Figure 2

Structural and sequence similarity scores of near-optimal sequence alignments and structural alignments for the protein pairs shown in Figure 1. Figures A. and B., 1 hdaB00 vs 1 mytA00 (pair 25). Figures C. and D., 1bcgA00 vs. 1b7dA00 (pair 42). Figures A. and C. show Zuker-generated alignments within 95% of the optimal score, using the BLOSUM50 scoring matrix and gap open/extension penalties of -10/-2. Figures B. and D. show 1000 probA-generated alignments using the BLOSUM50 scoring matrix, and gap open/extension penalties of -9.5/-1.2. The X-axis shows the semi-global sequence alignment score; the Y-axis shows the corresponding Levitt-Gerstein structural similarity score. Optimal sequence alignment, black circle; suboptimal alignments, gray circles. Blue X, Dali; green square, CE; red triangle, LSQMAN; magenta +, Matras. The optimal sequence alignment in Figure 2A has a structural similarity score of 2352, higher than any of the structure-based alignment scores (RMSD 1.51 Å, shift score of 0.94 with respect to the DALI alignment). The structural alignments have structural similarity scores ranging from 2330 to 2337, with RMSDs of 1.47 Å. In Figure 2C, the optimal sequence alignment has a structural alignment score of 2167 (RMSD 1.33 Å, shift score with respect to DALI of 0.66). Structural alignments have structural alignment scores ranging from 2210 to 2274, with RMSDs from 1.35 - 1.38Å. Matras did not produce an alignment for 1bcgA00 vs. 1b7dA00.