GTDB

GTDB compiles annotated glycosyltransferase (GT) data, including amino acid and coding sequences, tertiary structures, protein family classifications, catalytic reactions, and metabolic pathway associations, to support GT function annotation and structural-functional analyses.

Key Features:

• Extensive Data Collection: Compiles 520,179 GTs from approximately 21,647 species covering 394 reaction types and includes amino acid sequences, coding region sequences, available tertiary structures, protein classification families, catalytic reactions, and metabolic pathways.
• Text Search and Identifier Integration: Enables text searches that combine multiple identifiers and data sources to retrieve detailed GT annotations.
• Sequence Search (BLAST): Integrates BLAST (Basic Local Alignment Search Tool) for sequence similarity searches against predefined sequences to assist annotation of query GTs.
• Molecular Docking (GTdock): Implements GTdock using AutoDock Vina to perform docking simulations of multiple GTs against a single acceptor and employs 3Dmol.js for model visualization.

Scientific Applications:

• Function Annotation: Annotating biological functions of glycosyltransferases via integrated sequence and annotation data and BLAST-based similarity searches.
• Structural–Functional Analysis: Investigating sequence–structure–function relationships of GTs using available tertiary structures and docking simulations.
• Metabolic Pathway Analysis: Exploring GT roles in catalytic reactions and metabolic pathway associations.
• Natural Product and Agrochemical Discovery: Supporting discovery and optimization of glycosylated bioactive compounds relevant to pharmaceutical and agrochemical research.

Methodology:

Compiled datasets of amino acid sequences, coding region sequences, tertiary structures, protein family classifications, catalytic reactions, and metabolic pathways for 520,179 GTs from ~21,647 species spanning 394 reaction types; implemented text-based identifier searches, BLAST sequence searches, and molecular docking via GTdock with AutoDock Vina and visualization using 3Dmol.js.