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