.. code:: python
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.
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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.
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.. code:: python
from cameo import models
from cameo.strain_design import pathway_prediction
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.. code:: python
model = models.bigg.iMM904
.. code:: python
predictor = pathway_prediction.PathwayPredictor(model=model, compartment_regexp=re.compile(".*_c$"))
.. code:: python
pathways = predictor.run(product="vanillin", max_predictions=4)
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Pathway 1
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|
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 |
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Pathway 2
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|
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 |
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Pathway 3
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|
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 |
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Pathway 4
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|
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 |
.. code:: python
pathways.pathways[0].reactions[0]
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Id | MNXR5336 |
Name | rhea:13309 |
Stoichiometry | MNXM754 + MNXM2 + MNXM8 <=> MNXM10 + 2.0 MNXM1 + MNXM982 |
Lower bound | -1000.000000 |
Upper bound | 1000.000000 |
.. code:: python
pathways.plot_production_envelopes(model, objective=model.reactions.BIOMASS_SC5_notrace)
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