title: Physiological genomics of Escherichia coli protein families.
abstract: The well-researched Escherichia coli genome offers the opportunity to explore the value of using protein families within a single organism to enrich functional annotation procedures and to study mechanisms of protein evolution. Having identified multimodular proteins resulting from gene fusion, and treated each module as a separate protein, nonoverlapping sequence-similar families in E. coli could be assembled. Of 3,902 proteins of length 100 residues or more, 2,415 clustered into 609 protein families. The relatedness of function among members of each family was dissected in detail. Data on paralogous protein families provides valuable information in attributing putative function to unknown genes, supplementing existing function annotation. Enzymes, transporters, and regulators represent the three major types of proteins in E. coli. They are shown to have distinctive patterns in gene duplication and divergence and gene fusion, suggesting that details of protein evolution have been different for genes in these categories. Data for the complete list of paralogous protein families and updated functional annotation for E. coli K-12 are accessible in GenProtEC (http://genprotec.mbl.edu).
authors.affiliation: Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA. Ping.Liang@RoswellPark.org
authors.forename: Ping
authors.initials: P
authors.lastname: Liang
authors.forename: Bernard
authors.initials: B
authors.lastname: Labedan
authors.forename: Monica
authors.initials: M
authors.lastname: Riley
mesh_terms: D002352:Carrier Proteins / Q000737:chemistry / Q000235:genetics / Q000502:physiology; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D004798:Enzymes / Q000737:chemistry / Q000235:genetics / Q000502:physiology; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics* / Q000502:physiology*; D019143:Evolution, Molecular; D023281:Genomics / Q000379:methods; D020407:Internet; D005810:Multigene Family / Q000502:physiology*; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid
chemical_list: D002352:Carrier Proteins; D004798:Enzymes; D029968:Escherichia coli Proteins