dbCAN-PUL

dbCAN-PUL catalogs experimentally validated prokaryotic polysaccharide utilization loci (PULs) containing carbohydrate-active enzymes (CAZymes) and associated genes to support analysis of microbial carbohydrate metabolism.

Key Features:

• Experimental Validation: Focuses on experimentally verified CAZyme-containing PULs reported in the literature.
• Extensive Metadata and Annotations: Each entry records substrate specificity, methods of experimental characterization, and protein sequence information.
• Batch Download: Enables batch retrieval of data filtered by substrate, species/genome, genus, or experimental characterization method.
• Integration with External Resources: Links PUL entries to CAZy for CAZymes, UniProt for transporters and protein annotations, and other gene annotation pages.
• Homologous Gene Cluster Display: Provides MultiGeneBlast-based identification of homologous gene clusters in GenBank sequences.
• BLASTX Service Integration: Embeds a BLASTX service to query external sequences against PUL protein sets.

Scientific Applications:

• Microbial Ecology: Analysis of how microorganisms interact with their environment through carbohydrate metabolism mediated by PULs.
• Biotechnological Applications: Identification of CAZymes and PULs relevant to biofuel production, waste degradation, and bioremediation.
• Comparative Genomics: Investigation of the diversity and evolution of PULs across bacterial phyla, archaea, and metagenomes.

Methodology:

Entries were curated from literature reporting experimentally characterized PULs and linked to CAZy, UniProt and GenBank annotations; the resource integrates MultiGeneBlast for homolog detection, an embedded BLASTX service for sequence queries, and cross-references with dbCAN2 and dbCAN-seq.