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SUPERFAMILY Description
SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.
The SUPERFAMILY annotation is based on a collection of hidden Markov models, 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 over
1,200 completely sequenced genomes
against the hidden Markov models.
For each protein you can:
 Submit sequences for SCOP classification
View domain organisation, sequence alignments and protein sequence details
For each genome you can:
Examine superfamily assignments, phylogenetic trees, domain organisation lists and networks
Check for over- and under-represented superfamilies within a genome
For each superfamily you can:
Inspect SCOP classification, functional annotation, Gene Ontology annotation, InterPro abstract and genome assignments
Explore taxonomic distribution of a superfamily across the tree of life
All annotation, models and the database dump are freely available for download to everyone.
Description cont.
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Major Features
| Sequence search |
Submit your protein, or DNA, sequence for superfamily and family level classification.
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| Keyword search |
Search for superfamily names, family names, species names, sequence IDs,
SCOP IDs,
PDB IDs and hidden Markov model IDs.
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| Domain assignments |
Domain assignments, alignments and architectures for completely sequenced
eukaryotic, and
prokaryotic organisms.
Additional sequence collections
are also included.
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| Comparative genomics tools |
Browse unusual (over- and under-represented) superfamilies and families,
adjacent domain pair lists and graphs, unique domain pairs, domain combinations,
domain architecture co-occurrence networks and domain distribution across taxonomic kingdoms for each organism.
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| Genome statistics |
For each genome: number of sequences, number of sequences with assignment,
percentage of sequences with assignment, percentage total sequence coverage, number of domains assigned,
number of superfamilies assigned, number of families assigned, average superfamily size,
percentage produced by duplication, average sequence length, average length matched, number of domain pairs
and number of unique domain architectures.
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| Superfamily annotation |
InterPro have added abstracts for 1,052 superfamilies,
and 763 superfamilies have some Gene Ontology (GO) annotation.
Mapping file between SUPERFAMILY and GO: SUPERFAMILY2go.
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| Functional annotation |
Functional annotation of
SCOP 1.73 superfamilies. By
Christine Vogel.
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| Phylogenetic trees |
Genome combinations, or specific clades, can be displayed as individual trees.
The trees are based on protein domain architecture data for all genomes in SUPERFAMILY, and
are generated using heuristic parsimony methods.
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| Similar domain architectures |
Finds the 10 domain architectures which are most similar to a domain architecture of interest.
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| Profile comparison |
For finding remote domain matches. Available when the sequence search fails to find a significant match.
Profile comparison (PRC) for aligning and scoring two profile hidden Markov
models by Martin Madera.
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| Hidden Markov models |
Produce SCOP domain assignments for your
sequences using the SUPERFAMILY models. HMM visualisation by
Martin Madera,
e.g. model 0045110.
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| Web services |
Distributed Annotation Server and linking to SUPERFAMILY.
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| Downloads |
Sequences, assignments, models, MySQL database and scripts - updated weekly.
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Recent news
More details on recent updates to SUPERFAMILY can be found in the news archive.
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