{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Easy strain design using a high-level interface" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "
\n", " | InChI | \n", "SMILES | \n", "charge | \n", "formula | \n", "mass | \n", "name | \n", "source | \n", "search_rank | \n", "
---|---|---|---|---|---|---|---|---|
MNXM680 | \n", "InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)... | \n", "CN1C=NC2=C1C(=O)N(C)C(=O)N2C | \n", "0 | \n", "C8H10N4O2 | \n", "194.1906 | \n", "caffeine | \n", "chebi:27732 | \n", "0 | \n", "
\n", " | InChI | \n", "SMILES | \n", "charge | \n", "formula | \n", "mass | \n", "name | \n", "source | \n", "search_rank | \n", "
---|---|---|---|---|---|---|---|---|
MNXM680 | \n", "InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)... | \n", "CN1C=NC2=C1C(=O)N(C)C(=O)N2C | \n", "0 | \n", "C8H10N4O2 | \n", "194.1906 | \n", "caffeine | \n", "chebi:27732 | \n", "0 | \n", "
Id | \n", "Name | \n", "Formula | \n", " \n", " \n", "
---|---|---|
MNXM754 | vanillin | C8H8O3 |
\n", " \n", "
\n", " " ], "text/plain": [ "\n", " | equation | \n", "lower_bound | \n", "upper_bound | \n", "
---|---|---|---|
MNXR5340 | \n", "H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... | \n", "-1000 | \n", "1000 | \n", "
MNXR5336 | \n", "2.0 H(+) + NADH + vanillate <=> H2O + vanillin... | \n", "-1000 | \n", "1000 | \n", "
MNXR2795 | \n", "S-adenosyl-L-methionine + glycine <=> H(+) + S... | \n", "-1000 | \n", "1000 | \n", "
MNXR68718 | \n", "H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki... | \n", "-1000 | \n", "1000 | \n", "
\n", " | equation | \n", "lower_bound | \n", "upper_bound | \n", "
---|---|---|---|
MNXR5340 | \n", "H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... | \n", "-1000 | \n", "1000 | \n", "
MNXR5336 | \n", "2.0 H(+) + NADH + vanillate <=> H2O + vanillin... | \n", "-1000 | \n", "1000 | \n", "
MNXR84169 | \n", "(6R)-5,10-methylenetetrahydrofolate + glycine ... | \n", "-1000 | \n", "1000 | \n", "
MNXR68718 | \n", "H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki... | \n", "-1000 | \n", "1000 | \n", "
\n", " | equation | \n", "lower_bound | \n", "upper_bound | \n", "
---|---|---|---|
MNXR5340 | \n", "H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... | \n", "-1000 | \n", "1000 | \n", "
MNXR5336 | \n", "2.0 H(+) + NADH + vanillate <=> H2O + vanillin... | \n", "-1000 | \n", "1000 | \n", "
MNXR68718 | \n", "H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki... | \n", "-1000 | \n", "1000 | \n", "
MNXR651 | \n", "2.0 H(+) + NADH + formate <=> H2O + formaldehy... | \n", "-1000 | \n", "1000 | \n", "
\n", " | equation | \n", "lower_bound | \n", "upper_bound | \n", "
---|---|---|---|
MNXR5340 | \n", "H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... | \n", "-1000 | \n", "1000 | \n", "
MNXR5336 | \n", "2.0 H(+) + NADH + vanillate <=> H2O + vanillin... | \n", "-1000 | \n", "1000 | \n", "
MNXR230 | \n", "H(+) + 4-hydroxybenzoate + O2 + NADPH <=> H2O ... | \n", "-1000 | \n", "1000 | \n", "
MNXR640 | \n", "methanol + NAD(+) <=> H(+) + NADH + formaldehyde | \n", "-1000 | \n", "1000 | \n", "
\n", " | equation | \n", "lower_bound | \n", "upper_bound | \n", "
---|---|---|---|
MNXR5340 | \n", "H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... | \n", "-1000 | \n", "1000 | \n", "
MNXR5336 | \n", "2.0 H(+) + NADH + vanillate <=> H2O + vanillin... | \n", "-1000 | \n", "1000 | \n", "
MNXR68718 | \n", "H2O + 3,4-dihydroxybenzoate <=> 3-dehydroshiki... | \n", "-1000 | \n", "1000 | \n", "
\n", " | equation | \n", "lower_bound | \n", "upper_bound | \n", "
---|---|---|---|
MNXR5340 | \n", "H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... | \n", "-1000 | \n", "1000 | \n", "
MNXR5336 | \n", "2.0 H(+) + NADH + vanillate <=> H2O + vanillin... | \n", "-1000 | \n", "1000 | \n", "
MNXR230 | \n", "H(+) + 4-hydroxybenzoate + O2 + NADPH <=> H2O ... | \n", "-1000 | \n", "1000 | \n", "
\n", " | equation | \n", "lower_bound | \n", "upper_bound | \n", "
---|---|---|---|
MNXR4008 | \n", "H(+) + 3-oxoadipate <=> H2O + 5-oxo-4,5-dihydr... | \n", "-1000 | \n", "1000 | \n", "
MNXR184 | \n", "3-oxoadipyl-CoA + succinate <=> 3-oxoadipate +... | \n", "-1000 | \n", "1000 | \n", "
MNXR5340 | \n", "H(+) + NADH + O2 + vanillate <=> H2O + 3,4-dih... | \n", "-1000 | \n", "1000 | \n", "
MNXR5336 | \n", "2.0 H(+) + NADH + vanillate <=> H2O + vanillin... | \n", "-1000 | \n", "1000 | \n", "
MNXR228 | \n", "CO2 + 5-oxo-4,5-dihydro-2-furylacetate <=> H(+... | \n", "-1000 | \n", "1000 | \n", "
MNXR4119 | \n", "2.0 H(+) + 3-carboxy-cis,cis-muconate <=> 3,4-... | \n", "-1000 | \n", "1000 | \n", "
MNXR209 | \n", "CoA + 3-oxoadipyl-CoA <=> acetyl-CoA + succiny... | \n", "-1000 | \n", "1000 | \n", "
MNXR3655 | \n", "2-(carboxymethyl)-5-oxo-2,5-dihydro-2-furoate ... | \n", "-1000 | \n", "1000 | \n", "
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---|---|---|---|---|---|---|---|---|---|
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29 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(-reaction.13GS, -reaction.2OXOADPtim, -reacti... | \n", "(+reaction.MNXR5340#metanetx:MNXR5340, +reacti... | \n", "NaN | \n", "NaN | \n", "0.000000 | \n", "4.984455e-12 | \n", "PathwayPredictor+DifferentialFVA | \n", "
30 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(reaction.13GS(value=0.072594), reaction.2DDA7... | \n", "(+reaction.MNXR5340#metanetx:MNXR5340, +reacti... | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "PathwayPredictor+DifferentialFVA | \n", "
31 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(reaction.13GS(value=0.108891), reaction.2DDA7... | \n", "(+reaction.MNXR5340#metanetx:MNXR5340, +reacti... | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "PathwayPredictor+DifferentialFVA | \n", "
32 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(reaction.13GS(value=0.145187), reaction.2DDA7... | \n", "(+reaction.MNXR5340#metanetx:MNXR5340, +reacti... | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "PathwayPredictor+DifferentialFVA | \n", "
33 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(reaction.13GS(value=0.181484), reaction.2DDA7... | \n", "(+reaction.MNXR5340#metanetx:MNXR5340, +reacti... | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "PathwayPredictor+DifferentialFVA | \n", "
34 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(reaction.13GS(value=0.217781), reaction.2DDA7... | \n", "(+reaction.MNXR5340#metanetx:MNXR5340, +reacti... | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "PathwayPredictor+DifferentialFVA | \n", "
35 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(-reaction.SULR, -reaction.THRS, -reaction.TMD... | \n", "(+reaction.MNXR5340#metanetx:MNXR5340, +reacti... | \n", "0.000000 | \n", "-0.000000 | \n", "-0.000000 | \n", "0.000000e+00 | \n", "PathwayPredictor+DifferentialFVA | \n", "
36 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(-reaction.ENO, -reaction.ERGSTter, -reaction.... | \n", "(+reaction.MNXR5340#metanetx:MNXR5340, +reacti... | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "PathwayPredictor+DifferentialFVA | \n", "
37 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "() | \n", "(+reaction.MNXR5340#metanetx:MNXR5340, +reacti... | \n", "-0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "2.878657e-01 | \n", "PathwayPredictor+DifferentialFVA | \n", "
38 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(-reaction.13GS, -reaction.2OXOADPtim, -reacti... | \n", "(+reaction.MNXR5340#metanetx:MNXR5340, +reacti... | \n", "0.000000 | \n", "0.254043 | \n", "1.905325 | \n", "4.603305e-08 | \n", "PathwayPredictor+DifferentialFVA | \n", "
39 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(reaction.13GS(value=0.036297), reaction.2OXOA... | \n", "(+reaction.MNXR5340#metanetx:MNXR5340, +reacti... | \n", "0.005438 | \n", "0.226674 | \n", "1.700055 | \n", "3.198537e-02 | \n", "PathwayPredictor+DifferentialFVA | \n", "
40 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(reaction.13GS(value=0.072594), reaction.2OXOA... | \n", "(+reaction.MNXR5340#metanetx:MNXR5340, +reacti... | \n", "0.009562 | \n", "0.199305 | \n", "1.494785 | \n", "6.397013e-02 | \n", "PathwayPredictor+DifferentialFVA | \n", "
41 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(reaction.13GS(value=0.108891), reaction.2OXOA... | \n", "(+reaction.MNXR5340#metanetx:MNXR5340, +reacti... | \n", "0.012374 | \n", "0.171935 | \n", "1.289514 | \n", "9.595523e-02 | \n", "PathwayPredictor+DifferentialFVA | \n", "
42 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(reaction.13GS(value=0.145187), reaction.2OXOA... | \n", "(+reaction.MNXR5340#metanetx:MNXR5340, +reacti... | \n", "0.013872 | \n", "0.144566 | \n", "1.084244 | \n", "1.279406e-01 | \n", "PathwayPredictor+DifferentialFVA | \n", "
43 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(reaction.13GS(value=0.181484), reaction.2OXOA... | \n", "(+reaction.MNXR5340#metanetx:MNXR5340, +reacti... | \n", "0.014057 | \n", "0.117197 | \n", "0.878974 | \n", "1.599255e-01 | \n", "PathwayPredictor+DifferentialFVA | \n", "
44 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(reaction.13GS(value=0.21778), reaction.2OXOAD... | \n", "(+reaction.MNXR5340#metanetx:MNXR5340, +reacti... | \n", "0.012757 | \n", "0.088634 | \n", "0.664755 | \n", "1.919105e-01 | \n", "PathwayPredictor+DifferentialFVA | \n", "
45 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "() | \n", "(+reaction.MNXR5340#metanetx:MNXR5340, +reacti... | \n", "-0.000000 | \n", "-0.000000 | \n", "-0.000000 | \n", "2.878657e-01 | \n", "PathwayPredictor+DifferentialFVA | \n", "
46 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(-reaction.ACOTAim, -reaction.ACS, -reaction.A... | \n", "(+reaction.MNXR5340#metanetx:MNXR5340, +reacti... | \n", "NaN | \n", "NaN | \n", "-0.000000 | \n", "-1.316513e-12 | \n", "PathwayPredictor+DifferentialFVA | \n", "
47 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(-reaction.13GS, -reaction.2OXOADPtim, -reacti... | \n", "(+reaction.MNXR4008#metanetx:MNXR4008, +reacti... | \n", "-0.000000 | \n", "0.745631 | \n", "5.592233 | \n", "-7.750803e-11 | \n", "PathwayPredictor+DifferentialFVA | \n", "
48 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(reaction.13GS(value=0.036303), reaction.2OXOA... | \n", "(+reaction.MNXR4008#metanetx:MNXR4008, +reacti... | \n", "0.015942 | \n", "0.664458 | \n", "4.983433 | \n", "3.199022e-02 | \n", "PathwayPredictor+DifferentialFVA | \n", "
49 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(reaction.13GS(value=0.072605), reaction.2OXOA... | \n", "(+reaction.MNXR4008#metanetx:MNXR4008, +reacti... | \n", "0.027989 | \n", "0.583284 | \n", "4.374633 | \n", "6.398044e-02 | \n", "PathwayPredictor+DifferentialFVA | \n", "
50 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(reaction.13GS(value=0.108908), reaction.2OXOA... | \n", "(+reaction.MNXR4008#metanetx:MNXR4008, +reacti... | \n", "0.036141 | \n", "0.502111 | \n", "3.765833 | \n", "9.597049e-02 | \n", "PathwayPredictor+DifferentialFVA | \n", "
51 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(reaction.13GS(value=0.14521), reaction.2OXOAD... | \n", "(+reaction.MNXR4008#metanetx:MNXR4008, +reacti... | \n", "0.040398 | \n", "0.420938 | \n", "3.157035 | \n", "1.279606e-01 | \n", "PathwayPredictor+DifferentialFVA | \n", "
52 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(reaction.13GS(value=0.181513), reaction.2OXOA... | \n", "(+reaction.MNXR4008#metanetx:MNXR4008, +reacti... | \n", "0.040759 | \n", "0.339765 | \n", "2.548235 | \n", "1.599507e-01 | \n", "PathwayPredictor+DifferentialFVA | \n", "
53 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(reaction.13GS(value=0.217815), reaction.2OXOA... | \n", "(+reaction.MNXR4008#metanetx:MNXR4008, +reacti... | \n", "0.037226 | \n", "0.258591 | \n", "1.939434 | \n", "1.919409e-01 | \n", "PathwayPredictor+DifferentialFVA | \n", "
54 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "() | \n", "(+reaction.MNXR4008#metanetx:MNXR4008, +reacti... | \n", "0.000043 | \n", "0.000199 | \n", "0.001489 | \n", "2.879114e-01 | \n", "PathwayPredictor+DifferentialFVA | \n", "
55 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "(-reaction.GLCt1, -reaction.GLNS, -reaction.GL... | \n", "(+reaction.MNXR4008#metanetx:MNXR4008, +reacti... | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "PathwayPredictor+DifferentialFVA | \n", "
56 | \n", "Saccharomyces cerevisiae | \n", "iMM904 | \n", "() | \n", "(+reaction.MNXR4008#metanetx:MNXR4008, +reacti... | \n", "0.000043 | \n", "0.000199 | \n", "0.001489 | \n", "2.879114e-01 | \n", "PathwayPredictor+DifferentialFVA | \n", "