The MiST2 database: A comprehensive genomics resource on microbial signal transduction

Nucleic Acids Research

Volumn 38, Issue SUPPL.1, 2009, Pages

  Ulrich, Luke E ^a,b   Zhulin, Igor B ^b,c  

^a Agile Genomics LLC   (United States)

^b UNIVERSITY OF TENNESSEE   (United States)

^c OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN HISTIDINE KINASE; SIGMA FACTOR; ARCHAEAL PROTEIN; BACTERIAL PROTEIN;

AMINO ACID SEQUENCE; ARCHAEAL GENOME; ARTICLE; BACTERIAL GENOME; CHEMOTAXIS; CLASSIFICATION; COMPUTER INTERFACE; DATA BASE; GENOMICS; INFORMATION PROCESSING; INFORMATION RETRIEVAL; MICROBIAL SIGNAL TRANSDUCTION DATABASE; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; WEB BROWSER; ARCHAEBACTERIUM; BACTERIUM; BIOLOGY; COMPUTER PROGRAM; GENETIC DATABASE; GENETICS; INTERNET; METABOLISM; METHODOLOGY; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE;

ARCHAEA; BACTERIA (MICROORGANISMS);

ARCHAEA; ARCHAEAL PROTEINS; BACTERIA; BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DATABASES, PROTEIN; GENOME, ARCHAEAL; GENOME, BACTERIAL; INFORMATION STORAGE AND RETRIEVAL; INTERNET; PROTEIN STRUCTURE, TERTIARY; SIGNAL TRANSDUCTION; SOFTWARE;

EID: 75549092201     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp940     Document Type: Article

References (32)

1. Kofoid, E.C. and Parkinson, J.S. (1988) Transmitter and receiver modules in bacterial signaling proteins. Proc. Natl Acad. Sci. USA, 85, 4981-4985.
2. Stock, A.M., Robinson, V.L. and Goudreau, P.N. (2000) Two-component signal transduction. Annu. Rev. Biochem., 69, 183-215.
3. Ulrich, L.E., Koonin, E.V. and Zhulin, I.B. (2005) One-component systems dominate signal transduction in prokaryotes. Trends Microbiol., 13, 52-56.
4. Hengge, R. (2009) Principles of c-di-GMP signalling in bacteria. Nat. Rev. Microbiol, 7, 263-273.
5. Wadhams, G.H. and Armitage, J.P. (2004) Making sense of it all: bacterial chemotaxis. Nat. Rev. Mol. Cell Biol, 5, 1024-1037.
6. Butcher, B.G., Mascher, T. and Helmann, J.D. (2008) Environmental sensing and the role of extracytoplasmic function sigma factors. In El-Sharoud, W. (ed.), Bacterial Physiology. Springer, Berlin, Heidelberg, pp. 233-261.
7. Helmann, J.D. (2002) The extracytoplasmic function (ECF) sigma factors. Adv. Microb. Physiol., 46, 47-110.
8. Staroń, A., Sofia, H.J., Dietrich, S., Ulrich, L.E., Liesegang, H. and Mascher, T. (2009) The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) sigma factor protein family. Mol. Microbiol., 10.1111/j.1365-2958.2009.06870.x. Available at: http://www.ncbi.nlm.nih.gov/pubmed/19737356.
9. Tatusov, R.L., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Kiryutin, B., Koonin, E.V., Krylov, D.M., Mazumder, R., Mekhedov, S.L., Nikolskaya, A.N. et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 4, 4110.1186/1471-2105-4-41.
10. Ulrich, L.E. and Zhulin, I.B. (2006) MiST: a microbial signal transduction database. Nucleic Acids Res., 35, D386-D390.
11. Chain, P.S.G., Denef, V.J., Konstantinidis, K.T., Vergez, L.M., Agulló, L., Reyes, V.L., Hauser, L., Córdova, M., Gómez, L., González, M. et al. (2006) Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc. Natl Acad. Sci. USA, 103, 15280-15287.
12. Moran, M.A., Belas, R., Schell, M.A., González, J.M., Sun, F., Sun, S., Binder, B.J., Edmonds, J., Ye, W., Orcutt, B. et al. (2007) Ecological genomics of marine Roseobacters. Appl. Environ. Microbiol., 73, 4559-4569.
13. Anderson, I., Rodriguez, J., Susanti, D., Porat, I., Reich, C., Ulrich, L.E., Elkins, J.G., Mavromatis, K., Lykidis, A., Kim, E. et al. (2008) Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. J. Bacteriol., 190, 2957-2965.
14. Weiner, R.M., Taylor, L.E., Henrissat, B., Hauser, L., Land, M., Coutinho, P.M., Rancurel, C., Saunders, E.H., Longmire, A.G., Zhang, H. et al. (2008) Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T. PLoS Genet., 4, e100008710.1371/journal.pgen.1000087.
15. Anderson, I.J., Dharmarajan, L., Rodriguez, J., Hooper, S., Porat, I., Ulrich, L.E., Elkins, J.G., Mavromatis, K., Sun, H., Land, M. et al. (2009) The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota. BMC Genomics, 10, 14510.1186/1471-2164-10-145.
16. Anderson, I., Ulrich, L.E., Lupa, B., Susanti, D., Porat, I., Hooper, S.D., Lykidis, A., Sieprawska-Lupa, M., Dharmarajan, L., Goltsman, E. et al. (2009) Genomic characterization of methanomicrobiales reveals three classes of methanogens. PLoS ONE, 4, e579710.1371/journal.pone.0005797.
17. Lin, M., Zhang, C., Gibson, K. and Rikihisa, Y. (2009) Analysis of complete genome sequence of Neorickettsia risticii: causative agent of Potomac horse fever. Nucleic Acids Res, 37, 6076-6091.
18. Helmann, J.D. and Chamberlin, M.J. (1988) Structure and function of bacterial sigma factors. Annu. Rev. Biochem., 57, 839-872.
19. Finn, R.D., Tate, J., Mistry, J., Coggill, P.C., Sammut, S.J., Hotz, H., Ceric, G., Forslund, K., Eddy, S.R., Sonnhammer, E.L.L. et al. (2008) The Pfam protein families database. Nucleic Acids Res., 36, D281-D288.
20. Eddy, S. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
21. Galperin, M.Y., Natale, D.A., Aravind, L. and Koonin, E.V. (1999) A specialized version of the HD hydrolase domain implicated in signal transduction. J. Mol. Microbiol. Biotechnol., 1, 303-305.
22. Wuichet, K., Alexander, R.P. and Zhulin, I.B. (2007) Comparative genomic and protein sequence analyses of a complex system controlling bacterial chemotaxis. Meth. Enzymol., 422, 1-31.
23. Ermolaeva, M.D. (2005) Operon finding in bacteria. In Subramaniam, S. (ed.), Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics. John Wiley & Sons, New York, pp. 2886-2891.
24. Dam, P., Olman, V., Harris, K., Su, Z. and Xu, Y. (2006) Operon prediction using both genome-specific and general genomic information. Nucleic Acids Res., 35, 288-298.
25. Pertea, M., Ayanbule, K., Smedinghoff, M. and Salzberg, S.L. (2008) OperonDB: a comprehensive database of predicted operons in microbial genomes. Nucleic Acids Res., 37, D479-D482.
26. Wolf, Y.I., Rogozin, I.B., Kondrashov, A.S. and Koonin, E.V. (2001) Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res., 11, 356-372.
27. Dutta, S., Burkhardt, K., Young, J., Swaminathan, G.J., Matsuura, T., Henrick, K., Nakamura, H. and Berman, H.B. (2009) Data deposition and annotation at the worldwide protein data bank. Mol. Biotechnol., 42, 1-13.
28. The UniProt Consortium. (2009) The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res., 37, D169-D174.
29. Koretke, K.K., Lupas, A.N., Warren, P.V., Rosenberg, M. and Brown, J.R. (2000) Evolution of two-component signal transduction. Mol. Biol. Evol., 17, 1956-1970.
30. Altschul, S., Madden, T., Schaffer, A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
31. Suzek, B.E., Huang, H., McGarvey, P., Mazumder, R. and Wu, C.H. (2007) UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics, 23, 1282-1288.
32. van Dongen, S. (2000) A cluster algorithm for graphs. Inf. Syst., 1, 1-40.