GTDB: an integrated resource for glycosyltransferase sequences and annotations. (16th June 2020)

• Record Type: Journal Article
• Authors: Zhou, Chenfen; Xu, Qingwei; He, Sheng; Ye, Wei; Cao, Ruifang; Wang, Pengyu; Ling, Yunchao; Yan, Xing; Wang, Qingzhong; Zhang, Guoqing
• Is Part Of: Database. Volume 2020(2020)
• Publication Date: 2020-06-16
• Subjects: Biology -- Databases -- Periodicals; Bioinformatics -- Periodicals; 570.285
• DOI: 10.1093/database/baaa047
• Languages: English
• ISSNs: 1758-0463

Abstract

Abstract: Glycosyltransferases (GTs), a large class of carbohydrate-active enzymes, adds glycosyl moieties to various substrates to generate multiple bioactive compounds, including natural products with pharmaceutical or agrochemical values. Here, we first collected comprehensive information on GTs, including amino acid sequences, coding region sequences, available tertiary structures, protein classification families, catalytic reactions and metabolic pathways. Then, we developed sequence search and molecular docking processes for GTs, resulting in a GTs database (GTDB). In the present study, 520 179 GTs from approximately 21 647 species that involved in 394 kinds of different reactions were deposited in GTDB. GTDB has the following useful features: (i) text search is provided for retrieving the complete details of a query by combining multiple identifiers and data sources; (ii) a convenient browser allows users to browse data by different classifications and download data in batches; (iii) BLAST is offered for searching against pre-defined sequences, which can facilitate the annotation of the biological functions of query GTs; and lastly, (iv) GTdock using AutoDock Vina performs docking simulations of several GTs with the same single acceptor and displays the results based on 3Dmol.js allowing easy view of models.