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PULDB specifications

Information


Unique identifier OMICS_21872
Name PULDB
Alternative name Polysaccharide-Utilization Loci DataBase
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainers


  • person_outline Bernard Henrissat
  • person_outline Nicolas Terrapon

Publications for Polysaccharide-Utilization Loci DataBase

PULDB citations

 (6)
call_split

A novel acetyl xylan esterase enabling complete deacetylation of substituted xylans

2018
Biotechnol Biofuels
PMCID: 5863359
PMID: 29588659
DOI: 10.1186/s13068-018-1074-3
call_split See protocol

[…] The PUL database (PULDB, http://www.cazy.org/PULDB) [] was searched for PULs that contained at least two of the predicted xylan-active CAZyme families of interest, such as GH10, GH43, GH67, and GH115. From the obtained […]

library_books

SACCHARIS: an automated pipeline to streamline discovery of carbohydrate active enzyme activities within polyspecific families and de novo sequence datasets

2018
Biotechnol Biofuels
PMCID: 5798181
PMID: 29441125
DOI: 10.1186/s13068-018-1027-x

[…] help streamline the characterization of CAZyme function, several bioinformatic approaches have been developed. These include subfamily delineation within a defined group of GH families [, –]; PULDB (Polysaccharide Utilization Loci DataBase; []), an online tool associated with the CAZy website which provides comparative predictions of enzyme activities within Bacteroides spp. catabolic pathways ac […]

library_books

Comparative Metagenomics of Cellulose and Poplar Hydrolysate Degrading Microcosms from Gut Microflora of the Canadian Beaver (Castor canadensis) and North American Moose (Alces americanus) after Long Term Enrichment

2017
Front Microbiol
PMCID: 5742341
PMID: 29326667
DOI: 10.3389/fmicb.2017.02504

[…] c distances, the presence of CAZymes and of regulatory genes (e.g., hybrid two-component system protein, extracytoplasmic function (ECF) σ/anti-σ factors, etc.) following the automatic method used in PULDB (). The proteins with unknown functions from the PULs reported here and in PULDB were pooled and submitted to CD-HIT web server () to identify proteins that meet a similarity threshold, which wa […]

library_books

The 2018 Nucleic Acids Research database issue and the online molecular biology database collection

2017
Nucleic Acids Res
PMCID: 5753253
PMID: 29316735
DOI: 10.1093/nar/gkx1235

[…] the PANTHER database (). PANTHER full-length sequence based clustering is shown to be complementary to MEROP’s domain-based structure. Carbohydrate-active enzymes are covered by the arrival in NAR of PULDB (), covering polysaccharide utilization loci in the prominent gut bacteria of the phylum Bacteriodetes, and dbCAN-seq (), which usefully extrapolates information from the well-known CAZy databas […]

library_books

PULDB: the expanded database of Polysaccharide Utilization Loci

2017
Nucleic Acids Res
PMCID: 5753385
PMID: 29088389
DOI: 10.1093/nar/gkx1022

[…] In order to achieve a >10-fold increase in PULDB, we analyzed 820 complete genome sequences (∼3 million genes) mostly of the Bacteroidetes phylum downloaded from JGI (http://genome.jgi.doe.gov/) and NCBI (https://www.ncbi.nlm.nih.gov/nuccore) […]

library_books

Identification of a New Lipoprotein Export Signal in Gram Negative Bacteria

2016
MBio
PMCID: 5080379
PMID: 27795390
DOI: 10.1128/mBio.01232-16

[…] s fragilis NCTC 9343 surface-exposed lipoproteins () were processed in the same way (). Forty-two Flavobacterium johnsoniae UW101 predicted SusD-like lipoproteins were identified in the PUL database (PULDB) of the CAZY database (), and the corresponding sequences were extracted from the UniProt database and processed as described above (). […]

Citations

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PULDB institution(s)
Institut National de la Recherche Agronomique (INRA), UR454 Microbiologie, Centre de Clermont-Ferrand/Theix, Saint-Genès Champanelle, France; Department of Animal and Range Sciences, Montana State University, Bozeman, MT, USA; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, Université Aix-Marseille, Marseille, France; INRA, USC 1408 AFMB, Marseille, France; INRA, UMR408 Sécurité et Qualité des Produits d’Origine Végétale, Avignon, France; Université d’Avignon et des Pays de Vaucluse, UMR408 Sécurité et Qualité des Produits d’Origine Végétale, Avignon, France; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia

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