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- conserved partial reaction
- a partial reaction performed by all members
of a given superfamily
- evidence code
- a three-letter acronym
designating data source or method of derivation
- family
- a set of evolutionarily related enzymes that catalyze the same
overall reaction; a subset of a superfamily
- Hidden Markov Model (HMM) - a statistical
model used in the the SFLD to describe sequences in a
family, subgroup, or superfamily. Input sequences are
compared to the SFLD HMMs; highly significant hits suggest how proteins
may be classified, and by association, what reactions they may catalyze.
- mechanistically diverse superfamily
(within the SFLD, often shortened to superfamily)
- a set of evolutionarily related enzymes whose members retain a
conserved aspect of function. For example, all members of a
superfamily might catalyze the same partial reaction
or stabilize the same type of intermediate.
While the defining aspect of function is conserved among all members of
a superfamily, the members can be highly divergent and catalyze quite
different overall reactions.
(For more information, see reviews
[Babbitt, 2003]
and [Gerlt and Babbitt, 2001].)
- 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
- provisional
- families, subgroups, superfamilies, and suprafamilies that have not yet been through the complete
SFLD curation process and thus may not conform to the specific sequence, structure, and function-based
definition for their respective groups, but provide a starting point for more detailed curation work
- SMILES/SMARTS
- line notation systems for symbolizing chemical structures and reactions
(SMARTS is a generalization of
SMILES)
- subgroup - a set of evolutionarily
related enzymes from the same superfamily
but broader than a family; definitions are superfamily-specific
- suprafamily - a set of evolutionarily related enzymes whose members share a
common active site architecture but utilize this conserve architecture to catalyze reactions with no apparent
mechanistic relationship
- Suspect Annotations
- Missing Functionally Important Residues (MFR)
Used when a seqeuence is labeled as misannotated based upon the absence or mutation of residues known to be critical for the function to which the sequence was erroneously annotated.
- Superfamily Associated Only (SFA)
Used when a sequence is a labeled as misannotated because sequence similarity can only assign the sequence to the superfamily of the function to which it was annotated (and not to the family).
- No Superfamily Association (NSA)
Used when a sequence is labeled as misannotated because sequence similarity cannot assign the sequence to the superfamily of the function to which it was annotated.
- Below Trusted Cutoff (BTC)
Used when a sequence is labeled as misannotated because sequence similarity is too weak to assign the sequence to the funciton to which it was annotated (falls below family-defined cutoff). However, the sequence does exhibit detectable sequence similarity to other sequences that perform the function.
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