Table 4.
Gene loci identified to be both under positive selection and homologous recombination.
| Locus Tag | Locus | Gene Annotation | Positive Selection Analysis | FDR-p-value (Test 2 FDR p-value) | Recombination Method | Smallest significant p-value |
|---|---|---|---|---|---|---|
| CT681 | ompA | major outer membrane protein | Test 1 | 0.002606405 | NSS, MaxChi GeneCon, PHI | 0.00E+00 |
| CT824 | - | insulinase family zinc metalloprotease | Test 1 | 9.81E-05 | NSS, PHI | 5.00E-03 |
| CT852 | yhgN | Yhgn Family Protein/putative integral membrane protein | Test 2 (Clade 1) |
0.01888237 | MaxChi, GeneCon | 0.00E+00 |
| CT869 | pmpE | polymorphic outer membrane protein | Test 1 | 1.55E-32 | NSS, MaxChi GeneCon, PHI | 0.00E+00 |
| CT870 | pmpF | polymorphic outer membrane protein | Test 1 | 1.55E-32 | NSS, MaxChi GeneCon, PHI | 0.00E+00 |
| CT875 | - | hypothetical protein | Test 1, Test 2 (Clade 4) |
2.93E-07 (0.001) | MaxChi | 8.00E-03 |
| CT011 | - | hypothetical protein | Test 1, Test 2 (Clade 2) |
0.008772363 | MaxChi, GeneCon | 0.00E+00 |
| CT033 | recD_1 | exodeoxyribonuclease V alpha chain | Test 2 (Clade 4) |
0.0316283 | NSS | 4.40E-02 |
| CT049 | - | hypothetical protein | Test 1 | 6.42E-06 | NSS, MaxChi GeneCon, PHI | 0.00E+00 |
| CT107 | mutY | A/G-specific adenine DNA glycosylase | Test 1 | 2.44E-10 | MaxChi, GeneCon | 3.00E-04 |
| CT112 | pepF | oligoendopeptidase F | Test 2 (Clade 4) |
0.014 | GeneCon | 0.0127 |
| CT115 | incD | inclusion membrane protein D | Test 1, Test 2 (Clade 1) |
4.51E-04 (3.56E-04) | MaxChi | 1.10E-02 |
| CT144 | - | hypothetical protein | Test 1 | 5.78E-13 | NSS, MaxChi GeneCon, PHI | 0.00E+00 |
| CT244 | - | hypothetical protein | Test 1, Test 2 (Clade 3) |
2.95E-06 (1.56E-08) | MaxChi, GeneCon | 0.00E+00 |
| CT288 | - | Hypothetical protein/candidate inclusion membrane protein | Test 1, Test 2 (Clade 4) |
2.95E-06 (0.0058) | NSS | 5.00E-03 |
| CT315 | rpoB | DNA-directed RNA polymerase subunit beta | Test 2 (Clade 4) |
0.0067 | MaxChi | 2.10E-02 |
| CT448 | secD/secF | bifunctional preprotein translocase subunit SecD/SecF | Test 2 (Clade 3) |
2.50E-05 | MaxChi, GeneCon | 0.00E+00 |
| CT456 | - | hypothetical protein/translocated actin-recruiting protein (tarp) | Test 1, Test 2 (Clade 1) |
0.0021 (6.30E-06) | NSS, MaxChi, GeneCon | 0.00E+00 |
| CT470 | recO | DNA repair protein RecO | Test 1 | 0.0036 | MaxChi | 4.00E-03 |
| CT551 | dacC | D-alanyl-D-alanine carboxypeptidase | Test 2 (Clade 4) |
0.051 | MaxChi | 2.00E-02 |
| CT580 | - | hypothetical protein/putative integral membrane protein | Test 1 | 1.46E-09 | MaxChi | 1.10E-02 |
| CT604 | groEL_2 | 60 kDa chaperonin GroEL2 | Test 1, Test 2 (Clade 3) |
0.006 (1.35E-15) | MaxChi, GeneCon | 0.00E+00 |
| CT619 | - | hypothetical protein | Test 2 (Clade 1) |
0.008 | NSS, MaxChi, GeneCon | 0.00E+00 |
GeneCon -> GENECONV; NSS -> Neighbor Similarity Score; MaxChi -> Maximum χ2; PHI -> Pairwise Homoplasy Test