changes to the original iUma22 model:
allowing co2 uptake
model.reactions.get_by_id('EX_co2_e').lower_bound = -10
Enabling substrate uptake for 2-oxo-butanate
model.add_boundary(model.metabolites.get_by_id('2obut_e'), type="exchange", lb=0)
Enabling substrate uptake for formate
model.add_boundary(model.metabolites.get_by_id('for_e'), type="exchange", lb=0)
Correction of reaction directionality
model.reactions.get_by_id('FRUCTOSE-6-PHOSPHATE-PHOSPHOKETOLASE-RXN').lower_bound = 0
model.reactions.get_by_id('PHOSPHOKETOLASE-RXN').lower_bound = 0
Deactivating reactions to get fluxes more realistic
model.reactions.get_by_id('RXN-11453').bounds = 0,0
model.reactions.get_by_id('PRDXl').bounds = 0,0
model.reactions.get_by_id('RXN-12481').lower_bound = 0
model.reactions.get_by_id('ACITL').bounds = 0,0
Mannitol production
https://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-3881
Reported Mannitol pathway genes in U. maydis by Schipper, 2009:
https://d-nb.info/1000245756/34
I'MANNOSE-6P_c + nadph_c + h_c + h2o_c --> mnl_c + nadp_c + pi_c'
Adding Isocitrate lyase
'icit_c --> succ_c + glx_c'