DbCAN-PUL: a database of experimentally characterized CAZyme gene clusters and their substrates. Issue Volume 49:Issue D1(2021) (17th September 2020)

• Record Type: Journal Article
• Authors: Ausland, Catherine; Zheng, Jinfang; Yi, Haidong; Yang, Bowen; Li, Tang; Feng, Xuehuan; Zheng, Bo; Yin, Yanbin
• Is Part Of: Nucleic acids research. Volume 49:Issue D1(2021)
• Page Start: D523
• Page End: D528
• Publication Date: 2020-09-17
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkaa742
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: PULs (p olysaccharide u tilization l oci) are discrete gene clusters of CAZymes (C arbohydrate A ctive EnZymes ) and other genes that work together to digest and utilize carbohydrate substrates. While PULs have been extensively characterized in Bacteroidetes, there exist PULs from other bacterial phyla, as well as archaea and metagenomes, that remain to be catalogued in a database for efficient retrieval. We have developed an online database dbCAN-PUL (http://bcb.unl.edu/dbCAN_PUL/ ) to display experimentally verified CAZyme-containing PULs from literature with pertinent metadata, sequences, and annotation. Compared to other online CAZyme and PUL resources, dbCAN-PUL has the following new features: (i) Batch download of PUL data by target substrate, species/genome, genus, or experimental characterization method; (ii) Annotation for each PUL that displays associated metadata such as substrate(s), experimental characterization method(s) and protein sequence information, (iii) Links to external annotation pages for CAZymes (CAZy), transporters (UniProt) and other genes, (iv) Display of homologous gene clusters in GenBank sequences via integrated MultiGeneBlast tool and (v) An integrated BLASTX service available for users to query their sequences against PUL proteins in dbCAN-PUL. With these features, dbCAN-PUL will be an important repository for CAZyme and PUL research, complementing our other web servers and databases (dbCAN2, dbCAN-seq).