{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T04:36:03Z","timestamp":1784608563949,"version":"3.55.0"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,9,17]],"date-time":"2020-09-17T00:00:00Z","timestamp":1600300800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-1933521"],"award-info":[{"award-number":["DBI-1933521"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000199","name":"United States Department of Agriculture","doi-asserted-by":"publisher","award":["58-8042-9-089"],"award-info":[{"award-number":["58-8042-9-089"]}],"id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008114","name":"UNL","doi-asserted-by":"publisher","award":["2019-YIN"],"award-info":[{"award-number":["2019-YIN"]}],"id":[{"id":"10.13039\/100008114","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>PULs (polysaccharide utilization loci) are discrete gene clusters of CAZymes (Carbohydrate Active 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).<\/jats:p>","DOI":"10.1093\/nar\/gkaa742","type":"journal-article","created":{"date-parts":[[2020,8,26]],"date-time":"2020-08-26T03:46:11Z","timestamp":1598413571000},"page":"D523-D528","source":"Crossref","is-referenced-by-count":104,"title":["dbCAN-PUL: a database of experimentally characterized CAZyme gene clusters and their substrates"],"prefix":"10.1093","volume":"49","author":[{"given":"Catherine","family":"Ausland","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinfang","family":"Zheng","sequence":"additional","affiliation":[{"name":"Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haidong","family":"Yi","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of North Carolina at Chapel Hill,\u00a0Chapel Hill,\u00a0NC 27599, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bowen","family":"Yang","sequence":"additional","affiliation":[{"name":"Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tang","family":"Li","sequence":"additional","affiliation":[{"name":"Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuehuan","family":"Feng","sequence":"additional","affiliation":[{"name":"Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Zheng","sequence":"additional","affiliation":[{"name":"Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7667-881X","authenticated-orcid":false,"given":"Yanbin","family":"Yin","sequence":"additional","affiliation":[{"name":"Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,9,17]]},"reference":[{"key":"2021010313110807200_B1","doi-asserted-by":"crossref","first-page":"D490","DOI":"10.1093\/nar\/gkt1178","article-title":"The carbohydrate-active enzymes database (CAZy) in 2013","volume":"42","author":"Lombard","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2021010313110807200_B2","doi-asserted-by":"crossref","first-page":"D516","DOI":"10.1093\/nar\/gkx894","article-title":"dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation","volume":"46","author":"Huang","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2021010313110807200_B3","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1093\/bioinformatics\/btu716","article-title":"Automatic prediction of polysaccharide utilization loci in Bacteroidetes species","volume":"31","author":"Terrapon","year":"2015","journal-title":"Bioinformatics"},{"key":"2021010313110807200_B4","doi-asserted-by":"crossref","first-page":"36269","DOI":"10.1074\/jbc.M606509200","article-title":"Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period","volume":"281","author":"Bjursell","year":"2006","journal-title":"J. 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