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dbCAN-PUL: a database of experimentally characterized CAZyme gene clusters and their substrates.
Nucleic Acids Research ( IF 14.9 ) Pub Date : 2020-09-17 , DOI: 10.1093/nar/gkaa742
Catherine Ausland 1 , Jinfang Zheng 2 , Haidong Yi 3 , Bowen Yang 2 , Tang Li 2 , Xuehuan Feng 2 , Bo Zheng 2 , Yanbin Yin 2
Affiliation  

Abstract
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).


中文翻译:

dbCAN-PUL:通过实验表征的CAZyme基因簇及其底物的数据库。

摘要
PUL(多糖利用位点)是CAZymes(碳水化合物活性酶)和其他共同消化和利用碳水化合物底物的基因的离散基因簇。虽然PULs已在拟杆菌中得到广泛鉴定,存在其他细菌门,古细菌和元基因组的PUL,这些仍然需要在数据库中进行分类以进行有效检索。我们已经开发了在线数据库dbCAN-PUL(http://bcb.unl.edu/dbCAN_PUL/),以显示来自文献的经过实验验证的含CAZyme的PUL,以及相关的元数据,序列和注释。与其他在线CAZyme和PUL资源相比,dbCAN-PUL具有以下新功能:(i)通过目标底物,物种/基因组,属或实验表征方法批量下载PUL数据;(ii)每个PUL的注释,显示相关的元数据,例如底物,实验表征方法和蛋白质序列信息,(iii)链接到CAZymes(CAZy),转运蛋白(UniProt)和其他基因的外部注释页面,(iv)通过集成的MultiGeneBlast工具在GenBank序列中显示同源基因簇,以及(v)集成的BLASTX服务可供用户查询dbCAN-PUL中的PUL蛋白序列。有了这些功能,dbCAN-PUL将成为CAZyme和PUL研究的重要存储库,是对我们其他Web服务器和数据库(dbCAN2,dbCAN-seq)的补充。
更新日期:2020-09-17
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