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ESUBGEM description

Ectocarpus subulatus is a small filamentous brown alga that is able to live in freshwater. Its full genome was published in 2020 (Dittami et al., Marine Genomics), alongside with a first version of a genome-scale metabolic network (still available at http://gem-aureme.irisa.fr/sububftgem). In a follow-up study (Girard et al., in preparation) we are now curating specifically the sterol biosynthesis pathways (PWY-8191, PWY-8238).

Automatic reconstruction with AuReMe

Model summary: summary

Download AuReMe Input/Output [LINK OR MEDIA data]

The automatic reconstruction of Ectocarpus subulatus strain BFT results to a Genome scale Model containing 2086 reactions, 2204 metabolites, 5052 genes and 1152 pathways. This GeM was obtained based on the following sources:

  • Based on annotation data:
    • Tool: PathwayTools
    • Creation of a metabolic network containing 1459 reactions
  • Based on expertise:
    • 480 reaction(s) added
  • Based on orthology data:
    • Creation of a global metabolic network containing 417 reactions
    • Tool: Pantograph
      • From template a.taliana.aragem creation of a metabolic network containing: 417 reactions

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: gem-aureme[AT]inria.fr