BMC Immunology

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
	Mutation	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
	K138E^a	1.000	N	0.121	N	0.185	N	0.111	N	+0.52
	V176I^a	0.400	N	0.047	N	0.160	N	0.090	N	+0.22
	A177T^a	1.000	N	0.042	N	0.105	N	0.063	N	−0.17^b
	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
	F107L^a	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
	H264Q^a	0.074	N	0.074	N	0.225	N	0.078	N	−0.75^b
	M279K^a	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

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);
^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)

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