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Transporter Classification Database (TCDB)

The Transporter Classification Database (TCDB) is a comprehensive database that provides a functional and phylogenetic classification of membrane transport proteins found in living organisms. It is a critical resource for researchers in the fields of biochemistry, molecular biology, and pharmacology, offering insights into the mechanisms and evolutionary relationships of transport proteins.

Overview

Transport proteins are essential for the movement of molecules across cellular membranes, a process vital for cellular function and homeostasis. The TCDB classifies these proteins based on their transport mechanism, substrate specificity, and evolutionary origin. The database is curated by experts and is continuously updated to reflect new discoveries in the field.

History

The TCDB was established to provide a systematic and comprehensive classification of transport proteins, similar to the Enzyme Commission (EC) numbers used for enzymes. It was developed by Milton H. Saier, Jr. and his colleagues at the University of California, San Diego. The database has grown significantly since its inception, incorporating data from genomic, proteomic, and biochemical studies.

Classification System

The TCDB uses a hierarchical classification system that organizes transport proteins into classes, subclasses, families, and subfamilies. The primary classification is based on the mode of transport and energy coupling mechanism, which includes:

• Channels and Pores: Proteins that facilitate passive transport of ions and small molecules.
• Electrochemical Potential-driven Transporters: Proteins that use ion gradients to drive the transport of substrates.
• Primary Active Transporters: Proteins that use energy from ATP hydrolysis or other sources to transport substrates against their concentration gradient.
• Group Translocators: Proteins that modify their substrates during the transport process.
• Transmembrane Electron Carriers: Proteins involved in electron transport across membranes.

Each class is further divided into subclasses and families based on specific characteristics and evolutionary relationships.

Features

The TCDB provides several features to facilitate research and analysis:

• Search and Browse: Users can search for transport proteins by name, function, or classification number. The database also allows browsing by class, family, or organism.
• Sequence Data: The TCDB includes sequence data for each protein, allowing for comparative analysis and phylogenetic studies.
• Functional Annotations: Detailed annotations provide information on the function, structure, and mechanism of each transport protein.
• Cross-references: The database includes cross-references to other biological databases, such as UniProt, PDB, and KEGG.

Applications

The TCDB is used by researchers to:

• Identify and classify new transport proteins discovered in genomic and proteomic studies.
• Study the evolutionary relationships and functional diversity of transport proteins.
• Develop models of transport mechanisms and predict the function of uncharacterized proteins.
• Explore potential targets for drug development and therapeutic interventions.

Also see

• Membrane transport protein
• Ion channel
• Active transport
• Passive transport
• Bioinformatics databases

External Links

• [TCDB Official Website](http://www.tcdb.org)