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Table 2 Sequence and structure based evaluation of the effect of mutations (Table 1)

From: Insight into SNPs and epitopes of E protein of newly emerged genotype-I isolates of JEV from Midnapur, West Bengal, India

   Sequence based prediction Structure based prediction
Mutation SIFT PHD-SNP SNAP META-SNP SDM
Score Effect Score Effect Score Effect Score Effect ∆∆G
Kcal Mol−1
Domain I N002H 0.500 N 0.056 N 0.180 N 0.115 N +0.01
K138Ea 1.000 N 0.121 N 0.185 N 0.111 N +0.52
V176Ia 0.400 N 0.047 N 0.160 N 0.090 N +0.22
A177Ta 1.000 N 0.042 N 0.105 N 0.063 N −0.17b
Y183F 0.200 N 0.488 N 0.525 N 0.367 N +1.79
R193K 0.450 N 0.490 N 0.340 N 0.414 N −0.81
Domain II C060Y 0.000 D 0.935 D 0.800 D 0.882 D −2.33
N103K 0.000 D 0.833 D 0.780 D 0.771 D +1.61
F107La 1.000 N 0.218 N 0.310 N 0.155 N −0.97
T129M 0.070 N 0.106 N 0.410 N 0.143 N +0.86
A222S 0.420 N 0.177 N 0.115 N 0.162 N −0.77
G244E 1.000 N 0.070 N 0.215 N 0.065 N +1.85
G261S 0.200 N 0.152 N 0.105 N 0.134 N +1.74
H264Qa 0.074 N 0.074 N 0.225 N 0.078 N −0.75b
M279Ka 0.390 N 0.159 N 0.255 N 0.121 N −1.97
Domain III V315A 0.620 N 0.066 N 0.400 N 0.094 N −1.63
S327T 0.820 N 0.067 N 0.175 N 0.103 N +0.97
A366S 0.740 N 0.190 N 0.235 N 0.185 N −1.18
V372L 0.310 N 0.129 N 0.245 N 0.164 N −0.79
M374I 0.540 N 0.225 N 0.365 N 0.169 N +0.08
G388K 0.010 D 0.910 D 0.775 D 0.793 D +3.00
W396R 0.000 D 0.841 D 0.865 D 0.819 D −2.48
  1. D disease, N normal; aindicates these six mutations are not GI specific but also present in SA14, GIII isolates with reference to vaccine strain SA14-14-2 (Table 1);
  2. bindicates ∆∆G was calculated in reverse mutation form i.e. T177A and Q264H as WT E protein possesses T and Q at these positions respectively Server based four independent methods for sequence of ecto domain of E protein and Site Directed Mutator (SDM) [41] method for structure of all isolates was used for the purpose (see Materials and Methods for details)