Table 2

List of five S. sclerotiorum effector candidates selected based on Ka/Ks > 1 in pairwise comparisons with their B. cinerea orthologs
Protein ID Annotation PFAM domains Length Ka/Ks vs BC1T KaKs vs BcT4 Ka/Ks > 1 sites Prob
SS1G_04551 Pectinesterase A Pectinesterase (PF01095.14) 308 2 2 max Ka/Ks = 0.93 NA
SS1G_07158 - DUF1374 (PF07118) 328 6 ND max Ka/Ks = 0.4 NA
SS1G_07749 Xylanase Glycoside hydrolase family 11 (PF00457.12) 200 4 4 R36, L43, D74, Q76, S128, N174, S200 0.08224
SS1G_10165 Pectinesterase Pectinesterase (PF01095.14) 310 2 0,061669 P22, K31, T34, A36, S54, A63, S85, S86, G88, S89, Q95, A118, D146, I165, F191, D208, P211, S212, T213, L218, 226I, 230A, 233S, 236A, 237G, 238 T, S246, V253, M258, S259, N260, 261 V, N263, V269, S274, P275, N276, 278Q, H285, A286, A290, H301, S302, P306, S310, N316, K318, S319, S324 0.00038
SS1G_10617 Glycoside hydrolase family 15 protein Glycoside hydrolase family 15 (PF00723.16); Carbohydrate-binding module family 20 (PF00686.14); Carbohydrate-binding module family 25 (PF03423.8) 628 2 0,078172 N53, R56, M81, S91, N128, S313, S361, Q383, Q409, S416, N514, Y526, F537, V549, K586, V589, S605, S617, Q639 0.2987

Site specific Ka/Ks ratio estimated using Bayesian inference based on the M8 model of Yang et al., 2000. Only sites with Ka/Ks > 1 in the mature protein sequence are reported. P-value for positive selection estimated using a likelihood ratio test based on the comparison of twice the log likelihood difference obtained with the M8 and M8a null model with a chi-square probability table of degree of freedom 1. BC1T, Botrytis cinerea B.05 genome; BcT4, Botrytis cinerea T4 genome; ND, not determined.

Guyon et al.

Guyon et al. BMC Genomics 2014 15:336   doi:10.1186/1471-2164-15-336

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