Database Description

Database Description#

The built-in downloader uses the db_current HTTP snapshot from pro.unl.edu by default. You can also download the pinned S3 release for faster and more stable transfers by using the --aws_s3 flag with the run_dbcan database command (see Preparing Databases). The databases are generally updated annually between July and September.

The databases used by run_dbCAN are described below.

CAZyme Databases#

  • DIAMOND database - Description: Fast protein alignment database used to identify CAZyme sequences. - Filename: CAZy.dmnd

  • dbCAN HMM database - Description: HMM profiles for CAZyme families; sensitive identification. - Filename: dbCAN.hmm

  • dbCAN-sub HMM database - Description: Subfamily-level HMM profiles for fine-grained CAZyme subfamily identification. - Filename: dbCAN-sub.hmm

CGC Databases#

  • Transporter DIAMOND database (from TCDB) - Description: Transporter proteins used to identify transporters in CGCs. - Filename: TCDB.dmnd

  • Transcription Factor HMM database (fungi, from MycoCosm) - Description: HMM profiles for transcription factors used in fungal datasets. - Filename: TF.hmm

  • Transcription Factor DIAMOND database (prokaryotes, from PRODORIC) - Description: TF protein database used to identify TFs in prokaryotic CGCs. - Filename: TF.dmnd

  • Signal Transduction Protein HMM database - Description: HMM profiles for signal transduction proteins. - Filename: STP.hmm

  • Sulfatase DIAMOND database (from SulfAtlas) - Description: Sulfatase protein database used to identify sulfatases. - Filename: sulfatlas_db.dmnd

  • Peptidase DIAMOND database (from MEROPS) - Description: Peptidase protein database used to identify peptidases. - Filename: peptidase_db.dmnd

  • dbCAN-PUL DIAMOND database - Description: Polysaccharide Utilization Loci (PUL) protein database for PUL identification. - Filename: PUL.dmnd

Substrate Prediction Databases#

  • Substrate mapping table - Description: Mapping from CAZyme family/EC to known substrates. - Filename: fam-substrate-mapping.tsv

  • dbCAN-PUL substrate table - Description: Substrate mapping associated with PULs from the dbCAN-PUL database. - Directory: dbCAN-PUL/ - Spreadsheet: dbCAN-PUL.xlsx

Contents