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Unbalanced reactions not producing biomass metabolites

asked 2020-05-29 03:14:22 -0500

bcamara gravatar image

Hello !!! I am working on my PGDB using the module MetaFlux. For the biomass objective function, I am including different metaboites including amino acids, deoxynucleotides, nucleotides..etc. One of the biomass metabolites that I want to include is the Glycogen compound (ID: Glycogens). In the case of my PGDB, this metabolite can be generated and consumed using the glycogen biosynthesis I and glycogen degradation I pathways. I have checked every single step reaction of these pathways, checking that all the reactions are included with their corresponding genes, and are annotated in the right direction. However, several of these reactions are determined as unbalanced (GLYCOGEN-BRANCH-RXN, GLYCOGENSYN-RXN, GLYCOPHOSPHORYL-RXN,RXN0-5146,RXN-9025), and for that reason they are directly discarded by the solver when trying to find an optimal solution. I have checked these reactions and because of the way they are formulated it is imposible that this reactions can be balanced. What should I do to make the model produce glycogen as biomass metabolite?

Thank you so much for everything


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answered 2020-06-01 02:44:31 -0500

bcamara gravatar image

Dear Waikit,

I am not sure if I am understanding you correctly. For the last reaction of the glycogen pathway biosynthesis I, are you suggesting me to include ADP-D-GLUCOSE in the nutrient section, and ADP in the biomass section of the .fba file?

I do not know how to create the specific compound instances. What instances I have to create for the compound Glycogens or 1,4-a-D-glucan? Could you be more specific in the steps that I should do?

Thank you so much

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Hi Beatriz, I think it depends on how accurate you would like your model to be and what data you have. If you don't really know what specific glycogen compounds are needed for your biomass, perhaps you could stop earlier in the pathway as is done in the EcoCyc model. You should have access to the EcoCyc model files so you can refer to them (you can check the EcoCyc directory of your PT installation under data/fba/fba-examples/). Simply put, you would define ADP-D-GLUCOSE with a positive coefficient and ADP with a negative coefficient in the biomass section of the .fba file. If you do have more specific information about the glycogen compounds, and you want to model them, you would need to create compound instances for the compound classes of the unbalanced reactions such that they can balance. By having specific compound instances, the compounds will have ...(more)

waikit gravatar imagewaikit ( 2020-06-01 23:00:12 -0500 )edit

Hi waikit, Following your recommendation I have included ADP-D-GLUCOSE and ADP in the biomass section and it worked. However, I am still interested in including glycogen in the biomass section. As you indicated me, I have to create a new instance of the compound class glycogen. However, I have not been able to include the structural data of this compound. How can I include this information in the instance? This is also happening when creating instances of other compound class of lipids (e.g. cardiolipin) Is it possible to include the structural data with the Marvin compound editor tool? I have tried to install it but it seems that Pathway Tools does not recognize it. I think the chemaxon website has changed and there is no "Web Developers" to download "Marvin Applets" package. The instructions for the intallation of the marvin software in the Pathway Tools website does not work ...(more)

bcamara gravatar imagebcamara ( 2020-06-24 09:15:15 -0500 )edit

answered 2020-05-29 16:35:28 -0500

waikit gravatar image

Hi Beatriz,

Indeed, MetaFlux excludes unbalanced reactions before generating the lp file to be submitted to the solver. For the EcoCyc model, we simply stopped at the last step of the pathway with a balanced reaction. In this case, we defined ADP-D-GLUCOSE as a reactant in the biomass reaction and ADP as a product. If it is important for you to run a simulation with all the steps towards glycogen along with the genes associated with them, I recommend creating specific compound instances of the compound classes for all the relevant unbalanced reactions. That way, the generic reactions can be instantiated with your specific compounds to produce balanced reactions to produce glycogen with a specific chemical formula. In general, you do not want to include compound classes in the biomass.

Hope that helps. Let us know if you have additional questions.

Wai Kit

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Asked: 2020-05-29 03:14:22 -0500

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Last updated: Jun 01 '20