TranSyT

TranSyT automates identification and integration of transport systems into genome-scale metabolic models to generate transport reactions with Gene-Protein-Reaction (GPR) associations.

Key Features:

• Automatically updated internal database: Builds and maintains an internal database derived from curated records of the Transporter Classification Database (TCDB) and supplemented with additional data sources.
• Transporter family and protein compilation: Compiles comprehensive information about transporter families, proteins, and their associated reactions.
• Genome-wide annotation: Provides automated annotation of transport systems across complete genomes without requiring manual curation.
• Reaction derivation with GPRs: Derives transport reactions that include Gene-Protein-Reaction (GPR) associations.
• Cross-database reaction export: Exports transport reactions annotated with identifiers from four different metabolite databases.
• Metabolic model integration: Produces integration-ready transport reactions for incorporation into genome-scale metabolic models.

Scientific Applications:

• Genome-scale model refinement: Enhances completeness and accuracy of genome-scale metabolic models by adding transport reactions and GPR associations.
• Transport system annotation: Enables systematic identification and annotation of transporter proteins and families in sequenced genomes.
• Cross-database interoperability: Facilitates mapping of transport reactions across metabolite databases for comparative and integrative analyses.
• Study of cellular transport mechanisms: Supports investigations into cellular transport processes by providing curated reaction and transporter datasets.

Methodology:

Assembles an automatically updated internal database from TCDB and supplementary sources, compiles transporter family/protein/reaction data, derives transport reactions including GPR associations, and exports reactions annotated with identifiers from four metabolite databases.