FIGURE 19. Protein evolution.

The figure shows percentage residue identity and cumulative non-synonymous to synonymous codon rate ratios for total proteins and for regions with and without predicted InterPro domains, predicted SMART domains with or without known enzymatic activity, and SMART domains specific to three different subcellular compartments. The 12,845 orthologous gene pairs referred to in Table 12 were used for analysis. a, Proteins were divided into regions with and without InterPro domains, and per cent identity was calculated for total proteins (black) and for domain-containing (red line) and domain-free (grey line) regions. The higher conservation of domain-containing regions, relative to domain-free regions, is consistent with their greater functional conservation. The protein sequences are plotted in bins of 4% identity. In calculating the per cent amino acid identity between two sequences, the number of identical residues was divided by the total number of alignment positions, including positions where one sequence was aligned with a gap. b, Cumulative K_A/K_S ratios for total proteins (black line) and for regions with (red line) and without (grey line) predicted Interpro domains. Protein-domain-containing regions have low K_A/K_S ratios (<0.15), suggesting that they may be subject to greater degrees of purifying selection than are the domain-free regions. The differences in functional constraints between predicted domain regions and the rest of the protein may be found to be even more pronounced, as a significant proportion of sequences may contain as yet unpredicted protein domains. c, Cumulative K_A/K_S ratios for SMART domain predictions with (red line) or without (black line) known enzymatic activity. The higher proportion of catalytic domains with low K_A/K_S ratios is an indication of the greater purifying selection acting on these sequences. d, Cumulative K_A/K_S ratios for predicted SMART domains that are specific to one of three different subcellular compartments. Compared with intracellular (cytoplasmic (red) and nuclear (black)) domains, a greater proportion of secreted domains (grey) possess higher K_A/K_S values. This indicates that secreted, often extracellular domains are subject, on average, to greater positive diversifying selection.