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 shortest pathways search algorithm using an universal biochemical reaction database.
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)
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
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
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
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