Table 1.
Results of site-specific positive selection analysis of the slpA gene
| Model | P | lnL | Estimates of parameters | PS sites |
|---|---|---|---|---|
| M0: one ratio | 1 | −16877.369043 | ω = 0.1440 | None |
| M1: Neutral | 1 | −16292.610806 | p0 = 0.61757, p1 = 0.38243 ω0 = 0.08215, ω1 = 1.00000 |
Not allowed |
| M2: Selection | 4 | −16242.808880 | p0 = 0.59388, p1 = 0.32797 (p2 = 0.07815), ω0 = 0.08640, ω1 = 1.0000, ω2 = 68.75381 |
BEB 46 > 0.50 12 > 0.95 4 > 0.99 |
| M3: Discrete (K = 2) | 3 | −16210.1011 | p0 = 0.46054, (p1 = 0.53946) ω0 = 0.03195, ω1 = 0.35512 |
None |
| M3: Discrete (K = 3) | 5 | −16098.846498 | p0 = 0.38293, p1 = 0.51573, p2 = 0.10134 ω0 = 0.01892, ω1 = 0.24549, ω2 = 20.89735 |
None |
| M7: Beta | 2 | −16105.477356 | p = 0.41836, q = 1.29859 | Not allowed |
| M8: Beta&Omega > 1 | 4 | −16052.155863 | p0 = 0.92067, p = 0.47615, q = 1.96064 (p1 = 0.07933), ω = 29.20962 |
BEB 44 > 0.50 11 > 0.95 4 > 0.99 |
| M8a: Beta&Omega = 1 | 3 | −16095.794065 | p0 = 0.87118, p = 0.52389, q = 2.94963 (p1 = 0.12882), ω = 1.0000 |
Not allowed |
The table shows the number of residues predicted to be under positive selection for each site-specific model in the analyses. All models tested are displayed, along with number of parameters (P), log likelihood scores (lnL), estimates of parameters (where p = proportion of sites under a particular omega value, and ω = the ratio of non-synonymous substitution per non-synonymous site to synonymous substitution per synonymous site (DN/DS)). The number of positively selected sites with a given posterior probability is also shown