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 | freq | annotation | gene | description |
| RA | 290,626 | T→A | 6.1% | intergenic (‑116/+224) | yagM ← / ← yagN | CP4‑6 prophage; uncharacterized protein/CP4‑6 prophage; uncharacterized protein |
| RA | 290,627 | T→A | 6.1% | intergenic (‑117/+223) | yagM ← / ← yagN | CP4‑6 prophage; uncharacterized protein/CP4‑6 prophage; uncharacterized protein |
| RA | 344,307 | C→T | 6.0% | intergenic (‑153/‑86) | prpR ← / → prpB | propionate catabolism operon regulatory protein/2‑methylisocitrate lyase |
| RA | 344,308 | A→G | 6.1% | intergenic (‑154/‑85) | prpR ← / → prpB | propionate catabolism operon regulatory protein/2‑methylisocitrate lyase |
| RA | 447,314 | A→G | 5.5% | intergenic (‑248/+212) | cyoA ← / ← ampG | cytochrome o ubiquinol oxidase subunit II/muropeptide transporter |
| RA | 447,315 | A→T | 5.4% | intergenic (‑249/+211) | cyoA ← / ← ampG | cytochrome o ubiquinol oxidase subunit II/muropeptide transporter |
| RA | 447,316 | C→T | 5.8% | intergenic (‑250/+210) | cyoA ← / ← ampG | cytochrome o ubiquinol oxidase subunit II/muropeptide transporter |
| RA | 546,958 | G→T | 5.1% | intergenic (+170/+25) | ybcF → / ← purK | putative carbonate kinase/N5‑carboxyaminoimidazole ribonucleotide synthase |
| RA | 546,959 | C→T | 5.1% | intergenic (+171/+24) | ybcF → / ← purK | putative carbonate kinase/N5‑carboxyaminoimidazole ribonucleotide synthase |
| RA | 590,975 | T→A | 6.0% | intergenic (‑76/‑81) | cusR ← / → cusC | response regulator in two‑component regulatory system with CusS/copper/silver efflux system, outer membrane component |
| RA | 590,976 | T→A | 6.0% | intergenic (‑77/‑80) | cusR ← / → cusC | response regulator in two‑component regulatory system with CusS/copper/silver efflux system, outer membrane component |
| RA | 777,217 | C→T | 5.6% | intergenic (+109/‑324) | lysQ → / → nadA | tRNA‑Lys/quinolinate synthase, subunit A |
| RA | 1,162,870 | A→G | 6.5% | intergenic (+25/‑185) | ndh → / → ycfJ | respiratory NADH dehydrogenase 2/cupric reductase/uncharacterized protein |
| RA | 1,266,179 | T→G | 5.3% | intergenic (+263/+26) | rdlC → / ← chaA | sRNA antisense regulator affects LdrC translation; proposed addiction module in LDR‑C repeat, with toxic peptide LdrC/calcium/sodium:proton antiporter |
| RA | 1,331,584:1 | +A | 5.3% | coding (1497/2676 nt) | acnA → | aconitate hydratase 1 |
| RA | 1,331,588 | T→G | 5.3% | C501G (TGT→GGT) | acnA → | aconitate hydratase 1 |
| RA | 1,381,022 | G→A | 7.2% | E16K (GAA→AAA) | tyrR → | aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase |
| RA | 1,425,820 | G→A | 6.7% | A839T (GCT→ACT) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,510,660 | G→C | 5.4% | A276P (GCT→CCT) | patD → | gamma‑aminobutyraldehyde dehydrogenase |
| RA | 1,510,664 | G→T | 5.9% | G277V (GGA→GTA) ‡ | patD → | gamma‑aminobutyraldehyde dehydrogenase |
| RA | 1,510,665 | A→C | 5.0% | G277G (GGA→GGC) ‡ | patD → | gamma‑aminobutyraldehyde dehydrogenase |
| RA | 1,510,669 | G→C | 5.1% | D279H (GAT→CAT) | patD → | gamma‑aminobutyraldehyde dehydrogenase |
| RA | 1,537,486 | G→T | 5.5% | L278M (CTG→ATG) | narU ← | nitrate/nitrite transporter |
| RA | 1,537,487 | C→G | 5.0% | M277I (ATG→ATC) ‡ | narU ← | nitrate/nitrite transporter |
| RA | 1,537,488 | A→C | 5.1% | M277R (ATG→AGG) ‡ | narU ← | nitrate/nitrite transporter |
| RA | 1,551,376 | G→T | 5.7% | A307E (GCG→GAG) | ddpF ← | D,D‑dipeptide permease system, ATP‑binding component |
| RA | 1,570,045 | G→T | 6.2% | A611D (GCC→GAC) | yddB ← | putative TonB‑dependent outer membrane receptor |
| RA | 1,625,264 | G→A | 5.2% | pseudogene (1279/1284 nt) | ydfJ ← | pseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein |
| RA | 1,631,169 | A→G | 7.8% | K53E (AAA→GAA) | ynfO → | uncharacterized protein, Qin prophage |
| RA | 1,631,173 | G→C | 7.8% | R54T (AGA→ACA) ‡ | ynfO → | uncharacterized protein, Qin prophage |
| RA | 1,631,174 | A→T | 7.8% | R54S (AGA→AGT) ‡ | ynfO → | uncharacterized protein, Qin prophage |
| RA | 1,631,175 | G→C | 7.8% | V55L (GTT→CTT) | ynfO → | uncharacterized protein, Qin prophage |
| RA | 1,631,185 | Δ1 bp | 5.4% | coding (173/234 nt) | ynfO → | uncharacterized protein, Qin prophage |
| RA | 1,636,614 | C→T | 6.0% | intergenic (+290/+132) | cspF → / ← quuQ | Qin prophage; cold shock protein/Qin prophage; putative antitermination protein Q |
| RA | 1,636,616 | C→G | 5.6% | intergenic (+292/+130) | cspF → / ← quuQ | Qin prophage; cold shock protein/Qin prophage; putative antitermination protein Q |
| RA | 1,636,627 | C→G | 6.2% | intergenic (+303/+119) | cspF → / ← quuQ | Qin prophage; cold shock protein/Qin prophage; putative antitermination protein Q |
| RA | 1,636,630 | C→G | 6.2% | intergenic (+306/+116) | cspF → / ← quuQ | Qin prophage; cold shock protein/Qin prophage; putative antitermination protein Q |
| RA | 1,636,641 | C→G | 6.2% | intergenic (+317/+105) | cspF → / ← quuQ | Qin prophage; cold shock protein/Qin prophage; putative antitermination protein Q |
| RA | 1,636,643 | A→G | 6.1% | intergenic (+319/+103) | cspF → / ← quuQ | Qin prophage; cold shock protein/Qin prophage; putative antitermination protein Q |
| RA | 1,750,647 | C→G | 6.2% | D231E (GAC→GAG) | pykF → | pyruvate kinase I |
| RA | 1,750,650 | A→T | 5.7% | E232D (GAA→GAT) | pykF → | pyruvate kinase I |
| RA | 1,750,651 | A→T | 5.7% | I233F (ATC→TTC) | pykF → | pyruvate kinase I |
| RA | 1,750,654 | C→G | 6.2% | L234V (CTC→GTC) | pykF → | pyruvate kinase I |
| RA | 1,786,776 | G→T | 5.4% | R71R (CGC→CGA) | nlpC ← | putative C40 clan peptidase lipoprotein |
| RA | 1,898,849 | C→A | 5.9% | T233N (ACT→AAT) | manZ → | mannose‑specific enzyme IID component of PTS |
| RA | 1,898,852 | T→G | 5.8% | I234S (ATT→AGT) | manZ → | mannose‑specific enzyme IID component of PTS |
| RA | 1,930,988 | C→A | 5.0% | A27D (GCT→GAT) | yebK → | putative DNA‑binding transcriptional regulator |
| RA | 1,965,464 | G→C | 8.7% | A495A (GCC→GCG) | tar ← | methyl‑accepting chemotaxis protein II |
| RA | 1,965,467 | G→C | 8.7% | A494A (GCC→GCG) | tar ← | methyl‑accepting chemotaxis protein II |
| RA | 1,965,470 | A→C | 8.0% | A493A (GCT→GCG) | tar ← | methyl‑accepting chemotaxis protein II |
| RA | 2,056,835 | C→A | 5.1% | intergenic (‑31/+34) | ldtA ← / ← cobT | L,D‑transpeptidase linking Lpp to murein/nicotinate‑nucleotide‑‑dimethylbenzimidazole phosphoribosyltransferase |
| RA | 2,056,837 | G→T | 5.0% | intergenic (‑33/+32) | ldtA ← / ← cobT | L,D‑transpeptidase linking Lpp to murein/nicotinate‑nucleotide‑‑dimethylbenzimidazole phosphoribosyltransferase |
| RA | 2,069,884 | A→T | 6.2% | A32A (GCA→GCT) | yeeS → | CP4‑44 prophage; putative DNA repair protein |
| RA | 2,122,276 | A→C | 5.0% | F32V (TTT→GTT) | wcaF ← | putative acyl transferase |
| RA | 2,170,724 | G→T | 22.8% | intergenic (‑41/+267) | gatY ← / ← fbaB | D‑tagatose 1,6‑bisphosphate aldolase 2, catalytic subunit/fructose‑bisphosphate aldolase class I |
| RA | 2,180,978 | T→A | 5.3% | K306* (AAA→TAA) | yehA ← | putative fimbrial‑like adhesin protein |
| RA | 2,235,692 | T→C | 5.9% | Q252R (CAA→CGA) | yeiB ← | DUF418 family putative inner membrane protein |
| RA | 2,235,695 | A→C | 6.0% | L251R (CTG→CGG) ‡ | yeiB ← | DUF418 family putative inner membrane protein |
| RA | 2,235,696 | G→C | 6.0% | L251V (CTG→GTG) ‡ | yeiB ← | DUF418 family putative inner membrane protein |
| RA | 2,235,697 | G→T | 6.0% | A250A (GCC→GCA) | yeiB ← | DUF418 family putative inner membrane protein |
| RA | 2,235,700 | G→A | 5.8% | I249I (ATC→ATT) | yeiB ← | DUF418 family putative inner membrane protein |
| RA | 2,333,087 | C→T | 5.3% | H14H (CAC→CAT) | ubiG → | bifunctional 3‑demethylubiquinone‑9 3‑methyltransferase/ 2‑octaprenyl‑6‑hydroxy phenol methylase |
| RA | 2,353,918 | C→A | 5.2% | G326C (GGT→TGT) | rhmD ← | L‑rhamnonate dehydratase |
| RA | 2,406,123 | A→C | 5.3% | intergenic (‑50/+33) | yfbU ← / ← yfbV | UPF0304 family protein/UPF0208 family inner membrane protein |
| RA | 2,435,140 | C→A | 8.8% | intergenic (‑56/‑103) | fabB ← / → mnmC | 3‑oxoacyl‑[acyl‑carrier‑protein] synthase I/fused 5‑methylaminomethyl‑2‑thiouridine‑forming enzyme methyltransferase and FAD‑dependent demodification enzyme |
| RA | 2,435,141 | T→G | 8.8% | intergenic (‑57/‑102) | fabB ← / → mnmC | 3‑oxoacyl‑[acyl‑carrier‑protein] synthase I/fused 5‑methylaminomethyl‑2‑thiouridine‑forming enzyme methyltransferase and FAD‑dependent demodification enzyme |
| RA | 2,719,426 | T→C | 100% | intergenic (‑321/+2) | kgtP ← / ← rrfG | alpha‑ketoglutarate transporter/5S ribosomal RNA of rrnG operon |
| RA | 2,799,889 | C→T | 5.8% | P174L (CCG→CTG) | proW → | glycine betaine transporter subunit |
| RA | 2,815,288 | G→T | 5.1% | S28Y (TCC→TAC) | alaS ← | alanyl‑tRNA synthetase |
| RA | 3,032,212 | C→G | 5.7% | R297R (CGG→CGC) | xerD ← | site‑specific tyrosine recombinase |
| RA | 3,032,217 | G→C | 5.6% | P296A (CCG→GCG) | xerD ← | site‑specific tyrosine recombinase |
| RA | 3,039,409 | T→G | 10.2% | intergenic (‑149/+118) | ygfF ← / ← gcvP | putative NAD(P)‑dependent oxidoreductase with NAD(P)‑binding Rossmann‑fold domain/glycine decarboxylase, PLP‑dependent, subunit (protein P) of glycine cleavage complex |
| RA | 3,159,514 | G→C | 5.1% | Q522E (CAG→GAG) | ygiS ← | putative inner membrane ABC superfamily transporter permease |
| RA | 3,159,515 | G→A | 5.1% | P521P (CCC→CCT) | ygiS ← | putative inner membrane ABC superfamily transporter permease |
| RA | 3,165,200 | G→A | 5.0% | intergenic (+8/+38) | qseC → / ← ygiZ | quorum sensing sensory histidine kinase in two‑component regulatory system with QseB/inner membrane protein |
| RA | 3,260,190 | G→A | 5.2% | R79C (CGT→TGT) | tdcA ← | tdc operon transcriptional activator |
| RA | 3,262,694 | C→T | 5.3% | Y307Y (TAC→TAT) | yhaC → | pentapetide repeats‑related protein |
| RA | 3,262,701 | A→G | 5.4% | I310V (ATA→GTA) | yhaC → | pentapetide repeats‑related protein |
| RA | 3,333,192 | G→A | 5.1% | S78L (TCG→TTG) | mlaF ← | ABC transporter maintaining OM lipid asymmetry, ATP‑binding protein |
| RA | 3,499,668 | C→T | 5.2% | G343D (GGC→GAC) | yhfT ← | inner membrane protein |
| RA | 3,513,358 | G→T | 5.3% | N235K (AAC→AAA) | hofQ ← | DNA catabolic putative fimbrial transporter |
| RA | 3,702,549 | C→A | 6.0% | Q429H (CAG→CAT) | eptB ← | KDO phosphoethanolamine transferase, Ca(2+)‑inducible |
| RA | 3,822,340 | A→C | 14.1% | Q12H (CAA→CAC) | xanP → | xanthine permease |
| RA | 3,877,923 | A→G | 100% | Q24R (CAG→CGG) | rnpA → | protein C5 component of RNase P |
| RA | 3,986,663 | C→A | 5.1% | G717G (GGC→GGA) | cyaA → | adenylate cyclase |
| RA | 4,019,993 | Δ1 bp | 100% | coding (107/702 nt) | fre → | NAD(P)H‑flavin reductase |
| RA | 4,073,976 | C→A | 5.5% | G205C (GGC→TGC) | fdhE ← | formate dehydrogenase formation protein |
| RA | 4,127,924 | T→A | 6.2% | Q347L (CAG→CTG) | gldA ← | glycerol dehydrogenase, NAD+ dependent; 1,2‑propanediol:NAD+ oxidoreductase |
| RA | 4,264,609 | G→A | 5.1% | intergenic (+20/+79) | ssb → / ← yjcB | single‑stranded DNA‑binding protein/putative inner membrane protein |
| RA | 4,298,800 | A→C | 5.8% | F163V (TTT→GTT) | alsC ← | D‑allose transporter subunit |
| RA | 4,356,671 | T→G | 6.7% | intergenic (‑81/+37) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,356,672 | C→A | 6.6% | intergenic (‑82/+36) | dcuA ← / ← aspA | C4‑dicarboxylate antiporter/aspartate ammonia‑lyase |
| RA | 4,404,042 | C→A | 7.1% | intergenic (+34/‑50) | yjfC → / → aidB | ATP‑Grasp family ATPase/DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase |
| RA | 4,404,051 | G→C | 7.5% | intergenic (+43/‑41) | yjfC → / → aidB | ATP‑Grasp family ATPase/DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase |
| RA | 4,404,057 | A→T | 8.2% | intergenic (+49/‑35) | yjfC → / → aidB | ATP‑Grasp family ATPase/DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase |
| RA | 4,404,058 | C→A | 8.2% | intergenic (+50/‑34) | yjfC → / → aidB | ATP‑Grasp family ATPase/DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase |
| RA | 4,404,059 | T→G | 7.4% | intergenic (+51/‑33) | yjfC → / → aidB | ATP‑Grasp family ATPase/DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase |
| RA | 4,404,060 | A→T | 7.7% | intergenic (+52/‑32) | yjfC → / → aidB | ATP‑Grasp family ATPase/DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase |
| RA | 4,404,066 | G→C | 7.5% | intergenic (+58/‑26) | yjfC → / → aidB | ATP‑Grasp family ATPase/DNA alkylation damage repair protein; flavin‑containing DNA binding protein, weak isovaleryl CoA dehydrogenase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 463794 | 464330 | 537 | 51 [49] | [47] 50 | ybaO–[mdlA] | ybaO,[mdlA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | = 194377 | 109 (1.040) | 6 (0.060) | 6/240 | NT | 5.4% | coding (1345/1353 nt) | rseP | inner membrane zinc RIP metalloprotease; RpoE activator, by degrading RseA; cleaved signal peptide endoprotease |
| ? | CP009273 | = 194383 | 107 (1.060) | coding (1351/1353 nt) | rseP | inner membrane zinc RIP metalloprotease; RpoE activator, by degrading RseA; cleaved signal peptide endoprotease | |||||
| * | ? | CP009273 | 221558 = | NA (NA) | 6 (0.060) | 4/242 | NT | NA | noncoding (1301/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | CP009273 | 221597 = | NA (NA) | noncoding (1340/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | CP009273 | = 221765 | NA (NA) | 4 (0.040) | 4/236 | NT | NA | noncoding (1508/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon |
| ? | CP009273 | = 221796 | NA (NA) | noncoding (1539/1542 nt) | rrsH | 16S ribosomal RNA of rrnH operon | |||||
| * | ? | CP009273 | 222321 = | NA (NA) | 4 (0.040) | 4/246 | NT | NA | noncoding (76/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | CP009273 | 222356 = | NA (NA) | noncoding (111/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | CP009273 | = 222402 | NA (NA) | 9 (0.090) | 9/234 | NT | NA | noncoding (157/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | CP009273 | = 222413 | NA (NA) | noncoding (168/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | CP009273 | = 224641 | NA (NA) | 3 (0.030) | 3/240 | NT | NA | noncoding (2396/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | CP009273 | = 224671 | NA (NA) | noncoding (2426/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | CP009273 | 269746 = | NA (NA) | 3 (0.030) | 3/246 | NT | NA | noncoding (1115/1195 nt) | IS5 | repeat region |
| ? | CP009273 | 269797 = | NA (NA) | noncoding (1064/1195 nt) | IS5 | repeat region | |||||
| * | ? | CP009273 | 270657 = | NA (NA) | 6 (0.060) | 6/246 | NT | NA | noncoding (117/1221 nt) | IS30 | repeat region |
| ? | CP009273 | 270693 = | NA (NA) | noncoding (153/1221 nt) | IS30 | repeat region | |||||
| * | ? | CP009273 | = 286595 | NA (NA) | 4 (0.040) | 4/248 | NT | 11.8% | noncoding (518/768 nt) | IS1 | repeat region |
| ? | CP009273 | 1045783 = | 30 (0.290) | coding (301/504 nt) | insB1 | IS1 transposase B | |||||
| * | ? | CP009273 | 360104 = | 119 (1.140) | 133 (1.270) | 98/250 | NT | 52.8% | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | NA (NA) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | 377009 = | NA (NA) | 4 (0.040) | 4/244 | NT | NA | coding (203/366 nt) | insC1 | IS2 repressor TnpA |
| ? | CP009273 | 377076 = | NA (NA) | coding (270/366 nt) | insC1 | IS2 repressor TnpA | |||||
| * | ? | CP009273 | = 377057 | NA (NA) | 4 (0.040) | 4/242 | NT | NA | coding (251/366 nt) | insC1 | IS2 repressor TnpA |
| ? | CP009273 | = 377080 | NA (NA) | coding (274/366 nt) | insC1 | IS2 repressor TnpA | |||||
| * | ? | CP009273 | 377566 = | NA (NA) | 8 (0.080) | 7/240 | NT | NA | coding (437/906 nt) | insD1 | IS2 transposase TnpB |
| ? | CP009273 | 377597 = | NA (NA) | coding (468/906 nt) | insD1 | IS2 transposase TnpB | |||||
| * | ? | CP009273 | = 377639 | NA (NA) | 4 (0.040) | 4/242 | NT | NA | coding (510/906 nt) | insD1 | IS2 transposase TnpB |
| ? | CP009273 | = 377728 | NA (NA) | coding (599/906 nt) | insD1 | IS2 transposase TnpB | |||||
| * | ? | CP009273 | 377693 = | NA (NA) | 5 (0.050) | 5/238 | NT | NA | coding (564/906 nt) | insD1 | IS2 transposase TnpB |
| ? | CP009273 | 377723 = | NA (NA) | coding (594/906 nt) | insD1 | IS2 transposase TnpB | |||||
| * | ? | CP009273 | = 385697 | 75 (0.720) | 4 (0.040) | 4/240 | NT | 5.2% | intergenic (‑514/‑10) | hemB/yaiT | 5‑aminolevulinate dehydratase (porphobilinogen synthase)/pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein |
| ? | CP009273 | = 385711 | 74 (0.740) | pseudogene (5/1458 nt) | yaiT | pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein | |||||
| * | ? | CP009273 | 386400 = | 106 (1.010) | 8 (0.080) | 4/238 | NT | 7.9% | pseudogene (694/1458 nt) | yaiT | pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein |
| ? | CP009273 | 386441 = | 85 (0.850) | pseudogene (735/1458 nt) | yaiT | pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein | |||||
| * | ? | CP009273 | = 397377 | 69 (0.660) | 8 (0.080) | 6/246 | NT | 9.8% | coding (175/1416 nt) | phoA | bacterial alkaline phosphatase |
| ? | CP009273 | = 397423 | 79 (0.770) | coding (221/1416 nt) | phoA | bacterial alkaline phosphatase | |||||
| * | ? | CP009273 | = 817364 | 92 (0.880) | 7 (0.070) | 3/238 | NT | 7.8% | coding (591/957 nt) | ybhN | UPF0104 family inner membrane protein |
| ? | CP009273 | = 817392 | 78 (0.780) | coding (563/957 nt) | ybhN | UPF0104 family inner membrane protein | |||||
| * | ? | CP009273 | 1203246 = | 20 (0.190) | 45 (0.490) | 42/218 | NT | 68.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | 1205075 = | 24 (0.260) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1203261 | 19 (0.180) | 88 (0.960) | 66/218 | NT | 81.3% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 24 (0.260) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | = 1232284 | 81 (0.770) | 5 (0.050) | 5/242 | NT | 5.8% | coding (414/1533 nt) | ycgB | SpoVR family stationary phase protein |
| ? | CP009273 | = 1232323 | 84 (0.830) | coding (375/1533 nt) | ycgB | SpoVR family stationary phase protein | |||||
| * | ? | CP009273 | = 1293520 | 86 (0.820) | 6 (0.060) | 6/240 | NT | 7.3% | coding (58/2676 nt) | adhE | fused acetaldehyde‑CoA dehydrogenase/iron‑dependent alcohol dehydrogenase/pyruvate‑formate lyase deactivase |
| ? | CP009273 | = 1293555 | 70 (0.700) | coding (23/2676 nt) | adhE | fused acetaldehyde‑CoA dehydrogenase/iron‑dependent alcohol dehydrogenase/pyruvate‑formate lyase deactivase | |||||
| * | ? | CP009273 | = 1294757 | 91 (0.870) | 8 (0.080) | 7/232 | NT | 8.4% | intergenic (+56/‑682) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide transporter subunit |
| ? | CP009273 | = 1294794 | 90 (0.930) | intergenic (+93/‑645) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide transporter subunit | |||||
| * | ? | CP009273 | 1428689 = | 79 (0.750) | 4 (0.040) | 4/236 | NT | 5.0% | intergenic (‑208/+526) | ynaE/ttcC | cold shock protein, Rac prophage/pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related |
| ? | CP009273 | = 1627143 | 76 (0.770) | intergenic (‑601/‑186) | ydfJ/ydfK | pseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein/cold shock protein, function unknown, Qin prophage | |||||
| * | ? | CP009273 | 1457524 = | 69 (0.660) | 4 (0.040) | 4/242 | NT | 5.6% | coding (1143/1314 nt) | paaK | phenylacetyl‑CoA ligase |
| ? | CP009273 | 1457556 = | 69 (0.680) | coding (1175/1314 nt) | paaK | phenylacetyl‑CoA ligase | |||||
| * | ? | CP009273 | 1471741 = | 86 (0.820) | 4 (0.040) | 4/234 | NT | 5.0% | intergenic (+34/‑137) | ydbD/ynbA | PF10971 family putative periplasmic methylglyoxal resistance protein/inner membrane protein |
| ? | CP009273 | 1471777 = | 71 (0.720) | intergenic (+70/‑101) | ydbD/ynbA | PF10971 family putative periplasmic methylglyoxal resistance protein/inner membrane protein | |||||
| * | ? | CP009273 | 1509098 = | 105 (1.000) | 8 (0.080) | 6/244 | NT | 8.0% | coding (80/795 nt) | ydcV | putative spermidine/putrescine transporter subunit |
| ? | CP009273 | 1509140 = | 82 (0.800) | coding (122/795 nt) | ydcV | putative spermidine/putrescine transporter subunit | |||||
| * | ? | CP009273 | 1550719 = | 71 (0.680) | 5 (0.050) | 5/238 | NT | 6.8% | intergenic (‑182/‑163) | bdm/osmC | biofilm‑dependent modulation protein/lipoyl‑dependent Cys‑based peroxidase, hydroperoxide resistance; salt‑shock inducible membrane protein; peroxiredoxin |
| ? | CP009273 | 1550759 = | 69 (0.690) | intergenic (‑222/‑123) | bdm/osmC | biofilm‑dependent modulation protein/lipoyl‑dependent Cys‑based peroxidase, hydroperoxide resistance; salt‑shock inducible membrane protein; peroxiredoxin | |||||
| * | ? | CP009273 | = 1644120 | 66 (0.630) | 4 (0.040) | 4/234 | NT | 5.5% | coding (70/192 nt) | ydfD | Qin prophage; uncharacterized protein |
| ? | CP009273 | = 1644147 | 75 (0.760) | coding (97/192 nt) | ydfD | Qin prophage; uncharacterized protein | |||||
| * | ? | CP009273 | = 1683431 | 76 (0.720) | 5 (0.050) | 4/238 | NT | 6.1% | coding (599/1176 nt) | manA | mannose‑6‑phosphate isomerase |
| ? | CP009273 | = 1683454 | 81 (0.810) | coding (622/1176 nt) | manA | mannose‑6‑phosphate isomerase | |||||
| * | ? | CP009273 | 1972769 = | 3 (0.030) | 102 (0.980) | 82/248 | NT | 97.2% | intergenic (‑315/‑465) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | 3576788 = | NA (NA) | intergenic (+10/‑55) | yrhA/insA | pseudogene, interrupted by IS1E/IS1 repressor TnpA | |||||
| * | ? | CP009273 | = 1972777 | 3 (0.030) | 82 (0.780) | 63/250 | NT | 96.5% | intergenic (‑323/‑457) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | = 3577555 | NA (NA) | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E | |||||
| * | ? | CP009273 | = 1986278 | 76 (0.720) | 4 (0.040) | 4/238 | NT | 5.2% | coding (21/549 nt) | pgsA | phosphatidylglycerophosphate synthetase |
| ? | CP009273 | = 1986339 | 74 (0.740) | intergenic (‑41/+16) | pgsA/uvrC | phosphatidylglycerophosphate synthetase/excinuclease UvrABC, endonuclease subunit | |||||
| * | ? | CP009273 | = 1996103 | 73 (0.700) | 4 (0.040) | 4/246 | NT | 5.1% | coding (985/1497 nt) | fliC | flagellar filament structural protein (flagellin) |
| ? | CP009273 | = 1996129 | 76 (0.740) | coding (959/1497 nt) | fliC | flagellar filament structural protein (flagellin) | |||||
| * | ? | CP009273 | 2029140 = | 86 (0.820) | 4 (0.040) | 4/234 | NT | 5.1% | intergenic (+416/‑176) | yedS/hchA | pseudogene, outer membrane protein homology; putative outer membrane protein/glyoxalase III and Hsp31 molecular chaperone |
| ? | CP009273 | 2029239 = | 69 (0.700) | intergenic (+515/‑77) | yedS/hchA | pseudogene, outer membrane protein homology; putative outer membrane protein/glyoxalase III and Hsp31 molecular chaperone | |||||
| * | ? | CP009273 | 2059947 = | NA (NA) | 6 (0.060) | 4/240 | NT | NA | noncoding (888/1195 nt) | IS5 | repeat region |
| ? | CP009273 | 2095432 = | NA (NA) | noncoding (993/1195 nt) | IS5 | repeat region | |||||
| * | ? | CP009273 | = 2212968 | 110 (1.050) | 9 (0.090) | 5/236 | NT | 7.9% | intergenic (‑8/+203) | osmF/bglX | putative ABC superfamily transporter periplasmic‑binding protein/beta‑D‑glucoside glucohydrolase, periplasmic |
| ? | CP009273 | = 2213006 | 106 (1.070) | intergenic (‑46/+165) | osmF/bglX | putative ABC superfamily transporter periplasmic‑binding protein/beta‑D‑glucoside glucohydrolase, periplasmic | |||||
| * | ? | CP009273 | = 2278546 | 115 (1.100) | 6 (0.060) | 4/242 | NT | 5.0% | coding (692/1761 nt) | yejM | essential inner membrane DUF3413 domain‑containing protein; lipid A production and membrane permeability factor |
| ? | CP009273 | = 2278576 | 116 (1.140) | coding (722/1761 nt) | yejM | essential inner membrane DUF3413 domain‑containing protein; lipid A production and membrane permeability factor | |||||
| * | ? | CP009273 | 2515798 = | 109 (1.040) | 7 (0.070) | 5/248 | NT | 6.2% | coding (39/885 nt) | xapR | transcriptional activator of xapAB |
| ? | CP009273 | 2515852 = | 104 (1.000) | intergenic (‑16/+236) | xapR/xapB | transcriptional activator of xapAB/xanthosine transporter | |||||
| * | ? | CP009273 | 2518302 = | 114 (1.090) | 6 (0.060) | 6/234 | NT | 5.6% | intergenic (‑65/‑184) | xapA/yfeN | purine nucleoside phosphorylase II/putative outer membrane protein |
| ? | CP009273 | 2518392 = | 95 (0.970) | intergenic (‑155/‑94) | xapA/yfeN | purine nucleoside phosphorylase II/putative outer membrane protein | |||||
| * | ? | CP009273 | = 2638459 | 72 (0.690) | 4 (0.040) | 4/240 | NT | 5.2% | coding (2226/2313 nt) | pbpC | penicillin‑insensitive murein repair transglycosylase; inactive transpeptidase domain |
| ? | CP009273 | = 2638516 | 76 (0.760) | coding (2169/2313 nt) | pbpC | penicillin‑insensitive murein repair transglycosylase; inactive transpeptidase domain | |||||
| * | ? | CP009273 | 2645747 = | 88 (0.840) | 8 (0.080) | 4/234 | NT | 9.1% | intergenic (‑101/‑106) | yfhM/sseA | bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein/3‑mercaptopyruvate sulfurtransferase |
| ? | CP009273 | 2645810 = | 78 (0.790) | intergenic (‑164/‑43) | yfhM/sseA | bacterial alpha2‑macroglobulin colonization factor ECAM; anti‑host protease defense factor; periplasmic inner membrane‑anchored lipoprotein/3‑mercaptopyruvate sulfurtransferase | |||||
| * | ? | CP009273 | 2721870 = | NA (NA) | 4 (0.040) | 3/246 | NT | NA | noncoding (674/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon |
| ? | CP009273 | 2721910 = | NA (NA) | noncoding (634/2904 nt) | rrlG | 23S ribosomal RNA of rrnG operon | |||||
| * | ? | CP009273 | 2845465 = | 92 (0.880) | 5 (0.050) | 4/234 | NT | 5.3% | coding (243/273 nt) | hypC | hydrogenase maturation protein |
| ? | CP009273 | 2845525 = | 94 (0.960) | coding (31/1122 nt) | hypD | hydrogenase maturation protein | |||||
| * | ? | CP009273 | 3301217 = | 105 (1.000) | 6 (0.060) | 4/250 | NT | 5.5% | coding (3/1890 nt) coding (76/81 nt) |
deaD yrbN |
ATP‑dependent RNA helicase uncharacterized protein |
| ? | CP009273 | 3301262 = | 103 (0.980) | coding (31/81 nt) | yrbN | uncharacterized protein | |||||
| * | ? | CP009273 | 3417947 = | 46 (0.440) | 4 (0.040) | 4/238 | NT | 8.4% | noncoding (2196/2904 nt) | rrlD | 23S ribosomal RNA of rrnD operon |
| ? | CP009273 | 3418051 = | NA (NA) | noncoding (2092/2904 nt) | rrlD | 23S ribosomal RNA of rrnD operon | |||||
| * | ? | CP009273 | = 3422160 | NA (NA) | 3 (0.030) | 3/236 | NT | NA | intergenic (‑39/‑435) | rrsD/yrdA | 16S ribosomal RNA of rrnD operon/bacterial transferase hexapeptide domain protein |
| ? | CP009273 | = 3422185 | NA (NA) | intergenic (‑64/‑410) | rrsD/yrdA | 16S ribosomal RNA of rrnD operon/bacterial transferase hexapeptide domain protein | |||||
| * | ? | CP009273 | 3624559 = | 122 (1.160) | 7 (0.070) | 5/236 | NT | 6.0% | coding (1392/1623 nt) | yhiJ | DUF4049 family protein |
| ? | CP009273 | 3624609 = | 104 (1.050) | coding (1342/1623 nt) | yhiJ | DUF4049 family protein | |||||
| * | ? | CP009273 | 3802610 = | 102 (0.970) | 7 (0.070) | 5/240 | NT | 6.9% | coding (711/1278 nt) | waaA | 3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase) |
| ? | CP009273 | 3802644 = | 90 (0.890) | coding (745/1278 nt) | waaA | 3‑deoxy‑D‑manno‑octulosonic‑acid transferase (KDO transferase) | |||||
| * | ? | CP009273 | = 3878640 | 111 (1.060) | 8 (0.080) | 6/240 | NT | 6.7% | coding (205/1647 nt) | yidC | membrane protein insertase |
| ? | CP009273 | = 3878675 | 117 (1.160) | coding (240/1647 nt) | yidC | membrane protein insertase | |||||
| * | ? | CP009273 | = 4098513 | 101 (1.010) | 6 (0.060) | 6/238 | NT | 5.6% | noncoding (15/98 nt) | RIP302 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP302 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | CP009273 | = 4098576 | NA (NA) | noncoding (78/98 nt) | RIP302 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP302 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | CP009273 | 4122278 = | NA (NA) | 4 (0.040) | 4/250 | NT | NA | noncoding (4/34 nt) | REP306 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP306 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | CP009273 | 4122310 = | NA (NA) | intergenic (+115/‑234) | metL/metF | Bifunctional aspartokinase/homoserine dehydrogenase 2/5,10‑methylenetetrahydrofolate reductase | |||||
| * | ? | CP009273 | = 4173443 | 104 (0.990) | 6 (0.060) | 4/244 | NT | 5.3% | coding (2271/4029 nt) | rpoB | RNA polymerase, beta subunit |
| ? | CP009273 | = 4173499 | 112 (1.090) | coding (2327/4029 nt) | rpoB | RNA polymerase, beta subunit | |||||
| * | ? | CP009273 | 4398991 = | NA (NA) | 7 (0.080) | 6/220 | NT | 7.7% | noncoding (22/98 nt) | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | CP009273 | 4399052 = | 84 (0.910) | noncoding (83/98 nt) | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP331 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||