Figure 9.

Examples of structure pairs that are not correctly aligned by HHpred and/or SUPRB. For each example, the structure pairs are colored to indicate corresponding secondary structures in a structural alignment by TM-align on the top panel. On the bottom panel, aligned secondary structures by HHpred and SUPRB are shown by red (HHpred) and blue (SUPRB) arrows. The secondary structures of the same color on the top and the bottom panel correspond to each other. Arrows indicate β strands while boxes are α helices. Note that the length of the lines does not reflect the actual size of the proteins (two proteins do not necessarily have the same length). A, left, 2h7wB (query), right 1ifrA (template). TM-score (RMSD) of the predicted structure of the query inferred from the HHpred/SUPRB alignments are 0.346 (4.20 Å) and 0.290 (4.09 Å), respectively. B, Left, 1xsiC (query), right, 2c8nA (template). TM-score (RMSD) of the structure models using HHpred/SUPRB alignments are 0.410 (2.83 Å) and 0.269 (3.45 Å), respectively. C, Left, 1amxA (query), right, 1ayoA (template). TM-score (RMSD) of the structure models using HHpred/SUPRB alignments are 0.591 (3.50 Å) and 0.589 (3.30 Å), respectively. D, Left, 1uc8_B (query), right, 1auvA (template). TM-score (RMSD) of the structure models using HHpred/SUPRB alignments are 0.438 (2.91 Å) and 0.416 (2.62 Å), respectively