New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures

Abstract

CATH version 3.5 (Class, Architecture, Topology, Homology, available at http://www.cathdb.info/) contains 173 536 domains, 2626 homologous superfamilies and 1313 fold groups. When focusing on structural genomics (SG) structures, we observe that the number of new folds for CATH v3.5 is slightly less than for previous releases, and this observation suggests that we may now know the majority of folds that are easily accessible to structure determination. We have improved the accuracy of our functional family (FunFams) sub-classification method and the CATH sequence domain search facility has been extended to provide FunFam annotations for each domain. The CATH website has been redesigned. We have improved the display of functional data and of conserved sequence features associated with FunFams within each CATH superfamily.

Figure 1.

Screenshot of the CATH superfamily page for the aldolase superfamily. Sections displaying different types of data are labelled (a)–(i).

Figure 2.

Plot showing, for each enzyme superfamily in CATH, the number of unique EC terms, FunFams and SCs.

Figure 3.

2DSEC plot and structural superpositions of the structural representatives of a structural cluster in the aldolase superfamily. Structural features common to all the domains in the SC are shown in light blue on the superposition.

Figure 4.

Figures showing the protein domains 1h7oA00 (ALAD, left) and 1d3gA00 (DHODH) with common structural features coloured blue, embellishments green, substrates black and catalytic residues orange.

Figure 5.

Screenshot of the FunFam page associated with ALAD.

Figure 6.

Structural alignment of the two protein domains 1h7oA00 and 1d3gA00. The catalytic residues are highlighted according to their properties (aromatic residues are in red, polar residues in green and those with a positive charge are in purple).