title: Identification of efflux proteins using efficient radial basis function networks with position-specific scoring matrices and biochemical properties.
abstract: Efflux proteins are membrane proteins, which are involved in the transportation of multidrugs. The annotation of efflux proteins in genomic sequences would aid to understand the function. Although the percentage of membrane proteins in genomes is estimated to be 25-30%, there is no information about the content of efflux proteins. For annotating such class of proteins it is necessary to develop a reliable method to identify efflux proteins from amino acid sequence information. In this work, we have developed a method based on radial basis function networks using position specific scoring matrices (PSSM) and amino acid properties. We noticed that the C-terminal domain of efflux proteins contain vital information for discrimination. Our method showed an accuracy of 78 and 92% in discriminating efflux proteins from transporters and membrane proteins, respectively using fivefold cross-validation. We utilized our method for annotating the genomes E. coli and P. aeruginosa and it predicted 8.7 and 9.2% of proteins as efflux proteins in these genomes, respectively. The predicted efflux proteins have been compared with available experimental data and we observed a very good agreement between them. Further, we developed a web server for classifying efflux proteins and it is freely available at http://rbf.bioinfo.tw/∼sachen/EFFLUXpredict/Efflux-RBF.php. We suggest that our method could be an effective tool for annotating efflux proteins in genomic sequences.
authors.affiliation: Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, Taiwan.
authors.forename: Yu-Yen
authors.initials: YY
authors.lastname: Ou
authors.forename: Shu-An
authors.initials: SA
authors.lastname: Chen
authors.forename: Yun-Min
authors.initials: YM
authors.lastname: Chang
authors.forename: Devadasan
authors.initials: D
authors.lastname: Velmurugan
authors.forename: Kazuhiko
authors.initials: K
authors.lastname: Fukui
authors.forename: M
authors.initials: M
authors.lastname: Michael Gromiha
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D026901:Membrane Transport Proteins / Q000737:chemistry*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D056510:Position-Specific Scoring Matrices; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D026901:Membrane Transport Proteins
keywords: E. coli; annotation; genome; membrane protein; transporter