Mercurial > repos > bimib > cobraxy
diff COBRAxy/local/models/ENGRO2.xml @ 271:d8412f6c94be draft
Uploaded
| author | francesco_lapi |
|---|---|
| date | Mon, 10 Mar 2025 14:50:23 +0000 |
| parents | 41f35c2f0c7b |
| children |
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--- a/COBRAxy/local/models/ENGRO2.xml Mon Mar 10 14:49:39 2025 +0000 +++ b/COBRAxy/local/models/ENGRO2.xml Mon Mar 10 14:50:23 2025 +0000 @@ -400,13 +400,17 @@ <species metaid="meta_M_thymd_c" sboTerm="SBO:0000299" id="M_thymd_c" name="Thymidine" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0"/> <species metaid="meta_M_HC00576_e" sboTerm="SBO:0000299" id="M_HC00576_e" name="HC00576" compartment="C_e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0"/> <species metaid="meta_M_4abut_e" sboTerm="SBO:0000299" id="M_4abut_e" name="4abut" compartment="C_e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0"/> - <species id="M_chsterol_e" name="Cholesterol" compartment="C_e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:chemicalFormula="C27H46O"/> - <species id="M_gal_e" name="D-Galactose" compartment="C_e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:chemicalFormula="C6H12O6"/> - <species id="M_gal_c" name="D-Galactose" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:chemicalFormula="C6H12O6"/> - <species id="M_gal1p_c" name="D-galactopyranose 1-phosphate" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:chemicalFormula="C6H11O9P"/> - <species id="M_udpg_c" name="Uridine diphosphate glucose" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:chemicalFormula="C15H22N2O17P2"/> - <species id="M_g1p_c" name="Glucose 1-phosphate" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:chemicalFormula="C6H11O9P"/> - <species id="M_udpgal_c" name="Uridine diphosphategalactose" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:chemicalFormula="C6H11O9P"/> + <species id="M_chsterol_e" name="Cholesterol" compartment="C_e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C27H46O"/> + <species id="M_gal_e" name="D-Galactose" compartment="C_e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C6H12O6"/> + <species id="M_gal_c" name="D-Galactose" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C6H12O6"/> + <species id="M_gal1p_c" name="D-galactopyranose 1-phosphate" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C6H11O9P"/> + <species id="M_udpg_c" name="Uridine diphosphate glucose" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C15H22N2O17P2"/> + <species id="M_g1p_c" name="Glucose 1-phosphate" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C6H11O9P"/> + <species id="M_udpgal_c" name="Uridine diphosphategalactose" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C6H11O9P"/> + <species id="M_ac_c" name="Acetic acid" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C2H3O2"/> + <species id="M_acrn_c" name="Carnitine O-Acetyltransferase" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C9H17NO4"/> + <species id="M_acrn_m" name="Carnitine O-Acetyltransferase" compartment="C_m" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C9H17NO4"/> + <species id="M_ac_m" compartment="C_m" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0"/> </listOfSpecies> <listOfParameters> <parameter sboTerm="SBO:0000626" id="cobra_default_lb" value="-1000" constant="true"/> @@ -538,8 +542,8 @@ </reaction> <reaction metaid="meta_R_PYRt2" sboTerm="SBO:0000176" id="R_PYRt2" name="Pyruvate transport in via proton symport" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> + <speciesReference species="M_h_e" stoichiometry="1" constant="true"/> <speciesReference species="M_pyr_e" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_e" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> @@ -1391,7 +1395,7 @@ <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__117"/> </fbc:geneProductAssociation> </reaction> - <reaction metaid="meta_R_ICDHyr" sboTerm="SBO:0000176" id="R_ICDHyr" name="IDH1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <reaction metaid="meta_R_ICDHyr" sboTerm="SBO:0000176" id="R_ICDHyr" name="IDH1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> <speciesReference species="M_icit_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> @@ -2227,9 +2231,9 @@ <listOfProducts> <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> + <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4378"/> @@ -4419,9 +4423,9 @@ </reaction> <reaction metaid="meta_R_r0682" sboTerm="SBO:0000176" id="R_r0682" name="r0682" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> + <speciesReference species="M_but_2_enoyl_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_but_2_enoyl_ACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_butyryl_ACP_c" stoichiometry="1" constant="true"/> @@ -4433,13 +4437,13 @@ </reaction> <reaction metaid="meta_R_r0760" sboTerm="SBO:0000176" id="R_r0760" name="r0760" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> + <speciesReference species="M_butyryl_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_butyryl_ACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3_oxohexanoyl_ACP_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3594"/> @@ -4447,9 +4451,9 @@ </reaction> <reaction metaid="meta_R_r0761" sboTerm="SBO:0000176" id="R_r0761" name="r0761" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> + <speciesReference species="M_3_oxohexanoyl_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_3_oxohexanoyl_ACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_D_3_hydroxyhexanoyl_ACP_c" stoichiometry="1" constant="true"/> @@ -4473,9 +4477,9 @@ </reaction> <reaction metaid="meta_R_r0763" sboTerm="SBO:0000176" id="R_r0763" name="r0763" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> + <speciesReference species="M_2E_hexenoyl_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_2E_hexenoyl_ACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_hexanoyl_ACP_c" stoichiometry="1" constant="true"/> @@ -4487,13 +4491,13 @@ </reaction> <reaction metaid="meta_R_r0764" sboTerm="SBO:0000176" id="R_r0764" name="r0764" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> + <speciesReference species="M_hexanoyl_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_hexanoyl_ACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3_oxooctanoyl_ACP_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3594"/> @@ -4501,9 +4505,9 @@ </reaction> <reaction metaid="meta_R_r0694" sboTerm="SBO:0000176" id="R_r0694" name="r0694" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> + <speciesReference species="M_3_oxooctanoyl_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_3_oxooctanoyl_ACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_R_3_hydroxyoctanoyl_ACP_c" stoichiometry="1" constant="true"/> @@ -4527,13 +4531,13 @@ </reaction> <reaction metaid="meta_R_r0765" sboTerm="SBO:0000176" id="R_r0765" name="r0765" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> + <speciesReference species="M_2E_octenoyl_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_2E_octenoyl_ACP_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_octanoyl_ACP_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3594"/> @@ -4546,8 +4550,8 @@ </listOfReactants> <listOfProducts> <speciesReference species="M_3_oxodecanoyl_ACP_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3594"/> @@ -4555,9 +4559,9 @@ </reaction> <reaction metaid="meta_R_r0692" sboTerm="SBO:0000176" id="R_r0692" name="r0692" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> + <speciesReference species="M_3_oxodecanoyl_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_3_oxodecanoyl_ACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_R_3_hydroxydecanoyl_ACP_c" stoichiometry="1" constant="true"/> @@ -4581,9 +4585,9 @@ </reaction> <reaction metaid="meta_R_r0767" sboTerm="SBO:0000176" id="R_r0767" name="r0767" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> + <speciesReference species="M_2E_decenoyl_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_2E_decenoyl_ACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_decanoyl_ACP_c" stoichiometry="1" constant="true"/> @@ -4595,13 +4599,13 @@ </reaction> <reaction metaid="meta_R_r0768" sboTerm="SBO:0000176" id="R_r0768" name="r0768" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> + <speciesReference species="M_decanoyl_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_decanoyl_ACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3_oxododecanoyl_ACP_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3594"/> @@ -4609,9 +4613,9 @@ </reaction> <reaction metaid="meta_R_r0769" sboTerm="SBO:0000176" id="R_r0769" name="r0769" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> + <speciesReference species="M_3_oxododecanoyl_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_3_oxododecanoyl_ACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_D_3_hydroxydodecanoyl_ACP_c" stoichiometry="1" constant="true"/> @@ -4635,9 +4639,9 @@ </reaction> <reaction metaid="meta_R_r0712" sboTerm="SBO:0000176" id="R_r0712" name="r0712" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> + <speciesReference species="M_2E_dodecenoyl_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_2E_dodecenoyl_ACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_dodecanoyl_ACP_c" stoichiometry="1" constant="true"/> @@ -4649,13 +4653,13 @@ </reaction> <reaction metaid="meta_R_r0713" sboTerm="SBO:0000176" id="R_r0713" name="r0713" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> + <speciesReference species="M_dodecanoyl_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_dodecanoyl_ACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_3_oxotetradecanoyl_ACP_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3594"/> @@ -4663,9 +4667,9 @@ </reaction> <reaction metaid="meta_R_r0701" sboTerm="SBO:0000176" id="R_r0701" name="r0701" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> + <speciesReference species="M_3_oxotetradecanoyl_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_3_oxotetradecanoyl_ACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_HMA_c" stoichiometry="1" constant="true"/> @@ -4689,13 +4693,13 @@ </reaction> <reaction metaid="meta_R_r0771" sboTerm="SBO:0000176" id="R_r0771" name="r0771" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> + <speciesReference species="M_2E_tetradecenoyl_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_2E_tetradecenoyl_ACP_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_tetradecanoyl_ACP_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3594"/> @@ -4708,8 +4712,8 @@ </listOfReactants> <listOfProducts> <speciesReference species="M_3_oxohexadecanoyl_ACP_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3594"/> @@ -4717,9 +4721,9 @@ </reaction> <reaction metaid="meta_R_r0696" sboTerm="SBO:0000176" id="R_r0696" name="r0696" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> + <speciesReference species="M_3_oxohexadecanoyl_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_3_oxohexadecanoyl_ACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_R_3_hydroxypalmitoyl_ACP_c" stoichiometry="1" constant="true"/> @@ -4743,9 +4747,9 @@ </reaction> <reaction metaid="meta_R_r0773" sboTerm="SBO:0000176" id="R_r0773" name="r0773" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> + <speciesReference species="M_2E_hexadecenoyl_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_2E_hexadecenoyl_ACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_hexadecanoyl_ACP_c" stoichiometry="1" constant="true"/> @@ -4761,8 +4765,8 @@ <speciesReference species="M_hexadecanoyl_ACP_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> + <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> <speciesReference species="M_hdca_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> <fbc:or> @@ -4868,40 +4872,40 @@ <speciesReference species="M_arg__L_c" stoichiometry="0.35926" constant="true"/> <speciesReference species="M_asn__L_c" stoichiometry="0.279425" constant="true"/> <speciesReference species="M_asp__L_c" stoichiometry="0.352607" constant="true"/> - <speciesReference species="M_gln__L_c" stoichiometry="0.325996" constant="true"/> - <speciesReference species="M_glu__L_c" stoichiometry="0.385872" constant="true"/> - <speciesReference species="M_gly_c" stoichiometry="0.538891" constant="true"/> - <speciesReference species="M_pro__L_c" stoichiometry="0.412484" constant="true"/> - <speciesReference species="M_ser__L_c" stoichiometry="0.392525" constant="true"/> - <speciesReference species="M_met__L_c" stoichiometry="0.153018" constant="true"/> - <speciesReference species="M_thr__L_c" stoichiometry="0.31269" constant="true"/> - <speciesReference species="M_trp__L_c" stoichiometry="0.013306" constant="true"/> - <speciesReference species="M_his__L_c" stoichiometry="0.126406" constant="true"/> - <speciesReference species="M_lys__L_c" stoichiometry="0.592114" constant="true"/> - <speciesReference species="M_val__L_c" stoichiometry="0.352607" constant="true"/> - <speciesReference species="M_leu__L_c" stoichiometry="0.545544" constant="true"/> - <speciesReference species="M_ile__L_c" stoichiometry="0.286078" constant="true"/> - <speciesReference species="M_phe__L_c" stoichiometry="0.259466" constant="true"/> - <speciesReference species="M_tyr__L_c" stoichiometry="0.159671" constant="true"/> + <speciesReference species="M_atp_c" stoichiometry="20.704451" constant="true"/> + <speciesReference species="M_chsterol_c" stoichiometry="0.020401" constant="true"/> + <speciesReference species="M_ctp_c" stoichiometry="0.039036" constant="true"/> <speciesReference species="M_cys__L_c" stoichiometry="0.046571" constant="true"/> <speciesReference species="M_datp_c" stoichiometry="0.013183" constant="true"/> <speciesReference species="M_dctp_c" stoichiometry="0.009442" constant="true"/> <speciesReference species="M_dgtp_c" stoichiometry="0.009898" constant="true"/> <speciesReference species="M_dttp_c" stoichiometry="0.013091" constant="true"/> - <speciesReference 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species="M_hdca_c" stoichiometry="0.271039" constant="true"/> + <speciesReference species="M_val__L_c" stoichiometry="0.352607" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_BIOMASSA_c" stoichiometry="1" constant="true"/> <speciesReference species="M_adp_c" stoichiometry="20.650823" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="20.650823" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="20.650823" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="20.650823" constant="true"/> </listOfProducts> </reaction> <reaction metaid="meta_R_GLCt1" sboTerm="SBO:0000176" id="R_GLCt1" name="uptakeGlc" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> @@ -6856,12 +6860,12 @@ </reaction> <reaction id="R_TMDK1" name="TMDK1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> + <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_thymd_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_dtmp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> </listOfProducts> <fbc:geneProductAssociation> @@ -6924,9 +6928,9 @@ </listOfReactants> <listOfProducts> <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_glu__L_e" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - 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+6993,8 @@ </reaction> <reaction id="R_UGLT" name="UDPglucose-Hexose-1-Phosphate Uridylyltransferase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> <listOfReactants> + <speciesReference species="M_gal1p_c" stoichiometry="1" constant="true"/> <speciesReference species="M_udpg_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_gal1p_c" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="M_g1p_c" stoichiometry="1" constant="true"/> @@ -7089,6 +7093,182 @@ </fbc:and> </fbc:geneProductAssociation> </reaction> + <reaction id="R_CSNATr" name="Carnitine O-Acetyltransferase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_crn_c" stoichiometry="1" constant="true"/> + </listOfReactants> 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