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. 2002 Jan 1;30(1):268-72.
doi: 10.1093/nar/30.1.268.

SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments

Julian Gough  1 , Cyrus Chothia
Affiliations

SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments

Julian Gough et al. Nucleic Acids Res. .

Abstract

The SUPERFAMILY database contains a library of hidden Markov models representing all proteins of known structure. The database is based on the SCOP 'superfamily' level of protein domain classification which groups together the most distantly related proteins which have a common evolutionary ancestor. There is a public server at http://supfam.org which provides three services: sequence searching, multiple alignments to sequences of known structure, and structural assignments to all complete genomes. Given an amino acid or nucleotide query sequence the server will return the domain architecture and SCOP classification. The server produces alignments of the query sequences with sequences of known structure, and includes multiple alignments of genome and PDB sequences. The structural assignments are carried out on all complete genomes (currently 59) covering approximately half of the soluble protein domains. The assignments, superfamily breakdown and statistics on them are available from the server. The database is currently used by this group and others for genome annotation, structural genomics, gene prediction and domain-based genomic studies.

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Figures

Figure 1
Figure 1
An example of the result of a sequence query. The protein (sp│P2931│EPA2_HUMAN) is a multi-domain protein with five structural domains predicted with confidence, and shown in grey, three non-significant predictions. Each domain covers a different region of the query sequence and may be classified in a different SCOP superfamily with a different score. The ‘Align’ button links to a sequence alignment, and the ‘Assign.’ button links to all genome assignments for the given superfamily.
Figure 2
Figure 2
A section of a result of a nucleotide search of human contig AB019437.00001 clearly showing a DNA/RNA polymerase domain consisting of exons 3–7. The alignment shows how the exons combine in order to make up a complete domain.
See this image and copyright information in PMC

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