TABLE 1.
Simple sequence repeat variants in the seven S. agalactiae comparison genomes
| Genea | Annotationb | Repeatc | Positiond | Variantse | Commentsf |
|---|---|---|---|---|---|
| Sag0148 | Oligopeptide ABC transporter, lipoprotein | (TAAAAAAATG)3 | -103 | (−1); Cjb111 | Effect unknown |
| Sag0355 | CHP | (TA)4 | -40 | (−1); Coh1 | -10/-35 distance changes |
| Sag0466 | Thiolase | (A)8 | 116 | (−1); Nem316 | Truncation |
| Sag0972 | CHP, authentic frameshift | (A)9 | 145 | (−1); Nem316, Cjb111, H36b; and (−2); 515, Coh1 | Fusion in −1 |
| Sag0992 | Phosphate ABC transporter, lipoprotein | (A)8 | 2 | (−1); Coh1 | Truncation |
| Sag1033 | FtsK/SpoIIIE family protein | (G)7 | 13 | (+1); 515 | Truncation |
| Sag1133 | CHP, possible hydrolase | (AG)4 | 76 | (−1); 515, H36b | Truncation |
| Sag1236 | C5a peptidase, authentic frameshift | (A)8 | 3185 | (+1); 18rs21, Coh1 | LPXTG fusion |
| Sag1265 | Cadmium resistance transporter, putative | (T)8 | -1 | (−1); 18rs21 | Effect unknown |
| Sag1149 | Lipoprotein, putative | (A)8 | 11 | (−1); Coh1 | Truncation |
| Sag1555 | HP | (A)8 | 21 | (−1); 515, H36b, Coh1, Nem316 | Truncation |
| Sag1568 | Phosphoserine aminotransferase (SerC), frameshifted | (G)6 | 295 | (−1); Cjb111, H36b, Coh1, Nem316, 515 | Fusion |
| Sag1745 | HP | (A)8 | 18 | (−1); Cjb111 | Truncation |
| Sag1921 | Sensor histidine kinase | (A)9 | 3 | (−1); Cjb111 | Truncation |
| Sag2063 | BibA, CWP | (A)8 | 1120 | (−1); 515, Cjb111 | LPXTG truncation |
| Sag2094 | Competence/damage-inducible protein CinA, authentic frameshift | (T)8 | 301 | (−1); Cjb111, Coh1, H36b, Nem316 | Fusion |
| Sag2170 | CHP | (G)7 | 98 | (−1); A909 | Truncation |
a
That is, the gene identifier in the reference genome 2603v/r.
b
Abbreviations: HP, hypothetical protein; CHP, conserved hypothetical protein; CWP, cell wall-attached protein.
c
The repeat unit is shown in parenthesis, and the number of consecutive units is indicated.
d
The location of the SSR respective to the start codon of the closest ORF. SSRs with positive numbers are found in the coding sequence, whereas negative numbers indicate an upstream location.
e
The number of repeat units compared to the reference strain is given in parentheses, and the strain(s) where the variants are found are indicated.
f
The predicted effect of the variation relative to the reference strain.