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  • Altschul, S., Madden, T., Schaffer, A., Zhang, J., Zhang, Z. & Miller, W., et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 33893402.DOI: 10.1093/nar/25.17.3389
  • Blattner, F.R., Plunkett, G. & Bloch, C.A., et al. (1997 The complete gene sequence of Escherichia coli K-12. Science 277: 14531474.DOI: 10.1126/science.277.5331.1453
  • Bausch, C., Peekhaus, N., Utz, C., Blais, T., Murray, E. & Lowary, T., et al. (1998) Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for l-idonic acid catabolism in Escherichia coli. J Bacteriol 180: 37043710.
  • Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Rapp, B.A. & Wheeler, D.L. (2000) GenBank. Nucleic Acids Res 28: 1518.DOI: 10.1093/nar/28.1.15
  • Berg, O.G. & Von Hippel, P.H. (1987) Selection of DNA binding sites by regulatory proteins. Statistical–mechanical theory and application to operators and promoters. J Mol Biol 193: 723750.
  • Blanco, C. (1987) Transcriptional and translational signals of the uidA gene in Escherichia coli K12. Mol Gen Genet 208: 490498.
  • Bork, P. & Koonin, E.V. (1998) Predicting functions from protein sequences – where are the bottlenecks? Nature Genet 18: 313318.
  • Egan, S.E., Fliege, R., Tong, S., Shibata, A., Wolf, R.E. & Conway, T. (1992) Molecular characterization of the Entner–Doudoroff pathway in Escherichia coli: sequence analysis and localization of promoters for the edd–eda operon. J Bacteriol 174: 46384646.
  • Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F. & Kerlavage, A.R., et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496512.
  • Gelfand, M.S. (1999) Recognition of regulatory sites by genomic comparison. Res Microbiol 150: 755771.DOI: 10.1016/s0923-2508(99)00117-5
  • Gelfand, M.S., Koonin, E.V. & Mironov, A.A. (2000) Prediction of transcription regulatory sites in Archaea by a comparative genomic approach. Nucleic Acids Res 28: 695705.DOI: 10.1093/nar/28.3.695
  • Goodrich, J.A., Schwartz, M.L. & McClyre, W.R. (1990) Searching for and predicting the activity of sites for DNA binding proteins: compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF). Nucleic Acids Res 18: 49935000.
  • Hugouvieux-Cotte-Pattat, N., Condemine, G., Nasser, W. & Reverchon, S. (1996) Regulation of pectinolysis in Erwinia chrysanthemi. Annu Rev Microbiol 50: 213257.
  • Izu, H., Adachi, O. & Yamada, M. (1997) Gene organization and transcriptional regulation of the gntRKU operon involved in gluconate uptake and catabolism of Escherichia coli. J Mol Biol 267: 778793.DOI: 10.1006/jmbi.1996.0913
  • Klemm, P., Tong, S., Nielsen, H. & Conway, T. (1996) The gntP gene of Escherichia coli involved in gluconate uptake. J Bacteriol 178: 6167.
  • Lin, E.C.C. (1996) Dissimilatory pathways for sugars, polyols, and carboxylates. In Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edn, Vol. 1. Neidhardt, F.C., Curtiss, R., III, Ingraham, J.L., Lin, E.C.C., Low, K.B., Magasanik, B., et al. (eds). Washington, DC: American Society for Microbiology Press, pp. 307342.
  • Mironov, A.A., Koonin, E.V., Roytberg, M.A. & Gelfand, M.S. (1999) Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes. Nucleic Acids Res 27: 29812989.DOI: 10.1093/nar/27.14.2981
  • Mironov, A.A., Vinokurova, N.P. & Gelfand, M.S. (2000) GenomeExplorer: software for analysis of complete bacterial genomes. Mol Biol 34: 222231.
  • Mulligan, M.E., Hawley, D.K., Entriken, R. & McClure, W.R. (1984) Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity. Nucleic Acids Res 12: 789800.
  • Nasser, W., Reverchon, S., Condemine, G. & Robert-Baudouy, J. (1994) Specific interactions of Erwinia chrysanthemi KdgR repressor with different operators of genes involved in pectinolysis. J Mol Biol 18: 427440.
  • Nasser, W., Robert-Baudouy, J. & Reverchon, S. (1997) Antagonistic effect of CRP and KdgR in the transcription control of the Erwinia chrysanthemi pectinolysis genes. Mol Microbiol 26: 10711082.
  • Novichkova, E.S. (2000) Comparative Approach to Analysis of Regulation in Complete Genomes: Catabolite Repression in Gamma-proteobacteriae. MSc Thesis, Moscow State Engineering Physics Institute.
  • Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G.D. & Maltsev, N. (1999) The use of gene clusters to infer functional coupling. Proc Natl Acad Sci USA 96: 28962901.DOI: 10.1073/pnas.96.6.2896
  • Peekhaus, N. & Conway, T. (1998a) What's for dinner? Entner–Doudoroff metabolism in Escherichia coli. J Bacteriol 180: 34953502.
  • Peekhaus, N. & Conway, T. (1998b) Positive and negative transcriptional regulation of the Escherichia coli gluconate regulon gene gntT by GntR and the cyclic AMP (cAMP)–cAMP receptor protein complex. J Bacteriol 180: 17771785.
  • Ritzenthaler, P., Blanco, C. & Mata-Gilsinger, M. (1985) Genetic analysis of uxuR and exuR genes: evidence for ExuR and UxuR monomer repressors interactions. Mol Gen Genet 199: 507511.
  • Robison, K., McGuire, A.M. & Church, G.M. (1998) A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J Mol Biol 284: 241254.DOI: 10.1006/jmbi.1998.2160
  • Rouanet, C., Nomura, K., Tsuyumu, S. & Nasser, W. (1999) Regulation of pelD and pelE, encoding major alkaline pectate lyases in Erwinia chrysanthemi: involvement of the main transcriptional factors. J Bacteriol 181: 59485957.
  • Schneider, T.D., Stormo, G.D., Gold, L. & Ehrenfeucht, A. (1986) Information content of binding sites on nucleotide sequences. J Mol Biol 188: 415431.
  • Shevchik, V.E., Condemine, G., Robert-Baudouy, J. & Hugouvieux-Cotte-Pattat, N. (1999) The exopolygalacturonate lyase PelW and the oligogalacturonate lyase Ogl, two cytoplasmic enzymes of pectin catabolism in Erwinia chrysanthemi 3937. J Bacteriol 181: 39123919.
  • Stojanovic, N., Florea, L., Riemer, C., Gumucio, D., Slightom, J. & Goodman, M., et al. (1999) Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions. Nucleic Acids Res 27: 38993910.DOI: 10.1093/nar/27.19.3899
  • Tatusov, R.L., Galperin, M.Y., Natale, D.A. & Koonin, E.V. (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28: 3336.DOI: 10.1093/nar/28.1.33
  • Thieffry, D., Salgado, H., Huerta, A.M. & Collado-Vides, J. (1998) Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12. Bioinformatics 14: 391400.DOI: 10.1093/bioinformatics/14.5.391
  • Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. & Higgins, D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 48764882.DOI: 10.1093/nar/25.24.4876
  • Williams, S.G., Greenwood, J.A. & Jones, C.W. (1992) Molecular analysis of the lac operon encoding the binding-protein-dependent lactose transport system and beta-galactosidase in Agrobacterium radiobacter. Mol Microbiol 6: 17551768.