EffectiveDB--updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems

Research output: Contribution to journalArticlepeer-review

Authors

  • Valerie Eichinger
  • Thomas Nussbaumer
  • Alexander Platzer
  • Marc-André Jehl
  • Thomas Rattei

Colleges, School and Institutes

External organisations

  • University of Vienna

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.

Details

Original languageEnglish
Pages (from-to)D669-D674
JournalNucleic Acids Research
Volume44
Issue numberD1
Early online date20 Nov 2015
Publication statusPublished - 1 Jan 2016

Keywords

  • Bacterial Proteins, Databases, Protein, Genome, Bacterial, Molecular Sequence Annotation, Protein Sorting Signals, Protein Structure, Tertiary, Sequence Analysis, Protein, Type III Secretion Systems, Type IV Secretion Systems, Type VI Secretion Systems, Journal Article, Research Support, Non-U.S. Gov't