from IPython.display import display
import re
Predict heterologous pathways
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.
If you’re running this notebook on
try.cameo.bio, things might run very slow due
to our inability to provide access to the proprietary
CPLEX
solver on a public webserver. Furthermore, Jupyter kernels might crash
and restart due to memory limitations on the server.
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 |
Pathway 2
|
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 |
Pathway 3
|
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 |
Pathway 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 |
| 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)
