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COKAGEM description

Cladosiphon okamuranus is an edible brown alga cultivated around Okinawa, with 20 000 tons of fresh weight harvested yearly, representing around 4 billion japanese yens in 2006. Its draft genome sequence was published in 2016 (Nishitsuji et al., DNA Research). The paper describing this GEM reconstruction in more detail is in preparation. Manual curation is ongoing on carotenoid biosynthesis pathway (CAROTENOID-PWY) and on the first cycle of xanthophylls (PWY-5945).

The photograph used here is cropped from a work by Mr. Kenji Iwa, published as CC BY SA 4.0. The original version can be accessed in this paper.

Automatic reconstruction with AuReMe

Model summary: summary

The automatic reconstruction of Cladosiphon okamuranus results in a Genome-scale Metabolic Model containing 3390 reactions, 2255 metabolites, 5373 genes and 1403 pathways. This GeM was obtained based on the following sources:

  • Based on annotation data:
    • Tool: Pathway tools
      • Creation of a metabolic network containing 2494 reactions
  • Based on orthology data:
    • Tool: Pantograph
      • From template ECTOCARPUS_SILICULOSUS creation of a metabolic network containing: 1468 reactions
      • From template NANNOCHLOROPSIS_SALINA creation of a metabolic network containing: 595 reactions
      • From template SACCHARINA_JAPONICA creation of a metabolic network containing: 3020 reactions
      • From template ARABIDOPSIS_THALIANA creation of a metabolic network containing: 426 reactions
  • Based on expertise:
      • 64 reaction(s) added
  • Based on gap-filling:
    • Tool: meneco
      • 67 reaction(s) added

File:Venn.png


Collaborative curation

  • Suggest reactions to add or remove:
  • Suggest new reactions to create and add:
  • Follow the examples given in the form(s) to correctly share your suggestions
  • Send the filled form(s) to: gabriel.markov@sb-roscoff.fr