title: EffectiveDB--updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems.
abstract: Protein secretion systems play a key role in the interaction of bacteria and hosts. EffectiveDB (http://effectivedb.org) contains pre-calculated predictions of bacterial secreted proteins and of intact secretion systems. Here we describe a major update of the database, which was previously featured in the NAR Database Issue. EffectiveDB bundles various tools to recognize Type III secretion signals, conserved binding sites of Type III chaperones, Type IV secretion peptides, eukaryotic-like domains and subcellular targeting signals in the host. Beyond the analysis of arbitrary protein sequence collections, the new release of EffectiveDB also provides a 'genome-mode', in which protein sequences from nearly complete genomes or metagenomic bins can be screened for the presence of three important secretion systems (Type III, IV, VI). EffectiveDB contains pre-calculated predictions for currently 1677 bacterial genomes from the EggNOG 4.0 database and for additional bacterial genomes from NCBI RefSeq. The new, user-friendly and informative web portal offers a submission tool for running the EffectiveDB prediction tools on user-provided data.
authors.affiliation: Division of Computational System Biology, Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria.
authors.forename: Valerie
authors.initials: V
authors.lastname: Eichinger
authors.affiliation: Division of Computational System Biology, Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria.
authors.forename: Thomas
authors.initials: T
authors.lastname: Nussbaumer
authors.affiliation: Division of Computational System Biology, Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria.
authors.forename: Alexander
authors.initials: A
authors.lastname: Platzer
authors.affiliation: Division of Computational System Biology, Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria.
authors.forename: Marc-André
authors.initials: MA
authors.lastname: Jehl
authors.affiliation: Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.
authors.forename: Roland
authors.initials: R
authors.lastname: Arnold
authors.affiliation: Division of Computational System Biology, Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria thomas.rattei@univie.ac.at.
authors.forename: Thomas
authors.initials: T
authors.lastname: Rattei
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D030562:Databases, Protein; D016680:Genome, Bacterial; D058977:Molecular Sequence Annotation; D021382:Protein Sorting Signals; D017434:Protein Structure, Tertiary; D020539:Sequence Analysis, Protein; D000069296:Type III Secretion Systems; D000069319:Type IV Secretion Systems; D000069376:Type VI Secretion Systems
chemical_list: D001426:Bacterial Proteins; D021382:Protein Sorting Signals; D000069296:Type III Secretion Systems; D000069319:Type IV Secretion Systems; D000069376:Type VI Secretion Systems