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Table 1 Results of site-specific positive selection analysis of the slpA gene

From: Surface layer proteins from virulent Clostridium difficile ribotypes exhibit signatures of positive selection with consequences for innate immune response

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
  1. 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