TABLE 1 .
Clade-specific SNPs identified between clades B and C
| SNP position in EC958 | SNP identified in cladea: |
Impactb | Locus tag | Codon | Gene | Product | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| B | B0 |
C0 |
C | |||||||||||
| H17 | G216 | JJ1897 | C001 | JJ2244 | G213 | CD306 | ||||||||
| 1244787 | C | C | C | C | C | C | C | C | T | I→V | EC958_1322 | 23 | potB | Spermidine-putrescine transport system permease |
| 2715324 | G | G | G | G | G | G | G | G | A | Syn | EC958_5020 | 125 | Hypothetical protein | |
| 3536312 | C | C | C | C | C | C | C | C | T | |||||
| 3555316 | C | C | C | C | C | C | C | C | T | Syn | EC958_3511 | 39 | yhaK | Hypothetical protein |
| 3921426 | G | G | G | G | G | G | G | G | A | K→R | EC958_3887 | 78 | yhiM | Hypothetical protein |
| 2536291 | C | C | C | C | C | T | C | C | T | N→D | EC958_2567 | 87 | gyrA | DNA gyrase subunit A |
| 1504736 | C | C | C | C | C | C | C | G | G | Syn | EC958_1601 | 142 | yciK | Hypothetical oxidoreductase YciK |
| 2744500 | C | C | C | C | C | C | C | T | T | I→V | EC958_2766 | 224 | eutB | Probable regulatory subunit of ethanolamine ammonia-lyase |
| 2937986 | A | A | A | A | A | A | A | G | G | |||||
| 4032999 | C | C | C | C | C | C | C | T | T | C→R | EC958_3982 | 119 | yiaK | Hypothetical oxidoreductase YiaK |
| 1382365 | G | G | G | G | G | G | A | A | A | Syn | EC958_1478 | 204 | hemA | Glutamyl-tRNA reductase |
| 2756734 | C | C | C | C | C | C | T | T | T | Syn | EC958_2779 | 448 | maeB | NADP-dependent malate dehydrogenase |
| 3883417 | G | G | G | G | G | G | A | A | A | M→T | EC958_3846 | 231 | livG | ATP-binding component of high-affinity branched-chain amino acid transport system LivG |
| 53758 | T | T | T | T | A | A | A | A | A | R→S | EC958_0181 | 147 | kefC | Glutathione-regulated potassium efflux antiporter |
| 2705332 | G | G | G | G | A | A | A | A | A | Syn | EC958_5013 | 334 | nupC | Nucleoside-transport system protein NupC |
| 3549826 | A | A | A | A | T | T | T | T | T | F→Y | EC958_3501 | 184 | yqjA | Hypothetical protein |
| 3587935 | G | G | G | G | A | A | A | A | A | N→D | EC958_3544 | 20 | agaD | Phosphotransferase system, N-acetylgalactosamine-specific IID component |
| 642980 | C | C | T | T | T | T | T | T | T | Syn | EC958_0717 | 116 | ybdB | Hypothetical protein |
| 761921 | G | G | A | A | A | A | A | A | A | Syn | EC958_0832 | 150 | Putative C4-dicarboxylate transporter, small permease protein (DctQ-like) | |
| 1001668 | T | T | C | C | C | C | C | C | C | Syn | EC958_1062 | 115 | ycaP | Hypothetical protein |
| 1167464 | C | C | T | T | T | T | T | T | T | C→R | EC958_1238 | 268 | ymdC | Putative synthase |
| 1317794 | G | G | A | A | A | A | A | A | A | Syn | EC958_1416 | 36 | ycgK | Protein YcgK |
| 1727956 | G | G | T | T | T | T | T | T | T | S→A | EC958_1806 | 223 | Probable dimethyl sulfoxide reductase chain YnfF | |
| 2191491 | C | C | T | T | T | T | T | T | T | Syn | EC958_2289 | 527 | Putative peptide synthetase-like protein | |
| 2395814 | C | C | T | T | T | T | T | T | T | L→P | EC958_2450 | 556 | Hypothetical protein | |
| 2686010 | T | T | C | C | C | C | C | C | C | |||||
| 2692404 | C | C | T | T | T | T | T | T | T | C→R | EC958_5002 | 238 | ypdB | Hypothetical protein |
| 2706426 | C | C | T | T | T | T | T | T | T | Syn | EC958_5222 | 482 | yfeA | Hypothetical protein |
| 3030230 | G | G | T | T | T | T | T | T | T | K→N | EC958_3037 | 192 | Hypothetical protein | |
| 3798899 | G | G | A | A | A | A | A | A | A | Syn | EC958_3771 | 208 | yhfW | Hypothetical protein |
| 3802091 | G | G | T | T | T | T | T | T | T | |||||
| 3823737 | A | A | G | G | G | G | G | G | G | |||||
| 3913371 | G | G | A | A | A | A | A | A | A | T→A | EC958_3880 | 195 | Putative xylulose kinase | |
| 4009795 | C | C | T | T | T | T | T | T | T | V→A | EC958_3959 | 327 | yiaE | Putative dehydrogenase |
| 4216222 | C | C | T | T | T | T | T | T | T | |||||
| 4233771 | T | T | C | C | C | C | C | C | C | |||||
| 779389 | C | T | T | T | T | T | T | T | T | L→P | EC958_0846 | 476 | Putative glycosyl hydrolase | |
| 822709 | G | A | A | A | A | A | A | A | A | Syn | EC958_0888 | 281 | bioF | 8-Amino-7-oxononanoate synthase |
| 2406295 | G | A | A | A | A | A | A | A | A | |||||
| 3892567 | A | G | G | G | G | G | G | G | G | S→F | EC958_3856 | 69 | ftsX | Cell division membrane protein |
| 3941887 | G | A | A | A | A | A | A | A | A | Syn | EC958_3906 | 72 | chuW | Putative oxygen-independent coproporphyrinogen III oxidase |
| 4631378 | C | T | T | T | T | T | T | T | T | K→E | EC958_4497 | 567 | plsB | Glycerol-3-phosphate acyltransferase |
a
Boldface indicates clade B specific, and italic indicates clade C specific.
b
Impact of SNP in bold relative to ST131 clade C2 strain EC958. Syn, synonymous change; non-synonymous changes to protein-coding genes are shown with single letter amino acid codes (EC958 sequence on left, SNP impact on right); blank lines indicate SNP in intergenic region.