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GEM description

Automatic reconstruction with AuReMe

Model summary: summary

Download AuReMe Input/Output [LINK OR MEDIA data]

The automatic reconstruction of SJAPGEM results to a Genome scale Model containing 3344 reactions, 3242 metabolites, 5022 genes and 1388 pathways. This GeM was obtained based on the following sources:

  • Based on annotation data:
    • Tool: Pathway tools
      • Creation of a metabolic network containing 2560 reactions
  • Based on orthology data:
    • Tool: Pantograph
      • From template NANNOCHLOROPSIS_SALINA creation of a metabolic network containing: 595 reactions
      • From template ARABIDOPSIS_THALIANA creation of a metabolic network containing: 425 reactions
      • From template ECTOCARPUS_SILICULOSUS creation of a metabolic network containing: 1498 reactions
  • Based on expertise:
      • 74 reaction(s) added
  • Based on gap-filling:
    • Tool: meneco
      • 90 reaction(s) added


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: