reactions with -1000 or 1000 flux

[dtusso]

Hello 

I am writing to you because I am having a problem with these reactions that have a flux value with the maximum limit, when I am doing FBA.
When I make R00332 or R03035 irreversible,  the μ value decreases significantly. Additionally, other reactions appear with maximum values of upper limits, and the production of unwanted metabolites also begins.  I wanted to ask if somebody could possibly give me some suggestions to solve this problem. Thank you very much if you can help me with anything.

Name LB V UB
ATP + CoA + Tetradecanoic acid <=> Tetradecanoyl-CoA + AMP + Diphosphate FACOAL140__cyto -1000 -1000 1000
dATP + GMP <=> dADP + GDP GK2__cyto -1000 1000 1000
ATP + GMP <=> ADP + GDP R00332__cyto -1000 -999,96541 1000
ATP + Pantetheine 4'-phosphate => Diphosphate + Dephospho-CoA R03035__cyto -1000 -999,99552 1000
H2O + Dephospho-CoA <=> AMP + Pantetheine 4'-phosphate R03036__cyto -1000 -1000 1000
Orthophosphate (extr) + H+ (extr) <=> Orthophosphate (cyto) + H+ (cyto) TR1000009_CYTMEM__cytmem -1000 -999,6877 1000
Orthophosphate (extr) + Tetradecanoic acid (cyto) <=> Orthophosphate (cyto) + Tetradecanoic acid (extr) TR2901030__cytmem -1000 1000 1000

[dtusso]

[Moritz Beber]

Hi,

It is critical that you understand, that you cannot interpret "internal" reaction fluxes using FBA. Does your objective make sense? If so, that is the only value you should care about.

You can also run parsimonious FBA, which will minimize reaction fluxes, however, you should still not interpret them as having biological meaning.

Best,

Moritz

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[Brian]

If my objective is BIOMASS_reaction, how do I know that it makes sense? I have read that setting BIOMASS_reaction as your objective returns the growth rate (mu) for your model, but I am getting values of over 700, which seems quite high. I am using the Recon3D model.

[Moritz Beber]

Indeed, in most cases your objective will correspond to the model's biomass function, which will give you an estimate of the growth rate.

A value of 700 seems unreasonably high and probably means that you have created unrealistic uptake rates.