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.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  S. Greiner, X. Wang, R. G. Herrmann, U. Rauwolf, K. Mayer, G. Haberer, and J. Meurer The Complete Nucleotide Sequences of the 5 Genetically Distinct Plastid Genomes of Oenothera, Subsection Oenothera: II. A Microevolutionary View Using Bioinformatics and Formal Genetic Data Mol. Biol. Evol., September 1, 2008; 25(9): 2019 - 2030. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. F. Saccone, N. L. Saccone, G. E. Swan, P. A. F. Madden, A. M. Goate, J. P. Rice, and L. J. Bierut Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence Bioinformatics, August 15, 2008; 24(16): 1805 - 1811. [Abstract] [PDF]
|
|
|
|
 |
|
 A. F. Alvarez, H. M. Alvarez, R. Kalscheuer, M. Waltermann, and A. Steinbuchel Cloning and characterization of a gene involved in triacylglycerol biosynthesis and identification of additional homologous genes in the oleaginous bacterium Rhodococcus opacus PD630 Microbiology, August 1, 2008; 154(8): 2327 - 2335. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Eisenbeis, S. Lohmiller, M. Valdebenito, S. Leicht, and V. Braun NagA-Dependent Uptake of N-Acetyl-Glucosamine and N-Acetyl-Chitin Oligosaccharides across the Outer Membrane of Caulobacter crescentus J. Bacteriol., August 1, 2008; 190(15): 5230 - 5238. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Balasubramanian, T. R. Kannan, and J. B. Baseman The Surface-Exposed Carboxyl Region of Mycoplasma pneumoniae Elongation Factor Tu Interacts with Fibronectin Infect. Immun., July 1, 2008; 76(7): 3116 - 3123. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Mullane, P. O'Gaora, J. E. Nally, C. Iversen, P. Whyte, P. G. Wall, and S. Fanning Molecular Analysis of the Enterobacter sakazakii O-Antigen Gene Locus Appl. Envir. Microbiol., June 15, 2008; 74(12): 3783 - 3794. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. L. Hughes, C. L. Nolder, A. J. Nowalk, D. R. Clifton, R. R. Howison, V. L. Schmit, R. D. Gilmore Jr., and J. A. Carroll Borrelia burgdorferi Surface-Localized Proteins Expressed during Persistent Murine Infection Are Conserved among Diverse Borrelia spp. Infect. Immun., June 1, 2008; 76(6): 2498 - 2511. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S.-i. Arimura, M. Fujimoto, Y. Doniwa, N. Kadoya, M. Nakazono, W. Sakamoto, and N. Tsutsumi Arabidopsis ELONGATED MITOCHONDRIA1 Is Required for Localization of DYNAMIN-RELATED PROTEIN3A to Mitochondrial Fission Sites PLANT CELL, June 1, 2008; 20(6): 1555 - 1566. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. K. Bothe, J. Braun, L. Mundhenk, and A. D. Gruber Murine mCLCA6 Is an Integral Apical Membrane Protein of Non-goblet Cell Enterocytes and Co-localizes With the Cystic Fibrosis Transmembrane Conductance Regulator J. Histochem. Cytochem., May 1, 2008; 56(5): 495 - 509. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Musatovova, T. R. Kannan, and J. B. Baseman Genomic Analysis Reveals Mycoplasma pneumoniae Repetitive Element 1-Mediated Recombination in a Clinical Isolate Infect. Immun., April 1, 2008; 76(4): 1639 - 1648. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Lequette, E. Lanfroy, V. Cogez, J.-P. Bohin, and J.-M. Lacroix Biosynthesis of osmoregulated periplasmic glucans in Escherichia coli: the membrane-bound and the soluble periplasmic phosphoglycerol transferases are encoded by the same gene Microbiology, February 1, 2008; 154(2): 476 - 483. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Luo, T. Xu, C. Hunke, G. Gruber, S. G. Vasudevan, and J. Lescar Crystal Structure of the NS3 Protease-Helicase from Dengue Virus J. Virol., January 1, 2008; 82(1): 173 - 183. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. A. Bennett, R. M. Aimino, and J. R. McCormick Streptomyces coelicolor Genes ftsL and divIC Play a Role in Cell Division but Are Dispensable for Colony Formation J. Bacteriol., December 15, 2007; 189(24): 8982 - 8992. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Latijnhouwers, T. Gillespie, P. Boevink, V. Kriechbaumer, C. Hawes, and C. M. Carvalho Localization and domain characterization of Arabidopsis golgin candidates J. Exp. Bot., December 1, 2007; 58(15-16): 4373 - 4386. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Richter, U. Lindenstrauss, C. Lucke, R. Bayliss, and T. Bruser Functional Tat Transport of Unstructured, Small, Hydrophilic Proteins J. Biol. Chem., November 16, 2007; 282(46): 33257 - 33264. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. McCallum, A. K. C. Brassinga, C. D. Sifri, and B. Berger-Bachi Functional Characterization of TcaA: Minimal Requirement for Teicoplanin Susceptibility and Role in Caenorhabditis elegans Virulence Antimicrob. Agents Chemother., November 1, 2007; 51(11): 3836 - 3843. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Guillot and C. P. Moran Jr. Essential Internal Promoter in the spoIIIA Locus of Bacillus subtilis J. Bacteriol., October 15, 2007; 189(20): 7181 - 7189. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Castagna, A. Soragna, S. A. Mari, M. Santacroce, S. Bette, P. G. Mandela, G. Rudnick, A. Peres, and V. F. Sacchi Interaction between lysine 102 and aspartate 338 in the insect amino acid cotransporter KAAT1 Am J Physiol Cell Physiol, October 1, 2007; 293(4): C1286 - C1295. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Yao and C. Allen The Plant Pathogen Ralstonia solanacearum Needs Aerotaxis for Normal Biofilm Formation and Interactions with Its Tomato Host J. Bacteriol., September 1, 2007; 189(17): 6415 - 6424. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. F. Collins, M. Saleem, and J. P. Derrick Purification and Three-Dimensional Electron Microscopy Structure of the Neisseria meningitidis Type IV Pilus Biogenesis Protein PilG J. Bacteriol., September 1, 2007; 189(17): 6389 - 6396. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Almqvist, Y. Huang, A. Laaksonen, D.-N. Wang, and S. Hovmoller Docking and homology modeling explain inhibition of the human vesicular glutamate transporters Protein Sci., September 1, 2007; 16(9): 1819 - 1829. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Yu, Y.-W. Faan, W. Y. K. Chung, and J. S. H. Tsang Isolation and Characterization of a Novel Haloacid Permease from Burkholderia cepacia MBA4 Appl. Envir. Microbiol., August 1, 2007; 73(15): 4874 - 4880. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Seidel, L. J. Alderwick, H. L. Birch, H. Sahm, L. Eggeling, and G. S. Besra Identification of a Novel Arabinofuranosyltransferase AftB Involved in a Terminal Step of Cell Wall Arabinan Biosynthesis in Corynebacterianeae, such as Corynebacterium glutamicum and Mycobacterium tuberculosis J. Biol. Chem., May 18, 2007; 282(20): 14729 - 14740. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. E. Gentle, A. J. Perry, F. H. Alcock, V. A. Likic, P. Dolezal, E. T. Ng, A. W. Purcell, M. McConnville, T. Naderer, A.-L. Chanez, et al. Conserved Motifs Reveal Details of Ancestry and Structure in the Small TIM Chaperones of the Mitochondrial Intermembrane Space Mol. Biol. Evol., May 1, 2007; 24(5): 1149 - 1160. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Ruiz, S. Falcocchio, F. I. J. Pastor, L. Saso, and P. Diaz Helicobacter pylori EstV: Identification, Cloning, and Characterization of the First Lipase Isolated from an Epsilon-Proteobacterium Appl. Envir. Microbiol., April 15, 2007; 73(8): 2423 - 2431. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. A. Legaree, K. Daniels, J. T. Weadge, D. Cockburn, and A. J. Clarke Function of penicillin-binding protein 2 in viability and morphology of Pseudomonas aeruginosa J. Antimicrob. Chemother., March 1, 2007; 59(3): 411 - 424. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Kuo, K. R. Hurst, and P. S. Masters Exceptional Flexibility in the Sequence Requirements for Coronavirus Small Envelope Protein Function J. Virol., March 1, 2007; 81(5): 2249 - 2262. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Seidel, L. J. Alderwick, H. Sahm, G. S. Besra, and L. Eggeling Topology and mutational analysis of the single Emb arabinofuranosyltransferase of Corynebacterium glutamicum as a model of Emb proteins of Mycobacterium tuberculosis Glycobiology, February 1, 2007; 17(2): 210 - 219. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. F. Saccone, A. L. Hinrichs, N. L. Saccone, G. A. Chase, K. Konvicka, P. A.F. Madden, N. Breslau, E. O. Johnson, D. Hatsukami, O. Pomerleau, et al. Cholinergic nicotinic receptor genes implicated in a nicotine dependence association study targeting 348 candidate genes with 3713 SNPs Hum. Mol. Genet., January 1, 2007; 16(1): 36 - 49. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. W. Murcha, D. Elhafez, R. Lister, J. Tonti-Filippini, M. Baumgartner, K. Philippar, C. Carrie, D. Mokranjac, J. Soll, and J. Whelan Characterization of the Preprotein and Amino Acid Transporter Gene Family in Arabidopsis Plant Physiology, January 1, 2007; 143(1): 199 - 212. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. B. Duffy and B. Barquera Membrane Topology Mapping of the Na+-Pumping NADH: Quinone Oxidoreductase from Vibrio cholerae by PhoA- Green Fluorescent Protein Fusion Analysis J. Bacteriol., December 15, 2006; 188(24): 8343 - 8351. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Nakayama, S. Chen, N. Oyama, K. Nishiguchi, E. A. Azab, E. Tanaka, R. Kariyama, and K. Sonomoto Revised Model for Enterococcus faecalis fsr Quorum-Sensing System: the Small Open Reading Frame fsrD Encodes the Gelatinase Biosynthesis-Activating Pheromone Propeptide Corresponding to Staphylococcal AgrD J. Bacteriol., December 1, 2006; 188(23): 8321 - 8326. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. McDonald, S. Sheng, B. Stanley, D. Chen, Y. Ko, R. N. Cole, P. Pedersen, and J. E. Van Eyk Expanding the Subproteome of the Inner Mitochondria Using Protein Separation Technologies: One- and Two-dimensional Liquid Chromatography and Two-dimensional Gel Electrophoresis Mol. Cell. Proteomics, December 1, 2006; 5(12): 2392 - 2411. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Trujillo, L. Altschmied, P. Schweizer, K.-H. Kogel, and R. Huckelhoven Respiratory Burst Oxidase Homologue A of barley contributes to penetration by the powdery mildew fungus Blumeria graminis f. sp. hordei J. Exp. Bot., November 1, 2006; 57(14): 3781 - 3791. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. C. Elble, V. Walia, H.-c. Cheng, C. J. Connon, L. Mundhenk, A. D. Gruber, and B. U. Pauli The Putative Chloride Channel hCLCA2 Has a Single C-terminal Transmembrane Segment J. Biol. Chem., October 6, 2006; 281(40): 29448 - 29454. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Mundhenk, M. Alfalah, R. C. Elble, B. U. Pauli, H. Y. Naim, and A. D. Gruber Both Cleavage Products of the mCLCA3 Protein Are Secreted Soluble Proteins J. Biol. Chem., October 6, 2006; 281(40): 30072 - 30080. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Hiller, A. Grote, M. Maneck, R. Munch, and D. Jahn JVirGel 2.0: computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins Bioinformatics, October 1, 2006; 22(19): 2441 - 2443. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. J. J. B. Sibbald, A. K. Ziebandt, S. Engelmann, M. Hecker, A. de Jong, H. J. M. Harmsen, G. C. Raangs, I. Stokroos, J. P. Arends, J. Y. F. Dubois, et al. Mapping the Pathways to Staphylococcal Pathogenesis by Comparative Secretomics Microbiol. Mol. Biol. Rev., September 1, 2006; 70(3): 755 - 788. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Fujiki, S. Kawakami, R. W. Kim, and R. N. Beachy Domains of tobacco mosaic virus movement protein essential for its membrane association J. Gen. Virol., September 1, 2006; 87(9): 2699 - 2707. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. S. Lott, B. Paget, J. M. Johnston, L. T. J. Delbaere, J. A. Sigrell-Simon, M. J. Banfield, and E. N. Baker The Structure of an Ancient Conserved Domain Establishes a Structural Basis for Stable Histidine Phosphorylation and Identifies a New Family of Adenosine-specific Kinases J. Biol. Chem., August 4, 2006; 281(31): 22131 - 22141. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Zhao and E. London An amino acid "transmembrane tendency" scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: Relationship to biological hydrophobicity. Protein Sci., August 1, 2006; 15(8): 1987 - 2001. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. N. Stahler, S. Odenbreit, R. Haas, J. Wilrich, A. H. M. V. Vliet, J. G. Kusters, M. Kist, and S. Bereswill The Novel Helicobacter pylori CznABC Metal Efflux Pump Is Required for Cadmium, Zinc, and Nickel Resistance, Urease Modulation, and Gastric Colonization Infect. Immun., July 1, 2006; 74(7): 3845 - 3852. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Takenouchi-Ohkubo, L. M. Mortensen, K. R. Drasbek, M. Kilian, and K. Poulsen Horizontal transfer of the immunoglobulin A1 protease gene (iga) from Streptococcus to Gemella haemolysans Microbiology, July 1, 2006; 152(7): 2171 - 2180. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. J. Alderwick, M. Seidel, H. Sahm, G. S. Besra, and L. Eggeling Identification of a Novel Arabinofuranosyltransferase (AftA) Involved in Cell Wall Arabinan Biosynthesis in Mycobacterium tuberculosis J. Biol. Chem., June 9, 2006; 281(23): 15653 - 15661. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M.-J. Han and S. Y. Lee The Escherichia coli Proteome: Past, Present, and Future Prospects Microbiol. Mol. Biol. Rev., June 1, 2006; 70(2): 362 - 439. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Fu, A. Subramanya, D. Rozansky, and D. M. Cohen WNK kinases influence TRPV4 channel function and localization Am J Physiol Renal Physiol, June 1, 2006; 290(6): F1305 - F1314. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Krut, K. Wiegmann, H. Kashkar, B. Yazdanpanah, and M. Kronke Novel Tumor Necrosis Factor-responsive Mammalian Neutral Sphingomyelinase-3 Is a C-tail-anchored Protein J. Biol. Chem., May 12, 2006; 281(19): 13784 - 13793. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Xu, Y. Fu, W. Tian, and D. M. Cohen Glycosylation of the osmoresponsive transient receptor potential channel TRPV4 on Asn-651 influences membrane trafficking Am J Physiol Renal Physiol, May 1, 2006; 290(5): F1103 - F1109. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Zetterberg, W. A. Campbell, H. W. Yang, and W. Xia The Cytosolic Loop of the {gamma}-Secretase Component Presenilin Enhancer 2 Protects Zebrafish Embryos from Apoptosis J. Biol. Chem., April 28, 2006; 281(17): 11933 - 11939. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Campisano, C. Schroeder, M. Schemionek, J. Overhage, and B. H. A. Rehm PslD Is a Secreted Protein Required for Biofilm Formation by Pseudomonas aeruginosa Appl. Envir. Microbiol., April 1, 2006; 72(4): 3066 - 3068. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Lucas-Elio, D. Gomez, F. Solano, and A. Sanchez-Amat The Antimicrobial Activity of Marinocine, Synthesized by Marinomonas mediterranea, Is Due to Hydrogen Peroxide Generated by Its Lysine Oxidase Activity. J. Bacteriol., April 1, 2006; 188(7): 2493 - 2501. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. M. Burgess, D. J. Slotboom, E. R. Geertsma, R. H. Duurkens, B. Poolman, and D. van Sinderen The Riboflavin Transporter RibU in Lactococcus lactis: Molecular Characterization of Gene Expression and the Transport Mechanism. J. Bacteriol., April 1, 2006; 188(8): 2752 - 2760. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Pei, Z. Jia, and P. A. Watkins The Second Member of the Human and Murine "Bubblegum" Family Is a Testis- and Brainstem-specific Acyl-CoA Synthetase J. Biol. Chem., March 10, 2006; 281(10): 6632 - 6641. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. G. Kreft, L. Wang, and M. Hochstrasser Membrane Topology of the Yeast Endoplasmic Reticulum-localized Ubiquitin Ligase Doa10 and Comparison with Its Human Ortholog TEB4 (MARCH-VI) J. Biol. Chem., February 24, 2006; 281(8): 4646 - 4653. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. N. Amin, B. L. Taylor, and M. S. Johnson Topology and Boundaries of the Aerotaxis Receptor Aer in the Membrane of Escherichia coli J. Bacteriol., February 1, 2006; 188(3): 894 - 901. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. R. Couturier, E. Tasca, C. Montecucco, and M. Stein Interaction with CagF Is Required for Translocation of CagA into the Host via the Helicobacter pylori Type IV Secretion System Infect. Immun., January 1, 2006; 74(1): 273 - 281. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. L. Fink, R. N. Aturaliya, M. J. Davis, F. Zhang, K. Hanson, M. S. Teasdale, C. Kai, J. Kawai, P. Carninci, Y. Hayashizaki, et al. LOCATE: a mouse protein subcellular localization database Nucleic Acids Res., January 1, 2006; 34(suppl_1): D213 - D217. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Silvestri, V. Caputo, E. Bellacchio, L. Atorino, B. Dallapiccola, E. M. Valente, and G. Casari Mitochondrial import and enzymatic activity of PINK1 mutants associated to recessive parkinsonism Hum. Mol. Genet., November 15, 2005; 14(22): 3477 - 3492. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Schwartz, N. Grammel, E. Heinzelmann, U. Keller, and W. Wohlleben Phosphinothricin Tripeptide Synthetases in Streptomyces virido |