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Protein Science (2002), 11:233-244.
Copyright © 2002 The Protein Society

The CATH extended protein-family database: Providing structural annotations for genome sequences

Frances M.G. Pearl1,3, David Lee1,2,3, James E. Bray1, Daniel W.A. Buchan1, Adrian J. Shepherd1 and Christine A. Orengo1

1 Department of Biochemistry and Molecular Biology, University College London, University of London, London WC1E 6BT, UK
2 Department of Crystallography, Birkbeck College, University of London, London WC1E 7HX, UK

Reprint requests to: Dr. Frances Pearl, Department of Biochemistry and Molecular Biology, University College London, University of London, Gower Street, London WC1E 6BT, UK; e-mail: frances{at}biochem.ucl.ac.uk; fax: 44 (0) 20 7679 7193.

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.

Keywords: Structural genomics; fold assignment; homology; sequence profiles; CATH


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