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T3DB: an integrated database for bacterial type III secretion system.

Yejun Wang1, He Huang, Ming'an Sun

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

BMC Bioinformatics
|May 2, 2012
PubMed
Summary
This summary is machine-generated.

A new database, T3DB, integrates Type III Secretion System (T3SS) gene and protein data. This resource aids research into bacterial pathogenesis and symbiosis by standardizing nomenclature and facilitating communication among scientists.

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Area of Science:

  • Microbiology
  • Bacterial Pathogenesis
  • Molecular Biology

Background:

  • Type III Secretion System (T3SS) is crucial for bacterial pathogenesis and symbiosis in Gram-negative bacteria.
  • Lack of standardized nomenclature for T3SS genes impedes research progress.
  • A unified knowledgebase is needed to integrate T3SS data and improve inter-group communication.

Purpose of the Study:

  • To develop a comprehensive database (T3DB) for T3SS-related research.
  • To provide an integrated platform for sequence collection, function annotation, and ortholog classification of T3SS genes.
  • To facilitate communication and collaboration among researchers studying diverse bacterial species.

Main Methods:

  • Developed the T3SS-related Database (T3DB) as an integrated platform.
  • Manually curated data on T3SS-containing bacteria, genes, functions, and orthologs from scientific literature.
  • Implemented BPBAac, an efficient tool for predicting T3SS effectors.

Main Results:

  • T3DB is the first systematic platform for well-annotated T3SS gene and protein information.
  • The database includes curated data on T3SS apparatus, effectors, chaperones, and regulatory genes.
  • Ortholog clusters and curated data support feature analysis and evolutionary studies.

Conclusions:

  • T3DB significantly facilitates research on T3SS and bacterial pathogenicity.
  • The integrated data and ortholog clusters promote inter-researcher communication and new discoveries.
  • High-quality curated data on effectors and chaperones are valuable for further analysis.