Enquiry about cobrapy

[Xinrun Yang]

Recently, I reanalyzed the genome-scale metabolite model. Since some metabolites could not be annotated from genome, I wanted to see their fluxes by manually adding the reaction of this metabolite to determine whether it could be utilized by this strain. However, I encountered the problem that the flux of these manually added metabolites reactions always returned 0 values.

Here are my codes, taking ala_B as an example.  Note: bigg is my metabolites.

metabolite_cobra = cobra.Metabolite('ala_B', name=metabolite_name, compartment='C_e')

reaction_EX = cobra.Reaction("EX_" + 'ala_B'+'_e')

reaction_EX.name = metabolite_name + ' Exchange'

reaction_EX.lower_bound = -1000

reaction_EX.upper_bound = 1000

reaction_EX.add_metabolites({metabolite_cobra: -1})

I was wondering if you could provide some insights into why this might be occurring. I am keen to understand if there might be something I am overlooking.