Superfamily (proteins)
| Content | |
|---|---|
| Description | The SUPERFAMILY database provides structural and functional annotation for all proteins and genomes. |
| Data types captured |
Protein families, genome annotation, alignments, Hidden Markov models (HMMs) |
| Organisms | all |
| Contact | |
| Research center | University of Bristol |
| Laboratory | |
| Primary citation | PMID 19036790 |
| Access | |
| Data format | FASTA format |
| Website | supfam |
| Download URL | supfam |
| Miscellaneous | |
| License | GNU General Public License |
| Version | 1.75 |
SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes. It classifies amino acid sequences into known structural domains, especially into SCOP superfamilies. Domains are functional, structural, and evolutionary units that form proteins. Domains of common Ancestry are grouped into superfamilies. The domains and domain superfamilies are defined and described in SCOP.Superfamilies are groups of proteins which have structural evidence to support a common evolutionary ancestor but may not have detectable sequence homology.
The SUPERFAMILY annotation is based on a collection of hidden Markov models (HMM), which represent structural protein domains at the SCOP superfamily level. A superfamily groups together domains which have an evolutionary relationship. The annotation is produced by scanning protein sequences from completely sequenced genomes against the hidden Markov models.
For each protein you can:
For each genome you can:
For each superfamily you can:
All annotation, models and the database dump are freely available for download to everyone.
Sequence Search
Submit a protein or DNA sequence for SCOP superfamily and family level classification using the SUPERFAMILY HMM's. Sequences can be submitted either by raw input or by uploading a file, but all must be in FASTA format. Sequences can be amino acids, a fixed frame nucleotide sequence, or all frames of a submitted nucleotide sequence. Up to 1000 sequences can be run at a time.
Keyword Search
Search the database using a superfamily, family, or species name plus a sequence, SCOP, PDB, or HMM ID's. A successful search yields the class, folds, superfamilies, families, and individual proteins matching the query.
Domain Assignments
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Wikipedia