Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes

Nucleic Acids Research

Volumn 32, Issue 21, 2004, Pages 6321-6326

  Doerks, Tobias ^a,b   von Mering, Christian ^a,b   Bork, Peer ^a,b  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN;

ACTINOBACTERIA; ARCHAEBACTERIUM; ARTICLE; BACTERIAL GENOME; CELL ACTIVITY; CHLAMYDIACEAE; EUKARYOTE; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CONSERVATION; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; HYPOTHESIS; NONHUMAN; ORTHOLOGY; PRIORITY JOURNAL; PROKARYOTE; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN FUNCTION; RICKETTSIA; SPECIES DIFFERENCE;

BACTERIAL PROTEINS; GENOME, BACTERIAL; GENOMICS; SOFTWARE;

EID: 13444309602     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh973     Document Type: Article

References (33)

1. Roberts,R.J. (2004) Identifying protein function - a call for community action. PloS Biol., 2, E42.
2. Dandekar,T., Snel,B., Huynen,M. and Bork,P. (1998) Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci., 23, 324-328.
3. Enright,A.J., Iliopoulos,I., Kyrpides,N.C. and Ouzounis,C.A. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature, 402, 86-90.
4. Marcotte,E.M., Pellegrini,M., Ng,H.L., Rice,D.W., Yeates,T.O. and Eisenberg,D. (1999) Detecting protein function and protein-protein interactions. Science, 285, 751-753.
5. Overbeek,R., Fonstein,M., D'Souza,M., Pusch,G.D. and Maltsev,N. (1999) The use of gene clusters to infer functional coupling. Proc. Natl Acad. Sci. USA, 96, 2896-2901.
6. Pellegrini,M., Marcotte,E.M., Thompson,M.J., Eisenberg,D. and Yeates,T.O. (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl Acad. Sci. USA, 96, 4285-4288.
7. von Mering,C., Huynen,M., Jaeggi,D., Schmidt,S., Bork,P. and Snel,B. (2003) STRING: a database of predicted functional associations between proteins. Nucleic Acids Res., 31, 258-261.
8. Huynen,M., Snel,B., Lathe,W.,III and Bork,P. (2000) Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res., 10, 1204-1210.
9. Mellor,J.C., Yanai,I., Clodfelter,K.H., Mintseris,J. and DeLisi,C. (2002) Predictome: a database of putative functional links between proteins. Nucleic Acids Res., 30, 306-309.
10. Marcotte,E.M., Pellegrini,M., Thompson,M.J., Yeates,T.O. and Eisenberg,D. (1999) A combined algorithm for genome-wide prediction of protein function. Nature, 402, 83-86.
11. Makarova,K.S. and Koonin,E.V. (2003) Comparative genomics of Archaea: how much have we learned in six years, and what's next? Genome Biol., 4, 115.
12. von Mering,C., Zdobnov,E.M., Tsoka,S., Ciccarelli,F.D., Pereira-Leal,J.B., Ouzounis,C.A. and Bork,P. (2003) Genome evolution reveals biochemical networks and functional modules. Proc. Natl Acad. Sci. USA, 100, 15428-15433.
13. Makarova,K.S., Wolf,Y.I. and Koonin,E.V. (2003) Potential genomic determinants of hyperthermophily. Trends Genet., 19, 172-176.
14. Doerks,T., Andrade,M.A., Lathe,W.,III, von Mering,C. and Bork,P. (2004) Global analysis of bacterial transcription factors to predict cellular target processes. Trends Genet., 20, 126-131.
15. Karaoz,U., Murali,T.M., Letovsky,S., Zheng,Y., Ding,C., Cantor,C.R. and Kasif,S. (2004) Whole-genome annotation by using evidence integration in functional-linkage networks. Proc. Natl Acad. Sci. USA 101, 2888-2993.
16. Tatusov,R.L., Natale,D.A., Garkavtsev,I.V., Tatusova,T.A., Shankavaram,U.T., Rao,B.S., Kiryutin,B., Galperin,M.Y., Fedorova,N.D. and Koonin,E.V. (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29, 22-28.
17. Boeckmann,B., Bairoch,A., Apweiler,R., Blatter,M.C., Estreicher,A., Gasteiger,E., Martin,M.J., Michoud,K., O'Donovan,C., Phan,I., Pilbout,S. and Schneider,M. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31, 365-370.
18. Martin,P.R., Watson,A.A., McCaul,T.F. and Mattick,J.S. (1995) Characterization of a five-gene cluster required for the biogenesis of type 4 fimbriae in Pseudomonas aeruginosa. Mol. Microbiol., 16 497-508.
19. Ogawa,H., Haga,T. and Toyoshima,C. (2000) Soluble P-type ATPase from an archaeon, Methanococcus jannaschii. FEBS Lett., 471, 99-102.
20. Bramkamp,M., Gassel,M., Herkenhoff-Hesselmann,B., Bertrand,J. and Altendorf,K. (2003) The Methanocaldococcus jannaschii protein Mj0968 is not a P-type ATPase. FEBS Lett., 543, 31-36.
21. Chitnis,P.R., Reilly,P.A. and Nelson,N. (1989) Insertional inactivation of the gene encoding subunit II of photosystem I from the Cyanobacterium synechocystis sp. PCC 6803. J. Biol. Chem., 264, 18374-18380.
22. Buttner,D., Gurlebeck,D., Noel,L.D. and Bonas,U. (2004) HpaB from Xanthomonas campestris pv. vesicatoria acts as an exit control protein in type III-dependent protein secretion. Mol. Microbiol., 54, 755-768.
23. Stader,J., Matsumura,P., Vacante,D., Dean,G.E. and Macnab,R.M. (1986) Nucleotide sequence of the Escherichia coli motB gene and site-limited incorporation of its product into the cytoplasmic membrane. J. Bacteriol., 166, 244-252.
24. Freudl,R., Klose,M. and Henning,U. (1990) Export and sorting of the Escherichia coli outer membrane protein OmpA. J. Bioenerg. Biomembr., 22, 441-449.
25. Bouveret,E., Benedetti,H., Rigal,A., Loret,E. and Lazdunski,C. (1999) In vitro characterization of peptidoglycan-associated lipoprotein (PAL)-peptidoglycan and PAL-TolB interactions. J. Bacteriology, 181, 6306-6311.
26. Das,S., Chakrabortty,A., Banerjee,R. and Chaudhuri,K. (1999) Involvement of in vivo induced icmF gene of Vibrio cholerae in motility, adherence to epithelial cells, and conjugation frequency. Biochem. Biophys. Res. Commun., 295, 922-928.
27. Mintz,K.P. and Fives-Taylor,P.M. (2000) impA, a gene coding for an inner membrane protein, influences colonial morphology of Actinobacillus actinomycetemcomitans. Infect. Immun., 68, 6580-6586.
28. Shin,D.H., Yokota,H., Kim,R. and Kim,S.H. (2002) Crystal structure of conserved hypothetical protein Aq1575 from Aquifex aeolicus. Proc. Natl Acad. Sci. USA, 99, 7980-7985.
29. West,S.C. (1997) Processing of recombination intermediates by the RuvABC Proteins. Annu. Rev. Genet., 31, 213-244.
30. Sharples,G.J., Yokota,H., Kim,R. and Kim,S.H. (1999) Holliday junction processing in bacteria: insights from the evolutionary conservation of RuvABC, RecG, and RusA. J. Bacteriology, 181, 5543-5550.
31. Ingleston,S.M., Dickman,M.J., Grasby,J.A., Hornby,D.P., Sharples,G.J. and Lloyd,R.G. (2002) Holliday junction binding and processing by the RuvA protein of Mycoplasma pneumoniae. Eur. J. Biochem., 269, 1525-1533.
32. Gao,L.Y., Groger,R., Cox,J.S., Beverley,S.M., Lawson,E.H. and Brown,E.J. (2003) Transposon mutagenesis of Mycobacterium marinum identifies a locus linking pigmentation and intracellular survival. Infect. Immun., 71, 922-929.
33. 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.