Transport classification database (TCDB)

Transport classification database (TCDB) classifies membrane transport proteins and provides a hierarchical, phylogeny-informed reference analogous to the Enzyme Commission (EC) system for research into their structure, function, mechanism, and evolution.

Key Features:

• Content scope: Contains over 10,000 non-redundant protein entries representing all recognized families of transmembrane molecular transport systems.
• Five-level hierarchical classification: Organizes proteins into five levels — class and subclass (first two levels), family and subfamily (second two levels), and the specific transport system (fifth level).
• Phylogenetic integration: Incorporates phylogenetic information into the classification to clarify evolutionary relationships among transport proteins.
• Superfamilies: Includes superfamilies that encompass multiple families and are linked to the five-tier hierarchical classification.
• Coverage and recognition: Covers transport proteins across all types of living organisms and is recognized by the International Union of Biochemistry and Molecular Biology (IUBMB).
• Manual curation and annotations: Entries include extensive text descriptions covering structural, functional, mechanistic, and evolutionary aspects produced by manual curation.
• Integration with tools and databases: Provides links and interconnections to unique software tools and numerous other relevant databases.

Scientific Applications:

• Protein classification and annotation: Serves as a reference for classifying and annotating membrane transport proteins within a standardized hierarchical scheme.
• Comparative and evolutionary studies: Enables analysis of phylogenetic relationships, superfamily membership, and evolutionary history of transport proteins.
• Structure–function and mechanistic inference: Supports investigation of structural, functional, and mechanistic properties through curated descriptive entries.
• Cross-database bioinformatics analyses: Facilitates integrative analyses that combine TCDB data with external databases and software tools.

Methodology:

Uses a five-level hierarchical classification incorporating phylogenetic information, with entries manually curated and linked to external software tools and databases.