A gold standard set of mechanistically diverse enzyme superfamilies

Abstract

Superfamily and family analyses provide an effective tool for the functional classification of proteins, but must be automated for use on large datasets. We describe a 'gold standard' set of enzyme superfamilies, clustered according to specific sequence, structure, and functional criteria, for use in the validation of family and superfamily clustering methods. The gold standard set represents four fold classes and differing clustering difficulties, and includes five superfamilies, 91 families, 4,887 sequences and 282 structures.

Figure 1

Comparison of gold and silver standard family classifications to Pfam for the gold standard enolase superfamily. The outer ring represents Pfam family classifications. Sequences that match multiple Pfam HMMs, all of which correspond to a single SFLD functional domain (for example, 'Enolase_N', representing the amino terminus of the enzyme enolase and 'Enolase', representing the carboxyl terminus of the enzyme enolase), are shown with a single designation in the figure to simplify the illustration. (a) The inner ring represents gold standard family classifications. Gray regions represent enzymes that can be assigned to the gold standard enolase superfamily, but cannot be confidently assigned to a gold standard family. (b) The inner ring represents silver standard family classifications. Gray regions represent enzymes that can be assigned to the gold standard enolase superfamily, but cannot be confidently assigned to a silver standard family.