CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources

BackgroundThe functions of proteins are strongly related to their localization in cell compartments (for example the cytoplasm or membranes) but the experimental determination of the sub-cellular localization of proteomes is laborious and expensive. A fast and low-cost alternative approach is in silico prediction, based on features of the protein primary sequences. However, biologists are confronted with a very large number of computational tools that use different methods that address various localization features with diverse specificities and sensitivities. As a result, exploiting these computer resources to predict protein localization accurately involves querying all tools and comparing every prediction output; this is a painstaking task. Therefore, we developed a comprehensive database, called CoBaltDB, that gathers all prediction outputs concerning complete prokaryotic proteomes.DescriptionThe current version of CoBaltDB integrates the results of 43 localization predictors for 784 complete bacterial and archaeal proteomes (2.548.292 proteins in total). CoBaltDB supplies a simple user-friendly interface for retrieving and exploring relevant information about predicted features (such as signal peptide cleavage sites and transmembrane segments). Data are organized into three work-sets ("specialized tools", "meta-tools" and "additional tools"). The database can be queried using the organism name, a locus tag or a list of locus tags and may be browsed using numerous graphical and text displays.ConclusionsWith its new functionalities, CoBaltDB is a novel powerful platform that provides easy access to the results of multiple localization tools and support for predicting prokaryotic protein localizations with higher confidence than previously possible. CoBaltDB is available at http://www.umr6026.univ-rennes1.fr/english/home/research/basic/software/cobalten.

[1]  A. Krogh,et al.  A combined transmembrane topology and signal peptide prediction method. , 2004, Journal of molecular biology.

[2]  M. Madan Babu,et al.  A Database of Bacterial Lipoproteins (DOLOP) with Functional Assignments to Predicted Lipoproteins , 2006, Journal of bacteriology.

[3]  J. Kissinger,et al.  Identification of Diverse Archaeal Proteins with Class III Signal Peptides Cleaved by Distinct Archaeal Prepilin Peptidases , 2006, Journal of bacteriology.

[4]  Masami Ikeda,et al.  ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability , 2004, Nucleic Acids Res..

[5]  David Thybert,et al.  OxyGene: an innovative platform for investigating oxidative-response genes in whole prokaryotic genomes , 2008, BMC Genomics.

[6]  Liam J. McGuffin,et al.  Protein structure prediction servers at University College London , 2005, Nucleic Acids Res..

[7]  Dieter Jahn,et al.  PrediSi: prediction of signal peptides and their cleavage positions , 2004, Nucleic Acids Res..

[8]  Arne Elofsson,et al.  OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar , 2008, Bioinform..

[9]  Claudio Donati,et al.  Protein Homology Network Families Reveal Step-Wise Diversification of Type III and Type IV Secretion Systems , 2006, PLoS Comput. Biol..

[10]  Shigeki Mitaku,et al.  High performance system for signal peptide prediction: SOSUIsignal , 2004 .

[11]  Stavros J. Hamodrakas,et al.  waveTM: Wavelet-based transmembrane segment prediction , 2004, Silico Biol..

[12]  Yu-Yen Ou,et al.  TMBETADISC-RBF: Discrimination of beta-barrel membrane proteins using RBF networks and PSSM profiles , 2008, Comput. Biol. Chem..

[13]  Daniel Restrepo-Montoya,et al.  Validating subcellular localization prediction tools with mycobacterial proteins , 2009, BMC Bioinformatics.

[14]  Thomas Rattei,et al.  Sequence-Based Prediction of Type III Secreted Proteins , 2009, PLoS pathogens.

[15]  Hans Wolf-Watz,et al.  Protein delivery into eukaryotic cells by type III secretion machines , 2006, Nature.

[16]  Radhey S. Gupta,et al.  The Natural Evolutionary Relationships among Prokaryotes , 2000, Critical reviews in microbiology.

[17]  Burkhard Rost,et al.  PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins , 2006, Nucleic Acids Res..

[18]  A. Driessen,et al.  Sec- and Tat-mediated protein secretion across the bacterial cytoplasmic membrane--distinct translocases and mechanisms. , 2008, Biochimica et biophysica acta.

[19]  David T. Jones,et al.  Improving the accuracy of transmembrane protein topology prediction using evolutionary information , 2007, Bioinform..

[20]  S. Karamanou,et al.  Bacterial protein secretion through the translocase nanomachine , 2007, Nature Reviews Microbiology.

[21]  Gajendra P. S. Raghava,et al.  PSLpred: prediction of subcellular localization of bacterial proteins , 2005, Bioinform..

[22]  Shandar Ahmad,et al.  TMBETA-NET: discrimination and prediction of membrane spanning β-strands in outer membrane proteins , 2005, Nucleic Acids Res..

[23]  Yaoqi Zhou,et al.  Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations , 2005, Nucleic Acids Res..

[24]  R. Brasseur,et al.  Secretion of Yop proteins by Yersiniae , 1990, Infection and immunity.

[25]  David S. Wishart,et al.  PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation , 2008, Nucleic Acids Res..

[26]  T. Palmer,et al.  A new way out: protein localization on the bacterial cell surface via Tat and a novel Type II secretion system , 2008, Molecular microbiology.

[27]  George Georgiou,et al.  The bacterial twin-arginine translocation pathway. , 2006, Annual review of microbiology.

[28]  Jing Hu,et al.  A method for discovering transmembrane beta-barrel proteins in Gram-negative bacterial proteomes , 2008, Comput. Biol. Chem..

[29]  Erik L. L. Sonnhammer,et al.  Advantages of combined transmembrane topology and signal peptide prediction—the Phobius web server , 2007, Nucleic Acids Res..

[30]  Shigeki Mitaku,et al.  SOSUI: classification and secondary structure prediction system for membrane proteins , 1998, Bioinform..

[31]  Theodore D. Liakopoulos,et al.  A novel tool for the prediction of transmembrane protein topology based on a statistical analysis of the SwissProt database: the OrienTM algorithm. , 2001, Protein engineering.

[32]  M. Saier,et al.  The β‐barrel finder (BBF) program, allowing identification of outer membrane β‐barrel proteins encoded within prokaryotic genomes , 2002 .

[33]  Guang R. Gao,et al.  An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes , 2005, Bioinform..

[34]  Schuyler F. Baldwin,et al.  The Complete Genome Sequence of Escherichia coli DH10B: Insights into the Biology of a Laboratory Workhorse , 2008, Journal of bacteriology.

[35]  K. Hughes,et al.  How and when are substrates selected for type III secretion? , 2001, Trends in microbiology.

[36]  D. Thanassi,et al.  Mechanisms of Protein Export across the Bacterial Outer Membrane , 2005, Journal of bacteriology.

[37]  Gertraud Burger,et al.  'Unite and conquer': enhanced prediction of protein subcellular localization by integrating multiple specialized tools , 2007, BMC Bioinformatics.

[38]  Jenn-Kang Hwang,et al.  Prediction of protein subcellular localization , 2006, Proteins.

[39]  Michel Hébraud,et al.  Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. , 2009, Trends in microbiology.

[40]  Andrew G. Garrow,et al.  A consensus algorithm to screen genomes for novel families of transmembrane β barrel proteins , 2007, Proteins.

[41]  Burkhard Rost,et al.  The PredictProtein server , 2003, Nucleic Acids Res..

[42]  B. Rost,et al.  Mimicking cellular sorting improves prediction of subcellular localization. , 2005, Journal of molecular biology.

[43]  S J Hamodrakas,et al.  A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm. , 1999, Protein engineering.

[44]  Rolf Apweiler,et al.  A comparison of signal sequence prediction methods using a test set of signal peptides , 2000, Bioinform..

[45]  A. Bäumler,et al.  Evolution of the Chaperone/Usher Assembly Pathway: Fimbrial Classification Goes Greek , 2007, Microbiology and Molecular Biology Reviews.

[46]  Ingvar Eidhammer,et al.  BOMP: a program to predict integral ?barrel outer membrane proteins encoded within genomes of Gram-negative bacteria , 2004, Nucleic Acids Res..

[47]  Hongbin Shen,et al.  MemBrain: Improving the Accuracy of Predicting Transmembrane Helices , 2008, PloS one.

[48]  A. Edwards,et al.  Proteins Exported via the PrsD-PrsE Type I Secretion System and the Acidic Exopolysaccharide Are Involved in Biofilm Formation by Rhizobium leguminosarum , 2006, Journal of bacteriology.

[49]  Peter Clote,et al.  transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels , 2006, Nucleic Acids Res..

[50]  Jos Boekhorst,et al.  LocateP: Genome-scale subcellular-location predictor for bacterial proteins , 2008, BMC Bioinformatics.

[51]  K. Chou,et al.  Signal-3L: A 3-layer approach for predicting signal peptides. , 2007, Biochemical and biophysical research communications.

[52]  Wen-Lian Hsu,et al.  Protein subcellular localization prediction based on compartment-specific features and structure conservation , 2007, BMC Bioinformatics.

[53]  I. Henderson,et al.  Type V protein secretion: simplicity gone awry? , 2004, Current issues in molecular biology.

[54]  B. Rost,et al.  Topology prediction for helical transmembrane proteins at 86% accuracy–Topology prediction at 86% accuracy , 1996, Protein science : a publication of the Protein Society.

[55]  Aoife McLysaght,et al.  Porter: a new, accurate server for protein secondary structure prediction , 2005, Bioinform..

[56]  S. Genin,et al.  Secreted proteins from Ralstonia solanacearum: a hundred tricks to kill a plant. , 2009, Current opinion in microbiology.

[57]  S H White,et al.  MPtopo: A database of membrane protein topology , 2001, Protein science : a publication of the Protein Society.

[58]  John Chan,et al.  SecA2 functions in the secretion of superoxide dismutase A and in the virulence of Mycobacterium tuberculosis , 2003, Molecular microbiology.

[59]  S. Brunak,et al.  SHORT COMMUNICATION Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites , 1997 .

[60]  A Elofsson,et al.  Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. , 1997, Protein engineering.

[61]  G. Waksman,et al.  Fiber assembly by the chaperone-usher pathway. , 2004, Biochimica et biophysica acta.

[62]  Zhirong Sun,et al.  Support vector machine approach for protein subcellular localization prediction , 2001, Bioinform..

[63]  O. Schneewind,et al.  Yersinia enterocolitica type III secretion: an mRNA signal that couples translation and secretion of YopQ , 1999, Molecular microbiology.

[64]  A. Elofsson,et al.  Best α‐helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information , 2004 .

[65]  O. Steward,et al.  Evidence that protein constituents of postsynaptic membrane specializations are locally synthesized: Time course of appearance of recently synthesized proteins in synaptic junctions , 1991, Journal of neuroscience research.

[66]  S. Pukatzki,et al.  The type VI secretion system: translocation of effectors and effector-domains. , 2009, Current opinion in microbiology.

[67]  M. Pallen.  The ESAT-6/WXG100 superfamily -- and a new Gram-positive secretion system? , 2002, Trends in microbiology.

[68]  István Simon,et al.  The HMMTOP transmembrane topology prediction server , 2001, Bioinform..

[69]  Mamoon Rashid,et al.  Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs , 2007, BMC Bioinformatics.

[70]  G. Cornelis,et al.  The type III secretion system tip complex and translocon , 2008, Molecular microbiology.

[71]  Narayanaswamy Balakrishnan,et al.  Transmembrane helix prediction using amino acid property features and latent semantic analysis , 2008, BMC Bioinformatics.

[72]  Guo-Zheng Li,et al.  Using AdaBoost for the prediction of subcellular location of prokaryotic and eukaryotic proteins , 2008, Molecular Diversity.

[73]  B. Appelmelk,et al.  Type VII secretion in mycobacteria: classification in line with cell envelope structure. , 2009, Trends in microbiology.

[74]  I. Henderson,et al.  Type V Protein Secretion Pathway: the Autotransporter Story , 2004, Microbiology and Molecular Biology Reviews.

[75]  K. Chou,et al.  Gpos-PLoc: an ensemble classifier for predicting subcellular localization of Gram-positive bacterial proteins. , 2007, Protein engineering, design & selection : PEDS.

[76]  M. Michael Gromiha,et al.  TMBETA-GENOME: database for annotated β-barrel membrane proteins in genomic sequences , 2006, Nucleic Acids Res..

[77]  Lutz Schmitt,et al.  Type 1 protein secretion in bacteria, the ABC-transporter dependent pathway (Review) , 2005, Molecular membrane biology.

[78]  Terri K. Attwood,et al.  BPROMPT: a consensus server for membrane protein prediction , 2003, Nucleic Acids Res..

[79]  David R. Westhead,et al.  TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins , 2005, BMC Bioinformatics.

[80]  Piero Fariselli,et al.  SPEPlip: the detection of signal peptide and lipoprotein cleavage sites , 2003, Bioinform..

[81]  David R. Westhead,et al.  TMB-Hunt: a web server to screen sequence sets for transmembrane β-barrel proteins , 2005, Nucleic Acids Res..

[82]  M. Pallen,et al.  Type III secretion: what's in a name? , 2006, Trends in microbiology.

[83]  Marcin J. Skwark,et al.  Sequence analysis SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology , 2008 .

[84]  Andrei L. Lomize,et al.  OPM: Orientations of Proteins in Membranes database , 2006, Bioinform..

[85]  O. Schneewind,et al.  A mRNA signal for the type III secretion of Yop proteins by Yersinia enterocolitica. , 1997, Science.

[86]  Paul Horton,et al.  Discrimination of outer membrane proteins using support vector machines , 2005, Bioinform..

[87]  Zemin Zhang,et al.  Signal peptide prediction based on analysis of experimentally verified cleavage sites , 2004, Protein science : a publication of the Protein Society.

[88]  Wen-Lian Hsu,et al.  Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function. , 2008, Journal of proteome research.

[89]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[90]  A. Driessen,et al.  Protein secretion in the Archaea: multiple paths towards a unique cell surface , 2006, Nature Reviews Microbiology.

[91]  Zheng Yuan,et al.  SVMtm: Support vector machines to predict transmembrane segments , 2004, J. Comput. Chem..

[92]  Baldomero Oliva,et al.  'TransMem': a neural network implemented in Excel spreadsheets for predicting transmembrane domains of proteins , 1997, Comput. Appl. Biosci..

[93]  I. Henderson,et al.  The general secretory pathway: a general misnomer? , 2004, Trends in microbiology.

[94]  I. Eidhammer,et al.  Analysing the outer membrane subproteome of Methylococcus capsulatus (Bath) using proteomics and novel biocomputing tools , 2006, Archives of Microbiology.

[95]  M. Saier,et al.  The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes. , 2002, Protein science : a publication of the Protein Society.

[96]  Masami Ikeda,et al.  TMPDB: a database of experimentally-characterized transmembrane topologies , 2003, Nucleic Acids Res..

[97]  Jeff A. Bilmes,et al.  Transmembrane Topology and Signal Peptide Prediction Using Dynamic Bayesian Networks , 2008, PLoS Comput. Biol..

[98]  Pierre Baldi,et al.  TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins , 2008, Bioinform..

[99]  Johannes Söding,et al.  HHomp—prediction and classification of outer membrane proteins , 2009, Nucleic Acids Res..

[100]  I. Henderson,et al.  Outer membrane translocation: numerical protein secretion nomenclature in question in mycobacteria. , 2009, Trends in Microbiology.

[101]  P. Delepelaire.  Type I secretion in gram-negative bacteria. , 2004, Biochimica et biophysica acta.

[102]  T. Tsuji,et al.  SOSUI-GramN: high performance prediction for sub-cellular localization of proteins in Gram-negative bacteria , 2008, Bioinformation.

[103]  G von Heijne,et al.  The structure of signal peptides from bacterial lipoproteins. , 1989, Protein engineering.

[104]  S H White,et al.  Energetics, stability, and prediction of transmembrane helices. , 2001, Journal of molecular biology.

[105]  Kuo-Chen Chou,et al.  Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides. , 2007, Biochemical and biophysical research communications.

[106]  Patrick Argos,et al.  Prediction of Membrane Protein Topology Utilizing Multiple Sequence Alignments , 1997, Journal of protein chemistry.

[107]  D T Jones,et al.  Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.

[108]  Tin Wee Tan,et al.  SPdb – a signal peptide database , 2005, BMC Bioinformatics.

[109]  G. Schneider,et al.  Domain Organization of Long Signal Peptides of Single-Pass Integral Membrane Proteins Reveals Multiple Functional Capacity , 2008, PloS one.

[110]  Pantelis G Bagos,et al.  Prediction of lipoprotein signal peptides in Gram-positive bacteria with a Hidden Markov Model. , 2008, Journal of proteome research.

[111]  Sophie Bleves,et al.  The bacterial type VI secretion machine: yet another player for protein transport across membranes. , 2008, Microbiology.

[112]  S J Hamodrakas,et al.  An hierarchical artificial neural network system for the classification of transmembrane proteins. , 1999, Protein engineering.

[113]  Matthias Müller,et al.  Twin-arginine-specific protein export in Escherichia coli. , 2005, Research in microbiology.

[114]  J. Mekalanos,et al.  Characterization of the Vibrio cholerae ToxR regulon: identification of novel genes involved in intestinal colonization , 1988 .

[115]  S. Matsuyama,et al.  Effects of Lipoprotein Overproduction on the Induction of DegP (HtrA) Involved in Quality Control in the Escherichia coli Periplasm* , 2004, Journal of Biological Chemistry.

[116]  D. McGeoch,et al.  On the predictive recognition of signal peptide sequences. , 1985, Virus research.

[117]  C Combet,et al.  NPS@: network protein sequence analysis. , 2000, Trends in biochemical sciences.

[118]  Peilin Jia,et al.  Prediction of subcellular protein localization based on functional domain composition. , 2007, Biochemical and biophysical research communications.

[119]  Søren Brunak,et al.  Prediction of twin-arginine signal peptides , 2005, BMC Bioinformatics.

[120]  Stavros J. Hamodrakas,et al.  PRED-TMBB: a web server for predicting the topology of ?barrel outer membrane proteins , 2004, Nucleic Acids Res..

[121]  B. Berks.  A common export pathway for proteins binding complex redox cofactors? , 1996, Molecular microbiology.

[122]  W R Taylor,et al.  A model recognition approach to the prediction of all-helical membrane protein structure and topology. , 1994, Biochemistry.

[123]  J. Setubal,et al.  Lipoprotein computational prediction in spirochaetal genomes. , 2006, Microbiology.

[124]  Trinad Chakraborty,et al.  Augur - a computational pipeline for whole genome microbial surface protein prediction and classification , 2006, Bioinform..

[125]  N. Cianciotto.  Type II secretion: a protein secretion system for all seasons. , 2005, Trends in microbiology.

[126]  Kuang Lin,et al.  A simple and fast secondary structure prediction method using hidden neural networks , 2005, Bioinform..

[127]  Arne Elofsson,et al.  TOPCONS: consensus prediction of membrane protein topology , 2009, Nucleic Acids Res..

[128]  J. Anné,et al.  The role of protein secretion systems in the virulence of the intracellular pathogen Legionella pneumophila. , 2007, Microbiology.

[129]  Hedvig Tordai,et al.  Identification and correction of abnormal, incomplete and mispredicted proteins in public databases , 2008, BMC Bioinformatics.

[130]  G von Heijne,et al.  Patterns of amino acids near signal-sequence cleavage sites. , 1983, European journal of biochemistry.

[131]  Shigeki Mitaku,et al.  Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfaces , 2002, Bioinform..

[132]  B. Martoglio,et al.  Signal sequences: more than just greasy peptides. , 1998, Trends in cell biology.

[133]  Darren R Flower,et al.  LIPPRED: A web server for accurate prediction of lipoprotein signal sequences and cleavage sites , 2006, Bioinformation.

[134]  G Schneider,et al.  Analysis of cleavage-site patterns in protein precursor sequences with a perceptron-type neural network. , 1993, Biochemical and biophysical research communications.

[135]  Stavros J. Hamodrakas,et al.  Prediction of Cell Wall Sorting Signals in Gram-Positive bacteria with a Hidden Markov Model: Application to Complete genomes , 2008, J. Bioinform. Comput. Biol..

[136]  A. Krogh,et al.  Prediction of lipoprotein signal peptides in Gram‐negative bacteria , 2003, Protein science : a publication of the Protein Society.

[137]  Jaap Heringa,et al.  PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information , 2005, Nucleic Acids Res..

[138]  István Simon,et al.  TOPDB: topology data bank of transmembrane proteins , 2007, Nucleic Acids Res..

[139]  V. Goder,et al.  Topogenesis of membrane proteins: determinants and dynamics , 2001, FEBS letters.

[140]  Piero Fariselli,et al.  A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins , 2002, ISMB.

[141]  C DeLisi,et al.  The detection and classification of membrane-spanning proteins. , 1985, Biochimica et biophysica acta.

[142]  Judith Klein-Seetharaman,et al.  TMpro web server and web service: transmembrane helix prediction through amino acid property analysis , 2007, Bioinform..

[143]  Biao Kan,et al.  Pleiotropic effects of the twin-arginine translocation system on biofilm formation, colonization, and virulence in Vibrio cholerae , 2009, BMC Microbiology.

[144]  M. Saier,et al.  Type II protein secretion and its relationship to bacterial type IV pili and archaeal flagella. , 2003, Microbiology.

[145]  Jessica C Kissinger,et al.  Adaptation of protein secretion to extremely high‐salt conditions by extensive use of the twin‐arginine translocation pathway , 2002, Molecular microbiology.

[146]  Stavros J. Hamodrakas,et al.  Evaluation of methods for predicting the topology of β-barrel outer membrane proteins and a consensus prediction method , 2005, BMC Bioinformatics.

[147]  Zhiyong Lu,et al.  Predicting subcellular localization of proteins using machine-learned classifiers , 2004, Bioinform..

[148]  Stavros J. Hamodrakas,et al.  Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins , 2006, BMC Bioinformatics.

[149]  S. Brunak,et al.  Improved prediction of signal peptides: SignalP 3.0. , 2004, Journal of molecular biology.

[150]  R. W. Davis,et al.  A low rate of nucleotide changes in Escherichia coli K‐12 estimated from a comparison of the genome sequences between two different substrains , 1999, FEBS letters.

[151]  Gisbert Schneider,et al.  Prediction of Type III Secretion Signals in Genomes of Gram-Negative Bacteria , 2009, PloS one.

[152]  Burkhard Rost,et al.  LOCnet and LOCtarget: sub-cellular localization for structural genomics targets , 2004, Nucleic Acids Res..

[153]  Song Zhang,et al.  DBMLoc: a Database of proteins with multiple subcellular localizations , 2008, BMC Bioinformatics.

[154]  Jean-Philippe Vert,et al.  A novel representation of protein sequences for prediction of subcellular location using support vector machines , 2005, Protein science : a publication of the Protein Society.

[155]  H. Huber,et al.  The ultrastructure of Ignicoccus: evidence for a novel outer membrane and for intracellular vesicle budding in an archaeon. , 2002, Archaea.

[156]  M. Pallen,et al.  Genomic analysis of the protein secretion systems in Clostridium acetobutylicum ATCC 824. , 2005, Biochimica et biophysica acta.

[157]  Kuo-Chen Chou,et al.  Large-scale predictions of gram-negative bacterial protein subcellular locations. , 2006, Journal of proteome research.

[158]  Søren Brunak,et al.  Non-classical protein secretion in bacteria , 2005, BMC Microbiology.

[159]  J. Vivanco,et al.  Root-Microbe Communication through Protein Secretion* , 2008, Journal of Biological Chemistry.

[160]  Damián López,et al.  IgTM: An algorithm to predict transmembrane domains and topology in proteins , 2008, BMC Bioinformatics.

[161]  Kenneth E. Rudd,et al.  EcoGene: a genome sequence database for Escherichia coli K-12 , 2000, Nucleic Acids Res..

[162]  Christopher M. Bailey,et al.  Type VI secretion: a beginner's guide. , 2008, Current opinion in microbiology.

[163]  Sang Yup Lee,et al.  EcoProDB: the Escherichia coli protein database , 2007, Bioinform..

[164]  Dariusz Plewczynski,et al.  Prediction of signal peptides in protein sequences by neural networks. , 2008, Acta biochimica Polonica.

[165]  Christophe G. Lambert,et al.  PSORTdb: a protein subcellular localization database for bacteria , 2004, Nucleic Acids Res..

[166]  Anders Krogh,et al.  Prediction of Signal Peptides and Signal Anchors by a Hidden Markov Model , 1998, ISMB.

[167]  Nikitas Papangelopoulos,et al.  EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations , 2009, Bioinform..

[168]  Zsuzsanna Dosztányi,et al.  PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank , 2004, Nucleic Acids Res..

[169]  J. Mekalanos,et al.  Characterization of the Vibrio cholerae ToxR Regulon: Identification of Novel Genes Involved in Intestinal Colonization , 1989, Infection and immunity.

[170]  Yaoqi Zhou,et al.  Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method , 2003 .

[171]  A J Cuticchia,et al.  TM Finder: A prediction program for transmembrane protein segments using a combination of hydrophobicity and nonpolar phase helicity scales , 2001, Protein science : a publication of the Protein Society.

[172]  P. D. Rick,et al.  Roles of histidine-103 and tyrosine-235 in the function of the prolipoprotein diacylglyceryl transferase of Escherichia coli , 1997, Journal of bacteriology.

[173]  Sukanta Mondal,et al.  THGS: a web-based database of Transmembrane Helices in Genome Sequences , 2004, Nucleic Acids Res..

[174]  Aleksey A. Porollo,et al.  Combining prediction of secondary structure and solvent accessibility in proteins , 2005, Proteins.

[175]  Kuo-Chen Chou,et al.  MemType-2L: a web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM. , 2007, Biochemical and biophysical research communications.

[176]  Jae-Seong Yang,et al.  Construction of functional interaction networks through consensus localization predictions of the human proteome. , 2009, Journal of proteome research.

[177]  Jeff F. Miller,et al.  Virulence factor secretion and translocation by Bordetella species. , 2009, Current opinion in microbiology.

[178]  Konstantinos D. Tsirigos,et al.  Prediction of signal peptides in archaea. , 2008, Protein engineering, design & selection : PEDS.

[179]  D. Juretic,et al.  Basic Charge Clusters and Predictions of Membrane Protein Topology , 2002, J. Chem. Inf. Comput. Sci..

[180]  Henry R. Bigelow,et al.  Predicting transmembrane beta-barrels in proteomes. , 2004, Nucleic acids research.

[181]  Karl Frank,et al.  High-performance signal peptide prediction based on sequence alignment techniques , 2008, Bioinform..

[182]  István Csabai,et al.  Improving signal peptide prediction accuracy by simulated neural network , 1991, Comput. Appl. Biosci..

[183]  Kevin Karplus,et al.  SAM-T08, HMM-based protein structure prediction , 2009, Nucleic Acids Res..

[184]  Manuel G. Claros,et al.  TopPred II: an improved software for membrane protein structure predictions , 1994, Comput. Appl. Biosci..

[185]  J. Belisle,et al.  Identification of putative exported/secreted proteins in prokaryotic proteomes. , 2001, Gene.

[186]  B. Rost,et al.  Automatic prediction of protein function , 2003, Cellular and Molecular Life Sciences CMLS.

[187]  G. von Heijne,et al.  A new method for predkting signal sequence cleavage sites , 2022 .