Toggle Main Menu Toggle Search

ePrints

PULDB: The expanded database of Polysaccharide Utilization Loci

Lookup NU author(s): Professor Harry Gilbert

Downloads


Licence

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0).


Abstract

© 2017 The Author(s) . The Polysaccharide Utilization Loci (PUL) database was launched in 2015 to present PUL predictions in â 1/470 Bacteroidetes species isolated from the human gastrointestinal tract, as well as PULs derived from the experimental data reported in the literature. In 2018 PULDB offers access to 820 genomes, sampled from various environments and covering a much wider taxonomical range. A Krona dynamic chart was set up to facilitate browsing through taxonomy. Literature surveys now allows the presentation of the most recent (i) PUL repertoires deduced from RNAseq large-scale experiments, (ii) PULs that have been subjected to in-depth biochemical analysis and (iii) new Carbohydrate-Active enzyme (CAZyme) families that contributed to the refinement of PUL predictions. To improve PUL visualization and genome browsing, the previous annotation of genes encoding CAZymes, regulators, integrases and SusCD has now been expanded to include functionally relevant protein families whose genes are significantly found in the vicinity of PULs: Sulfatases, proteases, ROK repressors, epimerases and ATP-Binding Cassette and Major Facilitator Superfamily transporters. To cope with cases where susCD may be absent due to incomplete assemblies/split PULs, we present â CAZyme cluster' predictions. Finally, a PUL alignment tool, operating on the tagged families instead of amino-acid sequences, was integrated to retrieve PULs similar to a query of interest. The updated PULDB website is accessible at www.cazy.org/PULDB-new/


Publication metadata

Author(s): Terrapon N, Lombard V, Drula E, Lapebie P, Al-Masaudi S, Gilbert HJ, Henrissat B

Publication type: Article

Publication status: Published

Journal: Nucleic Acids Research

Year: 2018

Volume: 46

Issue: D1

Pages: D677-D683

Print publication date: 04/01/2018

Online publication date: 27/10/2017

Acceptance date: 25/10/2017

ISSN (print): 0305-1048

ISSN (electronic): 1362-4962

Publisher: Oxford University Press

URL: https://doi.org/10.1093/nar/gkx1022

DOI: 10.1093/nar/gkx1022


Altmetrics

Altmetrics provided by Altmetric


Actions

    Link to this publication


Share