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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
- 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
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