Glycoside Hydrolases GlycosylTransferases Polysaccharide Lyases Carbohydrate Esterases Auxiliary Activities

Polysaccharide-Utilization Loci DataBase (PULDB)

PULDB describes Polysaccharide Utilization Loci (PULs) experimentally characterized in the literature, but also 81,235 PUL predictions in 2,494 Bacteroidetes species.
A PUL is a set of physically-linked genes organized around a susCD gene pair. PULs are prevalent in the Bacteroidetes phylum. They provide an evolutionary advantage to these species by orchestrating the breakdown of complex glycans thanks to the encoded CAZymes. Please note that our PUL prediction tool tends to predict more PULs with multiple tandem susCD pairs than what is seen in experimentally determined cases.

Citing PULDB

A new reference for PULDB ! In the 2018 database issue of Nucleic Acids Research, we summarize the many changes that have occurred in the PULDB during the previous two years.
Terrapon N, Lombard V, Drula É, Lapébie P, Al-Masaudi S, Gilbert HJ, Henrissat B (2017) PULDB: the expanded database of Polysaccharide Utilization Loci; Nucleic Acids Research Link to the publication

To refer the prediction method
Terrapon, N., Lombard, V., Gilbert, H.J. and Henrissat, B. (2015) Automatic prediction of polysaccharide utilization loci in Bacteroidetes species from the human gut microbiota; Bioinformatics 31(5):647-55 - Link to the publication

List by species/taxon or browse PULDB taxonomy Name NCBI tax_id Include CAZyme clusters?	Search for PULs with specific modules Enter one or multiple modules (list available here) separated by '+' Module(s) Force order? Add CAZyme clusters? Restrict to a species/taxon or a NCBI tax_id	Search for a protein or a substrate
Note: [Fn], [Fc] and [F] indicate a possibly fragmented gene (e.g. a missing signal peptide or an incomplete catalytic module) at N- or C-terminus or both/undetermined, respectively, and [EC] denotes functional characterization of the gene in the litterature (EC number assigned by CAZy curators).

Organism name/NCBI id

Bacteroides thetaiotaomicron VPI-5482 - 226186

Identifier/JBrowse link

Literature-derived PUL 86

Modularity

◀ GH2_1

◀ GH53

◀ unk

◀ SusD

◀ SusC

◀ unk

◀ HTCS

Corresponding publication

Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont.
Martens EC, Chiang HC, Gordon JI
Cell host & microbe, 4(5):447-57 (2008)

Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts.
Martens EC, Lowe EC, Chiang H, Pudlo NA, Wu M, McNulty NP, Abbott DW, Henrissat B, Gilbert HJ, Bolam DN, Gordon JI
PLoS biology, 9(12):e1001221 (2011)

Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides.
Luis AS, Briggs J, Zhang X, Farnell B, Ndeh D, Labourel A, Baslé A, Cartmell A, Terrapon N, Stott K, Lowe EC, McLean R, Shearer K, Schückel J, Venditto I, Ralet MC, Henrissat B, Martens EC, Mosimann SC, Abbott DW, Gilbert HJ
Nature microbiology, 3(2):210-219 (2017)

Substrate

pectic galactan [Martens2011, Luis2017]

Protein details

Protein	Modularity	CAZy function		Genome Sequencing description	Pfam domains
BT4667	◀ GH2_1 [EC]	EC3.2.1.23	b-galactosidase	beta-galactosidase	PF02837 PF00703 PF02836 PF16355 PF18565
BT4668	◀ GH53 [EC]	EC3.2.1.89	endo-b-1,4-galactanase	arabinogalactan endo-1,4-beta-galactosidase	PF07745
BT4669	◀ unk			hypothetical protein	PF14292 PF17138 PF17141
BT4670	◀ SusD			putative outer membrane protein, probably involved in nutrient binding	PF07980
BT4671	◀ SusC			putative outer membrane protein, probably involved in nutrient binding	PF13715 PF07715 PF00593
BT4672	◀ unk			hypothetical protein
BT4673	◀ HTCS			two-component system sensor histidine kinase	PF07494 PF07495 PF00512 PF02518 PF12833

Overlap with PULs

Predicted PUL 84

◀ GH2_1

◀ GH53

◀ unk

◀ SusD

◀ SusC

◀ unk

◀ HTCS

unk ▶

PL13 ▶

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