############# Model summary Number of compounds: 2132 Number of reactions: 1977 Number of genes: 2281 Ratio rxn with genes/rxns: 79% ############# Analyzing targets #Topological analysis Number of targets: 50 Reading draft network from /shared/e_siliculosus/networks/ESiliculosus_final.sbml ... Warning: R_RXN__45__15490 listOfReactants=None done. Reading seeds from growth_medium/seeds_artefacts.sbml ... done. Reading targets from targets_compounds/targets.sbml ... done. Checking draftnet for unproducible targets ... done. 50 producible targets: "M_CPD__45__8117_c" "M_LEU_c" "M_DOCOSANOATE_c" "M_CIT_c" "M_GLC_c" "M_CPD__45__8120_c" "M_PALMITATE_c" "M_SER_c" "M_OLEATE__45__CPD_c" "M_GLT_c" "M_CPD__45__12653_c" "M_L__45__ALPHA__45__ALANINE_c" "M_LINOLENIC_ACID_c" "M_HIS_c" "M_ARG_c" "M_VAL_c" "M_SUC_c" "M_PHE_c" "M_GLUTATHIONE_c" "M_THREO__45__DS__45__ISO__45__CITRATE_c" "M_5Z8Z11Z14Z17Z__45__EICOSAPENTAENOATE_c" "M_L__45__ASPARTATE_c" "M_TYR_c" "M_LINOLEIC_ACID_c" "M_THR_c" "M_CPD__45__8121_c" "M_CPD__45__9247_c" "M_CYS_c" "M_STEARIC_ACID_c" "M_HOMO__45__SER_c" "M_LYS_c" "M_ARACHIDONIC_ACID_c" "M_TRP_c" "M_ILE_c" "M_GLY_c" "M_CPD__45__9245_c" "M_4__45__AMINO__45__BUTYRATE_c" "M_GLYCOLLATE_c" "M_ASN_c" "M_MANNITOL_c" "M_Eicosadienoates_c" "M_MET_c" "M_L__45__ORNITHINE_c" "M_PRO_c" "M_GLYCEROL_c" "M_GLN_c" "M_CPD__45__7836_c" "M_AMMONIUM_c" "M_GLYCERATE_c" "M_ARACHIDIC_ACID_c" 0 unproducible targets: #Flux Balance Analysis CPD__45__9245_c // CPD-9245_c 16.0319704207 positive CPD__45__9247_c // CPD-9247_c 14.2863727905 positive 4__45__AMINO__45__BUTYRATE_c // 4-AMINO-BUTYRATE_c 55.5118060463 positive GLYCOLLATE_c // GLYCOLLATE_c 1003.01750151 positive Eicosadienoates_c // Eicosadienoates_c 11.2173066452 positive CIT_c // CIT_c 571.428571429 positive AMMONIUM_c // AMMONIUM_c 1000.0 positive SUC_c // SUC_c 800.0 positive L__45__ASPARTATE_c // L-ASPARTATE_c 958.668673413 positive OLEATE__45__CPD_c // OLEATE-CPD_c 12.877781371 positive CPD__45__8120_c // CPD-8120_c 10.6018404891 positive ARACHIDONIC_ACID_c // ARACHIDONIC_ACID_c 14.160658715 positive LINOLEIC_ACID_c // LINOLEIC_ACID_c 12.0689024348 positive CPD__45__12653_c // CPD-12653_c 3.01750150875 positive CPD__45__8121_c // CPD-8121_c 3.01750150875 positive 5Z8Z11Z14Z17Z__45__EICOSAPENTAENOATE_c // 5Z8Z11Z14Z17Z-EICOSAPENTAENOATE_c 14.6324026196 positive LINOLENIC_ACID_c // LINOLENIC_ACID_c 3.01750150875 positive STEARIC_ACID_c // STEARIC_ACID_c 13.8402545852 positive PALMITATE_c // PALMITATE_c 15.4462710826 positive ARACHIDIC_ACID_c // ARACHIDIC_ACID_c 12.5917677472 positive CPD__45__7836_c // CPD-7836_c 17.589061178 positive DOCOSANOATE_c // DOCOSANOATE_c 11.6457103632 positive CPD__45__8117_c // CPD-8117_c 11.3795681155 positive GLYCERATE_c // GLYCERATE_c 1002.94242607 positive THREO__45__DS__45__ISO__45__CITRATE_c // THREO-DS-ISO-CITRATE_c 571.428571429 positive GLYCEROL_c // GLYCEROL_c 419.588298397 positive MANNITOL_c // MANNITOL_c 713.22220115 positive SER_c // SER_c 1001.75747388 positive L__45__ORNITHINE_c // L-ORNITHINE_c 102.698570504 positive HOMO__45__SER_c // HOMO-SER_c 590.553854536 positive LYS_c // LYS_c 68.5384585831 positive LEU_c // LEU_c 57.4443694689 positive ILE_c // ILE_c 57.4443694689 positive VAL_c // VAL_c 81.5685132298 positive GLT_c // GLT_c 763.84242434 positive TYR_c // TYR_c 67.022247566 positive PRO_c // PRO_c 110.296970893 positive GLN_c // GLN_c 438.29238167 positive TRP_c // TRP_c 47.2183699972 positive GLY_c // GLY_c 1001.75747388 positive ASN_c // ASN_c 497.646560002 positive PHE_c // PHE_c 49.2891048295 positive CYS_c // CYS_c 50.9139667185 positive THR_c // THR_c 590.553854536 positive HIS_c // HIS_c 267.73035218 positive L__45__ALPHA__45__ALANINE_c // L-ALPHA-ALANINE_c 490.502417047 positive ARG_c // ARG_c 148.245312745 positive MET_c // MET_c 34.0611974768 positive GLC_c // GLC_c 1003.01750151 positive GLUTATHIONE_c // GLUTATHIONE_c 53.3508192527 positive ############# Computing optimization Testing reaction biomass_rxn Growth rate: 3.01750150875 Status: optimal IN FLUXES OUT FLUXES OBJECTIVES ------------------------- ----------------- ----------------- AMMONIA_e 864 PROTON_e 689 biomass_rxn 3.02 SULFATE_e 1.81 BIOMASS_e 3.02 OXYGEN__45__... 0.0302 FVA analysis: Blocked reactions: 1382 Essential reactions: 63 Essential genes: 33 30/30 compounds with positive flux 0/30 compounds without flux GLC_c // GLC_c 724.244070252 positive GLN_c // GLN_c 40.8069249814 positive CYS_c // CYS_c 160.335846045 positive LEU_c // LEU_c 182.794866392 positive SUC_c // SUC_c 911.161731207 positive GLT_c // GLT_c 40.4579496921 positive GLYCERATE_c // GLYCERATE_c 1000.0 positive L__45__ORNITHINE_c // L-ORNITHINE_c 997.569014168 positive ARG_c // ARG_c 998.661493542 positive SER_c // SER_c 363.826278491 positive MANNITOL_c // MANNITOL_c 2.14952996259 positive GLYCEROL_c // GLYCEROL_c 175.81188178 positive L__45__ALPHA__45__ALANINE_c // L-ALPHA-ALANINE_c 18.3727812709 positive ILE_c // ILE_c 274.192299587 positive THREO__45__DS__45__ISO__45__CITRATE_c // THREO-DS-ISO-CITRATE_c 60.9849062357 positive MET_c // MET_c 104.380181328 positive VAL_c // VAL_c 92.9064925641 positive CIT_c // CIT_c 29.5992629784 positive ASN_c // ASN_c 661.127033604 positive PRO_c // PRO_c 79.7578333632 positive L__45__ASPARTATE_c // L-ASPARTATE_c 76.6055563421 positive 4__45__AMINO__45__BUTYRATE_c // 4-AMINO-BUTYRATE_c 999.500682907 positive GLY_c // GLY_c 303.371262018 positive THR_c // THR_c 906.33573305 positive HIS_c // HIS_c 999.119273527 positive GLYCOLLATE_c // GLYCOLLATE_c 1000.0 positive TYR_c // TYR_c 514.849086114 positive PHE_c // PHE_c 133.198106771 positive TRP_c // TRP_c 387.016417962 positive LYS_c // LYS_c 188.475405981 positive