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m-jahn / genome-scale-models

Genome scale metabolic models in SBML format
GNU General Public License v3.0
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heme production not functional in the model #8

Closed m-jahn closed 4 years ago

m-jahn commented 4 years ago

The RBA (resource allocation) model sitting on top of the genome scale model does not have a functioning TCA cycle. The reason for this is that succinate dehydrogenase (SUCDi/SUCD1) has two subunits that require heme as a cofactor, and heme synthesis is not functional in the genome scale model. However, technically this is not necessary as it is not a part of the the biomass reaction and the GEM is functional without. FOr the RBA model, it would be good to have.

m-jahn commented 4 years ago

Added 1 reaction to complete heme biosynthesis, added Fe2+ to medium which is now required for heme, and updated biomass reaction, see commit b8a3b2d.