from cameo import load_model
model = load_model("iJR904")
model
Name | MODELID_1461534 |
Number of metabolites | 761 |
Number of reactions | 1075 |
Reactions | 12ppd_dsh_S_e <=> 12ppd_dsh_S_c h_c + nadh_c + 2dhglcn_c --> glcn_c + nad_c h_c + nadph_c + 2dhglcn_c --> glcn_c + nadp_c h_c + nadh_c + 2dhguln_c --> idon_dsh_L_c + nad_c nadph_c + 2dhguln_c + h_c --> nadp_c + idon_dsh_L_c o2_c + h_c + nadh_c + 3hcinnm_c --> nad_c + h2o_c + dhcinnm_c h_c + nadh_c + o2_c + 3hpppn_c --> nad_c + dhpppn_c + h2o_c h2o_c + phthr_c --> 4hthr_c + pi_c 5dglcn_c + h_c + nadph_c <=> glcn_c + nadp_c ru5p_dsh_D_c <=> ara5p_c ttdca_c + ACP_c + atp_c --> amp_c + myrsACP_c + ppi_c ttdcea_c + atp_c + ACP_c --> amp_c + tdeACP_c + ppi_c ACP_c + atp_c + hdca_c --> amp_c + palmACP_c + ppi_c hdcea_c + ACP_c + atp_c --> amp_c + hdeACP_c + ppi_c ocdcea_c + atp_c + ACP_c --> amp_c + octeACP_c + ppi_c unagamu_c + dtdp4aaddg_c --> dtdp_c + unagamuf_c + h_c h2o_c + arbt6p_c --> g6p_c + hqn_c akg_c + 4abut_c --> glu_dsh_L_c + sucsal_c nad_c + h2o_c + 4abutn_c --> 4abut_c + 2.0 h_c + nadh_c h_e + 4abut_e --> 4abut_c + h_c accoa_c + acac_c --> aacoa_c + ac_c 2.0 accoa_c <=> aacoa_c + coa_c h_e + acac_e <=> acac_c + h_c coa_c + nad_c + acald_c --> h_c + nadh_c + accoa_c acald_e <=> acald_c gtp_c + h_c + adocbip_c --> agdpcbi_c + ppi_c hco3_c + atp_c + accoa_c <=> pi_c + h_c + adp_c + malcoa_c coa_c + atp_c + ppa_c --> ppcoa_c + pi_c + adp_c uacgam_c + udcpp_c --> ump_c + unaga_c pep_c + acgam_e --> acgam6p_c + pyr_c atp_c + acglu_c --> acg5p_c + adp_c glu_dsh_L_c + accoa_c --> h_c + coa_c + acglu_c h_c + pyr_c + 2obut_c --> co2_c + 2ahbut_c atp_c + ac_c <=> actp_c + adp_c h_c + 2.0 pyr_c --> co2_c + alac_dsh_S_c unaga_c + uacmamu_c --> h_c + udp_c + unagamu_c pep_c + acmana_e --> acmanap_c + pyr_c h_e + acnam_e --> acnam_c + h_c acnam_c --> acmana_c + pyr_c accoa_c + ACP_c <=> coa_c + acACP_c h2o_c + acorn_c --> orn_c + ac_c acon_dsh_T_c + amet_c --> ahcys_c + aconm_c cit_c <=> icit_c akg_c + acorn_c <=> acg5sa_c + glu_dsh_L_c apoACP_c + coa_c --> h_c + pap_c + ACP_c coa_c + ac_c + atp_c --> accoa_c + ppi_c + amp_c h_e + ac_e <=> ac_c + h_c h_c + h2o_c + adn_c --> ins_c + nh4_c 4adcho_c --> h_c + 4abz_c + pyr_c chor_c + gln_dsh_L_c --> glu_dsh_L_c + 4adcho_c h2o_c + ade_c + h_c --> nh4_c + hxan_c h_e + ade_e <=> ade_c + h_c 2.0 h_c + 2.0 nadh_c + accoa_c <=> coa_c + 2.0 nad_c + etoh_c atp_c + amp_c <=> 2.0 adp_c gtp_c + amp_c <=> gdp_c + adp_c itp_c + amp_c <=> idp_c + adp_c h_c + amet_c <=> co2_c + ametam_c atp_c --> camp_c + ppi_c atp_c + adn_c --> adp_c + amp_c + h_c h_e + adn_e --> adn_c + h_c h_e + adn_e <=> adn_c + h_c atp_c + adocbi_c --> adocbip_c + adp_c + h_c rdmbzi_c + agdpcbi_c --> gmp_c + adocbl_c + h_c prpp_c + ade_c --> amp_c + ppi_c atp_c + aps_c --> paps_c + adp_c + h_c dcamp_c <=> fum_c + amp_c 25aics_c <=> aicar_c + fum_c imp_c + asp_dsh_L_c + gtp_c --> pi_c + 2.0 h_c + gdp_c + dcamp_c h2o_c + acgam6p_c --> ac_c + gam6p_c adphep_dsh_DD_c --> adphep_dsh_LD_c h2o_c + agm_c --> ptrc_c + urea_c nadp_c + acg5sa_c + pi_c <=> acg5p_c + nadph_c + h_c h2o_c + ahcys_c <=> hcys_dsh_L_c + adn_c h2o_c + ahcys_c --> rhcys_c + ade_c 10fthf_c + aicar_c <=> fprica_c + thf_c hco3_c + air_c + atp_c --> pi_c + h_c + 5caiz_c + adp_c 5aizc_c <=> 5caiz_c coa_c + nad_c + akg_c --> succoa_c + co2_c + nadh_c akg_e + h_e <=> h_c + akg_c atp_c + 2.0 ala_dsh_D_c <=> pi_c + h_c + alaala_c + adp_c ala_dsh_L_c <=> ala_dsh_D_c ala_dsh_L_c --> ala_dsh_D_c ala_dsh_D_c + pydx5p_c --> pyam5p_c + pyr_c akg_c + ala_dsh_L_c <=> glu_dsh_L_c + pyr_c pydx5p_c + ala_dsh_L_c --> pyam5p_c + pyr_c atp_c + ala_dsh_L_e + h2o_c --> ala_dsh_L_c + pi_c + h_c + adp_c h_e + ala_dsh_L_e <=> ala_dsh_L_c + h_c h_c + glyald_c + nadh_c <=> glyc_c + nad_c pacald_c + nad_c + h2o_c --> nadh_c + 2.0 h_c + pac_c nad_c + acald_c + h2o_c --> ac_c + 2.0 h_c + nadh_c h2o_c + alltt_c --> urdglyc_c + urea_c h2o_c + alltn_c --> alltt_c + h_c h_e + alltn_e <=> alltn_c + h_c altrn_c --> 2ddglcn_c + h2o_c malt_c + malttr_c --> maltttr_c + glc_dsh_D_c malt_c + maltttr_c --> maltpt_c + glc_dsh_D_c malt_c + maltpt_c --> malthx_c + glc_dsh_D_c malt_c + malthx_c --> malthp_c + glc_dsh_D_c acmanap_c --> acgam6p_c acmana_c + atp_c --> h_c + adp_c + acmanap_c 8aonn_c + amet_c <=> amob_c + dann_c 2dmmq8_c + amet_c --> h_c + ahcys_c + mqn8_c air_c + h2o_c --> 4ampm_c + 2.0 for_c + 4.0 h_c h2o_c + amp_c --> ade_c + r5p_c prpp_c + anth_c --> ppi_c + pran_c gln_dsh_L_c + chor_c --> pyr_c + h_c + anth_c + glu_dsh_L_c h_c + ala_dsh_L_c + pmcoa_c <=> coa_c + 8aonn_c + co2_c h2o_c + ap4a_c --> 2.0 adp_c + 2.0 h_c h2o_c + ap5a_c --> atp_c + adp_c + 2.0 h_c nadph_c + 5apru_c + h_c --> 5aprbu_c + nadp_c arab_dsh_L_c <=> rbl_dsh_L_c atp_c + arab_dsh_L_e + h2o_c --> h_c + pi_c + arab_dsh_L_c + adp_c h_e + arab_dsh_L_e <=> arab_dsh_L_c + h_c h_c + arg_dsh_L_c --> agm_c + co2_c orn_c + arg_dsh_L_e <=> orn_e + arg_dsh_L_c argsuc_c <=> fum_c + arg_dsh_L_c atp_c + asp_dsh_L_c + citr_dsh_L_c --> amp_c + argsuc_c + h_c + ppi_c atp_c + arg_dsh_L_e + h2o_c --> arg_dsh_L_c + pi_c + h_c + adp_c nadp_c + pi_c + aspsa_c <=> nadph_c + h_c + 4pasp_c h2o_c + asn_dsh_L_c --> asp_dsh_L_c + nh4_c gln_dsh_L_c + atp_c + asp_dsh_L_c + h2o_c --> amp_c + h_c + glu_dsh_L_c + ppi_c + asn_dsh_L_c atp_c + asp_dsh_L_c + nh4_c --> amp_c + h_c + ppi_c + asn_dsh_L_c atp_c + asn_dsh_L_e + h2o_c --> asn_dsh_L_c + pi_c + h_c + adp_c h_e + asn_dsh_L_e <=> asn_dsh_L_c + h_c h_c + asp_dsh_L_c --> ala_dsh_B_c + co2_c cbp_c + asp_dsh_L_c --> cbasp_c + pi_c + h_c atp_c + asp_dsh_L_c <=> 4pasp_c + adp_c q8_c + asp_dsh_L_c --> iasp_c + q8h2_c mqn8_c + asp_dsh_L_c --> iasp_c + mql8_c fum_c + asp_dsh_L_c --> iasp_c + succ_c o2_c + asp_dsh_L_c --> h2o2_c + iasp_c asp_dsh_L_c --> fum_c + nh4_c akg_c + asp_dsh_L_c <=> glu_dsh_L_c + oaa_c atp_c + asp_dsh_L_e + h2o_c --> pi_c + h_c + asp_dsh_L_c + adp_c h_e + asp_dsh_L_e --> asp_dsh_L_c + h_c 2.0 h_e + asp_dsh_L_e --> asp_dsh_L_c + 2.0 h_c 3.0 h_e + asp_dsh_L_e --> asp_dsh_L_c + 3.0 h_c succoa_c + arg_dsh_L_c --> h_c + coa_c + sucarg_c atp_c + h2o_c --> pi_c + adp_c + h_c atp_c + prpp_c --> ppi_c + prbatp_c pi_c + 4.0 h_e + adp_c <=> 3.0 h_c + atp_c + h2o_c betald_c + nad_c + h2o_c --> glyb_c + 2.0 h_c + nadh_c nadp_c + betald_c + h2o_c --> nadph_c + glyb_c + 2.0 h_c h2o_c + pap_c --> amp_c + pi_c btnso_c + h_c + nadh_c --> btn_c + nad_c + h2o_c btnso_c + nadph_c + h_c --> nadp_c + h2o_c + btn_c cys_dsh_L_c + dtbt_c <=> ala_dsh_L_c + btn_c + 2.0 h_c but_c + accoa_c --> ac_c + btcoa_c h_e + but_e <=> but_c + h_c 0.035 ptrc_c + 0.000129 clpn_EC_c + 0.154 glycogen_c + 0.00013 nadp_c + 0.0084 lps_EC_c + 0.0247 dttp_c + 0.007 spmd_c + 0.326 lys_dsh_L_c + 0.0254 dctp_c + 0.09 his_dsh_L_c + 0.0254 dgtp_c + 0.001935 pe_EC_c + 0.203 gtp_c + 0.488 ala_dsh_L_c + 1e-05 fad_c + 6e-06 coa_c + 0.126 ctp_c + 0.00215 nad_c + 0.003 udpg_c + 0.25 glu_dsh_L_c + 0.205 ser_dsh_L_c + 5e-05 nadh_c + 0.428 leu_dsh_L_c + 0.000464 pg_EC_c + 0.0247 datp_c + 0.136 utp_c + 0.281 arg_dsh_L_c + 0.087 cys_dsh_L_c + 0.21 pro_dsh_L_c + 0.582 gly_c + 0.0276 peptido_EC_c + 45.5608 h2o_c + 0.054 trp_dsh_L_c + 0.276 ile_dsh_L_c + 0.25 gln_dsh_L_c + 0.131 tyr_dsh_L_c + 0.229 asn_dsh_L_c + 0.241 thr_dsh_L_c + 45.7318 atp_c + 5.2e-05 ps_EC_c + 0.0004 nadph_c + 3e-06 succoa_c + 5e-05 accoa_c + 0.229 asp_dsh_L_c + 0.176 phe_dsh_L_c + 0.001 amp_c + 0.05 5mthf_c + 0.146 met_dsh_L_c + 0.402 val_dsh_L_c --> 45.5628 pi_c + 45.5608 adp_c + 45.56035 h_c + 0.7302 ppi_c 4.0 malACP_c + 10.0 nadph_c + 14.0 h_c + actACP_c --> 10.0 nadp_c + ddcaACP_c + 4.0 co2_c + 5.0 h2o_c + 4.0 ACP_c actACP_c + 5.0 malACP_c + 12.0 nadph_c + 17.0 h_c --> 12.0 nadp_c + myrsACP_c + 6.0 h2o_c + 5.0 ACP_c + 5.0 co2_c 5.0 malACP_c + 11.0 nadph_c + 16.0 h_c + actACP_c --> 11.0 nadp_c + 5.0 ACP_c + 5.0 co2_c + 6.0 h2o_c + tdeACP_c 6.0 malACP_c + 14.0 nadph_c + 20.0 h_c + actACP_c --> 14.0 nadp_c + palmACP_c + 6.0 co2_c + 7.0 h2o_c + 6.0 ACP_c actACP_c + 6.0 malACP_c + 13.0 nadph_c + 19.0 h_c --> 13.0 nadp_c + 6.0 co2_c + 7.0 h2o_c + 6.0 ACP_c + hdeACP_c actACP_c + 7.0 malACP_c + 15.0 nadph_c + 22.0 h_c --> 15.0 nadp_c + 7.0 co2_c + 8.0 h2o_c + 7.0 ACP_c + octeACP_c 15dap_c + lys_dsh_L_e + h_e --> h_c + lys_dsh_L_c + 15dap_e 2.0 h2o2_c --> 2.0 h2o_c + o2_c cbi_c + atp_c + h2o_c <=> adocbi_c + pi_c + ppi_c cbl1_e + atp_c + h2o_c --> h_c + pi_c + cbl1_c + adp_c atp_c + h2o_c + cbl1_c <=> pi_c + adocbl_c + ppi_c atp_c + co2_c + nh4_c --> cbp_c + 2.0 h_c + adp_c gln_dsh_L_c + hco3_c + 2.0 atp_c + h2o_c --> cbp_c + pi_c + 2.0 adp_c + 2.0 h_c + glu_dsh_L_c 0.02 cdpdag_EC_c + h2o_c --> cmp_c + 0.02 pa_EC_c + 2.0 h_c 4c2me_c + atp_c --> 2p4c2me_c + adp_c + h_c chol_e + atp_c + h2o_c --> chol_c + h_c + pi_c + adp_c chol_e + h_e <=> h_c + chol_c chor_c --> pphn_c 3psme_c --> pi_c + chor_c chor_c --> 4hbz_c + pyr_c nadh_c + h_c + cinnm_c + o2_c --> nad_c + cenchddd_c cit_c --> ac_c + oaa_c cit_e + succ_c --> cit_c + succ_e 0.04 pg_EC_c <=> 0.02 clpn_EC_c + glyc_c h2o_c + cmp_c --> csn_c + r5p_c co2_e <=> co2_c o2_c + cpppg3_c + 2.0 h_c --> pppg9_c + 2.0 co2_c + 2.0 h2o_c crn_c + bbtcoa_c <=> crncoa_c + gbbtn_c ctbtcoa_c + crn_c <=> crncoa_c + ctbt_c crncoa_c <=> ctbtcoa_c + h2o_c crn_e + gbbtn_c --> crn_c + gbbtn_e oaa_c + h2o_c + accoa_c --> cit_c + coa_c + h_c h2o_c + h_c + csn_c --> nh4_c + ura_c csn_e + h_e --> csn_c + h_c gln_dsh_L_c + utp_c + atp_c + h2o_c --> ctp_c + pi_c + adp_c + 2.0 h_c + glu_dsh_L_c cyan_c + tsul_c --> so3_c + tcynt_c + h_c cynt_c + 3.0 h_c + hco3_c --> 2.0 co2_c + nh4_c h_e + cynt_e --> cynt_c + h_c cys_dsh_L_c + h2o_c --> pyr_c + h2s_c + nh4_c h2s_c + acser_c --> cys_dsh_L_c + h_c + ac_c cyst_dsh_L_c + h2o_c --> pyr_c + hcys_dsh_L_c + nh4_c atp_c + cys_dsh_L_e + h2o_c --> h_c + pi_c + cys_dsh_L_c + adp_c 2.0 h_c + 0.5 o2_c + q8h2_c --> q8_c + 2.0 h_e + h2o_c 2.5 h_c + 0.5 o2_c + q8h2_c --> q8_c + 2.5 h_e + h2o_c h2o_c + h_c + cytd_c --> nh4_c + uri_c gtp_c + cytd_c --> cmp_c + gdp_c + h_c cytd_e + h_e --> cytd_c + h_c cytd_e + h_e <=> cytd_c + h_c cmp_c + atp_c <=> cdp_c + adp_c atp_c + dcmp_c <=> dcdp_c + adp_c fad_c + ala_dsh_D_c + h2o_c --> pyr_c + fadh2_c + nh4_c h2o_c + h_c + dad_dsh_2_c --> nh4_c + din_c atp_c + damp_c <=> adp_c + dadp_c dad_dsh_2_e + h_e --> dad_dsh_2_c + h_c atp_c + 0.02 12dgr_EC_c --> 0.02 pa_EC_c + adp_c + h_c ala_dsh_D_e + h_e <=> ala_dsh_D_c + h_c 26dap_dsh_M_c + h_c --> co2_c + lys_dsh_L_c 26dap_dsh_LL_c <=> 26dap_dsh_M_c 26dap_dsh_M_e + atp_c + h2o_c --> 26dap_dsh_M_c + h_c + pi_c + adp_c h_c + 0.02 pa_EC_c + ctp_c <=> 0.02 cdpdag_EC_c + ppi_c ru5p_dsh_D_c --> h_c + db4p_c + for_c atp_c + co2_c + dann_c <=> dtbt_c + 3.0 h_c + pi_c + adp_c h_c + h2o_c + dctp_c --> dutp_c + nh4_c h_c + h2o_c + dcyt_c --> duri_c + nh4_c h_e + dcyt_e --> dcyt_c + h_c 2dh3dgal_c + atp_c --> 2dh3dgal6p_c + adp_c + h_c 2ddglcn_e + h_e <=> 2ddglcn_c + h_c 2ddglcn_c + atp_c --> h_c + adp_c + 2ddg6p_c h2o_c + e4p_c + pep_c --> pi_c + 2dda7p_c 2dh3dgal6p_c <=> g3p_c + pyr_c atp_c + dgmp_c <=> dgdp_c + adp_c dgsn_e + h_e --> dgsn_c + h_c 23dhmb_c --> 3mob_c + h2o_c 23dhmp_c --> 3mop_c + h2o_c dha_c + pep_c --> dhap_c + pyr_c dha_e <=> dha_c nad_c + 23ddhb_c <=> nadh_c + 23dhb_c + h_c 23dhb_c + atp_c <=> ppi_c + 23dhba_c cenchddd_c + nad_c --> dhcinnm_c + nadh_c + h_c dhcinnm_c + o2_c --> hkntd_c h_c + nadph_c + 23dhdp_c --> thdp_c + nadp_c aspsa_c + pyr_c --> h_c + 23dhdp_c + 2.0 h2o_c h_c + nadph_c + dhf_c <=> thf_c + nadp_c dhpt_c + atp_c + glu_dsh_L_c --> dhf_c + pi_c + adp_c octdp_c + dhna_c --> 2dmmq8_c + h_c + co2_c + ppi_c dhnpt_c --> 6hmhpt_c + gcald_c q8_c + dhor_dsh_S_c --> orot_c + q8h2_c mqn8_c + dhor_dsh_S_c --> orot_c + mql8_c h2o_c + dhor_dsh_S_c <=> cbasp_c + h_c cechddd_c + nad_c --> nadh_c + dhpppn_c + h_c 25drapp_c + h_c + h2o_c --> 5apru_c + nh4_c 4abz_c + 6hmhptpp_c --> h_c + dhpt_c + ppi_c dhptd_c --> h2o_c + hmfurn_c 3dhq_c <=> 3dhsk_c + h2o_c 2dda7p_c --> pi_c + 3dhq_c h_e + din_e --> din_c + h_c 25dkglcn_c + h_c + nadph_c --> 2dhguln_c + nadp_c 25dkglcn_c + h_c + nadh_c --> 5dglcn_c + nad_c 25dkglcn_c + h_c + nadph_c --> 5dglcn_c + nadp_c o2_c + h2o_c + dkmpp_c --> 2kmb_c + pi_c + 2.0 h_c + for_c 3.0 h2o_c + dkmpp_c --> 2kmb_c + pi_c + 6.0 h_c + for_c dmpp_c + ipdp_c --> ppi_c + grdp_c h2mb4p_c + h_c + nadh_c --> dmpp_c + nad_c + h2o_c amet_c + 2omhmbl_c --> q8h2_c + ahcys_c + h_c dmso_c + mql8_c --> dms_c + mqn8_c + h2o_c dmso_e + mql8_c --> dms_e + mqn8_c + h2o_e dmso_c + 2dmmql8_c --> 2dmmq8_c + dms_c + h2o_c dmso_e + 2dmmql8_c --> 2dmmq8_c + dms_e + h2o_e h2o_c + dhpmp_c --> dhnpt_c + pi_c h2o_c + ahdt_c --> dhpmp_c + ppi_c + h_c 23doguln_c + h_c + nadh_c --> 3dhguln_c + nad_c dpcoa_c + atp_c --> coa_c + adp_c + h_c nadph_c + h_c + 2dhp_c --> nadp_c + pant_dsh_R_c 2dr5p_c --> g3p_c + acald_c h_e + ser_dsh_D_e <=> h_c + ser_dsh_D_c atp_c + dtmp_c <=> dtdp_c + adp_c atp_c + duri_c --> dump_c + adp_c + h_c pi_c + duri_c <=> 2dr1p_c + ura_c h_e + duri_e --> duri_c + h_c h2o_c + dutp_c --> dump_c + ppi_c + h_c h_c + nadph_c + dxyl5p_c --> 2me4p_c + nadp_c g3p_c + h_c + pyr_c --> co2_c + dxyl5p_c atp_c + dxyl_c --> dxyl5p_c + adp_c + h_c h_e + lac_dsh_D_e <=> h_c + lac_dsh_D_c nad_c + e4p_c + h2o_c <=> 4per_c + 2.0 h_c + nadh_c unagamuf_c --> udcpdp_c + h_c + eca_EC_c 2ddg6p_c --> g3p_c + pyr_c 6pgc_c --> 2ddg6p_c + h2o_c kdo2lipid4_c + ddcaACP_c --> ACP_c + kdo2lipid4L_c myrsACP_c + kdo2lipid4L_c --> lipa_c + ACP_c kdo2lipid4_c + hdeACP_c --> kdo2lipid4p_c + ACP_c myrsACP_c + kdo2lipid4p_c --> lipa_cold_c + ACP_c 2pg_c <=> h2o_c + pep_c 3.0 23dhba_c + 3.0 seramp_c --> enter_c + 6.0 amp_c + 6.0 h_c etha_c --> acald_c + nh4_c h_e + etoh_e <=> etoh_c + h_c 12ppd_dsh_S_e --> 15dap_e --> 26dap_dsh_M_e --> 2ddglcn_e --> 3hcinnm_e --> 3hpppn_e --> 4abut_e --> ac_e --> acac_e --> acald_e --> acgam_e --> acmana_e --> acnam_e --> ade_e --> adn_e --> akg_e --> ala_dsh_D_e --> ala_dsh_L_e --> alltn_e --> amp_e --> arab_dsh_L_e --> arg_dsh_L_e --> asn_dsh_L_e --> asp_dsh_L_e --> but_e --> cbl1_e --> chol_e --> cit_e --> co2_e <=> crn_e --> csn_e --> cynt_e --> cys_dsh_L_e --> cytd_e --> dad_dsh_2_e --> dcyt_e --> dgsn_e --> dha_e --> din_e --> dms_e --> dmso_e --> duri_e --> etoh_e --> fe2_e <=> for_e --> fru_e --> fuc1p_dsh_L_e --> fuc_dsh_L_e --> fum_e --> g6p_e --> gal_e --> galct_dsh_D_e --> galctn_dsh_D_e --> galt_e --> galur_e --> gam_e --> gbbtn_e --> glc_dsh_D_e <-- glcn_e --> glcr_e --> glcur_e --> gln_dsh_L_e --> glu_dsh_L_e --> gly_e --> glyald_e --> glyb_e --> glyc3p_e --> glyc_e --> glyclt_e --> gsn_e --> gua_e --> h2o_e <=> h_e <=> hdca_e --> his_dsh_L_e --> hxan_e --> idon_dsh_L_e --> ile_dsh_L_e --> indole_e --> ins_e --> k_e <=> lac_dsh_D_e --> lac_dsh_L_e --> lcts_e --> leu_dsh_L_e --> lys_dsh_L_e --> mal_dsh_L_e --> malt_e --> malthx_e --> maltpt_e --> malttr_e --> maltttr_e --> man6p_e --> man_e --> melib_e --> met_dsh_D_e --> met_dsh_L_e --> mnl_e --> na1_e <=> nac_e --> nad_e --> nh4_e <=> nmn_e --> no2_e --> no3_e --> o2_e <-- ocdca_e --> orn_e --> phe_dsh_L_e --> pi_e <=> pnto_dsh_R_e --> pppn_e --> pro_dsh_L_e --> ptrc_e --> pyr_e --> rib_dsh_D_e --> rmn_e --> sbt_dsh_D_e --> ser_dsh_D_e --> ser_dsh_L_e --> so4_e <=> spmd_e --> succ_e --> sucr_e --> tartr_dsh_L_e --> taur_e --> thm_e --> thr_dsh_L_e --> thymd_e --> tma_e --> tmao_e --> tre_e --> trp_dsh_L_e --> tsul_e --> ttdca_e --> tyr_dsh_L_e --> ura_e --> urea_e --> uri_e --> val_dsh_L_e --> xan_e --> xtsn_e --> xyl_dsh_D_e --> f6p_c <=> dha_c + g3p_c 6.0 fad_c + 7.0 coa_c + atp_c + ttdca_c + 6.0 nad_c + 6.0 h2o_c --> 6.0 fadh2_c + 7.0 accoa_c + 6.0 h_c + 6.0 nadh_c + ppi_c + amp_c 7.0 fad_c + 8.0 coa_c + atp_c + 7.0 nad_c + hdca_c + 7.0 h2o_c --> 7.0 fadh2_c + 8.0 accoa_c + 7.0 h_c + 7.0 nadh_c + ppi_c + amp_c 8.0 fad_c + 9.0 coa_c + atp_c + 8.0 nad_c + ocdca_c + 8.0 h2o_c --> 8.0 fadh2_c + 9.0 accoa_c + 8.0 h_c + 8.0 nadh_c + ppi_c + amp_c fad_c + nad_c + btcoa_c + h2o_c --> h_c + fadh2_c + nadh_c + aacoa_c fdp_c <=> dhap_c + g3p_c fdp_c + h2o_c --> pi_c + f6p_c fuc_dsh_L_c <=> fcl_dsh_L_c atp_c + fcl_dsh_L_c --> fc1p_c + adp_c + h_c fc1p_c <=> dhap_c + lald_dsh_L_c fe2_c + ppp9_c --> 2.0 h_c + pheme_c 3.0 h_c + q8_c + for_c --> 2.0 h_e + q8h2_c + co2_c mqn8_c + 3.0 h_c + for_c --> 2.0 h_e + mql8_c + co2_c atp_c + fe2_e + h2o_c --> h_c + pi_c + fe2_c + adp_c h2o_c + suc6p_c --> g6p_c + fru_c h_c + for_c --> co2_c + h2_c atp_c + h_c + fmn_c --> ppi_c + fad_c for_e <=> for_c fum_c + mql8_c --> mqn8_c + succ_c fum_c + 2dmmql8_c --> 2dmmq8_c + succ_c atp_c + f1p_c --> adp_c + fdp_c + h_c fru_e + pep_c --> f1p_c + pyr_c fru_e + pep_c --> f6p_c + pyr_c 10fthf_c + h2o_c --> thf_c + for_c + h_c fuc1p_dsh_L_e + 2.0 pi_c --> 2.0 pi_e + fuc1p_dsh_L_c fuc_dsh_L_e + h_e <=> fuc_dsh_L_c + h_c fum_c + h2o_c <=> mal_dsh_L_c fum_e + 2.0 h_e --> fum_c + 2.0 h_c fum_e + 3.0 h_e --> fum_c + 3.0 h_c gam1p_c + accoa_c --> h_c + acgam1p_c + coa_c g1p_c + h2o_c --> pi_c + glc_dsh_D_c dttp_c + g1p_c + h_c --> ppi_c + dtdpglu_c glu1sa_c --> 5aop_c nadp_c + glyc3p_c <=> dhap_c + h_c + nadph_c q8_c + glyc3p_c --> dhap_c + q8h2_c mqn8_c + glyc3p_c --> dhap_c + mql8_c glyc3p_c + 2dmmq8_c --> dhap_c + 2dmmql8_c glu5sa_c --> 1pyr5c_c + h_c + h2o_c nadph_c + h_c + glu5p_c --> nadp_c + glu5sa_c + pi_c h2o_c + gam6p_c --> f6p_c + nh4_c nadp_c + g6p_c <=> h_c + 6pgl_c + nadph_c g6p_e + 2.0 pi_c --> g6p_c + 2.0 pi_e galct_dsh_D_c --> 5dh4dglc_c + h2o_c galctn_dsh_D_c --> 2dh3dgal_c + h2o_c h_e + galctn_dsh_D_e <=> galctn_dsh_D_c + h_c galct_dsh_D_e + h_e <=> galct_dsh_D_c + h_c atp_c + gal_c <=> adp_c + gal1p_c + h_c h2o_c + melib_c --> gal_c + glc_dsh_D_c pep_c + galt_e --> galt1p_c + pyr_c g1p_c + h_c + utp_c <=> udpg_c + ppi_c h_e + galur_e <=> galur_c + h_c g1p_c + h_c + utp_c --> udpg_c + ppi_c gal_e + atp_c + h2o_c --> gal_c + h_c + pi_c + adp_c gal_e + h_e --> gal_c + h_c gam_e + pep_c --> gam6p_c + pyr_c nad_c + pi_c + g3p_c <=> h_c + nadh_c + 13dpg_c 10fthf_c + gar_c <=> fgam_c + thf_c + h_c atp_c + for_c + gar_c --> fgam_c + pi_c + h_c + adp_c nad_c + gcald_c + h2o_c --> 2.0 h_c + glyclt_c + nadh_c gdpddman_c --> gdpofuc_c gln_dsh_L_c + f6p_c --> glu_dsh_L_c + gam6p_c thf_c + ser_dsh_L_c --> mlthf_c + h2o_c + gly_c atp_c + gmp_c <=> gdp_c + adp_c h2o_e + glc_dsh_D_e + q8_c --> glcn_e + h_e + q8h2_c glcn_e + h_e <=> glcn_c + h_c glycogen_c + pi_c --> g1p_c 5dh4dglc_c --> pyr_c + 2h3oppan_c glcr_c --> 5dh4dglc_c + h2o_c glcr_e + h_e <=> glcr_c + h_c adpglc_c --> glycogen_c + adp_c + h_c glcur_e + h_e <=> glcur_c + h_c glc_dsh_D_e + pep_c --> g6p_c + pyr_c glc_dsh_D_e + h_e --> glc_dsh_D_c + h_c atp_c + g1p_c + h_c --> adpglc_c + ppi_c glu_dsh_L_c + atp_c + nh4_c --> gln_dsh_L_c + h_c + pi_c + adp_c gln_dsh_L_e + atp_c + h2o_c --> gln_dsh_L_c + h_c + pi_c + adp_c galt1p_c + nad_c <=> h_c + nadh_c + tag6p_dsh_D_c atp_c + glu_dsh_L_c --> adp_c + glu5p_c glu_dsh_L_e + 4abut_c <=> glu_dsh_L_c + 4abut_e glu_dsh_L_c + cys_dsh_L_c + atp_c --> h_c + pi_c + glucys_c + adp_c h_c + glu_dsh_L_c --> 4abut_c + co2_c nadp_c + h2o_c + glu_dsh_L_c <=> akg_c + nadph_c + h_c + nh4_c gln_dsh_L_c + h2o_c --> glu_dsh_L_c + nh4_c gln_dsh_L_c + prpp_c + h2o_c --> glu_dsh_L_c + pram_c + ppi_c glu_dsh_D_c <=> glu_dsh_L_c gln_dsh_L_c + nadph_c + h_c + akg_c --> nadp_c + 2.0 glu_dsh_L_c nadph_c + h_c + glutrna_c --> nadp_c + glu1sa_c + trnaglu_c trnaglu_c + glu_dsh_L_c + atp_c --> amp_c + glutrna_c + ppi_c glu_dsh_L_e + atp_c + h2o_c --> pi_c + glu_dsh_L_c + h_c + adp_c h_e + glu_dsh_L_e <=> glu_dsh_L_c + h_c glu_dsh_L_e + na1_e --> glu_dsh_L_c + na1_c 2.0 glx_c + h_c --> co2_c + 2h3oppan_c glyald_e <=> glyald_c coa_c + 2aobut_c --> gly_c + accoa_c atp_c + glyb_e + h2o_c --> glyb_c + pi_c + h_c + adp_c h_e + glyb_e <=> glyb_c + h_c atp_c + glyc3p_e + h2o_c --> pi_c + glyc3p_c + h_c + adp_c glyc3p_e + pi_c --> glyc3p_c + pi_e glyc_c + nad_c --> dha_c + nadh_c + h_c atp_c + glyc_dsh_R_c --> 3pg_c + adp_c + h_c gly_c + thf_c + nad_c --> mlthf_c + nadh_c + co2_c + nh4_c glx_c + h_c + nadh_c --> glyclt_c + nad_c nadph_c + h_c + glx_c --> nadp_c + glyclt_c glyclt_e + h_e <=> glyclt_c + h_c glyclt_c + q8_c --> q8h2_c + glx_c glyclt_c + mqn8_c --> glx_c + mql8_c glyclt_c + 2dmmq8_c --> 2dmmql8_c + glx_c glyc_c <=> glyc_e atp_c + glyc_c --> glyc3p_c + adp_c + h_c h2o_c + lgt_dsh_S_c --> gthrd_c + lac_dsh_D_c + h_c h_e + gly_e <=> gly_c + h_c gdpmann_c --> gdpddman_c + h2o_c atp_c + gmhep1p_c + h_c --> adphep_dsh_DD_c + ppi_c atp_c + gmhep7p_c --> adp_c + gmhep17bp_c + h_c gmhep17bp_c + h2o_c --> pi_c + gmhep1p_c gmp_c + nadph_c + 2.0 h_c --> nadp_c + nh4_c + imp_c gln_dsh_L_c + xmp_c + atp_c + h2o_c --> amp_c + gmp_c + glu_dsh_L_c + 2.0 h_c + ppi_c nadp_c + 6pgc_c --> co2_c + ru5p_dsh_D_c + nadph_c atp_c + glcn_c --> 6pgc_c + adp_c + h_c nadph_c + h_c + gdpofuc_c --> nadp_c + gdpfuc_c gp4g_c + h2o_c --> 2.0 gdp_c + 2.0 h_c g3pc_c + h2o_c --> h_c + glyc3p_c + chol_c h2o_c + g3pe_c --> etha_c + glyc3p_c + h_c h2o_c + g3ps_c --> glyc3p_c + h_c + ser_dsh_L_c g3pg_c + h2o_c --> glyc_c + glyc3p_c + h_c g3pi_c + h2o_c --> inost_c + glyc3p_c + h_c grdp_c + ipdp_c --> ppi_c + frdp_c gsn_c + atp_c --> adp_c + gmp_c + h_c gsn_e + h_e --> gsn_c + h_c h2o_c + gtspmd_c --> gthrd_c + spmd_c atp_c + gthrd_c + spmd_c --> gtspmd_c + pi_c + h_c + adp_c nadph_c + h_c + gthox_c <=> nadp_c + 2.0 gthrd_c gly_c + glucys_c + atp_c --> gthrd_c + h_c + pi_c + adp_c h2o_c + gtp_c --> ahdt_c + for_c gtp_c + 3.0 h2o_c --> 25drapp_c + 2.0 h_c + for_c + ppi_c h_c + h2o_c + gua_c --> xan_c + nh4_c prpp_c + gua_c --> ppi_c + gmp_c gua_e <=> gua_c gua_e + h_e --> gua_c + h_c glcur_c <=> fruur_c galur_c <=> tagur_c h2o_e <=> h2o_c 4hbz_c + octdp_c --> ppi_c + 3ophb_c 3hcinnm_e + h_e <=> 3hcinnm_c + h_c h2o_c + co2_c <=> h_c + hco3_c h_e + hdca_e --> h_c + hdca_c h2o_c + pheme_c + frdp_c --> ppi_c + hemeO_c atp_c + 4mhetz_c --> 4mpetz_c + adp_c + h_c atp_c + glc_dsh_D_c --> g6p_c + adp_c + h_c histd_c + 2.0 nad_c + h2o_c --> his_dsh_L_c + 3.0 h_c + 2.0 nadh_c hisp_c + h2o_c --> histd_c + pi_c atp_c + his_dsh_L_e + h2o_c --> his_dsh_L_c + h_c + pi_c + adp_c h_e + his_dsh_L_e <=> his_dsh_L_c + h_c h2o_c + hkndd_c --> 2.0 h_c + op4en_c + succ_c hkntd_c + h2o_c --> fum_c + op4en_c + 2.0 h_c h2o_c + 4.0 ppbng_c --> hmbil_c + 4.0 nh4_c atp_c + 4ahmmp_c --> 4ampm_c + adp_c + h_c 4h2opntn_c --> acald_c + pyr_c atp_c + 6hmhpt_c --> 6hmhptpp_c + amp_c + h_c o2_c + dhpppn_c --> hkndd_c 3hpppn_e + h_e <=> 3hpppn_c + h_c hpyr_c <=> 2h3oppan_c hpyr_c + h_c + nadh_c --> glyc_dsh_R_c + nad_c hpyr_c + h_c + nadph_c --> glyc_dsh_R_c + nadp_c nadp_c + hom_dsh_L_c <=> h_c + aspsa_c + nadph_c atp_c + hom_dsh_L_c --> phom_c + adp_c + h_c succoa_c + hom_dsh_L_c --> suchms_c + coa_c imacp_c + glu_dsh_L_c --> akg_c + hisp_c prpp_c + hxan_c --> imp_c + ppi_c 2.0 h_c + h2_c + q8_c --> q8h2_c + 2.0 h_e 2.0 h_c + h2_c + mqn8_c --> mql8_c + 2.0 h_e 2.0 h_c + h2_c + 2dmmq8_c --> 2dmmql8_c + 2.0 h_e pyam5p_c + h2o_c --> pydam_c + pi_c hxan_e <=> hxan_c nadp_c + icit_c <=> co2_c + akg_c + nadph_c chor_c --> ichor_c h2o_c + ichor_c --> 23ddhb_c + pyr_c icit_c --> glx_c + succ_c 5dglcn_c + h_c + nadh_c <=> idon_dsh_L_c + nad_c 5dglcn_c + nadph_c + h_c --> nadp_c + idon_dsh_L_c h_e + idon_dsh_L_e <=> h_c + idon_dsh_L_c gln_dsh_L_c + prlp_c --> eig3p_c + aicar_c + h_c + glu_dsh_L_c eig3p_c --> imacp_c + h2o_c h_c + 2cpr5p_c --> co2_c + 3ig3p_c + h2o_c akg_c + ile_dsh_L_c <=> glu_dsh_L_c + 3mop_c atp_c + ile_dsh_L_e + h2o_c --> ile_dsh_L_c + pi_c + h_c + adp_c h_e + ile_dsh_L_e <=> h_c + ile_dsh_L_c h2o_c + imp_c <=> fprica_c nad_c + h2o_c + imp_c --> xmp_c + h_c + nadh_c indole_e + h_e <=> indole_c + h_c atp_c + ins_c --> imp_c + adp_c + h_c h_e + ins_e --> ins_c + h_c h_e + ins_e <=> ins_c + h_c ipdp_c --> dmpp_c h_c + h2mb4p_c + nadh_c --> nad_c + ipdp_c + h2o_c 3c2hmp_c + nad_c --> nadh_c + 3c4mop_c + h_c 3c2hmp_c <=> 2ippm_c + h2o_c h2o_c + 2ippm_c <=> 3c3hmp_c 3mob_c + h2o_c + accoa_c --> 3c3hmp_c + h_c + coa_c h_c + nadph_c + alac_dsh_S_c --> 23dhmb_c + nadp_c h_c + nadph_c + 2ahbut_c --> 23dhmp_c + nadp_c acACP_c + malACP_c + h_c --> co2_c + ACP_c + actACP_c malACP_c + h_c + accoa_c --> coa_c + actACP_c + co2_c malACP_c + nadph_c + ddcaACP_c + 2.0 h_c --> nadp_c + 3hmrsACP_c + co2_c + ACP_c ctp_c + kdo_c --> ckdo_c + ppi_c h2o_c + kdo8p_c --> kdo_c + pi_c h2o_c + ara5p_c + pep_c --> kdo8p_c + pi_c h_c + 3dhgulnp_c --> co2_c + xu5p_dsh_L_c atp_c + k_e + h2o_c --> k_c + pi_c + h_c + adp_c h_e + k_e <=> h_c + k_c h2o_c + lcts_c --> gal_c + glc_dsh_D_c lald_dsh_L_c + nad_c + h2o_c <=> 2.0 h_c + lac_dsh_L_c + nadh_c lald_dsh_L_c + nad_c + h2o_c --> 2.0 h_c + lac_dsh_L_c + nadh_c h_c + nadh_c + lald_dsh_L_c <=> nad_c + 12ppd_dsh_S_c h_e + lcts_e <=> h_c + lcts_c nad_c + lac_dsh_D_c <=> h_c + nadh_c + pyr_c q8_c + lac_dsh_D_c --> pyr_c + q8h2_c 4mop_c + glu_dsh_L_c --> akg_c + leu_dsh_L_c leu_dsh_L_e + atp_c + h2o_c --> pi_c + leu_dsh_L_c + h_c + adp_c h_e + leu_dsh_L_e <=> h_c + leu_dsh_L_c gthrd_c + mthgxl_c --> lgt_dsh_S_c u23ga_c + lipidX_c --> udp_c + h_c + lipidAds_c 0.02 agpg_EC_c + h2o_c --> g3pg_c + 0.07 hdcea_c + 0.5 ocdcea_c + h_c + 0.36 hdca_c + 0.02 ttdca_c + 0.05 ttdcea_c h2o_c + 0.02 agpe_EC_c --> 0.07 hdcea_c + 0.5 ocdcea_c + h_c + 0.36 hdca_c + 0.02 ttdca_c + 0.05 ttdcea_c + g3pe_c 0.02 agpc_EC_c + h2o_c --> h_c + 0.07 hdcea_c + 0.5 ocdcea_c + 0.36 hdca_c + g3pc_c + 0.02 ttdca_c + 0.05 ttdcea_c 0.02 agpe_EC_c + 0.02 pg_EC_c --> g3pe_c + 0.02 apg_EC_c 0.02 agpc_EC_c + 0.02 pg_EC_c --> 0.02 apg_EC_c + g3pc_c 0.02 agpg_EC_c + 0.02 pg_EC_c --> 0.02 apg_EC_c + g3pg_c 2.0 cdpea_c + 2.0 udpg_c + lipa_c + 3.0 ckdo_c + 3.0 adphep_dsh_LD_c --> 10.0 h_c + lps_EC_c + 3.0 cmp_c + 2.0 cdp_c + 2.0 udp_c + 3.0 adp_c h_c + lys_dsh_L_c --> co2_c + 15dap_c lys_dsh_L_e + atp_c + h2o_c --> lys_dsh_L_c + pi_c + h_c + adp_c h_e + lys_dsh_L_e <=> h_c + lys_dsh_L_c q8_c + lac_dsh_L_c --> pyr_c + q8h2_c mqn8_c + lac_dsh_L_c --> pyr_c + mql8_c h_e + lac_dsh_L_e <=> h_c + lac_dsh_L_c nad_c + mnl1p_c <=> nadh_c + f6p_c + h_c h_c + malACP_c --> co2_c + acACP_c glx_c + h2o_c + accoa_c --> coa_c + mal_dsh_L_c + h_c atp_c + malthx_e + h2o_c --> malthx_c + h_c + pi_c + adp_c maltpt_e + atp_c + h2o_c --> h_c + pi_c + maltpt_c + adp_c atp_c + malttr_e + h2o_c --> malttr_c + h_c + pi_c + adp_c maltttr_e + atp_c + h2o_c --> h_c + pi_c + maltttr_c + adp_c atp_c + malt_e + h2o_c --> malt_c + pi_c + h_c + adp_c malt_e + pep_c --> malt6p_c + pyr_c 2.0 h_e + mal_dsh_L_e --> 2.0 h_c + mal_dsh_L_c 3.0 h_e + mal_dsh_L_e --> 3.0 h_c + mal_dsh_L_c h_c + man1p_c + gdp_c --> pi_c + gdpmann_c man6p_c <=> f6p_c 2.0 pi_c + man6p_e --> man6p_c + 2.0 pi_e nad_c + mana_c <=> nadh_c + fruur_c + h_c man_e + pep_c --> man6p_c + pyr_c 2mcit_c --> 2mcacn_c + h2o_c micit_c <=> succ_c + pyr_c oaa_c + ppcoa_c + h2o_c --> coa_c + h_c + 2mcit_c malcoa_c + ACP_c <=> coa_c + malACP_c nad_c + mal_dsh_L_c <=> h_c + oaa_c + nadh_c q8_c + mal_dsh_L_c --> oaa_c + q8h2_c mqn8_c + mal_dsh_L_c --> oaa_c + mql8_c 5mdru1p_c --> dkmpp_c + h2o_c nad_c + mal_dsh_L_c --> co2_c + nadh_c + pyr_c nadp_c + mal_dsh_L_c --> pyr_c + co2_c + nadph_c h_c + 2mecdp_c --> h2mb4p_c + h2o_c 2p4c2me_c --> 2mecdp_c + cmp_c h_e + melib_e --> h_c + melib_c 2me4p_c + ctp_c + h_c --> ppi_c + 4c2me_c atp_c + h2o_c + met_dsh_L_c --> amet_c + pi_c + ppi_c atp_c + met_dsh_D_e + h2o_c --> met_dsh_D_c + pi_c + h_c + adp_c 5mthf_c + hcys_dsh_L_c --> met_dsh_L_c + thf_c atp_c + met_dsh_L_e + h2o_c --> pi_c + adp_c + h_c + met_dsh_L_c dhap_c --> mthgxl_c + pi_c h2o_c + mi1p_dsh_D_c --> pi_c + inost_c 2mcacn_c + h2o_c --> micit_c malttr_c + h2o_c --> malt_c + glc_dsh_D_c maltttr_c + h2o_c --> malttr_c + glc_dsh_D_c maltpt_c + h2o_c --> maltttr_c + glc_dsh_D_c malthx_c + h2o_c --> maltpt_c + glc_dsh_D_c malthp_c + h2o_c --> malthx_c + glc_dsh_D_c pi_c + maltpt_c <=> maltttr_c + g1p_c pi_c + malthx_c <=> maltpt_c + g1p_c pi_c + malthp_c <=> malthx_c + g1p_c mmcoa_dsh_S_c + h_c --> ppcoa_c + co2_c mmcoa_dsh_R_c <=> mmcoa_dsh_S_c succoa_c --> mmcoa_dsh_R_c mnl_e + pep_c --> mnl1p_c + pyr_c mana_c --> 2ddglcn_c + h2o_c ckdo_c + lipidA_c --> cmp_c + kdolipid4_c + h_c ckdo_c + kdolipid4_c --> cmp_c + kdo2lipid4_c + h_c 3mob_c + h2o_c + mlthf_c --> 2dhp_c + thf_c 5mta_c + h2o_c --> 5mtr_c + ade_c h2o_c + methf_c <=> 10fthf_c mlthf_c + nadp_c <=> h_c + methf_c + nadph_c mlthf_c + h_c + nadh_c --> nad_c + 5mthf_c 5mdr1p_c <=> 5mdru1p_c atp_c + 5mtr_c --> 5mdr1p_c + adp_c + h_c h2o_c + acg5sa_c --> glu5sa_c + ac_c nac_e --> nac_c h2o_c + nad_c --> nmn_c + amp_c + 2.0 h_c h2o_e + nad_e --> nmn_e + amp_e + 2.0 h_e h_c + nadh_c + mqn8_c --> mql8_c + nad_c h_c + nadh_c + q8_c --> q8h2_c + nad_c 4.5 h_c + q8_c + nadh_c --> nad_c + q8h2_c + 3.5 h_e mqn8_c + 3.0 h_c + nadh_c --> nad_c + 2.0 h_e + mql8_c 2dmmq8_c + 3.8 h_c + nadh_c --> nad_c + 2dmmql8_c + 2.8 h_e h_c + 2dmmq8_c + nadh_c --> 2dmmql8_c + nad_c atp_c + nad_c --> h_c + adp_c + nadp_c h2o_c + nadp_c --> pi_c + nad_c atp_c + dnad_c + nh4_c --> amp_c + h_c + nad_c + ppi_c nad_c + nadph_c --> nadh_c + nadp_c prpp_c + atp_c + nac_c + h2o_c --> nicrnt_c + pi_c + adp_c + ppi_c na1_c + h_e <=> na1_e + h_c 2.0 na1_c + 3.0 h_e --> 2.0 na1_e + 3.0 h_c na1_c + 2.0 h_e --> na1_e + 2.0 h_c atp_c + gdp_c <=> gtp_c + adp_c atp_c + udp_c <=> adp_c + utp_c cdp_c + atp_c <=> adp_c + ctp_c atp_c + dtdp_c <=> dttp_c + adp_c atp_c + dgdp_c <=> adp_c + dgtp_c atp_c + dudp_c <=> dutp_c + adp_c atp_c + dcdp_c <=> dctp_c + adp_c atp_c + dadp_c <=> adp_c + datp_c nh4_e <=> nh4_c atp_c + h_c + nmn_c --> nad_c + ppi_c h2o_c + nmn_c --> nicrnt_c + nh4_c h2o_c + nmn_c --> r5p_c + h_c + ncam_c nmn_e --> nmn_c h2o_c + nmn_e --> h_c + r5p_c + ncam_c ncam_c + h2o_c --> nac_c + nh4_c atp_c + h_c + nicrnt_c --> dnad_c + ppi_c dmbzid_c + nicrnt_c --> nac_c + 5prdmbz_c + h_c quln_c + prpp_c + 2.0 h_c --> nicrnt_c + co2_c + ppi_c h_e + no2_e <=> no2_c + h_c 2.0 h_c + q8h2_c + no3_c --> no2_c + q8_c + 2.0 h_e + h2o_c 2.0 h_c + no3_c + mql8_c --> mqn8_c + no2_c + 2.0 h_e + h2o_c no2_c + no3_e --> no3_c + no2_e sbzcoa_c --> dhna_c + coa_c h2o_c + dump_c --> duri_c + pi_c h2o_c + xmp_c --> pi_c + xtsn_c h2o_c + imp_c --> pi_c + ins_c h2o_c + ump_c --> pi_c + uri_c h2o_c + dcmp_c --> dcyt_c + pi_c h2o_c + cmp_c --> cytd_c + pi_c h2o_c + dtmp_c --> pi_c + thymd_c damp_c + h2o_c --> pi_c + dad_dsh_2_c h2o_c + amp_c --> pi_c + adn_c dgmp_c + h2o_c --> pi_c + dgsn_c gmp_c + h2o_c --> pi_c + gsn_c dgtp_c + h2o_c --> ppi_c + dgmp_c + h_c gtp_c + h2o_c --> ppi_c + gmp_c + h_c h2o_c + dctp_c --> dcmp_c + ppi_c + h_c ctp_c + h2o_c --> cmp_c + ppi_c + h_c datp_c + h2o_c --> h_c + ppi_c + damp_c atp_c + h2o_c --> amp_c + ppi_c + h_c dttp_c + h2o_c --> dtmp_c + ppi_c + h_c h2o_c + utp_c --> ump_c + ppi_c + h_c dgtp_c + h2o_c --> pppi_c + dgsn_c h2o_c + gtp_c --> pppi_c + gsn_c no2_c + 3.0 nadh_c + 5.0 h_c --> 3.0 nad_c + 2.0 h2o_c + nh4_c o2_e <=> o2_c 2obut_c + coa_c --> ppcoa_c + for_c orn_c + cbp_c <=> citr_dsh_L_c + pi_c + h_c h_e + ocdca_e --> ocdca_c + h_c 5.0 ipdp_c + frdp_c --> octdp_c + 5.0 ppi_c ohpb_c + glu_dsh_L_c <=> akg_c + phthr_c 2ohph_c + amet_c --> h_c + 2omph_c + ahcys_c amet_c + 2ombzl_c --> h_c + 2ommbl_c + ahcys_c h_c + 3c4mop_c --> 4mop_c + co2_c 0.5 o2_c + 2ommbl_c --> 2omhmbl_c h_c + orot5p_c --> co2_c + ump_c 0.5 o2_c + 2omph_c --> 2ombzl_c h2o_c + op4en_c --> 4h2opntn_c h_c + 3ophb_c --> 2oph_c + co2_c 0.5 o2_c + 2oph_c --> 2ohph_c orn_c + h_c --> ptrc_c + co2_c akg_c + orn_c --> glu_dsh_L_c + glu5sa_c atp_c + orn_e + h2o_c --> orn_c + pi_c + h_c + adp_c ppi_c + orot5p_c <=> prpp_c + orot_c akg_c + h_c + thmpp_c --> co2_c + ssaltpp_c nad_c + 1pyr5c_c + 2.0 h2o_c --> h_c + nadh_c + glu_dsh_L_c 2.0 h_c + nadph_c + 1pyr5c_c --> pro_dsh_L_c + nadp_c coa_c + atp_c + pac_c --> phaccoa_c + ppi_c + amp_c pant_dsh_R_c + atp_c + ala_dsh_B_c --> amp_c + h_c + ppi_c + pnto_dsh_R_c h2o_c + 0.02 pa_EC_c --> pi_c + 0.02 12dgr_EC_c ugmda_c + udcpp_c --> uagmda_c + ump_c paps_c + trdrd_c --> so3_c + trdox_c + pap_c + 2.0 h_c octeACP_c + 0.1 tdeACP_c + 0.72 palmACP_c + 0.04 myrsACP_c + glyc3p_c + 0.14 hdeACP_c --> 2.0 ACP_c + 0.02 pa_EC_c pyr_c + coa_c + nad_c --> co2_c + nadh_c + accoa_c o2_c + pdx5p_c <=> h2o2_c + pydx5p_c phthr_c + nad_c + dxyl5p_c --> pi_c + pdx5p_c + h_c + co2_c + 2.0 h2o_c + nadh_c pdx5p_c + h2o_c --> pi_c + pydxn_c o2_c + h2o_c + peamn_c --> pacald_c + h2o2_c + nh4_c h_c + 0.02 pe_EC_c + cmp_c <=> 0.02 12dgr_EC_c + cdpea_c nad_c + 4per_c <=> h_c + ohpb_c + nadh_c atp_c + f6p_c --> adp_c + fdp_c + h_c atp_c + tag6p_dsh_D_c --> tagdp_dsh_D_c + adp_c + h_c pyr_c + coa_c --> for_c + accoa_c gam1p_c <=> gam6p_c nad_c + 3pg_c --> 3php_c + nadh_c + h_c g6p_c <=> f6p_c atp_c + 3pg_c <=> 13dpg_c + adp_c 6pgl_c + h2o_c --> 6pgc_c + h_c h2o_c + 2pglyc_c --> glyclt_c + pi_c 2pg_c <=> 3pg_c g1p_c <=> g6p_c h2o_c + 0.02 pgp_EC_c --> pi_c + 0.02 pg_EC_c 0.02 cdpdag_EC_c + glyc3p_c <=> cmp_c + 0.02 pgp_EC_c + h_c akg_c + phe_dsh_L_c <=> glu_dsh_L_c + phpyr_c h_e + phe_dsh_L_e <=> phe_dsh_L_c + h_c atp_c + pi_e + h2o_c --> 2.0 pi_c + h_c + adp_c h_e + pi_e <=> h_c + pi_c 0.02 pg_EC_c + h2o_c --> 0.07 hdcea_c + 0.5 ocdcea_c + h_c + 0.36 hdca_c + 0.02 agpg_EC_c + 0.02 ttdca_c + 0.05 ttdcea_c 0.02 pe_EC_c + h2o_c --> 0.02 agpe_EC_c + 0.07 hdcea_c + 0.5 ocdcea_c + h_c + 0.36 hdca_c + 0.02 ttdca_c + 0.05 ttdcea_c h2o_c + 0.02 pc_EC_c --> h_c + 0.07 hdcea_c + 0.05 ttdcea_c + 0.02 agpc_EC_c + 0.36 hdca_c + 0.02 ttdca_c + 0.5 ocdcea_c man1p_c <=> man6p_c 5aprbu_c + h2o_c --> pi_c + 4r5au_c 4ampm_c + atp_c --> adp_c + 2mahmp_c atp_c + pnto_dsh_R_c --> 4ppan_c + adp_c + h_c na1_e + pnto_dsh_R_e --> na1_c + pnto_dsh_R_c pyr_c + q8_c + h2o_c --> ac_c + co2_c + q8h2_c h2o_c + ppi_c --> h_c + 2.0 pi_c adp_c + ppap_c <=> atp_c + ppa_c 2.0 5aop_c --> h_c + ppbng_c + 2.0 h2o_c pep_c + co2_c + h2o_c --> oaa_c + pi_c + h_c h_c + 4ppcys_c --> co2_c + pan4p_c atp_c + oaa_c --> co2_c + adp_c + pep_c ppcoa_c + succ_c --> succoa_c + ppa_c r1p_c <=> r5p_c 2dr1p_c <=> 2dr5p_c 4ppan_c + ctp_c + cys_dsh_L_c --> h_c + cmp_c + 4ppcys_c + ppi_c nad_c + pphn_c --> 34hpp_c + co2_c + nadh_c h_c + pphn_c --> co2_c + phpyr_c + h2o_c 1.5 o2_c + pppg9_c --> 3.0 h2o_c + ppp9_c pppn_c + h_c + o2_c + nadh_c --> cechddd_c + nad_c h_e + pppn_e <=> pppn_c + h_c pyr_c + atp_c + h2o_c --> amp_c + 2.0 h_c + pi_c + pep_c uaagmda_c --> udcpdp_c + h_c + peptido_EC_c atp_c + gly_c + pram_c <=> pi_c + h_c + gar_c + adp_c fpram_c + atp_c --> 2.0 h_c + pi_c + air_c + adp_c pran_c --> 2cpr5p_c h2o_c + prbamp_c --> prfp_c atp_c + asp_dsh_L_c + 5aizc_c <=> pi_c + h_c + 25aics_c + adp_c h2o_c + prbatp_c --> ppi_c + prbamp_c + h_c gln_dsh_L_c + atp_c + h2o_c + fgam_c --> fpram_c + h_c + pi_c + adp_c + glu_dsh_L_c prfp_c --> prlp_c fad_c + pro_dsh_L_c --> 1pyr5c_c + fadh2_c + h_c atp_c + pro_dsh_L_e + h2o_c --> pi_c + h_c + adp_c + pro_dsh_L_c h_e + pro_dsh_L_e <=> pro_dsh_L_c + h_c pro_dsh_L_e + na1_e --> na1_c + pro_dsh_L_c atp_c + r5p_c <=> amp_c + prpp_c + h_c skm5p_c + pep_c <=> 3psme_c + pi_c h_c + 0.02 ps_EC_c --> co2_c + 0.02 pe_EC_c glu_dsh_L_c + 3php_c --> akg_c + pser_dsh_L_c h2o_c + pser_dsh_L_c --> pi_c + ser_dsh_L_c 0.02 cdpdag_EC_c + ser_dsh_L_c <=> cmp_c + 0.02 ps_EC_c + h_c pi_c + ppcoa_c --> coa_c + ppap_c pi_c + accoa_c <=> coa_c + actp_c pan4p_c + h_c + atp_c --> dpcoa_c + ppi_c orn_c + ptrc_e <=> orn_e + ptrc_c ptrc_c + akg_c --> glu_dsh_L_c + 4abutn_c ptrc_e + atp_c + h2o_c --> ptrc_c + h_c + pi_c + adp_c ptrc_e + h_e <=> ptrc_c + h_c pi_c + adn_c <=> r1p_c + ade_c dad_dsh_2_c + pi_c <=> 2dr1p_c + ade_c gsn_c + pi_c <=> gua_c + r1p_c dgsn_c + pi_c <=> 2dr1p_c + gua_c ins_c + pi_c <=> hxan_c + r1p_c pi_c + din_c <=> 2dr1p_c + hxan_c xtsn_c + pi_c <=> r1p_c + xan_c o2_c + pyam5p_c + h2o_c --> pydx5p_c + h2o2_c + nh4_c pydam_c + atp_c --> pyam5p_c + h_c + adp_c pydx_c + atp_c --> pydx5p_c + adp_c + h_c pydxn_c + atp_c --> pdx5p_c + adp_c + h_c h2o_c + pydx5p_c --> pi_c + pydx_c h_c + pep_c + adp_c --> atp_c + pyr_c uri_c + pi_c <=> r1p_c + ura_c h_e + pyr_e <=> h_c + pyr_c dhap_c + iasp_c --> quln_c + h_c + pi_c + 2.0 h2o_c atp_c + ribflv_c --> fmn_c + adp_c + h_c 4r5au_c + db4p_c --> pi_c + dmlz_c + 2.0 h2o_c 2.0 dmlz_c --> 4r5au_c + ribflv_c atp_c + rib_dsh_D_c --> h_c + adp_c + r5p_c atp_c + rbl_dsh_L_c --> ru5p_dsh_L_c + adp_c + h_c ru5p_dsh_L_c <=> xu5p_dsh_D_c rhcys_c --> dhptd_c + hcys_dsh_L_c atp_c + rib_dsh_D_e + h2o_c --> pi_c + adp_c + h_c + rib_dsh_D_c rmn_c <=> rml_c atp_c + rml_c --> adp_c + rml1p_c + h_c h_e + rmn_e --> h_c + rmn_c rml1p_c <=> lald_dsh_L_c + dhap_c trdrd_c + adp_c --> trdox_c + h2o_c + dadp_c trdrd_c + gdp_c --> trdox_c + dgdp_c + h2o_c trdrd_c + cdp_c --> trdox_c + h2o_c + dcdp_c trdrd_c + udp_c --> dudp_c + trdox_c + h2o_c trdrd_c + atp_c --> trdox_c + h2o_c + datp_c trdrd_c + gtp_c --> trdox_c + h2o_c + dgtp_c trdrd_c + ctp_c --> trdox_c + h2o_c + dctp_c trdrd_c + utp_c --> trdox_c + h2o_c + dutp_c ru5p_dsh_D_c <=> xu5p_dsh_D_c r5p_c <=> ru5p_dsh_D_c 5prdmbz_c + h2o_c --> rdmbzi_c + pi_c s7p_c --> gmhep7p_c 2.0 h_c + sucarg_c + 2.0 h2o_c --> sucorn_c + co2_c + 2.0 nh4_c gtp_c + atp_c + so4_c + h2o_c --> aps_c + pi_c + gdp_c + ppi_c nad_c + sbt6p_c <=> nadh_c + f6p_c + h_c sbt_dsh_D_e + pep_c --> sbt6p_c + pyr_c h2o_c + sl26da_c --> 26dap_dsh_LL_c + succ_c akg_c + sl26da_c <=> glu_dsh_L_c + sl2a6o_c atp_c + seln_c + h2o_c --> amp_c + pi_c + selnp_c atp_c + h_c + ser_dsh_L_c <=> seramp_c + ppi_c ser_dsh_L_c + accoa_c <=> acser_c + coa_c ser_dsh_D_c --> nh4_c + pyr_c ser_dsh_L_c --> nh4_c + pyr_c h_e + ser_dsh_L_e <=> h_c + ser_dsh_L_c ser_dsh_L_e + na1_e --> na1_c + ser_dsh_L_c h2o_c + sucglu_c --> glu_dsh_L_c + succ_c nad_c + h2o_c + sucgsa_c --> 2.0 h_c + sucglu_c + nadh_c ssaltpp_c + ichor_c --> 2shchc_c + thmpp_c + pyr_c dscl_c + nad_c --> nadh_c + scl_c + h_c fe2_c + scl_c --> 3.0 h_c + sheme_c nadph_c + h_c + 3dhsk_c <=> nadp_c + skm_c atp_c + skm_c --> skm5p_c + adp_c + h_c suchms_c + cys_dsh_L_c --> cyst_dsh_L_c + succ_c + h_c sucorn_c + akg_c --> sucgsa_c + glu_dsh_L_c spmd_c + accoa_c --> N1aspmd_c + coa_c + h_c spmd_c + accoa_c --> coa_c + n8aspmd_c + h_c atp_c + h2o_c + spmd_e --> spmd_c + pi_c + h_c + adp_c ptrc_c + ametam_c --> 5mta_c + spmd_c + h_c 2.0 o2s_c + 2.0 h_c --> o2_c + h2o2_c sucsal_c + nad_c + h2o_c --> 2.0 h_c + nadh_c + succ_c nadp_c + sucsal_c + h2o_c --> 2.0 h_c + nadph_c + succ_c coa_c + atp_c + sucbz_c --> sbzcoa_c + ppi_c + amp_c 2shchc_c --> h2o_c + sucbz_c succ_e + atp_c + h2o_c --> pi_c + adp_c + h_c + succ_c 2.0 h_e + succ_e --> 2.0 h_c + succ_c 3.0 h_e + succ_e --> 3.0 h_c + succ_c h_c + succ_c --> h_e + succ_e fad_c + succ_c --> fadh2_c + fum_c q8_c + fadh2_c <=> fad_c + q8h2_c fum_e + succ_c <=> fum_c + succ_e coa_c + succ_c + atp_c <=> pi_c + succoa_c + adp_c pep_c + sucr_e --> pyr_c + suc6p_c 3.0 nadp_c + h2s_c + 3.0 h2o_c <=> so3_c + 3.0 nadph_c + 5.0 h_c so4_e + atp_c + h2o_c --> h_c + pi_c + so4_c + adp_c nad_c + altrn_c <=> h_c + nadh_c + tagur_c s7p_c + g3p_c <=> f6p_c + e4p_c tartr_dsh_L_c --> h2o_c + oaa_c tartr_dsh_L_e + succ_c <=> succ_e + tartr_dsh_L_c taur_c + o2_c + akg_c --> h_c + so3_c + co2_c + succ_c + aacald_c atp_c + taur_e + h2o_c --> taur_c + pi_c + h_c + adp_c dtdp4addg_c + accoa_c --> h_c + coa_c + dtdp4aaddg_c glu_dsh_L_c + dtdp4d6dg_c --> akg_c + dtdp4addg_c dtdp4d6dg_c --> dtdp4d6dm_c h_c + nadph_c + dtdp4d6dm_c --> dtdprmn_c + nadp_c dtdpglu_c --> h2o_c + dtdp4d6dg_c atp_c + lipidAds_c --> lipidA_c + adp_c + h_c tagdp_dsh_D_c <=> dhap_c + g3p_c nadp_c + nadh_c + 2.0 h_e --> nad_c + nadph_c + 2.0 h_c succoa_c + h2o_c + thdp_c --> coa_c + sl2a6o_c h_e + thymd_e --> h_c + thymd_c h_e + thymd_e <=> h_c + thymd_c thm_e + atp_c + h2o_c --> pi_c + h_c + thm_c + adp_c thr_dsh_L_c <=> acald_c + gly_c nad_c + thr_dsh_L_c --> nadh_c + 2aobut_c + h_c thr_dsh_L_c --> 2obut_c + nh4_c h2o_c + phom_c --> pi_c + thr_dsh_L_c thr_dsh_L_e + atp_c + h2o_c --> thr_dsh_L_c + h_c + pi_c + adp_c h_e + thr_dsh_L_e <=> h_c + thr_dsh_L_c na1_e + thr_dsh_L_e --> na1_c + thr_dsh_L_c tyr_dsh_L_c + dxyl5p_c + cys_dsh_L_c + atp_c --> ala_dsh_L_c + 4mpetz_c + h_c + co2_c + 4hba_c + h2o_c + ppi_c + amp_c xu5p_dsh_D_c + r5p_c <=> s7p_c + g3p_c xu5p_dsh_D_c + e4p_c <=> f6p_c + g3p_c mql8_c + h_c + tmao_c --> mqn8_c + tma_c + h2o_c tmao_e + h_e + mql8_c --> h2o_e + tma_e + mqn8_c 2dmmql8_c + h_c + tmao_c --> 2dmmq8_c + tma_c + h2o_c tmao_e + 2dmmql8_c + h_e --> h2o_e + tma_e + 2dmmq8_c atp_c + thymd_c --> adp_c + dtmp_c + h_c pi_c + thymd_c <=> 2dr1p_c + thym_c mlthf_c + dump_c --> dhf_c + dtmp_c atp_c + thm_c <=> thmmp_c + adp_c + h_c atp_c + thmmp_c <=> thmpp_c + adp_c 2mahmp_c + 4mpetz_c + h_c --> ppi_c + thmmp_c dhap_c <=> g3p_c nadph_c + trdox_c + h_c --> nadp_c + trdrd_c h2o_c + tre6p_c --> g6p_c + glc_dsh_D_c h2o_c + tre6p_c --> pi_c + tre_c udpg_c + g6p_c --> udp_c + tre6p_c + h_c h2o_c + tre_c --> 2.0 glc_dsh_D_c h2o_e + tre_e --> 2.0 glc_dsh_D_e tre_e + pep_c --> tre6p_c + pyr_c h2o_c + trp_dsh_L_c <=> pyr_c + indole_c + nh4_c 3ig3p_c + ser_dsh_L_c --> trp_dsh_L_c + g3p_c + h2o_c indole_c + ser_dsh_L_c --> trp_dsh_L_c + h2o_c 3ig3p_c --> g3p_c + indole_c h_e + trp_dsh_L_e <=> h_c + trp_dsh_L_c h_c + nadh_c + 2h3oppan_c --> glyc_dsh_R_c + nad_c tsul_e + atp_c + h2o_c --> h_c + pi_c + tsul_c + adp_c h_e + ttdca_e --> ttdca_c + h_c akg_c + tyr_dsh_L_c <=> 34hpp_c + glu_dsh_L_c h_e + tyr_dsh_L_e <=> tyr_dsh_L_c + h_c 3hmrsACP_c + u3hga_c --> u23ga_c + h_c + ACP_c 26dap_dsh_M_c + atp_c + uamag_c --> ugmd_c + pi_c + h_c + adp_c 2.0 nad_c + uacmam_c + h2o_c --> 3.0 h_c + 2.0 nadh_c + uacmamu_c uacgam_c --> uacmam_c 3hmrsACP_c + uacgam_c <=> u3aga_c + ACP_c pep_c + uacgam_c --> pi_c + uaccg_c h_c + utp_c + acgam1p_c --> ppi_c + uacgam_c uacgam_c + uagmda_c --> udp_c + uaagmda_c + h_c glu_dsh_D_c + uama_c + atp_c --> h_c + pi_c + uamag_c + adp_c uamr_c + ala_dsh_L_c + atp_c --> h_c + pi_c + adp_c + uama_c nadph_c + uaccg_c + h_c --> uamr_c + nadp_c h2o_c + udcpdp_c --> pi_c + udcpp_c + h_c frdp_c + 8.0 ipdp_c --> udcpdp_c + 8.0 ppi_c udpg_c <=> udpgal_c udpgal_c --> udpgalfur_c 2.0 nad_c + udpg_c + h2o_c --> udpglcur_c + 3.0 h_c + 2.0 nadh_c udpg_c + gal1p_c <=> g1p_c + udpgal_c urdglyc_c + 2.0 h_c + h2o_c --> glx_c + co2_c + 2.0 nh4_c atp_c + ugmd_c + alaala_c --> h_c + pi_c + ugmda_c + adp_c u3aga_c + h2o_c --> u3hga_c + ac_c atp_c + ump_c <=> adp_c + udp_c 2kmb_c + glu_dsh_L_c --> akg_c + met_dsh_L_c uppg3_c + 2.0 amet_c --> dscl_c + 2.0 ahcys_c + h_c hmbil_c --> h2o_c + uppg3_c 4.0 h_c + uppg3_c --> 4.0 co2_c + cpppg3_c prpp_c + ura_c --> ppi_c + ump_c h_e + ura_e --> ura_c + h_c h_e + ura_e <=> ura_c + h_c urea_e <=> urea_c atp_c + dump_c <=> dudp_c + adp_c uri_c + gtp_c --> gdp_c + ump_c + h_c h_e + uri_e --> uri_c + h_c h_e + uri_e <=> uri_c + h_c h2o_c + u23ga_c --> lipidX_c + ump_c + 2.0 h_c akg_c + val_dsh_L_c <=> glu_dsh_L_c + 3mob_c atp_c + val_dsh_L_e + h2o_c --> pi_c + h_c + adp_c + val_dsh_L_c h_e + val_dsh_L_e <=> h_c + val_dsh_L_c 3mob_c + ala_dsh_L_c --> pyr_c + val_dsh_L_c xu5p_dsh_L_c --> ru5p_dsh_L_c xan_e <=> xan_c h_e + xan_e --> xan_c + h_c prpp_c + xan_c --> ppi_c + xmp_c xtsn_e + h_e <=> xtsn_c + h_c xyl_dsh_D_c <=> xylu_dsh_D_c fru_c --> glc_dsh_D_c xylu_dsh_D_c + atp_c --> xu5p_dsh_D_c + h_c + adp_c atp_c + xyl_dsh_D_e + h2o_c --> xyl_dsh_D_c + pi_c + h_c + adp_c h_e + xyl_dsh_D_e --> h_c + xyl_dsh_D_c |
from cameo.flux_analysis import simulation
help(simulation)
Help on module cameo.flux_analysis.simulation in cameo.flux_analysis: NAME cameo.flux_analysis.simulation FILE /Users/joao/Documents/repos/cameo/cameo/flux_analysis/simulation.py DESCRIPTION Methods for simulating flux distributions. Currently implements: * fba - Flux Balance Analysis * pfba - Parsimonious Flux Balance Analysis * lmoma - (Linear) Minimization of Metabolic Adjustment * room - Regulatory On/Off Minimization FUNCTIONS fba(model, objective=None, *args, **kwargs) Flux Balance Analysis. Parameters ---------- model: SolverBasedModel objective: a valid objective - see SolverBaseModel.objective (optional) Returns ------- FluxDistributionResult Contains the result of the linear solver. lmoma(model, reference=None, cache={}, volatile=True, *args, **kwargs) Linear Minimization Of Metabolic Adjustment. Parameters ---------- model: SolverBasedModel reference: dict objective: str or reaction or optlang.Objective An objective to be minimized/maximized for volatile: boolean cache: dict Returns ------- FluxDistributionResult Contains the result of the linear solver. moma(model, reference=None, *args, **kwargs) pfba(model, objective=None, *args, **kwargs) Parsimonious Flux Balance Analysis. Parameters ---------- model: SolverBasedModel objective: str or reaction or optlang.Objective An objective to be minimized/maximized for Returns ------- FluxDistributionResult Contains the result of the linear solver. room(model, reference=None, cache={}, volatile=True, delta=0.03, epsilon=0.001, *args, **kwargs) Regulatory On/Off Minimization [1]. Parameters ---------- model: SolverBasedModel reference: dict objective: str or reaction or optlang.Objective An objective to be minimized/maximized for volatile: boolean cache: dict Returns ------- FluxDistributionResult Contains the result of the linear solver. References ---------- [1] Tomer Shlomi, Omer Berkman and Eytan Ruppin, "Regulatory on/off minimization of metabolic flux changes after genetic perturbations", PNAS 2005 102 (21) 7695-7700; doi:10.1073/pnas.0406346102 DATA __all__ = ['fba', 'pfba', 'moma', 'lmoma', 'room']
FBA and PFBA can be used to compute flux distributions for the Wild-Type (model as it as been described) as well as knockouts (next session)
%time
fba_result = simulation.fba(model)
CPU times: user 3 µs, sys: 1e+03 ns, total: 4 µs Wall time: 6.91 µs
%time
pfba_result = simulation.pfba(model)
CPU times: user 3 µs, sys: 1 µs, total: 4 µs Wall time: 6.91 µs
Although PFBA and FBA can be used to simulate the effect of knockouts, other methods have been proven more valuable for that task: MOMA and ROOM. In cameo we implement a linear version of MOMA.
Simulating knockouts:
model.reactions.PGI
Id | PGI |
Stoichiometry | g6p_c <=> f6p_c |
Lower bound | -999999.000000 |
Upper bound | 999999.000000 |
model.reactions.PGI.knock_out()
model.reactions.PGI
Id | PGI |
Stoichiometry | g6p_c --> f6p_c |
Lower bound | 0.000000 |
Upper bound | 0.000000 |
%time
fba_knockout_result = simulation.fba(model)
fba_knockout_result[model.objective]
CPU times: user 2 µs, sys: 0 ns, total: 2 µs Wall time: 5.01 µs
0.905983
pfba_knockout_result = simulation.pfba(model)
pfba_knockout_result[model.objective]
0.905983
MOMA and ROOM relly on a reference (wild-type) flux distribution and we can use the one previously computed.
Parsimonious FBA references seem to produce better results using this methods
lmoma_result["2 * EX_glc_lp_e_rp_"]
-18.7358
%time
lmoma_result = simulation.lmoma(model, reference=pfba_result.fluxes)
lmoma_result[model.objective]
CPU times: user 2 µs, sys: 1 µs, total: 3 µs Wall time: 5.01 µs
0.791393
%time
room_result = simulation.room(model, reference=pfba_result.fluxes)
room_result[model.objective]
CPU times: user 2 µs, sys: 1 µs, total: 3 µs Wall time: 5.01 µs
0.887440
room_result
<cameo.core.result.FluxDistributionResult at 0x10aa75b50>