Physiological genomics of E . coli protein families

Ping Liang, Bernard Labedan, and Monica Riley Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA 2 Present address: Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA Institut de Génétique et Microbiologie, CNRS UMR 8621, Bâtiment 409, Université de ParisSud, 91405 Orsay Cedex, France Corresponding author. Email: mriley@mbl.edu; Phone (508) 289-7612; FAX: (508) 289-7388.

[1]  M. Riley,et al.  Divergence of function in sequence-related groups of Escherichia coli proteins. , 2001, Genome research.

[2]  P. Babbitt,et al.  Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies. , 2001, Annual review of biochemistry.

[3]  Ann M Stock,et al.  Histidine kinases and response regulator proteins in two-component signaling systems. , 2001, Trends in biochemical sciences.

[4]  V. Thorsson,et al.  Genome sequence of Halobacterium species NRC-1. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Temple F. Smith,et al.  Operons in Escherichia coli: genomic analyses and predictions. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Gaston H. Gonnet,et al.  Darwin v. 2.0: an interpreted computer language for the biosciences , 2000, Bioinform..

[7]  B. Persson,et al.  SDR and MDR: completed genome sequences show these protein families to be large, of old origin, and of complex nature , 1999, FEBS letters.

[8]  M. Berlyn Linkage Map of Escherichia coli K-12, Edition 10: The Traditional Map , 1998, Microbiology and Molecular Biology Reviews.

[9]  M H Saier,et al.  Microbial genome analyses: global comparisons of transport capabilities based on phylogenies, bioenergetics and substrate specificities. , 1998, Journal of molecular biology.

[10]  K. Linton,et al.  The Escherichia coli ATP‐binding cassette (ABC) proteins , 1998, Molecular microbiology.

[11]  N. W. Davis,et al.  The complete genome sequence of Escherichia coli K-12. , 1997, Science.

[12]  M. Riley,et al.  Protein evolution viewed through Escherichia coli protein sequences: introducing the notion of a structural segment of homology, the module. , 1997, Journal of molecular biology.

[13]  P. Argos,et al.  An assessment of amino acid exchange matrices in aligning protein sequences: the twilight zone revisited. , 1995, Journal of molecular biology.

[14]  W. Pearson Comparison of methods for searching protein sequence databases , 1995, Protein science : a publication of the Protein Society.

[15]  M. Hermodson,et al.  Structural homology between rbs repressor and ribose binding protein implies functional similarity , 1992, Protein science : a publication of the Protein Society.

[16]  S. Altschul Amino acid substitution matrices from an information theoretic perspective , 1991, Journal of Molecular Biology.

[17]  J. Knappe,et al.  Pyruvate‐formate‐lyase‐deactivase and acetyl‐CoA reductase activities of Escherichia coli reside on a polymeric protein particle encoded by adhE , 1991, FEBS letters.

[18]  O. Kandler,et al.  Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[19]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[20]  J. Roth,et al.  Enzyme Evolution: Generation of a Bifunctional Enzyme by Fusion of Adjacent Genes , 1970, Nature.

[21]  W. Fitch Distinguishing homologous from analogous proteins. , 1970, Systematic zoology.

[22]  W. Fitch,et al.  Construction of phylogenetic trees. , 1967, Science.

[23]  M. Riley,et al.  Interim report on genomics of Escherichia coli. , 2000, Annual review of microbiology.

[24]  Kenneth E. Rudd,et al.  EcoGene: a genome sequence database for Escherichia coli K-12 , 2000, Nucleic Acids Res..

[25]  M. Riley,et al.  Genetic Inventory: Escherichia coli as a Window on Ancestral Proteins , 1999 .

[26]  L. Orgel,et al.  Phylogenetic Classification and the Universal Tree , 1999 .

[27]  H. Bisswanger,et al.  Multifunctional proteins. , 1976, Annual review of biochemistry.

[28]  Christus,et al.  A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins , 2022 .