Puzzle on GapFind results

[wh960823]

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• [ ] Tried to solve the issue on my own
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[wh960823]

I hereby confirm that I have:

[X] Tried to solve the issue on my own [X] Retried to run my code with the latest version of The COBRA Toolbox [X] Checked that a similar issue has not already been opened

Hello, When I used GapFind to find block metabolites in my draft model. Some of the results makes me quite puzzled. A metabolite both as reactant and product in my model. but the GapFind report this metabolite as block metabolite. I want to known why this metabolite is blocked. Best regards, Hao

[WegrzynAB]

Hi Hao, did you check if the metabolite can be made and removed from the model properly? It may happen that if other metabolites required to make your metabolite are not present, then that pathway will be blocked. Also if you cannot remove the products the pathway will be blocked.

You can test that in two steps: assuming this is the part of your network: rxn 1: A + B -> C rxn 2: C + D -> E

• add a temporary sink (sink_C: lb 0, ub 1000) for this metabolite and optimize for the rxn1 -> if your objective function flux value is >0, then it can be produced
• add a temporary demand (DM_C: lb -1000, ub 0) for this metabolite and optimize for the rxn 2 -> if your objective function flux value is >0, then it can be removed

Regards, Aga