Figure 4

GASH alignment format. The alignment between 1bwwA and 1jv5B using default GASH is shown. In addition to the total NER score (eqn. 1), the residue-based similarity score (eqn. 2) was evaluated and scaled to integer values between 0 and 9. The distribution of such equivalences is reported at the bottom of the alignment. In order to roughly define the beginning and end of the most important parts of each alignment the first and last set of 5 continuous residues where the average similarity score was 5 or more was located. We refer to this region as the core alignment, and report the number of gaps and aligned residue pairs within the region. Also, the number of residues aligned under the three RMSD cutoffs, N2-6 are indicated. The alignments were written out with the residue pairs and secondary structure color coded by the similarity scale (with red the most and blue the least similar), making it easy to recognize regions of structural similarity.