This article is part of the supplement: Ninth International Conference on Bioinformatics (InCoB2010): Bioinformatics

Open Access Proceedings

T3SEdb: data warehousing of virulence effectors secreted by the bacterial Type III Secretion System

Daniel Ming Ming Tay, Kunde Ramamoorthy Govindarajan, Asif M Khan, Terenze Yao Rui Ong, Hanif M Samad, Wei Wei Soh, Minyan Tong, Fan Zhang and Tin Wee Tan*

Author Affiliations

Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597

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BMC Bioinformatics 2010, 11(Suppl 7):S4  doi:10.1186/1471-2105-11-S7-S4

Published: 15 October 2010

Abstract

Background

Effectors of Type III Secretion System (T3SS) play a pivotal role in establishing and maintaining pathogenicity in the host and therefore the identification of these effectors is important in understanding virulence. However, the effectors display high level of sequence diversity, therefore making the identification a difficult process. There is a need to collate and annotate existing effector sequences in public databases to enable systematic analyses of these sequences for development of models for screening and selection of putative novel effectors from bacterial genomes that can be validated by a smaller number of key experiments.

Results

Herein, we present T3SEdb http://effectors.bic.nus.edu.sg/T3SEdb webcite, a specialized database of annotated T3SS effector (T3SE) sequences containing 1089 records from 46 bacterial species compiled from the literature and public protein databases. Procedures have been defined for i) comprehensive annotation of experimental status of effectors, ii) submission and curation review of records by users of the database, and iii) the regular update of T3SEdb existing and new records. Keyword fielded and sequence searches (BLAST, regular expression) are supported for both experimentally verified and hypothetical T3SEs. More than 171 clusters of T3SEs were detected based on sequence identity comparisons (intra-cluster difference up to ~60%). Owing to this high level of sequence diversity of T3SEs, the T3SEdb provides a large number of experimentally known effector sequences with wide species representation for creation of effector predictors. We created a reliable effector prediction tool, integrated into the database, to demonstrate the application of the database for such endeavours.

Conclusions

T3SEdb is the first specialised database reported for T3SS effectors, enriched with manual annotations that facilitated systematic construction of a reliable prediction model for identification of novel effectors. The T3SEdb represents a platform for inclusion of additional annotations of metadata for future developments of sophisticated effector prediction models for screening and selection of putative novel effectors from bacterial genomes/proteomes that can be validated by a small number of key experiments.