First Comprehensive In Silico Analysis of the Functional and Structural Consequences of SNPs in Human GalNAc-T1 Gene

Table 4

Top 10 templates used by I-TASSER to create the high-quality models for human GALNT1 secondary structure.

Rank	PDB Hit	Iden1	Iden2	Cov.	Norm. 𝑍-score
1	2ffuA	0.45	0.41	0.88	3.12
2	2d7iA	0.43	0.42	0.91	7.15
3	2ffuA	0.45	0.41	0.88	8.16
4	2ffuA	0.45	0.41	0.88	5.97
5	2ffuA	0.45	0.41	0.88	4.41
6	2d7iA	0.43	0.42	0.91	7.11
7	2ffuA	0.45	0.41	0.88	7.99
8	2d7rA	0.43	0.42	0.92	6.42
9	1xhbA	0.99	0.79	0.80	3.06
10	2ffuA	0.45	0.41	0.88	6.21

Rank of templates represents the top ten threading templates used by I-TASSER. “Ident1” is the percentage sequence identity of the templates in the threading aligned region with the query sequence. “Ident2” is the percentage sequence identity of the whole template chains with query sequence. “Cov” represents the coverage of the threading alignment and is equal to the number of aligned residues divided by the length of query protein. “Norm. 𝑍-score” is the normalized 𝑍-score of the threading alignments. Alignment with a Normalized 𝑍-score > 1 mean a good alignment and vice versa. The top 10 alignments reported above (in order of their ranking) are taken from the following threading programs: 1: MUSTER 2: HHSEARCH 3: SP3 4: PROSPECT2 5: PPA-I 6: HHSEARCH I 7: SPARKS 8: SAM T99 9: MUSTER 10: HHSEARCH.