Table 1. Relationship between evolutionary rates and the conservative nature of fixed amino acid substitutions.

Evolutionary rates of proteins in the human genome are represented by the percentage of identities between human proteins and their orthologs in Macaca monkey. The proteins are divided into groups of different evolutionary rates, and the proportion of conservative amino acid mismatches in each group are shown for the four different ranking matrixes. Not all proteins encoded by the macaque and human genomes are considered because some proteins do not have easily identifiable orthologs. Also, we limited our analysis to proteins that have length >200 amino acids and show >60% identity between macaque and human in order to reduce the chance of misidentifying orthologs.

Identity %	BLOSUM62	EX	delta-V	delta-P	# proteins	Length ave.
Protein length >1,102 amino acid with no gaps in alignment
>99	0.49	0.30	0.34	0.67	136	1532.7
98–99	0.44	0.25	0.32	0.63	137	1464.0
96–98	0.42	0.24	0.32	0.58	125	1539.4
87–96	0.38	0.20	0.31	0.55	57	1414.4
Protein length >1,102 amino acid with gaps in alignment
>99	0.47	0.31	0.42	0.70	61	1659.3
98–99	0.41	0.24	0.34	0.63	119	1855.8
96–98	0.36	0.21	0.32	0.56	320	1792.7
87–96	0.33	0.19	0.31	0.50	437	1727.3
Protein length 200–1,102 amino acid with no gaps in alignment
>95	0.43	0.25	0.32	0.63	6984	478.3
90–95	0.39	0.20	0.31	0.55	1229	407.9
80–90	0.38	0.20	0.32	0.52	276	350.9
60–80	0.41	0.25	0.37	0.57	91	372.8
Protein length 200–1,102 amino acid with gaps in alignment
>95	0.38	0.22	0.32	0.59	2001	601.1
90–95	0.33	0.19	0.31	0.51	1529	566.4
80–90	0.30	0.17	0.30	0.47	1050	489.1
60–80	0.33	0.20	0.33	0.48	467	447.1