Protein Engineering, Vol 10, 673-676, Copyright © 1997 by Oxford University Press
M Cserzo, E Wallin, I Simon, G von Heijne and A Elofsson
A new, simple method for predicting transmembrane segments in integral
membrane proteins has been developed. It is based on low-stringency dot-
plots of the query sequence against a collection of non-homologous membrane
proteins using a previously derived scoring matrix [Cserzo et al., 1994, J.
Mol. Biol., 243, 388-396]. This so-called dense alignment surface (DAS)
method is shown to perform on par with earlier methods that require extra
information in the form of multiple sequence alignments or the distribution
of positively charged residues outside the transmembrane segments, and thus
improves prediction abilities when only single-sequence information is
available or for classes of membrane proteins that do not follow the
'positive inside' rule.
ARTICLES
Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method
Institute of Enzymology, Biological Research Center Hungarian Academy of Sciences, Budapest.
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J.-R. Wei, Y.-H. Tsai, P.-C. Soo, Y.-T. Horng, S.-C. Hsieh, S.-W. Ho, and H.-C. Lai Biochemical Characterization of RssA-RssB, a Two-Component Signal Transduction System Regulating Swarming Behavior in Serratia marcescens J. Bacteriol., August 15, 2005; 187(16): 5683 - 5690. [Abstract] [Full Text] [PDF]
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S. Shipkowski and J. E. Brenchley Characterization of an Unusual Cold-Active {beta}-Glucosidase Belonging to Family 3 of the Glycoside Hydrolases from the Psychrophilic Isolate Paenibacillus sp. Strain C7 Appl. Envir. Microbiol., August 1, 2005; 71(8): 4225 - 4232. [Abstract] [Full Text] [PDF]
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C. Valentin, P. Dunoyer, G. Vetter, C. Schalk, A. Dietrich, and S. Bouzoubaa Molecular Basis for Mitochondrial Localization of Viral Particles during Beet Necrotic Yellow Vein Virus Infection J. Virol., August 1, 2005; 79(15): 9991 - 10002. [Abstract] [Full Text] [PDF]
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A. Gibson, A. P. Lewis, K. Affleck, A. J. Aitken, E. Meldrum, and N. Thompson hCLCA1 and mCLCA3 Are Secreted Non-integral Membrane Proteins and Therefore Are Not Ion Channels J. Biol. Chem., July 22, 2005; 280(29): 27205 - 27212. [Abstract] [Full Text] [PDF]
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L. Banci, I. Bertini, V. Calderone, F. Cramaro, R. Del Conte, A. Fantoni, S. Mangani, A. Quattrone, and M. S. Viezzoli A prokaryotic superoxide dismutase paralog lacking two Cu ligands: From largely unstructured in solution to ordered in the crystal PNAS, May 24, 2005; 102(21): 7541 - 7546. [Abstract] [Full Text] [PDF]
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R. Vicentefranqueira, M. A. Moreno, F. Leal, and J. A. Calera The zrfA and zrfB Genes of Aspergillus fumigatus Encode the Zinc Transporter Proteins of a Zinc Uptake System Induced in an Acid, Zinc-Depleted Environment Eukaryot. Cell, May 1, 2005; 4(5): 837 - 848. [Abstract] [Full Text] [PDF]
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M. Lohr, C.-S. Im, and A. R. Grossman Genome-Based Examination of Chlorophyll and Carotenoid Biosynthesis in Chlamydomonas reinhardtii Plant Physiology, May 1, 2005; 138(1): 490 - 515. [Abstract] [Full Text] [PDF]
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V. Yurchenko, T. Pushkarsky, J.-H. Li, W. W. Dai, B. Sherry, and M. Bukrinsky Regulation of CD147 Cell Surface Expression: INVOLVEMENT OF THE PROLINE RESIDUE IN THE CD147 TRANSMEMBRANE DOMAIN J. Biol. Chem., April 29, 2005; 280(17): 17013 - 17019. [Abstract] [Full Text] [PDF]
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T. Stein, S. Heinzmann, S. Dusterhus, S. Borchert, and K.-D. Entian Expression and Functional Analysis of the Subtilin Immunity Genes spaIFEG in the Subtilin-Sensitive Host Bacillus subtilis MO1099 J. Bacteriol., February 1, 2005; 187(3): 822 - 828. [Abstract] [Full Text] [PDF]
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T. P. Roosild and S. Choe Redesigning an integral membrane K+ channel into a soluble protein Protein Eng. Des. Sel., February 1, 2005; 18(2): 79 - 84. [Abstract] [Full Text] [PDF]
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W. R. Mathews, F. Wang, D. J. Eide, and M. Van Doren Drosophila fear of intimacy Encodes a Zrt/IRT-like Protein (ZIP) Family Zinc Transporter Functionally Related to Mammalian ZIP Proteins J. Biol. Chem., January 7, 2005; 280(1): 787 - 795. [Abstract] [Full Text] [PDF]
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U. Kappler, L. I. Sly, and A. G. McEwan Respiratory gene clusters of Metallosphaera sedula - differential expression and transcriptional organization Microbiology, January 1, 2005; 151(1): 35 - 43. [Abstract] [Full Text] [PDF]
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A. M. Raczko, J. M. Bujnicki, M. Pawlowski, R. Godlewska, M. Lewandowska, and E. K. Jagusztyn-Krynicka Characterization of new DsbB-like thiol-oxidoreductases of Campylobacter jejuni and Helicobacter pylori and classification of the DsbB family based on phylogenomic, structural and functional criteria Microbiology, January 1, 2005; 151(1): 219 - 231. [Abstract] [Full Text] [PDF]
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D. Schwartz, S. Berger, E. Heinzelmann, K. Muschko, K. Welzel, and W. Wohlleben Biosynthetic Gene Cluster of the Herbicide Phosphinothricin Tripeptide from Streptomyces viridochromogenes Tu494 Appl. Envir. Microbiol., December 1, 2004; 70(12): 7093 - 7102. [Abstract] [Full Text] [PDF]
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D. A. Brede, T. Faye, O. Johnsborg, I. Odegard, I. F. Nes, and H. Holo Molecular and Genetic Characterization of Propionicin F, a Bacteriocin from Propionibacterium freudenreichii Appl. Envir. Microbiol., December 1, 2004; 70(12): 7303 - 7310. [Abstract] [Full Text] [PDF]
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G. W. Turner and R. Croteau Organization of Monoterpene Biosynthesis in Mentha. Immunocytochemical Localizations of Geranyl Diphosphate Synthase, Limonene-6-Hydroxylase, Isopiperitenol Dehydrogenase, and Pulegone Reductase Plant Physiology, December 1, 2004; 136(4): 4215 - 4227. [Abstract] [Full Text] [PDF]
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J. L. McMurry, J. S. Van Arnam, M. Kihara, and R. M. Macnab Analysis of the Cytoplasmic Domains of Salmonella FlhA and Interactions with Components of the Flagellar Export Machinery J. Bacteriol., November 15, 2004; 186(22): 7586 - 7592. [Abstract] [Full Text] [PDF]
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C. Lefevre, B. Bouadjar, A. Karaduman, F. Jobard, S. Saker, M. Ozguc, M. Lathrop, J.-F. Prud'homme, and J. Fischer Mutations in ichthyin a new gene on chromosome 5q33 in a new form of autosomal recessive congenital ichthyosis Hum. Mol. Genet., October 1, 2004; 13(20): 2473 - 2482. [Abstract] [Full Text] [PDF]
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S. Trenkamp, W. Martin, and K. Tietjen Specific and differential inhibition of very-long-chain fatty acid elongases from Arabidopsis thaliana by different herbicides PNAS, August 10, 2004; 101(32): 11903 - 11908. [Abstract] [Full Text] [PDF]
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G. Anilkumar, R. Srinivasan, and P. Ajitkumar Genomic organization and in vivo characterization of proteolytic activity of FtsH of Mycobacterium smegmatis SN2 Microbiology, August 1, 2004; 150(8): 2629 - 2639. [Abstract] [Full Text] [PDF]
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A. V. Smirnova and M. S. Ullrich Topological and deletion analysis of CorS, a Pseudomonas syringae sensor kinase Microbiology, August 1, 2004; 150(8): 2715 - 2726. [Abstract] [Full Text] [PDF]
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G. L. Youngblood and D. H. Sweet Identification and functional assessment of the novel murine organic anion transporter Oat5 (Slc22a19) expressed in kidney Am J Physiol Renal Physiol, August 1, 2004; 287(2): F236 - F244. [Abstract] [Full Text] [PDF]
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M. Arai, H. Mitsuke, M. Ikeda, J.-X. Xia, T. Kikuchi, M. Satake, and T. Shimizu ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability Nucleic Acids Res., July 1, 2004; 32(suppl_2): W390 - W393. [Abstract] [Full Text] [PDF]
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Y. X. Guo, S.-W. Chan, and J. Kwang Membrane Association of Greasy Grouper Nervous Necrosis Virus Protein A and Characterization of Its Mitochondrial Localization Targeting Signal J. Virol., June 15, 2004; 78(12): 6498 - 6508. [Abstract] [Full Text] [PDF]
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