from IPython.display import display
import re
Predicting heterologous pathways is an important strategy to generate new viable strains. Because portfolio of available reactions is very large, computer assisted pathway design becomes essential. Cameo implements a pathway search algorithm using an universal biochemical reaction database that enumerates the shortest pathways.
from cameo import models
from cameo.strain_design import pathway_prediction
model = models.bigg.iMM904
predictor = pathway_prediction.PathwayPredictor(model=model, compartment_regexp=re.compile(".*_c$"))
pathways = predictor.run(product="vanillin", max_predictions=4)
equation | lower_bound | upper_bound | |
---|---|---|---|
MNXR5336 | vanillin + H2O + NAD(+) <=> NADH(2-) + 2.0 H(+... | -1000 | 1000 |
MNXR5340 | formaldehyde + H2O + NAD(+) + 3,4-dihydroxyben... | -1000 | 1000 |
MNXR68718 | H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki... | -1000 | 1000 |
equation | lower_bound | upper_bound | |
---|---|---|---|
MNXR230 | NADP(+) + H2O + 3,4-dihydroxybenzoate <=> O2 +... | -1000 | 1000 |
MNXR5336 | vanillin + H2O + NAD(+) <=> NADH(2-) + 2.0 H(+... | -1000 | 1000 |
MNXR5340 | formaldehyde + H2O + NAD(+) + 3,4-dihydroxyben... | -1000 | 1000 |
equation | lower_bound | upper_bound | |
---|---|---|---|
MNXR5336 | vanillin + H2O + NAD(+) <=> NADH(2-) + 2.0 H(+... | -1000 | 1000 |
MNXR5340 | formaldehyde + H2O + NAD(+) + 3,4-dihydroxyben... | -1000 | 1000 |
MNXR14769 | H2O + 3,4-dihydroxybenzoate + NAD(+) <=> NADH(... | -1000 | 1000 |
equation | lower_bound | upper_bound | |
---|---|---|---|
MNXR5336 | vanillin + H2O + NAD(+) <=> NADH(2-) + 2.0 H(+... | -1000 | 1000 |
MNXR5340 | formaldehyde + H2O + NAD(+) + 3,4-dihydroxyben... | -1000 | 1000 |
MNXR6101 | anthranilate + NADH(2-) + O2 + 3.0 H(+) <=> NH... | -1000 | 1000 |
MNXR7067 | 3,4-dihydroxybenzoate + H(+) <=> catechol + CO(2) | -1000 | 1000 |
pathways.pathways[0].reactions[0]
Id | MNXR5336 |
Name | rhea:13309 |
Stoichiometry | MNXM754 + MNXM2 + MNXM8 <=> MNXM10 + 2.0 MNXM1 + MNXM982 |
Lower bound | -1000.000000 |
Upper bound | 1000.000000 |
pathways.plot_production_envelopes(model, objective=model.reactions.BIOMASS_SC5_notrace)