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What is the right way to include transport reactions from experimental data?

asked 2020-04-06 04:16:55 -0500

bcamara gravatar image

Hello! I am trying to complete my model using information from experimental data. We have tested our strain with different carbon sources. For example, we have tested that our gram negative strain is able to use D-Mannose as the only carbon source. I have included the specific reaction that transport D-Mannose from periplasm to cytosol (RXN-15087) and I have included another reaction that is generic that transport sugars from extracellular to periplasm using a porin (RXN0-7209: Transport: a sugar). Supposely, these two reactions are the right ones that the strain shoud use to tranport D-Mannose from the extracellular space to the cytosol space. And D-Mannose is classify as (all carbohydrates -> a carbohydrate -> a glycan -> a sugar -> a monosaccharide -> a hexose). To evaluate if the model is able to use this nutrient, I have use MetaFlux. When D-Mannose is in the periplasm space, the model is working correctly. However, when D-Mannose is in the extracellular space, the model is not able to use it. Why is happening this? I cannot understand what is happening if the nutrient (D-Mannose) is classify as sugar and the reaction RXN0-7209 is a generic reacton that includes this sugar compound.

Could you help me, please?

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answered 2020-04-07 13:22:26 -0500

waikit gravatar image

Hi, I think you may be providing D-Mannose as the compound class MANNOSE instead of one of the compound instances under MANNOSE such as CPD-15373 (aldehydo-D-Mannose). When RXN0-7209 is instantiated to all possible instance reactions, only compound instances are considered. So, for RXN0-7209, there will be some instantiated reactions with CPD-15373 but not MANNOSE. This might be why MANNOSE worked in the periplasm but not in the extracellular space.

You may want to try providing the nutrient as one of the instances of MANNOSE rather than the compound class itself. If you looked at the .sol file that is generated after you run your .fba file, you can probably see that even when you provided MANNOSE as the nutrient in the periplasm, RXN-15087 gets instantiated to something like "an [HPr protein]-Npi-phospho-L-histidine + D-mannose[periplasm] -> beta-D-mannopyranose 6-phosphate + an [HPr]-L-histidine". This will depend on what reactions you have downstream in the network but most will have compound instances rather than compound classes.

In general, you may want to check the .sol file and/or the .log file to see if the reaction you are expecting is really present. Hopefully, this is the explanation for your situation. If not, please confirm whether you see the expected reaction in the .sol and .log files, and I can investigate further.

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Asked: 2020-04-06 04:16:55 -0500

Seen: 3,011 times

Last updated: Apr 07 '20