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PlantCAZyme
Cite: NAR/gkaa742 2020

Because CGCFinder predicted no CGC for this PUL, the gene cluster depicted below contains dbCAN2 and CGC signature predictions for all genes in the PUL, instead of a predicted CGC.


PUL General Information

Literature Information

PUL ID

PUL0181

PubMed

27083849, Int J Biol Macromol. 2016 Jul;88:578-85. doi: 10.1016/j.ijbiomac.2016.04.025. Epub 2016 Apr 13.

Characterization method

NMR,sugar utilization assay

Genomic accession number

AB812036

Nucelotide position range

1-20537

Substrate

O-antigen

Loci

galF-wzx-irf2-tld-orf4-wzy-orf6-orf7-gmd-fcl-gmm-manC-wfgS-manB-gnd

Species

Escherichia coli/562

Degradation or Biosynthesis

biosynthesis

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

wcaM - BAQ01287.1 0 - 898 (+) AB812036.1:1-899 -
galF - BAQ01288.1 1061 - 1967 (+) AB812036.1:1062-1968 -
wzx - BAQ01289.1 2378 - 3773 (+) AB812036.1:2379-3774 -
- - BAQ01290.1 3766 - 4384 (+) AB812036.1:3767-4385 -
- - BAQ01291.1 4385 - 5306 (+) AB812036.1:4386-5307 -
- - BAQ01292.1 5299 - 6439 (+) AB812036.1:5300-6440 -
wzy - BAQ01293.1 6440 - 7592 (+) AB812036.1:6441-7593 -
- - BAQ01294.1 7572 - 8715 (+) AB812036.1:7573-8716 -
- - BAQ01295.1 8711 - 9983 (+) AB812036.1:8712-9984 -
gmd - BAQ01296.1 9972 - 11097 (+) AB812036.1:9973-11098 -
fcl - BAQ01297.1 11100 - 12066 (+) AB812036.1:11101-12067 -
gmm - BAQ01298.1 12068 - 12530 (+) AB812036.1:12069-12531 -
manC - BAQ01299.1 12535 - 13942 (+) AB812036.1:12536-13943 -
- - BAQ01300.1 13941 - 14688 (+) AB812036.1:13942-14689 -
manB - BAQ01301.1 14693 - 16118 (+) AB812036.1:14694-16119 -
gnd - BAQ01302.1 16314 - 17721 (+) AB812036.1:16315-17722 -
ugd - BAQ01303.1 17967 - 19134 (+) AB812036.1:17968-19135 -
wzz - BAQ01304.1 19223 - 20258 (+) AB812036.1:19224-20259 -
hisI - BAQ01305.1 20354 - 20537 (-) AB812036.1:20355-20538 -

Cluster number

0

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 898 (+) CDS No
- 1062 - 1967 (+) CDS No
- 2379 - 3773 (+) CDS No
- 3767 - 4384 (+) CDS No
- 4386 - 5306 (+) CDS No
- 5300 - 6439 (+) CDS No
- 6441 - 7592 (+) CAZyme: GT4 No
- 7573 - 8715 (+) CDS No
- 8712 - 9983 (+) CDS No
- 9973 - 11097 (+) CDS No
- 11101 - 12066 (+) CDS No
- 12069 - 12530 (+) STP: STP|NUDIX No
- 12536 - 13942 (+) CAZyme: GT2_Glycos_transf_2|GT2 No
- 13942 - 14688 (+) CDS No
- 14694 - 16118 (+) CDS No
- 16315 - 17721 (+) CDS No
- 17968 - 19134 (+) CDS No
- 19224 - 20258 (+) CDS No
- 20355 - 20537 (-) CDS No

PUL ID

PUL0181

PubMed

27083849, Int J Biol Macromol. 2016 Jul;88:578-85. doi: 10.1016/j.ijbiomac.2016.04.025. Epub 2016 Apr 13.

Title

Structure of the beta-l-fucopyranosyl phosphate-containing O-specific polysaccharide of Escherichia coli O84.

Author

Knirel YA, Qian C, Senchenkova SN, Guo X, Shashkov AS, Chizhov AO, Perepelov AV, Liu B

Abstract

Fine structure of the O-polysaccharide chain of the lipopolysaccharide (O-antigen) defines the serospecificity of bacterial cells, which is the basis for O-serotyping of medically and agriculturally important gram-negative bacteria including Escherichia coli. In order to obtain the O-polysaccharide for structural analysis, the lipopolysaccharide was isolated from cells of E. coli O84a by phenol/water extraction and degraded with mild acid. However, the O-polysaccharide was cleaved at a highly acid-labile beta-l-fucopyranosyl phosphate (beta-l-Fucp-1-P) linkage to give mainly a pentasaccharide that corresponded to the O-polysaccharide repeat. Therefore, the lipopolysaccharide and the pentasaccharide as well as their O-deacylated derivatives were studied using sugar analysis, NMR spectroscopy, and (for oligosaccharides) ESI HR MS, and the O84-polysaccharide structure was established. The O-polysaccharide is distinguished by the presence of beta-l-Fucp-1-P and randomly di-O-acetylated 6-deoxy-d-talose, which are found for the first time in natural carbohydrates. The gene cluster for the O84-antigen biosynthesis was analysed and its content was found to be consistent with the O-polysaccharide structure.