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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

PUL0391

PubMed

21227922, Nucleic Acids Res. 2011 Apr;39(8):3240-54. doi: 10.1093/nar/gkq1281. Epub 2011 Jan 11.

Characterization method

microarray

Genomic accession number

CP001393.1

Nucelotide position range

1929397-1974000

Substrate

cellulose,xylan,xyloglucan,pectin,mannan

Loci

Athe_1853-Athe_1867

Species

Caldicellulosiruptor bescii/31899

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- Athe_1853 ACM60941.1 0 - 2502 (-) CP001393.1:1929397-1931899 3.2.1.91
- Athe_1854 ACM60942.1 2691 - 4074 (-) CP001393.1:1932088-1933471 4.2.2.2
- Athe_1855 ACM60943.1 4130 - 6092 (-) CP001393.1:1933527-1935489 4.2.2.9
- Athe_1856 ACM60944.1 6437 - 8819 (-) CP001393.1:1935834-1938216 -
- Athe_1857 ACM60945.1 9210 - 13647 (-) CP001393.1:1938607-1943044 -
- Athe_1858 ACM60946.1 14023 - 14155 (-) CP001393.1:1943420-1943552 -
- Athe_1859 ACM60947.1 14244 - 18129 (-) CP001393.1:1943641-1947526 -
- Athe_1860 ACM60948.1 18284 - 23999 (-) CP001393.1:1947681-1953396 -
- Athe_1861 ACM60949.1 24271 - 25294 (-) CP001393.1:1953668-1954691 -
- Athe_1862 ACM60950.1 25366 - 26905 (-) CP001393.1:1954763-1956302 -
- Athe_1863 ACM60951.1 26955 - 28416 (-) CP001393.1:1956352-1957813 -
- Athe_1864 ACM60952.1 28444 - 30145 (-) CP001393.1:1957841-1959542 -
- Athe_1865 ACM60953.1 30558 - 34668 (-) CP001393.1:1959955-1964065 -
- Athe_1866 ACM60954.1 34924 - 39169 (-) CP001393.1:1964321-1968566 3.2.1.78, 3.2.1.4
- Athe_1867 ACM60955.1 39324 - 44604 (-) CP001393.1:1968721-1974001 -

Cluster number

0

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2502 (-) CAZyme: PL11|CBM35|GH12|CBM3|CBM2|CE12 No
- 2692 - 4074 (-) CAZyme: PL3_1|PL3|CBM66 No
- 4131 - 6092 (-) CAZyme: PL9_1|CBM35|CBM66|PL9 No
- 6438 - 8819 (-) STP: STP|HTH_18 No
- 9211 - 13647 (-) CAZyme: CBM22|GH12|CBM0|CBM3|CBM2|CBM1|GH48|GH10|CBM9 No
- 14024 - 14155 (-) CDS No
- 14245 - 18129 (-) CAZyme: GH44|CBM35|GH12|CBM44|CBM3|CBM2|CBM76|CBM10|GH5|GH5_8 No
- 18285 - 23999 (-) CAZyme: CBM35|GH12|CBM5|CBM3|CBM2|GH74|CBM1|GH48 No
- 24272 - 25294 (-) CDS No
- 25367 - 26905 (-) CDS No
- 26956 - 28416 (-) CDS No
- 28445 - 30145 (-) CAZyme: GT39 No
- 30559 - 34668 (-) CAZyme: CBM3|GH9|GH5_8 No
- 34925 - 39169 (-) CAZyme: CBM3|GH5_1|GH5_8 No
- 39325 - 44604 (-) CAZyme: CBM3|GH48|GH9 No

PUL ID

PUL0391

PubMed

21227922, Nucleic Acids Res. 2011 Apr;39(8):3240-54. doi: 10.1093/nar/gkq1281. Epub 2011 Jan 11.

Title

Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725.

Author

Dam P, Kataeva I, Yang SJ, Zhou F, Yin Y, Chou W, Poole FL 2nd, Westpheling J, Hettich R, Giannone R, Lewis DL, Kelly R, Gilbert HJ, Henrissat B, Xu Y, Adams MW

Abstract

Caldicellulosiruptor bescii DSM 6725 utilizes various polysaccharides and grows efficiently on untreated high-lignin grasses and hardwood at an optimum temperature of approximately 80 degrees C. It is a promising anaerobic bacterium for studying high-temperature biomass conversion. Its genome contains 2666 protein-coding sequences organized into 1209 operons. Expression of 2196 genes (83%) was confirmed experimentally. At least 322 genes appear to have been obtained by lateral gene transfer (LGT). Putative functions were assigned to 364 conserved/hypothetical protein (C/HP) genes. The genome contains 171 and 88 genes related to carbohydrate transport and utilization, respectively. Growth on cellulose led to the up-regulation of 32 carbohydrate-active (CAZy), 61 sugar transport, 25 transcription factor and 234 C/HP genes. Some C/HPs were overproduced on cellulose or xylan, suggesting their involvement in polysaccharide conversion. A unique feature of the genome is enrichment with genes encoding multi-modular, multi-functional CAZy proteins organized into one large cluster, the products of which are proposed to act synergistically on different components of plant cell walls and to aid the ability of C. bescii to convert plant biomass. The high duplication of CAZy domains coupled with the ability to acquire foreign genes by LGT may have allowed the bacterium to rapidly adapt to changing plant biomass-rich environments.