TABLE 3 .
Homoplasic SNPs
| Positiona | Locus tag(s) | Gene | Branchesb | Bootstrapc | Changed | Product (distance to ATG in bp) |
Functional category | Localizatione | Bvgf |
|---|---|---|---|---|---|---|---|---|---|
| 612075 | BP0607 | gpm | 2 (1, 3) | 99 | Silent | Phosphoglycerate mutase 1 |
Energy metabolism | Cytoplasmic | |
| 667028 | BP0658 | 2 (1, 19) | 55 | Q30 | Putative dehydrogenase | Miscellaneous | Cytoplasmic | ||
| 925864 | BP0888 | 2 (7, 1) | 100 | Silent | GntR family transcriptional regulator |
Regulation | Cytoplasmic | ||
| 997017 | BP0958 | cysM | 5 (1, 1, 4, 2, 1) | 100 | G247E | Cysteine synthase B | Amino acid biosynthesis |
Cytoplasmic | |
| 1109310 | 1064BP | maeB | 2 (6, 1) | 100 | Silent | NADP-dependent malic enzyme |
Central/intermediary metabolism |
Cytoplasmic | |
| 1109312 | 1064BP | maeB | 2 (6, 1) | 100 | Q28P | NADP-dependent malic enzyme |
Central/intermediary metabolism |
Cytoplasmic | |
| 1175956 | 1119BP | fim2 | 2 (7, 9) | 100 | R177K | Serotype 2 fimbrial subunit precursor |
Virulence- associated genes |
Extracellular | + |
| 1565529 | 1487BP | smoM | 2 (1, 4) | 100 | R176K | Putative periplasmic solute-binding protein |
Transport/binding proteins |
Unknown | + |
| 1647989 | 1568BP | fim3 | 2 (1, 1) | 98 | T130A | Serotype 3 fimbrial subunit precursor |
Virulence- associated genes |
Extracellular | + |
| 2018882 | BP1914P | 2 (1, 2) | 100 | Intergenic | Transposase for IS1663 (321) |
Phage or transposon related |
Unknown | ||
| BP1915P | 2 (1, 2) | 100 | Intergenic | Conserved hypothetical protein (23) |
Conserved hypothetical |
Unknown | |||
| 2213448 | BP2090P | 2 (8, 1) | 100 | Intergenic | ABC transporter substrate-binding protein (306) |
Transport/binding proteins |
Periplasmic | − | |
| BP2091P | 2 (8, 1) | 100 | Intergenic | Dioxygenase hydroxylase component (53) |
Small molecule degradation |
Cytoplasmic | − | ||
| 2374322 | 2249BP | bscI | 2 (1, 97) | 60 | Y114C | Type III secretion protein | Virulence- associated genes |
Unknown | + |
| 3041105 | BP2862P | 2 (6, 1) | 100 | Intergenic | Conserved hypothetical protein (174) |
Unknown | Unknown | ||
| BP2863P | 2 (6, 1) | 100 | Intergenic | Conserved hypothetical protein (148) |
Unknown | Cytoplasmic | |||
| 3251279 | BP3052P | 2 (6, 2) | 100 | Intergenic | Putative gamma- glutamyl transpeptidase (242) |
Miscellaneous | Periplasmic | ||
| 3992064 | 3789BP | ptlB | 2 (1, 1) | 69 | Silent | Pertussis toxin transport protein |
Virulence- associated genes |
CM | + |
a
Position in reference genome B. pertussis Tohama I.
b
Number of branches in which the homoplasic SNP occurred (number of strains/branch).
c
Number of trees in which SNP is homoplasic (100 trees tested).
d
Change in amino acid.
e
Subcellular localization: CM, cytoplasmic membrane.
f
Regulation by Bvg: + activated; − repressed; blank cells, not activated or repressed.