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SIFT makes use of sequence homology and median evolutionary conservation scores to predict conserved protein function.
Consequently, we considered only protein identity that was 20% or higher as indication for functional conservation, a value that corresponds with previous reports that conserved protein function is indicated by at least 18 20% protein sequence identity [ 35].
The results demonstrated that mouse Syx1b can efficiently and functionally replace zebrafish Syx in developing embryos, indicating evolutionarily conserved protein function; and that the MO effects are specific to Syx.
Overall, there was greater amino acid conservation between DIA1 and DIA1R proteins in the central portion, which suggests this region mediates a key, conserved protein function.
The deduced BiP proteins and other BiP homologs were highly conserved with respect to functional domains and tertiary structures, suggesting the conserved protein function of BiP from different species.
Moreover, the characteristic motif of STT3, WWDYG was found in SaSTT3A and SaSTT3B, suggesting the potentially conserved protein function.
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Mitochondrial protein-coding genes normally have low rates of non-synonymous change (changes that alter amino acids) compared to synonymous change (dN/dS), due to strong purifying selection to conserve protein function [14], [15].
In contrast, more recent (terminal) snake branches have typical dN/dS ratios, indicating that strong purifying selection to conserve protein function subsequently resumed (Figures S1, S2, S3, S4, S5, S6, S7, S8).
Conversely, as species diverge the small number of radical mutations may be explained by the conservation of physiochemical properties, which are often conserved to maintain protein function even across evolutionary distant species [ 40].
Analysis of protein sequence shows that Drosophila and human Arl1 share 78% identity in their amino acids, suggestive of well-conserved protein function between species.
However, it appears that PH domains, despite sharing low-sequence homology and non-conserved protein function, have a conserved core structurally composed of seven β-strands and one C-terminal α-helix [32].
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