############# Model summary Number of compounds: 911 Number of reactions: 1117 Number of genes: 609 Ratio rxn with genes/rxns: 84% ############# Analyzing targets #Topological analysis Number of targets: 92 Reading draft network from /shared/e_faecalis_v583/networks/efaecalisV583_final.sbml ... Warning: R_EX_pi listOfProducts=None Warning: R_EX_co2 listOfProducts=None Warning: R_EX_lac__L listOfProducts=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. 72 producible targets: "M_succ_c" "M_akg_c" "M_tym_c" "M_gln__L_c" "M_pyr_c" "M_met__L_c" "M_RTAglc_c" "M_glx_c" "M_4abut_c" "M_val__L_c" "M_RNA_LPL_c" "M_PGlac2_c" "M_lys__L_c" "M_crtn_c" "M_nadph_c" "M_tyr__L_c" "M_ttdca_c" "M_DNA_LPL_c" "M_phe__L_c" "M_arg__L_c" "M_nac_c" "M_ins_c" "M_cit_c" "M_cbm_c" "M_gthox_c" "M_ocdca_c" "M_btn_c" "M_pydx5p_c" "M_ocdcea_c" "M_adn_c" "M_nadp_c" "M_bz_c" "M_ribflv_c" "M_uri_c" "M_dca_c" "M_salc_c" "M_amet_c" "M_hxan_c" "M_trp__L_c" "M_CPS_LPL2_c" "M_ala__L_c" "M_cytd_c" "M_pro__L_c" "M_gly_c" "M_asp__L_c" "M_nad_c" "M_acon_C_c" "M_his__L_c" "M_ala_B_c" "M_hom__L_c" "M_citr__L_c" "M_ile__L_c" "M_leu__L_c" "M_PreZ_c" "M_thr__L_c" "M_glu__L_c" "M_pydam_c" "M_fum_c" "M_2hb_c" "M_gsn_c" "M_asn__L_c" "M_acglu_c" "M_5oxpro_c" "M_unRTA_c" "M_L2aadp_c" "M_ser__L_c" "M_RTA_c" "M_cys__L_c" "M_oaa_c" "M_spmd_c" "M_orn_c" "M_ddca_c" 20 unproducible targets: "M_PROT_LPL_v60_c" "M_pgp_LPL_c" "M_ptdca_c" "M_moco_c" "M_lyspg_LPL_c" "M_MPT_c" "M_pa_LPL_c" "M_MCOSH_c" "M_mocogdp_c" "M_LTA_LPL_c" "M_dgdag_LPL_c" "M_pta_c" "M_orn__D_c" "M_pg_LPL_c" "M_clpn_LPL_c" "M_6ax_c" "M_malon_c" "M_dag_LPL_c" "M_cdpdag_LPL_c" "M_MCOOH_c" #Flux Balance Analysis ttdca_c // ttdca_c 90.9090909091 positive crtn_c // crtn_c 22.5445715197 positive unRTA_c // unRTA_c 22.5445715197 positive asp__L_c // asp__L_c 1027.95371514 positive pta_c // pta_c 22.5445715197 positive cys__L_c // cys__L_c 1021.94150423 positive ocdca_c // ocdca_c 68.9655172414 positive ser__L_c // ser__L_c 1022.624369 positive RNA_LPL_c // RNA_LPL_c 22.5445715197 positive val__L_c // val__L_c 1019.25757299 positive pg_LPL_c // pg_LPL_c 22.5445715197 positive thr__L_c // thr__L_c 1022.01468744 positive RTAglc_c // RTAglc_c 22.5445715197 positive 4abut_c // 4abut_c 1016.75123013 positive pgp_LPL_c // pgp_LPL_c 22.5445715197 positive adn_c // adn_c 363.636363636 positive CPS_LPL2_c // CPS_LPL2_c 71.4285714286 positive orn__D_c // orn__D_c 22.5445715197 positive hxan_c // hxan_c 1062.85545743 positive pydx5p_c // pydx5p_c 1022.54454898 positive leu__L_c // leu__L_c 1018.27147343 positive PROT_LPL_v60_c // PROT_LPL_v60_c 22.5445715197 positive ptdca_c // ptdca_c 22.5445715194 positive nadp_c // nadp_c 71.4285714286 positive PGlac2_c // PGlac2_c 51.9480519481 positive moco_c // moco_c 100.0 positive tyr__L_c // tyr__L_c 1021.01063887 positive MCOSH_c // MCOSH_c 22.5445715197 positive met__L_c // met__L_c 1021.33933873 positive acon_C_c // acon_C_c 750.0 positive arg__L_c // arg__L_c 1020.35323917 positive citr__L_c // citr__L_c 22.5445715197 positive ile__L_c // ile__L_c 1020.18888924 positive trp__L_c // trp__L_c 1022.21587167 positive pro__L_c // pro__L_c 1020.35323918 positive hom__L_c // hom__L_c 1007.46135213 positive ala_B_c // ala_B_c 1024.25220108 positive gthox_c // gthox_c 153.225806452 positive fum_c // fum_c 684.210526316 positive ala__L_c // ala__L_c 1029.86368112 positive L2aadp_c // L2aadp_c 840.0 positive his__L_c // his__L_c 1021.61325527 positive cbm_c // cbm_c 22.5445715197 positive LTA_LPL_c // LTA_LPL_c 22.5445715197 positive ddca_c // ddca_c 108.108108108 positive 5oxpro_c // 5oxpro_c 593.75 positive MPT_c // MPT_c 100.0 positive glu__L_c // glu__L_c 1022.54457152 positive btn_c // btn_c 1022.54434607 positive nac_c // nac_c 1022.49948238 positive 2hb_c // 2hb_c 777.777777778 positive RTA_c // RTA_c 22.5445715197 positive nad_c // nad_c 80.0 positive ribflv_c // ribflv_c 1022.54457152 positive cytd_c // cytd_c 266.666666667 positive pa_LPL_c // pa_LPL_c 22.5445715197 positive mocogdp_c // mocogdp_c 63.4920634921 positive phe__L_c // phe__L_c 1022.23907524 positive nadph_c // nadph_c 74.0740740741 positive PreZ_c // PreZ_c 173.913043478 positive asn__L_c // asn__L_c 1019.25757299 positive ocdcea_c // ocdcea_c 66.6666666667 positive MCOOH_c // MCOOH_c 22.5445715098 positive tym_c // tym_c 1015.63523686 positive ins_c // ins_c 1022.4716912 positive pyr_c // pyr_c 1011.27228576 positive cit_c // cit_c 1021.39095936 positive spmd_c // spmd_c 22.5445715197 positive dca_c // dca_c 133.333333333 positive orn_c // orn_c 22.5445715197 positive dgdag_LPL_c // dgdag_LPL_c 22.5445715197 positive succ_c // succ_c 697.674418605 positive pydam_c // pydam_c 1022.54457152 positive amet_c // amet_c 173.913043478 positive bz_c // bz_c 794.780915547 positive lyspg_LPL_c // lyspg_LPL_c 22.5445715197 positive dag_LPL_c // dag_LPL_c 22.5445715197 positive oaa_c // oaa_c 1011.2563866 positive gln__L_c // gln__L_c 1022.50497536 positive salc_c // salc_c 142.857142857 positive uri_c // uri_c 363.636363636 positive cdpdag_LPL_c // cdpdag_LPL_c 22.5445715197 positive glx_c // glx_c 880.0 positive gly_c // gly_c 1032.65228972 positive 6ax_c // 6ax_c 22.5445715197 positive malon_c // malon_c 22.5445715197 positive lys__L_c // lys__L_c 1022.477385 positive DNA_LPL_c // DNA_LPL_c 22.5445715197 positive clpn_LPL_c // clpn_LPL_c 22.5445715197 positive acglu_c // acglu_c 800.0 positive akg_c // akg_c 700.0 positive gsn_c // gsn_c 363.636363636 positive ############# Computing optimization Testing reaction biomass_LPL60 Growth rate: 22.5445715197 Status: optimal IN FLUXES OUT FLUXES OBJECTIVES -------------------- ----------------- ------------------- gln__L_e 252 co2_e 1e+03 biomass_LPL60 22.5 ins_e 240 lac__L_e 332 cit_e 189 glu__L_e 243 thr__L_e 36.1 gua_e 238 leu__L_e 4.27 lys__L_e 3.99 val__L_e 3.29 asn__L_e 3.29 ile__L_e 2.36 arg__L_e 2.19 pro__L_e 2.19 ade_e 2.07 ura_e 1.87 phe__L_e 1.86 tyr__L_e 1.53 thymd_e 1.47 met__L_e 1.21 his__L_e 0.931 cys__L_e 0.603 trp__L_e 0.329 nac_e 0.0451 pan4p_e 0.00451 4abz_e 0.000225 btn_e 0.000225 thm_e 0.000225 pydx5p_e 2.25e-05 FVA analysis: Blocked reactions: 506 Essential reactions: 167 Essential genes: 115 20/20 compounds with positive flux 0/20 compounds without flux coa_c // coa_c 13.1313463466 positive mocogdp_c // mocogdp_c 13.1312557403 positive thf_c // thf_c 13.131252712 positive lyspg_LPL_c // lyspg_LPL_c 13.1321313967 positive clpn_LPL_c // clpn_LPL_c 13.131479653 positive atp_c // atp_c 21.8290441176 positive LTA_LPL_c // LTA_LPL_c 13.1774897945 positive nad_c // nad_c 13.1318370202 positive h2o_c // h2o_c 13.1312530948 positive RTAglc_c // RTAglc_c 13.1822064522 positive PGlac2_c // PGlac2_c 13.1217141842 positive RNA_LPL_c // RNA_LPL_c 13.1710348242 positive CPS_LPL2_c // CPS_LPL2_c 13.1454718692 positive udcpdp_c // udcpdp_c 13.1312819153 positive pydx5p_c // pydx5p_c 13.1312530944 positive pg_LPL_c // pg_LPL_c 13.1351171595 positive btn_c // btn_c 13.1312530948 positive thmpp_c // thmpp_c 13.1312563107 positive DNA_LPL_c // DNA_LPL_c 13.1400788289 positive PROT_LPL_v60_c // PROT_LPL_v60_c 13.0880209554 positive