Mercurial > repos > bimib > marea_2
changeset 372:9cb6eaa3c2b8 draft
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--- a/marea_2/custom_data_generator.py Thu Sep 19 10:00:47 2024 +0000 +++ b/marea_2/custom_data_generator.py Wed Nov 06 18:02:22 2024 +0000 @@ -6,11 +6,11 @@ import pandas as pd import utils.general_utils as utils import utils.rule_parsing as rulesUtils -from typing import Optional, Tuple, Union, Dict +from typing import Optional, Tuple, Union, List, Dict import utils.reaction_parsing as reactionUtils ARGS : argparse.Namespace -def process_args() -> argparse.Namespace: +def process_args(args:List[str] = None) -> argparse.Namespace: """ Interfaces the script of a module with its frontend, making the user's choices for various parameters available as values in code. @@ -35,9 +35,8 @@ parser.add_argument("-id", "--input", type = str, required = True, help = "Input model") parser.add_argument("-mn", "--name", type = str, required = True, help = "Input model name") # ^ I need this because galaxy converts my files into .dat but I need to know what extension they were in - - argsNamespace = parser.parse_args() - argsNamespace.out_dir = "result" + parser.add_argument('-idop', '--output_path', type = str, default='result', help = 'output path for maps') + argsNamespace = parser.parse_args(args) # ^ can't get this one to work from xml, there doesn't seem to be a way to get the directory attribute from the collection return argsNamespace @@ -184,7 +183,7 @@ writer.writerow({ fieldNames[0] : key, fieldNames[1] : value }) ###############################- ENTRY POINT -################################ -def main() -> None: +def main(args:List[str] = None) -> None: """ Initializes everything and sets the program in motion based on the fronted input arguments. @@ -193,10 +192,10 @@ """ # get args from frontend (related xml) global ARGS - ARGS = process_args() + ARGS = process_args(args) # this is the worst thing I've seen so far, congrats to the former MaREA devs for suggesting this! - if os.path.isdir(ARGS.out_dir) == False: os.makedirs(ARGS.out_dir) + if os.path.isdir(ARGS.output_path) == False: os.makedirs(ARGS.output_path) # load custom model model = load_custom_model(
--- a/marea_2/local/medium/medium.csv Thu Sep 19 10:00:47 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ -engro2_name,RPMI 1640,DMEM,EMEM,DMEM:F12 = 1:1,McCoy's 5A,IMDM,MEM,GMEM,Leibovitz's L-15,F12,F10,AMEM,Waymouth MB 7521 medium,F12K,William's E Medium,Medium 199,MCDB 105,NEAA,RPMI:F12 = 1:1,RPMI:MEM = 1:1,RPMI:EMEM = 1:1,EMEM:F12 = 1:1,DMEM:RPMI = 2:1,DMEM:IMDM = 1:1,MCDB 105:Medium 199 = 1:1,allOpen -EX_Lcystin_e,0.20766774,0.20127796,0.09904154,0.09996805,0.0,0.29201278,0.09904154,0.09904154,0.0,0.0,0.0,0.09904154,0.0625,0.0,0.08329073,0.108333334,0.0,0.0,0.10383387,0.15335464,0.15335464,0.04952077,0.20340788666666665,0.24664537000000003,0.054166667,1000 -EX_ala__L_e,0.0,0.0,0.0,0.049999997,0.15617977,0.28089887,0.0,0.0,2.52809,0.099999994,0.101123594,0.28089887,0.0,0.20224719,1.011236,0.28089887,0.030337078,10.0,0.049999997,0.0,0.0,0.049999997,0.0,0.140449435,0.15561797400000002,1000 -EX_arg__L_e,1.1494253,0.39810428,0.5971564,0.69905216,0.19952606,0.39810428,0.5971564,0.19905214,2.8735633,1.0,1.0,0.49763033,0.35545024,2.0,0.28735632,0.33175355,0.29952607,0.0,1.07471265,0.8732908500000001,0.8732908500000001,0.7985782,0.64854462,0.39810428,0.31563980999999997,1000 -EX_asn__L_e,0.37878788,0.0,0.0,0.05,0.3409091,0.18939394,0.0,0.0,1.8939394,0.10006667,0.1,0.33333334,0.0,0.2,0.13333334,0.0,0.1,10.0,0.239427275,0.18939394,0.18939394,0.050033335,0.12626262666666668,0.09469697,0.05,1000 -EX_asp__L_e,0.15037593,0.0,0.0,0.05,0.15015037,0.22556391,0.0,0.0,0.0,0.1,0.09774436,0.22556391,0.45112783,0.2,0.22556391,0.22556391,0.1,10.0,0.125187965,0.075187965,0.075187965,0.05,0.05012531,0.112781955,0.162781955,1000 -EX_chsterol_e,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.00051679584,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.00025839792,1000 -EX_cys__L_e,0.0,0.0,0.0,0.09977272,0.2603306,0.0,0.0,0.0,0.9917355,0.19954544,0.20661157,0.5681818,0.5041322,0.39772728,0.3305785,0.0005681818,0.0,0.0,0.09977272,0.0,0.0,0.09977272,0.0,0.0,0.0002840909,1000 -EX_fol_e,0.0022675737,0.009070295,0.0022675737,0.0060090707,0.022675738,0.009070295,0.0022675737,0.0045351475,0.0022675737,0.0029478457,0.0029478457,0.0022675737,0.0011337869,0.0029478457,0.0022675737,2.2675737e-05,0.001171875,0.0,0.0026077097,0.0022675737,0.0022675737,0.0026077097,0.006802721233333334,0.009070295,0.0005972753685,1000 -EX_gal_e,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,5.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1000 -EX_glc__D_e,11.111111,25.0,5.5555553,17.505556,16.666666,25.0,5.5555553,25.0,0.0,10.011111,6.111111,5.5555553,27.777779,7.0,11.111111,5.5555553,5.5555553,0.0,10.561111,8.33333315,8.33333315,7.78333315,20.370370333333334,25.0,5.5555553,1000 -EX_gln__L_e,2.0547945,3.9726028,2.0,2.5,1.5013698,4.0,2.0,2.0,2.0547945,1.0,1.0,2.0,2.3972602,2.0,0.0,0.6849315,0.0,0.0,1.52739725,2.02739725,2.02739725,1.5,3.333333366666667,3.9863014000000003,0.34246575,1000 -EX_glu__L_e,0.13605443,0.0,0.0,0.05,0.15034014,0.5102041,0.0,0.0,0.0,0.1,0.1,0.5102041,1.0204082,0.19727892,0.34013605,0.5102041,0.029931974,10.0,0.118027215,0.068027215,0.068027215,0.05,0.04535147666666667,0.25510205,0.27006803700000004,1000 -EX_gly_e,0.13333334,0.4,0.0,0.25,0.1,0.4,0.0,0.0,2.6666667,0.1,0.1,0.6666667,0.6666667,0.2,0.6666667,0.6666667,0.030666666,10.0,0.11666667,0.06666667,0.06666667,0.05,0.31111111333333336,0.4,0.348666683,1000 -EX_gthrd_e,0.0032573289,0.0,0.0,0.0,0.0016286644,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.048859935,0.0,0.00016286645,0.00016286645,0.0,0.0,0.00162866445,0.00162866445,0.00162866445,0.0,0.0010857763,0.0,8.1433225e-05,1000 -EX_hdca_e,0.0,0.0,0.0,0.00014999999,0.0,0.0,0.0,0.0,0.0,0.00029999999,0.0,0.0,0.0,0.0,0.00010169491,0.0,0.0,0.0,0.000149999995,0.0,0.0,0.000149999995,0.0,0.0,0.0,1000 -EX_his__L_e,0.09677419,0.2,0.2,0.14990476,0.09980952,0.2,0.2,0.1,1.6129032,0.1,0.10952381,0.2,0.82580644,0.21809523,0.09677419,0.10419047,0.2,0.0,0.09838709500000001,0.148387095,0.148387095,0.15000000000000002,0.16559139666666667,0.2,0.152095235,1000 -EX_ile__L_e,0.3816794,0.8015267,0.39694658,0.41580153,0.300458,0.8015267,0.39694658,0.39694658,1.908397,0.030534351,0.019847328,0.4,0.1908397,0.060152672,0.3816794,0.3053435,0.5038168,0.0,0.2061068755,0.38931298999999997,0.38931298999999997,0.2137404655,0.6615776000000001,0.8015267,0.40458014999999997,1000 -EX_leu__L_e,0.3816794,0.8015267,0.39694658,0.45076334,0.300458,0.8015267,0.39694658,0.39694658,0.9541985,0.1,0.099236645,0.39694658,0.3816794,0.2,0.57251906,0.45801526,1.0,0.0,0.2408397,0.38931298999999997,0.38931298999999997,0.24847329,0.6615776000000001,0.8015267,0.72900763,1000 -EX_lys__L_e,0.2739726,0.7978142,0.3989071,0.4986339,0.19945355,0.7978142,0.3989071,0.3989071,0.51369864,0.19945355,0.15846995,0.3989071,1.3114754,0.3989071,0.47792348,0.38251367,0.9945355,0.0,0.236713075,0.33643985,0.33643985,0.299180325,0.6232003333333334,0.7978142,0.688524585,1000 -EX_met__L_e,0.10067114,0.20134228,0.10067114,0.11570469,0.099999994,0.20134228,0.10067114,0.10067114,0.5033557,0.030201342,0.030201342,0.10067114,0.33557048,0.06013423,0.10067114,0.10067114,0.10067114,0.0,0.065436241,0.10067114,0.10067114,0.065436241,0.16778523333333337,0.20134228,0.10067114,1000 -EX_phe__L_e,0.09090909,0.4,0.19393939,0.2150303,0.1,0.4,0.19393939,0.2,0.75757575,0.030303031,0.030303031,0.19393939,0.3030303,0.060121212,0.15151516,0.15151516,0.2,0.0,0.0606060605,0.14242423999999998,0.14242423999999998,0.1121212105,0.29696969666666667,0.4,0.17575758000000002,1000 -EX_pi_e,5.633803,0.91558444,1.0144928,0.9530394099999999,4.2028985,0.9057971,1.0144928,0.89855075,1.77920467,1.0,1.6926885,1.0144928,2.7001757,1.23784074,1.0144928,1.0144928,0.5,0.0,3.3169015,3.3241479000000003,3.3241479000000003,1.0072464,2.4883239600000002,0.91069077,0.7572464,1000 -EX_pro__L_e,0.17391305,0.0,0.0,0.15,0.15043478,0.3478261,0.0,0.0,0.0,0.3,0.1,0.3478261,0.4347826,0.6,0.26086956,0.3478261,0.1,10.0,0.236956525,0.086956525,0.086956525,0.15,0.05797101666666667,0.17391305,0.22391305,1000 -EX_ptrc_e,0.0,0.0,0.0,0.0005031056,0.0,0.0,0.0,0.0,0.0,0.001,0.0,0.0,0.0,0.0019875776,0.0,0.0,1.242236e-06,0.0,0.0005,0.0,0.0,0.0005,0.0,0.0,6.21118e-07,1000 -EX_pyr_e,0.0,0.0,0.0,0.5,0.0,1.0,0.0,0.0,5.0,1.0,1.0,1.0,0.0,2.0,0.22727273,0.0,1.0,0.0,0.5,0.0,0.0,0.5,0.0,0.5,0.5,1000 -EX_ser__L_e,0.2857143,0.4,0.0,0.25,0.25047618,0.4,0.0,0.0,1.9047619,0.1,0.1,0.23809524,0.0,0.2,0.0952381,0.23809524,0.30476192,10.0,0.19285714999999998,0.14285715,0.14285715,0.05,0.36190476666666666,0.4,0.27142858000000003,1000 -EX_thr__L_e,0.16806723,0.79831934,0.40336135,0.44915968,0.15042016,0.79831934,0.40336135,0.39999998,2.5210085,0.099999994,0.0302521,0.40336135,0.6302521,0.19327731,0.33613446,0.25210086,0.10084034,0.0,0.134033612,0.28571429000000004,0.28571429000000004,0.251680672,0.5882353033333333,0.79831934,0.17647059999999998,1000 -EX_thymd_e,0.0,0.0,0.0,0.0015082645,0.0,0.0,0.0,0.0,0.0,0.002892562,0.002892562,0.041322313,0.0,0.002892562,0.0,0.0,9.917356e-05,0.0,0.001446281,0.0,0.0,0.001446281,0.0,0.0,4.958678e-05,1000 -EX_trp__L_e,0.024509804,0.078431375,0.04901961,0.04421569,0.0151960775,0.078431375,0.04901961,0.039215688,0.09803922,0.01,0.0029411765,0.04901961,0.19607843,0.020098038,0.04901961,0.04901961,0.020098038,0.0,0.017254902,0.036764707,0.036764707,0.029509805,0.060457517999999995,0.078431375,0.034558824,1000 -EX_tyr__L_e,0.11111111,0.39779004,0.19923371,0.21375479,0.1,0.46222222,0.19923371,0.19923371,1.6574585,0.02980916,0.010038313,0.23111111,0.22099447,0.051526718,0.19406131,0.22222222,0.1,0.0,0.07046013500000001,0.15517241,0.15517241,0.114521435,0.3022303966666667,0.43000613,0.16111111,1000 -EX_val__L_e,0.17094018,0.8034188,0.3931624,0.4517094,0.15042736,0.8034188,0.3931624,0.4,0.85470086,0.1,0.02991453,0.3931624,0.5555556,0.1965812,0.42735043,0.21367522,1.0,0.0,0.13547009,0.28205129,0.28205129,0.2465812,0.5925925933333334,0.8034188,0.60683761,1000 -EX_o2_e,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,0.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000 -EX_h_e,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,0.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000 -EX_h2o_e,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,0.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000.0,1000
--- a/marea_2/local/models/ENGRO2.xml Thu Sep 19 10:00:47 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11558 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" metaid="meta_" sboTerm="SBO:0000624" level="3" version="1" fbc:required="false"> - <model metaid="meta_dc" id="dc" name="Empty model structure" fbc:strict="true"> - <listOfUnitDefinitions> - <unitDefinition id="mmol_per_gDW_per_hr"> - <listOfUnits> - <unit kind="mole" exponent="1" scale="-3" multiplier="1"/> - <unit kind="gram" exponent="-1" scale="0" multiplier="1"/> - <unit kind="second" exponent="-1" scale="0" multiplier="3600"/> - </listOfUnits> - </unitDefinition> - </listOfUnitDefinitions> - <listOfCompartments> - <compartment id="C_c" name="cytosol" constant="true"/> - <compartment id="C_m" name="mitochondrium" constant="true"/> - <compartment id="C_e" name="extracellular" constant="true"/> - </listOfCompartments> - <listOfSpecies> - <species metaid="meta_M_accoa_c" sboTerm="SBO:0000299" id="M_accoa_c" name="acetylCoAc" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C23H34N7O17P3S"/> - <species metaid="meta_M_accoa_m" sboTerm="SBO:0000299" id="M_accoa_m" name="acetylCoAm" compartment="C_m" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C23H34N7O17P3S"/> - <species metaid="meta_M_pyr_m" sboTerm="SBO:0000299" id="M_pyr_m" name="pyruvatem" compartment="C_m" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C3H3O3"/> - <species metaid="meta_M_pyr_c" sboTerm="SBO:0000299" id="M_pyr_c" name="pyruvatec" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C3H3O3"/> - <species metaid="meta_M_lac__L_c" sboTerm="SBO:0000299" id="M_lac__L_c" name="lactatec" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C3H5O3"/> - <species metaid="meta_M_lac__L_e" sboTerm="SBO:0000299" id="M_lac__L_e" name="lactatex" compartment="C_e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C3H5O3"/> - <species metaid="meta_M_f6p_c" sboTerm="SBO:0000299" id="M_f6p_c" name="fructose6phosphatec" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C6H11O9P"/> - <species metaid="meta_M_fdp_c" sboTerm="SBO:0000299" id="M_fdp_c" name="fructose1_6bisphosphatec" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C6H10O12P2"/> - <species metaid="meta_M_pep_c" sboTerm="SBO:0000299" id="M_pep_c" name="PEPc" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C3H2O6P"/> - <species metaid="meta_M_2pg_c" sboTerm="SBO:0000299" id="M_2pg_c" name="2phosphoDglyceratec" compartment="C_c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C3H4O7P"/> - 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<speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8889"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8888"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1093"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_PGM" sboTerm="SBO:0000176" id="R_PGM" name="PGM_1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_3pg_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_2pg_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8889"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8888"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1093"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ENO" sboTerm="SBO:0000176" id="R_ENO" name="ENO" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_2pg_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3350"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3354"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3353"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_PYK" sboTerm="SBO:0000176" id="R_PYK" name="PK" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9021"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9020"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_LDH_L" sboTerm="SBO:0000176" id="R_LDH_L" name="LDH" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_lac__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6541"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6535"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__30866"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6544"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__28335"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__21481"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_r0407" sboTerm="SBO:0000176" id="R_r0407" name="ALDO1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_HC00361_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_dhap_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_e4p_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__418"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__417"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__414"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_PRPPS" sboTerm="SBO:0000176" id="R_PRPPS" name="PRPS1" 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_r5p_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9465"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9462"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9463"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_G6PDH2r" sboTerm="SBO:0000176" id="R_G6PDH2r" name="G6PD" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_g6p_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_6pgl_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4057"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_PGL" sboTerm="SBO:0000176" id="R_PGL" name="PGLS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_6pgl_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_6pgc_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4795"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8903"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GND" sboTerm="SBO:0000176" id="R_GND" name="6PGD" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_6pgc_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ru5p__D_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8891"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_RPI" sboTerm="SBO:0000176" id="R_RPI" name="RPI" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_ru5p__D_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_r5p_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10297"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_TKT2" sboTerm="SBO:0000176" id="R_TKT2" name="TKT1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_e4p_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_xu5p__D_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11835"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__25313"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11834"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_RPE" sboTerm="SBO:0000176" id="R_RPE" name="RPE" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_ru5p__D_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_xu5p__D_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10293"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__45241"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_TKT1" sboTerm="SBO:0000176" id="R_TKT1" name="TKT" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_r5p_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_xu5p__D_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_s7p_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11835"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__25313"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11834"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_TALA" sboTerm="SBO:0000176" id="R_TALA" name="TALDO1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_g3p_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_s7p_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_e4p_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_f6p_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11559"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_r0408" sboTerm="SBO:0000176" id="R_r0408" name="SBPase" 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_s7p_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_HC00361_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> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8878"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8876"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8877"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_PDHm" sboTerm="SBO:0000176" id="R_PDHm" name="PDH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_pyr_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_accoa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2898"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__21350"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2896"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8808"/> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8806"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8807"/> - </fbc:or> - </fbc:and> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_PCm" sboTerm="SBO:0000176" id="R_PCm" name="PC" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_atp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_hco3_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_pyr_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_oaa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8636"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_PEPCK_re" sboTerm="SBO:0000176" id="R_PEPCK_re" name="PEPCK" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pep_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8724"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_CSm" sboTerm="SBO:0000176" id="R_CSm" name="CS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_accoa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_oaa_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_cit_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2422"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ACONTm" sboTerm="SBO:0000176" id="R_ACONTm" name="mACO" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_cit_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_icit_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__118"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__117"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ICDHxm" sboTerm="SBO:0000176" id="R_ICDHxm" name="IDH3" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_icit_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5386"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5385"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5384"/> - </fbc:and> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ICDHym" sboTerm="SBO:0000176" id="R_ICDHym" name="IDH2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_icit_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5383"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_AKGDm" sboTerm="SBO:0000176" id="R_AKGDm" name="AKGDH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_succoa_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2898"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8124"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2911"/> - </fbc:and> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_SUCOAS1m" sboTerm="SBO:0000176" id="R_SUCOAS1m" name="SCS" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_gdp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_succoa_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_gtp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_succ_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11449"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11450"/> - </fbc:and> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_SUCD1m" sboTerm="SBO:0000176" id="R_SUCD1m" name="SDH" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_fad_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_succ_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_fadh2_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_fum_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10680"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10681"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10682"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10683"/> - </fbc:and> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_FUMm" sboTerm="SBO:0000176" id="R_FUMm" name="FH1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_fum_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_mal__L_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3700"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_MDHm" sboTerm="SBO:0000176" id="R_MDHm" name="MDH2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_mal__L_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_oaa_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6971"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ME1m" sboTerm="SBO:0000176" id="R_ME1m" name="ME2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_mal__L_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_pyr_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6984"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ME2m" sboTerm="SBO:0000176" id="R_ME2m" name="ME3" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_mal__L_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_pyr_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6985"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ME2" sboTerm="SBO:0000176" id="R_ME2" name="ME1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6983"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ACITL" sboTerm="SBO:0000176" id="R_ACITL" name="ACLY" 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_cit_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__115"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_FUM" sboTerm="SBO:0000176" id="R_FUM" name="FH2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3700"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_MDH" sboTerm="SBO:0000176" id="R_MDH" name="MDH1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6970"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17836"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_AKGMALtm" sboTerm="SBO:0000176" id="R_AKGMALtm" name="SLC25A11" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_mal__L_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10981"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10980"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ACONT" sboTerm="SBO:0000176" id="R_ACONT" name="cACO" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_cit_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_icit_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <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"> - <listOfReactants> - <speciesReference species="M_icit_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5382"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_PPA" sboTerm="SBO:0000176" id="R_PPA" name="cPPA" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="2" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__30042"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9226"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_Complex1ROS" sboTerm="SBO:0000176" id="R_Complex1ROS" name="Complex1ROS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_h_m" stoichiometry="4.75" constant="true"/> - <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_o2_m" stoichiometry="0.05" constant="true"/> - <speciesReference species="M_q10_m" stoichiometry="0.95" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h_c" stoichiometry="3.8" constant="true"/> - <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_o2s_m" stoichiometry="0.05" constant="true"/> - <speciesReference species="M_q10h2_m" stoichiometry="0.95" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7694"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7707"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7699"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7697"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7702"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7705"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7715"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7714"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7698"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7692"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7683"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7688"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7684"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7685"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7700"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7693"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7696"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20372"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7704"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7706"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7708"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7701"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7703"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7716"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7712"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7686"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20371"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7717"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7695"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7690"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17194"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7462"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7456"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7461"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7458"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7459"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7455"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7460"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7710"/> - 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<listOfReactants> - <speciesReference species="M_ficytC_m" stoichiometry="2" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="2" constant="true"/> - <speciesReference species="M_q10h2_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_focytC_m" stoichiometry="2" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="4" constant="true"/> - <speciesReference species="M_q10_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__12585"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__30862"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__12586"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__12582"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29594"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__12587"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__12590"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2579"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__30863"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7427"/> - </fbc:and> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_CYOOm2i" sboTerm="SBO:0000176" id="R_CYOOm2i" name="Complex4" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_focytC_m" stoichiometry="4" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="8" constant="true"/> - <speciesReference species="M_o2_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_ficytC_m" stoichiometry="4" constant="true"/> - <speciesReference species="M_h2o_m" stoichiometry="2" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="4" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2292"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2269"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2285"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2267"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7421"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7419"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7422"/> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2277"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2279"/> - </fbc:or> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2288"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2287"/> - </fbc:or> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2280"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__24380"/> - </fbc:or> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__16232"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2265"/> - </fbc:or> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2291"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__24381"/> - </fbc:or> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2294"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__24382"/> - </fbc:or> - </fbc:and> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ATPS4mi" sboTerm="SBO:0000176" id="R_ATPS4mi" name="ATPsynthase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_adp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="4" constant="true"/> - <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_atp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="3" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__837"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__830"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__840"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__838"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__823"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__847"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__833"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__14247"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__845"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__846"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7414"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7415"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__848"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__850"/> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__842"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__843"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__841"/> - </fbc:or> - </fbc:and> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GLUCYS" sboTerm="SBO:0000176" id="R_GLUCYS" name="GCL" 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_cys__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_glucys_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4311"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4312"/> - </fbc:and> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GTHS" sboTerm="SBO:0000176" id="R_GTHS" name="GSS" 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_glucys_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_gthrd_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4624"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_SPODMm" sboTerm="SBO:0000176" id="R_SPODMm" name="SOD2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_h_m" stoichiometry="2" constant="true"/> - <speciesReference species="M_o2s_m" stoichiometry="2" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h2o2_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_o2_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11180"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GTHPi" sboTerm="SBO:0000176" id="R_GTHPi" name="GPcit" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_gthrd_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_gthox_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9352"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4556"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9353"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4554"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4553"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GTHPm" sboTerm="SBO:0000176" id="R_GTHPm" name="GPmit" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_gthrd_m" stoichiometry="2" constant="true"/> - <speciesReference species="M_h2o2_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_gthox_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_m" stoichiometry="2" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9354"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4556"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4553"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GDR" sboTerm="SBO:0000176" id="R_GDR" name="cGSRnadh" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_gthox_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_gthrd_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4623"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GTHOr" sboTerm="SBO:0000176" id="R_GTHOr" name="cGSRnadph" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_gthox_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_gthrd_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4623"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GDRm" sboTerm="SBO:0000176" id="R_GDRm" name="mGSRnadh" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_gthox_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_gthrd_m" stoichiometry="2" constant="true"/> - <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4623"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GTHOm" sboTerm="SBO:0000176" id="R_GTHOm" name="mGSRnadph" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_gthox_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_gthrd_m" stoichiometry="2" constant="true"/> - <speciesReference species="M_nadp_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4623"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_r0885" sboTerm="SBO:0000176" id="R_r0885" name="TrasportGSH" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_gthrd_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_gthrd_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10980"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_PYRt2m" sboTerm="SBO:0000176" id="R_PYRt2m" name="MPC" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_pyr_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__21606"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__24515"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10922"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HMR_4964" sboTerm="SBO:0000176" id="R_HMR_4964" name="SLC25A1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_cit_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_mal__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_cit_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_mal__L_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10979"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_r2420" sboTerm="SBO:0000176" id="R_r2420" name="SLC25A2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10989"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ATPtm" sboTerm="SBO:0000176" id="R_ATPtm" name="ANT" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_atp_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10991"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10990"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10992"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_FUMtm" sboTerm="SBO:0000176" id="R_FUMtm" name="SLC25A10" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_fum_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10980"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_CO2tm" sboTerm="SBO:0000176" id="R_CO2tm" name="TransportCO2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_O2tm" sboTerm="SBO:0000176" id="R_O2tm" name="TransportO2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_o2_m" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_r0801" sboTerm="SBO:0000176" id="R_r0801" name="GNT" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_gtp_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_gdp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10992"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_THD1m" sboTerm="SBO:0000176" id="R_THD1m" name="NNT" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7863"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_H2Otm" sboTerm="SBO:0000176" id="R_H2Otm" name="AQP8" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__642"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_NH4tm" sboTerm="SBO:0000176" id="R_NH4tm" name="TransportNH3" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_nh4_m" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_HCO3E" sboTerm="SBO:0000176" id="R_HCO3E" name="cCA" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_hco3_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1371"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1373"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1383"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1372"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1380"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1368"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1374"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1375"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1381"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__14914"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HCO3Em" sboTerm="SBO:0000176" id="R_HCO3Em" name="mCA" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_hco3_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1378"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1377"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GLUN" sboTerm="SBO:0000176" id="R_GLUN" name="cGLS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4331"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GLNS" sboTerm="SBO:0000176" id="R_GLNS" name="GS" 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_glu__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4341"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__21016"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GLUt2m" sboTerm="SBO:0000176" id="R_GLUt2m" name="GluCarrier" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__19954"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10988"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GLNtm_1" sboTerm="SBO:0000176" id="R_GLNtm_1" name="GlnCarrier" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_gln__L_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_GLUNm" sboTerm="SBO:0000176" id="R_GLUNm" name="mGLS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_gln__L_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nh4_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4331"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29570"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GLUPRT" sboTerm="SBO:0000176" id="R_GLUPRT" name="PPAT" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pram_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9238"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_PRAGSr" sboTerm="SBO:0000176" id="R_PRAGSr" name="GART1" 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_gly_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pram_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_gar_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4163"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GARFT" sboTerm="SBO:0000176" id="R_GARFT" name="GART2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_10fthf_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_gar_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_fgam_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4163"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_PRFGS" sboTerm="SBO:0000176" id="R_PRFGS" name="PFAS" 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_fgam_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_fpram_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8863"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_PRAIS" sboTerm="SBO:0000176" id="R_PRAIS" name="GART3" 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_fpram_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_air_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4163"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_AIRCr" sboTerm="SBO:0000176" id="R_AIRCr" name="PAICS1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_air_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_5aizc_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8587"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_PRASCSi" sboTerm="SBO:0000176" id="R_PRASCSi" name="PAICS2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_5aizc_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_25aics_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8587"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ADSL2r" sboTerm="SBO:0000176" id="R_ADSL2r" name="PAICS3" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_25aics_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_aicar_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__291"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_AICART" sboTerm="SBO:0000176" id="R_AICART" name="ATIC1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_10fthf_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_aicar_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_fprica_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__794"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_IMPC" sboTerm="SBO:0000176" id="R_IMPC" name="ATIC2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_fprica_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_imp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__794"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ADSS" sboTerm="SBO:0000176" id="R_ADSS" name="ADSS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_imp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_dcamp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__292"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20093"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ADSL1r" sboTerm="SBO:0000176" id="R_ADSL1r" name="ADSL" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_dcamp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__291"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_IMPDH2" sboTerm="SBO:0000176" id="R_IMPDH2" name="IMPDH2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_imp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_xmp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6052"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6053"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GMPS" sboTerm="SBO:0000176" id="R_GMPS" name="GMPS" 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_nh4_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_xmp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_amp_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"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GMPS2" sboTerm="SBO:0000176" id="R_GMPS2" name="GMPS2" 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_gln__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_xmp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <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"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4378"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GK1" sboTerm="SBO:0000176" id="R_GK1" name="GUK1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_gmp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4693"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_RNDR2" sboTerm="SBO:0000176" id="R_RNDR2" name="RRM2B1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_dgdp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10451"/> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17296"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10452"/> - </fbc:or> - </fbc:and> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ADK1" sboTerm="SBO:0000176" id="R_ADK1" name="cAK" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="2" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__362"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__361"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20091"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__365"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_RNDR1" sboTerm="SBO:0000176" id="R_RNDR1" name="RRM2B2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_dadp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10451"/> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17296"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10452"/> - </fbc:or> - </fbc:and> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_CBPS" sboTerm="SBO:0000176" id="R_CBPS" name="CAD1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_atp_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_hco3_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_cbp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1424"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ASPCT" sboTerm="SBO:0000176" id="R_ASPCT" name="CAD2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_cbp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_cbasp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1424"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_DHORTS" sboTerm="SBO:0000176" id="R_DHORTS" name="CAD3" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_cbasp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_dhor__S_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1424"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_DHORD9" sboTerm="SBO:0000176" id="R_DHORD9" name="DHODH" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_dhor__S_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_q10_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_orot_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_q10h2_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2867"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ORPT" sboTerm="SBO:0000176" id="R_ORPT" name="UMPS1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_orot_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_orot5p_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__12563"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_OMPDC" sboTerm="SBO:0000176" id="R_OMPDC" name="UMPS2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_orot5p_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ump_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__12563"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_UMPK" sboTerm="SBO:0000176" id="R_UMPK" name="CMPK1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ump_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18170"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_RNDR4" sboTerm="SBO:0000176" id="R_RNDR4" name="RRM2B3" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_dudp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10451"/> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17296"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10452"/> - </fbc:or> - </fbc:and> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_TMDS" sboTerm="SBO:0000176" id="R_TMDS" name="TYMS" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_dump_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_mlthf_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_dhf_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_dtmp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__12441"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_URIDK2r" sboTerm="SBO:0000176" id="R_URIDK2r" name="CMPK2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_dudp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_dump_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3061"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_NDPK2" sboTerm="SBO:0000176" id="R_NDPK2" name="NME1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_udp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_utp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7851"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20461"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20567"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7849"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7850"/> - </fbc:and> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_NDPK3" sboTerm="SBO:0000176" id="R_NDPK3" name="NME2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_cdp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7851"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20461"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20567"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7849"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7850"/> - </fbc:and> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_CTPS1" sboTerm="SBO:0000176" id="R_CTPS1" name="CTPS" 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_nh4_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_utp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ctp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2520"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2519"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_RNDR3" sboTerm="SBO:0000176" id="R_RNDR3" name="RRM2B4" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_cdp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_dcdp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10451"/> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17296"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10452"/> - </fbc:or> - </fbc:and> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GDHm" sboTerm="SBO:0000176" id="R_GDHm" name="GLUDnadh" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nh4_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4335"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4336"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GLUDym" sboTerm="SBO:0000176" id="R_GLUDym" name="GLUDnadph" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nh4_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4335"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4336"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ASPTA" sboTerm="SBO:0000176" id="R_ASPTA" name="cGOT" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_oaa_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4432"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ASPTAm" sboTerm="SBO:0000176" id="R_ASPTAm" name="mGOT" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_oaa_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_asp__L_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4433"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ASPGLUm" sboTerm="SBO:0000176" id="R_ASPGLUm" name="GLAST" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_asp__L_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10983"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10982"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ASPT" sboTerm="SBO:0000176" id="R_ASPT" name="FH3" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3700"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_CBPSam" sboTerm="SBO:0000176" id="R_CBPSam" name="CPS1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_atp_m" stoichiometry="2" constant="true"/> - <speciesReference species="M_hco3_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nh4_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_m" stoichiometry="2" constant="true"/> - <speciesReference species="M_cbp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="2" constant="true"/> - <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2323"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_OCBTm" sboTerm="SBO:0000176" id="R_OCBTm" name="OTC" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_cbp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_orn_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_citr__L_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8512"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ORNt4m" sboTerm="SBO:0000176" id="R_ORNt4m" name="ORNT" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_citr__L_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_orn_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_citr__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_orn_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10985"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__22921"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ARGSS" sboTerm="SBO:0000176" id="R_ARGSS" name="ASS1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_citr__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_argsuc_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__758"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ARGSL" sboTerm="SBO:0000176" id="R_ARGSL" name="ASL" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_argsuc_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_arg__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_fum_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__746"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ARGN" sboTerm="SBO:0000176" id="R_ARGN" name="ARG1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_arg__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_orn_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_urea_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__663"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ORNDC" sboTerm="SBO:0000176" id="R_ORNDC" name="ODC1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_orn_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ptrc_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8109"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_SPMS" sboTerm="SBO:0000176" id="R_SPMS" name="SpermidineSynthase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_ametam_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ptrc_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_5mta_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_spmd_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11296"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_SPRMS" sboTerm="SBO:0000176" id="R_SPRMS" name="SpermineSynthase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_ametam_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_spmd_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_5mta_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_sprm_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11123"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11296"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ADMDC" sboTerm="SBO:0000176" id="R_ADMDC" name="AMD1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_ametam_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__457"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_MTAP" sboTerm="SBO:0000176" id="R_MTAP" name="MTAP" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_5mta_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_5mdr1p_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ade_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7413"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ADPT" sboTerm="SBO:0000176" id="R_ADPT" name="APRT" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_ade_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_prpp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__626"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_MTRI" sboTerm="SBO:0000176" id="R_MTRI" name="MRI1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_5mdr1p_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_5mdru1p_c" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_MDRPD" sboTerm="SBO:0000176" id="R_MDRPD" name="MTRUD" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_5mdru1p_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_dkmpp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__642"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7103"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__638"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__634"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__637"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__633"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_DKMPPD" sboTerm="SBO:0000176" id="R_DKMPPD" name="dkmppDegradation" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_dkmpp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_2kmb_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_for_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_SPMDtex2" sboTerm="SBO:0000176" id="R_SPMDtex2" name="DMspermidine" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_spmd_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_spmd_e" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_SPRMti" sboTerm="SBO:0000176" id="R_SPRMti" name="DMspermine" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_sprm_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_sprm_e" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10963"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GLYAMDTRc" sboTerm="SBO:0000176" id="R_GLYAMDTRc" name="AGAT" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_arg__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_gudac_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_orn_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4175"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ARGDr" sboTerm="SBO:0000176" id="R_ARGDr" name="ARGAH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_arg__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_citr__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_r0074" sboTerm="SBO:0000176" id="R_r0074" name="ALDH18A1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="2" constant="true"/> - <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_glu5sa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__406"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GLU5SAtmc" sboTerm="SBO:0000176" id="R_GLU5SAtmc" name="TransportGLU5SA" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_glu5sa_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_glu5sa_c" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_G5SADs" sboTerm="SBO:0000176" id="R_G5SADs" name="ALDH4A1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_glu5sa_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_1pyr5c_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__406"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_PRO1x" sboTerm="SBO:0000176" id="R_PRO1x" name="P5CR2nadh" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_1pyr5c_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pro__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__30262"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_P5CR" sboTerm="SBO:0000176" id="R_P5CR" name="P5CR2nadph" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_1pyr5c_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pro__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__30262"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_PROD2" sboTerm="SBO:0000176" id="R_PROD2" name="PRODH2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pro__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_1pyr5c_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17325"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_TransportFAD" sboTerm="SBO:0000176" id="R_TransportFAD" name="TransportFAD" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_fad_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_fadh2_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_fad_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_fadh2_m" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_ASNS1" sboTerm="SBO:0000176" id="R_ASNS1" name="ASNS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_asn__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__753"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ASNN" sboTerm="SBO:0000176" id="R_ASNN" name="ASRGL1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_asn__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__16448"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20123"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_METS" sboTerm="SBO:0000176" id="R_METS" name="MTR" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_5mthf_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_hcys__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7468"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_METAT" sboTerm="SBO:0000176" id="R_METAT" name="MAT" 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_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6903"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6905"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6904"/> - </fbc:and> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HMR_3915" sboTerm="SBO:0000176" id="R_HMR_3915" name="HNMT" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_5mthf_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ahcys_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5028"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_AHCi" sboTerm="SBO:0000176" id="R_AHCi" name="AHCY" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_ahcys_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adn_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_hcys__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__642"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7103"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__638"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__634"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__637"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__633"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ADNK1" sboTerm="SBO:0000176" id="R_ADNK1" name="ADK" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_adn_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__257"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_CYSTS" sboTerm="SBO:0000176" id="R_CYSTS" name="CBS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_hcys__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_cyst__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1550"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_CYSTGL" sboTerm="SBO:0000176" id="R_CYSTGL" name="CTH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_cyst__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_2obut_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2501"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_MTHFR3" sboTerm="SBO:0000176" id="R_MTHFR3" name="MTHFR" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_mlthf_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_5mthf_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7436"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_UNK2" sboTerm="SBO:0000176" id="R_UNK2" name="MetSynthesis" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_2kmb_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_gln__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_UNK3" sboTerm="SBO:0000176" id="R_UNK3" name="TAT" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_2kmb_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_5MTHFt" sboTerm="SBO:0000176" id="R_5MTHFt" name="Dm5methylTHF" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_5mthf_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_5mthf_e" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3791"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3795"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ILETA" sboTerm="SBO:0000176" id="R_ILETA" name="cBCAT1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ile__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_3mop_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__976"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_3MOPt2im" sboTerm="SBO:0000176" id="R_3MOPt2im" name="Transport3mop" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_3mop_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_3mop_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_ILETAm" sboTerm="SBO:0000176" id="R_ILETAm" name="mBCAT1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_ile__L_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_3mop_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__977"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_LEUTA" sboTerm="SBO:0000176" id="R_LEUTA" name="cBCAT2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_leu__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_4mop_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__976"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_4MOPt2im" sboTerm="SBO:0000176" id="R_4MOPt2im" name="Transport4mop" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_4mop_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_4mop_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_LEUTAm" sboTerm="SBO:0000176" id="R_LEUTAm" name="mBCAT2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_leu__L_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_4mop_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__977"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_OIVD1m" sboTerm="SBO:0000176" id="R_OIVD1m" name="BCKD1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_4mop_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_ivcoa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__987"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2898"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2698"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__986"/> - </fbc:and> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ACOAD8m" sboTerm="SBO:0000176" id="R_ACOAD8m" name="IVD" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_fad_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_ivcoa_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_3mb2coa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_fadh2_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6186"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_MCCCrm" sboTerm="SBO:0000176" id="R_MCCCrm" name="MCC" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_3mb2coa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_atp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_hco3_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_3mgcoa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_adp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6936"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6937"/> - </fbc:and> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_MGCHrm" sboTerm="SBO:0000176" id="R_MGCHrm" name="MGCoAH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_3mgcoa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_hmgcoa_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__890"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HMGCOAtm" sboTerm="SBO:0000176" id="R_HMGCOAtm" name="TransportHMGCoA" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_hmgcoa_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_hmgcoa_c" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_VALTA" sboTerm="SBO:0000176" id="R_VALTA" name="cBCAT3" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_val__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_3mob_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__976"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_3MOBt2im" sboTerm="SBO:0000176" id="R_3MOBt2im" name="Transport3mob" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_3mob_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_3mob_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_VALTAim" sboTerm="SBO:0000176" id="R_VALTAim" name="mBCAT3" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_val__L_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_3mob_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__977"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_OIVD2m" sboTerm="SBO:0000176" id="R_OIVD2m" name="BCKD2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_3mob_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_ibcoa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__987"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2898"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2698"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__986"/> - </fbc:and> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ACOAD9m" sboTerm="SBO:0000176" id="R_ACOAD9m" name="ACOAD" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_fad_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_ibcoa_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_2mp2coa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_fadh2_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__89"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__87"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ECOAH12m" sboTerm="SBO:0000176" id="R_ECOAH12m" name="ECoAH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_2mp2coa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_3hibutcoa_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3151"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4801"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4803"/> - </fbc:and> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_3HBCOAHLm" sboTerm="SBO:0000176" id="R_3HBCOAHLm" name="HIBCH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_3hibutcoa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_3hmp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_HIBDm" sboTerm="SBO:0000176" id="R_HIBDm" name="HIBD" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_3hmp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_2mop_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4907"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_r0643" sboTerm="SBO:0000176" id="R_r0643" name="HIBADH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_2mop_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_HC00900_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="2" constant="true"/> - <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__403"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__404"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__407"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__412"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__877"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_MMSAD1m" sboTerm="SBO:0000176" id="R_MMSAD1m" name="MMAL1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_2mop_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_ppcoa_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7179"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_MMTSADm" sboTerm="SBO:0000176" id="R_MMTSADm" name="MMAL2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_2mop_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_mmcoa__R_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_PCC" sboTerm="SBO:0000176" id="R_PCC" name="PCC" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_atp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_hco3_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_ppcoa_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_mmcoa__S_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_MMALH" sboTerm="SBO:0000176" id="R_MMALH" name="MMALH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_HC00900_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_mmcoa__S_m" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_MMEm" sboTerm="SBO:0000176" id="R_MMEm" name="MCM1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_mmcoa__S_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_mmcoa__R_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__16732"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_MMMm" sboTerm="SBO:0000176" id="R_MMMm" name="MCM2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_mmcoa__R_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_succoa_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7526"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ILEtmi" sboTerm="SBO:0000176" id="R_ILEtmi" name="TransportIle" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_ile__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_ile__L_m" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_LEUt5m" sboTerm="SBO:0000176" id="R_LEUt5m" name="TransportLeu" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_leu__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_leu__L_m" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_VALt5m" sboTerm="SBO:0000176" id="R_VALt5m" name="TransportVal" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_val__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_val__L_m" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_PGCD" sboTerm="SBO:0000176" id="R_PGCD" name="PHGDH" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_3pg_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_3php_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8923"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_PSERT" sboTerm="SBO:0000176" id="R_PSERT" name="PSAT1" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_3php_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pser__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__19129"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_PSP_L" sboTerm="SBO:0000176" id="R_PSP_L" name="PSPH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pser__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9577"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GHMT2r" sboTerm="SBO:0000176" id="R_GHMT2r" name="cSHMT" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_mlthf_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10850"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_SERD_L" sboTerm="SBO:0000176" id="R_SERD_L" name="SDS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10691"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__30404"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ALATA_L" sboTerm="SBO:0000176" id="R_ALATA_L" name="GPT" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ala__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18062"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4552"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_r1435" sboTerm="SBO:0000176" id="R_r1435" name="TransportSer" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_ser__L_m" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_GLYtm" sboTerm="SBO:0000176" id="R_GLYtm" name="TransportGly" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_gly_m" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_GHMT2rm" sboTerm="SBO:0000176" id="R_GHMT2rm" name="mSHMT" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_ser__L_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_thf_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_gly_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_mlthf_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10852"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_MLTHFtm" sboTerm="SBO:0000176" id="R_MLTHFtm" name="mlthf Transport" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_mlthf_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_mlthf_m" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_r0962" sboTerm="SBO:0000176" id="R_r0962" name="Transport_folate" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_fol_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_fol_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29683"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_FORtm" sboTerm="SBO:0000176" id="R_FORtm" name="TransportFormate" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_for_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_for_c" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_r0514" sboTerm="SBO:0000176" id="R_r0514" name="DHFRL1_DHFR_5" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_fol_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_dhf_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2861"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_DHFRim" sboTerm="SBO:0000176" id="R_DHFRim" name="DHFRL1_DHFR_6" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_dhf_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_nadp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_thf_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2861"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_FTHFLmi" sboTerm="SBO:0000176" id="R_FTHFLmi" name="mMTHFD1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_atp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_for_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_thf_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_10fthf_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_adp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7432"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__21055"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_MTHFCm" sboTerm="SBO:0000176" id="R_MTHFCm" name="mMTHFD2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_10fthf_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_methf_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7434"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_MTHFDm" sboTerm="SBO:0000176" id="R_MTHFDm" name="mMTHFD3" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_methf_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_mlthf_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7434"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7432"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_FOLR2" sboTerm="SBO:0000176" id="R_FOLR2" name="cDHFR1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_fol_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_dhf_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2861"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_DHFR" sboTerm="SBO:0000176" id="R_DHFR" name="cDHFR2" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_dhf_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2861"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_FTHFLi" sboTerm="SBO:0000176" id="R_FTHFLi" name="cMTHFD1" 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_for_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_10fthf_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7432"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_FTHFDH" sboTerm="SBO:0000176" id="R_FTHFDH" name="cMTHFD2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_10fthf_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_co2_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_thf_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26777"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3978"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_MTHFC" sboTerm="SBO:0000176" id="R_MTHFC" name="cMTHFD3" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_10fthf_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_methf_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7432"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_MTHFD" sboTerm="SBO:0000176" id="R_MTHFD" name="cMTHFD4" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_methf_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_mlthf_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7432"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7436"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_MTHFD2i" sboTerm="SBO:0000176" id="R_MTHFD2i" name="cMTHFD5" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_methf_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_mlthf_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7434"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__31865"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ACACT1r" sboTerm="SBO:0000176" id="R_ACACT1r" name="cACAT" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_accoa_c" stoichiometry="2" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_aacoa_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__94"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HMGCOAS" sboTerm="SBO:0000176" id="R_HMGCOAS" name="cHMGCS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_aacoa_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_hmgcoa_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5007"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HMGCOAR" sboTerm="SBO:0000176" id="R_HMGCOAR" name="Hydroxymethylglutaryl CoA reductase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_hmgcoa_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="2" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_mev__R_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="2" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5006"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_MEVK1" sboTerm="SBO:0000176" id="R_MEVK1" name="Mevalonate kinase atp" 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_mev__R_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_5pmev_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> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7530"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_PMEVK" sboTerm="SBO:0000176" id="R_PMEVK" name="Phosphomevalonate kinase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_5pmev_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_5dpmev_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9141"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_IPDDI" sboTerm="SBO:0000176" id="R_IPDDI" name="Isopentenyl-diphosphate D-isomerase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_ipdp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_dmpp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5387"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__23487"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_DPMVD" sboTerm="SBO:0000176" id="R_DPMVD" name="Diphosphomevalonate decarboxylase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_5dpmev_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ipdp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7529"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_DMATT" sboTerm="SBO:0000176" id="R_DMATT" name="Dimethylallyltranstransferase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_dmpp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ipdp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_grdp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4249"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GRTT" sboTerm="SBO:0000176" id="R_GRTT" name="Geranyltranstransferase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_grdp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ipdp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_frdp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4249"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HMR_1465" sboTerm="SBO:0000176" id="R_HMR_1465" name="Farnesyl-Diphosphate:Farnesyl-Diphosphate Farnesyltransferase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_frdp_c" stoichiometry="2" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_HC01118_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3629"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HMR_1467" sboTerm="SBO:0000176" id="R_HMR_1467" name="Presqualene-Diphosphate Diphosphate-Lyase (Reducing, Squalene-Forming)" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_HC01118_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_sql_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3629"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_SMO" sboTerm="SBO:0000176" id="R_SMO" name="Squalene monooxygenase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_sql_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_Ssq23epx_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11279"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_LNSTLS" sboTerm="SBO:0000176" id="R_LNSTLS" name="Lanosterol synthase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_Ssq23epx_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_lanost_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6708"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HMR_1477" sboTerm="SBO:0000176" id="R_HMR_1477" name="Sterol 14Alpha-Demethylase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_lanost_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_M00939_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2649"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HMR_1478" sboTerm="SBO:0000176" id="R_HMR_1478" name="Sterol 14Alpha-Demethylase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_M00939_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_o2_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_M00937_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2649"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HMR_1479" sboTerm="SBO:0000176" id="R_HMR_1479" name="Sterol 14Alpha-Demethylase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_M00937_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_44mctr_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_for_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2649"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_C14STR" sboTerm="SBO:0000176" id="R_C14STR" name="C 14 sterol reductase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_44mctr_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_44mzym_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__6518"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11863"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HMR_1490" sboTerm="SBO:0000176" id="R_HMR_1490" name="Methylsterol Monooxygenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_44mzym_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_o2_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_M00961_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10545"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1334"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HMR_1493" sboTerm="SBO:0000176" id="R_HMR_1493" name="Methylsterol Monooxygenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_M00961_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_o2_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_M00957_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10545"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1334"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HMR_1494" sboTerm="SBO:0000176" id="R_HMR_1494" name="Methylsterol Monooxygenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_M00957_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_o2_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_4mzym_int1_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10545"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1334"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_C3STDH1" sboTerm="SBO:0000176" id="R_C3STDH1" name="C 3 sterol dehydrogenase 4 methylzymosterol" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_4mzym_int1_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_4mzym_int2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13398"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HMR_1495" sboTerm="SBO:0000176" id="R_HMR_1495" name="3Beta-Hydroxysteroid-4Alpha-Carboxylate 3-Dehydrogenase (Decarboxylating)" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_4mzym_int1_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_4mzym_int2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13398"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__19340"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HMR_1500" sboTerm="SBO:0000176" id="R_HMR_1500" name="3Beta-Hydroxysteroid 3-Dehydrogenase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_4mzym_int2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="3" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_HC02110_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5215"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HMR_1502" sboTerm="SBO:0000176" id="R_HMR_1502" name="Methylsterol Monooxygenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_HC02110_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_o2_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_M00963_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10545"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1334"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HMR_1503" sboTerm="SBO:0000176" id="R_HMR_1503" name="Methylsterol Monooxygenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_M00963_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_o2_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_M00959_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10545"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1334"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HMR_1504" sboTerm="SBO:0000176" id="R_HMR_1504" name="Methylsterol Monooxygenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_M00959_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_o2_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_M00955_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10545"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1334"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HMR_1505" sboTerm="SBO:0000176" id="R_HMR_1505" name="3Beta-Hydroxysteroid-4Alpha-Carboxylate 3-Dehydrogenase (Decarboxylating)" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_M00955_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_M01067_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - 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<speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_hco3_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_malcoa_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__85"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__84"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_FASN" sboTerm="SBO:0000176" id="R_FASN" name="FASN" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_accoa_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_acACP_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3594"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_MCAT" sboTerm="SBO:0000176" id="R_MCAT" name="MCAT" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_malcoa_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_coa_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3594"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_AcetoacetylACPsynthesis" sboTerm="SBO:0000176" id="R_AcetoacetylACPsynthesis" name="AcetoacetylACPsynthesis" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_acACP_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_malACP_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_ACP_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_HC01587_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3594"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_r0691" sboTerm="SBO:0000176" id="R_r0691" name="r0691" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_HC01587_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_R_3_hydroxybutanoyl_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"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_r0681" sboTerm="SBO:0000176" id="R_r0681" name="r0681" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_R_3_hydroxybutanoyl_ACP_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_but_2_enoyl_ACP_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3594"/> - </fbc:geneProductAssociation> - </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_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"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3594"/> - </fbc:geneProductAssociation> - 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<speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3594"/> - </fbc:geneProductAssociation> - </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_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"/> - <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3594"/> - </fbc:geneProductAssociation> - </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_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_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"/> - </fbc:geneProductAssociation> - </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"> - 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<speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3594"/> - </fbc:geneProductAssociation> - </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_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> - <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"/> - </fbc:geneProductAssociation> - 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<fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13557"/> - </fbc:and> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_r0963" sboTerm="SBO:0000176" id="R_r0963" name="ExFolate" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_0_bound"> - <listOfReactants> - <speciesReference species="M_fol_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_fol_e" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3791"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3795"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3793"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_THBPTt" sboTerm="SBO:0000176" id="R_THBPTt" name="ExTetrahydrobiopterinc" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_0_bound"> - <listOfReactants> - <speciesReference species="M_thbpt_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_thbpt_e" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_arg_L_t" sboTerm="SBO:0000176" id="R_arg_L_t" name="ExArg" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_0_bound"> - <notes> - <html xmlns="http://www.w3.org/1999/xhtml"> - <p>gpr_old: ENSG00000003989 or ENSG00000139209 or ENSG00000139514 or ENSG00000165349 or ENSG00000268104</p> - </html> - </notes> - <listOfReactants> - <speciesReference species="M_arg__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_arg__L_e" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11067"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26441"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11057"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11060"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11061"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11026"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11065"/> - </fbc:and> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11026"/> - </fbc:and> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_phe_L_t" sboTerm="SBO:0000176" id="R_phe_L_t" name="ExPhe" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_0_bound"> - <notes> - <html xmlns="http://www.w3.org/1999/xhtml"> - <p>gpr_old: ENSG00000112394 or ENSG00000149150 or ENSG00000167703</p> - </html> - </notes> - <listOfReactants> - <speciesReference species="M_phe__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_phe__L_e" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13448"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11061"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11060"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13447"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11057"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__14679"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13557"/> - </fbc:or> - </fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17027"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__23087"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9225"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11063"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11066"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26441"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ile_L_t" sboTerm="SBO:0000176" id="R_ile_L_t" name="ExIle" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_0_bound"> - <notes> - <html xmlns="http://www.w3.org/1999/xhtml"> - <p>gpr_old: ENSG00000149150 or ENSG00000167703</p> - </html> - </notes> - <listOfReactants> - <speciesReference species="M_ile__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_ile__L_e" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13557"/> - </fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9225"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__23087"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11063"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26441"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_leu_L_t" sboTerm="SBO:0000176" id="R_leu_L_t" name="ExLeu" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_0_bound"> - <notes> - <html xmlns="http://www.w3.org/1999/xhtml"> - <p>gpr_old: ENSG00000149150 or ENSG00000167703</p> - </html> - </notes> - <listOfReactants> - <speciesReference species="M_leu__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_leu__L_e" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13447"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11061"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11026"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11060"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11057"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__14679"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13557"/> - </fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9225"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__23087"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11063"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26441"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_val_L_t" sboTerm="SBO:0000176" id="R_val_L_t" name="ExVal" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_0_bound"> - <notes> - <html xmlns="http://www.w3.org/1999/xhtml"> - <p>gpr_old: ENSG00000149150 or ENSG00000167703</p> - </html> - </notes> - <listOfReactants> - <speciesReference species="M_val__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_val__L_e" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13557"/> - </fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9225"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__23087"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11063"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26441"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_met_L_t" sboTerm="SBO:0000176" id="R_met_L_t" name="ExMet" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_0_bound"> - <notes> - <html xmlns="http://www.w3.org/1999/xhtml"> - <p>gpr_old: ENSG00000149150 or ENSG00000167703</p> - </html> - </notes> - <listOfReactants> - <speciesReference species="M_met__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_met__L_e" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13447"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13448"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10969"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13557"/> - </fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9225"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__23087"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11063"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26441"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ser_L_t" sboTerm="SBO:0000176" id="R_ser_L_t" name="ExSer" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <notes> - <html xmlns="http://www.w3.org/1999/xhtml"> - <p>gpr_old: ENSG00000017483 or ENSG00000111371 or ENSG00000123643 or ENSG00000134294 or ENSG00000139209 or ENSG00000149150 or ENSG00000268104 or (ENSG00000130234 and ENSG00000174358) or (ENSG00000147003 and ENSG00000164363) or (ENSG00000147003 and ENSG00000174358)</p> - </html> - </notes> - <listOfReactants> - <speciesReference species="M_ser__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_ser__L_e" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13447"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13448"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__14679"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13557"/> - </fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18070"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11063"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18761"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9225"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26441"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_gly_t" sboTerm="SBO:0000176" id="R_gly_t" name="ExGly" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <notes> - <html xmlns="http://www.w3.org/1999/xhtml"> - <p>gpr_old: ENSG00000017483 or ENSG00000111371 or ENSG00000123643 or ENSG00000134294 or ENSG00000139209 or ENSG00000165970 or ENSG00000186335 or ENSG00000196517 or ENSG00000268104 or (ENSG00000130234 and ENSG00000174358) or (ENSG00000147003 and ENSG00000164363) or (ENSG00000147003 and ENSG00000174358)</p> - </html> - </notes> - <listOfReactants> - <speciesReference species="M_gly_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_gly_e" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11058"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11026"/> - </fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13447"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13448"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__14679"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13557"/> - </fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11056"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11056"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11063"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11051"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18070"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26441"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18762"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18761"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_asn_L_t" sboTerm="SBO:0000176" id="R_asn_L_t" name="ExAsn" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <notes> - <html xmlns="http://www.w3.org/1999/xhtml"> - <p>gpr_old: ENSG00000017483 or ENSG00000111371 or ENSG00000134294 or ENSG00000139209 or ENSG00000149150 or ENSG00000188338 or ENSG00000268104 or (ENSG00000130234 and ENSG00000174358) or (ENSG00000147003 and ENSG00000164363) or (ENSG00000147003 and ENSG00000174358)</p> - </html> - </notes> - <listOfReactants> - <speciesReference species="M_asn__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_asn__L_e" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13447"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13448"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__14679"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13557"/> - </fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18070"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18044"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11063"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__9225"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26441"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - 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<listOfProducts> - <speciesReference species="M_hdca_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4433"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10995"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1663"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10998"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GTHRDt2" sboTerm="SBO:0000176" id="R_GTHRDt2" name="ExGSH" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_0_bound"> - <listOfReactants> - <speciesReference species="M_gthrd_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_gthrd_e" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_DmLact" sboTerm="SBO:0000176" id="R_DmLact" name="DmLact" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - 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</listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10919"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10918"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_DmBiomass" sboTerm="SBO:0000176" id="R_DmBiomass" name="DmBiomass" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_BIOMASSA_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_BIOMASSA_e" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_NH4t" sboTerm="SBO:0000176" id="R_NH4t" name="ExNH3" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_nh4_e" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_PTRCtex2" sboTerm="SBO:0000176" id="R_PTRCtex2" name="DmPutrescine" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_ptrc_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_ptrc_e" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_GUDACtr2" sboTerm="SBO:0000176" id="R_GUDACtr2" name="ExGA" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_gudac_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_gudac_e" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_CE2705t" sboTerm="SBO:0000176" id="R_CE2705t" name="ExDihydrobiopterinc" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_CE2705_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_CE2705_e" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11003"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11004"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_Dm2oxobutyrate" sboTerm="SBO:0000176" id="R_Dm2oxobutyrate" name="Dm2oxobutyrate" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_2obut_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_2obut_e" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_H2Ot" sboTerm="SBO:0000176" id="R_H2Ot" name="ExH2O" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - 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<speciesReference species="M_h_e" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_CO2t" sboTerm="SBO:0000176" id="R_CO2t" name="ExCO2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_co2_e" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_DmGSSG" sboTerm="SBO:0000176" id="R_DmGSSG" name="DmGSSG" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_gthox_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_gthox_e" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_glu_L_t" sboTerm="SBO:0000176" id="R_glu_L_t" name="DmGlu" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <notes> - <html xmlns="http://www.w3.org/1999/xhtml"> - <p>gpr_old: ENSG00000188338</p> - </html> - </notes> - <listOfReactants> - <speciesReference species="M_glu__L_e" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10944"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10939"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10941"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10940"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10945"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18044"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10971"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26441"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ala_L_t" sboTerm="SBO:0000176" id="R_ala_L_t" name="ExAla" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <notes> - <html xmlns="http://www.w3.org/1999/xhtml"> - <p>gpr_old: ENSG00000003989 or ENSG00000017483 or ENSG00000111371 or ENSG00000123643 or ENSG00000134294 or ENSG00000139209 or ENSG00000139514 or ENSG00000165349 or ENSG00000180773 or ENSG00000186335 or ENSG00000188338 or ENSG00000268104 or (ENSG00000130234 and ENSG00000174358) or (ENSG00000147003 and ENSG00000164363) or (ENSG00000147003 and ENSG00000174358)</p> - </html> - </notes> - <listOfReactants> - <speciesReference species="M_ala__L_e" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_ala__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13448"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11060"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11057"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13447"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__14679"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11061"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13557"/> - </fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18070"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18044"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11063"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10942"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26441"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - 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<fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10941"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10940"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10945"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18044"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ATPM" sboTerm="SBO:0000176" id="R_ATPM" name="ATPmaintenance" 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_h2o_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_GACMTRc" sboTerm="SBO:0000176" id="R_GACMTRc" name="GAMT" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_amet_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_gudac_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_ahcys_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_creat_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4136"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_CKc_cho" sboTerm="SBO:0000176" id="R_CKc_cho" name="CK" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_creat_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pcreat_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1994"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1991"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_CRTNsyn_cho" sboTerm="SBO:0000176" id="R_CRTNsyn_cho" name="CRTNsynthase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_pcreat_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_crtn_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_CRTNtr" sboTerm="SBO:0000176" id="R_CRTNtr" name="DmCreatinine" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_crtn_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_crtn_e" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_NDPK1" sboTerm="SBO:0000176" id="R_NDPK1" name="GTPsynth" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_gdp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_gtp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7851"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20461"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20567"/> - 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<fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7850"/> - </fbc:and> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_NDPK7" sboTerm="SBO:0000176" id="R_NDPK7" name="dCTPsynth" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_dcdp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_dctp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7851"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20461"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20567"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7849"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7850"/> - </fbc:and> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_DTMPK" sboTerm="SBO:0000176" id="R_DTMPK" name="dTDPsynth" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_dtmp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_dtdp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3061"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_NDPK4" sboTerm="SBO:0000176" id="R_NDPK4" name="dTTPsynth" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_dtdp_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_dttp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7851"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20461"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__20567"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7849"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7850"/> - </fbc:and> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_his_L_t" sboTerm="SBO:0000176" id="R_his_L_t" name="ExHis" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_0_bound"> - <notes> - <html xmlns="http://www.w3.org/1999/xhtml"> - <p>gpr_old: ENSG00000139209</p> - </html> - </notes> - <listOfReactants> - <speciesReference species="M_his__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_his__L_e" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13448"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__14679"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18044"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11067"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18070"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11056"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_PTRCOX1" sboTerm="SBO:0000176" id="R_PTRCOX1" name="PTRCOX1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ptrc_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_4abutn_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__80"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__550"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__549"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ABUTD" sboTerm="SBO:0000176" id="R_ABUTD" name="ABUTD" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_4abutn_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_4abut_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> - <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__412"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_r0465_1" sboTerm="SBO:0000176" id="R_r0465_1" name="HisAbutLigase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_4abut_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_his__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_HC00576_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_amp_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__29268"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ABUTH" sboTerm="SBO:0000176" id="R_ABUTH" name="ABUTH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_HC00576_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_4abut_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_his__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__642"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7103"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__638"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__634"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__637"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__633"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GLUDC" sboTerm="SBO:0000176" id="R_GLUDC" name="GLUDC" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_4abut_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4093"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4092"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HISDr" sboTerm="SBO:0000176" id="R_HISDr" name="HISD" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_his__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_urcan_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4806"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_URCN" sboTerm="SBO:0000176" id="R_URCN" name="URCN" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_urcan_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_4izp_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__642"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7103"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__638"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__634"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__637"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__633"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_IZPN" sboTerm="SBO:0000176" id="R_IZPN" name="IZPN" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_4izp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_forglu_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__28577"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GluForTx" sboTerm="SBO:0000176" id="R_GluForTx" name="GluForTx" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_forglu_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_thf_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_5forthf_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3974"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_FTCD" sboTerm="SBO:0000176" id="R_FTCD" name="FTCD" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_5forthf_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_methf_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__3974"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_NBAHH_ir" sboTerm="SBO:0000176" id="R_NBAHH_ir" name="NBAHH" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_carn_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_ala_B_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_his__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__642"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__7103"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__638"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__634"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__637"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__633"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_r0283" sboTerm="SBO:0000176" id="R_r0283" name="HisAlaLigase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_ala_B_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_his__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_carn_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29268"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_ASP1DC" sboTerm="SBO:0000176" id="R_ASP1DC" name="ASP1DC" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_ala_B_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4092"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_lys_L_t" sboTerm="SBO:0000176" id="R_lys_L_t" name="ExLys" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_0_bound"> - <notes> - <html xmlns="http://www.w3.org/1999/xhtml"> - <p>gpr_old: ENSG00000003989 or ENSG00000139209 or ENSG00000139514 or ENSG00000165349</p> - </html> - </notes> - <listOfReactants> - <speciesReference species="M_lys__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_lys__L_e" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10969"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11057"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11060"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__14679"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11061"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11067"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_LYStm" sboTerm="SBO:0000176" id="R_LYStm" name="TransportLys" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_lys__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_lys__L_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10985"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__22921"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_SACCD3m" sboTerm="SBO:0000176" id="R_SACCD3m" name="SACCD3m" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_lys__L_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadph_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_saccrp__L_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17366"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_r0525" sboTerm="SBO:0000176" id="R_r0525" name="SACCRPOX" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_saccrp__L_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_L2aadp6sa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> - 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<listOfReactants> - <speciesReference species="M_L2aadp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_2oxoadp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17929"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_2OXOADOXm" sboTerm="SBO:0000176" id="R_2OXOADOXm" name="OXOADPOR" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_2oxoadp_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_glutcoa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2898"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8124"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__21350"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__2911"/> - </fbc:and> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_GLUTCOADHm" sboTerm="SBO:0000176" id="R_GLUTCOADHm" name="GLUTCOADHm" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_fad_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_glutcoa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_b2coa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_co2_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_fadh2_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4189"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_3HBCDm" sboTerm="SBO:0000176" id="R_3HBCDm" name="ECOAH1m" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_b2coa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_3hbcoa__R_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__23408"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HACD1m" sboTerm="SBO:0000176" id="R_HACD1m" name="HACD1m" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_3hbcoa__R_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nad_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_aacoa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_nadh_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4799"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4800"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4801"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4803"/> - </fbc:and> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HMGCOASm" sboTerm="SBO:0000176" id="R_HMGCOASm" name="mHMGCS" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_aacoa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_accoa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_coa_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_hmgcoa_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5008"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_cys_L_t" sboTerm="SBO:0000176" id="R_cys_L_t" name="ExCys" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <notes> - <html xmlns="http://www.w3.org/1999/xhtml"> - <p>gpr_old: ENSG00000167703</p> - </html> - </notes> - <listOfReactants> - <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_cys__L_e" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13448"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13557"/> - </fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__23087"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11063"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__18070"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26441"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_CYSO" sboTerm="SBO:0000176" id="R_CYSO" name="CDO1" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_cys__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_3sala_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="2" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__1795"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_3SALATAi" sboTerm="SBO:0000176" id="R_3SALATAi" name="3SALATAc" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_3sala_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_3snpyr_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4432"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_3SALAASPm" sboTerm="SBO:0000176" id="R_3SALAASPm" name="Transport3SALA" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_3sala_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_asp__L_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_3sala_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_asp__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10983"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__10982"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_3SALATAim" sboTerm="SBO:0000176" id="R_3SALATAim" name="3SALATAm" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_3sala_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_akg_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_3snpyr_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_m" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4433"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_3SPYRSP" sboTerm="SBO:0000176" id="R_3SPYRSP" name="3SPYRSTc" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_3snpyr_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_pyr_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_3SPYRSPm" sboTerm="SBO:0000176" id="R_3SPYRSPm" name="3SPYRSTm" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_3snpyr_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_h_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_pyr_m" stoichiometry="1" constant="true"/> - <speciesReference species="M_so3_m" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_HMR_3951" sboTerm="SBO:0000176" id="R_HMR_3951" name="ExSulfitec" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_so3_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_so3_e" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_ExSulfitem" sboTerm="SBO:0000176" id="R_ExSulfitem" name="ExSulfitem" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_so3_m" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_so3_e" stoichiometry="1" constant="true"/> - </listOfProducts> - </reaction> - <reaction metaid="meta_R_PHETHPTOX2" sboTerm="SBO:0000176" id="R_PHETHPTOX2" name="PHETHPTOX2" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_phe__L_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_thbpt_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_CE2705_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_tyr__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__8582"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_tyr_L_t" sboTerm="SBO:0000176" id="R_tyr_L_t" name="ExTyr" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <notes> - <html xmlns="http://www.w3.org/1999/xhtml"> - <p>gpr_old: ENSG00000112394</p> - </html> - </notes> - <listOfReactants> - <speciesReference species="M_tyr__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_tyr__L_e" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__17027"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11047"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__27960"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__13557"/> - </fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11063"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11064"/> - <fbc:and> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__26441"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__29437"/> - </fbc:and> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_TYRTA" sboTerm="SBO:0000176" id="R_TYRTA" name="TYRTA" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_akg_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_tyr__L_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_34hpp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_glu__L_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:or> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__4432"/> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__11573"/> - </fbc:or> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_34HPPOR" sboTerm="SBO:0000176" id="R_34HPPOR" name="HPPOR" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - <listOfReactants> - <speciesReference species="M_34hpp_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_o2_c" stoichiometry="1" constant="true"/> - </listOfReactants> - <listOfProducts> - <speciesReference species="M_co2_c" stoichiometry="1" constant="true"/> - <speciesReference species="M_hgentis_c" stoichiometry="1" constant="true"/> - </listOfProducts> - <fbc:geneProductAssociation> - <fbc:geneProductRef fbc:geneProduct="G_HGNC__58__5147"/> - </fbc:geneProductAssociation> - </reaction> - <reaction metaid="meta_R_HGNTOR" sboTerm="SBO:0000176" id="R_HGNTOR" name="HGNTOR" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> - 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<p>HGNC symbol: GPI</p> - <p>ENSG: ENSG00000105220</p> - <p>HGNC ID: HGNC:4458</p> - </html> - </notes> - </fbc:geneProduct> - <fbc:geneProduct fbc:id="G_HGNC__58__8877" fbc:name="G_HGNC:8877" fbc:label="G_HGNC__58__8877"> - <notes> - <html xmlns="http://www.w3.org/1999/xhtml"> - <p>HGNC symbol: PFKM</p> - <p>ENSG: ENSG00000152556</p> - <p>HGNC ID: HGNC:8877</p> - </html> - </notes> - </fbc:geneProduct> - <fbc:geneProduct fbc:id="G_HGNC__58__8876" fbc:name="G_HGNC:8876" fbc:label="G_HGNC__58__8876"> - <notes> - <html xmlns="http://www.w3.org/1999/xhtml"> - <p>HGNC symbol: PFKL</p> - <p>ENSG: ENSG00000141959</p> - <p>HGNC ID: HGNC:8876</p> - </html> - </notes> - </fbc:geneProduct> - <fbc:geneProduct fbc:id="G_HGNC__58__8878" fbc:name="G_HGNC:8878" fbc:label="G_HGNC__58__8878"> - <notes> - <html xmlns="http://www.w3.org/1999/xhtml"> - <p>HGNC symbol: PFKP</p> - <p>ENSG: ENSG00000067057</p> - <p>HGNC ID: HGNC:8878</p> - </html> - </notes> - </fbc:geneProduct> - <fbc:geneProduct fbc:id="G_HGNC__58__3606" fbc:name="G_HGNC:3606" fbc:label="G_HGNC__58__3606"> - 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y="817.547" - id="tspan547">Palm</tspan></text> - </g> - <g - id="Group 76"> - <text - id="text7967-8" - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="16px" - font-weight="bold" - letter-spacing="0em"><tspan - x="1936.13" - y="817.547" - id="tspan548">AcAcACP</tspan></text> - <text - id="text6997-5-1-8-3-7-4-7" - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em"><tspan - x="2096.1399" - y="833.15997" - id="tspan549">14 NADPH</tspan></text> - <g - id="text6997-5-1-8-3-7-7-9-3"> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em" - id="text550"><tspan - x="2022.37" - y="794.15997" - id="tspan550">14 NADP</tspan></text> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em" - id="text551"><tspan - x="2072.4199" - y="794.15997" - id="tspan551">⁺</tspan></text> - </g> - <g - id="text6997-5-1-8-3-71-5-6-17"> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em" - id="text553"><tspan - x="2178.3701" - y="794.15997" - id="tspan552">6 H</tspan><tspan - x="2201.29" - y="794.15997" - id="tspan553">O</tspan></text> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em" - id="text554"><tspan - x="2197.0601" - y="794.15997" - id="tspan554">₂</tspan></text> - </g> - <g - id="text6997-5-1-8-3-71-5-7-3-5-8"> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em" - id="text555"><tspan - x="2134.48" - y="794.15997" - id="tspan555">6 CO</tspan></text> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - 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fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em" - id="text1046"><tspan - x="2362.0601" - y="1990.16" - id="tspan1046">H</tspan></text> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em" - id="text1047"><tspan - x="2370.73" - y="1990.16" - id="tspan1047">⁺</tspan></text> - </g> - <g - id="text7967-0-3-0-02-3-6"> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="16px" - font-weight="bold" - letter-spacing="0em" - id="text1048"><tspan - x="2297.3201" - y="2027.55" - id="tspan1048">CO</tspan></text> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="16px" - font-weight="bold" - letter-spacing="0em" - id="text1049"><tspan - x="2321.3401" - y="2027.55" - id="tspan1049">₂</tspan></text> - </g> - <g - id="text7967-0-3-0-2-78-8-7"> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="16px" - font-weight="bold" - letter-spacing="0em" - id="text1050"><tspan - x="2396.3" - y="2027.55" - id="tspan1050">HCO</tspan></text> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="16px" - font-weight="bold" - letter-spacing="0em" - id="text1051"><tspan - x="2431.8701" - y="2027.55" - id="tspan1051">₃</tspan></text> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="16px" - font-weight="bold" - letter-spacing="0em" - id="text1052"><tspan - x="2437.51" - y="2027.55" - id="tspan1052">⁻</tspan></text> - </g> - <path - id="R_HCO3E" - d="m 2379.5,2022.65 h -48 m 28.12,-0.28 c 7.89,-2.16 5.88,-20.34 5.88,-20.34 m -14.5,21.25 c -7.97,2.41 -7.29,20.3 -7.29,20.3" - stroke="#000000" - stroke-width="2.1163" /> - <g - id="text7967-0-3-9-1-2-1-3-9-7"> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em" - id="text1054"><tspan - x="2332.3799" - y="2056.1599" - id="tspan1053">H</tspan><tspan - x="2345.28" - y="2056.1599" - id="tspan1054">O</tspan></text> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em" - id="text1055"><tspan - x="2341.05" - y="2056.1599" - id="tspan1055">₂</tspan></text> - </g> - <path - id="F_HCO3E" - d="m 2368.22,2005.03 c -1.78,-9.37 -1.78,-9.37 -1.78,-9.37 l -2.48,9.17 2.22,-2.22 z m 10.66,19.84 c 9.66,-3.1 9.66,-3.1 9.66,-3.1 l -9.8,-2.65 2.5,2.82 z" - stroke="#000000" - stroke-width="2.23952" /> - <text - id="text4057" - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="16px" - font-weight="bold" - letter-spacing="0em"><tspan - x="2239.1001" - y="2027.55" - id="tspan1056">ADP</tspan></text> - <text - id="text4065-4" - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em"><tspan - x="2182.8201" - y="1996.03" - id="tspan1057">Pi</tspan></text> - <g - id="text4073-2"> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em" - id="text1059"><tspan - x="2131.25" - y="1995.97" - id="tspan1058">H</tspan><tspan - x="2144.1399" - y="1995.97" - id="tspan1059">O</tspan></text> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em" - id="text1060"><tspan - x="2139.9199" - y="1995.97" - id="tspan1060">₂</tspan></text> - </g> - <text - id="text4077" - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="16px" - font-weight="bold" - letter-spacing="0em"><tspan - x="2089.0901" - y="2027.55" - id="tspan1061">ATP</tspan></text> - <path - id="R_ATPM" - d="m 2184.01,2022.45 c 7.16,-1.67 6.53,-18.98 6.53,-18.98 m -67.04,19.69 102.91,-0.4 m -20.4,-0.31 c 7.16,-1.67 6.53,-18.98 6.53,-18.98 m -63.68,-1.55 c -3.59,12.96 4.73,21.24 4.73,21.24" - stroke="#000000" - stroke-width="3.03597" /> - <path - id="F_ATPM" - d="m 2192.62,2009.17 c -1.78,-9.37 -1.78,-9.37 -1.78,-9.37 l -2.48,9.17 2.22,-2.21 z m 33.48,16.55 c 8.44,-2.95 8.44,-2.95 8.44,-2.95 l -8.63,-2.29 2.23,2.54 z m -11.48,-16.55 c -1.78,-9.37 -1.78,-9.37 -1.78,-9.37 l -2.48,9.17 2.22,-2.21 z" - stroke="#000000" - stroke-width="2.23952" /> - <g - id="text4101-5"> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em" - id="text1062"><tspan - x="2208.72" - y="1996.03" - id="tspan1062">H</tspan></text> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em" - id="text1063"><tspan - x="2217.3899" - y="1996.03" - id="tspan1063">⁺</tspan></text> - </g> - <text - id="text7967-0-3-9-8-3" - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="16px" - font-weight="bold" - letter-spacing="0em"><tspan - x="2462.1001" - y="2029.55" - id="tspan1064">PPi</tspan></text> - <text - id="text7967-0-3-2-6-5-8-4" - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em"><tspan - x="2516.1599" - y="1996.16" - id="tspan1065">Pi</tspan></text> - <text - id="text7967-0-3-9-14-7-5" - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="16px" - font-weight="bold" - letter-spacing="0em"><tspan - x="2543.4399" - y="2029.55" - id="tspan1066">Pi</tspan></text> - <g - id="text7967-0-3-7-5-5-1"> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em" - id="text1068"><tspan - x="2497.3799" - y="2051.1599" - id="tspan1067">H</tspan><tspan - x="2510.28" - y="2051.1599" - id="tspan1068">O</tspan></text> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em" - id="text1069"><tspan - x="2506.05" - y="2051.1599" - id="tspan1069">₂</tspan></text> - </g> - <path - id="R_PPA" - d="M 2529.72,2024.25 H 2496 m 17.64,-1.07 c -8.28,1.46 -6.19,13.81 -6.19,13.81 m 1.8,-13.18 c 8.37,-1.63 7.67,-13.79 7.67,-13.79" - stroke="#000000" - stroke-width="2.4681" /> - <path - id="F_PPA" - d="m 2527.61,2026.74 c 9.67,-3.1 9.67,-3.1 9.67,-3.1 l -9.8,-2.65 2.5,2.82 z m -7.66,-16.32 c -1.78,-9.37 -1.78,-9.37 -1.78,-9.37 l -2.48,9.17 2.22,-2.22 z" - stroke="#000000" - stroke-width="2.23952" /> - </g> - <g - id="Group 32"> - <text - id="text5640-6" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2034.53" - y="1290.37" - id="tspan1070">0.01 dTTP</tspan></text> - <text - id="text5562-2" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2033.84" - y="1209.63" - id="tspan1071">0.01 dATP</tspan></text> - <text - id="text5543-5" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2031.09" - y="1263.46" - id="tspan1072">0.01 dGTP</tspan></text> - <text - id="text7967-0-3-6-2-0-0" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2042.22" - y="1182.1899" - id="tspan1073">0.05 UTP</tspan></text> - <text - id="text5590-1" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2032.47" - y="1236.55" - id="tspan1074">0.01 dCTP</tspan></text> - <text - id="text7967-0-3-6-2-7-4-6" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2048.21" - y="1155.49" - id="tspan1075">0.04CTP</tspan></text> - <text - id="text7967-0-5-1-1" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2034.42" - y="1331.8199" - id="tspan1076">0.27 Palm</tspan></text> - <text - id="text7967-0-8" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2037.84" - y="1357.36" - id="tspan1077">0.20 Chol</tspan></text> - <g - id="a14389-3"> - <text - id="text6883-6" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16px" - letter-spacing="0em"><tspan - x="2041.97" - y="1394.83" - id="tspan1078">0.28 G6P</tspan></text> - </g> - <g - id="a14389-3-9"> - <text - id="text6883-6-8" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16px" - letter-spacing="0em"><tspan - x="2031" - y="1419.7" - id="tspan1079">20.65 H20</tspan></text> - <text - id="text6883-6-8-0" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16px" - letter-spacing="0em"><tspan - x="2032.34" - y="1443.1899" - id="tspan1080">20.70 ATP</tspan></text> - </g> - <text - id="text4694-5" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2043.4" - y="1128.58" - id="tspan1081">0.04 GTP</tspan></text> - <text - id="text5640-6-2" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2448.8" - y="1177.9" - id="tspan1082">0.36 Arg</tspan></text> - <text - id="text5562-2-6" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2448.1001" - y="1248.71" - id="tspan1083">0.05 Cys</tspan></text> - <text - id="text5543-5-4" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2448.1001" - y="1319.61" - id="tspan1084">0.39 Glu</tspan></text> - <text - id="text7967-0-3-6-2-0-0-7" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2448.8" - y="1224.96" - id="tspan1085">0.35 Asp</tspan></text> - <text - id="text5590-1-2" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2448.1001" - y="1296.08" - id="tspan1086">0.33 Gln</tspan></text> - <text - id="text7967-0-3-6-2-7-4-6-0" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2448.8" - y="1201.4301" - id="tspan1087">0.28 Asn</tspan></text> - <text - id="text7967-0-5-1-1-1" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2097.46" - y="1489.5699" - id="tspan1088">0.29 Ile</tspan></text> - <text - id="text7967-0-8-1" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2096.72" - y="1466.76" - id="tspan1089">0.12 His</tspan></text> - <text - id="text6883-6-0" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2448.1001" - y="1272.55" - id="tspan1090">0.54 Gly</tspan></text> - <text - id="text5640-6-2-3" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2172.45" - y="1546.84" - id="tspan1091">0.59Lys</tspan></text> - <text - id="text7967-0-3-6-2-0-0-7-5" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2447.4299" - y="1342.62" - id="tspan1092">0.41 Pro</tspan></text> - <text - id="text7967-0-3-6-2-0-0-7-5-7" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2389.76" - y="1489.92" - id="tspan1093">0.26 Phe</tspan></text> - <text - id="text7967-0-3-6-2-7-4-6-0-8" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2389.77" - y="1471.21" - id="tspan1094">0.15 Met</tspan></text> - <text - id="text4694-5-1-8" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2097.05" - y="1508.79" - id="tspan1095">0.55 Leu</tspan></text> - <text - id="text5640-6-2-3-7" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2326.96" - y="1547.46" - id="tspan1096">0.01 Trp</tspan></text> - <text - id="text7967-0-3-6-2-0-0-7-5-4" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2391.01" - y="1510.1" - id="tspan1097">0.31Thr</tspan></text> - <text - id="text7967-0-3-6-2-7-4-6-0-8-0" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2449.01" - 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y="794.15997" - id="tspan555">6 CO</tspan></text> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em" - id="text556"><tspan - x="2162.51" - y="794.15997" - id="tspan556">₂</tspan></text> - </g> - <text - id="text7967-5-3" - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em"><tspan - x="2033.48" - y="833.15997" - id="tspan557">6 MalACP</tspan></text> - <text - id="text6997-5-1-8-3-71-5-6-1-4" - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em"><tspan - x="2088.48" - y="794.15997" - id="tspan558">7 ACP</tspan></text> - <path - id="F_FA160ACPH" - d="M 2194.58,804.595 C 2193.12,799 2193.12,799 2193.12,799 l -1.12,5.65 1.25,-1.433 z m -43.12,-0.5 C 2150,798.5 2150,798.5 2150,798.5 l -1.12,5.649 1.25,-1.432 z m -43.96,-0.878 c -1.46,-5.595 -1.46,-5.595 -1.46,-5.595 l -1.12,5.649 1.25,-1.433 z m -52.5,0 c -1.46,-5.595 -1.46,-5.595 -1.46,-5.595 l -1.12,5.649 1.25,-1.433 z m 145.46,10.961 c 5.83,-1.962 5.83,-1.962 5.83,-1.962 l -5.96,-1.524 1.54,1.688 z" - 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y="1236.55" - id="tspan1074">0.01 dCTP</tspan></text> - <text - id="text7967-0-3-6-2-7-4-6" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2048.21" - y="1155.49" - id="tspan1075">0.04CTP</tspan></text> - <text - id="text7967-0-5-1-1" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2034.42" - y="1331.8199" - id="tspan1076">0.27 Palm</tspan></text> - <text - id="text7967-0-8" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2037.84" - y="1357.36" - id="tspan1077">0.20 Chol</tspan></text> - <g - id="a14389-3"> - <text - id="text6883-6" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16px" - letter-spacing="0em"><tspan - x="2041.97" - y="1394.83" - id="tspan1078">0.28 G6P</tspan></text> - </g> - <g - id="a14389-3-9"> - <text - id="text6883-6-8" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16px" - letter-spacing="0em"><tspan - x="2031" - y="1419.7" - id="tspan1079">20.65 H20</tspan></text> - <text - id="text6883-6-8-0" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16px" - letter-spacing="0em"><tspan - x="2032.34" - y="1443.1899" - id="tspan1080">20.70 ATP</tspan></text> - </g> - <text - id="text4694-5" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2043.4" - y="1128.58" - id="tspan1081">0.04 GTP</tspan></text> - <text - id="text5640-6-2" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2448.8" - y="1177.9" - id="tspan1082">0.36 Arg</tspan></text> - <text - id="text5562-2-6" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2448.1001" - y="1248.71" - id="tspan1083">0.05 Cys</tspan></text> - <text - id="text5543-5-4" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2448.1001" - y="1319.61" - id="tspan1084">0.39 Glu</tspan></text> - <text - id="text7967-0-3-6-2-0-0-7" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2448.8" - y="1224.96" - id="tspan1085">0.35 Asp</tspan></text> - <text - id="text5590-1-2" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2448.1001" - y="1296.08" - id="tspan1086">0.33 Gln</tspan></text> - <text - id="text7967-0-3-6-2-7-4-6-0" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2448.8" - y="1201.4301" - id="tspan1087">0.28 Asn</tspan></text> - <text - id="text7967-0-5-1-1-1" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2097.46" - y="1489.5699" - id="tspan1088">0.29 Ile</tspan></text> - <text - id="text7967-0-8-1" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2096.72" - y="1466.76" - id="tspan1089">0.12 His</tspan></text> - <text - id="text6883-6-0" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2448.1001" - y="1272.55" - id="tspan1090">0.54 Gly</tspan></text> - <text - id="text5640-6-2-3" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2172.45" - y="1546.84" - id="tspan1091">0.59Lys</tspan></text> - <text - id="text7967-0-3-6-2-0-0-7-5" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2447.4299" - y="1342.62" - id="tspan1092">0.41 Pro</tspan></text> - <text - id="text7967-0-3-6-2-0-0-7-5-7" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2389.76" - y="1489.92" - id="tspan1093">0.26 Phe</tspan></text> - <text - id="text7967-0-3-6-2-7-4-6-0-8" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2389.77" - y="1471.21" - id="tspan1094">0.15 Met</tspan></text> - <text - id="text4694-5-1-8" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2097.05" - y="1508.79" - id="tspan1095">0.55 Leu</tspan></text> - <text - id="text5640-6-2-3-7" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2326.96" - y="1547.46" - id="tspan1096">0.01 Trp</tspan></text> - <text - id="text7967-0-3-6-2-0-0-7-5-4" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2391.01" - y="1510.1" - id="tspan1097">0.31Thr</tspan></text> - <text - id="text7967-0-3-6-2-7-4-6-0-8-0" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2449.01" - y="1389.6801" - id="tspan1098">0.16 Tyr</tspan></text> - <text - id="text7967-0-3-6-2-7-4-6-0-8-0-4" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2252.9199" - y="1548.21" - id="tspan1099">0.35Val</tspan></text> - <text - id="text4694-5-1-8-1" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2447.95" - y="1366.36" - id="tspan1100">0.39 Ser</tspan></text> - <text - id="text4694-5-1" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16.1333px" - letter-spacing="0em"><tspan - x="2448.8" - y="1154.9" - id="tspan1101">0.51 Ala</tspan></text> - <text - id="text11603-4-6" - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="20px" - font-weight="bold" - letter-spacing="0em"><tspan - x="2232.73" - y="1058.27" - id="tspan1102">Biomass</tspan></text> - <text - id="text11603-4-6-6" - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16px" - letter-spacing="0em"><tspan - x="2390.53" - y="1080.3101" - id="tspan1103">20.65 Pi</tspan></text> - <text - id="text11603-4-6-6-0" - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16px" - letter-spacing="0em"><tspan - x="2098.0601" - y="1099.96" - id="tspan1104">20.65ADP</tspan></text> - <text - id="text11603-4-6-6-8" - fill="#2b0000" - xml:space="preserve" - style="white-space:pre" - font-family="Inter" - font-size="16px" - letter-spacing="0em"><tspan - x="2391.05" - y="1109.83" - id="tspan1105">20.65 H</tspan></text> - <path - d="m 2197.91,1437.75 v -316.97 m -77.68,318.12 h 77.26 m -77.26,-21.95 h 77.26 m -77.26,-25.96 h 77.26 m -77.26,-37.96 h 77.26 m -76.89,-24.33 h 77.25 m -77.25,-43.95 h 77.25 m -77.25,-25.96 h 77.25 m -77.25,-27.96 h 77.25 m -77.25,-27.95 h 77.25 m -77.25,-27.96 h 77.25 m -77.25,-25.95 h 77.25 m -77.25,-29.41 h 77.25 m 167.19,265.81 v -239.38 m 1.79,237.09 h 77.25 m -79.07,-20.78 h 77.26 m -77.26,-23.96 h 77.26 m -77.26,-23.95 h 77.26 m -77.26,-23.96 h 77.26 m -77.26,-23.95 h 77.26 m -77.26,-23.96 h 77.26 m -77.26,-23.96 h 77.26 m -77.26,-23.95 h 77.26 m -77.26,-23.96 h 77.26 m -77.26,-23.95 h 77.26 m -240.93,91.85 h 162.63 m -57.04,245.8 h -60.45 m 86.11,34.74 H 2218.1 m 27.59,-16.32 v -39.56 m 62.83,41.38 v -39.57 m -140.29,38.11 h 77.26 m -77.72,-17.87 h 77.26 m -76.8,-21.69 h 77.26 m 63.29,40.88 h 77.26 m -77.71,-19.87 h 77.26 m -76.81,-19.69 h 77.26 m -168.08,68.36 v -14.96 m 59.71,15.86 v -14.96 m 54.45,13.46 v -14.96 M 2278.47,1075.5 V 1484 m 73.21,-375.43 v -32.75 m 0.16,0.71 h 25.49 m -186.71,20.44 h 162.64 m -2.15,11.35 h 28.94" - 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id="text1114"><tspan - x="695.50201" - y="854.15997" - id="tspan1114">₂</tspan></text> - </g> - <text - id="text7967-0-3-65-1-2-4-9-6-3-3-1-6-3_2" - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em"><tspan - x="719.492" - y="854.15997" - id="tspan1115">GDP</tspan></text> - <g - id="F_PEPCK_re"> - <path - d="m 677.5,868.5 6,-4 1.5,4.5 -0.5,-9 z" - stroke="#000000" - stroke-width="2.23952" - id="path1115" /> - <path - d="m 725.5,868.5 5.5,-4 3,6.5 -2,-10.5 z" - stroke="#000000" - stroke-width="2.23952" - id="path1116" /> - <path - d="m 287,877 -3.5,3.5 2.5,3 -11.5,-3 z" - stroke="#000000" - stroke-width="2.23952" - id="path1117" /> - </g> - <path - id="R_PEPCK_re" - d="m 1101,847 v -8.5 H 832.5 V 880 c 0,0 -81.06,0 -133,0 m -416,0 h 416 m 31,-16.651 C 727.5,880 738,880 738,880 m 48,0 c 12.5,0 12.5,-16.651 12.5,-16.651 M 699.5,880 C 678,880 683,863.349 683,863.349" - stroke="#000000" - stroke-width="2.22" /> - </g> - <g - id="Group 68"> - <path - id="R_ACONT" - d="m 1357.62,919.994 c -16.83,-0.009 -37.12,-10e-4 -37.12,-10e-4" - stroke="#000000" - stroke-width="2.43338" /> - <path - id="B_ACONT" - d="m 1355.21,923.238 c 9.62,-3.228 9.62,-3.228 9.62,-3.228 l -9.83,-2.521 2.54,2.786 z" - stroke="#000000" - stroke-width="2.66667" /> - <path - id="F_ACONT" - d="m 1324.66,917.489 -9.66,3.101 9.8,2.65 -2.5,-2.819 z" - stroke="#000000" - stroke-width="2.66667" /> - </g> - <g - id="Group 67"> - <text - id="text7967-0-3-65-1-3-2-82-8-9-6" - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="16px" - font-weight="bold" - letter-spacing="0em"><tspan - x="1145.21" - y="927.547" - id="tspan1117">AKG</tspan></text> - <text - id="text7967-0-3-9-2" - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="16px" - font-weight="bold" - letter-spacing="0em"><tspan - x="1283.4301" - y="926.547" - id="tspan1118">Iso</tspan></text> - <text - id="text7967-0-3-2-6-9" - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em"><tspan - x="1213.49" - y="897.15997" - id="tspan1119">NADPH</tspan></text> - <g - id="text7967-0-3-2-6-9_2"> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em" - id="text1120"><tspan - x="1195.0601" - y="904.15997" - id="tspan1120">H</tspan></text> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em" - id="text1121"><tspan - x="1203.73" - y="904.15997" - id="tspan1121">⁺</tspan></text> - </g> - <g - id="text7967-0-3-7-5-8"> - <text - fill="#000000" - xml:space="preserve" - style="white-space:pre" - font-family="Arial" - font-size="12px" - letter-spacing="0em" - id="text1122"><tspan - x="1236.22" - y="946.15997" - id="tspan1122">NADP</tspan></text> - <text - 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--- a/marea_2/marea.py Thu Sep 19 10:00:47 2024 +0000 +++ b/marea_2/marea.py Wed Nov 06 18:02:22 2024 +0000 @@ -15,11 +15,12 @@ import argparse import pyvips from typing import Tuple, Union, Optional, List, Dict +import copy ERRORS = [] ########################## argparse ########################################## ARGS :argparse.Namespace -def process_args() -> argparse.Namespace: +def process_args(args:List[str] = None) -> argparse.Namespace: """ Interfaces the script of a module with its frontend, making the user's choices for various parameters available as values in code. @@ -146,11 +147,17 @@ help='custom map to use') parser.add_argument( + '-idop', '--output_path', + type = str, + default='result', + help = 'output path for maps') + + parser.add_argument( '-mc', '--choice_map', type = utils.Model, default = utils.Model.HMRcore, choices = [utils.Model.HMRcore, utils.Model.ENGRO2, utils.Model.Custom]) - args :argparse.Namespace = parser.parse_args() + args :argparse.Namespace = parser.parse_args(args) if args.using_RAS and not args.using_RPS: args.net = False return args @@ -650,7 +657,7 @@ # all output files: I don't care, this was never the performance bottleneck of the tool and # there is no other net gain in saving and re-using the built string. ext, - prefix = "result") + prefix = ARGS.output_path) FIELD_NOT_AVAILABLE = '/' def writeToCsv(rows: List[list], fieldNames :List[str], outPath :utils.FilePath) -> None: @@ -761,7 +768,7 @@ return tmp, max_z_score -def computeEnrichment(metabMap :ET.ElementTree, class_pat :Dict[str, List[List[float]]], ids :List[str], *, fromRAS = True) -> None: +def computeEnrichment(metabMap: ET.ElementTree, class_pat: Dict[str, List[List[float]]], ids: List[str], *, fromRAS=True) -> List[Tuple[str, str, dict, float]]: """ Compares clustered data based on a given comparison mode and applies enrichment-based styling on the provided metabolic map. @@ -773,58 +780,52 @@ fromRAS : whether the data to enrich consists of RAS scores. Returns: - None - + List[Tuple[str, str, dict, float]]: List of tuples with pairs of dataset names, comparison dictionary, and max z-score. + Raises: sys.exit : if there are less than 2 classes for comparison Side effects: - metabMap : mut - ids : mut + metabMap : mutates based on calculated enrichment """ - class_pat = { k.strip() : v for k, v in class_pat.items() } - #TODO: simplfy this stuff vvv and stop using sys.exit (raise the correct utils error) - if (not class_pat) or (len(class_pat.keys()) < 2): sys.exit('Execution aborted: classes provided for comparisons are less than two\n') + class_pat = {k.strip(): v for k, v in class_pat.items()} + if (not class_pat) or (len(class_pat.keys()) < 2): + sys.exit('Execution aborted: classes provided for comparisons are less than two\n') + + enrichment_results = [] if ARGS.comparison == "manyvsmany": for i, j in it.combinations(class_pat.keys(), 2): - #TODO: these 2 functions are always called in pair and in this order and need common data, - # some clever refactoring would be appreciated. comparisonDict, max_z_score = compareDatasetPair(class_pat.get(i), class_pat.get(j), ids) - temp_thingsInCommon(comparisonDict, metabMap, max_z_score, i, j, fromRAS) + enrichment_results.append((i, j, comparisonDict, max_z_score)) elif ARGS.comparison == "onevsrest": for single_cluster in class_pat.keys(): - t :List[List[List[float]]] = [] - for k in class_pat.keys(): - if k != single_cluster: - t.append(class_pat.get(k)) - - rest :List[List[float]] = [] - for i in t: - rest = rest + i - + rest = [item for k, v in class_pat.items() if k != single_cluster for item in v] comparisonDict, max_z_score = compareDatasetPair(class_pat.get(single_cluster), rest, ids) - temp_thingsInCommon(comparisonDict, metabMap, max_z_score, single_cluster, fromRAS) + enrichment_results.append((single_cluster, "rest", comparisonDict, max_z_score)) elif ARGS.comparison == "onevsmany": controlItems = class_pat.get(ARGS.control) for otherDataset in class_pat.keys(): - if otherDataset == ARGS.control: continue - + if otherDataset == ARGS.control: + continue comparisonDict, max_z_score = compareDatasetPair(controlItems, class_pat.get(otherDataset), ids) - temp_thingsInCommon(comparisonDict, metabMap, max_z_score, ARGS.control, otherDataset, fromRAS) + enrichment_results.append((ARGS.control, otherDataset, comparisonDict, max_z_score)) + + return enrichment_results -def createOutputMaps(dataset1Name :str, dataset2Name :str, core_map :ET.ElementTree) -> None: - svgFilePath = buildOutputPath(dataset1Name, dataset2Name, details = "SVG Map", ext = utils.FileFormat.SVG) +def createOutputMaps(dataset1Name: str, dataset2Name: str, core_map: ET.ElementTree) -> None: + svgFilePath = buildOutputPath(dataset1Name, dataset2Name, details="SVG Map", ext=utils.FileFormat.SVG) utils.writeSvg(svgFilePath, core_map) if ARGS.generate_pdf: - pngPath = buildOutputPath(dataset1Name, dataset2Name, details = "PNG Map", ext = utils.FileFormat.PNG) - pdfPath = buildOutputPath(dataset1Name, dataset2Name, details = "PDF Map", ext = utils.FileFormat.PDF) - convert_to_pdf(svgFilePath, pngPath, pdfPath) + pngPath = buildOutputPath(dataset1Name, dataset2Name, details="PNG Map", ext=utils.FileFormat.PNG) + pdfPath = buildOutputPath(dataset1Name, dataset2Name, details="PDF Map", ext=utils.FileFormat.PDF) + convert_to_pdf(svgFilePath, pngPath, pdfPath) - if not ARGS.generate_svg: os.remove(svgFilePath.show()) + if not ARGS.generate_svg: + os.remove(svgFilePath.show()) ClassPat = Dict[str, List[List[float]]] def getClassesAndIdsFromDatasets(datasetsPaths :List[str], datasetPath :str, classPath :str, names :List[str]) -> Tuple[List[str], ClassPat]: @@ -870,7 +871,7 @@ return { id : list(map(utils.Float("Dataset values, not an argument"), values)) for id, values in dataset.items() }, IDs ############################ MAIN ############################################# -def main() -> None: +def main(args:List[str] = None) -> None: """ Initializes everything and sets the program in motion based on the fronted input arguments. @@ -880,46 +881,33 @@ Raises: sys.exit : if a user-provided custom map is in the wrong format (ET.XMLSyntaxError, ET.XMLSchemaParseError) """ - global ARGS - ARGS = process_args() + ARGS = process_args(args) - if os.path.isdir('result') == False: os.makedirs('result') + if not os.path.isdir(ARGS.output_path): + os.makedirs(ARGS.output_path) - core_map :ET.ElementTree = ARGS.choice_map.getMap( + core_map: ET.ElementTree = ARGS.choice_map.getMap( ARGS.tool_dir, utils.FilePath.fromStrPath(ARGS.custom_map) if ARGS.custom_map else None) - # TODO: ^^^ ugly but fine for now, the argument is None if the model isn't custom because no file was given. - # getMap will None-check the customPath and panic when the model IS custom but there's no file (good). A cleaner - # solution can be derived from my comment in FilePath.fromStrPath - + if ARGS.using_RAS: ids, class_pat = getClassesAndIdsFromDatasets(ARGS.input_datas, ARGS.input_data, ARGS.input_class, ARGS.names) - computeEnrichment(core_map, class_pat, ids) + enrichment_results = computeEnrichment(core_map, class_pat, ids) + for i, j, comparisonDict, max_z_score in enrichment_results: + map_copy = copy.deepcopy(core_map) + temp_thingsInCommon(comparisonDict, map_copy, max_z_score, i, j, ras_enrichment=True) + createOutputMaps(i, j, map_copy) if ARGS.using_RPS: ids, class_pat = getClassesAndIdsFromDatasets(ARGS.input_datas_rps, ARGS.input_data_rps, ARGS.input_class_rps, ARGS.names_rps) - computeEnrichment(core_map, class_pat, ids, fromRAS = False) - - # create output files: TODO: this is the same comparison happening in "maps", find a better way to organize this - if ARGS.comparison == "manyvsmany": - for i, j in it.combinations(class_pat.keys(), 2): createOutputMaps(i, j, core_map) - return - - if ARGS.comparison == "onevsrest": - for single_cluster in class_pat.keys(): createOutputMaps(single_cluster, "rest", core_map) - return - - for otherDataset in class_pat.keys(): - if otherDataset != ARGS.control: createOutputMaps(i, j, core_map) + enrichment_results = computeEnrichment(core_map, class_pat, ids, fromRAS=False) + for i, j, comparisonDict, max_z_score in enrichment_results: + map_copy = copy.deepcopy(core_map) + temp_thingsInCommon(comparisonDict, map_copy, max_z_score, i, j, ras_enrichment=False) + createOutputMaps(i, j, map_copy) - if not ERRORS: return - utils.logWarning( - f"The following reaction IDs were mentioned in the dataset but weren't found in the map: {ERRORS}", - ARGS.out_log) - - print('Execution succeded') - + print('Execution succeeded') ############################################################################### if __name__ == "__main__": main() \ No newline at end of file
--- a/marea_2/marea.xml Thu Sep 19 10:00:47 2024 +0000 +++ b/marea_2/marea.xml Wed Nov 06 18:02:22 2024 +0000 @@ -307,11 +307,11 @@ .. class:: infomark -**TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_. +**TIP**: If your dataset is not split into classes, use MaREA cluster analysis. .. class:: infomark -**TIP**: This tool using the RAS scores computed by `Ras tool`_. +**TIP**: This tool using the RAS scores computed by Ras generator tool. @REFERENCE@
--- a/marea_2/marea_cluster.py Thu Sep 19 10:00:47 2024 +0000 +++ b/marea_2/marea_cluster.py Wed Nov 06 18:02:22 2024 +0000 @@ -20,7 +20,7 @@ from typing import Optional, Dict, List ################################# process args ############################### -def process_args(args :List[str]) -> argparse.Namespace: +def process_args(args :List[str] = None) -> argparse.Namespace: """ Processes command-line arguments. @@ -86,9 +86,13 @@ type = str, help = 'output of best cluster tsv') - + parser.add_argument( + '-idop', '--output_path', + type = str, + default='result', + help = 'output path for maps') - args = parser.parse_args() + args = parser.parse_args(args) return args ########################### warning ########################################### @@ -217,8 +221,8 @@ Returns: None """ - if not os.path.exists('clustering'): - os.makedirs('clustering') + if not os.path.exists(args.output_path): + os.makedirs(args.output_path) if elbow == 'true': @@ -259,7 +263,7 @@ if (i + k_min == best): prefix = '_BEST' - write_to_csv(dataset, all_labels[i], 'clustering/kmeans_with_' + str(i + k_min) + prefix + '_clusters.tsv') + write_to_csv(dataset, all_labels[i], f'{args.output_path}/kmeans_with_' + str(i + k_min) + prefix + '_clusters.tsv') if (prefix == '_BEST'): @@ -272,7 +276,7 @@ if silhouette: - silhouette_draw(dataset, all_labels[i], i + k_min, 'clustering/silhouette_with_' + str(i + k_min) + prefix + '_clusters.png') + silhouette_draw(dataset, all_labels[i], i + k_min, f'{args.output_path}/silhouette_with_' + str(i + k_min) + prefix + '_clusters.png') if elbow: @@ -303,7 +307,7 @@ plt.plot(x, distortions, marker = 'o') plt.xlabel('Number of clusters (k)') plt.ylabel('Distortion') - s = 'clustering/elbow_plot.png' + s = f'{args.output_path}/elbow_plot.png' fig = plt.gcf() fig.set_size_inches(18.5, 10.5, forward = True) fig.savefig(s, dpi=100) @@ -406,8 +410,8 @@ Returns: None """ - if not os.path.exists('clustering'): - os.makedirs('clustering') + if not os.path.exists(args.output_path): + os.makedirs(args.output_path) if eps is not None: clusterer = DBSCAN(eps = eps, min_samples = min_samples) @@ -445,14 +449,14 @@ Returns: None """ - if not os.path.exists('clustering'): - os.makedirs('clustering') + if not os.path.exists(args.output_path): + os.makedirs(args.output_path) plt.figure(figsize=(10, 7)) plt.title("Customer Dendograms") shc.dendrogram(shc.linkage(dataset, method='ward'), labels=dataset.index.values.tolist()) fig = plt.gcf() - fig.savefig('clustering/dendogram.png', dpi=200) + fig.savefig(f'{args.output_path}/dendogram.png', dpi=200) range_n_clusters = [i for i in range(k_min, k_max+1)] @@ -466,7 +470,7 @@ cluster.fit_predict(dataset) cluster_labels = cluster.labels_ labels.append(cluster_labels) - write_to_csv(dataset, cluster_labels, 'clustering/hierarchical_with_' + str(n_clusters) + '_clusters.tsv') + write_to_csv(dataset, cluster_labels, f'{args.output_path}/hierarchical_with_' + str(n_clusters) + '_clusters.tsv') best = max_index(scores) + k_min @@ -475,7 +479,7 @@ if (i + k_min == best): prefix = '_BEST' if silhouette == 'true': - silhouette_draw(dataset, labels[i], i + k_min, 'clustering/silhouette_with_' + str(i + k_min) + prefix + '_clusters.png') + silhouette_draw(dataset, labels[i], i + k_min, f'{args.output_path}/silhouette_with_' + str(i + k_min) + prefix + '_clusters.png') for i in range(len(labels)): if (i + k_min == best): @@ -486,17 +490,18 @@ ############################# main ########################################### -def main() -> None: +def main(args_in:List[str] = None) -> None: """ Initializes everything and sets the program in motion based on the fronted input arguments. Returns: None """ - if not os.path.exists('clustering'): - os.makedirs('clustering') + global args + args = process_args(args_in) - args = process_args(sys.argv) + if not os.path.exists(args.output_path): + os.makedirs(args.output_path) #Data read
--- a/marea_2/marea_macros.xml Thu Sep 19 10:00:47 2024 +0000 +++ b/marea_2/marea_macros.xml Wed Nov 06 18:02:22 2024 +0000 @@ -140,7 +140,56 @@ url = {https://doi.org/10.1016/j.csbj.2020.04.008}, } </citation> + <citation type="bibtex"> + @article{ebrahim2013cobrapy, + title={COBRApy: constraints-based reconstruction and analysis for python}, + author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R}, + journal={BMC systems biology}, + volume={7}, + pages={1--6}, + year={2013}, + publisher={Springer} + } + </citation> </citations> </xml> + <xml name="citations_fluxes"> + <citations> + <citation type="bibtex"> + @article{galuzzi2024adjusting, + title={Adjusting for false discoveries in constraint-based differential metabolic flux analysis}, + author={Galuzzi, Bruno G and Milazzo, Luca and Damiani, Chiara}, + journal={Journal of Biomedical Informatics}, + volume={150}, + pages={104597}, + year={2024}, + publisher={Elsevier} + } + </citation> + <citation type="bibtex"> + @inproceedings{galuzzi2022best, + title={Best practices in flux sampling of constrained-based models}, + author={Galuzzi, Bruno G and Milazzo, Luca and Damiani, Chiara}, + booktitle={International Conference on Machine Learning, Optimization, and Data Science}, + pages={234--248}, + year={2022}, + organization={Springer} + } + </citation> + <citation type="bibtex"> + @article{ebrahim2013cobrapy, + title={COBRApy: constraints-based reconstruction and analysis for python}, + author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R}, + journal={BMC systems biology}, + volume={7}, + pages={1--6}, + year={2013}, + publisher={Springer} + } + </citation> + </citations> + </xml> + + </macros>
--- a/marea_2/ras_generator.py Thu Sep 19 10:00:47 2024 +0000 +++ b/marea_2/ras_generator.py Wed Nov 06 18:02:22 2024 +0000 @@ -12,7 +12,7 @@ ERRORS = [] ########################## argparse ########################################## ARGS :argparse.Namespace -def process_args() -> argparse.Namespace: +def process_args(args:List[str] = None) -> argparse.Namespace: """ Processes command-line arguments. @@ -61,8 +61,9 @@ '-ra', '--ras_output', type = str, required = True, help = 'ras output') + - return parser.parse_args() + return parser.parse_args(args) ############################ dataset input #################################### def read_dataset(data :str, name :str) -> pd.DataFrame: @@ -231,7 +232,9 @@ elif args.rules_selector == 'ENGRO2': gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/ENGRO2_genes.p', 'rb')) - + print(f"{args.tool_dir}'/local/pickle files/ENGRO2_genes.p'") + utils.logWarning(f"{args.tool_dir}'/local/pickle files/ENGRO2_genes.p'", ARGS.out_log) + print(args.rules_selector) gene_in_rule = gene_in_rule.get(type_gene) else: @@ -645,7 +648,7 @@ # csv rules need to be parsed, those in a pickle format are taken to be pre-parsed. return { line[0] : ruleUtils.parseRuleToNestedList(line[1]) for line in utils.readCsv(datFilePath) } -def main() -> None: +def main(args:List[str] = None) -> None: """ Initializes everything and sets the program in motion based on the fronted input arguments. @@ -654,8 +657,8 @@ """ # get args from frontend (related xml) global ARGS - ARGS = process_args() - + ARGS = process_args(args) + print(ARGS.rules_selector) # read dataset dataset = read_dataset(ARGS.input, "dataset") dataset.iloc[:, 0] = (dataset.iloc[:, 0]).astype(str)
--- a/marea_2/ras_generator.xml Thu Sep 19 10:00:47 2024 +0000 +++ b/marea_2/ras_generator.xml Wed Nov 06 18:02:22 2024 +0000 @@ -32,13 +32,13 @@ </when> </conditional> <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="Gene Expression dataset:" /> - <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" /> + <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset_RAS" help="Default: Dataset_RAS. Do not use white spaces." /> <param name="none" argument="--none" type="boolean" checked="true" label="(A and NaN) solved as (A)?" /> </inputs> <outputs> <data format="txt" name="log" label="Expression2RAS - $name - Log" /> - <data format="tabular" name="ras_output" label="$name RAS"/> + <data format="tabular" name="ras_output" label='$name'/> </outputs> <help>
--- a/marea_2/rps_generator.py Thu Sep 19 10:00:47 2024 +0000 +++ b/marea_2/rps_generator.py Wed Nov 06 18:02:22 2024 +0000 @@ -16,7 +16,7 @@ ########################## argparse ########################################## ARGS :argparse.Namespace -def process_args() -> argparse.Namespace: +def process_args(args:List[str] = None) -> argparse.Namespace: """ Processes command-line arguments. @@ -51,7 +51,7 @@ required = True, help = 'rps output') - args = parser.parse_args() + args = parser.parse_args(args) return args ############################ dataset name ##################################### @@ -222,7 +222,7 @@ df.to_csv(ARGS.rps_output, sep = '\t', na_rep = "None", index = False) ############################ main #################################### -def main() -> None: +def main(args:List[str] = None) -> None: """ Initializes everything and sets the program in motion based on the fronted input arguments. @@ -230,7 +230,7 @@ None """ global ARGS - ARGS = process_args() + ARGS = process_args(args) # TODO:use utils functions vvv with open(ARGS.tool_dir + '/local/pickle files/black_list.pickle', 'rb') as bl:
--- a/marea_2/rps_generator.xml Thu Sep 19 10:00:47 2024 +0000 +++ b/marea_2/rps_generator.xml Wed Nov 06 18:02:22 2024 +0000 @@ -24,7 +24,7 @@ </command> <inputs> <param name="input" argument="--input" type="data" format="tabular, tsv, csv" label="Abundance dataset:" /> - <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" /> + <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset_RPS" help="Default: Dataset_RPS. Do not use white spaces." /> <conditional name="cond_reactions"> <param name="reaction_choice" argument="--reaction_choice" type="select" label="Choose reaction dataset:"> @@ -39,7 +39,7 @@ <outputs> <data format="txt" name="log" label="Expression2RPS - $name - Log" /> - <data format="tabular" name="rps_output" label="$name RPS"/> + <data format="tabular" name="rps_output" label="$name"/> </outputs> <help>
--- a/marea_2/testing.py Thu Sep 19 10:00:47 2024 +0000 +++ b/marea_2/testing.py Wed Nov 06 18:02:22 2024 +0000 @@ -1,4 +1,4 @@ -# This is a general-purpose "testing utilities" module for the MaREA tool. +# This is a general-purpose "testing utilities" module for the COBRAxy tool. # This code was written entirely by m.ferrari133@campus.unimib.it and then (hopefully) many # more people contributed by writing tests for this tool's modules, feel free to send an email for # any questions. @@ -495,8 +495,8 @@ # ^^^ Manually applied an extra newline of space. ## Unit testing all the modules: -def unit_marea() -> None: - import marea as m +def unit_cobraxy() -> None: + import cobraxy as m import math import lxml.etree as ET import utils.general_utils as utils @@ -521,7 +521,7 @@ [math.nan, math.nan, math.nan, math.nan, math.nan, math.nan, math.nan]] } - unitTester = UnitTester("marea", LogMode.Pedantic, False, + unitTester = UnitTester("cobraxy", LogMode.Pedantic, False, UnitTest(m.name_dataset, ["customName", 12], ExactValue("customName")), UnitTest(m.name_dataset, ["Dataset", 12], ExactValue("Dataset_12")), @@ -800,7 +800,7 @@ ).testModule() if __name__ == "__main__": - unit_marea() + unit_cobraxy() unit_custom_data_generator() unit_utils() unit_ras_generator() \ No newline at end of file
--- a/marea_2/utils/custom_data_generator.py Thu Sep 19 10:00:47 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,218 +0,0 @@ -import os -import csv -import cobra -import pickle -import argparse -import pandas as pd -import utils.general_utils as utils -import utils.rule_parsing as rulesUtils -from typing import Optional, Tuple, Union, Dict -import utils.reaction_parsing as reactionUtils - -ARGS : argparse.Namespace -def process_args() -> argparse.Namespace: - """ - Interfaces the script of a module with its frontend, making the user's choices for - various parameters available as values in code. - - Args: - args : Always obtained (in file) from sys.argv - - Returns: - Namespace : An object containing the parsed arguments - """ - parser = argparse.ArgumentParser( - usage = "%(prog)s [options]", - description = "generate custom data from a given model") - - parser.add_argument("-ol", "--out_log", type = str, required = True, help = "Output log") - - parser.add_argument("-orules", "--out_rules", type = str, required = True, help = "Output rules") - parser.add_argument("-orxns", "--out_reactions", type = str, required = True, help = "Output reactions") - parser.add_argument("-omedium", "--out_medium", type = str, required = True, help = "Output medium") - parser.add_argument("-obnds", "--out_bounds", type = str, required = True, help = "Output bounds") - - parser.add_argument("-id", "--input", type = str, required = True, help = "Input model") - parser.add_argument("-mn", "--name", type = str, required = True, help = "Input model name") - # ^ I need this because galaxy converts my files into .dat but I need to know what extension they were in - - argsNamespace = parser.parse_args() - argsNamespace.out_dir = "result" - # ^ can't get this one to work from xml, there doesn't seem to be a way to get the directory attribute from the collection - - return argsNamespace - -################################- INPUT DATA LOADING -################################ -def load_custom_model(file_path :utils.FilePath, ext :Optional[utils.FileFormat] = None) -> cobra.Model: - """ - Loads a custom model from a file, either in JSON or XML format. - - Args: - file_path : The path to the file containing the custom model. - ext : explicit file extension. Necessary for standard use in galaxy because of its weird behaviour. - - Raises: - DataErr : if the file is in an invalid format or cannot be opened for whatever reason. - - Returns: - cobra.Model : the model, if successfully opened. - """ - ext = ext if ext else file_path.ext - try: - if ext is utils.FileFormat.XML: - return cobra.io.read_sbml_model(file_path.show()) - - if ext is utils.FileFormat.JSON: - return cobra.io.load_json_model(file_path.show()) - - except Exception as e: raise utils.DataErr(file_path, e.__str__()) - raise utils.DataErr(file_path, - f"Formato \"{file_path.ext}\" non riconosciuto, sono supportati solo file JSON e XML") - -################################- DATA GENERATION -################################ -ReactionId = str -def generate_rules(model: cobra.Model, *, asParsed = True) -> Union[Dict[ReactionId, rulesUtils.OpList], Dict[ReactionId, str]]: - """ - Generates a dictionary mapping reaction ids to rules from the model. - - Args: - model : the model to derive data from. - asParsed : if True parses the rules to an optimized runtime format, otherwise leaves them as strings. - - Returns: - Dict[ReactionId, rulesUtils.OpList] : the generated dictionary of parsed rules. - Dict[ReactionId, str] : the generated dictionary of raw rules. - """ - # Is the below approach convoluted? yes - # Ok but is it inefficient? probably - # Ok but at least I don't have to repeat the check at every rule (I'm clinically insane) - _ruleGetter = lambda reaction : reaction.gene_reaction_rule - ruleExtractor = (lambda reaction : - rulesUtils.parseRuleToNestedList(_ruleGetter(reaction))) if asParsed else _ruleGetter - - return { - reaction.id : ruleExtractor(reaction) - for reaction in model.reactions - if reaction.gene_reaction_rule } - -def generate_reactions(model :cobra.Model, *, asParsed = True) -> Dict[ReactionId, str]: - """ - Generates a dictionary mapping reaction ids to reaction formulas from the model. - - Args: - model : the model to derive data from. - asParsed : if True parses the reactions to an optimized runtime format, otherwise leaves them as they are. - - Returns: - Dict[ReactionId, str] : the generated dictionary. - """ - - unparsedReactions = { - reaction.id : reaction.reaction - for reaction in model.reactions - if reaction.reaction - } - - if not asParsed: return unparsedReactions - - return reactionUtils.create_reaction_dict(unparsedReactions) - -def get_medium(model:cobra.Model) -> pd.DataFrame: - trueMedium=[] - for r in model.reactions: - positiveCoeff=0 - for m in r.metabolites: - if r.get_coefficient(m.id)>0: - positiveCoeff=1; - if (positiveCoeff==0 and r.lower_bound<0): - trueMedium.append(r.id) - - df_medium = pd.DataFrame() - df_medium["reaction"] = trueMedium - return df_medium - -def generate_bounds(model:cobra.Model) -> pd.DataFrame: - - rxns = [] - for reaction in model.reactions: - rxns.append(reaction.id) - - bounds = pd.DataFrame(columns = ["lower_bound", "upper_bound"], index=rxns) - - for reaction in model.reactions: - bounds.loc[reaction.id] = [reaction.lower_bound, reaction.upper_bound] - return bounds - - -###############################- FILE SAVING -################################ -def save_as_csv_filePath(data :dict, file_path :utils.FilePath, fieldNames :Tuple[str, str]) -> None: - """ - Saves any dictionary-shaped data in a .csv file created at the given file_path as FilePath. - - Args: - data : the data to be written to the file. - file_path : the path to the .csv file. - fieldNames : the names of the fields (columns) in the .csv file. - - Returns: - None - """ - with open(file_path.show(), 'w', newline='') as csvfile: - writer = csv.DictWriter(csvfile, fieldnames = fieldNames, dialect="excel-tab") - writer.writeheader() - - for key, value in data.items(): - writer.writerow({ fieldNames[0] : key, fieldNames[1] : value }) - -def save_as_csv(data :dict, file_path :str, fieldNames :Tuple[str, str]) -> None: - """ - Saves any dictionary-shaped data in a .csv file created at the given file_path as string. - - Args: - data : the data to be written to the file. - file_path : the path to the .csv file. - fieldNames : the names of the fields (columns) in the .csv file. - - Returns: - None - """ - with open(file_path, 'w', newline='') as csvfile: - writer = csv.DictWriter(csvfile, fieldnames = fieldNames, dialect="excel-tab") - writer.writeheader() - - for key, value in data.items(): - writer.writerow({ fieldNames[0] : key, fieldNames[1] : value }) - -###############################- ENTRY POINT -################################ -def main() -> None: - """ - Initializes everything and sets the program in motion based on the fronted input arguments. - - Returns: - None - """ - # get args from frontend (related xml) - global ARGS - ARGS = process_args() - - # this is the worst thing I've seen so far, congrats to the former MaREA devs for suggesting this! - if os.path.isdir(ARGS.out_dir) == False: os.makedirs(ARGS.out_dir) - - # load custom model - model = load_custom_model( - utils.FilePath.fromStrPath(ARGS.input), utils.FilePath.fromStrPath(ARGS.name).ext) - - # generate data - rules = generate_rules(model, asParsed = False) - reactions = generate_reactions(model, asParsed = False) - bounds = generate_bounds(model) - medium = get_medium(model) - - # save files out of collection: path coming from xml - save_as_csv(rules, ARGS.out_rules, ("ReactionID", "Rule")) - save_as_csv(reactions, ARGS.out_reactions, ("ReactionID", "Reaction")) - bounds.to_csv(ARGS.out_bounds, sep = '\t') - medium.to_csv(ARGS.out_medium, sep = '\t') - -if __name__ == '__main__': - main() \ No newline at end of file
--- a/marea_2/utils/general_utils.py Thu Sep 19 10:00:47 2024 +0000 +++ b/marea_2/utils/general_utils.py Wed Nov 06 18:02:22 2024 +0000 @@ -10,7 +10,6 @@ from typing import Any, Callable, Dict, Generic, List, Optional, TypeVar, Union import pandas as pd -import cobra # FILES class FileFormat(Enum): @@ -516,9 +515,7 @@ Recon = "Recon" ENGRO2 = "ENGRO2" - ENGRO2_no_legend = "ENGRO2_no_legend" HMRcore = "HMRcore" - HMRcore_no_legend = "HMRcore_no_legend" Custom = "Custom" # Exists as a valid variant in the UI, but doesn't point to valid file paths. def __raiseMissingPathErr(self, path :Optional[FilePath]) -> None: @@ -550,24 +547,5 @@ path = customPath if self is Model.Custom else FilePath(f"{self.name}_map", FileFormat.SVG, prefix = f"{toolDir}/local/svg metabolic maps/") self.__raiseMissingPathErr(path) return readSvg(path, customErr = DataErr(path, f"custom map in wrong format")) - - def getCOBRAmodel(self, toolDir = ".", customPath :Optional[FilePath] = None, customExtension :Optional[FilePath]=None)->cobra.Model: - if(self is Model.Custom): - return self.load_custom_model(customPath, customExtension) - else: - return cobra.io.read_sbml_model(FilePath(f"{self.name}", FileFormat.XML, prefix = f"{toolDir}/local/models/").show()) - - def load_custom_model(self, file_path :FilePath, ext :Optional[FileFormat] = None) -> cobra.Model: - ext = ext if ext else file_path.ext - try: - if ext is FileFormat.XML: - return cobra.io.read_sbml_model(file_path.show()) - - if ext is FileFormat.JSON: - return cobra.io.load_json_model(file_path.show()) - - except Exception as e: raise DataErr(file_path, e.__str__()) - raise DataErr(file_path, - f"Fomat \"{file_path.ext}\" is not recognized, only JSON and XML files are supported.") def __str__(self) -> str: return self.value \ No newline at end of file