In [1]:
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](http://try.cameo.bio), things might run very slow due to our inability to provide access to the proprietary [CPLEX](https://www-01.ibm.com/software/commerce/optimization/cplex-optimizer/) solver on a public webserver. Furthermore, Jupyter kernels might crash and restart due to memory limitations on the server.
In [2]:
from cameo import models
from cameo.strain_design import pathway_prediction
In [3]:
model = models.bigg.iMM904
In [4]:
predictor = pathway_prediction.PathwayPredictor(model=model, compartment_regexp=re.compile(".*_c$"))
In [5]:
pathways = predictor.run(product="vanillin", max_predictions=4)
Pathway 1
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
In [6]:
pathways.pathways[0].reactions[0]
Out[6]:
IdMNXR5336
Namerhea:13309
StoichiometryMNXM754 + MNXM2 + MNXM8 <=> MNXM10 + 2.0 MNXM1 + MNXM982
Lower bound-1000.000000
Upper bound1000.000000
In [7]:
pathways.plot_production_envelopes(model, objective=model.reactions.BIOMASS_SC5_notrace)