EXPANDING CSDB_GT GLYCOSYLTRANSFERASE DATABASE WITH ESCHERICHIA COLI

K.S Egorova, Yu.A. Knirel, Ph.V. Toukach

N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia

KEYWORDS: CSDB, CSDB_GT, database, Escherichia coli, glycosyltransferase

Glycobiology, 2019, .29(4), .285-287

DOI: 10.1093/glycob/cwz006, PMID: 30759212


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/) 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 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.


Science :