Expanding CSDB_GT glycosyltransferase database with Escherichia coli. (31st January 2019)

• Record Type: Journal Article
• Authors: Egorova, Ksenia S; Knirel, Yuriy A; Toukach, Philip V
• Is Part Of: Glycobiology. Volume 29:Number 4(2019)
• Page Start: 285
• Page End: 287
• Publication Date: 2019-01-31
• Subjects: CSDB -- CSDB_GT -- database -- Escherichia coli -- glycosyltransferase; Glycoproteins -- Periodicals; Glycolipids -- Periodicals; Glycoconjugates -- Periodicals; 572.567
• DOI: 10.1093/glycob/cwz006
• Languages: English
• ISSNs: 0959-6658

Abstract

Abstract: In 2017, we reported a new database on glycosyltransferase (GT) activities, CSDB_GT (http://csdb.glycoscience.ru/gt.html ), which was built at the platform of the Carbohydrate Structure Database (CSDB, http://csdb.glycoscience.ru/database/index.html ) and contained data on experimentally confirmed GT activities from Arabidopsis thaliana . All entries in CSDB_GT are curated manually upon the analysis of scientific publications, and the key features of the database are accurate structural, genetic, protein and bibliographic references and close-to-complete coverage on experimentally proven GT activities in selected species. In 2018, CSDB_GT was supplemented with data on Escherichia coli GT activities. Now it contains ca. 800 entries on E. coli GTs, including ca. 550 entries with functions predicted in silico . This information was extracted from research papers published up to the year 2018 or was obtained by the authors' efforts on GT annotation. Thus, CSDB_GT was extended to provide not only experimentally confirmed GT activities, but also those predicted on the basis of gene or protein sequence homology that could carry valuable information. Accordingly, a new confirmation status—predicted in silico —was introduced. In addition, the coverage on A. thaliana was extended up to ca. 900 entries, all of which had experimental confirmation. Currently, CSDB_GT provides close-to-complete coverage on experimentally confirmed GT activities from A. thaliana and E. coli presented up to the year 2018.