Pfam - Protein families database of alignments and HMMs PROSITE - Database of protein domains, families and functional sites PIRSF - SuperFamily Classification System PASS2 - Protein Alignment as Structural Superfamilies v2 - PASS2@NCBS[6] SUPERFAMILY - Library of HMMs representing superfamilies and database of (superfamily and family) annotations for all completely sequenced organisms SCOP and CATH - classifications of protein structures into superfamilies, families and domains