Genome Analysis of Pass2 a Semi-Automated Database of Protein Alignments Organised as Structural Superfamilies

. Success of genomic sequencing projects has lead to an ever-increasing gap in the number of protein sequences and structure that are deposited in the databanks[1,2]. Homologous sequences sharing a degree of sequence, structural, and functional similarity[3,4] can be grouped though simple search programs. According to SCOP[5] (a dictionary of protein structural entrie), Superfamily of proteins are those sharing an insignificant sequence similarity yet possessing a similar function and fold, maintaining an evolutionary relationship among themselves. CAMPASS[6] forms the first version of a protein superfamily database, corresponding to 69 superfamilies, which records the alignments of proteins aligned using COMPARER[7]. Availability of such alignment databases over the World Wide Web offers the possibility to study and design experiments on specific superfamilies; they also permit systematic survey and analysis of various structural properties and to perform fold predictions. Analyses of structural and sequence differences amongst known superfamily members can hopefully provide useful guidelines for modelling distant related proteins. We report the genome analysis conducted for each Superfamily member for the semi-automated updated version of the superfamily alignment database, which has been designed to be in direct correspondence with SCOP database (1.53 release; [5]). The updated version of the database (PASS2) has 110 multimember superfamilies and 613 single member superfamilies. The analysis was conducted across 72 genomes (41 complete).