C necator (#12)

* Cupriavidus necator model based on iCN1361

* RehMBEL1391 model as updated by Jahn

* core model by Janasch

C_necator_RehMBEL1391_Jahn/PHB_from_fructose.scen

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+{"fluxes": {"EX_h_e": [0, 100], "EX_h2_e": [0.0, 0.0], "EX_ac_e": [0.0, 0.0], "EX_acac_e": [0.0, 0.0], "EX_acal_e": [0.0, 0.0], "EX_ad_e": [0.0, 0.0], "EX_adn_e": [0.0, 0.0], "EX_ala__L_e": [0.0, 0.0], "EX_an_e": [0.0, 0.0], "EX_arg__L_e": [0.0, 0.0], "EX_asn__L_e": [0.0, 0.0], "EX_asp__L_e": [0.0, 0.0], "EX_ccmuc_e": [0.0, 0.0], "EX_cit_e": [0.0, 0.0], "EX_cytd_e": [0.0, 0.0], "EX_dala_e": [0.0, 0.0], "EX_eth_e": [0.0, 0.0], "EX_formate_e": [0.0, 0.0], "EX_fum_e": [0.0, 0.0], "EX_gaba_e": [0.0, 0.0], "EX_gl_e": [0.0, 0.0], "EX_glu__L_e": [0.0, 0.0], "EX_gly__L_e": [0.0, 0.0], "EX_glycolate_e": [0.0, 0.0], "EX_gn_e": [0.0, 0.0], "EX_his__L_e": [0.0, 0.0], "EX_hyxn_e": [0.0, 0.0], "EX_icit_e": [0.0, 0.0], "EX_ile__L_e": [0.0, 0.0], "EX_indole_e": [0.0, 0.0], "EX_ins_e": [0.0, 0.0], "EX_lac__D_e": [0.0, 0.0], "EX_lac__L_e": [0.0, 0.0], "EX_leu__L_e": [0.0, 0.0], "EX_lys__L_e": [0.0, 0.0], "EX_mclact_e": [0.0, 0.0], "EX_orn_e": [0.0, 0.0], "EX_phe__L_e": [0.0, 0.0], "EX_pro__L_e": [0.0, 0.0], "EX_ptrc_e": [0.0, 0.0], "EX_pyr_e": [0.0, 0.0], "EX_ser__L_e": [0.0, 0.0], "EX_succ_e": [0.0, 0.0], "EX_t3_e": [0.0, 0.0], "EX_thr__L_e": [0.0, 0.0], "EX_thymd_e": [0.0, 0.0], "EX_trp__L_e": [0.0, 0.0], "EX_tyr__L_e": [0.0, 0.0], "EX_urea_e": [0.0, 0.0], "EX_uri_e": [0.0, 0.0], "EX_urocan_e": [0.0, 0.0], "EX_val__L_e": [0.0, 0.0], "EX_xan_e": [0.0, 0.0], "EX_xtsine_e": [0.0, 0.0], "EX_fru_e": [-3, 0]}, "pinned_reactions": [], "description": "", "objective_direction": "max", "objective_coefficients": {"PHBt": 1.0}, "use_scenario_objective": true, "version": 1}

C_necator_RehMBEL1391_Jahn/meta.json

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+{"format version": 2, "description": "Based on RehMBEL1391_sbml_L3V1.xml downloaded from https://github.com/m-jahn/genome-scale-models/tree/master/Ralstonia_eutropha/sbml, the map is also taken from this repository.\n\nmaximum ATP/H2 yield is 2.3333\n\nno maintenance ATP set in this model\n\nremoved proton symport in PHBt\n"}

C_necator_core/box_positions.json

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+{"Map": {"name": "Map", "background": "map1.svg", "bg-size": 1, "box-size": 1.610510000000001, "zoom": -6, "pos": [0, 0], "boxes": {"ACK": [767.3684210526311, 1951.5789473684197], "ACS": [873.7358319643101, 1745.7793722746853], "AKGDH": [1624.1341007049402, 1632.761639088499], "Ex_PHB": [318.0861244019136, 2032.5358851674623], "ALD": [1416.4671306085556, 194.98060340634262], "CITL": [1070.5970150184105, 2026.230592182495], "EDA": [257.80352776624886, 1185.3035759367763], "EDD": [242.98723306703914, 788.2268779979563], "PGL": [251.87700988656496, 601.541564787914], "GPD": [248.91375094672304, 405.9664747583459], "RUBISCO": [1073.895280964101, 943.1574542352311], "PRK": [1456.026556466288, 834.877612652688], "FDH": [1300.870674590612, 1069.7364772829408], "TKT2": [1476.2350542657782, 480.10299331210047], "TAL": [1459.9050204796524, 300.4726216647159], "SBPase": [1858.3578448611236, 300.4726216647159], "RPE": [1407.6489123640497, 578.0831960288557], "STH": [1793.0377097166202, 937.3439393236247], "SUCOA": [1685.2594867281894, 1430.510959664626], "ICD": [1701.5895205143152, 1760.3776421443683], "ACH": [1466.4370339941029, 1969.4020746067795], "SUCD": [1548.0872029247319, 1267.210621803367], "FUMC": [1191.2973932366294, 1400.0885358088963], "PGI": [267.8125540924642, 179.63037164738452], "FBPase": [689.1274257745115, 182.8963784046097], "FBA": [715.255479832313, 355.9947365375439], "PGK": [721.7874933467633, 757.7135676762401], "TPI": [525.8270879132529, 499.6990338554515], "GAPD": [682.5954122600612, 597.6792365722067], "GAPDH": [865.4917906646709, 594.4132298149815], "PGM": [725.0535001039884, 927.5459190519492], "ENO": [734.851520375664, 1110.442297456559], "PPS": [604.2112500866571, 1322.7327366761951], "PYK": [930.8119258091743, 1319.46672991897], "PEPC": [1156.1663920577114, 1250.8805880172413], "MAS": [1458.0904326275634, 1508.1292626388242], "MDH": [1205.156493416089, 1639.5353921270369], "PYRC": [1035.32414204038, 1626.4713650981362], "PTA": [527.4220047293355, 1726.0464846309742], "PhaA": [398.45282438147115, 1570.9492502253083], "PhaB": [280.8765811213649, 1757.1116353871432], "PhaCE": [254.7485270635635, 1904.081939462276], "AclAB": [1087.5802501559826, 1855.0918381038985], "XFPK1": [1054.920182583731, 111.04422974565588], "TKT1": [950.4079663525254, 313.5366486936166], "XFPK2": [1025.5261217687043, 695.6594392889618], "Ex_for": [1537.4356574502071, 1095.5597526030583], "Ex_frc": [946.348091724864, -62.62478273933855], "MAE": [1019.4420381476009, 1409.8191862347567], "ICL": [1458.8951705657134, 1713.197998462489], "CITS": [1021.7601933312297, 1714.2488293430931], "APPS": [719.6450531103678, 1758.3780071281628], "Ex_pyr": [31.94122949683308, 1403.3402929713077], "PDH": [675.5158753252981, 1486.8138361431184], "RPI": [1649.752338734145, 641.5703539521675], "BIOMASS": [1778.7453199520412, 1921.3165097191893]}}}

C_necator_core/meta.json

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+{"format version": 2, "description": "Read the Excel file from the publication \nhttps://doi.org/10.1016/j.ymben.2022.08.005\nwith \nhttps://github.com/MJanasch/ThermoCup/blob/main/CupriavidusCoreFBA/ThermoCup_ReadExcel_FBA.m\nand exported model to SBML. The model now contains the reaction needed for both growth on fructose and on formate.\nThe map is figure 1c from the publication.\n"}