. Author manuscript; available in PMC: 2015 Oct 1.

Published in final edited form as: J Mol Evol. 2014 Sep 13;79(0):130–142. doi: 10.1007/s00239-014-9644-x

Table 2.

Availability of homologous crystal structures

Viral Protein	BLAST hits^a	Unique sequences
		all	≥2%^b	≥5%^b	≥ 10%^b
Hemagglutinin precursor	63	17	10	9	7
Dengue protease helicase	31	13	7	7	7
West nile protease	21	16	10	7	6
Japanese encephalitis helicase	31	12	7	7	7
Hepatitis C protease	302	33	10	5	4
Rift valley fever nucleoprotein	95	9	5	5	5
Crimean congo nucleocapsid	7	4	3	2	2
Marburg RNA binding domain	63	9	5	3	3
Influenza nucleoprotein	69	15	4	4	2

Although most viral proteins have many PDB structures available, the sequence divergence among these structures is low. Therefore, when calculating RMSF from crystal structures, we considered only those proteins with at least five homologous structures at 5 % pairwise sequence divergence (highlighted in bold).

BLAST hits against all sequences in the PDB, excluding hits with < 35 % sequence identity and < 90 % alignment length

Unique sequences at indicated minimum pairwise sequence divergence