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 85

Modularity

◀ PL15_2

◀ MFS

◀ ROK

◀ unk

◀ Sulf1_11

◀ PL12_2

◀ GH88

◀ SusD

◀ SusC

◀ unk

◀ PL12_2

◀ HTCS

PL13 ▶

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)

How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans.
Cartmell A, Lowe EC, Baslé A, Firbank SJ, Ndeh DA, Murray H, Terrapon N, Lombard V, Henrissat B, Turnbull JE, Czjzek M, Gilbert HJ, Bolam DN
Proceedings of the National Academy of Sciences of the United States of America, (2017)

Substrate

heparin/heparan sulfate [Martens2008, Cartmell2017]

Protein details

Protein	Modularity	CAZy function		Genome Sequencing description	Pfam domains
BT4652	◀ PL15_2 [EC]	EC4.2.2.-	exo-heparin lyase (reducing-end specific)	hypothetical protein	PF16332 PF07940
BT4653	◀ MFS			glucose/galactose transporter	PF07690
BT4654	◀ ROK			ROK family transcriptional repressor, with glucokinase domain	PF00480
BT4655	◀ unk			hypothetical protein
BT4656	◀ Sulf1_11			N-acetylglucosamine-6-sulfatase precursor	PF00884 PF16347
BT4657	◀ PL12_2 [EC]	EC4.2.2.7	heparin lyase / heparin lyase I	heparinase III protein	PF16889 PF07940
BT4657	◀ PL12_2 [EC]	EC4.2.2.8	heparin-sulfate lyase / heparin lyase III	heparinase III protein	PF16889 PF07940
BT4658	◀ GH88 [EC]	EC3.2.1.-	d-4,5-unsaturated b-glucuronyl hydrolase	glucuronyl hydrolase	PF16386 PF07470
BT4659	◀ SusD			putative outer membrane protein, probably involved in nutrient binding	PF14322 PF07980
BT4660	◀ SusC			putative outer membrane protein, probably involved in nutrient binding	PF13715 PF07715 PF00593
BT4661	◀ unk			hypothetical protein	PF16319
BT4662	◀ PL12_2 [EC]	EC4.2.2.7	heparin lyase / heparin lyase I	heparinase III protein, heparitin sulfate lyase	PF16889 PF07940
BT4662	◀ PL12_2 [EC]	EC4.2.2.8	heparin-sulfate lyase / heparin lyase III	heparinase III protein, heparitin sulfate lyase	PF16889 PF07940
BT4663	◀ HTCS			two-component system sensor histidine kinase/response	PF07494 PF07495 PF00512 PF02518 PF00072 PF12833
BT4675	PL13 ▶ [EC]	EC4.2.2.7	heparin lyase / heparin lyase I	heparin lyase I precursor	PF14099

Overlap with PULs

Predicted PUL 83			◀ Sulf1_11 ◀ PL12_2 ◀ GH88 ◀ SusD ◀ SusC ◀ unk ◀ PL12_2 ◀ HTCS
Predicted PUL 84			◀ GH2_1 ◀ GH53 ◀ unk ◀ SusD ◀ SusC ◀ unk ◀ HTCS unk ▶ PL13 ▶

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