mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 7,240 | A→G | S240S (AGT→AGC) | yaaJ ← | putative transporter YaaJ |
| RA | 18,179 | (G)5→4 | coding (691/1167 nt) | nhaA → | Na(+):H(+) antiporter NhaA |
| RA | 25,107 | A→G | H906R (CAC→CGC) | ileS → | isoleucine‑‑tRNA ligase |
| RA | 49,008 | A→G | T414A (ACC→GCC) | kefC → | K(+) : H(+) antiporter KefC |
| RA | 55,555 | A→G | Y519H (TAT→CAT) | lptD ← | lipopolysaccharide assembly protein LptD |
| RA | 93,294 | T→C | G43G (GGT→GGC) | murE → | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate‑‑2, 6‑diaminopimelate ligase |
| RA | 141,108 | A→G | S40P (TCC→CCC) | gcd ← | quinoprotein glucose dehydrogenase |
| RA | 195,355 | A→G | I151M (ATA→ATG) | ispU → | undecaprenyl diphosphate synthase |
| RA | 204,483 | A→G | E379G (GAG→GGG) | lpxB → | lipid A disaccharide synthase |
| RA | 210,131 | +G | coding (453/2142 nt) | ldcC → | lysine decarboxylase 2 |
| RA | 217,044 | A→G | intergenic (‑41/+13) | yaeF ← / ← proS | peptidase C92 family protein/proline‑‑tRNA ligase |
| RA | 243,501 | C→T | intergenic (‑198/‑42) | fadE ← / → lpcA | acyl‑CoA dehydrogenase/D‑sedoheptulose 7‑phosphate isomerase |
| RA | 257,015 | T→C | R163R (CGT→CGC) | frsA → | fermentation‑respiration switch protein |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 289,044 | A→G | L40P (CTC→CCC) | xynR ← | CP4‑6 prophage; DNA‑binding transcriptional repressor XynR |
| RA | 308,771 | +C | coding (562/2526 nt) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | 369,543 | T→C | G311G (GGT→GGC) | mhpA → | putative 3‑(3‑hydroxyphenyl)propanoate/3‑hydroxycinnamate hydroxylase |
| RA | 375,247 | A→G | intergenic (+366/‑212) | mhpE → / → mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| RA | 375,269 | A→G | intergenic (+388/‑190) | mhpE → / → mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| RA | 375,277 | G→A | intergenic (+396/‑182) | mhpE → / → mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | DNA‑binding transcriptional repressor FrmR/outer membrane protein YaiO |
| RA | 391,703 | (G)6→7 | pseudogene (1453/1458 nt) | yaiT → | putative autotransporter YaiT |
| RA | 395,434 | G→A | T285M (ACG→ATG) | ampH ← | peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase |
| RA | 397,197 | Δ1 bp | coding (559/1221 nt) | sbmA → | peptide antibiotic/peptide nucleic acid transporter |
| RA | 428,237 | T→C | H197H (CAT→CAC) | secD → | Sec translocon accessory complex subunit SecD |
| RA | 435,614 | (T)6→7 | intergenic (+58/‑20) | nusB → / → thiL | transcription antitermination protein NusB/thiamine monophosphate kinase |
| RA | 503,225 | +G | coding (14/1677 nt) | ybaL ← | putative transporter YbaL |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 544,082 | Δ1 bp | coding (1211/1236 nt) | allC ← | allantoate amidohydrolase |
| RA | 595,675 | C→T | R26C (CGT→TGT) | cusC → | copper/silver export system outer membrane channel |
| RA | 601,164 | T→A | N817K (AAT→AAA) | cusA → | copper/silver export system RND permease |
| RA | 609,948 | A→G | R44R (CGT→CGC) | entD ← | phosphopantetheinyl transferase EntD |
| RA | 616,008 | A→G | T618A (ACG→GCG) | entF → | apo‑serine activating enzyme |
| RA | 634,194 | A→G | E203E (GAA→GAG) | ybdL → | methionine‑oxo‑acid transaminase, PLP‑dependent |
| RA | 712,538 | A→G | S89P (TCC→CCC) | ybfF ← | esterase |
| RA | 796,504 | A→G | I215V (ATT→GTT) | modB → | molybdate ABC transporter membrane subunit |
| RA | 799,693 | T→C | T295A (ACT→GCT) | ybhD ← | putative DNA‑binding transcriptional regulator YbhD |
| RA | 815,306 | T→G | V594G (GTC→GGC) | uvrB → | excision nuclease subunit B |
| RA | 828,749 | A→G | L78P (CTG→CCG) | ybhF ← | putative ABC exporter ATP binding subunit |
| RA | 880,671 | A→G | intergenic (‑191/‑56) | gstB ← / → dacC | glutathione S‑transferase GstB/D‑alanyl‑D‑alanine carboxypeptidase DacC |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 917,719 | A→G | Q416R (CAG→CGG) | ybjD → | DUF2813 domain‑containing protein YbjD |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 940,462 | A→G | V345V (GTA→GTG) | serS → | serine‑‑tRNA ligase |
| RA | 971,326 | A→G | T159A (ACC→GCC) | kdsB → | 3‑deoxy‑manno‑octulosonate cytidylyltransferase |
| RA | 973,349 | A→G | L18P (CTG→CCG) | elyC ← | envelope biogenesis factor |
| RA | 979,986 | C→T | R1221C (CGT→TGT) | mukB → | chromosome partitioning protein MukB |
| RA | 1,004,161 | A→G | E72G (GAA→GGA) | ycbF → | putative fimbrial chaperone YcbF |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,049,478 | A→G | G89G (GGT→GGC) | gfcA ← | threonine‑rich inner membrane protein GfcA |
| RA | 1,067,692 | A→G | V6A (GTG→GCG) | wrbA ← | NAD(P)H:quinone oxidoreductase |
| RA | 1,070,255 | A→G | F34L (TTC→CTC) | rutF ← | flavin reductase |
| RA | 1,079,601 | G→A | V99V (GTG→GTA) | putP → | proline:Na(+) symporter |
| RA | 1,093,346 | (T)6→7 | coding (471/1359 nt) | dgcT → | putative diguanylate cyclase DgcT |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,147,993 | A→G | I125V (ATT→GTT) | plsX → | putative phosphate acyltransferase |
| RA | 1,162,592 | (G)5→6 | coding (346/378 nt) | ycfL → | DUF1425 domain‑containing protein YcfL |
| RA | 1,167,286 | A→G | Y401C (TAC→TGC) | ndh → | NADH:quinone oxidoreductase II |
| RA | 1,205,638 | T→G | G30G (GGT→GGG) | ymfR → | e14 prophage; protein YmfR |
| RA | 1,206,043 | A→G | T105A (ACC→GCC) | beeE → | e14 prophage; putative protein BeeE |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,222,786 | C→T | G68D (GGT→GAT) | ymgG ← | PF13488 family protein YmgG |
| RA | 1,245,511 | A→G | T118A (ACC→GCC) | ycgY → | uncharacterized protein YcgY |
| RA | 1,294,524 | C→T | pseudogene (799/897 nt) | insZ ← | putative transposase InsZ |
| RA | 1,303,637 | T→C | S247P (TCT→CCT) | oppB → | murein tripeptide ABC transporter/oligopeptide ABC transporter inner membrane subunit OppB |
| RA | 1,304,427 | G→T | A198A (GCG→GCT) | oppC → | murein tripeptide ABC transporter/oligopeptide ABC transporter inner membrane subunit OppC |
| RA | 1,370,708 | A→G | S165G (AGC→GGC) | ycjM → | glucosylglycerate phosphorylase |
| RA | 1,404,074 | A→G | L164L (CTT→CTC) | abgA ← | p‑aminobenzoyl‑glutamate hydrolase subunit A |
| RA | 1,421,650 | (C)7→6 | coding (532/858 nt) | ydaU → | Rac prophage; DUF1376 domain‑containing protein YdaU |
| RA | 1,437,648 | A→G | L1046P (CTG→CCG) | ydbK ← | putative pyruvate‑flavodoxin oxidoreductase |
| RA | 1,445,005 | G→A | G652D (GGC→GAC) | ydbH → | PF11739 family protein YdbH |
| RA | 1,493,384 | A→G | E305E (GAA→GAG) | trg → | methyl‑accepting chemotaxis protein Trg |
| RA | 1,535,229 | A→C | G210G (GGT→GGG) | yddE ← | PF02567 family protein YddE |
| RA | 1,535,877 | G→A | intergenic (‑19/+60) | yddE ← / ← narV | PF02567 family protein YddE/nitrate reductase Z subunit gamma |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,570,741 | T→C | E435E (GAA→GAG) | gadB ← | glutamate decarboxylase B |
| RA | 1,576,260 | A→G | Y454H (TAT→CAT) | yddB ← | putative TonB‑dependent receptor |
| RA | 1,592,043 | A→G | L45P (CTG→CCG) | hipA ← | serine/threonine kinase HipA |
| RA | 1,594,131 | (C)8→6 | pseudogene (3955‑3956/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,594,256 | (C)8→9 | pseudogene (3831/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| JC | 1,597,313 | (C)7→10 | pseudogene (774/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,614,688 | C→A | A6S (GCA→TCA) | sad ← | NAD(+)‑dependent succinate semialdehyde dehydrogenase |
| RA | 1,620,752 | A→G | V129A (GTG→GCG) | eamA ← | cysteine/O‑acetylserine exporter EamA |
| RA | 1,624,188 | G→A | P104S (CCG→TCG) | ydeI ← | BOF family protein YdeI |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,651,822 | T→C | pseudogene (311/1197 nt) | intQ → | Qin prophage; putative defective integrase |
| RA | 1,674,655 | (C)6→7 | coding (743/1035 nt) | tqsA → | autoinducer 2 exporter |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,687,513 | A→G | F289L (TTT→CTT) | fumA ← | fumarase A |
| RA | 1,713,392 | T→C | G208G (GGT→GGC) | dtpA → | dipeptide/tripeptide:H(+) symporter DtpA |
| RA | 1,718,598 | G→A | A335A (GCC→GCT) | anmK ← | anhydro‑N‑acetylmuramic acid kinase |
| RA | 1,735,789 | T→C | S138P (TCA→CCA) | sodB → | superoxide dismutase (Fe) |
| RA | 1,756,145 | G→A | G150S (GGT→AGT) | pykF → | pyruvate kinase I |
| RA | 1,786,943 | T→C | N57S (AAC→AGC) | ppsA ← | phosphoenolpyruvate synthetase |
| RA | 1,788,844 | T→C | V137A (GTC→GCC) | aroH → | 3‑deoxy‑7‑phosphoheptulonate synthase, Trp‑sensitive |
| RA | 1,797,729 | A→T | D72E (GAT→GAA) | pheT ← | phenylalanine‑‑tRNA ligase subunit beta |
| RA | 1,823,934 | (C)5→4 | coding (420/888 nt) | cho → | endonuclease of nucleotide excision repair |
| RA | 1,832,698 | A→G | I91V (ATT→GTT) | xthA → | exodeoxyribonuclease III |
| RA | 1,847,995 | G→T | S5* (TCG→TAG) | selD ← | selenide, water dikinase |
| RA | 1,849,394 | T→C | G186G (GGT→GGC) | sppA → | protease IV, a signal peptide peptidase |
| RA | 1,850,034 | G→A | V400I (GTT→ATT) | sppA → | protease IV, a signal peptide peptidase |
| RA | 1,858,333 | T→C | K167K (AAA→AAG) | ydjJ ← | putative zinc‑binding dehydrogenase YdjJ |
| RA | 1,859,352 | G→A | T293I (ACC→ATC) | ydjK ← | putative transporter YdjK |
| RA | 1,868,282 | T→C | F459L (TTC→CTC) | yeaG → | protein kinase YeaG |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,885,377 | T→C | L238P (CTG→CCG) | yeaW → | carnitine monooxygenase subunit YeaW |
| RA | 1,888,441 | T→C | T436A (ACC→GCC) | fadD ← | fatty acyl‑CoA synthetase |
| RA | 1,892,288 | T→C | E316E (GAA→GAG) | yoaA ← | putative 5' to 3' DNA helicase implicated in DNA repair |
| RA | 1,899,034 | T→C | V203A (GTA→GCA) | pdeD → | putative c‑di‑GMP phosphodiesterase PdeD |
| RA | 1,923,469 | T→C | T80A (ACC→GCC) | yebY ← | DUF2511 domain‑containing protein YebY |
| RA | 1,936,414 | T→C | intergenic (‑100/‑238) | zwf ← / → yebK | NADP(+)‑dependent glucose‑6‑phosphate dehydrogenase/DNA‑binding transcriptional repressor YebK |
| RA | 1,975,233 | T→C | Q31R (CAG→CGG) | cheA ← | chemotaxis protein CheA |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,001,935 | +G | intergenic (‑146/+175) | fliA ← / ← fliC | RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein |
| RA | 2,030,962 | (T)5→6 | coding (1356/1419 nt) | dcm ← | DNA‑cytosine methyltransferase |
| RA | 2,033,994 | (T)8→7 | intergenic (+255/‑57) | rseX → / → yedS | small regulatory RNA RseX/putative outer membrane protein YedS, N‑terminal fragment |
| MC | 2,067,354 | Δ35,590 bp | between IS5 | yoeA–insH‑7 | 41 genes yoeA, insD‑3, insC‑3, yoeA, yeeP, isrC, flu, yeeR, yeeS, yeeT, cbeA, cbtA, yeeW, yoeF, yeeX, yeeA, sbmC, dacD, sbcB, yeeD, yeeE, plaP, yoeI, yeeY, yeeZ, yoeB, yefM, hisL, hisG, hisD, hisC, hisB, hisH, hisA, hisF, hisI, wzzB, ugd, gnd, wbbL, insH‑7 |
| RA | 2,114,707 | G→A | S397L (TCA→TTA) | wcaM ← | putative colanic acid biosynthesis protein WcaM |
| RA | 2,116,513 | G→A | G205G (GGC→GGT) | wcaL ← | putative colanic biosynthesis glycosyl transferase |
| RA | 2,117,829 | T→C | K192K (AAA→AAG) | wcaK ← | putative colanic acid biosynthesis pyruvyl transferase |
| RA | 2,137,049 | T→C | P65P (CCA→CCG) | wza ← | outer membrane polysaccharide export protein Wza |
| RA | 2,144,943 | A→G | T560A (ACG→GCG) | dgcE → | putative diguanylate cyclase DgcE |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,187,068 | T→C | Y37H (TAT→CAT) | rcnB → | periplasmic protein involved in nickel/cobalt export |
| RA | 2,213,464 | A→G | V394A (GTG→GCG) | btsS ← | high‑affinity pyruvate receptor |
| RA | 2,224,154 | G→C | G239G (GGC→GGG) | pbpG ← | peptidoglycan DD‑endopeptidase PbpG |
| RA | 2,233,515 | A→G | H213R (CAC→CGC) | sanA → | DUF218 domain‑containing protein SanA |
| RA | 2,262,962 | (C)5→6 | coding (534/1131 nt) | fruB ← | fructose‑specific PTS multiphosphoryl transfer protein FruB |
| RA | 2,267,665 | T→C | V474A (GTA→GCA) | yeiQ → | putative dehydrogenase, NAD‑dependent |
| RA | 2,285,722 | C→T | A449A (GCC→GCT) | yejM → | putative cardiolipin transport protein |
| RA | 2,304,988 | T→C | intergenic (+595/+120) | eco → / ← mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| RA | 2,305,013 | A→G | intergenic (+620/+95) | eco → / ← mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| RA | 2,305,027 | G→A | intergenic (+634/+81) | eco → / ← mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| RA | 2,312,373 | T→C | D126G (GAC→GGC) | ompC ← | outer membrane porin C |
| RA | 2,339,176 | T→C | D82G (GAC→GGC) | gyrA ← | DNA gyrase subunit A |
| RA | 2,350,215 | G→A | A266V (GCC→GTC) | glpQ ← | glycerophosphoryl diester phosphodiesterase |
| RA | 2,369,665 | G→A | G543S (GGT→AGT) | arnA → | fused UDP‑4‑amino‑4‑deoxy‑L‑arabinose formyltransferase/UDP‑glucuronate dehydrogenase |
| RA | 2,386,665 | A→G | H269R (CAC→CGC) | yfbL → | putative peptidase YfbL |
| RA | 2,396,080 | T→C | E124G (GAA→GGA) | nuoI ← | NADH:quinone oxidoreductase subunit I |
| RA | 2,397,693 | A→G | S825P (TCA→CCA) | nuoG ← | NADH:quinone oxidoreductase subunit G |
| RA | 2,405,651 | (C)5→6 | intergenic (‑579/+52) | nuoA ← / ← lrhA | NADH:quinone oxidoreductase subunit A/DNA‑binding transcriptional dual regulator LrhA |
| RA | 2,437,681 | T→C | K57K (AAA→AAG) | pdxB ← | erythronate‑4‑phosphate dehydrogenase |
| RA | 2,442,175 | T→C | C138R (TGC→CGC) | mnmC → | fused 5‑methylaminomethyl‑2‑thiouridine‑forming methyltransferase and FAD‑dependent demodification enzyme |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,496,504 | A→G | Y287C (TAC→TGC) | lpxP → | palmitoleoyl acyltransferase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,615,271 | T→C | E204G (GAG→GGG) | yfgO ← | putative transporter YfgO |
| RA | 2,648,364 | T→C | V1308V (GTA→GTG) | yfhM ← | alpha2‑macroglobulin |
| RA | 2,663,259 | G→A | A22V (GCC→GTC) | trmJ ← | tRNA Cm32/Um32 methyltransferase |
| RA | 2,667,775 | T→C | L24L (CTA→CTG) | hcaT ← | putative 3‑phenylpropionate transporter |
| RA | 2,675,097 | T→C | D222G (GAT→GGT) | yphC ← | putative zinc‑binding dehydrogenase YphC |
| RA | 2,710,553 | C→T | S45L (TCA→TTA) | nadB → | L‑aspartate oxidase |
| RA | 2,718,291 | T→C | T80A (ACG→GCG) | yfiF ← | putative methyltransferase |
| RA | 2,742,347 | T→C | V158A (GTC→GCC) | yfiR → | DUF4154 domain‑containing protein YfiR |
| RA | 2,742,729 | T→C | F116S (TTC→TCC) | dgcN → | diguanylate cyclase DgcN |
| RA | 2,743,395 | T→C | V338A (GTA→GCA) | dgcN → | diguanylate cyclase DgcN |
| RA | 2,757,662 | (T)8→9 | coding (939/957 nt) | yfjH ← | CP4‑57 prophage; protein YfjH |
| RA | 2,764,948 | Δ1 bp | coding (206/1617 nt) | abpA ← | CP4‑57 prophage; anti‑bacteriophage protein |
| RA | 2,765,414 | A→G | intergenic (‑261/+99) | abpA ← / ← yfjM | CP4‑57 prophage; anti‑bacteriophage protein/CP4‑57 prophage; protein YfjM |
| RA | 2,778,930 | (C)6→7 | coding (3797/4581 nt) | ypjA ← | adhesin‑like autotransporter YpjA |
| RA | 2,805,736 | C→T | R308C (CGC→TGC) | proV → | glycine betaine ABC transporter ATP binding subunit ProV |
| RA | 2,809,002 | A→G | pseudogene (687/1178 nt) | ygaY → | putative transporter YgaY, N‑terminal fragment |
| RA | 2,810,197 | A→G | Q194R (CAG→CGG) | ygaZ → | L‑valine exporter subunit YgaZ |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,817,834 | T→C | noncoding (27/77 nt) | argQ ← | tRNA‑Arg |
| RA | 2,818,784 | T→C | intergenic (‑139/+177) | serV ← / ← csrA | tRNA‑Ser/carbon storage regulator |
| RA | 2,821,137 | G→A | A292V (GCG→GTG) | alaS ← | alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor |
| RA | 2,835,963 | T→C | Q488R (CAG→CGG) | hypF ← | carbamoyltransferase HypF |
| RA | 2,837,711 | T→C | D132G (GAC→GGC) | hydN ← | putative electron transport protein HydN |
| RA | 2,839,090 | T→C | T59A (ACT→GCT) | ascG ← | DNA‑binding transcriptional repressor AscG |
| RA | 2,844,085 | G→A | R42R (CGC→CGT) | hycG ← | formate hydrogenlyase subunit HycG |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,891,910 | T→C | intergenic (‑12/‑304) | cysJ ← / → queD | sulfite reductase, flavoprotein subunit/6‑carboxy‑5,6,7,8‑tetrahydropterin synthase |
| RA | 2,900,874 | T→C | Y95H (TAT→CAT) | yqcE → | putative transport protein YqcE |
| RA | 2,902,963 | G→A | T356T (ACG→ACA) | ygcE → | putative sugar kinase YgcE |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,990,434 | A→C | intergenic (‑74/‑120) | yqeK ← / → ygeF | protein YqeK/protein YgeF |
| RA | 2,997,971 | T→C | pseudogene (18/300 nt) | ygeP ← | protein YgeP |
| RA | 2,999,755 | (C)6→7 | coding (137/756 nt) | ygeR ← | LysM domain‑containing putative peptidase lipoprotein YgeR |
| RA | 3,001,304 | (G)7→8 | coding (960/2259 nt) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | 3,003,479 | (G)6→7 | coding (866/879 nt) | xdhB → | putative xanthine dehydrogenase FAD‑binding subunit XdhB |
| RA | 3,060,772 | (T)8→9 | intergenic (+126/‑78) | argP → / → scpA | DNA‑binding transcriptional dual regulator ArgP/methylmalonyl‑CoA mutase |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| MC JC | 3,131,341 | Δ191 bp | IS5‑mediated | yghQ ← | putative transport protein YghQ |
| RA | 3,162,717 | T→C | intergenic (‑48/+27) | ftsP ← / ← plsC | cell division protein required during stress conditions/1‑acylglycerol‑3‑phosphate O‑acyltransferase |
| RA | 3,177,509 | (C)6→7 | coding (402/630 nt) | nudF ← | ADP‑sugar pyrophosphatase |
| RA | 3,200,205 | A→G | V254A (GTG→GCG) | ygiF ← | inorganic triphosphatase |
| RA | 3,231,441 | A→G | intergenic (+202/‑224) | ygjK → / → fadH | glycoside hydrolase/2,4‑dienoyl‑CoA reductase |
| RA | 3,240,406 | T→C | W155R (TGG→CGG) | sstT → | serine/threonine:Na(+) symporter |
| RA | 3,240,984 | (G)7→8 | coding (1041/1245 nt) | sstT → | serine/threonine:Na(+) symporter |
| RA | 3,250,078 | T→C | R132R (CGT→CGC) M1A (GTG→GCG) † |
yqjE → yqjK → |
conserved inner membrane protein YqjE conserved protein YqjK |
| RA | 3,257,649 | A→G | V121A (GTA→GCA) | cyuP ← | putative D/L‑serine transporter |
| RA | 3,275,916 | G→A | G212D (GGC→GAC) | garD → | galactarate dehydratase |
| RA | 3,304,212 | G→A | G255G (GGG→GGA) | yhbW → | putative luciferase‑like monooxygenase |
| RA | 3,304,813 | (C)7→8 | coding (1005/1245 nt) | mtr ← | tryptophan:H(+) symporter Mtr |
| RA | 3,319,940 | G→A | G435D (GGC→GAC) | argG → | argininosuccinate synthetase |
| RA | 3,321,393 | T→C | D74G (GAC→GGC) | yhbX ← | putative hydrolase, inner membrane |
| RA | 3,337,816 | T→C | N26D (AAT→GAT) | mlaC ← | intermembrane phospholipid transport system ‑ periplasmic binding protein |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,361,696 | A→G | H174R (CAC→CGC) | gltF → | periplasmic protein GltF |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,423,458 | C→T | noncoding (85/120 nt) | rrfF ← | 5S ribosomal RNA |
| RA | 3,448,477 | T→C | H31R (CAC→CGC) | rpsQ ← | 30S ribosomal subunit protein S17 |
| RA | 3,475,447 | G→A | T91M (ACG→ATG) | tusD ← | sulfurtransferase complex subunit TusD |
| RA | 3,484,970 | T→C | W161R (TGG→CGG) | prkB → | putative phosphoribulokinase |
| RA | 3,486,448 | A→C | N110T (AAC→ACC) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,531,110 | G→A | Q444* (CAA→TAA) | yhgE ← | putative transport protein YhgE |
| RA | 3,534,231 | A→G | T472A (ACC→GCC) | pck → | phosphoenolpyruvate carboxykinase (ATP) |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,561,621 | C→T | G68D (GGC→GAC) | glpE ← | thiosulfate sulfurtransferase GlpE |
| RA | 3,662,411 | A→G | L666L (TTA→TTG) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | 3,692,258 | T→C | Y117C (TAC→TGC) | bcsB ← | cellulose synthase periplasmic subunit |
| RA | 3,708,091 | T→C | intergenic (‑386/+525) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,725,214 | G→A | V35V (GTC→GTT) | glyQ ← | glycine‑‑tRNA ligase subunit alpha |
| RA | 3,747,700 | A→G | H206R (CAC→CGC) | lyxK → | L‑xylulose kinase |
| RA | 3,772,577 | T→C | G99G (GGT→GGC) | mtlA → | mannitol‑specific PTS enzyme IICBA component |
| RA | 3,777,538 | T→C | V47A (GTG→GCG) | lldP → | lactate/glycolate:H(+) symporter LldP |
| RA | 3,788,824 | C→T | Q242* (CAG→TAG) | yibQ → | divergent polysaccharide deacetylase domain‑containing protein YibQ |
| RA | 3,802,925 | Δ1 bp | coding (134/1020 nt) | waaO ← | UDP‑D‑glucose:(glucosyl)LPS alpha‑1,3‑glucosyltransferase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,831,149 | T→C | R231R (CGT→CGC) | yicH → | AsmA famly protein YicH |
| RA | 3,844,073 | T→C | V37A (GTC→GCC) | adeD → | adenine deaminase |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,882,822 | A→G | V303A (GTG→GCG) | dnaA ← | chromosomal replication initiator protein DnaA |
| RA | 3,905,125 | A→G | I158T (ATC→ACC) | bglF ← | beta‑glucoside specific PTS enzyme II/BglG kinase/BglG phosphatase |
| RA | 3,908,180 | A→G | Y63H (TAC→CAC) | pstB ← | phosphate ABC transporter ATP binding subunit |
| RA | 3,911,408 | C→G | V40L (GTG→CTG) | pstS ← | phosphate ABC transporter periplasmic binding protein |
| RA | 3,931,183 | (G)7→8 | intergenic (‑90/‑133) | ravA ← / → kup | regulatory ATPase RavA/K(+):H(+) symporter Kup |
| RA | 3,955,352 | T→C | S8P (TCC→CCC) | ilvA → | threonine deaminase |
| RA | 3,967,388 | T→C | G324G (GGT→GGC) | rho → | transcription termination factor Rho |
| RA | 3,982,684 | (C)8→9 | noncoding (79/87 nt) | leuT → | tRNA‑Leu |
| RA | 4,020,242 | T→C | V6A (GTA→GCA) | ubiB → | ubiquinone biosynthesis protein UbiB |
| RA | 4,065,386 | T→C | G127G (GGA→GGG) | yihO ← | putative sulfoquinovose transporter |
| RA | 4,105,746 | (C)5→6 | intergenic (‑76/‑74) | cpxR ← / → cpxP | DNA‑binding transcriptional dual regulator CpxR/periplasmic protein CpxP |
| RA | 4,200,155 | (C)6→5 | intergenic (+61/‑126) | yjaG → / → hupA | conserved protein YjaG/DNA‑binding protein HU‑alpha |
| RA | 4,206,123 | A→G | G470G (GGT→GGC) | purH ← | bifunctional AICAR transformylase/IMP cyclohydrolase |
| RA | 4,223,381 | G→A | A83V (GCA→GTA) | iclR ← | DNA‑binding transcriptional repressor IclR |
| RA | 4,231,763 | (A)7→6 | intergenic (‑132/+121) | yjbD ← / ← lysC | conserved protein YjbD/aspartate kinase III |
| RA | 4,235,842 | A→G | intergenic (+435/‑64) | pgi → / → yjbE | glucose‑6‑phosphate isomerase/uncharacterized protein YjbE |
| RA | 4,258,235 | T→C | V165A (GTA→GCA) | dinF → | DNA damage‑inducible protein F |
| RA | 4,264,913 | A→G | P200P (CCA→CCG) | dnaB → | replicative DNA helicase |
| RA | 4,271,898 | G→A | A658A (GCC→GCT) | uvrA ← | excision nuclease subunit A |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,300,614 | C→T | G139G (GGG→GGA) | mdtP ← | putative multidrug efflux pump outer membrane channel |
| RA | 4,357,799 | A→G | G273G (GGT→GGC) | cadA ← | lysine decarboxylase 1 |
| RA | 4,406,165 | (T)6→5 | intergenic (+180/‑25) | purA → / → nsrR | adenylosuccinate synthetase/DNA‑binding transcriptional repressor NsrR |
| RA | 4,413,140 | A→G | Y38C (TAC→TGC) | yjfC → | putative acid‑‑amine ligase YjfC |
| RA | 4,435,385 | T→A | D394V (GAT→GTT) | cpdB ← | 2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase |
| RA | 4,442,353 | +G | intergenic (‑177/‑29) | msrA ← / → tamA | methionine sulfoxide reductase A/translocation and assembly module subunit TamA |
| RA | 4,443,061 | A→G | N227S (AAC→AGC) | tamA → | translocation and assembly module subunit TamA |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,534,210 | T→C | intergenic (‑157/+220) | topAI ← / ← yjhZ | KpLE2 phage‑like element; toxin of the TopAI‑YjhQ toxin‑antitoxin system, TopA inhibitor/KpLE2 phage‑like element; putative acetyltransferase YjhZ |
| RA | 4,534,223 | A→G | intergenic (‑170/+207) | topAI ← / ← yjhZ | KpLE2 phage‑like element; toxin of the TopAI‑YjhQ toxin‑antitoxin system, TopA inhibitor/KpLE2 phage‑like element; putative acetyltransferase YjhZ |
| RA | 4,545,573 | A→T | I160F (ATC→TTC) | fimD → | type I fimbriae usher protein |
| RA | 4,556,769 | (T)9→10 | coding (116/144 nt) | ytiD → | protein YtiD |
| RA | 4,556,939 | T→C | G9G (GGT→GGC) | idlP → | iraD leader peptide |
| RA | 4,606,215 | (G)8→9 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 580696 | 581288–581123 | 428–593 | 45 [41] | [41] 42 | [nohD] | [nohD] |
| * | * | ÷ | NC_000913 | 3423770–3424234 | 3424526–3424238 | 5–757 | 43 [34] | [37] 42 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 64 (0.450) | 106 (0.840) | 60/244 | 0.5 | 64.1% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 62 (0.490) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 64 (0.450) | 77 (0.610) | 52/244 | 0.8 | 56.5% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 62 (0.490) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 151 (1.090) | 72/268 | 0.3 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3363001 = | 239 (1.670) | 246 (1.740) | 94/274 | 0.1 | 67.0% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 5 (0.040) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 203 (1.420) | 90/276 | 0.1 | 97.1% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 6 (0.040) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 4101721 | 18 (0.130) | 39 (0.290) +GGGGGG |
28/250 | 2.8 | 68.8% | coding (32/984 nt) | kdgT | 2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| ? | NC_000913 | 4101722 = | 18 (0.130) | coding (33/984 nt) | kdgT | 2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter | |||||