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SMART 5: domains in the context of genomes and networks
EMBL Meyerhofstrasse 1, 69012 Heidelberg, Germany 1Wellcome Trust Centre for Human Genetics Roosevelt Drive, Oxford OX3 7BN, UK 2Bioinformatik, Biozentrum, Am Hubland, University of Wuerzburg 97074 Wuerzburg, Germany
*To whom correspondence should be addressed. Tel: +49 6221 387 8526; Fax: +49 6221 387 517; Email: bork{at}embl.de
Received September 13, 2005. Revised October 11, 2005. Accepted October 11, 2005.
The Simple Modular Architecture Research Tool (SMART) is an online resource (http://smart.embl.de/) used for protein domain identification and the analysis of protein domain architectures. Many new features were implemented to make SMART more accessible to scientists from different fields. The new ‘Genomic’ mode in SMART makes it easy to analyze domain architectures in completely sequenced genomes. Domain annotation has been updated with a detailed taxonomic breakdown and a prediction of the catalytic activity for 50 SMART domains is now available, based on the presence of essential amino acids. Furthermore, intrinsically disordered protein regions can be identified and displayed. The network context is now displayed in the results page for more than 350 000 proteins, enabling easy analyses of domain interactions.
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M. Lloret-Llinares, C. Carre, A. Vaquero, N. de Olano, and F. Azorin Characterization of Drosophila melanogaster JmjC+N histone demethylases Nucleic Acids Res., May 1, 2008; 36(9): 2852 - 2863. [Abstract] [Full Text] [PDF]
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I. Anderson, J. Rodriguez, D. Susanti, I. Porat, C. Reich, L. E. Ulrich, J. G. Elkins, K. Mavromatis, A. Lykidis, E. Kim, et al. Genome Sequence of Thermofilum pendens Reveals an Exceptional Loss of Biosynthetic Pathways without Genome Reduction J. Bacteriol., April 15, 2008; 190(8): 2957 - 2965. [Abstract] [Full Text] [PDF]
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E. Frittoli, A. Palamidessi, A. Pizzigoni, L. Lanzetti, M. Garre, F. Troglio, A. Troilo, M. Fukuda, P. P. Di Fiore, G. Scita, et al. The Primate-specific Protein TBC1D3 Is Required for Optimal Macropinocytosis in a Novel ARF6-dependent Pathway Mol. Biol. Cell, April 1, 2008; 19(4): 1304 - 1316. [Abstract] [Full Text] [PDF]
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J. C. Gauntlett, S. Gebhard, S. Keis, J. M. Manson, K. M. Pos, and G. M. Cook Molecular Analysis of BcrR, a Membrane-bound Bacitracin Sensor and DNA-binding Protein from Enterococcus faecalis J. Biol. Chem., March 28, 2008; 283(13): 8591 - 8600. [Abstract] [Full Text] [PDF]
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D. Avisar, A. I. Prokhnevsky, and V. V. Dolja Class VIII Myosins Are Required for Plasmodesmatal Localization of a Closterovirus Hsp70 Homolog J. Virol., March 15, 2008; 82(6): 2836 - 2843. [Abstract] [Full Text] [PDF]
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H. Geng, J. B. Bruhn, K. F. Nielsen, L. Gram, and R. Belas Genetic Dissection of Tropodithietic Acid Biosynthesis by Marine Roseobacters Appl. Envir. Microbiol., March 1, 2008; 74(5): 1535 - 1545. [Abstract] [Full Text] [PDF]
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M. K. Basu, L. Carmel, I. B. Rogozin, and E. V. Koonin Evolution of protein domain promiscuity in eukaryotes Genome Res., March 1, 2008; 18(3): 449 - 461. [Abstract] [Full Text] [PDF]
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M. Yan, D. A. Rachubinski, S. Joshi, R. A. Rachubinski, and S. Subramani Dysferlin Domain-containing Proteins, Pex30p and Pex31p, Localized to Two Compartments, Control the Number and Size of Oleate-induced Peroxisomes in Pichia pastoris Mol. Biol. Cell, March 1, 2008; 19(3): 885 - 898. [Abstract] [Full Text] [PDF]
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