A strategy to retrieve the whole set of protein modules in microbial proteomes

Genome Research

Volumn 12, Issue 12, 2002, Pages 1961-1973

  Le Bouder Langevin, Stéphanie ^a   Capron Montaland, Isabelle ^b   De Rosa, Renaud ^c   Labedan, Bernard ^d  

^a ValiGen   (France)

^b INSTITUT CURIE   (France)

^c CNRS   (France)

^d UNIVERSITÉ PARIS SACLAY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

AUTOANALYSIS; CAMPYLOBACTER JEJUNI; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; DOCUMENTATION; ESCHERICHIA COLI; EVOLUTIONARY HOMOLOGY; GENE DUPLICATION; GENE FUSION; GRAM NEGATIVE BACTERIUM; HAEMOPHILUS INFLUENZAE; HELICOBACTER PYLORI; INFORMATION RETRIEVAL; METHODOLOGY; NONHUMAN; PRIORITY JOURNAL; REVIEW; SEQUENCE HOMOLOGY;

BACTERIAL PROTEINS; CAMPYLOBACTER JEJUNI; DATABASES, PROTEIN; ESCHERICHIA COLI PROTEINS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENES, BACTERIAL; GRAM-NEGATIVE BACTERIA; HAEMOPHILUS INFLUENZAE; HELICOBACTER PYLORI; PROTEOME; RECOMBINATION, GENETIC; RESEARCH DESIGN; SEQUENCE HOMOLOGY, AMINO ACID; SPECIES SPECIFICITY;

BACTERIA (MICROORGANISMS); CAMPYLOBACTER; CAMPYLOBACTER JEJUNI; ESCHERICHIA COLI; HAEMOPHILUS; HAEMOPHILUS INFLUENZAE; HELICOBACTER; HELICOBACTER PYLORI; NEGIBACTERIA; PROKARYOTA; PROTEOBACTERIA;

EID: 0036916747     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.393902     Document Type: Review

References (23)

1. Altschul, S.F. 1991. Amino acid substitution matrices from an information theoretic perspective. J. Mol. Biol. 219: 555-565.
2. Altschul, S.F. 1993. A protein alignment scoring system sensitive at all evolutionary distances J. Mol. Evol. 36: 290-300
3. Benner, S.A., Cohen, M.A., and Gonnet., G.H. 1993. Empirical and structural models for insertions and deletions in the divergent evolution of proteins. J. Mol. Biol. 229: 1065-1082.
4. Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., Griffiths-Jones, S., Howe, K.L., Marshall, M., and Sonnhammer, E.L. 2002. The Pfam protein families database. Nucleic Acids Res. 30: 276-280
5. Clausen, T., Schlegel, A., Peist, R., Schneider, E., Steegborn, C., Chang, Y.-S., Haase, A., Bourenkov, G.P., Bartunik, H.D., and Boos, W. 2000. X-ray structure of MalY from Escherichia coli: A pyridoxal 5′-phosphate-dependent enzyme acting as a modulator in mal gene expression. EMBO J. 19: 831-842
6. Corpet, F., Servant, F., Gouzy, J., and Kahn, D. 2000. ProDom and ProDom-CG: Tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res. 28: 267-269
7. Dayhoff, M.O., Schwartz, R.M., and Orcutt, B.C. 1978. A model for evolutionary change. In Atlas of protein sequence and structure (ed. M.O. Dayhoff), Vol. 5, Suppl. 3, pp. 345-352. National Biomedical Research Foundation, Washington, D.C.
8. De Rosa, R. and Labedan, B. 1998. The evolutionary relationships between the two bacteria Escherichia coli and Haemophilus influenzae and their putative last common ancestor. Mol. Biol. Evol. 15: 17-27.
9. Falquet, L., Pagni, M., Bucher, P., Hulo, N., Sigrist, C.J.A., Hofmann, K., and Bairoch, A. 2002. The PROSITE database, its status in 2002. Nucleic Acids Res. 30: 235-238.
10. Feng, D.F., Johnson, M.S., and Doolittle, R.F. 1985. Aligning amino acid sequences: Comparison of commonly used methods. J. Mol. Evol. 21: 112-125.
11. Fitch, W.M. 1970. Distinguishing homologous from analogous proteins. Syst. Zool. 19: 99-113.
12. Fitch, W.M. 2000. Homology: A personal view on some of the problems. Trends Genet. 16: 227-231.
13. Gonnet, G. and Hallett, M. 1997. The DARWIN Manual. http://www.wr.inf.ethz.ch/personal/gonnet/DarwinManual/DarwinManual.html
14. Gonnet, G.H., Cohen, M.A., and Benner, S.A. 1992. Exhaustive matching of the entire protein sequence database. Science 256: 1443-1445.
15. Gracy, J. and Argos, P. 1998. DOMO: A new database of aligned protein domains. Trends Biochem. Sci. 12: 495-497.
16. Labedan, B. and Riley, M. 1999. Genetic inventory: Escherichia coli as a window on ancestral proteins. In Organization of the prokaryotic genome (ed. R. Charlebois), Ch. 17, pp. 311-329. ASM Press, Washington, D.C.
17. Letunic, I., Goodstadt, L., Dickens, N.J., Doerks, T., Schultz, J., Mott, R., Ciccarelli, F., Copley, R.R., Ponting, C.P., and Bork, P. 2002. Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res. 30: 242-244.
18. Mira, A., Ochman, H., and Moran, N.A. 2001. Deletional bias and the evolution of bacterial genomes. Trends Genet. 17: 589-596.
19. Needleman, S.B. and Wunsch, C.D. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48: 443-453.
20. Ohno, S. 1970. Evolution by gene duplication. Springer-Verlag, New York.
21. Riley, M. and Labedan, B. 1997. Protein evolution viewed through Escherichia coli protein sequences: Introducing the notion of a structural segment of homology, the module. J. Mol. Biol. 268: 857-868.
22. Schwartz, R.M. and Dayhoff, M.O. 1978. Matrices for detecting distant relationships. In Atlas of Protein Sequence and Structure (ed. M.O. Dayoff), Vol. 5, Suppl. 3, pp. 353-358. National Biomedical Research Foundation, Washington, D.C.
23. Smith, T.F. and Waterman, M.S. 1981. Identification of common molecular subsequences. J. Mol. Biol. 147: 195-197.