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

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 (D_N/D_S)). The number of positively selected sites with a given posterior probability is also shown

ISSN: 2730-7182