An Automated Program to Screen Databases for Members of Protein Families

We have developed a program, ScreenTransporter (ST), to screen for potential members of recognized transporter families. This program uses Blastpgp as the engine to search a nonredundant database, NRDB90, based on an adjustable E-value cut-off as well as adjustable protein size criteria. Additional parameters can be integrated in later versions. ST is convenient for easily obtaining nonredundant members of transporter families starting from several homologous query sequences. The program can be applied to any protein family.

[1]  Adam Godzik,et al.  Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology , 2000, Bioinform..

[2]  M. Saier,et al.  Computer-aided analyses of transport protein sequences: gleaning evidence concerning function, structure, biogenesis, and evolution , 1994, Microbiological reviews.

[3]  A. Lesk.  COMPUTATIONAL MOLECULAR BIOLOGY , 1988, Proceeding of Data For Discovery.

[4]  J. M. Sauder,et al.  Large‐scale comparison of protein sequence alignment algorithms with structure alignments , 2000, Proteins.

[5]  R F Doolittle,et al.  Progressive alignment and phylogenetic tree construction of protein sequences. , 1990, Methods in enzymology.

[6]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

[7]  Yufeng Zhai,et al.  A web-based Tree View (TV) program for the visualization of phylogenetic trees. , 2002, Journal of molecular microbiology and biotechnology.

[8]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 , 2000, Nucleic Acids Res..

[9]  Yufeng Zhai,et al.  A simple sensitive program for detecting internal repeats in sets of multiply aligned homologous proteins. , 2002, Journal of molecular microbiology and biotechnology.

[10]  P. Mitchell.  Translocations through natural membranes. , 2006, Advances in enzymology and related areas of molecular biology.

[11]  M. Saier.  A Functional-Phylogenetic Classification System for Transmembrane Solute Transporters , 2000, Microbiology and Molecular Biology Reviews.

[12]  Sean R. Eddy,et al.  Pfam: multiple sequence alignments and HMM-profiles of protein domains , 1998, Nucleic Acids Res..

[13]  David L. Wheeler,et al.  GenBank , 2015, Nucleic Acids Res..

[14]  Y Zhai,et al.  A web-based program (WHAT) for the simultaneous prediction of hydropathy, amphipathicity, secondary structure and transmembrane topology for a single protein sequence. , 2001, Journal of molecular microbiology and biotechnology.

[15]  Chris Sander,et al.  Removing near-neighbour redundancy from large protein sequence collections , 1998, Bioinform..

[16]  Richard Hughey,et al.  Hidden Markov models for detecting remote protein homologies , 1998, Bioinform..

[17]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[18]  Kathryn E. Sidman,et al.  The protein identification resource (PIR). , 1986, Nucleic acids research.

[19]  Petra Mutzel,et al.  Computational Molecular Biology , 1996 .

[20]  D. Haussler,et al.  Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. , 1998, Journal of molecular biology.

[21]  M. Saier,et al.  Molecular phylogeny as a basis for the classification of transport proteins from bacteria, archaea and eukarya. , 1998, Advances in microbial physiology.

[22]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[23]  M H Saier,et al.  A web-based program for the prediction of average hydropathy, average amphipathicity and average similarity of multiply aligned homologous proteins. , 2001, Journal of molecular microbiology and biotechnology.

[24]  P. Mitchell.  Proton-translocation phosphorylation in mitochondria, chloroplasts and bacteria: natural fuel cells and solar cells. , 1967, Federation proceedings.