The CATH extended protein-family database: providing structural annotations for genome sequences.
An automatic sequence search and analysis protocol (DomainFinder) based on PSI-BLAST and IMPALA, and using conservative thresholds, has been developed for reliably integrating gene sequences from GenBank into their respective structural families within the CATH domain database (http://www.biochem.ucl.ac.uk/bsm/cath_new). DomainFinder assigns a new gene sequence to a CATH homologous superfamily provided that PSI-BLAST identifies a clear relationship to at least one other Protein Data Bank sequence within that superfamily. This has resulted in an expansion of the CATH protein family database (CATH-PFDB v1.6) from 19,563 domain structures to 176,597 domain sequences. A further 50,000 putative homologous relationships can be identified using less stringent cut-offs and these relationships are maintained within neighbour tables in the CATH Oracle database, pending further evidence of their suggested evolutionary relationship. Analysis of the CATH-PFDB has shown that only 15% of the sequence families are close enough to a known structure for reliable homology modeling. IMPALA/PSI-BLAST profiles have been generated for each of the sequence families in the expanded CATH-PFDB and a web server has been provided so that new sequences may be scanned against the profile library and be assigned to a structure and homologous superfamily.
Pearl
Frances M G
FM
Department of Biochemistry and Molecular Biology, University College London, University of London, London WC1E 6BT, UK. frances@biochem.ucl.ac.uk
Lee
David
D
Bray
James E
JE
Buchan
Daniel W A
DW
Shepherd
Adrian J
AJ
Orengo
Christine A
CA
D000465:Algorithms; D005075:Biological Evolution; D016208:Databases, Factual; D030562:Databases, Protein; D016678:Genome; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D013329:Structure-Activity Relationship
D011506:Proteins