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FigFams are sets of ProteinSequences? that are similar? along their full length.

Proteins are thought of as implementing one or more abstract FunctionalRoles. All of the members of a single FigFam are believed to implement precisely this same set of functional roles.

The FigFams are based on the subsystems view of the cell metabolism, in which the cell is composed of a set of functional subsystems, and each active variant? of a subsystem is thought of as a set of functional roles. Each protein implements one or more functional roles. The SubsystemsApproach to annotation consists of assigning the roles in a subsystem to the ProteinEncodingGenes in a genome.

The FigFam effort may be thought of as building the infrastructure needed to automatically project the manual annotations maintained within the subsystem collection onto new genomes (see GenomePipeline).

The construction of FigFams is based on grouping proteins when it can reliably be asserted that they implement identical functions. Currently, there are three cases in which we place different sequences into the same group:

1. families constructed from subsystems
2. families constructed from closely related genomes
3. families constructed by comparison of the ChromosomeContext?

The actual FigFams are constructed using a set of rules for determining which pairs of genes must be placed in the same group. The set of FigFams is the maximum set of groups consistent with the pairwise constraints. A post-processing step checks for the rare case in which a resulting FigFam contains two protein sequences which have different subsystem FunctionalRoles. Such a case is evidence of an error in the subsystems themselves and is corrected manually.

The following graphic depicts the gene context of several protein sequences from closely-related Bacillus anthracis genomes. The proteins belong to the same FigFam because they share similar ChromosomeContexts? and participate in the same subsystems.

For more about FigFams:

• Read the FigFamDescription article.
• Look at the FigFam pages for HPPK or 4-hydroxyphenylpyruvate dioxygenase

or enter a protein sequence in FastaFormat in the form below to search for a matching family.