Metabolic Pathway Flux Simulator

Metabolic Engineering

Substrate feed rate 100%

Enzyme E1 expression (S → M1) 100%

Enzyme E2 expression (M1 → Product) 100%

Product yield

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Byproduct flux

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Pathway efficiency

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How it works

Substrate molecules (cyan) enter the network at S and are converted to intermediate M1 by enzyme E1. At the branch point, M1 either continues down the engineered production pathway to Product P (green, catalyzed by E2) or leaks into the competing branch to Byproduct Bp (red, catalyzed by native enzyme E3). Each reaction's speed follows Michaelis–Menten kinetics, and the branch a molecule takes is weighted by the relative expression of E2 versus E3 — exactly the two levers a metabolic engineer pulls to raise yield.

v = Vmax·[S] / (Km + [S])
P(product) = E2 / (E2 + E3)   (E3 = 0 after knockout)

Substrate feed rate — how fast S molecules are supplied to the network; more feed means more flux everywhere, but only if downstream enzymes can keep up.
Enzyme E1 expression — throughput of the first conversion step; low expression starves the whole pathway even with plenty of substrate.
Enzyme E2 expression — throughput and pull-strength of the production step; raising it draws more flux away from the competing branch.
Knock out competing enzyme E3 — the classic engineering move: deleting the competing gene forces every molecule of M1 down the production pathway, maximizing yield at the cost of that branch's natural product.

Real-world relevance: this loop mirrors what happens in an engineered microbial strain — biologists tune promoter strength (enzyme expression) and knock out competing genes to redirect metabolic flux toward a target compound, then verify the result with flux balance analysis and omics measurements.

Substrate S Intermediate M1 Product P Byproduct Bp

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