Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli.

[1]  N H Horowitz,et al.  On the Evolution of Biochemical Syntheses. , 1945, Proceedings of the National Academy of Sciences of the United States of America.

[2]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[3]  Jacques Monod,et al.  On the Regulation of Gene Activity , 1961 .

[4]  N. Horowitz,et al.  The Evolution of Biochemical Syntheses — Retrospect and Prospect , 1965 .

[5]  M. Yčas,et al.  On earlier states of the biochemical system. , 1974, Journal of theoretical biology.

[6]  R. Jensen.  Enzyme recruitment in evolution of new function. , 1976, Annual review of microbiology.

[7]  Larry Wall,et al.  Programming Perl , 1991 .

[8]  G. Petsko,et al.  On the origin of enzymatic species. , 1993, Trends in biochemical sciences.

[9]  Stanley L. Miller,et al.  The Origin and Early Evolution of Life: Prebiotic Chemistry, the Pre-RNA World, and Time , 1996, Cell.

[10]  Larry Wall,et al.  Programming Perl (2nd ed.) , 1996 .

[11]  David C. Jones,et al.  CATH--a hierarchic classification of protein domain structures. , 1997, Structure.

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

[13]  Gapped BLAST and PSI-BLAST: A new , 1997 .

[14]  A. Valencia,et al.  Conserved Clusters of Functionally Related Genes in Two Bacterial Genomes , 1997, Journal of Molecular Evolution.

[15]  Sarah A. Teichmann,et al.  DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins , 1998, Bioinform..

[16]  Monica Riley,et al.  Genes and proteins of Escherichia coli K-12 , 1998, Nucleic Acids Res..

[17]  C. Chothia,et al.  Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[18]  A. Murzin.  How far divergent evolution goes in proteins. , 1998, Current opinion in structural biology.

[19]  B. Snel,et al.  Conservation of gene order: a fingerprint of proteins that physically interact. , 1998, Trends in biochemical sciences.

[20]  Thomas Lengauer,et al.  Pathway analysis in metabolic databases via differetial metabolic display (DMD) , 2000, German Conference on Bioinformatics.

[21]  R. Overbeek,et al.  The use of gene clusters to infer functional coupling. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Alejandro A. Schäffer,et al.  IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices , 1999, Bioinform..

[23]  B. Snel,et al.  Pathway alignment: application to the comparative analysis of glycolytic enzymes. , 1999, The Biochemical journal.

[24]  P. Bork,et al.  Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways. , 2000, Journal of molecular biology.

[25]  Sophia Tsoka,et al.  Prediction of protein interactions: metabolic enzymes are frequently involved in gene fusion , 2000, Nature Genetics.

[26]  Janet M. Thornton,et al.  Comparison of functional annotation schemes for genomes , 2000, Functional & Integrative Genomics.

[27]  P. Bork,et al.  Homology among (βα) 8 barrels: implications for the evolution of metabolic pathways 1 1Edited by G. Von Heijne , 2000 .

[28]  Natalia Maltsev,et al.  WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction , 2000, Nucleic Acids Res..

[29]  Peter D. Karp,et al.  The EcoCyc and MetaCyc databases , 2000, Nucleic Acids Res..

[30]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[31]  Sarah A. Teichmann,et al.  Fast assignment of protein structures to sequences using the Intermediate Sequence Library PDB-ISL , 2000, Bioinform..

[32]  Peter D. Karp,et al.  An ontology for biological function based on molecular interactions , 2000, Bioinform..

[33]  P Bork,et al.  Gene context conservation of a higher order than operons. , 2000, Trends in biochemical sciences.

[34]  S. Copley,et al.  Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach. , 2000, Trends in biochemical sciences.

[35]  R. Albert,et al.  The large-scale organization of metabolic networks , 2000, Nature.

[36]  中尾 光輝,et al.  KEGG(Kyoto Encyclopedia of Genes and Genomes)〔和文〕 (特集 ゲノム医学の現在と未来--基礎と臨床) -- (データベース) , 2000 .

[37]  P D Karp,et al.  Global properties of the metabolic map of Escherichia coli. , 2000, Genome research.

[38]  B. Snel,et al.  Gene and context: integrative approaches to genome analysis. , 2000, Advances in protein chemistry.

[39]  K. Schulten,et al.  Phylogenetic Analysis of Metabolic Pathways , 2001, Journal of Molecular Evolution.

[40]  M J Sternberg,et al.  A structural census of metabolic networks for E. coli. , 2001, Journal of molecular biology.

[41]  Javier Tamames,et al.  Evolution of gene order conservation in prokaryotes , 2001, Genome Biology.

[42]  Annabel E. Todd,et al.  Evolution of function in protein superfamilies, from a structural perspective. , 2001, Journal of molecular biology.

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

[44]  Julio Collado-Vides,et al.  RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12 , 2001, Nucleic Acids Res..

[45]  James E. Bray,et al.  A rapid classification protocol for the CATH Domain Database to support structural genomics , 2001, Nucleic Acids Res..

[46]  H. Mewes,et al.  SNAPping up functionally related genes based on context information: a colinearity-free approach. , 2001, Journal of molecular biology.

[47]  C. Chothia,et al.  The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli. , 2001, Journal of molecular biology.

[48]  S Tsoka,et al.  Functional versatility and molecular diversity of the metabolic map of Escherichia coli. , 2001, Genome research.

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

[50]  Frances M. G. Pearl,et al.  Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database. , 2002, Genome research.

[51]  Janet M Thornton,et al.  Pathway evolution, structurally speaking. , 2002, Current opinion in structural biology.