Table 3. Site analysis. Selective pressures and Likelihood-ratio-tests in protamine 1 and protamine 2 sequences.
| Protein (domain) | N | Lc | Selective pressures: | % class 1 (ω<1) | % class 2 (ω = 1) | % class 3 (ω>1) | Best fit model | 2Δl | parameter estimates | PSS |
| All sites | 41 | 51 | 8 | M2a (selection) | 9.71** | p0 = 0.41, p1 = 0.50993, p2 = 0.07950, ω0 = 069, | 33C*, 39V | |||
| Protamine1 | 16 | 153 | Anchoring domains | 70 | 16.6 | 13.3 | M8 (beta and ω) | 7.34* | p0 = 0.58495, p = 0.0050, q = 0.04910, p1 = 0.41505, ω = 2.65844 | 33C*, 38T*, 39V** |
| Phosphorylation sites | 57.1 | 28.6 | 14.3 | |||||||
| All sites | 63.02 | 36.98 | M1a (neutral) | 2.64 | p0 = 0.63016, p1 = 0.36984, ω1 = 1.00 | not allowed | ||||
| cleaved-Protamine 2 | 16 | 165 | Cleaving sites | 57.14 | 42.86 | M7 (beta) | 3.57 | p = 0.09398, q = 0.13753 | not allowed | |
| Phosphorylation sites | 100 | 0 | ||||||||
| All sites | 13.32 | 86.67 | M1a (neutral) | 2.12 | p0 = 0.13325, p1 = 0.86675, ω1 = 1.00 | not allowed | ||||
| mature-Protamine 2 | 16 | 162 | Anchoring domains | 0 | 100 | M7 (beta) | 2.52 | p = 35.58178, q = 0.00500 | not allowed | |
| Phosphorylation sites | 0 | 100 |
Parameter estimation and likelihood scores under models of variable ω ratios among sites for protamine 1, cleaved region of protamine 2 and the mature form of protamine 2. The data have N sequences, each of Lc codons after alignment gaps are removed. Differences between log-likelihood values of models with 99% statistical significance level for 2 d. f. are indicated in ** and with 95% of statistical significance in *. The proportion of sites under positive selection (p1), or under selective constraint (p0) and parameters p and q for the beta distribution are given. Positively selected sites (PSS) with a posterior probability >0.95 (*) and >0.99 (**) in a Bayes Empirical Bayes are indicated. Selectives pressures are shown as proportion of amino acid sites for different classes of selective regimes. Class 1: sites under purifying selection (0<ω<1); Class 2: sites neutrally evolving (ω = 1); Class 3: sites subject to positive selection or relaxation (ω>1). Proportions of sites in each selective class were also calculated for DNA-anchoring domains, phosphorylation motifs and cleaving sites.