The SFLD Glossary
Evidence code
A three-letter code designating data source or method of derivation. See the list of codes.
Enzyme Structure Function Ontology
An ontology designed to capture the relationships between enzyme sequence, structure, and function that underlie the SFLD. For more information, see:
Family
A set of evolutionarily related enzymes that catalyze the same overall reaction; a subset of a superfamily.
Functional domain
A single member of a family, either a whole protein or the domain(s) responsible for the enzymatic activity. Also known as an enzyme functional domain (EFD).
Hidden Markov Model (HMM)
A statistical model used in the SFLD to describe sequences in a family, subgroup, or superfamily. Sequences may be compared to the SFLD HMMs to determine their likely superfamily, subgroup, or family membership; highly significant hits suggest how proteins may be classified, and by association, what reactions they may catalyze. HMMs may be downloaded from the Download Archived Data tab of the appropriate Superfamily page.
Molecule similarity network
Representation of a set of molecules (substrates or products or both) as nodes, with links between the nodes indicating similarity (Tanimoto coefficient
calculated by Small Molecule Subgraph Detector (Rahman et al., Journal of Cheminformatics 1(1):12
(2009)). These networks can be viewed, manipulated, and analyzed using
Cytoscape
.
(More...)
Overall reaction
The chemical transformation of substrate(s) to product(s) catalyzed by an enzyme, often expressed as a series of partial reactions.
Partial reaction
A mechanistic step within the overall reaction catalyzed by an enzyme.
Reaction similarity network
Representation of a set of reactions as nodes, with links between the nodes indicating similarity in reaction, as calculated by the Reaction Decoder Tool (Rahman
et al., Bioinformatics 32(13):2065-6 (2016)). These networks can be viewed, manipulated, and analyzed using
Cytoscape
.
(More...)
When available, reaction
similarity networks can be downloaded from the Download Archived Data tab of the appropriate Superfamily, Subgroup, or Family page.
Sequence similarity network
Representation of a set of proteins as nodes, with links between the nodes
indicating similarity in amino acid sequence. The SFLD provides two types of
sequence similarity networks:
One Sequence per Node,
in which each node represents a unique sequence,
and Representative, in which each node can represent
multiple related sequences.
These networks can be viewed, manipulated, and analyzed using
Cytoscape
.
(More...)
Sequence similarity networks can be downloaded from the Download Archived Data tab of the appropriate Superfamily, Subgroup, or Family page.
Subgroup
A set of evolutionarily related enzymes from the same superfamily but broader than a family; definitions are superfamily-specific.
Superfamily
A set of evolutionarily related enzymes whose members retain a conserved aspect of function, performed by conserved active site features. For example, all members of a superfamily might catalyze the same partial reaction or stabilize the same type of intermediate using a characteristic set of conserved residues. Although the defining aspect of function is conserved across a superfamily, its members can be highly divergent and catalyze quite different overall reactions (such a superfamily may be called mechanistically diverse or functionally diverse). For more information, see the references.