Very low oxygen usage in sims with new flat files

[tahorst]

With the updated files from EcoCyc (#1065), the model consumes very little oxygen during simulations as seen with external_exchange_fluxes single analysis plots below.

Before EcoCyc files (768d8d7):

After (3fb3632):

This might be linked to ubiquinone and ubiquinol since reactions that convert between and consume oxygen are much lower in the new sims.

[ggsun]

I'm looking into this right now - thanks for pointing this out. There were a lot of metabolic redox reactions that started using different cofactors, so this might be easy as adding a single different version of a metabolic reaction.

[ggsun]

Based on what I've looked at so far, I'm suspecting that this issue is connected to the lower GLC[p] import that we can also see in the same plot. There's something funny going on in the first few reactions of glycolysis that imports GLC[p] and phosphorylates it to get G6P that I'm not fully grasping yet.