Figure 8. Substitution matrix adjustment.

Substitution matrices were generated for the alignment of the human protein CDK5RAP2 with its fly homolog cnn. The difference between the respective matrix and the adjusted matrix for the whole proteins is shown. This reference matrix is the one that BLAST uses for the alignment of these two proteins. When the difference is above zero (blue), then the two amino acids are more rare in the considered part of the protein. For example, proline is known to disrupt helices and hence also coiled-coils, therefore the scores for proline in the coiled-coil matrix are higher. In the substitution matrix for the hydrophobic interface (registers A/D), hydrophobic residues are more common, resulting in lower scores.