yeast-GEM
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SysBioChalmers
ATP/NADH issue
In our model, 1 NADH is equivalent to 1 NADPH. 1 NADH can produce 1.266ATP through respiratory chain. However, when you set one glucose as input, it can produce 12 NADH but produce 20.5253 ATP if you use NGAM reaction as the objective due to the hydrogen[c] serve as the proton pump in the model. Do you think it is a problem we should fix?
Can we compare it with the general yield of NADH, NADPH and ATP? If they very much, I think we can fix it.
@feiranl I don't fully understand the problem here. One thing is the ratio ATP/NADH in Ox.Pho. and another thing is the overall ATP/NADH ratio, which includes other processes (glycolysis, TCA, transport of phosphate to mitochondria, etc). I don't think both ratios have to match. Last time we checked with @edkerk the P/O ratio in the model was reasonable, around 1.5. But maybe I'm missing something?
@hongzhonglu @feiranl I remember you mention that you were comparing yields to exp data. Have you found data for NADH, NADPH and ATP yields? If so, have you compared them to the model?
@BenjaSanchez We don't do this work now. @feiranl Can you find the related data? I remember that you have written the codes to do such kind of analysis.
This is probably affected by changes that will be applied in #12, but should be specifically checked afterwards.
