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TCDB: the Transporter Classification Database for membrane transport protein analyses and information
Milton H Saier1, Can V Tran, Ravi D Barabote
1Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA. msaier@ucsd.edu
Nucleic Acids Research
|December 31, 2005
Summary
The Transporter Classification Database (TCDB) provides comprehensive information on transport systems. This curated resource aids in classifying and analyzing transport proteins across diverse organisms.
Area of Science:
- Biochemistry
- Molecular Biology
- Bioinformatics
Background:
- Transport systems are crucial for cellular function and are found in all living organisms.
- Accurate classification and information on transporters are essential for biological research.
- Existing databases may lack comprehensive, curated data on transport proteins.
Purpose of the Study:
- To present the Transporter Classification Database (TCDB) as a comprehensive resource for transport systems.
- To highlight the database's utility for classification, analysis, and annotation of transporters.
- To provide a freely accessible platform for researchers studying transport proteins.
Main Methods:
- Compilation of data from over 10,000 references.
- Classification of approximately 3000 transporters into over 400 families using the transporter classification (TC) system.
- Development of a web interface for data access, including hierarchical classification, sequence search, TC number search, and full-text searching.
- Integration of a functional ontology for enhanced query capabilities.
- Inclusion of specialized tools for transport protein analysis.
Main Results:
- TCDB is a curated, relational database with sequence, classification, structural, functional, and evolutionary information on transport systems.
- The database encompasses ~3000 transporters classified into >400 families.
- The TC system, approved by the International Union of Biochemistry and Molecular Biology, provides standardized nomenclature.
- The TCDB website offers multiple data access methods and analytical tools.
- TCDB serves as a valuable genome transporter-annotation tool.
Conclusions:
- TCDB is a vital, freely accessible resource for researchers studying transport proteins.
- The database facilitates efficient data retrieval, classification of new transporters, and genome annotation.
- TCDB supports a deeper understanding of the structure, function, and evolution of transport systems.