TABLE 2.
Additional homopolymeric tract variations in seven S. agalactiae comparison genomes
| Genea | Annotationb | Repeatc | Positiond | Variantse | Commentsf |
|---|---|---|---|---|---|
| Sag0003 | Diacylglycerol kinase domain, putative | (C)5 | 427 | (−1); Cjb111 | Truncation (74) |
| Sag0078 | Preprotein translocase SecY subunit | (A)7 | 1024 | (−1); 18rs21 | Truncation (21) |
| Sag0157 | DNase related, frameshift | (A)7 | 146 | (+1); A909, Nem316, 515, Cjb111, H36b | Fusion |
| Sag0203 | Polyribonucleotide nucleotidyltransferase | (A)7 | -20 | (−1); Coh1 | Unknown (NR) |
| Sag0232 | HP | (A)7 | 158 | (−1); Cjb111 | Truncation (71) |
| Sag0412-3 | Reg. protein RecX and RNA methyl transferase | (T/A)7 | -50/-55 | (−1); 515 | Unknown/in put. promoter |
| Sag0416 | CspA, serine protease, CWP | (A)7 | 1325 | (+1); A909; and (−1); Coh1 | Truncation (64) |
| Sag0679 | CHP | (A)7 | 714 | (−1); H36b | Truncation (29) |
| Sag0708 | Alpha amylase family protein | (T)7 | -11 | (−1); 515 | Unknown (NR) |
| Sag0723 | RNase III | (A)7 | 0 | (−1); Coh1, 515 | Unknown (NR) |
| Sag0771 | CWP | (A)7 | 594 | (−1); Coh1 | Truncation (61) |
| Sag0792-3 | CHP/glycerate kinase 2 | (T/A)7 | -120/-39 | (−1); Coh1 | -10 promoter element/unknown (NR) |
| Sag0817 | Probable thiamine transporter | (A)7 | -11 | (−2); Coh1 | Unknown (NR) |
| Sag0820 | Ribonucleoside-diphosphate reductase 2 | (A)7 | -13 | (+1); Coh1 | Unknown (NR) |
| Sag0833 | HP | (A)7 | 4 | (−1); Coh1 | Truncation (99) |
| Sag0835 | CHP | (A)7 | 16 | (−1); 515 | Truncation (98) |
| Sag0858 | ATP synthase F0, subunit | (A)7 | -13 | (−1); Coh1 | Unknown (NR) |
| Sag0878 | Acetoin dehydrogenase | (T)7 | -10 | (−1); 515 | Unknown (NR) |
| Sag0913 | Chloramphenicol acetyltransferase | (A)7 | 14 | (−1); Nem316, Cjb111 | Truncation (98) |
| Sag1003 | Putative permease, MP | (A)7 | 744 | (−1); Coh1 | Truncation (74) |
| Sag1041 | HP | (A)7 | -43 | (−1); Coh1, Cjb111 | Unknown (NR) |
| Sag1063 | Flavoprotein-related protein | (A)7 | 670 | (+1); Coh1 | Truncation (1) |
| Sag1086 | Xanthine phosphoribosyl transferase | (T)7 | -26 | (+2); Coh1 | In put. promoter |
| Sag1127 | Conserved domain protein | (A)7 | 1068 | (+1); A909, H36b, 515 | None (prior independent truncation) |
| Sag1175 | CpsA | (T)7 | -18 | (−1); A909, 18rs21, 515 | Unknown (NR) |
| Sag1183 | Ribose 5-phosphate isomerase | (T)7 | 92 | (+2); 18rs21 | Truncation (85) |
| Sag1215 | Putative exfoliative toxin A | (T)7/(T)7 | 133/-12 | (−1/0); 515 | Truncation (85) |
| (0/-1); A909, H36b | Unknown (NR) | ||||
| Sag1221 | Glycerophosphoryl diester phosphodiesterase, inactivated by PM | (A)6 | 71 | (+1); A909, H36b | Truncation (96), PM generates new start downstream |
| Sag1409 | RogB transcriptional reg., frameshift | (T)7 | 957 | (+1); Cjb111, 18rs21, H36b | Fusion |
| Sag1465 | Protease, putative | (T)7 | 173 | (−1); Cjb111 | Truncation (80) |
| Sag1503 | HP | (T)7 | 7 | (+1): Cjb111, H36b | Truncation (94) |
| Sag1554 | HP | (A)7 | 0 | (−1); Coh1, Cjb111, H36b | Unknown (NR) |
| Sag1576 | Transposase IS30 family, frameshift | (G)5 | 366 | (−1); A909, Coh1, 18rs21 | Fusion |
| Sag1734 | Transporter, putative | (A)7 | -13 | (−1); A909, NeM316, Coh1, 515, Cjb111, H26b | Unknown (NR) |
| Sag1756 | CHP/threonin aldolase | (T)7 | -21 | (+1); NeM316, 515 | Unknown (NR) |
| Sag1896 | RegR, sugar-binding transcriptional reg. | (A)7 | -32 | (−1); Cjb111 | Unknown (NR) |
| Sag1933 | PTS system, IIC component, putative | (A)7 | 357 | (+2); Coh1 | Truncation (75) |
| Sag2072 | Uridine phosphorylase | (A)7 | -28 | (+1); A909, H36b; and (+2); Coh1 | Unknown (NR) |
| Sag2170 | CHP | (G)7 | 98 | (−1); A909 | Truncation |
That is, the gene identifier in the reference genome 2603v/r.
Abbreviations: HP, hypothetical protein; CHP, conserved hypothetical protein; CWP, cell wall-attached protein; reg., regulator.
The repeat unit is shown in parenthesis, and the number of consecutive units is indicated. When the SSR is located between two ORFs on different strands, the form “(A/T)” “is used. When two separate SSRs relate to the same ORF, the form” “(T)/(T)” is used.
The location of the SSR respective to the start codon of the closest ORF. SSRs with positive numbers are found in coding sequence, whereas negative numbers indicate an upstream location.
The number of repeat units compared to the reference strain, and the strain(s) where variants are found.
The predicted effect of the variation relative to the reference strain. Percentage values are indicated in parentheses. NR, near RBS. put., putative.