notebook.community

Edit and run

Easy strain design using a high-level interface

WARNING: 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 [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. To avoid that, we encourage the users to shutdown previously opened notebooks. You can do from the `Home` page that by selecting the notebooks highlighted in green and pressing the `Shutdown` button on the top of the menu.

Users primarily interested in using cameo as a tool for enumerating metabolic engineering strategies have access to cameo's advanced programming interface via cameo.api that provides access to potential products (cameo.api.products), host organisms (cameo.api.hosts) and a configurable design function (cameo.api.design). Running cameo.api.design requires only minimal input and will run the following workflow.

Import the advanced interface.





In [1]:



    


from cameo import api

Searching for products

Search by trivial name.





In [2]:



    


api.products.search('caffeine')



    


















    
Out[2]:











  
    

      
      InChI
      SMILES
      charge
      formula
      mass
      name
      source
      search_rank
    

  
  
    

      MNXM680
      InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)...
      CN1C=NC2=C1C(=O)N(C)C(=O)N2C
      0
      C8H10N4O2
      194.1906
      caffeine
      chebi:27732
      0

Search by ChEBI ID.





In [3]:



    


api.products.search('chebi:27732')



    


















    
Out[3]:











  
    

      
      InChI
      SMILES
      charge
      formula
      mass
      name
      source
      search_rank
    

  
  
    

      MNXM680
      InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)...
      CN1C=NC2=C1C(=O)N(C)C(=O)N2C
      0
      C8H10N4O2
      194.1906
      caffeine
      chebi:27732
      0

Host organisms

Currently the following host organisms and respective models are available in cameo. More hosts and models will be added in the future (please get in touch with us if you'd like to get a particular host organism included).





In [4]:



    


for host in api.hosts:
    for model in host.models:
        print(host.name, model.id)



    


















    






Escherichia coli iJO1366
Saccharomyces cerevisiae iMM904

Computing strain engineering strategies

For demonstration purposes, we'll set a few options to limit the computational time. Also we'll create a multiprocessing view to take advantage of multicore CPUs (strain design algorithms will be run in parallel for individually predicted heterologous pathways).





In [5]:



    


from cameo.parallel import MultiprocessingView
mp_view = MultiprocessingView()

Limit the number of predicted heterlogous pathways to 4.





In [6]:



    


api.design.options.max_pathway_predictions = 4

Set a time limit of 30 minutes on individual heuristic optimizations.





In [7]:



    


api.design.options.heuristic_optimization_timeout = 30



    











In [8]:



    


report = api.design(product='vanillin', view=mp_view)



    


















    






Starting searching for compound vanillin









    






Found 1 compounds that match query 'vanillin'









    







            

                
                    
Id
                    Name
                    Formula
                

                
                    
MNXM754vanillinC8H8O3

                
            

            









    






Choosing best match (vanillin) ... please interrupt if this is not the desired compound.









    







        

            
        

        









    







        
        









    






Predicting pathways for product vanillin in Escherichia coli (using model iJO1366).









    






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
    

    

      MNXR2795
      S-adenosyl-L-methionine + glycine <=> H(+) + S...
      -1000
      1000
    

    

      MNXR68718
      H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki...
      -1000
      1000
    

  













    






Max flux: 4.29196










    






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
    

    

      MNXR84169
      (6R)-5,10-methylenetetrahydrofolate + glycine ...
      -1000
      1000
    

    

      MNXR68718
      H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki...
      -1000
      1000
    

  













    






Max flux: 7.28363










    






Pathway 3









    











  
    

      
      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
    

    

      MNXR651
      2.0 H(+) + NADH + formate <=> H2O + formaldehy...
      -1000
      1000
    

  













    






Max flux: 7.58479










    






Pathway 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
    

    

      MNXR230
      H(+) + 4-hydroxybenzoate + O2 + NADPH <=> H2O ...
      -1000
      1000
    

    

      MNXR640
      methanol + NAD(+) <=> H(+) + NADH + formaldehyde
      -1000
      1000
    

  













    




















    






This is the format of your plot grid:
[ (1,1) x1,y1 ]  [ (1,2) x2,y2 ]
[ (2,1) x3,y3 ]  [ (2,2) x4,y4 ]











    
















    

















    







        
        









    






Predicting pathways for product vanillin in Saccharomyces cerevisiae (using model iMM904).









    






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
    

    

      MNXR68718
      H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki...
      -1000
      1000
    

  













    






Max flux: 3.36842










    






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
    

    

      MNXR230
      H(+) + 4-hydroxybenzoate + O2 + NADPH <=> H2O ...
      -1000
      1000
    

  













    






Max flux: 1.90533










    






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










    




















    






This is the format of your plot grid:
[ (1,1) x1,y1 ]  [ (1,2) x2,y2 ]
[ (2,1) x3,y3 ]  [ (2,2) x4,y4 ]











    

















    






Optimizing 6 pathways
Starting optimization at Tue, 06 Feb 2018 14:06:57
Starting optimization at Tue, 06 Feb 2018 14:07:50
Starting optimization at Tue, 06 Feb 2018 14:07:57
Starting optimization at Tue, 06 Feb 2018 14:07:58










    






 
 















    






Finished after 00:32:09
Starting optimization at Tue, 06 Feb 2018 14:39:37










    






 
 















    






Finished after 00:33:45










    






 
 















    






Finished after 00:33:43










    






 
 















    






Finished after 00:33:43
Starting optimization at Tue, 06 Feb 2018 14:41:56










    






 
 















    






 
 















    






Finished after 00:30:09
Finished after 00:30:02










    






/Users/joaca/Documents/repositories/cameo/cameo/strain_design/heuristic/evolutionary/objective_functions.py:287: RuntimeWarning:

invalid value encountered in double_scalars

/Users/joaca/Documents/repositories/cameo/cameo/strain_design/heuristic/evolutionary/objective_functions.py:354: RuntimeWarning:

invalid value encountered in double_scalars


















In [9]:



    


report



    


















    
Out[9]:











  
    

      
      host
      model
      manipulations
      heterologous_pathway
      fitness
      yield
      product
      biomass
      method
    

  
  
    

      0
      Saccharomyces cerevisiae
      iMM904
      (-YPL110C)
      (+reaction.MNXR4008#metanetx:MNXR4008, +reacti...
      0.000043
      0.000199
      0.001489
      2.879114e-01
      PathwayPredictor+OptGene
    

    

      1
      Escherichia coli
      iJO1366
      (-reaction.3OAR140, -reaction.3OAS140, -reacti...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.000000
      0.572262
      4.291964
      8.136452e-08
      PathwayPredictor+DifferentialFVA
    

    

      2
      Escherichia coli
      iJO1366
      (-reaction.3OAR140, -reaction.3OAS140, -reacti...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.000000
      0.000000
      0.000000
      0.000000e+00
      PathwayPredictor+DifferentialFVA
    

    

      3
      Escherichia coli
      iJO1366
      (reaction.3OAR140(value=0.01699), reaction.3OA...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.000000
      0.508185
      3.351657
      0.000000e+00
      PathwayPredictor+DifferentialFVA
    

    

      4
      Escherichia coli
      iJO1366
      (reaction.3OAR140(value=0.025534), reaction.3O...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.093738
      0.381679
      2.862596
      3.274580e-01
      PathwayPredictor+DifferentialFVA
    

    

      5
      Escherichia coli
      iJO1366
      (reaction.3OAR140(value=0.034045), reaction.3O...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.000000
      0.475180
      3.563847
      0.000000e+00
      PathwayPredictor+DifferentialFVA
    

    

      6
      Escherichia coli
      iJO1366
      (reaction.3OAR140(value=0.042474), reaction.3O...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.104223
      0.254625
      1.909686
      5.457622e-01
      PathwayPredictor+DifferentialFVA
    

    

      7
      Escherichia coli
      iJO1366
      (reaction.3OAR140(value=0.050969), reaction.3O...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.093864
      0.191097
      1.433230
      6.549146e-01
      PathwayPredictor+DifferentialFVA
    

    

      8
      Escherichia coli
      iJO1366
      ()
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.000000
      0.000000
      0.000000
      9.823718e-01
      PathwayPredictor+DifferentialFVA
    

    

      9
      Escherichia coli
      iJO1366
      ()
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      -0.000000
      0.000000
      0.000000
      9.823718e-01
      PathwayPredictor+DifferentialFVA
    

    

      10
      Escherichia coli
      iJO1366
      (-reaction.3OAR140, -reaction.3OAS140, -reacti...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.000000
      0.971150
      7.283628
      0.000000e+00
      PathwayPredictor+DifferentialFVA
    

    

      11
      Escherichia coli
      iJO1366
      (-reaction.3OAR140, -reaction.3OAS140, -reacti...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      NaN
      NaN
      0.000000
      0.000000e+00
      PathwayPredictor+DifferentialFVA
    

    

      12
      Escherichia coli
      iJO1366
      (-reaction.3OAR140, -reaction.3OAS140, -reacti...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      NaN
      NaN
      0.000000
      0.000000e+00
      PathwayPredictor+DifferentialFVA
    

    

      13
      Escherichia coli
      iJO1366
      (-reaction.3OAR140, -reaction.3OAS140, -reacti...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      NaN
      NaN
      -0.000000
      0.000000e+00
      PathwayPredictor+DifferentialFVA
    

    

      14
      Escherichia coli
      iJO1366
      (-reaction.3OAR140, -reaction.3OAS140, -reacti...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      NaN
      NaN
      0.000000
      0.000000e+00
      PathwayPredictor+DifferentialFVA
    

    

      15
      Escherichia coli
      iJO1366
      (reaction.3OAR140(value=0.042474), reaction.3O...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.178214
      0.435389
      3.265417
      5.457622e-01
      PathwayPredictor+DifferentialFVA
    

    

      16
      Escherichia coli
      iJO1366
      (reaction.3OAR140(value=0.050969), reaction.3O...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.160501
      0.326762
      2.450714
      6.549146e-01
      PathwayPredictor+DifferentialFVA
    

    

      17
      Escherichia coli
      iJO1366
      ()
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.000000
      0.000000
      0.000000
      9.823718e-01
      PathwayPredictor+DifferentialFVA
    

    

      18
      Escherichia coli
      iJO1366
      ()
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      -0.000000
      0.000000
      0.000000
      9.823718e-01
      PathwayPredictor+DifferentialFVA
    

    

      19
      Escherichia coli
      iJO1366
      (-reaction.3OAR140, -reaction.3OAS140, -reacti...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.000000
      1.011305
      7.584790
      0.000000e+00
      PathwayPredictor+DifferentialFVA
    

    

      20
      Escherichia coli
      iJO1366
      (-reaction.3OAR140, -reaction.3OAS140, -reacti...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      NaN
      NaN
      -0.000000
      0.000000e+00
      PathwayPredictor+DifferentialFVA
    

    

      21
      Escherichia coli
      iJO1366
      (-reaction.3OAR140, -reaction.3OAS140, -reacti...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      NaN
      NaN
      0.000000
      0.000000e+00
      PathwayPredictor+DifferentialFVA
    

    

      22
      Escherichia coli
      iJO1366
      (reaction.3OAR140(value=0.025485), reaction.3O...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      NaN
      NaN
      NaN
      NaN
      PathwayPredictor+DifferentialFVA
    

    

      23
      Escherichia coli
      iJO1366
      (reaction.3OAR140(value=0.034045), reaction.3O...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.000000
      0.668001
      4.390359
      0.000000e+00
      PathwayPredictor+DifferentialFVA
    

    

      24
      Escherichia coli
      iJO1366
      (reaction.3OAR140(value=0.042474), reaction.3O...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.185581
      0.453387
      3.400405
      5.457622e-01
      PathwayPredictor+DifferentialFVA
    

    

      25
      Escherichia coli
      iJO1366
      (reaction.3OAR140(value=0.050969), reaction.3O...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.167136
      0.340270
      2.552028
      6.549146e-01
      PathwayPredictor+DifferentialFVA
    

    

      26
      Escherichia coli
      iJO1366
      ()
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      -0.000000
      0.000000
      0.000000
      9.823718e-01
      PathwayPredictor+DifferentialFVA
    

    

      27
      Escherichia coli
      iJO1366
      ()
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      -0.000000
      0.000000
      0.000000
      9.823718e-01
      PathwayPredictor+DifferentialFVA
    

    

      28
      Saccharomyces cerevisiae
      iMM904
      (-reaction.13GS, -reaction.2OXOADPtim, -reacti...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.000000
      0.449123
      3.368421
      5.205722e-09
      PathwayPredictor+DifferentialFVA
    

    

      29
      Saccharomyces cerevisiae
      iMM904
      (-reaction.13GS, -reaction.2OXOADPtim, -reacti...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      NaN
      NaN
      0.000000
      4.984455e-12
      PathwayPredictor+DifferentialFVA
    

    

      30
      Saccharomyces cerevisiae
      iMM904
      (reaction.13GS(value=0.072594), reaction.2DDA7...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      NaN
      NaN
      NaN
      NaN
      PathwayPredictor+DifferentialFVA
    

    

      31
      Saccharomyces cerevisiae
      iMM904
      (reaction.13GS(value=0.108891), reaction.2DDA7...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      NaN
      NaN
      NaN
      NaN
      PathwayPredictor+DifferentialFVA
    

    

      32
      Saccharomyces cerevisiae
      iMM904
      (reaction.13GS(value=0.145187), reaction.2DDA7...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      NaN
      NaN
      NaN
      NaN
      PathwayPredictor+DifferentialFVA
    

    

      33
      Saccharomyces cerevisiae
      iMM904
      (reaction.13GS(value=0.181484), reaction.2DDA7...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      NaN
      NaN
      NaN
      NaN
      PathwayPredictor+DifferentialFVA
    

    

      34
      Saccharomyces cerevisiae
      iMM904
      (reaction.13GS(value=0.217781), reaction.2DDA7...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      NaN
      NaN
      NaN
      NaN
      PathwayPredictor+DifferentialFVA
    

    

      35
      Saccharomyces cerevisiae
      iMM904
      (-reaction.SULR, -reaction.THRS, -reaction.TMD...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.000000
      -0.000000
      -0.000000
      0.000000e+00
      PathwayPredictor+DifferentialFVA
    

    

      36
      Saccharomyces cerevisiae
      iMM904
      (-reaction.ENO, -reaction.ERGSTter, -reaction....
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      NaN
      NaN
      NaN
      NaN
      PathwayPredictor+DifferentialFVA
    

    

      37
      Saccharomyces cerevisiae
      iMM904
      ()
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      -0.000000
      0.000000
      0.000000
      2.878657e-01
      PathwayPredictor+DifferentialFVA
    

    

      38
      Saccharomyces cerevisiae
      iMM904
      (-reaction.13GS, -reaction.2OXOADPtim, -reacti...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.000000
      0.254043
      1.905325
      4.603305e-08
      PathwayPredictor+DifferentialFVA
    

    

      39
      Saccharomyces cerevisiae
      iMM904
      (reaction.13GS(value=0.036297), reaction.2OXOA...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.005438
      0.226674
      1.700055
      3.198537e-02
      PathwayPredictor+DifferentialFVA
    

    

      40
      Saccharomyces cerevisiae
      iMM904
      (reaction.13GS(value=0.072594), reaction.2OXOA...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.009562
      0.199305
      1.494785
      6.397013e-02
      PathwayPredictor+DifferentialFVA
    

    

      41
      Saccharomyces cerevisiae
      iMM904
      (reaction.13GS(value=0.108891), reaction.2OXOA...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.012374
      0.171935
      1.289514
      9.595523e-02
      PathwayPredictor+DifferentialFVA
    

    

      42
      Saccharomyces cerevisiae
      iMM904
      (reaction.13GS(value=0.145187), reaction.2OXOA...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.013872
      0.144566
      1.084244
      1.279406e-01
      PathwayPredictor+DifferentialFVA
    

    

      43
      Saccharomyces cerevisiae
      iMM904
      (reaction.13GS(value=0.181484), reaction.2OXOA...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.014057
      0.117197
      0.878974
      1.599255e-01
      PathwayPredictor+DifferentialFVA
    

    

      44
      Saccharomyces cerevisiae
      iMM904
      (reaction.13GS(value=0.21778), reaction.2OXOAD...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      0.012757
      0.088634
      0.664755
      1.919105e-01
      PathwayPredictor+DifferentialFVA
    

    

      45
      Saccharomyces cerevisiae
      iMM904
      ()
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      -0.000000
      -0.000000
      -0.000000
      2.878657e-01
      PathwayPredictor+DifferentialFVA
    

    

      46
      Saccharomyces cerevisiae
      iMM904
      (-reaction.ACOTAim, -reaction.ACS, -reaction.A...
      (+reaction.MNXR5340#metanetx:MNXR5340, +reacti...
      NaN
      NaN
      -0.000000
      -1.316513e-12
      PathwayPredictor+DifferentialFVA
    

    

      47
      Saccharomyces cerevisiae
      iMM904
      (-reaction.13GS, -reaction.2OXOADPtim, -reacti...
      (+reaction.MNXR4008#metanetx:MNXR4008, +reacti...
      -0.000000
      0.745631
      5.592233
      -7.750803e-11
      PathwayPredictor+DifferentialFVA
    

    

      48
      Saccharomyces cerevisiae
      iMM904
      (reaction.13GS(value=0.036303), reaction.2OXOA...
      (+reaction.MNXR4008#metanetx:MNXR4008, +reacti...
      0.015942
      0.664458
      4.983433
      3.199022e-02
      PathwayPredictor+DifferentialFVA
    

    

      49
      Saccharomyces cerevisiae
      iMM904
      (reaction.13GS(value=0.072605), reaction.2OXOA...
      (+reaction.MNXR4008#metanetx:MNXR4008, +reacti...
      0.027989
      0.583284
      4.374633
      6.398044e-02
      PathwayPredictor+DifferentialFVA
    

    

      50
      Saccharomyces cerevisiae
      iMM904
      (reaction.13GS(value=0.108908), reaction.2OXOA...
      (+reaction.MNXR4008#metanetx:MNXR4008, +reacti...
      0.036141
      0.502111
      3.765833
      9.597049e-02
      PathwayPredictor+DifferentialFVA
    

    

      51
      Saccharomyces cerevisiae
      iMM904
      (reaction.13GS(value=0.14521), reaction.2OXOAD...
      (+reaction.MNXR4008#metanetx:MNXR4008, +reacti...
      0.040398
      0.420938
      3.157035
      1.279606e-01
      PathwayPredictor+DifferentialFVA
    

    

      52
      Saccharomyces cerevisiae
      iMM904
      (reaction.13GS(value=0.181513), reaction.2OXOA...
      (+reaction.MNXR4008#metanetx:MNXR4008, +reacti...
      0.040759
      0.339765
      2.548235
      1.599507e-01
      PathwayPredictor+DifferentialFVA
    

    

      53
      Saccharomyces cerevisiae
      iMM904
      (reaction.13GS(value=0.217815), reaction.2OXOA...
      (+reaction.MNXR4008#metanetx:MNXR4008, +reacti...
      0.037226
      0.258591
      1.939434
      1.919409e-01
      PathwayPredictor+DifferentialFVA
    

    

      54
      Saccharomyces cerevisiae
      iMM904
      ()
      (+reaction.MNXR4008#metanetx:MNXR4008, +reacti...
      0.000043
      0.000199
      0.001489
      2.879114e-01
      PathwayPredictor+DifferentialFVA
    

    

      55
      Saccharomyces cerevisiae
      iMM904
      (-reaction.GLCt1, -reaction.GLNS, -reaction.GL...
      (+reaction.MNXR4008#metanetx:MNXR4008, +reacti...
      NaN
      NaN
      NaN
      NaN
      PathwayPredictor+DifferentialFVA
    

    

      56
      Saccharomyces cerevisiae
      iMM904
      ()
      (+reaction.MNXR4008#metanetx:MNXR4008, +reacti...
      0.000043
      0.000199
      0.001489
      2.879114e-01
      PathwayPredictor+DifferentialFVA

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