Method in brief#
Flux balance analysis runs in COBRApy on the iML1515 model of Escherichia coli in minimal M9 medium under aerobic conditions. We compute two scenarios:
- Full knockout of the target gene, with the reaction switched off entirely.
- Partial inhibition, where enzyme occupancy follows from the ratio of the intracellular concentration to the dissociation constant.
The output is a relative growth rate and a four-level phenotype label.
Why this block does not enter the objective function#
With the intracellular concentration fixed at 1 µM, the growth rate is a deterministic function of affinity alone. A simple threshold rule on KD (0.11 / 1.00 / 9.00 µM) reproduces 100% of the labels. The systems biology block therefore duplicates the affinity signal. It serves data inspection and choices in later stages, not the ranking.
Limits of static flux balance#
Knocking out the DHFR reaction in iML1515 is lethal, but knocking out the folA gene itself is not: the model annotates folM as an isoenzyme, which is an artefact of the gene-protein-reaction rules rather than a real bypass route.
Simultaneous inhibition of folA and folP produces no synergy in this model (Loewe index 2.0), even though the combination of trimethoprim and sulfamethoxazole suggests it should. That is an expected limitation of static flux balance analysis.
Stage 6 describes the effect on growth within a metabolic model. It does not replace growth assays in culture or a full analysis of bypass routes.