Figure 3.

Similarity scores and dN values. (a) Similarity scores and the average dN values of motifs 1 and 3 plus 10-residue flanking fragments. The curve indicates the similarity scores along the upstream flanking region, the motif region (peak), and the downstream flanking region. The dashed line shows the average similarity value for the entire alignment. The vertical axis is the score obtained from the scoring matrix BLOSUM62, with scores ranging from -4 to 11. The horizontal axis indicates the position of the alignment. The three values indicate the nonsynonymous substitution (dN) values in the upstream flanking region, the motif region (peak), and the downstream flanking region, respectively. Diagrams for other motifs are given in Additional data file 9. (b) Distribution of pairwise dN values of motifs 1 and 3. Most dN values of motifs are equal to or less than 0.6. In contrast, the counterparts of flanking regions are equal to or greater than 1. This result indicates that sites in motif regions are highly conserved and less frequently subject to substitution than those in flanking regions. White boxes, amino-terminal regions; gray boxes, motif regions; black boxes, carboxy-terminal regions. Histograms for other motifs are given in Additional data file 10.