mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 47,858 | G→A | S30S (TCG→TCA) | kefC → | potassium:proton antiporter |
| RA | 67,598 | C→T | G247D (GGC→GAC) | araA ← | L‑arabinose isomerase |
| RA | 155,463 | A→T | *247K (TAA→AAA) | ecpD ← | predicted periplasmic pilin chaperone |
| RA | 257,873 | A→G | K15K (AAA→AAG) | crl → | DNA‑binding transcriptional regulator |
| RA | 267,502 | G→T | P228H (CCT→CAT) | ykfA ← | predicted GTP‑binding protein |
| RA | 275,785 | G→A | V413I (GTA→ATA) | mmuP → | predicted S‑methylmethionine transporter |
| RA | 285,498 | G→A | A294T (GCC→ACC) | yagG → | predicted sugar transporter |
| RA | 330,092 | A→G | N469S (AAC→AGC) | betT → | choline transporter of high affinity |
| RA | 345,099 | C→T | A155T (GCC→ACC) | yahN ← | neutral amino‑acid efflux system |
| RA | 349,140 | C→T | intergenic (+344/‑96) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 429,850 | T→C | Y8H (TAT→CAT) | yajD → | conserved hypothetical protein |
| RA | 453,398 | +G | intergenic (‑7/‑298) | yajG ← / → bolA | predicted lipoprotein/regulator of penicillin binding proteins and beta lactamase transcription (morphogene) |
| RA | 460,284 | G→T | A725S (GCA→TCA) | lon → | DNA‑binding ATP‑dependent protease La |
| RA | 464,946 | A→G | F531L (TTC→CTC) | ybaE ← | predicted transporter subunit |
| RA | 478,343 | C→T | A45T (GCT→ACT) | ylaC ← | predicted inner membrane protein |
| RA | 527,659 | A→G | K163E (AAA→GAA) | ylbH → | conserved hypothetical protein, rhs‑like |
| RA | 547,694 | A→G | pseudogene (114/261 nt) pseudogene (114/1259 nt) |
ylbE → ylbE → |
ECK0512:JW0507:b4507; hypothetical protein, N‑ter fragment ECK0512:JW0508+JW0507:b4572; hypothetical protein |
| RA | 547,835 | +G | pseudogene (255/261 nt) pseudogene (255/1259 nt) |
ylbE → ylbE → |
ECK0512:JW0507:b4507; hypothetical protein, N‑ter fragment ECK0512:JW0508+JW0507:b4572; hypothetical protein |
| RA | 548,801 | G→A | pseudogene (1221/1259 nt) pseudogene (964/1002 nt) |
ylbE → ylbE → |
ECK0512:JW0508+JW0507:b4572; hypothetical protein ECK0512:JW0508:b0519; hypothetical protein, C‑ter fragment |
| RA | 556,858 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional 5,10‑methylene‑tetrahydrofolate dehydrogenase and 5,10‑methylene‑tetrahydrofolate cyclohydrolase |
| RA | 563,782 | C→T | intergenic (‑79/‑164) | fimZ ← / → argU | predicted DNA‑binding transcriptional regulator/tRNA‑Arg |
| RA | 593,201 | A→G | F265L (TTC→CTC) | cusS ← | sensory histidine kinase in two‑component regulatory system with CusR, senses copper ions |
| RA | 631,602 | A→G | *66* (TAA→TAG) | ybdD → | conserved hypothetical protein |
| RA | 639,164 | G→A | P63P (CCG→CCA) | ahpF → | alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)‑binding |
| RA | 647,863 | A→G | M311T (ATG→ACG) | citF ← | citrate lyase, citrate‑ACP transferase (alpha) subunit |
| RA | 651,069 | T→C | N4S (AAT→AGT) | citC ← | citrate lyase synthetase |
| MC JC | 654,214 | Δ1,199 bp | [dcuC]–[dcuC] | [dcuC], insH, [dcuC] | |
| RA | 707,707 | A→G | N398S (AAC→AGC) | glnS → | glutamyl‑tRNA synthetase |
| RA | 711,161 | C→T | intergenic (‑93/+196) | fur ← / ← fldA | DNA‑binding transcriptional dual regulator/flavodoxin 1 |
| RA | 811,947 | G→T | G382V (GGC→GTC) A2S (GCA→TCA) |
bioF → bioC → |
8‑amino‑7‑oxononanoate synthase predicted methltransferase, enzyme of biotin synthesis |
| RA | 833,307 | G→T | T22T (ACC→ACA) | ybiA ← | conserved hypothetical protein |
| RA | 861,111 | G→A | L640L (CTG→TTG) | ybiW ← | predicted pyruvate formate lyase |
| RA | 862,250 | G→T | T260N (ACT→AAT) | ybiW ← | predicted pyruvate formate lyase |
| RA | 891,153 | C→T | R8H (CGT→CAT) | grxA ← | glutaredoxin 1, redox coenzyme for ribonucleotide reductase (RNR1a) |
| RA | 912,695 | C→T | P514P (CCG→CCA) | hcp ← | hybrid‑cluster [4Fe‑2S‑2O] protein in anaerobic terminal reductases |
| RA | 922,613 | G→A | L615L (CTG→CTA) | macB → | fused macrolide transporter subunits and ATP‑binding component and membrane component of ABC superfamily |
| RA | 976,718 | G→A | E216E (GAG→GAA) | mukE → | protein involved in chromosome partitioning |
| RA | 1,007,501 | A→C | N174K (AAT→AAG) | ycbX ← | predicted 2Fe‑2S cluster‑containing protein |
| RA | 1,008,014 | T→A | T3T (ACA→ACT) | ycbX ← | predicted 2Fe‑2S cluster‑containing protein |
| RA | 1,008,134 | C→T | intergenic (‑112/‑132) | ycbX ← / → ycbY | predicted 2Fe‑2S cluster‑containing protein/predicted methyltransferase |
| RA | 1,032,415 | C→T | intergenic (‑281/‑146) | serT ← / → hyaA | tRNA‑Ser/hydrogenase 1, small subunit |
| RA | 1,036,407 | A→G | E72E (GAA→GAG) | hyaD → | protein involved in processing of HyaA and HyaB proteins |
| RA | 1,055,413 | A→G | D396D (GAT→GAC) | torS ← | hybrid sensory histidine kinase in two‑component regulatory system with TorR |
| RA | 1,074,318 | G→T | A39E (GCG→GAG) | ycdM ← | predicted monooxygenase |
| RA | 1,084,947 | A→G | K384E (AAA→GAA) | ycdB → | conserved hypothetical protein |
| RA | 1,088,483 | C→T | Q599Q (CAG→CAA) | ycdR ← | predicted enzyme associated with biofilm formation |
| RA | 1,093,686 | T→C | V130A (GTA→GCA) | ycdT → | predicted diguanylate cyclase |
| RA | 1,097,861 | G→A | noncoding (33/88 nt) | serX ← | tRNA‑Ser |
| RA | 1,099,547 | C→T | A143V (GCC→GTC) | ycdX → | predicted zinc‑binding hydrolase |
| RA | 1,115,786 | T→C | intergenic (‑28/+55) | msyB ← / ← mdtG | hypothetical protein/predicted drug efflux system |
| RA | 1,142,123 | A→G | I172V (ATA→GTA) | flgL → | flagellar hook‑filament junction protein |
| RA | 1,210,070 | C→T | S121F (TCC→TTC) | ymfS → | hypothetical protein |
| RA | 1,224,919 | G→A | intergenic (‑423/‑123) | ymgG ← / → ymgH | hypothetical protein/hypothetical protein |
| RA | 1,234,526 | T→C | T28A (ACG→GCG) | dsbB ← | oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I |
| RA | 1,254,608 | T→C | intergenic (+46/+54) | dhaR → / ← ycgV | predicted DNA‑binding transcriptional regulator, dihydroxyacetone/predicted adhesin |
| RA | 1,255,918 | C→T | G538S (GGC→AGC) | ycgV ← | predicted adhesin |
| RA | 1,268,022 | A→G | T118A (ACG→GCG) | prmC → | N5‑glutamine methyltransferase, modifies release factors RF‑1 and RF‑2 |
| RA | 1,274,854 | G→A | T108M (ACG→ATG) | ychN ← | conserved hypothetical protein |
| RA | 1,295,635 | T→C | Y178H (TAC→CAC) | tdk → | thymidine kinase/deoxyuridine kinase |
| MC JC | 1,301,041 | Δ1,336 bp | insC–insD | insC, insD | |
| RA | 1,303,631 | C→T | Q246Y (CAG→TAT) | oppA → | oligopeptide transporter subunit |
| RA | 1,303,633 | G→T | Q246Y (CAG→TAT) | oppA → | oligopeptide transporter subunit |
| RA | 1,364,882 | G→A | V142V (GTG→GTA) | puuC → | gamma‑Glu‑gamma‑aminobutyraldehyde dehydrogenase, NAD(P)H‑dependent |
| RA | 1,393,837 | C→T | R45* (CGA→TGA) | ycjZ → | predicted DNA‑binding transcriptional regulator |
| RA | 1,394,475 | (A)8→9 | coding (771/900 nt) | ycjZ → | predicted DNA‑binding transcriptional regulator |
| RA | 1,413,523 | G→A | S47F (TCC→TTC) | ydaO ← | predicted C32 tRNA thiolase |
| RA | 1,430,136 | C→T | pseudogene (965/1527 nt) R102H (CGC→CAC) |
lomR → insH ← |
ECK1366:JW5884+JW5904:b4570; Rac prophage region; hypothetical protein IS5 transposase and trans‑activator |
| RA | 1,454,872 | +C | coding (485/2046 nt) | maoC ← | fused aldehyde dehydrogenase and enoyl‑CoA hydratase |
| RA | 1,516,711 | C→T | A79V (GCG→GTG) | ydcV → | predicted spermidine/putrescine transporter subunit |
| RA | 1,516,927 | A→G | N151S (AAT→AGT) | ydcV → | predicted spermidine/putrescine transporter subunit |
| RA | 1,559,619 | A→G | L45S (TTA→TCA) | ddpF ← | D‑Ala‑D‑Ala transporter subunit |
| RA | 1,584,624 | A→G | intergenic (‑386/+16) | ydeN ← / ← ydeO | conserved hypothetical protein/predicted DNA‑binding transcriptional acfivator |
| RA | 1,607,958 | G→A | G49S (GGT→AGT) | lsrF → | predicted aldolase |
| RA | 1,636,349 | G→A | A84V (GCG→GTG) | tfaQ ← | predicted tail fibre assembly protein |
| RA | 1,851,762 | C→T | G404G (GGC→GGT) | sppA → | protease IV |
| RA | 1,857,513 | C→T | G58E (GGA→GAA) | ydjG ← | predicted oxidoreductase |
| RA | 1,874,182 | A→G | Y143C (TAC→TGC) | yeaJ → | predicted diguanylate cyclase |
| RA | 1,878,701 | C→T | P27S (CCG→TCG) | yeaO → | conserved hypothetical protein |
| RA | 1,891,326 | (C)5→6 | coding (135/1686 nt) | fadD ← | acyl‑CoA synthetase |
| RA | 1,930,964 | T→A | D153V (GAT→GTT) | yebE ← | conserved hypothetical protein |
| RA | 2,002,152 | T→C | Y124C (TAC→TGC) | fliY ← | cystine transporter subunit |
| RA | 2,099,387 | T→C | intergenic (+25/+71) | hisI → / ← cld | fused phosphoribosyl‑AMP cyclohydrolase and phosphoribosyl‑ATP pyrophosphatase/regulator of length of O‑antigen component of lipopolysaccharide chains |
| RA | 2,176,396 | C→T | M6I (ATG→ATA) | gatC ← | galactitol‑specific enzyme IIC component of PTS |
| MC JC | 2,176,983 | Δ1,199 bp | [gatA]–[gatA] | [gatA], insH, [gatA] | |
| RA | 2,238,432 | T→C | L356L (TTA→CTA) | yeiT → | predicted oxidoreductase |
| RA | 2,266,989 | T→C | intergenic (‑160/‑208) | fruB ← / → setB | fused fructose‑specific PTS enzyme IIA component and HPr component/lactose/glucose efflux system |
| MC JC | 2,320,795 | Δ1,336 bp | insD–[rcsC] | insD, insC, [rcsC] | |
| RA | 2,358,400 | G→A | A362T (GCT→ACT) | glpA → | sn‑glycerol‑3‑phosphate dehydrogenase (anaerobic), large subunit, FAD/NAD(P)‑binding |
| RA | 2,493,033 | C→T | Q1072* (CAG→TAG) | evgS → | hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
| RA | 2,523,255 | (T)6→7 | coding (24/2190 nt) | yfeA ← | predicted diguanylate cyclase |
| RA | 2,792,695 | C→T | intergenic (+24/‑214) | gabT → / → gabP | 4‑aminobutyrate aminotransferase, PLP‑dependent/gamma‑aminobutyrate transporter |
| RA | 2,841,531 | G→A | R57* (CGA→TGA) | hycI ← | protease involved in processing C‑terminal end of HycE |
| RA | 2,863,059 | G→A | L56L (CTG→CTA) | ygbM → | conserved hypothetical protein |
| RA | 2,866,110 | T→A | intergenic (‑20/+160) | rpoS ← / ← nlpD | RNA polymerase, sigma S (sigma 38) factor/predicted outer membrane lipoprotein |
| RA | 2,966,215 | T→G | K292N (AAA→AAC) | ptsP ← | fused PEP‑protein phosphotransferase (enzyme I) of PTS system |
| RA | 3,001,511 | T→C | I81T (ATA→ACA) | xdhB → | xanthine dehydrogenase, FAD‑binding subunit |
| RA | 3,084,437 | Δ1 bp | coding (131/1977 nt) | speA ← | biosynthetic arginine decarboxylase, PLP‑binding |
| RA | 3,139,938 | C→T | R2H (CGT→CAT) | hybD ← | predicted maturation element for hydrogenase 2 |
| RA | 3,191,865 | G→A | A116T (GCC→ACC) | yqiK → | conserved hypothetical protein |
| RA | 3,213,568 | C→T | intergenic (+24/+55) | rpoD → / ← ygjF | RNA polymerase, sigma 70 (sigma D) factor/G/U mismatch‑specific DNA glycosylase |
| RA | 3,220,824 | C→A | P235T (CCG→ACG) | ebgR → | DNA‑binding transcriptional repressor |
| RA | 3,224,816 | C→T | H147Y (CAT→TAT) | ebgC → | cryptic beta‑D‑galactosidase, beta subunit |
| RA | 3,244,017 | G→A | Q86Q (CAG→CAA) | exuT → | hexuronate transporter |
| RA | 3,259,237 | G→A | S613F (TCT→TTT) | tdcE ← | pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase |
| MC JC | 3,261,134 | Δ1,199 bp | insH–[tdcD] | insH, [tdcD] | |
| RA | 3,294,438 | T→C | L395S (TTG→TCG) | yraM → | conserved hypothetical protein |
| RA | 3,306,434 | G→A | L428L (CTG→TTG) | deaD ← | ATP‑dependent RNA helicase |
| RA | 3,332,615 | T→A | intergenic (‑25/+102) | yhbE ← / ← rpmA | conserved inner membrane protein/50S ribosomal subunit protein L27 |
| RA | 3,338,549 | G→A | F185F (TTC→TTT) | yrbE ← | predicted toluene transporter subunit |
| RA | 3,375,433 | A→G | D237G (GAT→GGT) | dcuD → | predicted transporter |
| RA | 3,459,280 | T→C | E15G (GAA→GGA) | secE ← | preprotein translocase membrane subunit |
| RA | 3,472,611 | G→A | G144G (GGC→GGT) | btuB ← | vitamin B12/cobalamin outer membrane transporter |
| RA | 3,497,165 | G→A | A65T (GCG→ACG) | fsaB → | fructose‑6‑phosphate aldolase 2 |
| RA | 3,516,285 | T→C | intergenic (+20/‑47) | hslU → / → menA | molecular chaperone and ATPase component of HslUV protease/1,4‑dihydroxy‑2‑naphthoate octaprenyltransferase |
| RA | 3,532,412 | T→C | M236T (ATG→ACG) | cpxA → | sensory histidine kinase in two‑component regulatory system with CpxR |
| RA | 3,584,576 | G→A | P21S (CCA→TCA) | hemN ← | coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent |
| RA | 3,609,702 | C→T | E151E (GAG→GAA) | fre ← | flavin reductase |
| RA | 3,639,730 | T→C | K222R (AAA→AGA) | xerC ← | site‑specific tyrosine recombinase |
| RA | 3,657,262 | C→T | E273E (GAG→GAA) | wzyE ← | predicted Wzy protein involved in ECA polysaccharide chain elongation |
| RA | 3,704,876 | C→T | M164I (ATG→ATA) | trkD ← | potassium transporter |
| RA | 3,707,036 | G→A | A483T (GCC→ACC) | yieN → | fused predicted transcriptional regulators |
| RA | 3,727,747 | T→C | V168V (GTT→GTC) | pstA → | phosphate transporter subunit |
| RA | 3,735,429 | G→A | A323T (GCA→ACA) | bglH → | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,739,327 | C→T | V195I (GTT→ATT) | yieH ← | predicted hydrolase |
| MC JC | 3,742,938 | Δ1,336 bp | insD–insC | insD, insC | |
| MC JC | 3,746,913 | Δ1,199 bp | [tnaB]–[tnaB] | [tnaB], insH, [tnaB] | |
| MC JC | 3,750,593 | Δ1,199 bp | insH | insH | |
| RA | 3,806,473 | G→A | P198P (CCG→CCA) | yicI → | predicted alpha‑glucosidase |
| RA | 3,824,280 | T→C | pseudogene (413/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,326 | T→C | pseudogene (459/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,362 | A→T | pseudogene (495/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,368 | G→A | pseudogene (501/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,374 | C→T | pseudogene (507/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,380 | 2 bp→AA | pseudogene (513‑514/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,410 | T→A | pseudogene (543/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,514 | T→C | pseudogene (647/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,524 | T→G | pseudogene (657/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,824,537 | +G | pseudogene (670/687 nt) | rph → | ECK3633:JW3618:b3643; ribonuclease PH |
| RA | 3,915,241 | A→G | E48G (GAG→GGG) | glyQ → | glycine tRNA synthetase, alpha subunit |
| RA | 3,980,009 | T→C | intergenic (‑6/+19) | mdtF ← / ← mdtE | multidrug transporter, RpoS‑dependent/multidrug resistance efflux transporter |
| RA | 3,996,085 | C→T | A284V (GCC→GTC) | prlC → | oligopeptidase A |
| RA | 4,012,376 | G→A | A500T (GCC→ACC) | rbbA → | fused ribosome‑associated ATPases |
| RA | 4,017,703 | T→C | N1175D (AAC→GAC) | rhsB ← | rhsB element core protein RshB |
| RA | 4,032,019 | C→T | D650N (GAC→AAC) | zntA ← | zinc, cobalt and lead efflux system |
| RA | 4,036,723 | G→A | A184T (GCT→ACT) | ftsY → | fused Signal Recognition Particle (SRP) receptor |
| RA | 4,064,477 | A→G | E374E (GAA→GAG) | gntU → | gluconate transporter, low affinity GNT 1 system |
| RA | 4,083,312 | G→A | G325E (GGG→GAG) | rtcB → | conserved hypothetical protein |
| RA | 4,123,875 | G→A | R255H (CGC→CAC) | damX → | hypothetical protein |
| MC JC | 4,310,365 | Δ1,199 bp | insH–[alsK] | insH, [alsK] | |
| RA | 4,328,660 | C→T | V125I (GTC→ATC) | phnD ← | phosphonate/organophosphate ester transporter subunit |
| RA | 4,350,232 | G→A | R3C (CGC→TGC) | yjdF ← | conserved inner membrane protein |
| RA | 4,371,276 | (A)5→3 | intergenic (‑9/+296) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,392,090 | G→T | L655M (CTG→ATG) | yjeP ← | predicted mechanosensitive channel |
| RA | 4,407,692 | C→T | R325C (CGT→TGT) | hflK → | modulator for HflB protease specific for phage lambda cII repressor |
| RA | 4,443,410 | G→A | L179L (CTG→TTG) | ytfJ ← | predicted transcriptional regulator |
| RA | 4,477,260 | G→A | intergenic (‑45/+236) | pyrL ← / ← yjgH | pyrBI operon leader peptide/predicted mRNA endoribonuclease |
| RA | 4,561,090 | G→A | intergenic (‑88/‑585) | yjiC ← / → yjiD | hypothetical protein/DNA replication/recombination/repair protein |
| RA | 4,563,589 | T→A | K207M (AAG→ATG) | iadA ← | isoaspartyl dipeptidase |
| RA | 4,580,803 | C→T | pseudogene (1987/2721 nt) | yjiV → | ECK4334:JW5954:b4486; conserved hypothetical protein |
| RA | 4,586,637 | G→A | P365L (CCG→CTG) | hsdM ← | DNA methylase M |
| RA | 4,588,402 | C→T | L1032L (CTG→CTA) | hsdR ← | endonuclease R |
| RA | 4,591,445 | G→A | T18I (ACA→ATA) | hsdR ← | endonuclease R |
| RA | 4,606,089 | G→A | N37N (AAC→AAT) | dnaT ← | DNA biosynthesis protein |
| RA | 4,643,405 | T→C | H182H (CAT→CAC) | creD → | inner membrane protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | W3110S.gb | 14522 | 14528 | 7 | 9 [0] | [0] 5 | dnaJ | chaperone Hsp40, co‑chaperone with DnaK |
| * | * | ÷ | W3110S.gb | 15248 | 15253 | 6 | 9 [0] | [0] 3 | dnaJ | chaperone Hsp40, co‑chaperone with DnaK |
| * | * | ÷ | W3110S.gb | 88491 | 88497 | 7 | 2 [0] | [0] 8 | fruR | DNA‑binding transcriptional dual regulator |
| * | * | ÷ | W3110S.gb | 122325 | 122334 | 10 | 15 [1] | [1] 4 | pdhR | DNA‑binding transcriptional dual regulator |
| * | * | ÷ | W3110S.gb | 159998 | 160000 | 3 | 2 [0] | [0] 3 | yadB | glutamyl‑Q tRNA(Asp) synthetase |
| * | * | ÷ | W3110S.gb | 205159 | 205168 | 10 | 6 [0] | [0] 4 | dnaE | DNA polymerase III alpha subunit |
| * | * | ÷ | W3110S.gb | 299130 | 299131 | 2 | 6 [1] | [0] 6 | yagR | predicted oxidoreductase with molybdenum‑binding domain |
| * | * | ÷ | W3110S.gb | 371048 | 371077 | 30 | 10 [1] | [0] 3 | mhpC | 2‑hydroxy‑6‑ketonona‑2,4‑dienedioic acid hydrolase |
| * | * | ÷ | W3110S.gb | 379244 | 379254 | 11 | 2 [0] | [1] 8 | frmR/yaiO | regulator protein that represses frmRAB operon/hypothetical protein |
| * | * | ÷ | W3110S.gb | 422752 | 422775 | 24 | 7 [0] | [0] 9 | malZ | maltodextrin glucosidase |
| * | * | ÷ | W3110S.gb | 464057 | 464074 | 18 | 2 [1] | [1] 5 | ybaW/ybaX | conserved hypothetical protein/predicted aluminum resistance protein |
| * | * | ÷ | W3110S.gb | 482484 | 482506 | 23 | 19 [0] | [0] 2 | acrB | multidrug efflux system protein |
| * | * | ÷ | W3110S.gb | 489762 | 489776 | 15 | 2 [1] | [0] 2 | priC | primosomal replication protein N'' |
| * | * | ÷ | W3110S.gb | 573868–575008 | 575999 | 992–2132 | 4 [0] | [0] 146 | insH–[nmpC] | insH,[nmpC] |
| * | * | ÷ | W3110S.gb | 649172 | 649177 | 6 | 4 [0] | [0] 24 | citE | citrate lyase, citryl‑ACP lyase (beta) subunit |
| * | * | ÷ | W3110S.gb | 672860 | 672872 | 13 | 2 [0] | [0] 4 | leuS | leucyl‑tRNA synthetase |
| * | * | ÷ | W3110S.gb | 685594 | 685612 | 19 | 2 [1] | [0] 2 | gltL | glutamate and aspartate transporter subunit |
| * | * | ÷ | W3110S.gb | 721512 | 721547 | 36 | 11 [0] | [0] 6 | kdpE | DNA‑binding response regulator in two‑component regulatory system with KdpD |
| * | * | ÷ | W3110S.gb | 777547 | 777557 | 11 | 3 [0] | [1] 2 | tolA | membrane anchored protein in TolA‑TolQ‑TolR complex |
| * | * | ÷ | W3110S.gb | 779950 | 779957 | 8 | 4 [0] | [0] 5 | pal | peptidoglycan‑associated outer membrane lipoprotein |
| * | * | ÷ | W3110S.gb | 785656 | 785667 | 12 | 4 [1] | [0] 9 | ybgS | conserved hypothetical protein |
| * | * | ÷ | W3110S.gb | 804648 | 804668 | 21 | 2 [0] | [0] 4 | ybhJ | predicted hydratase |
| * | * | ÷ | W3110S.gb | 829012 | 829018 | 7 | 6 [1] | [0] 4 | ybhF | fused predicted transporter subunits and ATP‑binding components of ABC superfamily |
| * | * | ÷ | W3110S.gb | 835105 | 835109 | 5 | 2 [0] | [0] 13 | dinG | ATP‑dependent DNA helicase |
| * | * | ÷ | W3110S.gb | 907993 | 908007 | 15 | 8 [0] | [0] 2 | ybjT | conserved hypothetical protein with NAD(P)‑binding Rossmann‑fold domain |
| * | * | ÷ | W3110S.gb | 915614–915616 | 915647 | 32–34 | 9 [0] | [0] 14 | ybjE/aqpZ | predicted transporter/aquaporin |
| * | * | ÷ | W3110S.gb | 964726 | 964744 | 19 | 6 [0] | [0] 6 | [ycaI] | [ycaI] |
| * | * | ÷ | W3110S.gb | 1028972 | 1028978 | 7 | 9 [0] | [0] 2 | yccV | DNA‑binding protein, hemimethylated |
| * | * | ÷ | W3110S.gb | 1117473 | 1117476 | 4 | 4 [0] | [0] 24 | lpxL | lauryl‑acyl carrier protein (ACP)‑dependent acyltransferase |
| * | * | ÷ | W3110S.gb | 1172355 | 1172362 | 8 | 6 [0] | [1] 5 | mfd | transcription‑repair coupling factor |
| * | * | ÷ | W3110S.gb | 1192374 | 1192378 | 5 | 3 [0] | [1] 6 | purB | adenylosuccinate lyase |
| * | * | ÷ | W3110S.gb | 1209512 | 1209517 | 6 | 2 [0] | [0] 2 | ycfK | hypothetical protein |
| * | * | ÷ | W3110S.gb | 1227502 | 1227525 | 24 | 3 [1] | [1] 2 | minC | cell division inhibitor |
| * | * | ÷ | W3110S.gb | 1263917 | 1263928 | 12 | 3 [0] | [1] 6 | ispE | 4‑diphosphocytidyl‑2‑C‑methylerythritol kinase |
| * | * | ÷ | W3110S.gb | 1267740 | 1267742 | 3 | 14 [0] | [0] 5 | prmC | N5‑glutamine methyltransferase, modifies release factors RF‑1 and RF‑2 |
| * | * | ÷ | W3110S.gb | 1276090 | 1276100 | 11 | 5 [0] | [0] 5 | ychP | predicted invasin |
| * | * | ÷ | W3110S.gb | 1292420 | 1292424 | 5 | 2 [1] | [1] 3 | rssB | response regulator of RpoS |
| * | * | ÷ | W3110S.gb | 1313176 | 1313183 | 8 | 7 [0] | [1] 4 | tonB | membrane spanning protein in TonB‑ExbB‑ExbD complex |
| * | * | ÷ | W3110S.gb | 1317658 | 1317675 | 18 | 4 [0] | [1] 7 | yciG | hypothetical protein |
| * | * | ÷ | W3110S.gb | 1352917 | 1352926 | 10 | 4 [0] | [0] 9 | fabI/ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/conserved hypothetical protein |
| * | * | ÷ | W3110S.gb | 1359945 | 1359955 | 11 | 4 [1] | [0] 3 | puuP | putrescine importer |
| * | * | ÷ | W3110S.gb | 1386111 | 1386119 | 9 | 4 [0] | [0] 2 | ycjX | conserved hypothetical protein with nucleoside triphosphate hydrolase domain |
| * | * | ÷ | W3110S.gb | 1413582 | 1413582 | 1 | 3 [0] | [0] 11 | ydaO | predicted C32 tRNA thiolase |
| * | * | ÷ | W3110S.gb | 1421315 | 1421330 | 16 | 6 [0] | [0] 5 | ydaG/racR | hypothetical protein/predicted DNA‑binding transcriptional regulator |
| * | * | ÷ | W3110S.gb | 1431230 | 1431244 | 15 | 7 [0] | [1] 2 | stfR | predicted tail fiber protein |
| * | * | ÷ | W3110S.gb | 1431621 | 1431625 | 5 | 9 [0] | [1] 3 | stfR | predicted tail fiber protein |
| * | * | ÷ | W3110S.gb | 1463479 | 1463499 | 21 | 13 [1] | [0] 8 | paaJ | predicted beta‑ketoadipyl CoA thiolase |
| * | * | ÷ | W3110S.gb | 1491877 | 1491880 | 4 | 4 [1] | [0] 3 | gapC gapC |
ECK1409:JW5906+JW1413:b4493; glyceraldehyde‑3‑phosphate dehydrogenase C ECK1409:JW5906:b1417; glyceraldehyde‑3‑phosphate dehydrogenase C, C‑ter fragment |
| * | * | ÷ | W3110S.gb | 1513303 | 1513310 | 8 | 6 [0] | [1] 2 | ydcR/ydcS | fused predicted DNA‑binding transcriptional regulator and predicted amino transferase/predicted spermidine/putrescine transporter subunit |
| * | * | ÷ | W3110S.gb | 1648467 | 1648492 | 26 | 2 [1] | [1] 7 | flxA/ydfW | hypothetical protein/hypothetical protein |
| * | * | ÷ | W3110S.gb | 1672513 | 1672530 | 18 | 3 [1] | [1] 4 | ynfM | predicted transporter |
| * | * | ÷ | W3110S.gb | 1732390 | 1732393 | 4 | 9 [1] | [0] 7 | lhr | predicted ATP‑dependent helicase |
| * | * | ÷ | W3110S.gb | 1792034 | 1792034 | 1 | 7 [0] | [0] 6 | ydiU | conserved hypothetical protein |
| * | * | ÷ | W3110S.gb | 1831086 | 1831096 | 11 | 2 [0] | [1] 10 | astD | succinylglutamic semialdehyde dehydrogenase |
| * | * | ÷ | W3110S.gb | 1836788 | 1836796 | 9 | 4 [0] | [0] 2 | ydjZ | conserved inner membrane protein |
| * | * | ÷ | W3110S.gb | 1853601 | 1853607 | 7 | 2 [0] | [0] 3 | pncA | nicotinamidase/pyrazinamidase |
| * | * | ÷ | W3110S.gb | 1868233 | 1868240 | 8 | 6 [1] | [0] 8 | mipA/yeaG | scaffolding protein for murein synthesizing machinery/conserved hypothetical protein with nucleoside triphosphate hydrolase domain |
| * | * | ÷ | W3110S.gb | 2041768 | 2041795 | 28 | 12 [0] | [0] 2 | yedY | predicted reductase |
| * | * | ÷ | W3110S.gb | 2079303 | 2079309 | 7 | 12 [0] | [0] 4 | yeeU | antitoxin of the YeeV‑YeeU toxin‑antitoxin system |
| * | * | ÷ | W3110S.gb | 2186663 | 2186693 | 31 | 4 [1] | [1] 6 | yegX | predicted hydrolase |
| * | * | ÷ | W3110S.gb | 2202199 | 2202201 | 3 | 8 [0] | [0] 11 | molR molR |
DNA‑binding transcriptional regulator; ECK2108:JW2102+JW5915+JW5916:b4499 DNA‑binding transcriptional regulator, middle fragment; ECK2108:JW5915:b2116 |
| * | * | ÷ | W3110S.gb | 2210260 | 2210261 | 2 | 5 [0] | [0] 6 | yehM | hypothetical protein |
| * | * | ÷ | W3110S.gb | 2232522 | 2232570–2232543 | 22–49 | 5 [0] | [1] 2 | yohH/dusC | conserved hypothetical protein/tRNA‑dihydrouridine synthase C |
| * | * | ÷ | W3110S.gb | 2355268 | 2355299 | 32 | 4 [1] | [0] 4 | glpQ | periplasmic glycerophosphodiester phosphodiesterase |
| * | * | ÷ | W3110S.gb | 2403200 | 2403214 | 15 | 5 [0] | [1] 5 | nuoG | NADH:ubiquinone oxidoreductase, chain G |
| * | * | ÷ | W3110S.gb | 2472080 | 2472083 | 4 | 7 [0] | [0] 3 | intS | predicted prophage CPS‑53 integrase |
| * | * | ÷ | W3110S.gb | 2498099 | 2498099 | 1 | 13 [0] | [0] 7 | frc | formyl‑CoA transferase, NAD(P)‑binding |
| * | * | ÷ | W3110S.gb | 2569115 | 2569147 | 33 | 5 [1] | [0] 3 | eutE | predicted aldehyde dehydrogenase, ethanolamine utilization protein |
| * | * | ÷ | W3110S.gb | 2647056 | 2647062 | 7 | 2 [0] | [0] 3 | yfhM | conserved hypothetical protein |
| * | * | ÷ | W3110S.gb | 2749325 | 2749332 | 8 | 3 [0] | [0] 7 | grpE | heat shock protein |
| * | * | ÷ | W3110S.gb | 2803992 | 2803997 | 6 | 5 [0] | [0] 2 | proV | glycine betaine transporter subunit |
| * | * | ÷ | W3110S.gb | 2827387 | 2827403 | 17 | 3 [1] | [1] 2 | gutM | DNA‑binding transcriptional activator |
| * | * | ÷ | W3110S.gb | 2940001 | 2940001 | 1 | 3 [0] | [0] 5 | ygdD | conserved inner membrane protein |
| * | * | ÷ | W3110S.gb | 3007124 | 3007132 | 9 | 7 [1] | [0] 3 | ygeX | 2,3‑diaminopropionate ammonia‑lyase |
| * | * | ÷ | W3110S.gb | 3010354 | 3010357 | 4 | 4 [1] | [0] 5 | yqeA | predicted amino acid kinase |
| * | * | ÷ | W3110S.gb | 3315157 | 3315182 | 26 | 3 [0] | [1] 2 | infB | fused protein chain initiation factor 2, IF2 |
| * | * | ÷ | W3110S.gb | 3438714 | 3438721 | 8 | 4 [0] | [0] 17 | hemE | uroporphyrinogen decarboxylase |
| * | * | ÷ | W3110S.gb | 3759296 | 3759304 | 9 | 4 [0] | [0] 3 | recF | gap repair protein |
| * | * | ÷ | W3110S.gb | 3859257 | 3859260 | 4 | 3 [0] | [0] 2 | yibK/lldD | predicted rRNA methylase/L‑lactate dehydrogenase, FMN‑linked |
| * | * | ÷ | W3110S.gb | 3875061 | 3875069–3875062 | 2–9 | 4 [0] | [0] 7 | rhsA | rhsA element core protein RshA |
| * | * | ÷ | W3110S.gb | 4083703 | 4083711 | 9 | 4 [0] | [0] 2 | rtcA | RNA 3'‑terminal phosphate cyclase |
| * | * | ÷ | W3110S.gb | 4120616 | 4120626 | 11 | 2 [1] | [0] 4 | hofQ | predicted fimbrial transporter |
| * | * | ÷ | W3110S.gb | 4521187 | 4521192 | 6 | 3 [0] | [0] 3 | fecA | ferric citrate outer membrane transporter |
| * | * | ÷ | W3110S.gb | 4554534 | 4554538 | 5 | 2 [0] | [0] 7 | fimH/gntP | minor component of type 1 fimbriae/fructuronate transporter |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | W3110S.gb | = 274373 | NA (NA) | 146 (3.040) | 9/110 | 0.3 | 100% | intergenic (‑32/‑176) | insH/mmuP | IS5 transposase and trans‑activator/predicted S‑methylmethionine transporter |
| ? | W3110S.gb | 576000 = | 0 (0.000) | pseudogene (109/1128 nt) | nmpC | DLP12 prophage region; ECK0544:JW5078:b0553; truncated outer membrane porin | |||||
| * | ? | W3110S.gb | 314453 = | 45 (0.940) | 26 (0.570) +TCA |
7/104 | 0.4 | 55.0% | coding (873/888 nt) | eaeH | attaching and effacing protein, pathogenesis factor |
| ? | W3110S.gb | = 3920281 | 0 (0.000) | coding (88/213 nt) | cspA | major cold shock protein | |||||
| * | ? | W3110S.gb | 314453 = | 45 (0.940) | 109 (2.360) +TC |
17/106 | 0.0 | 81.6% | coding (873/888 nt) | eaeH | attaching and effacing protein, pathogenesis factor |
| ? | W3110S.gb | 3932930 = | 6 (0.120) | coding (219/1608 nt) | dppA | dipeptide transporter | |||||
| * | ? | W3110S.gb | = 315707 | NA (NA) | 46 (0.960) | 8/110 | 0.4 | 100% | coding (654/687 nt) | ykgA | predicted DNA‑binding transcriptional regulator |
| ? | W3110S.gb | 576911 = | 0 (0.000) | coding (76/498 nt) | ybcS | predicted lysozyme | |||||
| * | ? | W3110S.gb | 566000 = | NA (NA) | 43 (0.900) | 10/110 | 0.3 | 100% | intergenic (+90/‑56) | ybcD/insE | DLP12 prophage region; ECK0532:JW0527:b4508; predicted replication protein fragment/IS3 element protein InsE |
| ? | W3110S.gb | = 576913 | 0 (0.000) | coding (78/498 nt) | ybcS | predicted lysozyme | |||||
| * | ? | W3110S.gb | 1209367 = | 5 (0.100) | 40 (1.180) | 7/78 | 0.3 | 85.5% | coding (290/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | 1211196 = | 10 (0.300) | pseudogene (37/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | = 1209382 | 5 (0.100) | 30 (0.890) | 6/78 | 0.3 | 81.6% | coding (305/630 nt) | ycfK | hypothetical protein |
| ? | W3110S.gb | = 1211179 | 10 (0.300) | pseudogene (54/537 nt) | stfE | ECK1143:JW5172:b1157; e14 prophage region; predicted side tail fiber protein fragment | |||||
| * | ? | W3110S.gb | 2018571 = | 7 (0.150) | 39 (0.860) | 10/104 | 0.2 | 85.5% | coding (567/687 nt) | fliH | flagellar biosynthesis protein |
| ? | W3110S.gb | 2519723 = | NA (NA) | intergenic (+33/‑54) | nupC/insL | nucleoside (except guanosine) transporter/predicted transposase | |||||
| * | ? | W3110S.gb | = 2018583 | 11 (0.230) | 52 (1.120) | 7/106 | 0.5 | 83.1% | coding (579/687 nt) | fliH | flagellar biosynthesis protein |
| ? | W3110S.gb | = 2521059 | NA (NA) | intergenic (+170/+30) | insL/yfeA | predicted transposase/predicted diguanylate cyclase | |||||
| * | ? | W3110S.gb | = 2173564 | NA (NA) | 52 (1.100) | 12/108 | 0.2 | 88.3% | pseudogene (307/2041 nt) pseudogene (307/339 nt) |
gatR gatR |
DNA‑binding transcriptional regulator; ECK2083:JW5340+JW2074:b4498 DNA‑binding transcriptional regulator, C‑ter fragment; ECK2083:JW2074:b2090 |
| ? | W3110S.gb | 3920278 = | 7 (0.150) | coding (91/213 nt) | cspA | major cold shock protein | |||||
| * | ? | W3110S.gb | = 2412225 | NA (NA) | 55 (1.150) | 13/110 | 0.1 | 77.5% | intergenic (‑55/‑782) | insA/yfbQ | IS1 element protein/predicted aminotransferase |
| ? | W3110S.gb | = 3748807 | 16 (0.330) | coding (176/984 nt) | tnaB | tryptophan transporter of low affinity | |||||
| * | ? | W3110S.gb | 3748799 = | 15 (0.310) | 79 (1.650) | 13/110 | 0.1 | 84.0% | coding (184/984 nt) | tnaB | tryptophan transporter of low affinity |
| ? | W3110S.gb | 4056222 = | NA (NA) | intergenic (‑564/+15) | yrhB/insB | hypothetical protein/IS1 transposase InsAB' | |||||
| * | ? | W3110S.gb | = 4547372 | 16 (0.330) | 26 (0.650) | 6/92 | 0.4 | 75.0% | intergenic (+57/‑425) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin |
| ? | W3110S.gb | = 4547668 | 4 (0.100) | intergenic (+353/‑129) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin | |||||