Draw energy generating cycles

[hgscott]

MEMOTE just gives me a list of reactions with non-zero flux:

I want to see how those reactions are connected and what they are actually doing.

I started doing this manually and gave up because of how tedious it was, but Devlin says that is the best way to find these cycles.

[hgscott]

I could start with a much simpler cycle- memote locally just identifies three reactions: #41, try those.

[hgscott]

That 3 reaction cycle was exactly what the paper gave as a simple example: A symporter that exports a metabolite and a proton acts together with a transporter that takes the same metabolite up without a proton. A combination of both reactions builds up a proton gradient that can then be utilized to generate energy (e.g., via an ATP synthase). One reaction in the pair is irreversible, the other is:

[hgscott]

I can't make any more progress on drawing cycles until I have a stable list of reactions that are in cycles, so I will mark this as blocked until #41 is resolved.

[hgscott]

Luckily, the simple one I drew was the one that was real, so there's no more that I need to draw.

But do double-check the direction of the flux for those reactions.

[hgscott]

Here are the fluxes: Which means that, just like the example from the paper, the symporter is going from c to e, and the energy-free transporter is going e to c.

How is 5206 having a positive flux at all?

[hgscott]

The bounds after solution are different form when I looked up the model before:

I checked it is correct immediately after reading in the model:

It's only after the model is solved, that the bounds change, and the direction of the reaction changes too: