Figure 8
From: Species-specific protein sequence and fold optimizations
Sequence to structural domain alignment Sequence to structural domain alignments (A, B). A genomic sequence (SEQ) is aligned to a homologous sequence with a 3D structure (STR) using a secondary structure profile using ClustalW. Note the insertion of gaps (denoted by -, red) in non-structured regions of the 3D structure. In the MERGE step, gaps in the structure are masked out, and eliminated in the compression step (COMP). At this point, the number of identical residues and the number of residues in the genomic sequence occupying a domain position in the structure are counted. Since domain 1 alignment passes the minimal 25% identity and 75% occupancy, it is used for further analysis. However, the %identity in the domain 2 alignment (B) is lower than the threshold of 25%, and the entire domain alignment is masked out and not used in any further analyses.