Home Repository Download Help About Statistics Taxonomy Blastx
Links
PULDB
CAZy
dbCAN2
dbCAN-seq
run_dbcan
CAZypedia
PlantCAZyme
Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0542

PubMed

10368143, J Bacteriol. 1999 Jun;181(12):3695-704. doi: 10.1128/JB.181.12.3695-3704.1999.

Characterization method

substrate binding assay

Genomic accession number

DQ868502.2

Nucelotide position range

38552-76554

Substrate

xylan

Loci

xynDCEFG-xylM-axe1-xynB2A2-aguEFGA-xynB1-kdgKA-uxuR-uxaC-uxuAB-orfABC-xynAX-aze2-xynB3-xylAB

Species

Geobacillus stearothermophilus/1422

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

xynD - ABI49930.1 237 - 1965 (+) DQ868502.2:38789-40517 -
xynC - ABI49931.1 1957 - 2737 (+) DQ868502.2:40509-41289 -
xynE - ABI49932.1 2841 - 4167 (+) DQ868502.2:41393-42719 -
xynF - ABI49933.1 4229 - 5099 (+) DQ868502.2:42781-43651 -
xynG - ABI49934.1 5113 - 5980 (+) DQ868502.2:43665-44532 -
xylM - ABI49935.1 6172 - 7141 (+) DQ868502.2:44724-45693 -
axe1 - ABI49936.1 7164 - 7779 (+) DQ868502.2:45716-46331 -
xynB2 - ABI49956.1 7858 - 9976 (+) DQ868502.2:46410-48528 -
xynA2 - ABI49937.2 9978 - 10974 (+) DQ868502.2:48530-49526 -
- - ABI49960.1 11738 - 13196 (+) DQ868502.2:50290-51748 -
aguF - ABI49938.1 14708 - 15791 (+) DQ868502.2:53260-54343 -
aguG - ABI49939.1 15806 - 16697 (+) DQ868502.2:54358-55249 -
aguA - ABI49940.1 16714 - 18754 (+) DQ868502.2:55266-57306 -
xynB1 - ABI49941.1 18769 - 20284 (+) DQ868502.2:57321-58836 -
kdgK - ABI49942.1 20315 - 21260 (+) DQ868502.2:58867-59812 -
kdgA - ABI49943.1 21275 - 21926 (+) DQ868502.2:59827-60478 -
uxuR - ABI49944.1 21990 - 22740 (+) DQ868502.2:60542-61292 -
uxaC - ABI49945.1 22776 - 24198 (+) DQ868502.2:61328-62750 -
uxuA - ABI49946.1 24205 - 25321 (+) DQ868502.2:62757-63873 -
uxuB - ABI49947.1 25296 - 26142 (+) DQ868502.2:63848-64694 -
orfA - ABI49948.1 26218 - 26863 (+) DQ868502.2:64770-65415 -
orfB - ABI49949.1 27134 - 27650 (+) DQ868502.2:65686-66202 -
- - ABI49958.1 27831 - 29085 (+) DQ868502.2:66383-67637 -
orfC - ABI49950.1 29077 - 29878 (+) DQ868502.2:67629-68430 -
xynA - ABI49951.1 30215 - 31563 (-) DQ868502.2:68767-70115 -
xynX - ABI49952.1 32070 - 32742 (+) DQ868502.2:70622-71294 -
axe2 - ABI49953.1 32915 - 33575 (+) DQ868502.2:71467-72127 -
xynB3 - ABI49959.1 33619 - 35227 (+) DQ868502.2:72171-73779 -
xylA - ABI49954.1 35335 - 36673 (+) DQ868502.2:73887-75225 -
xylB - ABI49955.1 36680 - 38189 (+) DQ868502.2:75232-76741 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 238 - 1965 (+) TC: gnl|TC-DB|F4LXP4|8.A.59.2.1 Yes
- 1958 - 2737 (+) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes
- 2842 - 4167 (+) STP: STP|SBP_bac_1 Yes
- 4230 - 5099 (+) TC: gnl|TC-DB|Q8RJU9|3.A.1.1.18 Yes
- 5114 - 5980 (+) TC: gnl|TC-DB|G4FGN6|3.A.1.1.41 Yes
- 6173 - 7141 (+) other Yes
- 7165 - 7779 (+) CAZyme: CE4 Yes
- 7859 - 9976 (+) CAZyme: GH52 Yes
- 9979 - 10974 (+) CAZyme: GH10 Yes
- 11739 - 13196 (+) other Yes
- 14709 - 15791 (+) TC: gnl|TC-DB|Q09LY7|3.A.1.1.9 Yes
- 15807 - 16697 (+) TC: gnl|TC-DB|Q09LY6|3.A.1.1.9 Yes
- 16715 - 18754 (+) CAZyme: GH67 Yes
- 18770 - 20284 (+) CAZyme: GH39 Yes
- 20316 - 21260 (+) STP: STP|PfkB Yes
- 21276 - 21926 (+) other Yes
- 21991 - 22740 (+) TF: DBD-Pfam|GntR,DBD-SUPERFAMILY|0039384 Yes
- 22777 - 24198 (+) other Yes
- 24206 - 25321 (+) other Yes
- 25297 - 26142 (+) other Yes
- 26219 - 26863 (+) TC: gnl|TC-DB|G4PA66|9.B.28.1.5 Yes
- 27135 - 27650 (+) other Yes
- 27832 - 29085 (+) other Yes
- 29078 - 29878 (+) STP: STP|AAA Yes
- 30216 - 31454 (-) other Yes
- 32071 - 32742 (+) other Yes
- 32916 - 33575 (+) other Yes
- 33620 - 35227 (+) CAZyme: GH43_11 Yes
- 35336 - 36673 (+) CDS No
- 36681 - 38189 (+) CDS No

PUL ID

PUL0542

PubMed

10368143, J Bacteriol. 1999 Jun;181(12):3695-704. doi: 10.1128/JB.181.12.3695-3704.1999.

Title

The glucuronic acid utilization gene cluster from Bacillus stearothermophilus T-6.

Author

Shulami S, Gat O, Sonenshein AL, Shoham Y

Abstract

A lambda-EMBL3 genomic library of Bacillus stearothermophilus T-6 was screened for hemicellulolytic activities, and five independent clones exhibiting beta-xylosidase activity were isolated. The clones overlap each other and together represent a 23.5-kb chromosomal segment. The segment contains a cluster of xylan utilization genes, which are organized in at least three transcriptional units. These include the gene for the extracellular xylanase, xylanase T-6; part of an operon coding for an intracellular xylanase and a beta-xylosidase; and a putative 15.5-kb-long transcriptional unit, consisting of 12 genes involved in the utilization of alpha-D-glucuronic acid (GlcUA). The first four genes in the potential GlcUA operon (orf1, -2, -3, and -4) code for a putative sugar transport system with characteristic components of the binding-protein-dependent transport systems. The most likely natural substrate for this transport system is aldotetraouronic acid [2-O-alpha-(4-O-methyl-alpha-D-glucuronosyl)-xylotriose] (MeGlcUAXyl3). The following two genes code for an intracellular alpha-glucuronidase (aguA) and a beta-xylosidase (xynB). Five more genes (kdgK, kdgA, uxaC, uxuA, and uxuB) encode proteins that are homologous to enzymes involved in galacturonate and glucuronate catabolism. The gene cluster also includes a potential regulatory gene, uxuR, the product of which resembles repressors of the GntR family. The apparent transcriptional start point of the cluster was determined by primer extension analysis and is located 349 bp from the initial ATG codon. The potential operator site is a perfect 12-bp inverted repeat located downstream from the promoter between nucleotides +170 and +181. Gel retardation assays indicated that UxuR binds specifically to this sequence and that this binding is efficiently prevented in vitro by MeGlcUAXyl3, the most likely molecular inducer.