Protein Alignments organised as Structural Superfamilies
The superfamilies are named after their codes in SCOP database: for example, 46548 refers to 'alpha-helical ferredoxin' superfamily. The superfamilies are chosen from SCOP and all the representative members are extracted by using cut-off of 40% sequence identity and good resolution. For NMR structures we assigned 3.2 as the resolution cutoff, and for CA only structures, we considered its homologous proteins. For all Multi Member Superfamilies the alignment of family members is based on the conservation of structural features like solvent accessibility, hydrogen bonding and the presence of secondary structures. We have employed COMPARER (Sali et al., 1990; Sali et al.,1992) to obtain the multiple sequence alignment of distantly related proteins. The final alignment of multi Member Superfamilies and Single Member Superfamilies are presented in JOY format (Mizuguchi et al., 1998) to display three-dimensional (3D) structural information in a sequence alignment and help to understand the conservation of amino acids in their specific local environment.