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)
pathways = predictor.run(product="vanillin", max_predictions=4)
Pathway 1
equation lower_bound upper_bound
MNXR5340 H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... -1000 1000
MNXR5336 2.0 H(+) + NADH + vanillate <=> H2O + vanillin... -1000 1000
MNXR230 H(+) + 4-hydroxybenzoate + O2 + NADPH <=> H2O ... -1000 1000
Max flux: 1.90533
Pathway 2
equation lower_bound upper_bound
MNXR5340 H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... -1000 1000
MNXR5336 2.0 H(+) + NADH + vanillate <=> H2O + vanillin... -1000 1000
MNXR68718 H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki... -1000 1000
Max flux: 3.36842
Pathway 3
equation lower_bound upper_bound
MNXR4008 H(+) + 3-oxoadipate <=> H2O + 5-oxo-4,5-dihydr... -1000 1000
MNXR184 3-oxoadipyl-CoA + succinate <=> 3-oxoadipate +... -1000 1000
MNXR5340 H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... -1000 1000
MNXR5336 2.0 H(+) + NADH + vanillate <=> H2O + vanillin... -1000 1000
MNXR228 CO2 + 5-oxo-4,5-dihydro-2-furylacetate <=> H(+... -1000 1000
MNXR4119 2.0 H(+) + 3-carboxy-cis,cis-muconate <=> 3,4-... -1000 1000
MNXR209 CoA + 3-oxoadipyl-CoA <=> acetyl-CoA + succiny... -1000 1000
MNXR3655 2-(carboxymethyl)-5-oxo-2,5-dihydro-2-furoate ... -1000 1000
Max flux: 5.59223
Pathway 4
equation lower_bound upper_bound
MNXR5338 2.0 H(+) + NADH + 3,4-dihydroxybenzoate <=> H2... -1000 1000
MNXR1041 diphosphate + AMP + caffeoyl-CoA <=> CoA + ATP... -1000 1000
MNXR4974 O2 + 2.0 trans-4-coumarate <=> 2.0 trans-caffeate -1000 1000
MNXR227 diphosphate + AMP + 4-coumaroyl-CoA <=> CoA + ... -1000 1000
MNXR5340 H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... -1000 1000
MNXR5336 2.0 H(+) + NADH + vanillate <=> H2O + vanillin... -1000 1000
MNXR18369 CoA + H2O + 4-coumaroyl-CoA + NAD(+) <=> H(+) ... -1000 1000
MNXR232 H(+) + CoA + 4-hydroxybenzoate <=> H2O + 4-hyd... -1000 1000
MNXR1039 acetyl-CoA + 3,4-dihydroxybenzaldehyde <=> H2O... -1000 1000
Max flux: 2.24390
pathways.pathways[0].reactions[0]
Reaction identifierMNXR5340
Namerhea:13021
Memory address 0x01227016d8
Stoichiometry

MNXM1 + MNXM10 + MNXM4 + MNXM982 <=> MNXM2 + MNXM204 + MNXM56 + MNXM8

H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dihydroxybenzoate + formaldehyde + NAD(+)

GPR
Lower bound-1000
Upper bound1000
pathways.plot_production_envelopes(model, objective=model.reactions.BIOMASS_SC5_notrace)
This is the format of your plot grid:
[ (1,1) x1,y1 ]  [ (1,2) x2,y2 ]
[ (2,1) x3,y3 ]  [ (2,2) x4,y4 ]