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biosustain / cameo

cameo - computer aided metabolic engineering & optimization
http://cameo.bio
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Max flux value in http://cameo.bio/07-predict-heterologous-pathways.html #238

Open mauriceling opened 5 years ago

mauriceling commented 5 years ago

Hi,

I am trying to repeat Predict heterologous pathways (http://cameo.bio/07-predict-heterologous-pathways.html) on Python code. This is what I have:

from cameo import load_model from cameo.strain_design import pathway_prediction model = load_model('iMM904') predictor = pathway_prediction.PathwayPredictor(model) pathways = predictor.run(product="vanillin", max_predictions=2)

and the output is

Pathway 1 equation lower_bound upper_bound MNXR5340 H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... -1000 1000 MNXR5336 2.0 H(+) + NADH + vanillate <=> H2O + vanillin... -1000 1000 MNXR230 H(+) + 4-hydroxybenzoate + O2 + NADPH <=> H2O ... -1000 1000 Pathway 2 equation lower_bound upper_bound MNXR5340 H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... -1000 1000 MNXR5336 2.0 H(+) + NADH + vanillate <=> H2O + vanillin... -1000 1000 MNXR68718 H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki... -1000 1000

which is the same as in http://cameo.bio/07-predict-heterologous-pathways.html.

However, where can I get "Max flux" value (ie, Max flux: 3.36842 for Pathway 2)?

Is higher max flux predictive of higher vanillin production?

jjczajka commented 4 years ago

I am running into the same issue, was there ever a resolution to this?

mauriceling commented 4 years ago

No comments from the developers. Please kindly help out here.

Midnighter commented 4 years ago

Hi, you can 'apply' a pathway to your base model and then optimize for the pathway target. That will give you the theoretical maximum flux through your heterologous pathway.

Higher flux is indeed an indication that your carbon source can be used more efficiently.