PULDB: the expanded database of Polysaccharide Utilization Loci - INRAE - Institut national de recherche pour l’agriculture, l’alimentation et l’environnement Access content directly
Journal Articles Nucleic Acids Research Year : 2018

PULDB: the expanded database of Polysaccharide Utilization Loci


The Polysaccharide Utilization Loci (PUL) database was launched in 2015 to present PUL predictions in ∼70 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 '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/.
Fichier principal
Vignette du fichier
gkx1022.pdf (3.42 Mo) Télécharger le fichier
Origin : Publisher files allowed on an open archive

Dates and versions

hal-02094620 , version 1 (09-04-2019)


Attribution - NonCommercial



Nicolas Terrapon, Vincent Lombard, Elodie Drula, Pascal Lapébie, Saad Al-Masaudi, et al.. PULDB: the expanded database of Polysaccharide Utilization Loci. Nucleic Acids Research, 2018, 46 (D1), pp.D677-D683. ⟨10.1093/nar/gkx1022⟩. ⟨hal-02094620⟩
155 View
181 Download



Gmail Facebook X LinkedIn More