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 | 6,809 | T→G | K384T (AAA→ACA) | yaaJ ← | putative transporter |
| RA | 25,474 | T→G | S90A (TCG→GCG) | lspA → | prolipoprotein signal peptidase (signal peptidase II) |
| RA | 76,539 | T→G | E254A (GAA→GCA) | sgrR ← | transcriptional DNA‑binding transcriptional activator of sgrS sRNA |
| RA | 95,418 | T→G | S257A (TCG→GCG) | murF → | UDP‑N‑acetylmuramoyl‑tripeptide:D‑alanyl‑D‑ alanine ligase |
| JC JC | 111,051 | IS1 (–) +9 bp | coding (8‑16/390 nt) | mutT → | dGTP‑preferring nucleoside triphosphate pyrophosphohydrolase |
| RA | 142,754 | A→C | intergenic (‑84/‑25) | can ← / → yadG | carbonic anhydrase/putative ABC transporter ATPase |
| RA | 143,263 | A→C | E162A (GAA→GCA) | yadG → | putative ABC transporter ATPase |
| RA | 162,349 | A→C | Y82S (TAC→TCC) | hrpB → | putative ATP‑dependent helicase |
| RA | 246,246 | A→C | I86S (ATT→AGT) | dinJ ← | antitoxin of YafQ‑DinJ toxin‑antitoxin system |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 299,214 | A→C | F574C (TTC→TGC) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| RA | 301,463 | T→G | E142A (GAA→GCA) | paoB ← | PaoABC aldehyde oxidoreductase, FAD‑containing subunit |
| RA | 313,275 | T→G | intergenic (‑33/+441) | ykgR ← / ← ykgP | uncharacterized protein/pseudogene, oxidoreductase family |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| RA | 385,074 | T→G | intergenic (‑458/‑158) | yaiS ← / → tauA | putative PIG‑L family deacetylase/taurine ABC transporter periplasmic binding protein |
| RA | 394,041 | T→G | pseudogene (1072/1449 nt) | yaiT → | pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein |
| RA | 400,871 | T→G | E18A (GAA→GCA) | ddlA ← | D‑alanine‑D‑alanine ligase A |
| RA | 467,350 | A→C | intergenic (‑38/‑62) | ybaE ← / → cof | putative ABC transporter periplasmic binding protein/thiamine pyrimidine pyrophosphate hydrolase; HMP‑PP phosphatase |
| RA | 467,975 | T→G | N188K (AAT→AAG) | cof → | thiamine pyrimidine pyrophosphate hydrolase; HMP‑PP phosphatase |
| RA | 480,566 | A→C | L48W (TTG→TGG) | tomB ← | Hha toxicity attenuator; conjugation‑related protein |
| RA | 529,043 | A→C | pseudogene (404/491 nt) | ybbD → | pseudogene |
| RA | 533,167 | C→T | P53S (CCG→TCG) | allR → | glyoxylate‑inducible transcriptional repressor of all and gcl operons |
| RA | 546,173 | T→G | E64A (GAA→GCA) | allD ← | ureidoglycolate dehydrogenase |
| RA | 564,046 | T→G | S145S (TCA→TCC) | sfmZ ← | response regulator family protein |
| RA | 576,137 | T→G | pseudogene (689/1040 nt) | nmpC ← | DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage |
| RA | 585,035 | T→C | Y200C (TAC→TGC) | ompT ← | DLP12 prophage; outer membrane protease VII; outer membrane protein 3b |
| RA | 594,105 | A→C | N222K (AAT→AAG) | cusS ← | copper‑sensing histidine kinase in two‑component regulatory system with CusR |
| RA | 611,121 | A→C | S458R (AGT→AGG) | fepA ← | ferrienterobactin outer membrane transporter |
| RA | 615,736 | A→C | E527A (GAA→GCA) | entF → | enterobactin synthase multienzyme complex component, ATP‑dependent |
| RA | 619,006 | A→C | G251G (GGA→GGC) | fepE → | regulator of length of O‑antigen component of lipopolysaccharide chains |
| RA | 623,458 | T→G | L387V (TTG→GTG) | entS → | enterobactin exporter, iron‑regulated |
| RA | 626,842 | A→C | D258A (GAT→GCT) | entE → | 2,3‑dihydroxybenzoate‑AMP ligase component of enterobactin synthase multienzyme complex |
| RA | 658,782 | A→C | pseudogene (558/594 nt) | ybeM → | pseudogene, C‑N hydrolase superfamily homology;putative enzyme; Not classified; putative amidase |
| RA | 711,781 | T→G | N40H (AAC→CAC) | ybfE ← | LexA‑regulated protein, CopB family |
| RA | 741,597 | T→G | A320A (GCA→GCC) | dtpD ← | dipeptide and tripeptide permease D |
| RA | 750,404 | +C | coding (1766/2448 nt) | ybgQ ← | putative outer membrane protein |
| RA | 754,738 | A→C | intergenic (‑270/‑439) | gltA ← / → sdhC | citrate synthase/succinate dehydrogenase, membrane subunit, binds cytochrome b556 |
| RA | 783,757 | A→C | I198L (ATT→CTT) | pnuC → | nicotinamide riboside transporter |
| RA | 813,480 | A→C | intergenic (+533/‑46) | bioD → / → uvrB | dethiobiotin synthetase/exision nuclease of nucleotide excision repair, DNA damage recognition component |
| RA | 825,545 | T→G | V188V (GTA→GTC) | ybhR ← | putative ABC transporter permease |
| RA | 846,198 | A→C | F89C (TTC→TGC) | glnQ ← | glutamine transporter subunit |
| RA | 868,422 | (C)8→7 | coding (903/1872 nt) | gsiA → | glutathione ABC transporter ATPase |
| RA | 880,543 | A→C | intergenic (‑63/‑184) | gstB ← / → dacC | glutathione S‑transferase/D‑alanyl‑D‑alanine carboxypeptidase; penicillin‑binding protein 6a |
| RA | 917,078 | T→G | D202E (GAT→GAG) | ybjD → | putative OLD family ATP‑dependent endonuclease; DUF2813 family protein |
| RA | 921,236 | A→C | K297T (AAA→ACA) | macB → | macrolide ABC transporter peremase/ATPase |
| RA | 930,957 | A→C | N2K (AAT→AAG) | cydD ← | glutathione/cysteine ABC transporter export permease/ATPase |
| RA | 955,795 | A→C | F280V (TTT→GTT) | ycaO ← | ribosomal protein S12 methylthiotransferase accessory factor |
| RA | 960,657 | C→T | L132L (CTG→TTG) | ycaL → | putative peptidase‑related chaperone |
| RA | 979,391 | T→G | A1022A (GCT→GCG) | mukB → | chromosome condensin MukBEF, ATPase and DNA‑binding subunit |
| RA | 988,789 | A→C | L66R (CTG→CGG) | asnS ← | asparaginyl tRNA synthetase |
| RA | 1,035,960 | T→G | L64R (CTC→CGC) | hyaD → | hydrogenase 1 maturation protease |
| RA | 1,048,134 | A→C | N186K (AAT→AAG) | gfcC ← | putative O‑antigen capsule production periplasmic protein |
| RA | 1,064,004 | T→G | intergenic (‑229/‑32) | cbpA ← / → yccE | DnaK co‑chaperone; curved DNA‑binding protein/uncharacterized protein |
| RA | 1,068,370 | T→G | intergenic (+116/+141) | ymdF → / ← rutG | KGG family protein/pyrimidine permease |
| RA | 1,078,882 | T→G | M1M (ATG→CTG) † | putA ← | fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase |
| RA | 1,083,693 | A→C | A106A (GCA→GCC) | efeB → | deferrrochelatase, periplasmic |
| RA | 1,130,388 | G→A | A159V (GCA→GTA) | flgA ← | assembly protein for flagellar basal‑body periplasmic P ring |
| RA | 1,134,118 | A→C | Q106P (CAG→CCG) | flgF → | flagellar component of cell‑proximal portion of basal‑body rod |
| RA | 1,139,916 | T→G | D513E (GAT→GAG) | flgK → | flagellar hook‑filament junction protein 1 |
| RA | 1,183,048 | T→G | L191F (TTA→TTC) | potC ← | spermidine/putrescine ABC transporter permease |
| RA | 1,192,931 | C→T | R281R (CGG→CGA) | mnmA ← | tRNA(Gln,Lys,Glu) U34 2‑thiouridylase |
| RA | 1,216,638 | T→G | intergenic (+3/‑110) | ariR → / → ymgC | RcsB connector protein for regulation of biofilm and acid‑resistance/Blue light, low temperature and stress induced protein |
| RA | 1,224,314 | T→G | N78H (AAC→CAC) | minE ← | cell division topological specificity factor |
| RA | 1,244,222 | G→A | T102T (ACC→ACT) | ycgR ← | flagellar velocity braking protein, c‑di‑GMP‑regulated |
| RA | 1,250,644 | A→C | G65G (GGT→GGG) | dhaK ← | dihydroxyacetone kinase, PTS‑dependent, dihydroxyacetone‑binding subunit |
| RA | 1,290,933 | T→G | L231R (CTT→CGT) | rssB → | PcnB‑degradosome interaction factor; response regulator |
| RA | 1,343,516 | A→C | intergenic (‑188/+81) | osmB ← / ← yciT | osmotically and stress inducible lipoprotein/global regulator of transcription; DeoR family |
| RA | 1,438,947 | T→G | E613A (GAA→GCA) | pfo ← | pyruvate‑flavodoxin oxidoreductase |
| RA | 1,467,477 | A→C | pseudogene (2086/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,479,936 | A→C | N267H (AAC→CAC) | ynbC → | putative esterase |
| RA | 1,539,359 | G→T | P1078T (CCA→ACA) | narZ ← | nitrate reductase 2 (NRZ), alpha subunit |
| RA | 1,552,310 | T→G | intergenic (+319/+88) | fdnI → / ← yddM | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator |
| RA | 1,571,816 | T→G | D77A (GAT→GCT) | gadB ← | glutamate decarboxylase B, PLP‑dependent |
| RA | 1,597,313 | (C)7→8 | pseudogene (675/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,597,634 | A→C | pseudogene (354/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,598,136 | A→C | intergenic (‑149/+481) | yneO ← / ← lsrK | pseudogene, AidA homolog/autoinducer‑2 (AI‑2) kinase |
| RA | 1,605,170 | A→C | G40G (GGA→GGC) | lsrB → | autoinducer 2‑binding protein |
| RA | 1,668,951 | T→G | R214R (CGA→CGC) | ynfL ← | LysR family putative transcriptional regulator |
| RA | 1,669,235 | A→C | Y120D (TAT→GAT) | ynfL ← | LysR family putative transcriptional regulator |
| RA | 1,670,038 | T→G | C114G (TGT→GGT) | ynfM → | putative arabinose efflux transporter |
| RA | 1,673,237 | T→G | I89L (ATT→CTT) | mdtJ ← | multidrug efflux system transporter |
| RA | 1,681,460 | T→G | M162R (ATG→AGG) | folM → | dihydromonapterin reductase, NADPH‑dependent; dihydrofolate reductase isozyme |
| RA | 1,714,643 | T→G | I89M (ATT→ATG) | gstA → | glutathionine S‑transferase |
| RA | 1,738,006 | A→C | K55Q (AAG→CAG) | purR → | transcriptional repressor, hypoxanthine‑binding |
| RA | 1,738,276 | A→C | M145L (ATG→CTG) | purR → | transcriptional repressor, hypoxanthine‑binding |
| RA | 1,741,263 | A→C | intergenic (+141/‑150) | ydhC → / → cfa | putative arabinose efflux transporter/cyclopropane fatty acyl phospholipid synthase, SAM‑dependent |
| RA | 1,756,929 | T→G | L411R (CTG→CGG) | pykF → | pyruvate kinase I |
| RA | 1,775,251 | T→G | L189R (CTG→CGG) | aroD → | 3‑dehydroquinate dehydratase |
| RA | 1,792,490 | T→G | E81A (GAA→GCA) | nlpC ← | putative C40 clan peptidase lipoprotein |
| RA | 1,800,753 | A→C | V606V (GTT→GTG) | thrS ← | threonyl‑tRNA synthetase |
| RA | 1,815,451 | T→G | F529V (TTT→GTT) | katE → | catalase HPII, heme d‑containing |
| RA | 1,822,043 | T→G | I72L (ATC→CTC) | osmE ← | osmotically‑inducible lipoprotein |
| RA | 1,830,953 | T→G | N344H (AAT→CAT) | astC ← | succinylornithine transaminase, PLP‑dependent |
| RA | 1,849,711 | A→C | E292A (GAA→GCA) | sppA → | protease IV (signal peptide peptidase) |
| RA | 1,871,066 | T→G | Y228D (TAC→GAC) | yeaI → | putative membrane‑anchored diguanylate cyclase |
| RA | 1,896,050 | A→C | N416H (AAC→CAC) | pabB → | aminodeoxychorismate synthase, subunit I |
| RA | 1,906,661 | A→C | F134V (TTT→GTT) | rlmA ← | 23S rRNA m(1)G745 methyltransferase, SAM‑dependent |
| RA | 1,921,059 | T→G | P279P (CCT→CCG) | rsmF → | 16S rRNA m(5)C1407 methyltransferase, SAM‑dependent |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,008,526 | A→C | I84L (ATC→CTC) | yedE → | UPF0394 family sulphur transport domain‑containing inner membrane protein |
| RA | 2,036,444 | T→G | Y204D (TAT→GAT) | hchA → | glyoxalase III and Hsp31 molecular chaperone |
| RA | 2,056,867 | A→C | K4Q (AAA→CAA) | yeeN → | UPF0082 family protein |
| RA | 2,075,512 | T→G | L245R (CTG→CGG) | yeeR → | CP4‑44 prophage; putative membrane protein |
| RA | 2,114,029 | A→G | M100T (ATG→ACG) | wcaN ← | putative regulatory subunit for GalU |
| RA | 2,125,822 | A→C | L134R (CTG→CGG) | wcaH ← | GDP‑mannose mannosyl hydrolase |
| RA | 2,127,751 | T→G | E188D (GAA→GAC) | gmd ← | GDP‑D‑mannose dehydratase, NAD(P)‑binding |
| RA | 2,142,253 | A→C | intergenic (‑38/+54) | dcd ← / ← udk | deoxycytidine triphosphate deaminase; dCTP deaminase/uridine/cytidine kinase |
| RA | 2,151,093 | T→G | intergenic (‑108/‑92) | yegI ← / → yegJ | protein kinase‑related putative non‑specific DNA‑binding protein/uncharacterized protein |
| RA | 2,155,954 | G→A | G231D (GGC→GAC) | mdtB → | multidrug efflux system, subunit 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 | 2,185,875 | (G)7→8 | intergenic (‑79/‑42) | rcnR ← / → rcnA | transcriptional repressor of rcnA/membrane protein conferring nickel and cobalt resistance |
| RA | 2,221,860 | T→G | K44Q (AAA→CAA) | bglX ← | beta‑D‑glucoside glucohydrolase, periplasmic |
| RA | 2,234,442 | T→G | L137W (TTG→TGG) | preT → | dihydropyrimidine dehydrogenase, NADH‑dependent, subunit N |
| RA | 2,281,112 | A→C | I161L (ATC→CTC) | yejH → | putative ATP‑dependent DNA or RNA helicase |
| RA | 2,288,561 | (C)7→8 | pseudogene (354/2525 nt) | yejO ← | pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system |
| RA | 2,288,707 | T→G | pseudogene (208/2525 nt) | yejO ← | pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system |
| RA | 2,292,894 | A→C | L24R (CTG→CGG) | dsbE ← | periplasmic thioredoxin of cytochrome c‑type biogenesis |
| RA | 2,298,174 | A→C | L29R (CTG→CGG) | napC ← | quinol dehydrogenase, electron source for NapAB |
| RA | 2,307,348 | T→G | Q423P (CAA→CCA) | yojI ← | microcin J25 efflux ABC transporter permease/ATPase |
| RA | 2,318,639 | A→C | F413C (TTT→TGT) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,323,353 | T→G | intergenic (+102/‑94) | atoC → / → atoD | fused response regulator of ato operon, in two‑component system with AtoS: response regulator/sigma54 interaction protein/acetyl‑CoA:acetoacetyl‑CoA transferase, alpha subunit |
| RA | 2,361,316 | Δ1 bp | coding (99/1206 nt) | rhmD ← | L‑rhamnonate dehydratase |
| RA | 2,387,305 | G→A | P124P (CCG→CCA) | yfbM → | DUF1877 family protein |
| RA | 2,391,940 | T→C | T368A (ACC→GCC) | nuoM ← | NADH:ubiquinone oxidoreductase, membrane subunit M |
| RA | 2,393,051 | T→G | intergenic (‑10/+154) | nuoM ← / ← nuoL | NADH:ubiquinone oxidoreductase, membrane subunit M/NADH:ubiquinone oxidoreductase, membrane subunit L |
| RA | 2,406,402 | T→G | K80N (AAA→AAC) | lrhA ← | transcriptional repressor of flagellar, motility and chemotaxis genes |
| RA | 2,411,354 | A→C | intergenic (‑2/+85) | yfbS ← / ← yfbT | putative transporter/sugar phosphatas |
| RA | 2,420,409 | A→C | L26W (TTG→TGG) | yfcF ← | glutathione S‑transferase |
| RA | 2,462,889 | (C)9→8 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane transporter/uncharacterized protein |
| RA | 2,488,822 | A→C | L116R (CTT→CGT) | yfdE ← | acetyl‑CoA:oxalate CoA‑transferase |
| RA | 2,518,687 | A→C | E74A (GAA→GCA) | yfeC → | DUF1323 family putative DNA‑binding protein |
| RA | 2,574,749 | A→C | F85L (TTT→TTG) | eutQ ← | RmlC‑like cupin domain protein |
| RA | 2,575,120 | T→G | K113T (AAG→ACG) | eutP ← | putative P‑loop NTPase ethanolamine utilization protein |
| RA | 2,602,017 | (C)7→8 | coding (200/2019 nt) | hyfB → | hydrogenase 4, membrane subunit |
| RA | 2,612,663 | T→G | L255* (TTA→TGA) | hyfR → | hydrogenase‑4 transcriptional activator |
| RA | 2,620,311 | T→G | N188H (AAC→CAC) | upp ← | uracil phosphoribosyltransferase |
| RA | 2,635,996 | C→T | R454H (CGT→CAT) | der ← | GTPase; multicopy suppressor of ftsJ |
| RA | 2,698,512 | T→C | L13L (TTA→TTG) | pgpC ← | phosphatidylglycerophosphatase C, membrane bound |
| RA | 2,717,422 | A→C | V223V (GTA→GTC) | ung → | uracil‑DNA‑glycosylase |
| RA | 2,722,319 | A→C | Q789H (CAA→CAC) | pka → | protein lysine acetyltransferase |
| RA | 2,769,648 | (C)6→7 | intergenic (+162/‑55) | yfjQ → / → yfjR | CP4‑57 prophage; uncharacterized protein/CP4‑57 prophage; putative DNA‑binding transcriptional regulator |
| RA | 2,788,675 | A→C | intergenic (+26/‑310) | ygaQ → / → csiD | uncharacterized protein; putative enzyme/carbon starvation protein |
| RA | 2,869,491 | A→C | L10R (CTG→CGG) | pcm ← | L‑isoaspartate protein carboxylmethyltransferase type II |
| RA | 2,899,375 | A→C | I15S (ATT→AGT) | ygcU ← | putative FAD‑linked oxidoreductase |
| RA | 2,904,306 | T→G | intergenic (+932/+441) | ygcE → / ← queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| RA | 2,906,363 | T→G | L218* (TTA→TGA) | ygcG → | TPM domain protein, putative phosphatase |
| RA | 2,934,721 | T→G | S163A (TCG→GCG) | fucP → | L‑fucose transporter |
| RA | 2,968,180 | T→G | I85I (ATA→ATC) | ptsP ← | PEP‑protein phosphotransferase enzyme I; GAF domain containing protein |
| RA | 2,969,899 | A→C | T80P (ACT→CCT) | mutH → | methyl‑directed mismatch repair protein |
| RA | 2,999,680 | (G)7→8 | coding (212/756 nt) | ygeR ← | LysM domain‑containing M23 family putative peptidase; septation lipoprotein |
| RA | 3,009,624 | A→C | K287N (AAA→AAC) | ygeY → | putative peptidase |
| RA | 3,014,506 | T→G | Q184H (CAA→CAC) | yqeC ← | putative selenium‑dependent hydroxylase accessory protein |
| RA | 3,040,512 | A→C | G104G (GGT→GGG) | cptA ← | toxin of CptAB toxin‑antitoxin pair |
| RA | 3,044,628 | A→C | K323Q (AAG→CAG) | bglA → | 6‑phospho‑beta‑glucosidase A |
| RA | 3,082,025 | A→C | Y38S (TAC→TCC) | loiP → | Phe‑Phe periplasmic metalloprotease, OM lipoprotein; low salt‑inducible; Era‑binding heat shock protein |
| RA | 3,086,195 | A→C | I3I (ATA→ATC) | yqgC → | uncharacterized protein |
| RA | 3,089,170 | T→G | V296G (GTC→GGC) | galP → | D‑galactose transporter |
| RA | 3,101,594 | T→G | A10A (GCA→GCC) | yggN ← | DUF2884 family putative periplasmic protein |
| RA | 3,174,035 | T→G | E454D (GAA→GAC) | parE ← | DNA topoisomerase IV, subunit B |
| RA | 3,174,612 | A→C | L262R (CTG→CGG) | parE ← | DNA topoisomerase IV, subunit B |
| RA | 3,182,529 | A→C | intergenic (‑122/‑21) | ygiD ← / → zupT | 4,5‑ DOPA‑extradiol‑dioxygenase/zinc transporter |
| RA | 3,197,496 | T→G | T716P (ACT→CCT) | glnE ← | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| RA | 3,198,644 | A→C | F333C (TTC→TGC) | glnE ← | fused deadenylyltransferase/adenylyltransferase for glutamine synthetase |
| RA | 3,224,462 | T→G | T610T (ACT→ACG) | ebgA → | evolved beta‑D‑galactosidase, alpha subunit |
| RA | 3,231,189 | A→C | S768R (AGT→CGT) | ygjK → | alpha‑glucosidase |
| RA | 3,237,742 | A→C | K144N (AAA→AAC) | ygjR → | putative NAD(P)‑dependent dehydrogenase |
| RA | 3,240,984 | (G)7→8 | coding (1041/1245 nt) | sstT → | sodium:serine/threonine symporter |
| RA | 3,271,880 | T→G | E291A (GAA→GCA) | garR ← | tartronate semialdehyde reductase |
| RA | 3,276,692 | A→C | N471H (AAT→CAT) | garD → | D‑galactarate dehydrogenase |
| RA | 3,290,794 | A→C | I661L (ATC→CTC) | yraJ → | putative outer membrane protein |
| RA | 3,397,618 | T→G | I60L (ATT→CTT) | rng ← | ribonuclease G |
| RA | 3,399,779 | A→C | L67R (CTG→CGG) | mreC ← | cell wall structural complex MreBCD transmembrane component MreC |
| RA | 3,414,497 | T→G | Y212D (TAC→GAC) | acrE → | cytoplasmic membrane lipoprotein |
| RA | 3,437,278 | A→C | D254A (GAT→GCT) | trkA → | NAD‑binding component of TrK potassium transporter |
| RA | 3,438,864 | T→G | R89S (AGA→AGC) | zntR ← | zntA gene transcriptional activator |
| RA | 3,468,138 | T→G | G572G (GGA→GGC) | chiA ← | periplasmic endochitinase |
| RA | 3,473,612 | A→C | L157* (TTA→TGA) | rpsG ← | 30S ribosomal subunit protein S7 |
| RA | 3,479,233 | A→C | S459A (TCT→GCT) | kefB ← | potassium:proton antiporter |
| RA | 3,515,115 | A→C | L267V (TTG→GTG) | dam ← | DNA adenine methyltransferase |
| RA | 3,520,438 | A→C | L89R (CTC→CGC) | hofQ ← | DNA catabolic putative fimbrial transporter |
| 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 | 3,568,664 | T→G | Y222S (TAT→TCT) | glgC ← | glucose‑1‑phosphate adenylyltransferase |
| RA | 3,577,196 | T→G | M133L (ATG→CTG) | gntK ← | gluconate kinase 2 |
| RA | 3,602,989 | T→G | I419L (ATT→CTT) | ftsY ← | Signal Recognition Particle (SRP) receptor |
| RA | 3,623,709 | T→G | I104S (ATT→AGT) | yhhH → | putative NTF2 fold immunity protein for polymorphic toxin RhsB |
| RA | 3,655,917 | (A)5→4 | intergenic (‑15/+49) | yhiD ← / ← hdeB | putative Mg(2+) transport ATPase, inner membrane protein/acid‑resistance protein |
| RA | 3,679,181 | T→G | R3R (AGG→CGG) | yhjH ← | cyclic‑di‑GMP phosphodiesterase, FlhDC‑regulated |
| RA | 3,689,996 | A→C | L89* (TTA→TGA) | bcsZ ← | endo‑1,4‑D‑glucanase |
| RA | 3,697,854 | A→C | Q466P (CAA→CCA) | bcsE → | cellulose production protein |
| RA | 3,716,242 | A→C | V51V (GTT→GTG) | bisC ← | biotin sulfoxide reductase |
| RA | 3,725,176 | T→G | E48A (GAG→GCG) | glyQ ← | glycine tRNA synthetase, alpha subunit |
| RA | 3,749,326 | A→C | D32A (GAT→GCT) | sgbU → | putative L‑xylulose 5‑phosphate 3‑epimerase |
| RA | 3,752,058 | A→C | I23L (ATC→CTC) | yiaU → | putative DNA‑binding transcriptional regulator |
| RA | 3,790,919 | A→C | L143V (TTA→GTA) | tdh ← | L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| RA | 3,791,137 | A→G | V70A (GTA→GCA) | tdh ← | L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| RA | 3,807,410 | T→G | K230T (AAA→ACA) | waaQ ← | lipopolysaccharide core biosynthesis protein |
| JC | 3,815,859 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
| RA | 3,823,774 | A→C | N459H (AAC→CAC) | spoT → | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 3,841,270 | A→C | L157R (CTG→CGG) | nepI ← | putative transporter |
| RA | 3,966,875 | T→G | S153S (TCT→TCG) | rho → | transcription termination factor |
| RA | 3,972,452 | A→C | Q398P (CAG→CCG) | wecC → | UDP‑N‑acetyl‑D‑mannosaminuronic acid dehydrogenase |
| RA | 4,008,222 | A→C | I156L (ATC→CTC) | rhtC → | threonine efflux pump |
| RA | 4,012,707 | A→C | F37C (TTT→TGT) | metR ← | methionine biosynthesis regulon transcriptional regulator |
| RA | 4,032,068 | A→C | Q303P (CAG→CCG) | pepQ → | proline dipeptidase |
| RA | 4,046,716 | A→C | intergenic (‑114/‑250) | yihG ← / → polA | inner membrane protein, inner membrane acyltransferase/5' to 3' DNA polymerase and 3' to 5'/5' to 3' exonuclease |
| RA | 4,046,941 | A→C | intergenic (‑339/‑25) | yihG ← / → polA | inner membrane protein, inner membrane acyltransferase/5' to 3' DNA polymerase and 3' to 5'/5' to 3' exonuclease |
| RA | 4,061,235 | A→C | Y24S (TAT→TCT) | yihM → | putative sugar phosphate isomerase |
| RA | 4,143,312 | T→G | T261T (ACT→ACG) | frwC → | putative enzyme IIC component of PTS |
| RA | 4,186,531 | T→G | I394M (ATT→ATG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,186,603 | A→C | E418D (GAA→GAC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,190,100 | T→G | I105M (ATT→ATG) | yjaZ → | stationary phase growth adaptation protein |
| RA | 4,215,122 | T→G | G281G (GGT→GGG) | metA → | homoserine O‑transsuccinylase |
| RA | 4,221,645 | T→G | E281D (GAA→GAC) | arpA ← | ankyrin repeat protein |
| RA | 4,269,654 | T→G | F81V (TTC→GTC) | aphA → | acid phosphatase/phosphotransferase, class B, non‑specific |
| RA | 4,280,134 | T→G | F52C (TTT→TGT) | yjcE → | putative cation/proton antiporter |
| RA | 4,285,713 | A→C | N553K (AAT→AAG) | acs ← | acetyl‑CoA synthetase |
| RA | 4,291,339 | T→G | I288M (ATT→ATG) | nrfD → | formate‑dependent nitrite reductase, membrane subunit |
| RA | 4,291,923 | A→C | I138L (ATC→CTC) | nrfE → | heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfE |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,313,090 | T→G | intergenic (‑99/‑260) | alsR ← / → rpiB | d‑allose‑inducible als operon transcriptional repressor; autorepressor; repressor of rpiR/ribose 5‑phosphate isomerase B/allose 6‑phosphate isomerase |
| RA | 4,358,695 | A→C | intergenic (‑78/+2) | cadA ← / ← cadB | lysine decarboxylase, acid‑inducible/putative lysine/cadaverine transporter |
| RA | 4,362,301 | T→G | pseudogene (53/84 nt) | yjdQ ← | pseudogene, P4‑like integrase remnant |
| RA | 4,403,148 | A→C | N371H (AAC→CAC) | hflK → | modulator for HflB protease specific for phage lambda cII repressor |
| RA | 4,413,167 | A→C | E47A (GAG→GCG) | yjfC → | ATP‑Grasp family ATPase |
| RA | 4,474,971 | A→G | H37R (CAC→CGC) | tabA → | biofilm modulator regulated by toxins; DUF386 family protein, cupin superfamily protein |
| RA | 4,475,797 | A→C | I121L (ATT→CTT) | yjgL → | SopA‑central‑domain‑like hexapeptide repeat protein |
| RA | 4,485,560 | T→G | E131A (GAG→GCG) | pepA ← | multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor |
| RA | 4,517,027 | C→T | A231T (GCA→ACA) | fecR ← | anti‑sigma transmembrane signal transducer for ferric citrate transport; periplasmic FecA‑bound ferric citrate sensor and cytoplasmic FecI ECF sigma factor activator |
| RA | 4,522,275 | T→G | H607P (CAT→CCT) | yjhG ← | putative dehydratase |
| RA | 4,534,711 | T→G | intergenic (‑36/‑80) | yjhZ ← / → yjhR | pseudogene, rimK paralog, C‑terminal fragment/pseudogene, helicase family; putative frameshift suppressor |
| RA | 4,542,142 | T→G | Y36D (TAT→GAT) | fimE → | tyrosine recombinase/inversion of on/off regulator of fimA |
| RA | 4,548,617 | A→C | L111L (CTA→CTC) | fimG → | minor component of type 1 fimbriae |
| RA | 4,576,712 | T→G | pseudogene (2794/2937 nt) | yjiV → | pseudogene; conserved hypothetical protein |
| RA | 4,595,235 | A→C | F206C (TTT→TGT) | lgoR ← | putative transcriptional activator for L‑galactonate catabolism |
| RA | 4,599,353 | G→A | A30V (GCC→GTC) | opgB ← | OPG periplasmic biosynthetic phosphoglycerol transferases I (membrane‑bound) and II (soluble) |
| RA | 4,613,561 | C→T | R27R (CGC→CGT) | yjjV → | putative DNase |
| RA | 4,624,394 | A→C | I132M (ATT→ATG) | ytjB ← | SMP_2 family putative membrane‑anchored periplasmic protein |
| RA | 4,628,114 | A→C | Y267S (TAT→TCT) | nadR → | trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423692–3424234 | 3424617–3424238 | 5–926 | 133 [132] | [132] 134 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 27 (0.120) | 138 (0.750) | 87/166 | 0.8 | 85.3% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 25 (0.140) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 25 (0.110) | 136 (0.740) | 80/166 | 1.3 | 85.5% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 25 (0.140) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 224 (1.060) | 118/190 | 0.1 | 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 | |||||