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T3DB: an integrated database for bacterial type III secretion system

Yejun Wang1, He Huang2, Ming’an Sun1, Qing Zhang1 and Dianjing Guo1*

Author affiliations

1 School of Life Science, The Chinese University of Hong Kong, Shatin, NT, Hong Kong

2 Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China

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Citation and License

BMC Bioinformatics 2012, 13:66  doi:10.1186/1471-2105-13-66

Published: 30 April 2012

Abstract

Background

Type III Secretion System (T3SS), which plays important roles in pathogenesis or symbiosis, is widely expressed in a variety of gram negative bacteria. However, lack of unique nomenclature for T3SS genes has hindered T3SS related research. It is necessary to set up a knowledgebase integrating T3SS-related research data to facilitate the communication between different research groups interested in different bacteria.

Description

A T3SS-related Database (T3DB) was developed. T3DB serves as an integrated platform for sequence collection, function annotation, and ortholog classification for T3SS related apparatus, effector, chaperone and regulatory genes. The collection of T3SS-containing bacteria, T3SS-related genes, function annotation, and the ortholog information were all manually curated from literature. BPBAac, a highly efficient T3SS effector prediction tool, was also implemented.

Conclusions

T3DB is the first systematic platform integrating well-annotated T3SS-related gene and protein information to facilitate T3SS and bacterial pathogenecity related research. The newly constructed T3 ortholog clusters may faciliate effective communication between different research groups and will promote de novo discoveries. Besides, the manually-curated high-quality effector and chaperone data are useful for feature analysis and evolutionary studies of these important proteins.