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 | 14,991 | C→T | A275V (GCG→GTG) | dnaJ → | chaperone Hsp40, DnaK co‑chaperone |
| RA | 39,967 | A→G | Y140Y (TAT→TAC) | caiA ← | crotonobetaine reductase subunit II, FAD‑binding |
| RA | 44,792 | A→G | N205D (AAT→GAT) | fixC → | putative oxidoreductase |
| RA | 134,458 | T→C | V24A (GTC→GCC) | yacL → | UPF0231 family protein |
| RA | 143,271 | G→A | A165T (GCA→ACA) | yadG → | putative ABC transporter ATPase |
| RA | 232,838 | C→T | G373E (GGA→GAA) | mltD ← | putative membrane‑bound lytic murein transglycosylase D |
| RA | 249,034 | G→A | pseudogene (1037/1713 nt) | lfhA ← | pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 283,790 | A→G | D197G (GAC→GGC) | yagF → | CP4‑6 prophage; dehydratase family protein |
| RA | 284,450 | A→G | E417G (GAG→GGG) | yagF → | CP4‑6 prophage; dehydratase family protein |
| RA | 285,648 | C→G | A85G (GCC→GGC) | yagG → | CP4‑6 prophage; putative sugar transporter |
| JC | 308,054 | (C)7→10 | coding (1279/2526 nt) | ecpC ← | ECP production outer membrane protein |
| MC JC | 381,211 | Δ1,383 bp | [yaiX]–[yaiX] | [yaiX], insC1, insD1, [yaiX] | |
| RA | 474,975 | A→G | Y63H (TAC→CAC) | tesB ← | acyl‑CoA thioesterase 2 |
| RA | 483,535 | C→T | G290E (GGG→GAG) | acrB ← | multidrug efflux system protein |
| RA | 484,337 | (C)6→7 | coding (67/3150 nt) | acrB ← | multidrug efflux system protein |
| RA | 545,039 | A→G | V85A (GTG→GCG) | allC ← | allantoate amidohydrolase |
| JC JC | 572,172 | IS2 (–) +5 bp | coding (719‑723/798 nt) | ybcM → | DLP12 prophage; putative DNA‑binding transcriptional regulator |
| RA | 581,913 | (A)6→7 | pseudogene (254/438 nt) | tfaD → | pseudogene, DLP12 prophage; tail fiber assembly protein family;Phage or Prophage Related |
| RA | 590,771 | C→T | D62N (GAC→AAC) | nfrA ← | bacteriophage N4 receptor, outer membrane subunit |
| RA | 657,377 | T→C | V29A (GTG→GCG) | cspE → | constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein |
| RA | 667,534 | T→C | E228E (GAA→GAG) | mrdA ← | penicillin‑binding protein 2, transpeptidase involved in peptidoglycan synthesis |
| RA | 699,916 | A→G | G137G (GGT→GGC) | umpH ← | UMP phosphatase |
| RA | 702,597 | (G)5→6 | coding (155/1149 nt) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 736,382 | T→C | intergenic (+163/‑63) | ybfC → / → ybfQ | putative secreted protein/pseudogene, H repeat‑associated protein |
| RA | 738,795 | C→T | T235I (ACC→ATC) | ybfD → | H repeat‑associated putative transposase |
| RA | 738,829 | G→A | E246E (GAG→GAA) | ybfD → | H repeat‑associated putative transposase |
| RA | 758,260 | A→G | D191G (GAC→GGC) | sdhB → | succinate dehydrogenase, FeS subunit |
| RA | 773,267 | C→T | P76S (CCG→TCG) | cydB → | cytochrome d terminal oxidase, subunit II |
| RA | 798,120 | A→G | G104G (GGT→GGC) | ybhA ← | pyridoxal phosphate (PLP) phosphatase |
| RA | 817,261 | A→G | E73G (GAG→GGG) | moaA → | molybdopterin biosynthesis protein A |
| RA | 838,311 | +G | coding (146/267 nt) | ybiI ← | DksA‑type zinc finger protein |
| RA | 841,490 | C→T | S14S (TCG→TCA) | fiu ← | catecholate siderophore receptor |
| RA | 845,744 | A→G | S240S (TCT→TCC) | glnQ ← | glutamine transporter subunit |
| RA | 858,789 | T→C | K91K (AAA→AAG) | ybiU ← | DUF1479 family protein |
| RA | 867,112 | C→G | A182G (GCC→GGC) | iaaA → | Isoaspartyl peptidase |
| RA | 892,409 | +G | coding (443/903 nt) | rimK → | ribosomal protein S6 modification protein |
| RA | 932,884 | T→C | V97A (GTA→GCA) | lrp → | leucine‑responsive global transcriptional regulator |
| RA | 942,738 | C→T | R594W (CGG→TGG) | dmsA → | dimethyl sulfoxide reductase, anaerobic, subunit A |
| RA | 958,916 | A→G | A35A (GCA→GCG) | aroA → | 5‑enolpyruvylshikimate‑3‑phosphate synthetase |
| RA | 997,179 | C→T | A112T (GCC→ACC) | ssuE ← | NAD(P)H‑dependent FMN reductase |
| RA | 1,013,706 | T→C | L150L (TTG→CTG) | pqiB → | paraquat‑inducible, SoxRS‑regulated MCE domain protein |
| RA | 1,013,807 | A→G | V183V (GTA→GTG) | pqiB → | paraquat‑inducible, SoxRS‑regulated MCE domain protein |
| RA | 1,022,584 | T→C | T434A (ACG→GCG) | yccS ← | putative transporter, FUSC superfamily inner membrane protein |
| RA | 1,053,037 | A→G | V109A (GTC→GCC) | yccM ← | putative 4Fe‑4S membrane protein |
| RA | 1,088,769 | C→T | G363G (GGG→GGA) | pgaB ← | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein |
| RA | 1,124,108 | (G)6→7 | intergenic (‑54/+10) | grxB ← / ← mdtH | glutaredoxin 2 (Grx2)/multidrug resistance efflux transporter conferring overexpression resistance to norfloxacin and enoxacin |
| RA | 1,132,321 | C→T | T156T (ACC→ACT) | flgD → | flagellar hook assembly protein |
| RA | 1,163,578 | G→A | A107T (GCA→ACA) | thiK → | thiamine kinase |
| RA | 1,172,139 | A→G | I609T (ATT→ACT) | mfd ← | transcription‑repair coupling factor |
| RA | 1,203,537 | C→T | D90D (GAC→GAT) | ymfL → | e14 prophage; putative DNA‑binding transcriptional regulator |
| RA | 1,214,838 | T→C | E213G (GAA→GGA) | bluF ← | anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; inactive c‑di‑GMP phosphodiesterase‑like EAL domain protein |
| RA | 1,225,326 | C→T | G12G (GGG→GGA) | minD ← | inhibitor of FtsZ ring polymerization; chromosome‑membrane tethering protein; membrane ATPase of the MinCDEE system |
| RA | 1,270,311 | T→C | H12R (CAC→CGC) | ldrC ← | toxic polypeptide, small |
| RA | 1,281,664 | C→T | R601C (CGT→TGT) | narG → | nitrate reductase 1, alpha subunit |
| RA | 1,290,753 | G→A | C171Y (TGC→TAC) | rssB → | PcnB‑degradosome interaction factor; response regulator |
| RA | 1,307,516 | A→G | V377A (GTC→GCC) | clsA ← | cardiolipin synthase 1 |
| RA | 1,308,099 | C→T | G183R (GGG→AGG) | clsA ← | cardiolipin synthase 1 |
| RA | 1,324,641 | A→G | T182A (ACA→GCA) | yciO → | putative RNA binding protein |
| RA | 1,358,190 | A→G | V333A (GTG→GCG) | puuP ← | putrescine importer |
| RA | 1,380,716 | T→A | I190N (ATC→AAC) | ycjU → | beta‑phosphoglucomutase |
| RA | 1,382,785 | A→G | Q280R (CAG→CGG) | ompG → | outer membrane porin G |
| RA | 1,383,697 | C→T | A89T (GCC→ACC) | ycjW ← | LacI family putative transcriptional repressor |
| RA | 1,392,489 | G→A | A167T (GCT→ACT) | pgrR → | murein peptide degradation regulator |
| RA | 1,393,223 | A→G | intergenic (+333/‑4) | pgrR → / → mppA | murein peptide degradation regulator/murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit |
| RA | 1,407,641 | A→G | V52A (GTC→GCC) | ydaM ← | diguanylate cyclase, csgD regulator |
| RA | 1,419,721 | (G)7→6 | intergenic (‑265/+44) | ydaG ← / ← racR | Rac prophage; uncharacterized protein/Rac prophage; putative DNA‑binding transcriptional regulator |
| RA | 1,420,793 | (G)6→7 | coding (110/423 nt) | ydaT → | Rac prophage; uncharacterized protein |
| RA | 1,444,706 | C→T | G552G (GGC→GGT) | ydbH → | putative membrane‑anchored protein, function unknown |
| RA | 1,448,822 | T→C | V435A (GTC→GCC) | feaB → | phenylacetaldehyde dehydrogenase |
| RA | 1,449,092 | A→G | L753P (CTG→CCG) | tynA ← | tyramine oxidase, copper‑requiring |
| RA | 1,570,650 | T→C | T466A (ACC→GCC) | gadB ← | glutamate decarboxylase B, PLP‑dependent |
| RA | 1,580,435 | C→G | G119A (GGC→GCC) | ydeM ← | putative YdeN‑specific sulfatase‑maturating enzyme |
| RA | 1,595,660 | A→G | pseudogene (2328/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,603,562 | T→C | F182L (TTT→CTT) | lsrC → | autoinducer 2 import system permease protein |
| RA | 1,646,854 | C→T | intergenic (+117/+320) | flxA → / ← intK | Qin prophage; uncharacterized protein/pseudogene, integrase fragment, Qin prophage;Phage or Prophage Related |
| RA | 1,691,784 | A→G | S356S (AGT→AGC) | uidC ← | putative outer membrane porin for beta‑glucuronides porin protein |
| RA | 1,717,165 | T→C | T20A (ACG→GCG) | tyrS ← | tyrosyl‑tRNA synthetase |
| MC JC | 1,755,661 | Δ2,703 bp | pykF–[ldtE] | pykF, lpp, [ldtE] | |
| RA | 1,769,222 | C→T | P50L (CCG→CTG) | ydiK → | UPF0118 family inner membrane protein |
| RA | 1,803,248 | T→C | pseudogene (155/426 nt) | arpB → | pseudogene, ankyrin repeats |
| RA | 1,844,948 | T→A | intergenic (‑77/+51) | ynjI ← / ← topB | inner membrane protein/DNA topoisomerase III |
| RA | 1,877,132 | A→G | H75R (CAC→CGC) | yeaO → | DUF488 family protein |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 family protein, nitrate‑inducible |
| RA | 1,915,005 | T→C | H177R (CAC→CGC) | proQ ← | RNA chaperone, putative ProP translation regulator |
| RA | 1,916,069 | T→C | G20G (GGA→GGG) | msrC ← | free methionine‑(R)‑sulfoxide reductase |
| RA | 1,932,865 | T→C | G580G (GGA→GGG) | edd ← | 6‑phosphogluconate dehydratase |
| RA | 1,946,069 | T→C | intergenic (‑93/+46) | ruvA ← / ← yobI | component of RuvABC resolvasome, regulatory subunit/uncharacterized protein |
| RA | 1,955,053 | T→C | H652R (CAC→CGC) | torZ ← | trimethylamine N‑oxide reductase system III, catalytic subunit |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 1,982,132 | G→A | R86C (CGC→TGC) | otsB ← | trehalose‑6‑phosphate phosphatase, biosynthetic |
| RA | 1,994,904 | T→C | E152E (GAA→GAG) | uvrY ← | response regulator in two‑component regulatory system with BarA |
| RA | 2,017,429 | (C)6→7 | coding (876/1374 nt) | fliI → | flagellum‑specific ATP synthase |
| RA | 2,063,976 | T→C | A164A (GCA→GCG) | cobT ← | nicotinate‑nucleotide‑‑dimethylbenzimidazole phosphoribosyltransferase |
| RA | 2,088,373 | G→A | G252G (GGC→GGT) | yeeZ ← | putative epimerase |
| RA | 2,129,612 | G→A | L13L (CTC→CTT) | wcaE ← | putative glycosyl transferase |
| RA | 2,151,290 | T→C | S36P (TCT→CCT) | yegJ → | uncharacterized protein |
| RA | 2,161,380 | T→C | Y999H (TAT→CAT) | mdtC → | multidrug efflux system, subunit C |
| RA | 2,168,009 | T→C | T100A (ACA→GCA) | yegR ← | uncharacterized protein |
| 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 | 2,173,933 | T→C | pseudogene (346/914 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,175,182 | A→G | S380S (AGT→AGC) | gatZ ← | D‑tagatose 1,6‑bisphosphate aldolase 2, subunit |
| RA | 2,223,301 | T→C | F373L (TTC→CTC) | dld → | D‑lactate dehydrogenase, FAD‑binding, NADH independent |
| RA | 2,258,212 | T→C | E52E (GAA→GAG) | psuG ← | pseudouridine 5'‑phosphate glycosidase |
| RA | 2,261,739 | T→C | A209A (GCA→GCG) | fruK ← | fructose‑1‑phosphate kinase |
| RA | 2,269,424 | T→C | W191R (TGG→CGG) | lpxT → | lipid A 1‑diphosphate synthase; undecaprenyl pyrophosphate:lipid A 1‑phosphate phosphotransferase |
| RA | 2,325,637 | T→C | R294R (CGT→CGC) | atoE → | short chain fatty acid transporter |
| RA | 2,339,460 | C→T | intergenic (‑40/‑107) | gyrA ← / → ubiG | DNA gyrase (type II topoisomerase), subunit A/bifunctional 3‑demethylubiquinone‑9 3‑methyltransferase/ 2‑octaprenyl‑6‑hydroxy phenol methylase |
| RA | 2,367,405 | G→A | R112H (CGC→CAC) | arnC → | undecaprenyl phosphate‑L‑Ara4FN transferase |
| RA | 2,379,241 | T→A | N7Y (AAC→TAC) | menD ← | 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase; SEPHCHC synthase |
| RA | 2,435,409 | C→T | A76A (GCG→GCA) | truA ← | tRNA pseudouridine(38‑40) synthase |
| RA | 2,441,945 | T→C | V61A (GTG→GCG) | mnmC → | fused 5‑methylaminomethyl‑2‑thiouridine‑forming enzyme methyltransferase and FAD‑dependent demodification enzyme |
| RA | 2,454,272 | A→G | pseudogene (730/2646 nt) | yfcU ← | pseudogene, FimD fimbrial export usher family;putative membrane; Not classified; putative outer membrane protein |
| RA | 2,471,762 | G→C | pseudogene (361/579 nt) | yfdL ← | pseudogene, CPS‑53 (KpLE1) prophage;Phage or Prophage Related |
| RA | 2,476,116 | A→T | I82F (ATC→TTC) | yfdT → | CPS‑53 (KpLE1) prophage; uncharacterized protein |
| RA | 2,477,942 | G→A | A32A (GCG→GCA) | dsdX → | D‑serine transporter |
| RA | 2,536,495 | G→A | A248V (GCG→GTG) | pdxK ← | pyridoxal‑pyridoxamine kinase/hydroxymethylpyrimidine kinase |
| RA | 2,595,335 | T→C | A175A (GCA→GCG) | tmcA ← | elongator methionine tRNA (ac4C34) acetyltransferase |
| RA | 2,602,017 | (C)7→8 | coding (200/2019 nt) | hyfB → | hydrogenase 4, membrane subunit |
| RA | 2,616,013 | T→C | intergenic (‑132/‑81) | yfgO ← / → bepA | putative UPF0118 family inner membrane permease/OM protein maintenance and assembly metalloprotease and chaperone, periplasmic |
| RA | 2,682,157 | (C)7→8 | coding (589/3282 nt) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 2,687,347 | G→A | A21V (GCC→GTC) | glnB ← | regulatory protein P‑II for glutamine synthetase |
| RA | 2,688,468 | C→T | A112A (GCG→GCA) | glrR ← | response regulator regulating glmY sRNA in two‑component system with sensor protein GlrK |
| RA | 2,747,020 | G→A | A259V (GCG→GTG) | ffh ← | Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) |
| RA | 2,764,549 | T→C | D202G (GAC→GGC) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,765,124 | G→A | A10A (GCC→GCT) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,801,859 | A→G | Q171R (CAG→CGG) | nrdE → | ribonucleoside‑diphosphate reductase 2, alpha subunit |
| RA | 2,805,310 | T→C | S166P (TCT→CCT) | proV → | glycine betaine/proline ABC transporter periplasmic binding protein |
| RA | 2,809,534 | T→C | intergenic (+41/‑83) | ygaY → / → ygaZ | pseudogene, major facilitator transporter superfamily;putative transport; Not classified; putative transport protein/putative L‑valine exporter, norvaline resistance protein |
| RA | 2,812,356 | T→C | G310G (GGT→GGC) | emrA → | multidrug efflux system |
| RA | 2,858,929 | A→C | T613P (ACC→CCC) | mutS → | methyl‑directed mismatch repair protein |
| RA | 2,913,035 | A→G | L206P (CTC→CCC) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,913,196 | T→C | K152K (AAA→AAG) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,968,723 | A→G | R85R (CGT→CGC) | rppH ← | RNA pyrophosphohydrolase |
| JC | 3,018,356 | (GTC)4→3 | coding (2297‑2299/3099 nt) | ygfK → | putative Fe‑S subunit oxidoreductase subunit |
| RA | 3,036,196 | G→A | A4V (GCC→GTC) | prfB ← | peptide chain release factor RF‑2 |
| RA | 3,037,738 | A→T | D123E (GAT→GAA) | recJ ← | ssDNA exonuclease, 5' ‑‑> 3'‑specific |
| RA | 3,068,614 | C→T | S65S (TCG→TCA) | argO ← | arginine transporter |
| RA | 3,088,189 | T→C | intergenic (+329/‑95) | metK → / → galP | S‑adenosylmethionine synthetase/D‑galactose transporter |
| RA | 3,139,485 | A→G | K253K (AAA→AAG) | yghU → | putative S‑transferase |
| RA | 3,158,129 | C→T | A160A (GCC→GCT) | yqhG → | DUF3828 family putative periplasmic protein |
| RA | 3,162,669 | T→C | M1M (ATG→GTG) † | ftsP ← | septal ring component that protects the divisome from stress; multicopy suppressor of ftsI(Ts) |
| RA | 3,163,010 | G→A | P158S (CCG→TCG) | plsC ← | 1‑acyl‑sn‑glycerol‑3‑phosphate acyltransferase |
| RA | 3,175,651 | G→A | S119L (TCA→TTA) | yqiA ← | acyl CoA esterase |
| RA | 3,211,471 | G→A | G122D (GGT→GAT) | dnaG → | DNA primase |
| RA | 3,235,399 | G→A | L159L (CTC→CTT) | rlmG ← | 23S rRNA m(2)G1835 methyltransferase, SAM‑dependent |
| RA | 3,252,977 | T→C | Y23H (TAC→CAC) | yhaI → | DUF805 family inner membrane protein |
| RA | 3,362,012 | A→G | intergenic (+72/‑100) | gltF → / → yhcA | periplasmic protein/putative periplasmic chaperone protein |
| RA | 3,368,566 | G→A | G247E (GGG→GAG) | yhcG → | DUF1016 family protein in the PD‑(D/E)XK nuclease superfamily |
| RA | 3,391,786 | A→G | A81A (GCT→GCC) | tldD ← | putative peptidase |
| RA | 3,439,982 | A→G | S6S (AGT→AGC) | rplQ ← | 50S ribosomal subunit protein L17 |
| RA | 3,457,324 | T→C | D316D (GAT→GAC) | gspD → | general secretory pathway component, cryptic |
| RA | 3,462,301 | A→G | T110A (ACG→GCG) | gspI → | general secretory pathway component, cryptic |
| RA | 3,466,888 | A→G | V35A (GTC→GCC) | bfd ← | bacterioferritin‑associated ferredoxin |
| RA | 3,497,615 | T→C | F205L (TTC→CTC) | nirC → | nitrite transporter |
| RA | 3,505,884 | A→G | L46P (CTG→CCG) | yhfS ← | FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
| RA | 3,532,256 | +T | coding (184/1725 nt) | yhgE ← | DUF4153 family putative inner membrane protein |
| RA | 3,546,644 | T→C | V29A (GTC→GCC) | gntT → | gluconate transporter, high‑affinity GNT I system |
| 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 | 3,563,193 | A→G | D394G (GAC→GGC) | glpD → | sn‑glycerol‑3‑phosphate dehydrogenase, aerobic, FAD/NAD(P)‑binding |
| RA | 3,572,038 | T→C | T489A (ACC→GCC) | glgB ← | 1,4‑alpha‑glucan branching enzyme |
| RA | 3,572,259 | T→C | Y415C (TAC→TGC) | glgB ← | 1,4‑alpha‑glucan branching enzyme |
| RA | 3,575,146 | T→C | S26P (TCC→CCC) | yhgN → | UPF0056 family inner membrane protein |
| RA | 3,578,677 | A→G | V17A (GTG→GCG) | gntR ← | d‑gluconate inducible gluconate regulon transcriptional repressor |
| RA | 3,629,003 | T→C | D179G (GAC→GGC) | rbbA ← | ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein |
| RA | 3,648,144 | (T)7→8 | intergenic (‑356/‑384) | dinQ ← / → arsR | UV‑inducible membrane toxin, DinQ‑AgrB type I toxin‑antitoxin system/arsenical resistance operon transcriptional repressor; autorepressor |
| RA | 3,689,711 | G→A | P184L (CCG→CTG) | bcsZ ← | endo‑1,4‑D‑glucanase |
| RA | 3,696,621 | A→G | H55R (CAC→CGC) | bcsE → | cellulose production protein |
| RA | 3,700,370 | A→G | intergenic (‑283/‑193) | ldrD ← / → yhjV | toxic polypeptide, small/putative transporter |
| RA | 3,715,195 | T→C | E400E (GAA→GAG) | bisC ← | biotin sulfoxide reductase |
| RA | 3,779,043 | A→G | M549V (ATG→GTG) | lldP → | L‑lactate permease |
| RA | 3,815,521 | A→G | V83A (GTG→GCG) | pyrE ← | orotate phosphoribosyltransferase |
| RA | 3,815,808 | (A)8→7 | intergenic (‑40/+26) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,843,430 | C→T | W120* (TGG→TGA) | adeQ ← | adenine permease, high affinity; adenine:H+ symporter |
| RA | 3,844,146 | T→C | G61G (GGT→GGC) | adeD → | cryptic adenine deaminase |
| RA | 3,859,124 | A→G | G331G (GGT→GGC) | yidK ← | putative transporter |
| RA | 3,878,843 | T→C | D426G (GAC→GGC) | gyrB ← | DNA gyrase, subunit B |
| RA | 3,889,885 | T→C | Y386H (TAT→CAT) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 3,895,826 | A→G | L262L (TTG→CTG) | adeP ← | adenine permease, high affinity; adenine:H+ symporter |
| RA | 3,928,167 | T→C | R479R (AGA→AGG) | viaA ← | stimulator of RavA ATPase activity; von Willebrand factor domain protein |
| RA | 3,947,067 | (T)8→7 | intergenic (+35/+61) | trpT → / ← hdfR | tRNA‑Trp/flhDC operon transcriptional repressor |
| RA | 3,967,132 | A→G | H239R (CAC→CGC) | rho → | transcription termination factor |
| RA | 3,979,674 | T→C | G358G (GGT→GGC) | wzyE → | putative ECA polysaccharide chain elongation protein |
| RA | 4,032,787 | T→C | V99A (GTA→GCA) | yigZ → | UPF0029 family protein |
| RA | 4,114,622 | A→G | S320P (TCC→CCC) | glpX ← | fructose 1,6‑bisphosphatase II |
| RA | 4,128,247 | C→T | R50H (CGT→CAT) | metJ ← | transcriptional repressor, S‑adenosylmethionine‑binding |
| RA | 4,134,394 | A→G | D187G (GAC→GGC) | katG → | catalase‑peroxidase HPI, heme b‑containing |
| RA | 4,139,721 | Δ1 bp | coding (2501/2502 nt) | frwA ← | putative PTS enzyme: Hpr, enzyme I and II components |
| RA | 4,157,132 | A→G | K95E (AAA→GAA) | argH → | argininosuccinate lyase |
| RA | 4,173,601 | C→T | P174S (CCT→TCT) | birA → | bifunctional biotin‑[acetylCoA carboxylase] holoenzyme synthetase/ DNA‑binding transcriptional repressor, bio‑5'‑AMP‑binding |
| RA | 4,237,614 | A→G | T240A (ACG→GCG) | yjbG → | extracellular polysaccharide export OMA protein |
| RA | 4,281,575 | (A)5→4 | coding (1596/1650 nt) | yjcE → | putative cation/proton antiporter |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,320,065 | T→C | D200G (GAC→GGC) | phnI ← | ribophosphonate triphosphate synthase complex putative catalytic subunit |
| RA | 4,334,049 | T→C | Q514Q (CAA→CAG) | eptA ← | lipid A phosphoethanolamine transferase |
| RA | 4,339,313 | A→G | R403R (CGT→CGC) | adiA ← | arginine decarboxylase |
| RA | 4,341,617 | A→T | D4E (GAT→GAA) | melR ← | melibiose operon transcriptional regulator; autoregulator |
| RA | 4,359,666 | A→G | G122G (GGT→GGC) | cadB ← | putative lysine/cadaverine transporter |
| RA | 4,381,504 | T→C | E272G (GAA→GGA) | frdA ← | anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit |
| RA | 4,391,867 | A→G | A88A (GCA→GCG) | orn → | oligoribonuclease |
| RA | 4,407,982 | T→C | R443R (CGT→CGC) | rnr → | exoribonuclease R, RNase R |
| RA | 4,415,887 | (G)6→7 | coding (1613/1626 nt) | aidB → | DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase |
| RA | 4,485,819 | C→T | A45T (GCC→ACC) | pepA ← | multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor |
| RA | 4,491,790 | A→G | L246L (TTA→CTA) | idnT ← | L‑idonate and D‑gluconate transporter |
| RA | 4,494,883 | (A)7→8 | coding (261/564 nt) | idnK → | D‑gluconate kinase, thermosensitive |
| RA | 4,583,861 | A→G | R967R (CGT→CGC) | hsdR ← | endonuclease R Type I restriction enzyme |
| RA | 4,606,331 | A→G | noncoding (71/87 nt) | leuQ ← | tRNA‑Leu |
| RA | 4,620,670 | T→C | G356G (GGT→GGC) | deoB → | phosphopentomutase |
| RA | 4,641,366 | T→C | L142P (CTC→CCC) | yjtD → | putative methyltransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 226131–226601 | 228595–226988 | 388–2465 | 18 [16] | [17] 18 | rrlH | 23S ribosomal RNA of rrnH operon |
| * | * | ÷ | NC_000913 | 738053 | 738766 | 714 | 18 [16] | [17] 18 | [ybfD] | [ybfD] |
| * | * | ÷ | NC_000913 | 3423727–3424232 | 3424553–3424238 | 7–827 | 18 [17] | [17] 18 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 3 (0.070) | 36 (0.930) | 30/266 | 0.5 | 89.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 6 (0.160) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 3 (0.070) | 26 (0.670) | 26/266 | 0.8 | 85.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 6 (0.160) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 25 (0.590) | 24/290 | 1.3 | 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 | |||||
| * | ? | NC_000913 | = 4606207 | 8 (0.200) | 28 (0.660) +GGG |
26/276 | 0.9 | 77.6% | noncoding (80/87 nt) | leuP | tRNA‑Leu |
| ? | NC_000913 | 4606208 = | 8 (0.180) | noncoding (79/87 nt) | leuP | tRNA‑Leu | |||||