HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) All Versions of this Article: 9/1/15    most recent 00086.2001v1 Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in Web of Science Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Web of Science (15) Citing Articles via Google Scholar Google Scholar Articles by Liang, P. Articles by Riley, M. Search for Related Content PubMed PubMed Citation Articles by Liang, P. Articles by Riley, M.

Physiological genomics of Escherichia coli protein families

¹ Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543
² Institut de Génétique et Microbiologie, Centre National de la Recherche Scientifique UMR 8621, Bâtiment 409, Université de Paris-Sud, 91405 Orsay Cedex, France

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).

module; sequence similarity; protein family; predicting protein function; annotation; evolution

This article has been cited by other articles:

				L. A. Nahum, S. Goswami, and M. H. Serres Protein families reflect the metabolic diversity of organisms and provide support for functional prediction Physiol Genomics, August 7, 2009; 38(3): 250 - 260. [Abstract] [Full Text] [PDF]

				A. Sivakumar, C. Wilton, and L. Holm From sequences to a functional unit Physiol Genomics, March 13, 2006; 25(1): 1 - 8. [Abstract] [Full Text] [PDF]

				M. H. Serres, S. Goswami, and M. Riley GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins Nucleic Acids Res., January 1, 2004; 32(90001): D300 - 302. [Abstract] [Full Text] [PDF]

				A. Matte, J. Sivaraman, I. Ekiel, K. Gehring, Z. Jia, and M. Cygler Contribution of Structural Genomics to Understanding the Biology of Escherichia coli J. Bacteriol., July 15, 2003; 185(14): 3994 - 4002. [Full Text] [PDF]