SUPERFAMILY
Encyclopedia
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 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.
into known structural domains
, especially into SCOP
superfamilies. The 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, which represent structural protein domains at the SCOP
Structural Classification of Proteins
The Structural Classification of Proteins database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences. A motivation for this classification is to determine the evolutionary relationship between proteins...
superfamily level.
A superfamily groups together domains which have an evolutionary relationship. The annotation is produced by scanning protein sequences from completely sequenced genomes
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
against the hidden Markov models.
For each protein you can:
- Submit sequences for SCOP classification
- View domain organisation, sequence alignmentsSequence alignmentIn bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are...
and protein sequence details
For each genome you can:
- Examine superfamily assignments, phylogenetic treesPhylogenetic treeA phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics...
, 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 OntologyGene OntologyThe Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species...
annotation, InterPro abstract and genome assignments - Explore taxonomicBiological classificationBiological classification, or scientific classification in biology, is a method to group and categorize organisms by biological type, such as genus or species. Biological classification is part of scientific taxonomy....
distribution of a superfamily across the tree of life
All annotation, models and the database dump are freely available for download to everyone.
Purpose
SUPERFAMILY classifies amino acid sequencesPeptide sequence
Peptide sequence or amino acid sequence is the order in which amino acid residues, connected by peptide bonds, lie in the chain in peptides and proteins. The sequence is generally reported from the N-terminal end containing free amino group to the C-terminal end containing free carboxyl group...
into known structural domains
Protein domain
A protein domain is a part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural...
, especially into SCOP
Structural Classification of Proteins
The Structural Classification of Proteins database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences. A motivation for this classification is to determine the evolutionary relationship between proteins...
superfamilies. The superfamilies are groups of proteins which have structural evidence to support a common evolutionary ancestor but may not have detectable sequence homology
Homology (biology)
Homology forms the basis of organization for comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying...
.
See also
- SCOPStructural Classification of ProteinsThe Structural Classification of Proteins database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences. A motivation for this classification is to determine the evolutionary relationship between proteins...
- PfamPfamPfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.- Features :For each family in Pfam one can:* Look at multiple alignments* View protein domain architectures...
- InterProInterProInterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them....
- Protein familyProtein familyA protein family is a group of evolutionarily-related proteins, and is often nearly synonymous with gene family. The term protein family should not be confused with family as it is used in taxonomy....
- Structural domain