Introduction

dbCAN-seq is a database of CAZyme sequence and annotation built upon the dbCAN CAZyme HMMs database, which is further built from the GenBank protein sequences classified/annotated at the CAZy database. Compared to other CAZyme web resources, dbCAN-seq has the following unique features:

1. It provides a convenient download page for users to batch download all the precomputed CAZyme sequence and annotation data for over 5,000 fully sequenced bacterial genomes;


2. It provides the most comprehensive annotation data (e.g., WP_007212487.1) for computationally identified CAZymes including signature domains, molecular weight, PI, CDD (conserved domains), signalP (signal peptide), lipoP (lipoprotein prediction), TMHMM (transmembrane protein prediction), EC/enzyme prediction, and sequence homologs in the Swiss-Prot database, PDB database, and CAZy database;


3. It organizes the bacterial genomes according to the metadata such as disease, ecosystems, habitats, oxygen requirement, temperature, metabolism, etc.;


4. It provides a tool (CGC-Finder) to identify CAZyme gene clusters (CGCs). CGCs are defined as genomic regions containing at least one CAZyme gene, one transporter gene and one transcription factor gene. The rational is that CAZyme genes often work together with each other and with other important genes (e.g. TFs, sugar transporters) to synergistically degrade or synthesize various highly complex carbohydrates.