Figure 2.

An example of colored alignment produced by the PROMALS server. These sequences are adenylate/guanylate cyclase catalytic domains selected from the PFAM database (Accession number: PF00211) (23). The first line in each alignment block begins with ‘Conservation:’ and shows conservation index numbers for conserved positions. The last line in each block begins with ‘Consensus_ss:’ and shows the consensus secondary structure predictions (‘h’: α-helix; ‘e’: β-strand). Each representative sequence has a magenta name and is colored according to PSIPRED secondary structure predictions (red: α-helix, blue: β-strand). A representative sequence and the immediate sequences below it with black names, if there are any, form a closely related group (determined by the option ‘Identity threshold’). Sequences within each group are aligned in a fast way. The groups are aligned using profile consistency with enhanced information from database searches and secondary structure predictions.