Superfamily database
SUPERFAMILY is a database and search platform 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. Annotations. The SUPERFAMILY annotation is based on a collection of hidden Markov models (HMM), which represent structural  protein domains at the SCOP superfamily level. 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. Features. 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 The database has domain assignments, alignments, and architectures for completely sequence 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. Due to the growing gap between sequenced proteins and known functions of proteins, it is becoming increasingly important to develop a more automated method for functionally annotating proteins, especially for proteins with known domains. SUPERFAMILY uses  protein-level GO annotations taken from the Genome Ontology Annotation (GOA) project, which offers high-quality GO annotations directly associated to proteins in the UniprotKB over a wide spectrum of species. SUPERFAMILY has generated GO annotations for evolutionarily closed domains (at the SCOP family level) and distant domains (at the SCOP superfamily level). Phenotype 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, and Arabidopsis Plant. Superfamily Annotation InterPro abstracts for over 1,000 superfamilies, and Gene Ontology (GO) annotation for over 700 superfamilies. This  feature allows for the direct annotation of key features, functions, and structures of a superfamily. Functional Annotation Functional annotation of SCOP 1.73 superfamilies. The SUPERFAMILY database uses a scheme of 50 detailed function categories which map to 7 general function categories, similar to the scheme used in the COG database. A general function assigned to a superfamily was used to reflect the major function for that superfamily. The general categories of function are: Each domain superfamily in SCOP classes a to g were manually annotated using this scheme and the information used was provided by SCOP, InterPro, Pfam, Swiss Prot , and various literature sources. Phylogenetic Trees Create custom phylogenetic trees by selecting 3 or more available genomes on the SUPERFAMILY site. 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 This feature allows the user to find the 10 domain architectures which are most similar to the domain architecture of interest. Hidden Markov Models Produce SCOP domain assignments for a sequence using the SUPERFAMILY hidden Markov models. 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 HMM's are used. Web Services Distributed Annotation Server and linking to SUPERFAMILY. Downloads Sequences, assignments, models, MySQL database, and scripts - updated weekly. Use in Research. The SUPERFAMILY database has numerous research applications and has been used by many research groups for various studies. It can serve either as a database for proteins that the user wishes to examine with other methods, or to assign a function and structure to a novel or uncharacterized protein. One study found SUPERFAMILY to be very adept  at correctly assigning an appropriate function and structure to a large number of domains of unknown function by comparing them to the databases hidden Markov models. Another study used SUPERFAMILY to generate a data set of 1,733 Fold superfamily domains (FSF) in use of a comparison of proteomes and functionomes for to identify the origin of cellular diversification.