SUPERFAMILY 1.75 HMM library and genome assignments server

SUPERFAMILY 2 can be accessed from Please contact us if you experience any problems.


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 2,478 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 SCOP superfamily and family level classification.

Keyword search

Search for superfamily, family or species names plus sequence, SCOP, PDB or hidden Markov model IDs.

Domain assignments

Domain assignments, alignments and architectures for completely sequenced eukaryotic and prokaryotic organisms, plus sequence collections.

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.

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.

Gene Ontology Domain-centric Gene Ontology (GO) automatically annotated by Hai Fang.
Phenptype Ontology Domain-centric phenotype/anatomy ontology including Disease Ontology, Human Phenotype, Mouse Phenotype, Worm Phenotype, Yeast Phenotype, Fly Phenotype, Fly Anatomy, Zebrafish Anatomy, Xenopus Anatomy, Arabidopsis Plant.
Superfamily annotation InterPro abstracts for 1,052 superfamilies, and Gene Ontology (GO) annotation for 763 superfamilies.
Functional annotation

Functional annotation of SCOP 1.73 superfamilies, by Christine Vogel.

Phylogenetic trees Trees are generated using heuristic parsimony methods, and are based on protein domain architecture data for all genomes in SUPERFAMILY. Genome combinations, or specific clades, can be displayed as individual trees.
Similar domain architectures Find the 10 domain architectures which are most similar to a domain architecture of interest.
Hidden Markov models

Produce SCOP domain assignments for your sequences using the SUPERFAMILY models. HMM visualisation by Martin Madera, e.g. model 0045110.

Profile comparison

Find remote domain matches when the HMM search fails to find a significant match. Profile comparison (PRC) for aligning and scoring two profile hidden Markov models by Martin Madera

Web services

Distributed Annotation Server and linking to SUPERFAMILY.


Sequences, assignments, models, MySQL database and scripts - updated weekly.

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