nanR ← | sialic acid‑inducible nan operon repressor |
| RA | 3,398,511 | T→G | E122A (GAG→GCG) | mreD ← | cell wall structural complex MreBCD transmembrane component MreD |
| RA | 3,400,678 | T→G | E137A (GAA→GCA) | mreB ← | cell wall structural complex MreBCD, actin‑like component MreB |
| RA | 3,448,548 | A→C | T7T (ACT→ACG) | rpsQ ← | 30S ribosomal subunit protein S17 |
| RA | 3,476,689 | T→G | E244A (GAG→GCG) | fkpA ← | FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase) |
| RA | 3,484,500 | A→C | K4T (AAA→ACA) | prkB → | putative phosphoribulokinase |
| RA | 3,541,448 | A→C | N348H (AAC→CAC) | feoB → | ferrous iron transporter protein B and GTP‑binding protein; membrane protein |
| RA | 3,549,583 | T→G | D163A (GAT→GCT) | malQ ← | 4‑alpha‑glucanotransferase (amylomaltase) |
| RA | 3,554,067 | T→G | L328R (CTG→CGG) | malT → | mal regulon transcriptional activator |
| RA | 3,559,217 | A→C | D317A (GAT→GCT) | rtcR → | sigma 54‑dependent transcriptional regulator of rtcBA expression |
| 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 | 3,635,992 | T→G | intergenic (+99/+216) | yhiM → / ← yhiN | acid resistance protein, inner membrane/putative oxidoreductase |
| RA | 3,657,161 | T→G | L56* (TTA→TGA) | hdeD → | acid‑resistance membrane protein |
| RA | 3,659,521 | T→G | L97* (TTA→TGA) | mdtE → | anaerobic multidrug efflux transporter, ArcA‑regulated |
| RA | 3,671,117 | A→C | E509A (GAA→GCA) | treF → | cytoplasmic trehalase |
| RA | 3,681,475 | T→G | I156L (ATC→CTC) | yhjJ ← | putative periplasmic M16 family chaperone |
| RA | 3,683,667 | A→C | I651S (ATT→AGT) | yhjK ← | cyclic‑di‑GMP phosphodiesterase |
| RA | 3,791,001 | A→C | V115V (GTT→GTG) | tdh ← | L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| RA | 3,814,738 | A→C | K82T (AAA→ACA) | slmA → | nucleoid occlusion factor, anti‑FtsZ division inhibitor |
| RA | 3,824,507 | A→C | *703S (TAA→TCA) | spoT → | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 3,833,231 | A→C | M436R (ATG→AGG) | yicI ← | putative alpha‑glucosidase |
| RA | 3,864,379 | A→C | I161L (ATT→CTT) | yidP → | UTRA domain‑containing GntR family putative transcriptional regulator |
| RA | 3,882,059 | A→C | I88S (ATT→AGT) | dnaN ← | DNA polymerase III, beta subunit |
| RA | 3,898,162 | T→G | Y47* (TAT→TAG) | cbrC → | UPF0167 family protein |
| RA | 3,941,081 | A→C | W83G (TGG→GGG) | yieP ← | putative transcriptional regulator |
| RA | 3,972,742 | A→C | Q74P (CAG→CCG) | rffG → | dTDP‑glucose 4,6‑dehydratase |
| RA | 3,972,815 | T→G | I98M (ATT→ATG) | rffG → | dTDP‑glucose 4,6‑dehydratase |
| RA | 3,981,539 | T→G | L218R (CTG→CGG) | yifK → | putative APC family amino acid transporter |
| RA | 4,004,063 | A→C | L39R (CTG→CGG) | rarD ← | putative chloramphenical resistance permease |
| RA | 4,029,177 | T→G | K599Q (AAG→CAG) | fadB ← | fused 3‑hydroxybutyryl‑CoA epimerase/delta(3)‑cis‑delta(2)‑trans‑enoyl‑CoA isomerase/enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase |
| RA | 4,034,898 | T→G | R97R (CGT→CGG) | hemG → | protoporphyrin oxidase, flavoprotein |
| RA | 4,055,097 | T→G | D61A (GAC→GCC) | glnG ← | fused DNA‑binding response regulator in two‑component regulatory system with GlnL: response regulator/sigma54 interaction protein |
| RA | 4,073,504 | T→G | Q23P (CAA→CCA) | yihU ← | 3‑sulpholactaldehyde (SLA) reductase, NADH‑dependent; gamma‑hydroxybutyrate dehydrogenase, NADH‑dependent |
| RA | 4,073,554 | A→C | F6L (TTT→TTG) | yihU ← | 3‑sulpholactaldehyde (SLA) reductase, NADH‑dependent; gamma‑hydroxybutyrate dehydrogenase, NADH‑dependent |
| RA | 4,084,783 | A→C | F347C (TTC→TGC) | fdoG ← | formate dehydrogenase‑O, large subunit |
| RA | 4,093,592 | T→G | L227F (TTA→TTC) | rhaD ← | rhamnulose‑1‑phosphate aldolase |
| RA | 4,097,080 | A→C | I123M (ATT→ATG) | rhaB ← | rhamnulokinase |
| RA | 4,101,056 | A→C | S83R (AGC→CGC) | sodA → | superoxide dismutase, Mn |
| RA | 4,116,511 | T→G | I238L (ATT→CTT) | glpK ← | glycerol kinase |
| RA | 4,146,701 | A→C | S148S (TCA→TCC) | pflC → | putative [formate‑C‑acetyltransferase 2]‑activating enzyme; pyruvate formate‑lyase 1‑activating enzyme |
| RA | 4,149,302 | A→C | Y322D (TAT→GAT) | eptC ← | LPS heptose I phosphoethanolamine transferase |
| RA | 4,173,777 | T→G | N232K (AAT→AAG) | birA → | bifunctional biotin‑[acetylCoA carboxylase] holoenzyme synthetase/ DNA‑binding transcriptional repressor, bio‑5'‑AMP‑binding |
| RA | 4,179,038 | A→C | K54Q (AAA→CAA) | rplA → | 50S ribosomal subunit protein L1 |
| RA | 4,179,175 | T→G | D99E (GAT→GAG) | rplA → | 50S ribosomal subunit protein L1 |
| RA | 4,182,877 | T→G | F545V (TTC→GTC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,187,714 | A→C | K789Q (AAA→CAA) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,220,666 | T→G | K608Q (AAA→CAA) | arpA ← | ankyrin repeat protein |
| RA | 4,268,001 | T→G | A296A (GCT→GCG) | tyrB → | tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent |
| RA | 4,284,935 | A→C | L93L (CTT→CTG) | yjcH ← | DUF485 family inner membrane protein |
| RA | 4,285,155 | T→G | E20A (GAA→GCA) | yjcH ← | DUF485 family inner membrane protein |
| RA | 4,285,977 | T→G | V465V (GTA→GTC) | acs ← | acetyl‑CoA synthetase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,299,529 | A→C | intergenic (‑163/+35) | fdhF ← / ← mdtP | formate dehydrogenase‑H, selenopolypeptide subunit/outer membrane factor of efflux pump |
| RA | 4,310,903 | T→G | L26F (TTA→TTC) | alsA ← | D‑allose ABC transporter ATPase |
| RA | 4,313,825 | A→C | intergenic (+26/‑43) | rpiB → / → yjdP | ribose 5‑phosphate isomerase B/allose 6‑phosphate isomerase/putative periplasmic protein |
| RA | 4,335,035 | T→G | N186H (AAC→CAC) | eptA ← | lipid A phosphoethanolamine transferase |
| RA | 4,351,371 | T→G | I98L (ATT→CTT) | dcuS ← | sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration |
| RA | 4,399,742 | A→C | D164A (GAT→GCT) | miaA → | delta(2)‑isopentenylpyrophosphate tRNA‑adenosine transferase |
| RA | 4,424,756 | A→C | L12L (CTT→CTG) | yjfY ← | YhcN family protein, periplasmic |
| RA | 4,445,958 | A→C | Q616P (CAA→CCA) | tamB → | translocation and assembly module for autotransporter export, inner membrane subunit |
| RA | 4,510,292 | A→C | intergenic (+159/+398) | yjhV → / ← fecE | pseudogene, KpLE2 phage‑like element/ferric citrate ABC transporter ATPase |
| RA | 4,525,988 | A→C | intergenic (‑185/+118) | yjhI ← / ← sgcR | putative DNA‑binding transcriptional regulator/putative DNA‑binding transcriptional regulator |
| RA | 4,530,170 | A→C | F25C (TTC→TGC) | sgcC ← | putative PTS system EIIC permease component |
| RA | 4,543,958 | T→G | V77V (GTT→GTG) | fimI → | fimbrial protein involved in type 1 pilus biosynthesis |
| RA | 4,560,365 | A→C | L106V (TTA→GTA) | yjiH ← | nucleoside recognition pore and gate family putative inner membrane transporter |
| RA | 4,563,842 | A→C | intergenic (‑239/+80) | yjiK ← / ← yjiL | SdiA‑regulated family putative membrane‑anchored protein; putative phytase‑like esterase/putative ATPase, activator of (R)‑hydroxyglutaryl‑CoA dehydratase |
| RA | 4,568,563 | A→C | intergenic (‑44/‑435) | mdtM ← / → yjiP | multidrug efflux system protein/pseudogene, transposase_31 family protein |
| RA | 4,594,311 | T→G | I138L (ATC→CTC) | lgoT ← | putative L‑galactonate:H+ symporter |
| RA | 4,598,247 | T→G | N399H (AAC→CAC) | opgB ← | OPG periplasmic biosynthetic phosphoglycerol transferases I (membrane‑bound) and II (soluble) |
| RA | 4,615,781 | T→G | I429L (ATC→CTC) | yjjI ← | DUF3029 family protein, putative glycine radical enzyme |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423729–3424234 | 3424560–3424238 | 5–832 | 30 [29] | [29] 31 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 4 (0.070) | 47 (0.880) | 41/266 | 0.5 | 93.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 3 (0.060) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 4 (0.070) | 29 (0.540) | 28/266 | 1.9 | 89.8% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 3 (0.060) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 61 (1.050) | 55/290 | 0.2 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||