The SFLD Glossary

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 similar active site architecture but utilize this conserved architecture in substantially different ways. In some cases, the alpha carbons of key catalytic residues may be superimposable, while in other cases the side chains of key catalytic residues may superimpose though the corresponding alpha carbons come from different regions in the fold. In still other cases, cofactors or substrates may assume the position of key catalytic residues.