(a) Output page of the PROMALS3D server. This page allows access of PROMALS3D alignments in three formats with various adjustable parameters. Links to inputs and intermediate results are also provided. (b) An example of colored alignment. This alignment is for input of four SH2 domain sequences selected from PFAM database (23) and four SH2 structures (pdb ids are 1aya, 1jyr, 1lkk and 1mil). The first line in each alignment block begins with ‘Conservation:’ and shows conservation index numbers for conserved positions. The line in each block beginning with ‘Consensus_ss:’ shows the consensus secondary structure predictions (‘h’: α-helix; ‘e’: β-strand). The line in each block beginning with ‘Consensus_aa’ shows consensus amino acids. If the weighted frequency of certain type of residues is above a certain threshold, the consensus symbol of that type is displayed. Symbols are provided for the following types: conserved amino acid residues: bold and uppercase letters; aliphatic residues (I, V, L): l; aromatic residues (Y, H, W, F): @; hydrophobic residues (W, F, Y, M, L, I, V, A, C, T, H): h; alcohol residues (S, T): o; polar residues (D, E, H, K, N, Q, R, S, T): p; tiny residues (A, G, C, S): t; small residues (A, G, C, S, V, N, D, T, P): s; bulky residues (E, F, I, K, L, M, Q, R, W, Y): b; positively charged residues (K, R, H): +; negatively charged residues (D, E): −; charged (D, E, K, R, H): c. 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 and they are aligned in the first stage.