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. 2003 Jan 1;31(1):469-73.
doi: 10.1093/nar/gkg051.

Gene3D: structural assignments for the biologist and bioinformaticist alike

Daniel W A Buchan  1 , Stuart C G Rison, James E Bray, David Lee, Frances Pearl, Janet M Thornton, Christine A Orengo
Affiliations

Gene3D: structural assignments for the biologist and bioinformaticist alike

Daniel W A Buchan et al. Nucleic Acids Res. .

Abstract

The Gene3D database (http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/) provides structural assignments for genes within complete genomes. These are available via the internet from either the World Wide Web or FTP. Assignments are made using PSI-BLAST and subsequently processed using the DRange protocol. The DRange protocol is an empirically benchmarked method for assessing the validity of structural assignments made using sequence searching methods where appropriate assignment statistics are collected and made available. Gene3D links assignments to their appropriate entries in relevent structural and classification resources (PDBsum, CATH database and the Dictionary of Homologous Superfamilies). Release 2.0 of Gene3D includes 62 genomes, 2 eukaryotes, 10 archaea and 40 bacteria. Currently, structural assignments can be made for between 30 and 40 percent of any given genome. In any genome, around half of those genes assigned a structural domain are assigned a single domain and the other half of the genes are assigned multiple structural domains. Gene3D is linked to the CATH database and is updated with each new update of CATH.

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Figures

Figure 1
Figure 1
Populating the Gene3D Database. (A) CATH Representative sequences (S95Reps) are scanned against the GenBank non-redundant database containing the sequences from the completed genomes using PSI-BLAST. Search results (B) are processed by DomainFinder to generate ‘Ranges’ (C). These are ‘cleaned-up’ by the DRange package (D) and final assignments are assimilated in the Gene3D database (E).
Figure 2
Figure 2
Bar chart showing the distribution domains assigned to genes in three typical organisms: Caenorhabdatis elegans, Methanococcus jannaschii and Escherichia coli. The Y axis has been truncated.
Figure 3
Figure 3
Bar chart showing the relative percentage of domain classes from the four major CATH classes for genes that have been assigned a CATH domain. The four classes are: Class 1: all alpha folds; Class 2: all beta folds; Class: 3 mixed alpha and beta folds and Class 4: folds with little secondary structure.
Figure 4
Figure 4
Diagram shows a typical entry page (A) for a given genome (e.g. Mycoplasma genitalium) and the statistics presented and an (B) example of the diagram and data that can be retrieved for a gene.
See this image and copyright information in PMC

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