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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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Incomplete cyanobacteria universe - lacks photosynthesis related reactions #203

Open GediminasA opened 3 months ago

GediminasA commented 3 months ago

Hi,

I was trying to model the metabolism of a cyanobacteria species using the cyanobacteria universe file. However, I encountered some unexpected results. Upon examining the file "carveme/data/generated/universe_cyanobacteria.xml.gz," I noticed that it does not contain any photosynthesis-related reactions.

Could you please suggest a way to proceed and obtain a metabolic model that includes these reactions?

Thank you in advance.

Best regards, Gediminas

cdanielmachado commented 3 months ago

Hi,

You are right, the photosynthetic reactions are missing, it is surprising how this issue was not detected before.

The photosynthetic reactions in our universal model should come from the Synechocystis model in BiGG. However, I just realized that the photons in that model have a chemical formula "Z" (http://bigg.ucsd.edu/models/iJN678/metabolites/photon_c). There is a step during curation of the universal model where we remove any unbalanced reactions, which must have been the case here because of the fake element "Z".

I will fix this in a future release, but it might take a while... :)