GlycoPathDB

GlycoPathDB catalogs experimentally characterized enzymes and their sequence homologs involved in monosaccharide biosynthesis to enable analysis of biosynthetic pathways and evolutionary relationships.

Key Features:

• Extensive Enzyme Repository: GlycoPathDB compiles 542 experimentally characterized enzymes annotated with catalyzed reactions, substrate specificity, and associated monosaccharide biosynthesis pathways.
• Literature Integration: Each enzyme entry includes PubMed IDs linking to primary experimental characterizations.
• Genomic Contextualization: The database incorporates sequence homologs of characterized enzymes identified across nearly 13,000 completely sequenced Bacteria and Archaea genomes, enabling comparison of enzyme families such as aminotransferases, nucleotidyltransferases, acetyltransferases, and SDR family enzymes.

Scientific Applications:

• Evolutionary analysis: Enables deduction of evolutionary relationships among enzyme classes by comparative analysis of characterized enzymes and their homologs.
• Experimental validation: Supports design and interpretation of direct enzyme assays, structure–function relationship analyses, and expression profiling to validate enzyme annotations.
• Functional genomics and genetics: Facilitates determination of phenotypic consequences of gene knock-out/knock-in experiments and complementation studies using annotated enzyme information and homolog distributions.

Methodology:

Entries were produced by comprehensive literature curation to identify and catalog experimentally characterized monosaccharide biosynthesis enzymes, annotated with PubMed identifiers, and by incorporating sequence homologs identified across nearly 13,000 completely sequenced Bacteria and Archaea genomes.