FIGfams

FIGfams are sets of Protein Sequences? that are similar along their full length. Further, all of the proteins within a single FIGfam are believed to implement the same function. Sometimes, we simply state that a FIGfam is a set of isofunctional homologs.

FIGfams logoProteins are thought of as implementing one or more abstract Functional Roles. 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 Subsystems Approach to annotation consists of assigning the roles in a subsystem to the Protein Encoding Genes 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 Genome Pipeline).

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 Chromosome Context

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 Functional Roles. 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 Chromosome Contexts and participate in the same subsystems.

FIGfams-closeGenomes.png

Further Reading:

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Topic revision: r15 - 27 Jan 2009 - 16:33:43 - TWiki Guest
 
Notice to NMPDR Users - The NMPDR BRC contract has ended and bacterial data from NMPDR has been transferred to PATRIC (http://www.patricbrc.org), a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois. NMPDR is funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract HHSN266200400042C. Banner images are copyright © Dennis Kunkel.