from cameo import models, phenotypic_phase_plane
model = models.bigg.e_coli_core.copy()
model.reactions.EX_o2_e.lower_bound = 0
model.reactions.EX_succ_e
Id | EX_succ_e |
Name | Succinate exchange |
Stoichiometry | succ_e --> |
Lower bound | 0.000000 |
Upper bound | 1000.000000 |
ppp = phenotypic_phase_plane(model,
variables=[model.reactions.BIOMASS_Ecoli_core_w_GAM],
objective=model.reactions.EX_succ_e)
ppp.plot()
mutant1 = model.copy()
mutant1.reactions.ACKr.knock_out()
mutant1.reactions.ATPS4r.knock_out()
mutant1.reactions.ATPM.knock_out()
mutant1.reactions.FUM.knock_out()
ppp = phenotypic_phase_plane(mutant1,
variables=[mutant1.reactions.BIOMASS_Ecoli_core_w_GAM],
objective=mutant1.reactions.EX_succ_e)
ppp.plot()
mutant2 = model.copy()
mutant2.reactions.ACALD.knock_out()
mutant2.reactions.PYK.knock_out()
mutant2.reactions.ME2.knock_out()
ppp = phenotypic_phase_plane(mutant2,
variables=[mutant2.reactions.BIOMASS_Ecoli_core_w_GAM],
objective=mutant2.reactions.EX_succ_e)
ppp.plot()
mutant3 = model.copy()
mutant3.reactions.ACALD.knock_out()
mutant3.reactions.LDH_D.knock_out()
ppp = phenotypic_phase_plane(mutant3,
variables=[mutant3.reactions.BIOMASS_Ecoli_core_w_GAM],
objective=mutant3.reactions.EX_succ_e)
ppp.plot()
### Solution 1
mutant1.reactions.EX_o2_e.lower_bound = -20
ppp = phenotypic_phase_plane(mutant1,
variables=[mutant1.reactions.BIOMASS_Ecoli_core_w_GAM],
objective=mutant1.reactions.EX_succ_e)
ppp.plot()
mutant2.reactions.EX_o2_e.lower_bound = -20
ppp = phenotypic_phase_plane(mutant2,
variables=[mutant2.reactions.BIOMASS_Ecoli_core_w_GAM],
objective=mutant2.reactions.EX_succ_e)
ppp.plot()
mutant3.reactions.EX_o2_e.lower_bound = -20
ppp = phenotypic_phase_plane(mutant3,
variables=[mutant3.reactions.BIOMASS_Ecoli_core_w_GAM],
objective=mutant3.reactions.EX_succ_e)
ppp.plot()
The anwer is no!
mutant3.reactions.ACALD.gene_name_reaction_rule
'mhpF or adhE'
mutant3.reactions.LDH_D.gene_name_reaction_rule
'dld or ldhA'
for gene in mutant3.reactions.ACALD.genes:
print(gene.name, gene.reactions)
adhE frozenset({<Reaction ALCD2x at 0x7f8f21a0e908>, <Reaction ACALD at 0x7f8f21a0e668>}) mhpF frozenset({<Reaction ACALD at 0x7f8f21a0e668>})
for gene in mutant3.reactions.LDH_D.genes:
print(gene.name, gene.reactions)
ldhA frozenset({<Reaction LDH_D at 0x7f8f21a26208>}) dld frozenset({<Reaction LDH_D at 0x7f8f21a26208>})
mutant4 = model.copy()
mutant4.reactions.ACALD.knock_out()
mutant4.reactions.LDH_D.knock_out()
mutant4.reactions.ALCD2x.knock_out()
ppp = phenotypic_phase_plane(mutant4,
variables=[mutant4.reactions.BIOMASS_Ecoli_core_w_GAM],
objective=mutant4.reactions.EX_succ_e)
ppp.plot()
The answer is yes!