Low-level interface for developers¶
import pandas
pandas.options.display.max_rows = 8
from cameo import load_model
model = load_model('iJO1366')
cameo vs. cobrapy¶
Importing a model¶
cobrapy (load a model in SBML format):
from cobra.io import read_sbml_model
cobrapy_model = read_sbml_model('../tests/data/EcoliCore.xml')
cameo (load models from different formats):
from cameo import load_model
# read SBML model
model = load_model('../tests/data/EcoliCore.xml')
# ... or read a pickled model
model = load_model('../tests/data/iJO1366.pickle')
# ... or just import a model by ID from http://darwin.di.uminho.pt/models
iAF1260 = load_model('iAF1260')
Solving models¶
When optimizing models with cobrapy, the status of a returned solution needs to be checked to figure out if the solver found and optimal solution.
cobrapy_solution = cobrapy_model.optimize()
if cobrapy_solution.status == 'optimal':
pass # do something
cameo will raise an exception if non-optimal solution was found.
print model.objective
Maximize
1.0*Ec_biomass_iJO1366_core_53p95M
model.solve() # no exception
cp_model = model.copy()
# demand a very high biomass production rendering the model infeasible
cp_model.reactions.Ec_biomass_iJO1366_core_53p95M.lower_bound = 1000
cp_model.solve()
---------------------------------------------------------------------------
Infeasible Traceback (most recent call last)
<ipython-input-13-286e284739c2> in <module>()
2 cp_model = model.copy()
3 cp_model.reactions.Ec_biomass_iJO1366_core_53p95M.lower_bound = 1000 # demand an unrealistically high biomass production
----> 4 cp_model.solve()
/Users/niko/Arbejder/Dev/cameo/cameo/solver_based_model.pyc in solve(self, *args, **kwargs)
881 raise exceptions._OPTLANG_TO_EXCEPTIONS_DICT.get(status, SolveError)(
882 'Solving model %s did not return an optimal solution. The returned solution status is "%s"' % (
--> 883 self, status))
884 return solution
885 else:
Infeasible: Solving model iJO1366 did not return an optimal solution. The returned solution status is "infeasible"
Therefore, :code:try-except-else-finally statements should be used in code that utilizes :py:meth:cameo.solver_based_model.SolverBasedModel.solve.
try:
solution = model.solve()
except cameo.exceptions.SolverError:
print "A non-optimal solution was returned by the solver"
else:
pass # do something
It is important to note that cameo models maintain optimize to maintain compatibility with cobrapy but we discourage its use.
Solution object¶
solution
Formulating and solving optimization problems¶
Importing models¶
cameo has a single function (load_model) that can import models stored in different formats.
SBML¶
Models available on the web¶
cameo provides an interface to models hosted online by the University of Minho.
from cameo.webmodels import index_models
index_models()
| id | name | doi | author | year | formats | organism | taxonomy | |
|---|---|---|---|---|---|---|---|---|
| 0 | 1 | iJR904 | 10.1186/gb-2003-4-9-r54 | Reed | 2003 | [sbml] | Escherichia coli str. K12 substr. MG1655 | Bacteria; Proteobacteria; Gammaproteobacteria;... |
| 1 | 2 | iAF1260 | 10.1038/msb4100155 | Feist | 2007 | [sbml] | Escherichia coli str. K12 substr. MG1655 | Bacteria; Proteobacteria; Gammaproteobacteria;... |
| 2 | 3 | iMM904 | 10.1186/1752-0509-3-37 | Mo | 2007 | [sbml] | Saccharomyces cerevisiae | Eukaryota; Opisthokonta; Fungi; Dikarya; Ascom... |
| 3 | 4 | iJP815 | 10.1371/journal.pcbi.1000210 | Puchalka | 2008 | [sbml] | Pseudomonas putida str. KT2440 | Bacteria; Proteobacteria; Gammaproteobacteria;... |
| ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 132 | 133 | iTT548 | 10.1186/1475-2859-13-61 | Na-Rae Lee | 2014 | [sbml, excel] | Thermus thermophilus | Bacteria; Deinococcus-Thermus; Deinococci; The... |
| 133 | 134 | EctoGEM-1.0 | 10.1111/tpj.12627 | Prigent | 2014 | [sbml] | Ectocarpus siliculosus | Eukaryota; Stramenopiles; PX clade; Phaeophyce... |
| 134 | 135 | iMF721 | 10.1111/1462-2920.12513 | Fondi | 2014 | [sbml] | Pseudoalteromonas haloplanktis TAC125 | Bacteria; Proteobacteria; Gammaproteobacteria;... |
| 135 | 136 | Arabidopsis core model | 10.1104/pp.114.235358 | Arnold | 2014 | [sbml] | Arabidopsis thaliana | Eukaryota; Viridiplantae; Streptophyta; Strept... |
136 rows × 8 columns
If load_model is provided with a valid model name, it will automatically download the model in SBML format and import it.
load_model('iMM904')
| Name | iMM904 |
| Number of metabolites | 1228 |
| Number of reactions | 1577 |
| Reactions | h2o_c + 13BDglcn_c --> glc_D_c 13BDglcn_e + h2o_e --> glc_D_e udpg_c --> h_c + udp_c + 13BDglcn_c udpg_c --> 16BDglcn_c + udp_c + h_c h2o_c + h_c + 23camp_c --> amp2p_c 2dda7p_c <=> 2dda7p_m 2dhp_c <=> 2dhp_m h2o_c + 2doxg6p_c --> 2dglc_c + pi_c 2hb_c + nad_c <=> 2obut_c + h_c + nadh_c 2hb_e + h_e <=> 2hb_c + h_c 2hpmhmbq_m + amet_m --> ahcys_m + h_m + q6_m 2hp6mp_m + o2_m --> h2o_m + 2hp6mbq_m 2hp6mbq_m + amet_m --> h_m + 2hpmmbq_m + ahcys_m 0.5 o2_m + 2hpmmbq_m --> 2hpmhmbq_m 2mbac_c --> 2mbac_e 2mbald_c <=> 2mbald_e 2mbald_c <=> 2mbald_m 2mbtoh_c <=> 2mbtoh_e 2mbtoh_c <=> 2mbtoh_m 2mppal_c <=> 2mppal_e 2mppal_c <=> 2mppal_m 2obut_c <=> 2obut_m 2oxoadp_m --> 2oxoadp_c 2phetoh_e <=> 2phetoh_c 2phetoh_m <=> 2phetoh_c nadh_m + h_m + 34hpp_m --> 34hpl_m + nad_m 34hpp_c + o2_c --> co2_c + hgentis_c 34hpp_c + h_c <=> h_m + 34hpp_m 34hpp_c + h_c <=> 34hpp_x + h_x 3c3hmp_c <=> 3c3hmp_e 3c3hmp_c <=> 3c3hmp_m 3c4mop_c <=> 3c4mop_m amet_m + 3dh5hpb_m --> 3hph5mb_m + h_m + ahcys_m 3dh5hpb_c <=> 3dh5hpb_m 3dsphgn_c + nadph_c + h_c --> sphgn_c + nadp_c o2_c + 3hanthrn_c --> cmusa_c + h_c 3hph5mb_m --> 2hp6mp_m + co2_m amet_c + 3c2hmp_c --> 3ipmmest_c + ahcys_c 3mbald_c <=> 3mbald_e 3mbald_c <=> 3mbald_m h_c + 3mob_c --> 2mppal_c + co2_c 3mob_c <=> 3mob_m h_c + 3mop_c --> 2mbald_c + co2_c 3mop_e <=> 3mop_c 3mop_c <=> 3mop_m 0.5 o2_c + 3ophb_5_c --> 3dh5hpb_c 3ophb_5_c <=> 3ophb_5_m 4abutn_c <=> 4abutn_m 4abut_c <=> 4abut_m 4abz_c <=> 4abz_e 4abz_c <=> 4abz_m 4h2oglt_c <=> 4h2oglt_m 4h2oglt_c <=> 4h2oglt_x coucoa_m + coa_m + nad_m + h2o_m --> accoa_m + 4hbzcoa_m + h_m + nadh_m h2o_m + 4hbzcoa_m --> 4hbz_m + h_m + coa_m 4hbz_c <=> 4hbz_m nad_m + 4hglusa_m + h2o_m <=> e4hglu_m + 2.0 h_m + nadh_m 4hpro_LT_c <=> 4hpro_LT_m h2o_c + phthr_c --> pi_c + 4hthr_c h_c + 4mop_c --> 3mbald_c + co2_c 5aop_e + h_e --> 5aop_c + h_c 5aop_c <=> 5aop_m 6pgl_c <=> 6pgl_r 8aonn_e + h_e <=> 8aonn_c + h_c h2o_c + 4aabutn_c --> ac_c + 4abut_c h2o_c + o2_c + aact_c --> h2o2_c + nh4_c + mthgxl_c atp_c + h_c + nadph_c + L2aadp_c --> L2aadp6sa_c + ppi_c + amp_c + nadp_c atp_c + nadh_c + h_c + L2aadp_c --> L2aadp6sa_c + ppi_c + amp_c + nad_c glu_L_c + 2oxoadp_c <=> L2aadp_c + akg_c akg_c + 4abut_c --> glu_L_c + sucsal_c abt_e <=> abt_c nad_m + 4abutn_m + h2o_m --> 4abut_m + nadh_m + 2.0 h_m 4abut_e + h_e <=> 4abut_c + h_c 2.0 accoa_c --> aacoa_c + coa_c 2.0 accoa_m --> aacoa_m + coa_m 3odcoa_x + coa_x --> accoa_x + occoa_x coa_x + 3oddcoa_x --> accoa_x + dcacoa_x coa_x + 3otdcoa_x --> accoa_x + ddcacoa_x 3ohdcoa_x + coa_x --> tdcoa_x + accoa_x 3ohodcoa_x + coa_x --> accoa_x + pmtcoa_x 3ohxccoa_x + coa_x --> ttccoa_x + accoa_x 2.0 acald_c --> actn_R_c acald_e <=> acald_c acald_m <=> acald_c hco3_c + accoa_c + atp_c <=> malcoa_c + adp_c + h_c + pi_c atp_m + hco3_m + accoa_m <=> malcoa_m + pi_m + adp_m + h_m accoa_c <=> accoa_n aces_c --> aces_e accoa_c + gam6p_c <=> acgam6p_c + coa_c + h_c acgam6p_c <=> acgam1p_c atp_m + acglu_m --> adp_m + acg5p_m accoa_m + glu_L_m --> h_m + acglu_m + coa_m 2obut_m + pyr_m + h_m --> co2_m + 2ahbut_m iamac_c + h2o_c --> ac_c + h_c + iamoh_c ibutac_c + h2o_c --> ac_c + h_c + ibutoh_c aces_c + h2o_c --> ac_c + etoh_c + h_c 2.0 pyr_m + h_m --> co2_m + alac_S_m accoa_m + h2o_m --> ac_m + h_m + coa_m o2_x + dcacoa_x --> dc2coa_x + h2o2_x ddcacoa_x + o2_x --> dd2coa_x + h2o2_x o2_x + tdcoa_x --> h2o2_x + td2coa_x o2_x + pmtcoa_x --> hdd2coa_x + h2o2_x o2_x + stcoa_x --> h2o2_x + od2coa_x hexccoa_x + o2_x --> hxc2coa_x + h2o2_x accoa_c + ACP_c <=> coa_c + acACP_c accoa_m + ACP_m <=> acACP_m + coa_m amet_c + acon_T_c --> acon5m_c + ahcys_c cit_c <=> icit_c 2mcit_m <=> micit_m cit_m <=> icit_m acg5sa_m + glu_L_m --> acorn_m + akg_m h2o_e + fmn_e --> pi_e + ribflv_e coa_m + h2o_m --> 2.0 h_m + pan4p_m + pap_m acrn_c --> acrn_m acrn_x --> acrn_c atp_c + ac_c + coa_c --> ppi_c + amp_c + accoa_c coa_m + ac_m + atp_m --> accoa_m + amp_m + ppi_m ac_x + atp_x + coa_x --> accoa_x + ppi_x + amp_x ac_e + h_e <=> ac_c + h_c ac_c <=> ac_m ac_c <=> ac_x ac_e <=> ac_c h2o_c + h_c + adn_c --> nh4_c + ins_c 4adcho_c --> 4abz_c + pyr_c + h_c gln_L_c + chor_c --> glu_L_c + 4adcho_c h2o_c + ade_c + h_c --> hxan_c + nh4_c ade_e + h_e --> ade_c + h_c ade_c <=> ade_m 0.01 1agly3p_SC_c + h_c + nadph_c --> 0.01 1ag3p_SC_c + nadp_c atp_c + amp_c <=> 2.0 adp_c amp_m + atp_m <=> 2.0 adp_m gtp_c + amp_c <=> adp_c + gdp_c amp_m + gtp_m <=> adp_m + gdp_m itp_c + amp_c <=> idp_c + adp_c amp_m + itp_m <=> idp_m + adp_m amet_c + h_c --> ametam_c + co2_c atp_c --> camp_c + ppi_c atp_c + adn_c --> h_c + adp_c + amp_c adn_c + h2o_c --> ade_c + rib_D_c h_e + adn_e --> h_c + adn_c prpp_c + ade_c --> amp_c + ppi_c aps_c + atp_c --> adp_c + h_c + paps_c dcamp_c <=> amp_c + fum_c 25aics_c <=> aicar_c + fum_c asp_L_c + imp_c + gtp_c --> gdp_c + 2.0 h_c + dcamp_c + pi_c 0.02 dcacoa_c + 0.1 tdcoa_c + 0.06 ddcacoa_c + 0.24 odecoa_c + 0.27 pmtcoa_c + 0.05 stcoa_c + 0.01 1ag3p_SC_c + 0.09 ocdycacoa_c + 0.17 hdcoa_c --> coa_c + 0.01 pa_SC_c nadph_m + acg5p_m + h_m --> pi_m + nadp_m + acg5sa_m glx_c + ala_L_c --> gly_c + pyr_c ahcys_c <=> ahcys_m h2o_c + ahcys_c --> hcys_L_c + adn_c air_c + 2.0 h_c --> 4ahmmp_c + pi_c + gcald_c ch4s_c + achms_c --> ac_c + h_c + met_L_c h2s_c + achms_c --> ac_c + h_c + hcys_L_c 10fthf_c + aicar_c <=> fprica_c + thf_c air_c + co2_c <=> 5aizc_c + h_c akg_m + h_m + lpam_m <=> sdhlam_m + co2_m coa_m + sdhlam_m --> succoa_m + dhlam_m akg_c + mal_L_e <=> mal_L_c + akg_e akg_c + h_c <=> h_n + akg_n akg_e + h_e <=> akg_c + h_c akg_c <=> akg_x 3.0 h2o_c + ahdt_c --> dhnpt_c + 3.0 pi_c + 2.0 h_c h_m + gly_m + succoa_m --> co2_m + coa_m + 5aop_m akg_c + ala_L_c <=> glu_L_c + pyr_c ala_L_m + akg_m <=> pyr_m + glu_L_m trnaala_c + atp_c + ala_L_c --> ppi_c + alatrna_c + amp_c h_e + ala_L_e <=> h_c + ala_L_c ala_L_m --> ala_L_c h_c + nadph_c + glyald_c --> glyc_c + nadp_c 2mbald_c + h_c + nadh_c --> 2mbtoh_c + nad_c nadh_m + h_m + 2mbald_m --> 2mbtoh_m + nad_m 2mbald_c + nadph_c + h_c --> 2mbtoh_c + nadp_c h_c + nadh_c + 2mppal_c --> ibutoh_c + nad_c nadh_m + 2mppal_m + h_m --> ibutoh_m + nad_m h_c + 2mppal_c + nadph_c --> ibutoh_c + nadp_c h_c + nadh_c + 3mbald_c --> iamoh_c + nad_c nadh_m + h_m + 3mbald_m --> iamoh_m + nad_m h_c + nadph_c + 3mbald_c --> iamoh_c + nadp_c h_c + nadh_c + pacald_c --> nad_c + 2phetoh_c nadh_m + pacald_m + h_m --> nad_m + 2phetoh_m h_c + nadph_c + pacald_c --> 2phetoh_c + nadp_c h_c + id3acald_c + nadh_c --> ind3eth_c + nad_c id3acald_m + h_m + nadh_m --> ind3eth_m + nad_m etoh_c + nad_c --> h_c + acald_c + nadh_c h_c + nadh_c + acald_c --> etoh_c + nad_c acald_m + h_m + nadh_m --> etoh_m + nad_m etoh_c + nad_c <=> h_c + acald_c + nadh_c h2o_c + pacald_c + nad_c --> pac_c + nadh_c + 2.0 h_c id3acald_m + nad_m + h2o_m --> ind3ac_m + 2.0 h_m + nadh_m h2o_c + nadp_c + id3acald_c --> ind3ac_c + 2.0 h_c + nadph_c id3acald_m + nadp_m + h2o_m --> ind3ac_m + nadph_m + 2.0 h_m h2o_c + aproa_c + nad_c --> nadh_c + 2.0 h_c + ala_B_c acald_m + nad_m + h2o_m --> 2.0 h_m + nadh_m + ac_m h2o_c + nadp_c + acald_c --> 2.0 h_c + nadph_c + ac_c acald_m + h2o_m + nadp_m --> nadph_m + ac_m + 2.0 h_m h2o_c + alltt_c <=> urdglyc_c + urea_c h2o_c + alltn_c <=> alltt_c + h_c alltn_e --> alltn_c alltt_e --> alltt_c h2o_c + 3.0 h_c + allphn_c --> 2.0 co2_c + 2.0 nh4_c amet_c + 8aonn_c <=> amob_c + dann_c amet_e + h_e --> amet_c + h_c amet_c <=> amet_m h2o_c + 4gudbd_c --> 4gudbutn_c + nh4_c h2o_c + pad_c --> nh4_c + pac_c h2o_c + iad_c --> ind3ac_c + nh4_c h2o_c + h_c + amp_c --> nh4_c + imp_c h2o_c + amp_c --> ade_c + r5p_c amp_n <=> amp_c anth_c + prpp_c --> ppi_c + pran_c gln_L_c + chor_c --> anth_c + glu_L_c + pyr_c + h_c h_c + 2aobut_c --> aact_c + co2_c h2o_c + ap4a_c <=> 2.0 adp_c + 2.0 h_c aprut_c + h2o_c + o2_c --> h2o2_c + nh4_c + n4abutn_c o2_c + Dara14lac_c <=> h2o2_c + ertascb_D_c nadp_c + arab_D_c --> Dara14lac_c + h_c + nadph_c arab_L_c + nadph_c + h_c --> nadp_c + abt_c arab_D_e <=> arab_D_c arab_L_e <=> arab_L_c h2o_c + arg_L_c --> orn_c + urea_c argsuc_c <=> arg_L_c + fum_c atp_c + asp_L_c + citr_L_c <=> ppi_c + argsuc_c + amp_c + h_c atp_c + arg_L_c + trnaarg_c --> ppi_c + amp_c + argtrna_c atp_m + trnaarg_m + arg_L_m --> amp_m + argtrna_m + ppi_m h_c + arg_L_c <=> arg_L_m + h_m arg_L_e + h_e <=> arg_L_c + h_c h_v + arg_L_c --> h_c + arg_L_v his_L_c + amet_c --> NPmehis_c + h_c + ahcys_c 4pasp_c + h_c + nadph_c --> nadp_c + aspsa_c + pi_c h2o_c + asn_L_c --> asp_L_c + nh4_c h2o_e + asn_L_e --> nh4_e + asp_L_e h2o_c + atp_c + asp_L_c + gln_L_c --> asn_L_c + ppi_c + amp_c + glu_L_c + h_c atp_c + asn_L_c + trnaasn_c --> ppi_c + asntrna_c + amp_c trnaasn_m + asn_L_m + atp_m --> asntrna_m + amp_m + ppi_m h_c + asn_L_c <=> asn_L_m + h_m asn_L_e + h_e <=> asn_L_c + h_c h_v + asn_L_c --> h_c + asn_L_v h_v + asn_L_v --> asn_L_c + h_c asp_L_c + cbp_c --> cbasp_c + pi_c + h_c asp_L_m + glu_L_c --> asp_L_c + glu_L_m glu_L_x + asp_L_c <=> glu_L_c + asp_L_x asp_L_c + atp_c --> adp_c + 4pasp_c asp_L_c + fad_m --> h_c + iasp_c + fadh2_m asp_L_c + akg_c <=> glu_L_c + oaa_c asp_L_m + akg_m <=> glu_L_m + oaa_m akg_x + asp_L_x <=> oaa_x + glu_L_x atp_c + asp_L_c + trnaasp_c --> ppi_c + asptrna_c + amp_c trnaasp_m + asp_L_m + atp_m --> amp_m + asptrna_m + ppi_m asp_L_c + h_c <=> h_m + asp_L_m asp_L_c + h_c <=> asp_L_n + h_n asp_L_e + h_e <=> asp_L_c + h_c asp_L_n <=> asp_L_c h_v + asp_L_v --> asp_L_c + h_c athr_L_c + nadp_c <=> h_c + 2aobut_c + nadph_c atp_c + h_x + amp_x --> amp_c + h_c + atp_x h_c + atp_c + adp_c --> pi_c + ap4a_c gtp_c + h_c + adp_c --> pi_c + ap4g_c gtp_c + h_c + gdp_c --> pi_c + gp4g_c 2.0 h2o_c + atp_c --> amp_c + 2.0 pi_c + 2.0 h_c h2o_c + atp_c --> adp_c + pi_c + h_c prpp_c + atp_c --> ppi_c + prbatp_c h2o_c + atp_c --> adp_c + h_e + pi_c pi_g + adp_g + 3.0 h_c --> 2.0 h_g + atp_g + h2o_g pi_m + 3.0 h_c + adp_m --> 2.0 h_m + h2o_m + atp_m adp_v + pi_v + 3.0 h_c --> atp_v + 2.0 h_v + h2o_v atp_m + adp_c + h_c --> atp_c + adp_m + h_m atp_c + adp_x + h_x --> adp_c + h_c + atp_x h_c + btn_c + atp_c --> ppi_c + btamp_c h2o_c + pap_c --> amp_c + pi_c btd_RR_c + nad_c <=> actn_R_c + h_c + nadh_c btd_RR_c <=> btd_RR_e btn_e + h_e --> btn_c + h_c dtbt_c + s_c <=> btn_c + 2.0 h_c h_c + 44mctr_c + nadph_c --> nadp_c + 44mzym_c ergtrol_c + o2_c + h_c + nadph_c --> 2.0 h2o_c + nadp_c + ergtetrol_c ergtrol_c + o2_c + nadh_c + h_c --> 2.0 h2o_c + nad_c + ergtetrol_c ergtetrol_r + nadph_r + h_r --> ergst_r + nadp_r nad_c + 4mzym_int1_c --> 4mzym_int2_c + h_c + nadh_c + co2_c zym_int1_c + nad_c --> nadh_c + h_c + co2_c + zym_int2_c 4mzym_int2_c + nadph_c + h_c --> 4mzym_c + nadp_c h_c + zym_int2_c + nadph_c --> nadp_c + zymst_c 44mzym_c + 3.0 o2_c + 3.0 h_c + 3.0 nadph_c --> 4.0 h2o_c + 3.0 nadp_c + 4mzym_int1_c 3.0 o2_c + 3.0 nadph_c + 3.0 h_c + 4mzym_c --> 4.0 h2o_c + zym_int1_c + 3.0 nadp_c o2_c + nadph_c + h_c + epist_c --> 2.0 h2o_c + ergtrol_c + nadp_c fecost_c --> epist_c 2.0 h2o2_c --> 2.0 h2o_c + o2_c 2.0 h2o2_x --> 2.0 h2o_x + o2_x cbasp_n <=> cbasp_c h2o_c + gln_L_c + 2.0 atp_c + hco3_c --> glu_L_c + 2.0 adp_c + cbp_c + 2.0 h_c + pi_c cbp_c <=> cbp_n 2.0 focytc_m + h2o2_m --> 2.0 ficytc_m + 2.0 h2o_m glyc3p_m + 0.01 cdpdag_SC_m <=> cmp_m + h_m + 0.01 pgp_SC_m cdp_c <=> cdp_n cer1_24_c <=> cer1_24_r cer1_26_c <=> cer1_26_r cer2_24_c <=> cer2_24_r cer2_26_c <=> cer2_26_r cer1_24_r + coa_r + h_r --> ttccoa_r + sphgn_r cer1_26_r + h_r + coa_r --> sphgn_r + hexccoa_r cer2_24_r + coa_r + h_r --> psphings_r + ttccoa_r cer2_26_r + h_r + coa_r --> hexccoa_r + psphings_r o2_c + h_c + cer1_24_c + nadph_c --> h2o_c + cer2_24_c + nadp_c cer1_26_c + o2_c + h_c + nadph_c --> h2o_c + cer2_26_c + nadp_c sphgn_c + ttccoa_c --> cer1_24_c + coa_c + h_c sphgn_r + ttccoa_r --> cer1_24_r + h_r + coa_r sphgn_c + hexccoa_c --> cer1_26_c + coa_c + h_c sphgn_r + hexccoa_r --> cer1_26_r + h_r + coa_r psphings_c + ttccoa_c --> h_c + cer2_24_c + coa_c psphings_r + ttccoa_r --> cer2_24_r + h_r + coa_r hexccoa_c + psphings_c --> cer2_26_c + coa_c + h_c hexccoa_r + psphings_r --> cer2_26_r + h_r + coa_r o2_c + h_c + cer1_24_c + nadph_c --> h2o_c + cer2__24_c + nadp_c cer1_26_c + o2_c + h_c + nadph_c --> h2o_c + cer2__26_c + nadp_c o2_c + cer2_24_c + h_c + nadph_c --> h2o_c + cer3_24_c + nadp_c o2_c + cer2_26_c + nadph_c + h_c --> h2o_c + cer3_26_c + nadp_c h_c + ctp_c + cholp_c --> ppi_c + cdpchol_c amet_c + o2_c + zymst_c --> ahcys_c + 2.0 h2o_c + ergtetrol_c + h_c chol_e + h_e --> chol_c + h_c chol_c + atp_c --> h_c + adp_c + cholp_c chor_c --> pphn_c 3psme_c --> chor_c + pi_c chor_c --> 4hbz_c + pyr_c h2o_c + chitin_c --> ac_c + chitos_c + h_c udpacgal_c --> h_c + udp_c + chitin_c h_e + cit_e <=> cit_c + h_c cit_c + mal_L_m <=> mal_L_c + cit_m cit_x + mal_L_c <=> cit_c + mal_L_x pep_m + cit_c <=> pep_c + cit_m cit_c + icit_m <=> cit_m + icit_c cit_c + icit_x <=> cit_x + icit_c 0.01 pg_SC_m + 0.01 cdpdag_SC_m --> 0.01 clpn_SC_m + h_m + cmp_m h2o_c + cmp_c --> r5p_c + csn_c co2_e <=> co2_c co2_c <=> co2_g co2_c <=> co2_m co2_n <=> co2_c co2_c <=> co2_x co2_c <=> co2_v coa_x + h2o_x --> pan4p_x + 2.0 h_x + pap_x coa_c --> coa_m coa_c <=> coa_n T4hcinnm_m + coa_m + atp_m --> coucoa_m + amp_m + ppi_m o2_c + cpppg3_c + 2.0 h_c --> 2.0 h2o_c + 2.0 co2_c + pppg9_c crn_m + acrn_c --> crn_c + acrn_m acrn_x + crn_c --> acrn_c + crn_x crn_e <=> crn_c crn_m --> crn_c crn_c --> crn_x coa_m + acrn_m <=> accoa_m + crn_m crn_x + accoa_x <=> acrn_x + coa_x accoa_c + crn_c <=> acrn_c + coa_c h2o_c + h_c + csn_c --> ura_c + nh4_c h_e + csn_e --> h_c + csn_c accoa_m + oaa_m + h2o_m --> coa_m + cit_m + h_m oaa_x + h2o_x + accoa_x --> h_x + cit_x + coa_x atp_c + utp_c + nh4_c --> ctp_c + adp_c + 2.0 h_c + pi_c h2o_c + atp_c + utp_c + gln_L_c --> glu_L_c + ctp_c + adp_c + 2.0 h_c + pi_c cmp_m + ctp_c + 2.0 h_c --> ctp_m + cmp_c + 2.0 h_m 6.0 h_m + o2_m + 4.0 focytc_m --> 4.0 ficytc_m + 6.0 h_c + 2.0 h2o_m q6h2_m + 1.5 h_m + 2.0 ficytc_m --> q6_m + 2.0 focytc_m + 1.5 h_c h2s_c + acser_c --> ac_c + h_c + cys_L_c h2o_c + cyst_L_c --> 2obut_c + cys_L_c + nh4_c h2o_c + cyst_L_c --> hcys_L_c + pyr_c + nh4_c cyst_L_x + h2o_x --> hcys_L_x + nh4_x + pyr_x atp_c + cys_L_c + trnacys_c --> ppi_c + cystrna_c + amp_c hcys_L_c + ser_L_c --> h2o_c + cyst_L_c cyst_L_c <=> cyst_L_x cys_L_e + h_e <=> cys_L_c + h_c h2o_c + h_c + cytd_c --> nh4_c + uri_c cytd_c + gtp_c --> h_c + gdp_c + cmp_c h_e + cytd_e --> cytd_c + h_c cmp_c + atp_c <=> adp_c + cdp_c dcmp_c + atp_c <=> adp_c + dcdp_c h2o_c + h_c + dad_2_c --> din_c + nh4_c damp_c + atp_c <=> adp_c + dadp_c h_e + dad_2_e --> h_c + dad_2_c dadp_c <=> dadp_n 0.01 12dgr_SC_c + cdpchol_c --> cmp_c + h_c + 0.01 pc_SC_c h2o_c + 0.01 pa_SC_c --> 0.01 12dgr_SC_c + pi_c dann_e + h_e <=> dann_c + h_c h_c + ctp_c + 0.01 pa_SC_c <=> 0.01 cdpdag_SC_c + ppi_c ctp_m + h_m + 0.01 pa_SC_m <=> 0.01 cdpdag_SC_m + ppi_m ru5p_D_c --> db4p_c + h_c + for_c atp_c + dann_c + co2_c <=> dtbt_c + adp_c + 3.0 h_c + pi_c dcdp_c <=> dcdp_n dcmp_c + h_c + h2o_c <=> dump_c + nh4_c h2o_c + h_c + dctp_c --> nh4_c + dutp_c h2o_c + h_c + dcyt_c --> duri_c + nh4_c h_e + dcyt_e --> h_c + dcyt_c pep_c + h2o_c + e4p_c --> pi_c + 2dda7p_c h2o_m + pep_m + e4p_m --> pi_m + 2dda7p_m o2_c + tdcoa_c + h_c + nadph_c --> 2.0 h2o_c + tdecoa_c + nadp_c pmtcoa_c + o2_c + nadph_c + h_c --> 2.0 h2o_c + hdcoa_c + nadp_c o2_c + h_c + stcoa_c + nadph_c --> 2.0 h2o_c + odecoa_c + nadp_c o2_c + odecoa_c + nadph_c + h_c --> 2.0 h2o_c + ocdycacoa_c + nadp_c dgdp_c <=> dgdp_n h2o_c + 6dg_c --> gal_c + glc_D_c dgmp_c + atp_c <=> adp_c + dgdp_c h_e + dgsn_e --> h_c + dgsn_c 23dhmb_m --> h2o_m + 3mob_m 23dhmp_m --> 3mop_m + h2o_m atp_c + dha_c --> h_c + dhap_c + adp_c dhap_m --> dhap_c nadph_c + h_c + dhf_c --> thf_c + nadp_c dhf_m + nadph_m + h_m --> thf_m + nadp_m dhpt_c + atp_c + glu_L_c --> adp_c + dhf_c + h_c + pi_c dhf_c <=> dhf_m dhnpt_m --> 2ahhmp_m + h_m + gcald_m dhnpt_c <=> dhnpt_m q6_m + dhor_S_c --> orot_c + q6h2_m fum_c + dhor_S_c --> orot_c + succ_c o2_c + dhor_S_c --> h2o2_c + orot_c h2o_c + dhor_S_c <=> cbasp_c + h_c 2ahhmp_m + 4abz_m --> h2o_m + dhpt_m dhpt_c <=> dhpt_m 2dda7p_c --> pi_c + 3dhq_c 3dhq_c --> h2o_c + 3dhsk_c accoa_c + sprm_c --> N1sprm_c + coa_c + h_c din_e + h_e --> din_c + h_c amet_c + caphis_c --> h_c + ahcys_c + cmaphis_c 3.0 h2o_c + dkmpp_c --> 2kmb_c + for_c + 6.0 h_c + pi_c dmpp_c + ipdp_c --> grdp_c + ppi_c h2o_c + dhpmp_c --> pi_c + dhnpt_c h2o_c + ahdt_c --> ppi_c + dhpmp_c + h_c dolichol_c + ctp_c --> cdp_c + h_c + dolp_c dolmanp_r --> mannan_r + dolp_r + h_r dolp_c + gdpmann_c --> dolmanp_r + gdp_c dolp_c + h_c <=> h_r + dolp_r dpcoa_c + atp_c --> adp_c + coa_c + h_c dpcoa_m + atp_m --> adp_m + h_m + coa_m 13dpg_c <=> 23dpg_c + h_c 5dpmev_c + atp_c --> adp_c + ipdp_c + co2_c + pi_c 2dhp_c + nadph_c + h_c --> pant_R_c + nadp_c h_m + nadph_m + 2dhp_m --> nadp_m + pant_R_m atp_c + drib_c --> 2dr5p_c + adp_c + h_c 25dhpp_c + nadph_c + h_c --> 25dthpp_c + nadp_c h2o_c + h_c + 25dthpp_c --> 5aprbu_c + nh4_c atp_c + dtmp_c <=> dtdp_c + adp_c dttp_e <=> dttp_c dump_c <=> dump_n atp_c + duri_c --> h_c + adp_c + dump_c pi_c + duri_c <=> 2dr1p_c + ura_c duri_e + h_e --> duri_c + h_c h2o_c + dutp_c --> ppi_c + dump_c + h_c h2o_c + spmd_c + q6_m --> 13dampp_c + 4abutn_c + q6h2_m lac_D_c + 2.0 ficytc_m --> pyr_c + 2.0 focytc_m lac_D_m + 2.0 ficytc_m --> pyr_m + 2.0 focytc_m h_e + lac_D_e <=> h_c + lac_D_c lac_D_c + pyr_m <=> pyr_c + lac_D_m h_c + lac_D_c <=> h_m + lac_D_m e4hglu_c <=> e4hglu_m e4hglu_c <=> e4hglu_x e4p_c <=> e4p_m h2o_x + hxc2coa_x <=> 3hxccoa_x 3hdcoa_x <=> dc2coa_x + h2o_x 3hddcoa_x <=> h2o_x + dd2coa_x 3htdcoa_x <=> h2o_x + td2coa_x 3hhdcoa_x <=> hdd2coa_x + h2o_x 3hodcoa_x <=> h2o_x + od2coa_x e4hglu_c + akg_c --> glu_L_c + 4h2oglt_c e4hglu_m + akg_m --> 4h2oglt_m + glu_L_m akg_x + e4hglu_x --> 4h2oglt_x + glu_L_x 2pg_c <=> h2o_c + pep_c h2o_e + pectin_e --> galur_e 0.015 tdcoa_c + 0.27 odecoa_c + 0.02 pmtcoa_c + 0.03 stcoa_c + 0.01 hexccoa_c + 0.01 epist_c + 0.655 hdcoa_c --> 0.01 epistest_SC_c + coa_c h2o_c + 0.01 epistest_SC_c --> 0.02 hdca_c + 0.27 ocdcea_c + 0.01 hexc_c + h_c + 0.655 hdcea_c + 0.015 ttdca_c + 0.01 epist_c + 0.03 ocdca_c h2o_e + 0.01 epistest_SC_e --> 0.03 ocdca_e + 0.02 hdca_e + 0.27 ocdcea_e + 0.015 ttdca_e + 0.01 epist_e + h_e + 0.01 hexc_e + 0.655 hdcea_e epist_e <=> epist_c h2o_c + epm_c <=> man_c + gal_c 0.01 ergst_c + 0.015 tdcoa_c + 0.27 odecoa_c + 0.655 hdcoa_c + 0.03 stcoa_c + 0.01 hexccoa_c + 0.02 pmtcoa_c --> 0.01 ergstest_SC_c + coa_c h2o_c + 0.01 ergstest_SC_c --> 0.27 ocdcea_c + 0.01 ergst_c + 0.02 hdca_c + 0.01 hexc_c + h_c + 0.655 hdcea_c + 0.015 ttdca_c + 0.03 ocdca_c h2o_e + 0.01 ergstest_SC_e --> 0.03 ocdca_e + 0.02 hdca_e + 0.01 ergst_e + 0.015 ttdca_e + h_e + 0.27 ocdcea_e + 0.01 hexc_e + 0.655 hdcea_e ergst_c + udpg_c --> h_c + udp_c + ergst3glc_c ergst_e <=> ergst_c ergst_r <=> ergst_c ergtetrol_c <=> ergtetrol_r atp_c + etha_c --> ethamp_c + adp_c + h_c 0.01 12dgr_SC_c + cdpea_c <=> cmp_c + 0.01 pe_SC_c + h_c etha_e <=> etha_c etoh_e <=> etoh_c etoh_c <=> etoh_m 13BDglcn_e --> 2hb_e --> 2mbac_e --> 2mbald_e --> 2mbtoh_e --> 2mppal_e --> 2phetoh_e --> 3c3hmp_e --> 3mbald_e --> 3mop_e --> 4abut_e --> 4abz_e --> 5aop_e --> 8aonn_e --> Nbfortyr_e --> abt_e --> ac_e --> acald_e --> aces_e --> ade_e --> adn_e --> akg_e --> ala_L_e --> alltn_e --> alltt_e --> amet_e --> arab_D_e --> arab_L_e --> arg_L_e --> asn_L_e --> asp_L_e --> btd_RR_e --> btn_e --> chol_e --> cit_e --> co2_e --> crn_e --> csn_e --> cys_L_e --> cytd_e --> dad_2_e --> dann_e --> dca_e --> dcyt_e --> ddca_e --> dgsn_e --> din_e --> dttp_e --> duri_e --> epist_e --> epistest_SC_e --> ergst_e --> ergstest_SC_e --> etha_e --> etoh_e --> fe2_e <=> fecost_e --> fecostest_SC_e --> fmn_e --> for_e --> fru_e --> fum_e --> g3pc_e --> g3pi_e --> gal_e --> galur_e --> gam6p_e --> gcald_e --> glc_D_e <=> gln_L_e --> glu_L_e --> glx_e --> gly_e --> glyc_e --> gsn_e --> gthox_e --> gthrd_e --> gua_e --> h2o_e <=> h_e <=> hdca_e --> hdcea_e --> hexc_e --> his_L_e --> hxan_e --> iamac_e --> iamoh_e --> ibutac_e --> ibutoh_e --> id3acald_e --> ile_L_e --> ind3eth_e --> inost_e --> ins_e --> k_e <=> lac_D_e --> lac_L_e --> lanost_e --> lanostest_SC_e --> leu_L_e --> lys_L_e --> mal_L_e --> malt_e --> man_e --> melib_e --> met_L_e --> mmet_e --> na1_e <=> nac_e --> nadp_e --> nh4_e <=> nmn_e --> o2_e <=> oaa_e --> ocdca_e --> ocdcea_e --> ocdcya_e --> orn_e --> pacald_e --> pap_e --> pc_SC_e --> pectin_e --> pepd_e --> phe_L_e --> pheac_e --> pi_e <=> pnto_R_e --> pro_L_e --> ptd1ino_SC_e --> ptrc_e --> pyr_e --> rib_D_e --> ribflv_e --> sbt_D_e --> sbt_L_e --> ser_L_e --> so3_e --> so4_e <=> spmd_e --> sprm_e --> srb_L_e --> succ_e --> sucr_e --> taur_e --> thm_e --> thmmp_e --> thmpp_e --> thr_L_e --> thym_e --> thymd_e --> tre_e --> trp_L_e --> ttdca_e --> tyr_L_e --> ura_e --> urea_e --> uri_e --> val_L_e --> xan_e --> xtsn_e --> xyl_D_e --> xylt_e --> zymst_e --> zymstest_SC_e --> dca_c --> dca_x h2o_c + ddcaACP_c <=> ACP_c + h_c + ddca_c ddcaACP_m --> ddcaACP_c ddca_c --> ddca_x myrsACP_c + h2o_c <=> ttdca_c + ACP_c + h_c myrsACP_m --> myrsACP_c atp_x + tdcoa_c + h2o_x --> pi_x + adp_x + h_x + tdcoa_x ttdca_c --> ttdca_x h2o_c + tdeACP_c <=> ACP_c + h_c + ttdcea_c tdeACP_m --> tdeACP_c atp_x + tdecoa_c + h2o_x --> tdecoa_x + h_x + adp_x + pi_x ttdcea_c --> ttdcea_x h2o_c + palmACP_c <=> ACP_c + hdca_c + h_c palmACP_m --> palmACP_c atp_x + pmtcoa_c + h2o_x --> pmtcoa_x + h_x + adp_x + pi_x hdca_c --> hdca_x hdeACP_c + h2o_c <=> ACP_c + hdcea_c + h_c hdeACP_m --> hdeACP_c atp_x + hdcoa_c + h2o_x --> h_x + adp_x + pi_x + hdcoa_x hdcea_c --> hdcea_x h2o_c + ocdcaACP_c <=> ACP_c + ocdca_c + h_c ocdcaACP_m --> ocdcaACP_c atp_x + h2o_x + stcoa_c --> h_x + pi_x + stcoa_x + adp_x octeACP_c + h2o_c <=> ocdcea_c + h_c + ACP_c octeACP_m --> octeACP_c atp_x + odecoa_c + h2o_x --> pi_x + h_x + odecoa_x + adp_x ocdcyaACP_c + h2o_c <=> ocdcya_c + ACP_c + h_c ocdcyaACP_m --> ocdcyaACP_c atp_x + ocdycacoa_c + h2o_x --> h_x + adp_x + ocdycacoa_x + pi_x ttc_c --> ttc_x hexc_c --> hexc_x octa_c --> octa_x atp_x + dca_x + coa_x <=> dcacoa_x + ppi_x + amp_x coa_x + ddca_x + atp_x <=> amp_x + ddcacoa_x + ppi_x atp_c + ttdca_c + coa_c <=> ppi_c + tdcoa_c + amp_c atp_x + coa_x + ttdca_x <=> tdcoa_x + ppi_x + amp_x atp_c + ttdcea_c + coa_c <=> ppi_c + amp_c + tdecoa_c atp_x + ttdcea_x + coa_x <=> tdecoa_x + ppi_x + amp_x atp_c + hdca_c + coa_c <=> ppi_c + pmtcoa_c + amp_c hdca_x + coa_x + atp_x <=> pmtcoa_x + ppi_x + amp_x atp_c + hdcea_c + coa_c <=> ppi_c + hdcoa_c + amp_c atp_x + hdcea_x + coa_x <=> hdcoa_x + ppi_x + amp_x atp_c + ocdca_c + coa_c <=> ppi_c + stcoa_c + amp_c ocdcea_c + atp_c + coa_c <=> ppi_c + odecoa_c + amp_c atp_c + ocdcya_c + coa_c <=> ppi_c + amp_c + ocdycacoa_c coa_x + ttc_x + atp_x <=> amp_x + ttccoa_x + ppi_x atp_x + hexc_x + coa_x <=> hexccoa_x + ppi_x + amp_x atp_x + coa_x + octa_x <=> occoa_x + ppi_x + amp_x fad_c + fmn_m --> fad_m + fmn_c gthrd_c + nad_c + fald_c <=> nadh_c + Sfglutth_c + h_c 6.0 nad_x + nadph_x + tdecoa_x + 6.0 o2_x + 6.0 coa_x + 6.0 h2o_x --> 7.0 accoa_x + 6.0 nadh_x + 6.0 h2o2_x + nadp_x + 5.0 h_x 6.0 nad_x + 6.0 coa_x + 5.0 o2_x + tdecoa_x + 6.0 h2o_x --> 6.0 nadh_x + 5.0 h2o2_x + 7.0 accoa_x + 6.0 h_x 7.0 nad_x + nadph_x + 7.0 o2_x + hdcoa_x + 7.0 coa_x + 7.0 h2o_x --> 6.0 h_x + nadp_x + 7.0 nadh_x + 7.0 h2o2_x + 8.0 accoa_x 7.0 nad_x + 6.0 o2_x + 7.0 coa_x + 7.0 h2o_x + hdcoa_x --> 7.0 nadh_x + 8.0 accoa_x + 6.0 h2o2_x + 7.0 h_x 8.0 nad_x + nadph_x + 8.0 o2_x + 8.0 coa_x + odecoa_x + 8.0 h2o_x --> 7.0 h_x + 9.0 accoa_x + 8.0 nadh_x + 8.0 h2o2_x + nadp_x 8.0 nad_x + 8.0 coa_x + 7.0 o2_x + odecoa_x + 8.0 h2o_x --> 8.0 nadh_x + 7.0 h2o2_x + 9.0 accoa_x + 8.0 h_x 8.0 nad_x + 2.0 nadph_x + 8.0 o2_x + 8.0 coa_x + ocdycacoa_x + 8.0 h2o_x --> 6.0 h_x + 9.0 accoa_x + 8.0 nadh_x + 8.0 h2o2_x + 2.0 nadp_x 8.0 nad_x + nadph_x + 7.0 o2_x + 8.0 coa_x + ocdycacoa_x + 8.0 h2o_x --> 7.0 h_x + 9.0 accoa_x + 8.0 nadh_x + 7.0 h2o2_x + nadp_x 8.0 nad_x + 6.0 o2_x + ocdycacoa_x + 8.0 coa_x + 8.0 h2o_x --> 8.0 nadh_x + 6.0 h2o2_x + 9.0 accoa_x + 8.0 h_x 3.0 nad_x + ttccoa_x + 3.0 coa_x + 3.0 o2_x + 3.0 h2o_x --> stcoa_x + 3.0 nadh_x + 3.0 h2o2_x + 3.0 accoa_x + 3.0 h_x 3.0 nad_x + 3.0 coa_x + 3.0 o2_x + occoa_x + 3.0 h2o_x --> 3.0 nadh_x + 3.0 h2o2_x + 4.0 accoa_x + 3.0 h_x octa_c + malcoa_c + 3.0 h_c + 2.0 nadph_c --> h2o_c + 2.0 nadp_c + co2_c + dca_c + coa_c ocACP_m + 3.0 h_m + 2.0 nadph_m + malACP_m --> ACP_m + co2_m + dcaACP_m + 2.0 nadp_m + h2o_m malcoa_c + 3.0 h_c + occoa_c + 2.0 nadph_c --> h2o_c + dcacoa_c + co2_c + coa_c + 2.0 nadp_c dca_c + malcoa_c + 3.0 h_c + 2.0 nadph_c --> h2o_c + 2.0 nadp_c + co2_c + coa_c + ddca_c dcaACP_m + 3.0 h_m + 2.0 nadph_m + malACP_m --> co2_m + ACP_m + 2.0 nadp_m + ddcaACP_m + h2o_m dcacoa_c + malcoa_c + 3.0 h_c + 2.0 nadph_c --> h2o_c + ddcacoa_c + co2_c + coa_c + 2.0 nadp_c 2.0 nadph_c + ddca_c + 3.0 h_c + malcoa_c --> h2o_c + 2.0 nadp_c + co2_c + ttdca_c + coa_c 2.0 nadph_m + 3.0 h_m + ddcaACP_m + malACP_m --> ACP_m + myrsACP_m + co2_m + 2.0 nadp_m + h2o_m ddcacoa_c + malcoa_c + 3.0 h_c + 2.0 nadph_c --> h2o_c + 2.0 nadp_c + tdcoa_c + co2_c + coa_c 3.0 nadph_c + o2_c + 4.0 h_c + ddca_c + malcoa_c --> 3.0 h2o_c + 3.0 nadp_c + co2_c + ttdcea_c + coa_c o2_m + 3.0 nadph_m + 4.0 h_m + ddcaACP_m + malACP_m --> tdeACP_m + ACP_m + 3.0 nadp_m + 3.0 h2o_m + co2_m malcoa_c + 3.0 h_c + ttdca_c + 2.0 nadph_c --> h2o_c + hdca_c + 2.0 nadp_c + co2_c + coa_c myrsACP_m + 2.0 nadph_m + 3.0 h_m + malACP_m --> ACP_m + co2_m + 2.0 nadp_m + palmACP_m + h2o_m 2.0 nadph_c + tdcoa_c + 3.0 h_c + malcoa_c --> h2o_c + 2.0 nadp_c + pmtcoa_c + co2_c + coa_c 3.0 nadph_c + o2_c + 4.0 h_c + malcoa_c + ttdca_c --> 3.0 h2o_c + hdcea_c + co2_c + coa_c + 3.0 nadp_c myrsACP_m + 3.0 nadph_m + 4.0 h_m + malACP_m + o2_m --> hdeACP_m + ACP_m + 3.0 nadp_m + 3.0 h2o_m + co2_m 2.0 nadph_c + hdca_c + 3.0 h_c + malcoa_c --> h2o_c + 2.0 nadp_c + ocdca_c + co2_c + coa_c 3.0 h_m + 2.0 nadph_m + palmACP_m + malACP_m --> co2_m + ACP_m + 2.0 nadp_m + h2o_m + ocdcaACP_m 3.0 h_c + pmtcoa_c + 2.0 nadph_c + malcoa_c --> h2o_c + 2.0 nadp_c + coa_c + co2_c + stcoa_c hdca_c + o2_c + 4.0 h_c + malcoa_c + 3.0 nadph_c --> ocdcea_c + 3.0 h2o_c + 3.0 nadp_c + co2_c + coa_c o2_m + 3.0 nadph_m + 4.0 h_m + palmACP_m + malACP_m --> ACP_m + co2_m + 3.0 nadp_m + octeACP_m + 3.0 h2o_m 4.0 nadph_m + 2.0 o2_m + 5.0 h_m + palmACP_m + malACP_m --> ocdcyaACP_m + 4.0 nadp_m + ACP_m + 5.0 h2o_m + co2_m 9.0 h_c + ocdca_c + 6.0 nadph_c + 3.0 malcoa_c --> 3.0 h2o_c + 6.0 nadp_c + ttc_c + 3.0 co2_c + 3.0 coa_c 2.0 nadph_c + ttc_c + malcoa_c + 3.0 h_c --> h2o_c + 2.0 nadp_c + co2_c + coa_c + hexc_c 6.0 nadph_m + 9.0 h_m + acACP_m + 3.0 malACP_m --> 3.0 ACP_m + 6.0 nadp_m + 3.0 co2_m + ocACP_m + 3.0 h2o_m 6.0 nadph_c + accoa_c + 3.0 malcoa_c + 9.0 h_c --> 3.0 h2o_c + 6.0 nadp_c + 3.0 co2_c + 3.0 coa_c + occoa_c accoa_c + 3.0 malcoa_c + 8.0 h_c + 6.0 nadph_c --> 2.0 h2o_c + octa_c + 6.0 nadp_c + 3.0 co2_c + 4.0 coa_c fdp_c <=> dhap_c + g3p_c f1p_c <=> dhap_c + glyald_c s17bp_c <=> dhap_c + e4p_c h2o_c + fdp_c --> pi_c + f6p_c h2o_c + f26bp_c --> pi_c + f6p_c ppp9_m + fe2_m --> pheme_m + 2.0 h_m for_c + nad_c --> co2_c + nadh_c h_c + q6_m + for_c --> q6h2_m + co2_c fe2_e --> fe2_c fe2_c --> fe2_m 0.01 fecost_c + 0.27 odecoa_c + 0.02 pmtcoa_c + 0.03 stcoa_c + 0.01 hexccoa_c + 0.015 tdcoa_c + 0.655 hdcoa_c --> 0.01 fecostest_SC_c + coa_c h2o_c + 0.01 fecostest_SC_c --> 0.02 hdca_c + 0.27 ocdcea_c + 0.01 hexc_c + h_c + 0.655 hdcea_c + 0.015 ttdca_c + 0.01 fecost_c + 0.03 ocdca_c h2o_e + 0.01 fecostest_SC_e --> 0.03 ocdca_e + 0.02 hdca_e + 0.27 ocdcea_e + 0.015 ttdca_e + 0.01 fecost_e + h_e + 0.01 hexc_e + 0.655 hdcea_e fecost_e <=> fecost_c fe2_m --> fe2_c h2o_c + Lfmkynr_c --> Lkynr_c + for_c + h_c mettrna_m + 10fthf_m --> thf_m + h_m + fmettrna_m fmn_c + atp_c + h_c --> ppi_c + fad_c fmn_m + h_m + atp_m --> ppi_m + fad_m fmn_c + h_c + nadh_c --> fmnh2_c + nad_c fmn_c + nadph_c + h_c --> fmnh2_c + nadp_c 2ahhmd_m + 4abz_m --> dhpt_m + ppi_m for_e <=> for_c for_m --> for_c frdp_c <=> frdp_m fadh2_m + fum_c --> succ_c + fad_m fadh2_m + fum_m --> fad_m + succ_m ipdp_c + frdp_c --> ggdp_c + ppi_c f1p_c + atp_c --> adp_c + fdp_c + h_c h_e + fru_e --> fru_c + h_c 5fthf_c + atp_c --> adp_c + methf_c + pi_c atp_m + 5fthf_m --> pi_m + adp_m + methf_m h2o_c + atp_c + 5fthf_c --> 10fthf_c + adp_c + h_c + pi_c atp_c + thf_c + for_c --> 10fthf_c + adp_c + pi_c for_m + thf_m + atp_m --> pi_m + 10fthf_m + adp_m h2o_c + fum_c <=> mal_L_c h2o_c + 4fumacac_c --> acac_c + h_c + fum_c fum_m + h2o_m <=> mal_L_m h_e + fum_e <=> h_c + fum_c m2macchitppdol_g + gdpmann_g --> m3macchitppdol_g + gdp_g + h_g m3macchitppdol_g + gdpmann_g --> h_g + gdp_g + m4macchitppdol_g macchitppdol_g + gdpmann_g --> m1macchitppdol_g + gdp_g + h_g gdpmann_g + m1macchitppdol_g --> m2macchitppdol_g + gdp_g + h_g g3pc_e <=> g3pc_c h_c + nadh_c + dhap_c --> nad_c + glyc3p_c nadh_m + h_m + dhap_m --> glyc3p_m + nad_m fad_m + glyc3p_m --> dhap_m + fadh2_m g3pi_e <=> g3pi_c h2o_c + glyc3p_c --> glyc_c + pi_c glu5sa_c <=> h2o_c + h_c + 1pyr5c_c glu5sa_m <=> 1pyr5c_m + h2o_m + h_m glu5p_c + h_c + nadph_c --> glu5sa_c + pi_c + nadp_c glu5p_c + nadh_c + h_c --> glu5sa_c + pi_c + nad_c h2o_c + gam6p_c --> f6p_c + nh4_c g6p_c + nadp_c --> h_c + 6pgl_c + nadph_c g6p_r + nadp_r --> h_r + nadph_r + 6pgl_r g6p_c <=> g6p_B_c g6p_B_c <=> f6p_c g6p_c <=> g6p_r h2o_c + 1Dgali_c <=> inost_c + gal_c gal_c + atp_c --> h_c + adp_c + gal1p_c h2o_c + melib_c --> gal_c + glc_D_c utp_c + gal1p_c + h_c <=> udpgal_c + ppi_c h_c + utp_c + g1p_c <=> ppi_c + udpg_c h_e + gal_e --> h_c + gal_c gam6p_e <=> gam6p_c g3p_c + pi_c + nad_c <=> 13dpg_c + nadh_c + h_c gar_c + 10fthf_c --> thf_c + h_c + fgam_c 0.27 pmtcoa_c + 0.02 dcacoa_c + glyc3p_c + 0.06 ddcacoa_c + 0.24 odecoa_c + 0.17 hdcoa_c + 0.05 stcoa_c + 0.09 ocdycacoa_c + 0.1 tdcoa_c --> coa_c + 0.01 1ag3p_SC_c 0.02 dcacoa_c + dhap_c + 0.06 ddcacoa_c + 0.24 odecoa_c + 0.17 hdcoa_c + 0.05 stcoa_c + 0.09 ocdycacoa_c + 0.1 tdcoa_c + 0.27 pmtcoa_c --> 0.01 1agly3p_SC_c + coa_c 14glun_c --> h2o_c + glycogen_c gcald_e <=> gcald_c gcald_c <=> gcald_m h_m + gly_m + lpam_m <=> alpam_m + co2_m alpam_m + thf_m --> mlthf_m + nh4_m + dhlam_m dhlam_m + nad_m <=> h_m + lpam_m + nadh_m h_m + gly_m + lpro_m <=> co2_m + alpro_m thf_m + alpro_m --> dhlpro_m + mlthf_m + nh4_m dhlpro_m + nad_m <=> h_m + lpro_m + nadh_m gdpmann_c + gmp_g --> gdpmann_g + gmp_c h_c + gdp_g <=> gdp_c + h_g gdp_c <=> gdp_n gln_L_c + f6p_c --> glu_L_c + gam6p_c h2o_c + ggl_c <=> glyc_c + gal_c ggdp_c + ipdp_c --> ppi_c + pendp_c thf_c + ser_L_c <=> h2o_c + gly_c + mlthf_c thf_m + ser_L_m <=> gly_m + mlthf_m + h2o_m gmp_c + atp_c <=> adp_c + gdp_c datp_c + gmp_c <=> gdp_c + dadp_c glycogen_c + h2o_c --> glc_D_c h2o_v + glycogen_v --> glc_D_v glycogen_c --> glycogen_v glycogen_c + pi_c --> g1p_c udpg_c --> glycogen_c + udp_c + h_c glc_D_e --> glc_D_c glc_D_c <=> glc_D_v glu_L_c + nh4_c + atp_c --> pi_c + adp_c + h_c + gln_L_c atp_c + trnagln_c + gln_L_c --> ppi_c + glntrna_c + amp_c h_c + gln_L_c <=> gln_L_n + h_n gln_L_e + h_e <=> gln_L_c + h_c h_v + gln_L_c --> h_c + gln_L_v h_v + gln_L_v --> gln_L_c + h_c glp_c + tdcoa_c --> coa_c + tglp_c glu_L_c + atp_c --> adp_c + glu5p_c glu_L_c + cys_L_c + atp_c --> pi_c + glucys_c + adp_c + h_c glu_L_c + h_c --> co2_c + 4abut_c h2o_c + glu_L_c + nad_c --> akg_c + nadh_c + h_c + nh4_c h_c + nh4_c + akg_c + nadph_c --> h2o_c + glu_L_c + nadp_c glc_D_c + atp_c --> h_c + adp_c + g6p_B_c h2o_c + gln_L_c --> glu_L_c + nh4_c h2o_c + gln_L_c + prpp_c --> glu_L_c + ppi_c + pram_c gln_L_c + nadh_c + h_c + akg_c --> 2.0 glu_L_c + nad_c atp_c + trnaglu_c + glu_L_c --> glutrna_c + ppi_c + amp_c trnaglu_m + atp_m + glu_L_m --> glutrna_m + amp_m + ppi_m glu_L_c + h_c <=> h_n + glu_L_n h_e + glu_L_e <=> glu_L_c + h_c glu_L_c + oh1_m --> oh1_c + glu_L_m h_v + glu_L_v --> glu_L_c + h_c glu_L_c --> glu_L_m glx_c <=> glx_e glx_c <=> glx_x coa_c + 2aobut_c --> accoa_c + gly_c glyc3p_c --> glyc3p_m nadp_c + glyc_c --> h_c + dha_c + nadph_c nad_m + gly_m + thf_m --> mlthf_m + nadh_m + nh4_m + co2_m glyc_c <=> glyc_e glyc_e + h_e --> glyc_c + h_c h2o_c + udpg_c --> udp_c + 14glun_c + h_c glyc_c + atp_c --> h_c + adp_c + glyc3p_c h2o_c + lgt_S_c --> h_c + gthrd_c + lac_D_c h2o_m + lgt_S_m --> h_m + gthrd_m + lac_D_m atp_c + gly_c + trnagly_c --> glytrna_c + ppi_c + amp_c gly_c + h_c <=> h_m + gly_m h_e + gly_e <=> gly_c + h_c h2o_c + gln_L_c + xmp_c + atp_c --> glu_L_c + gmp_c + ppi_c + amp_c + 2.0 h_c nadp_c + 6pgc_c --> co2_c + ru5p_D_c + nadph_c h2o_c + gsn_c --> rib_D_c + gua_c h2o_c + g3pc_c --> chol_c + glyc3p_c + h_c grdp_c + ipdp_c --> frdp_c + ppi_c gsn_c + atp_c --> adp_c + gmp_c + h_c gsn_e + h_e --> gsn_c + h_c gsn_c + h_c <=> h_m + gsn_m gthox_c + nadph_c + h_c --> 2.0 gthrd_c + nadp_c gthox_e --> gthox_c h_m + nadph_m + gthox_m --> nadp_m + 2.0 gthrd_m h2o2_c + 2.0 gthrd_c <=> 2.0 h2o_c + gthox_c h2o2_m + 2.0 gthrd_m <=> gthox_m + 2.0 h2o_m atp_v + gthrd_c + h2o_v --> adp_v + h_v + gthrd_v + pi_v gthrd_e --> gthrd_c glucys_c + gly_c + atp_c --> pi_c + gthrd_c + adp_c + h_c gthrd_c + ala_L_c --> cgly_c + gluala_c h2o_c + gtp_c --> ahdt_c + for_c + h_c 3.0 h2o_c + gtp_c --> 2.0 h_c + ppi_c + for_c + 25dhpp_c 2.0 h2o_c + gtp_c --> gmp_c + 2.0 pi_c + 2.0 h_c gdp_m + h_c + gtp_c --> gdp_c + gtp_m + h_m h2o_c + h_c + gua_c --> xan_c + nh4_c prpp_c + gua_c --> gmp_c + ppi_c h_e + gua_e <=> h_c + gua_c gua_c <=> gua_m h2o2_c <=> h2o2_n h2o_e <=> h2o_c h2o_c <=> h2o_r h2o_c <=> h2o_m h2o_n <=> h2o_c h2o_c <=> h2o_x h2o_c <=> h2o_v nad_x + 3hxccoa_x <=> 3ohxccoa_x + h_x + nadh_x h_x + nadh_x + 3odcoa_x <=> nad_x + 3hdcoa_x nadh_x + 3oddcoa_x + h_x <=> nad_x + 3hddcoa_x 3otdcoa_x + nadh_x + h_x <=> nad_x + 3htdcoa_x h_x + nadh_x + 3ohdcoa_x <=> nad_x + 3hhdcoa_x h_x + nadh_x + 3ohodcoa_x <=> nad_x + 3hodcoa_x b124tc_m + h2o_m <=> hicit_m 4hbz_m + hexdp_m --> ppi_m + 3ophb_5_m accoa_m + akg_m + h2o_m --> coa_m + hcit_m + h_m akg_n + h2o_n + accoa_n --> hcit_n + coa_n + h_n h2o_c + co2_c <=> hco3_c + h_c h2o_m + co2_m <=> hco3_m + h_m co2_n + h2o_n <=> h_n + hco3_n hco3_c <=> hco3_n amet_c + hcys_L_c --> ahcys_c + met_L_c + h_c h_c + hcys_L_c <=> hcys_L_x + h_x hdca_e --> hdca_c hdcea_e --> hdcea_c nadh_m + o2_m + hemeO_m --> hemeA_m + nad_m + h2o_m frdp_m + h2o_m + pheme_m --> hemeO_m + ppi_m 4mhetz_c + atp_c --> 4mpetz_c + adp_c + h_c atp_c + glc_D_c --> g6p_c + adp_c + h_c man_c + atp_c --> h_c + adp_c + man6p_c fru_c + atp_c --> adp_c + f6p_c + h_c hexccoa_c <=> hexccoa_x hexdp_c <=> hexdp_m hgentis_c + o2_c --> 4mlacac_c + h_c hicit_m + nad_m <=> h_m + oxag_m + nadh_m h2o_c + histd_c + 2.0 nad_c --> his_L_c + 2.0 nadh_c + 3.0 h_c hisp_c + h2o_c --> histd_c + pi_c atp_c + his_L_c + trnahis_c --> ppi_c + amp_c + histrna_c trnahis_m + his_L_m + atp_m --> amp_m + ppi_m + histrna_m his_L_m + h_m <=> h_c + his_L_c his_L_e + h_e <=> h_c + his_L_c h_v + his_L_c --> his_L_v + h_c h2o_c + hLkynr_c --> ala_L_c + 3hanthrn_c 4.0 ppbng_c + h2o_c --> hmbil_c + 4.0 nh4_c mev_R_c + 2.0 nadp_c + coa_c <=> hmgcoa_c + 2.0 nadph_c + 2.0 h_c hmgcoa_c + h_c + coa_c <=> h2o_c + aacoa_c + accoa_c hmgcoa_m + h_m + coa_m <=> aacoa_m + accoa_m + h2o_m hmgcoa_c <=> hmgcoa_m atp_c + 4ahmmp_c --> h_c + adp_c + 4ampm_c 2ahhmp_m + atp_m --> 2ahhmd_m + h_m + amp_m 1p3h5c_c + 2.0 h_c + nadh_c --> 4hpro_LT_c + nad_c 1p3h5c_c + nadph_c + 2.0 h_c --> 4hpro_LT_c + nadp_c nad_m + 4hpro_LT_m --> 1p3h5c_m + nadh_m + 2.0 h_m 4hpro_LT_m + nadp_m --> 1p3h5c_m + 2.0 h_m + nadph_m aspsa_c + h_c + nadh_c --> hom_L_c + nad_c aspsa_c + nadph_c + h_c --> hom_L_c + nadp_c accoa_c + hom_L_c <=> coa_c + achms_c hom_L_c + atp_c --> adp_c + phom_c + h_c glu_L_c + imacp_c --> akg_c + hisp_c h_e + hxan_e <=> hxan_c + h_c hxan_c + prpp_c --> ppi_c + imp_c pyam5p_c + h2o_c --> pydam_c + pi_c iamac_c --> iamac_e iamoh_c <=> iamoh_e iamoh_c <=> iamoh_m ibutac_c --> ibutac_e ibutoh_c <=> ibutoh_e ibutoh_c <=> ibutoh_m icit_m + nad_m --> nadh_m + co2_m + akg_m icit_c + nadp_c --> co2_c + nadph_c + akg_c icit_m + nadp_m --> akg_m + co2_m + nadph_m icit_x + nadp_x --> akg_x + nadph_x + co2_x icit_c --> glx_c + succ_c id3acald_c <=> id3acald_e id3acald_c <=> id3acald_m gln_L_c + prlp_c --> glu_L_c + h_c + eig3p_c + aicar_c eig3p_c --> h2o_c + imacp_c h_c + 2cpr5p_c --> h2o_c + co2_c + 3ig3p_c ile_L_c + akg_c <=> glu_L_c + 3mop_c ile_L_m + akg_m <=> 3mop_m + glu_L_m atp_c + trnaile_c + ile_L_c --> ppi_c + iletrna_c + amp_c ile_L_m + trnaile_m + atp_m --> iletrna_m + amp_m + ppi_m ile_L_e + h_e <=> h_c + ile_L_c ile_L_c + h_v --> ile_L_v + h_c h_v + ile_L_v --> h_c + ile_L_c ile_L_m --> ile_L_c h2o_c + imp_c <=> fprica_c h2o_c + imp_c + nad_c --> nadh_c + h_c + xmp_c ind3ac_c <=> ind3ac_m ind3eth_c <=> ind3eth_e ind3eth_c <=> ind3eth_m h_c + indpyr_c <=> id3acald_c + co2_c ins_c + atp_c --> h_c + adp_c + imp_c inost_e + h_e --> inost_c + h_c ins_e + h_e --> h_c + ins_c h2o_c + 0.01 ipc124_SC_c --> h_c + mi1p_D_c + cer1_24_c h2o_c + 0.01 ipc126_SC_c --> cer1_26_c + mi1p_D_c + h_c h2o_c + 0.01 ipc224_SC_c --> cer2_24_c + mi1p_D_c + h_c h2o_c + 0.01 ipc226_SC_c --> cer2_26_c + mi1p_D_c + h_c h2o_c + 0.01 ipc324_SC_c --> cer3_24_c + mi1p_D_c + h_c h2o_c + 0.01 ipc326_SC_c --> mi1p_D_c + cer3_26_c + h_c 0.01 ptd1ino_SC_c + cer1_24_c --> 0.01 ipc124_SC_c + 0.01 12dgr_SC_c 0.01 ptd1ino_SC_c + cer1_26_c --> 0.01 12dgr_SC_c + 0.01 ipc126_SC_c 0.01 ptd1ino_SC_c + cer2_24_c --> 0.01 12dgr_SC_c + 0.01 ipc224_SC_c cer2_26_c + 0.01 ptd1ino_SC_c --> 0.01 ipc226_SC_c + 0.01 12dgr_SC_c 0.01 ptd1ino_SC_c + cer3_24_c --> 0.01 12dgr_SC_c + 0.01 ipc324_SC_c 0.01 ptd1ino_SC_c + cer3_26_c --> 0.01 12dgr_SC_c + 0.01 ipc326_SC_c ipdp_c <=> dmpp_c ipdp_c <=> ipdp_m 3c2hmp_c + nad_c --> h_c + 3c4mop_c + nadh_c 3c2hmp_c <=> h2o_c + 2ippm_c h2o_c + 2ippm_c <=> 3c3hmp_c h2o_c + 3mob_c + accoa_c --> 3c3hmp_c + h_c + coa_c 3mob_m + h2o_m + accoa_m --> h_m + coa_m + 3c3hmp_m itacon_m + coa_m + atp_m <=> itaccoa_m + pi_m + adp_m alac_S_m + h_m + nadph_m --> nadp_m + 23dhmb_m 2ahbut_m + nadph_m + h_m --> nadp_m + 23dhmp_m h2o_c + Lkynr_c --> ala_L_c + anth_c + h_c Lkynr_c + o2_c + nadph_c + h_c --> h2o_c + hLkynr_c + nadp_c k_e + h_e <=> h_c + k_c h_c + mthgxl_c + nadph_c --> lald_L_c + nadp_c 0.01 lanost_c + 0.015 tdcoa_c + 0.03 stcoa_c + 0.27 odecoa_c + 0.655 hdcoa_c + 0.01 hexccoa_c + 0.02 pmtcoa_c --> 0.01 lanostest_SC_c + coa_c h2o_c + 0.01 lanostest_SC_c --> 0.02 hdca_c + 0.27 ocdcea_c + 0.01 lanost_c + 0.03 ocdca_c + 0.655 hdcea_c + h_c + 0.015 ttdca_c + 0.01 hexc_c 0.01 lanostest_SC_e + h2o_e --> 0.03 ocdca_e + 0.02 hdca_e + 0.27 ocdcea_e + 0.015 ttdca_e + h_e + 0.01 hexc_e + 0.655 hdcea_e + 0.01 lanost_e lanost_e <=> lanost_c h2o_c + lald_L_c + nad_c --> lac_L_c + nadh_c + 2.0 h_c Lcystin_v + h_v --> h_c + Lcystin_c leu_L_c + akg_c <=> glu_L_c + 4mop_c leu_L_m + akg_m <=> 4mop_m + glu_L_m atp_c + leu_L_c + trnaleu_c --> ppi_c + leutrna_c + amp_c trnaleu_m + leu_L_m + atp_m --> leutrna_m + amp_m + ppi_m leu_L_e + h_e <=> h_c + leu_L_c h_v + leu_L_c --> h_c + leu_L_v h_v + leu_L_v --> h_c + leu_L_c gthrd_c + mthgxl_c --> lgt_S_c lanost_c + 3.0 o2_c + 2.0 h_c + 3.0 nadph_c --> 4.0 h2o_c + for_c + 44mctr_c + 3.0 nadp_c lanost_c + 3.0 nadh_c + 3.0 o2_c + 2.0 h_c --> 4.0 h2o_c + for_c + 44mctr_c + 3.0 nad_c Ssq23epx_c --> lanost_c 0.01 1agpc_SC_c + 0.02 dcacoa_c + 0.1 tdcoa_c + 0.06 ddcacoa_c + 0.24 odecoa_c + 0.17 hdcoa_c + 0.05 stcoa_c + 0.09 ocdycacoa_c + 0.27 pmtcoa_c --> 0.01 pc_SC_c + coa_c h2o_c + 0.01 dagpy_SC_c --> pi_c + 0.01 pa_SC_c + h_c nadp_c + ser_L_c <=> h_c + 2amsa_c + nadph_c lys_L_c + atp_c + trnalys_c --> lystrna_c + ppi_c + amp_c lys_L_m + atp_m + trnalys_m --> amp_m + ppi_m + lystrna_m lys_L_c + h_c <=> lys_L_m + h_m lys_L_e + h_e <=> lys_L_c + h_c h_v + lys_L_c --> lys_L_v + h_c lac_L_c + 2.0 ficytc_m --> 2.0 focytc_m + pyr_c lac_L_e + h_e <=> h_c + lac_L_c lac_L_c + h_c <=> lac_L_m + h_m 4mlacac_c --> 4fumacac_c mal_L_x + oaa_c <=> mal_L_c + oaa_x h2o_c + glx_c + accoa_c --> mal_L_c + h_c + coa_c glx_x + h2o_x + accoa_x --> mal_L_x + coa_x + h_x h2o_c + malt_c --> 2.0 glc_D_c malt_e + h_e --> h_c + malt_c mal_L_e + h_e <=> h_c + mal_L_c pi_m + mal_L_c <=> pi_c + mal_L_m gtp_c + h_c + man1p_c --> ppi_c + gdpmann_c man6p_c <=> f6p_c mannan_c <=> mannan_r man_e + h_e --> h_c + man_c hcit_m <=> b124tc_m + h2o_m micit_m --> succ_m + pyr_m oaa_m + ppcoa_m + h2o_m --> h_m + 2mcit_m + coa_m malcoa_c + ACP_c <=> malACP_c + coa_c malcoa_m + ACP_m <=> coa_m + malACP_m nad_c + mal_L_c <=> h_c + oaa_c + nadh_c mal_L_m + nad_m <=> h_m + oaa_m + nadh_m nad_x + mal_L_x <=> h_x + oaa_x + nadh_x 5mdru1p_c --> dkmpp_c + h2o_c mal_L_m + nad_m --> co2_m + pyr_m + nadh_m mal_L_m + nadp_m --> nadph_m + pyr_m + co2_m melib_e + h_e --> h_c + melib_c melt_c + h2o_c <=> sbt_D_c + gal_c h2o_c + atp_c + met_L_c --> amet_c + ppi_c + pi_c achms_c + cys_L_c --> ac_c + cyst_L_c + h_c 5mthf_c + hcys_L_c --> thf_c + met_L_c + h_c atp_c + met_L_c + trnamet_c --> ppi_c + mettrna_c + amp_c atp_m + trnamet_m + met_L_m --> mettrna_m + amp_m + ppi_m met_L_m + h_m <=> h_c + met_L_c met_L_e + h_e <=> h_c + met_L_c mev_R_c + atp_c --> adp_c + 5pmev_c + h_c mev_R_c + ctp_c --> 5pmev_c + cdp_c + h_c gtp_c + mev_R_c --> 5pmev_c + gdp_c + h_c mev_R_c + utp_c --> udp_c + 5pmev_c + h_c amet_c + 0.01 ptdmeeta_SC_c --> h_c + ahcys_c + 0.01 ptd2meeta_SC_c dhap_c --> mthgxl_c + pi_c hcys_L_c + mhpglu_c --> hpglu_c + met_L_c mi13456p_n + atp_n --> adp_n + h_n + minohp_n atp_n + mi1345p_n --> adp_n + mi13456p_n + h_n mi1456p_n + atp_n --> h_n + adp_n + mi13456p_n mi145p_n + atp_n --> h_n + adp_n + mi1456p_n mi145p_n + atp_n --> h_n + adp_n + mi1345p_n mi145p_c <=> mi145p_n h2o_c + mi1p_D_c --> inost_c + pi_c g6p_c --> mi1p_D_c minohp_c <=> minohp_n h2o_c + 0.01 mip2c124_SC_c --> h_c + man2mi1p_D_c + cer1_24_c h2o_c + 0.01 mip2c126_SC_c --> cer1_26_c + man2mi1p_D_c + h_c h2o_c + 0.01 mip2c224_SC_c --> cer2_24_c + man2mi1p_D_c + h_c h2o_c + 0.01 mip2c226_SC_c --> cer2_26_c + man2mi1p_D_c + h_c h2o_c + 0.01 mip2c324_SC_c --> cer3_24_c + man2mi1p_D_c + h_c 0.01 mip2c326_SC_c + h2o_c --> cer3_26_c + man2mi1p_D_c + h_c 0.01 mipc124_SC_c + 0.01 ptd1ino_SC_c --> 0.01 mip2c124_SC_c + 0.01 12dgr_SC_c 0.01 ptd1ino_SC_c + 0.01 mipc126_SC_c --> 0.01 12dgr_SC_c + 0.01 mip2c126_SC_c 0.01 mipc224_SC_c + 0.01 ptd1ino_SC_c --> 0.01 mip2c224_SC_c + 0.01 12dgr_SC_c 0.01 mipc226_SC_c + 0.01 ptd1ino_SC_c --> 0.01 mip2c226_SC_c + 0.01 12dgr_SC_c 0.01 ptd1ino_SC_c + 0.01 mipc324_SC_c --> 0.01 mip2c324_SC_c + 0.01 12dgr_SC_c 0.01 mipc326_SC_c + 0.01 ptd1ino_SC_c --> 0.01 mip2c326_SC_c + 0.01 12dgr_SC_c 0.01 mipc124_SC_c + h2o_c --> manmi1p_D_c + cer1_24_c + h_c 0.01 mipc126_SC_c + h2o_c --> cer1_26_c + manmi1p_D_c + h_c 0.01 mipc224_SC_c + h2o_c --> manmi1p_D_c + h_c + cer2_24_c 0.01 mipc226_SC_c + h2o_c --> manmi1p_D_c + cer2_26_c + h_c 0.01 mipc324_SC_c + h2o_c --> manmi1p_D_c + h_c + cer3_24_c 0.01 mipc326_SC_c + h2o_c --> manmi1p_D_c + cer3_26_c + h_c gdpmann_c + 0.01 ipc124_SC_c --> h_c + gdp_c + 0.01 mipc124_SC_c gdpmann_c + 0.01 ipc126_SC_c --> gdp_c + 0.01 mipc126_SC_c + h_c 0.01 ipc224_SC_c + gdpmann_c --> 0.01 mipc224_SC_c + h_c + gdp_c gdpmann_c + 0.01 ipc226_SC_c --> gdp_c + h_c + 0.01 mipc226_SC_c gdpmann_c + 0.01 ipc324_SC_c --> h_c + gdp_c + 0.01 mipc324_SC_c gdpmann_c + 0.01 ipc326_SC_c --> gdp_c + 0.01 mipc326_SC_c + h_c mmet_e + h_e --> h_c + mmet_c mlthf_c + h2o_c + 3mob_c --> 2dhp_c + thf_c 5mta_c + pi_c --> ade_c + 5mdr1p_c h2o_c + methf_c <=> 10fthf_c + h_c methf_m + h2o_m <=> h_m + 10fthf_m mlthf_c + nadp_c <=> methf_c + nadph_c mlthf_c + nad_c --> methf_c + nadh_c nadp_m + mlthf_m <=> nadph_m + methf_m mlthf_c + 2.0 h_c + nadph_c --> 5mthf_c + nadp_c 5mdr1p_c <=> 5mdru1p_c h2o_c + nad_c + n4abutn_c --> nadh_c + 4aabutn_c + 2.0 h_c nac_e <=> nac_c nad_x + h2o_x --> nmn_x + 2.0 h_x + amp_x h_c + nadh_c + q6_m --> q6h2_m + nad_c nadh_m + h_m + q6_m --> q6h2_m + nad_m atp_c + nad_c --> h_c + adp_c + nadp_c nad_m + atp_m --> adp_m + h_m + nadp_m h2o_c + nad_c --> adprib_c + h_c + ncam_c nad_m + h2o_m --> adprib_m + h_m + ncam_m h2o_c + nadp_c --> pi_c + nad_c h2o_m + nadp_m --> pi_m + nad_m nadp_c <=> nadp_e atp_c + dnad_c + nh4_c --> ppi_c + h_c + amp_c + nad_c nh4_n + atp_n + dnad_n --> ppi_n + h_n + amp_n + nad_n nad_n <=> nad_c h_c + nac_c + prpp_c --> ppi_c + nicrnt_c prpp_m + nac_m + h_m --> nicrnt_m + ppi_m h_e + na1_c <=> h_c + na1_e h2o_c + adp_c --> amp_c + pi_c + h_c h2o_c + gdp_c --> gmp_c + pi_c + h_c h2o_g + gdp_g --> gmp_g + pi_g + h_g h2o_c + dgdp_c --> dgmp_c + pi_c + h_c h2o_c + udp_c --> h_c + pi_c + ump_c gdp_c + atp_c <=> gtp_c + adp_c atp_c + udp_c <=> adp_c + utp_c cdp_c + atp_c <=> adp_c + ctp_c dtdp_c + atp_c <=> adp_c + dttp_c dgdp_c + atp_c <=> dgtp_c + adp_c dudp_c + atp_c <=> adp_c + dutp_c dcdp_c + atp_c <=> dctp_c + adp_c atp_c + dadp_c <=> datp_c + adp_c idp_c + atp_c <=> adp_c + itp_c Nbfortyr_c --> Nbfortyr_e 2.0 Nfortyr_c + nadph_c + h_c --> Nbfortyr_c + nadp_c nh4_e <=> nh4_c nh4_c --> nh4_e nh4_c <=> nh4_m nh4_c <=> nh4_n nh4_c <=> nh4_x h_c + nmn_c + atp_c --> ppi_c + nad_c h_m + nmn_m + atp_m --> nad_m + ppi_m h_e + nmn_e --> h_c + nmn_c h_c + nmn_c <=> nmn_m + h_m h_c + nmn_c <=> nmn_x + h_x h2o_c + ncam_c <=> nh4_c + nac_c ncam_m + h2o_m <=> nac_m + nh4_m h_c + nicrnt_c + atp_c --> ppi_c + dnad_c h_m + nicrnt_m + atp_m --> ppi_m + dnad_m quln_c + 2.0 h_c + prpp_c --> nicrnt_c + ppi_c + co2_c quln_m + 2.0 h_m + prpp_m --> nicrnt_m + co2_m + ppi_m amet_c + ncam_c --> 1mncam_c + ahcys_c h2o_c + dump_c --> pi_c + duri_c h2o_c + xmp_c --> pi_c + xtsn_c h2o_c + imp_c --> ins_c + pi_c h2o_c + ump_c --> pi_c + uri_c h2o_c + dcmp_c --> dcyt_c + pi_c h2o_c + cmp_c --> pi_c + cytd_c h2o_c + dtmp_c --> thymd_c + pi_c h2o_c + damp_c --> dad_2_c + pi_c h2o_c + amp_c --> pi_c + adn_c h2o_c + dgmp_c --> pi_c + dgsn_c h2o_c + gmp_c --> gsn_c + pi_c h2o_c + gtp_c --> gdp_c + pi_c + h_c h2o_c + dgtp_c --> pi_c + dgdp_c + h_c 2.0 h2o_c + ind3acnl_c --> ind3ac_c + nh4_c 2.0 h2o_c + aprop_c --> ala_L_c + nh4_c 2.0 h2o_c + acybut_c --> glu_L_c + nh4_c o2_e <=> o2_c o2_c <=> o2_r o2_c <=> o2_m oaa_c <=> oaa_e h_c + oaa_c <=> h_m + oaa_m coa_m + nad_m + 2obut_m --> nadh_m + ppcoa_m + co2_m cbp_c + orn_c --> h_c + pi_c + citr_L_c ocdca_e --> ocdca_c ocdcea_e --> ocdcea_c ocdcya_e --> ocdcya_c accoa_c + etoh_c --> aces_c + coa_c accoa_c + iamoh_c --> coa_c + iamac_c accoa_c + 2mbtoh_c --> 2mbac_c + coa_c accoa_c + ibutoh_c --> coa_c + ibutac_c accoa_c + 2phetoh_c --> coa_c + pheac_c glu_L_c + ohpb_c <=> phthr_c + akg_c h_c + 3c4mop_c --> 4mop_c + co2_c h_m + 3c4mop_m --> 4mop_m + co2_m h_c + orot5p_c --> co2_c + ump_c h_c + orn_c --> ptrc_c + co2_c orn_c + akg_c --> glu5sa_c + glu_L_c acorn_m + glu_L_m --> orn_m + acglu_m orn_e + h_e <=> h_c + orn_c h_c + orn_m <=> orn_c + h_m ppi_c + orot5p_c <=> orot_c + prpp_c h_m + oxag_m <=> 2oxoadp_m + co2_m oxag_c + akg_m <=> akg_c + oxag_m nad_m + 1pyr5c_m + 2.0 h2o_m --> nadh_m + h_m + glu_L_m 2.0 h_c + nadph_c + 1pyr5c_c --> nadp_c + pro_L_c pacald_c <=> pacald_e pacald_c <=> pacald_m 0.01 pa_SC_c + atp_c --> 0.01 dagpy_SC_c + adp_c pan4p_c <=> pan4p_m pant_R_c + ala_B_c + atp_c --> ppi_c + amp_c + h_c + pnto_R_c pant_R_c <=> pant_R_m trdrd_c + paps_c --> so3_c + 2.0 h_c + trdox_c + pap_c pap_e <=> pap_c pap_c <=> pap_m pa_SC_c <=> pa_SC_m hco3_c + pyr_c + atp_c --> adp_c + h_c + oaa_c + pi_c 12dgr_SC_c + pc_SC_c --> 1agpc_SC_c + triglyc_SC_c h2o_c + camp_c --> amp_c + h_c h2o_c + 35cdamp_c --> damp_c + h_c h2o_c + 35cimp_c --> h_c + imp_c h2o_c + 35cgmp_c --> gmp_c + h_c h2o_c + 35ccmp_c --> cmp_c + h_c dhlam_m + nad_m --> h_m + lpam_m + nadh_m nad_m + pyr_m + coa_m --> nadh_m + accoa_m + co2_m o2_c + pdx5p_c <=> h2o2_c + pydx5p_c pendp_c <=> pendp_m pepd_c + accoa_c --> apep_c + h_c + coa_c pepd_e + h_e --> h_c + pepd_c ethamp_c + h_c + ctp_c --> ppi_c + cdpea_c amet_c + 0.01 pe_SC_c --> ahcys_c + 0.01 ptdmeeta_SC_c + h_c pe_SC_c <=> pe_SC_g pe_SC_c <=> pe_SC_m pe_SC_c <=> pe_SC_v f6p_c + atp_c --> fdp_c + adp_c + h_c f6p_c + atp_c --> f26bp_c + adp_c + h_c atp_c + tag6p_D_c --> tagdp_D_c + adp_c + h_c atp_c + s7p_c --> h_c + adp_c + s17bp_c gam1p_c <=> gam6p_c 3pg_c + nad_c --> 3php_c + h_c + nadh_c g6p_c <=> f6p_c atp_c + 3pg_c <=> 13dpg_c + adp_c h2o_c + 6pgl_c --> 6pgc_c + h_c 2pg_c <=> 3pg_c g1p_c <=> g6p_c 0.01 pgp_SC_m + h2o_m --> pi_m + 0.01 pg_SC_m 1p3h5c_m + nad_m + 2.0 h2o_m --> nadh_m + h_m + e4hglu_m 1p3h5c_m + h2o_m + h_m <=> 4hglusa_m pheac_c --> pheac_e akg_c + phe_L_c <=> glu_L_c + phpyr_c atp_c + phe_L_c + trnaphe_c --> ppi_c + amp_c + phetrna_c phe_L_m + trnaphe_m + atp_m --> amp_m + phetrna_m + ppi_m phe_L_m + h_m <=> h_c + phe_L_c phe_L_e + h_e <=> h_c + phe_L_c h2o_c + 0.01 ptd135bp_SC_c --> 0.01 ptd3ino_SC_c + pi_c 0.01 ptd3ino_SC_c + atp_c --> h_c + adp_c + 0.01 ptd134bp_SC_c 0.01 ptd3ino_SC_c + atp_c --> h_c + adp_c + 0.01 ptd135bp_SC_c h2o_c + 0.01 ptd145bp_SC_c --> pi_c + 0.01 ptd4ino_SC_c 0.01 ptd145bp_SC_c + h2o_c --> mi145p_c + 0.01 12dgr_SC_c + h_c atp_c + 0.01 ptd4ino_SC_c --> h_c + adp_c + 0.01 ptd145bp_SC_c 0.01 ptd1ino_SC_c + atp_c --> adp_c + 0.01 ptd3ino_SC_c + h_c 0.01 ptd1ino_SC_c + atp_c --> adp_c + 0.01 ptd4ino_SC_c + h_c 0.01 ptd1ino_SC_n + atp_n --> h_n + adp_n + 0.01 ptd4ino_SC_n inost_c + 0.01 cdpdag_SC_c --> cmp_c + h_c + 0.01 ptd1ino_SC_c pi_c + h_c <=> pi_m + h_m h_c + pi_c <=> h_n + pi_n h_c + pi_c <=> h_x + pi_x pi_e + h_e <=> h_c + pi_c h_c + pi_c <=> h_v + pi_v oh1_m + pi_c <=> pi_m + oh1_c h2o_e + 0.005 ptd1ino_SC_e --> 0.05 ocdca_e + 0.27 hdca_e + 0.02 dca_e + 0.06 ddca_e + 0.09 ocdcya_e + 0.1 ttdca_e + h_e + 0.24 ocdcea_e + 0.5 g3pi_e + 0.17 hdcea_e h2o_c + 0.005 pc_SC_c --> 0.24 ocdcea_c + 0.27 hdca_c + 0.5 g3pc_c + 0.06 ddca_c + h_c + 0.17 hdcea_c + 0.02 dca_c + 0.1 ttdca_c + 0.09 ocdcya_c + 0.05 ocdca_c h2o_e + 0.005 pc_SC_e --> 0.05 ocdca_e + 0.27 hdca_e + 0.02 dca_e + 0.06 ddca_e + 0.09 ocdcya_e + 0.5 g3pc_e + 0.1 ttdca_e + h_e + 0.24 ocdcea_e + 0.17 hdcea_e h2o_c + 0.01 pc_SC_c --> chol_c + 0.01 pa_SC_c + h_c man1p_c <=> man6p_c h2o_c + 5aprbu_c --> 4r5au_c + pi_c amet_c + 0.01 ptd2meeta_SC_c --> h_c + ahcys_c + 0.01 pc_SC_c atp_c + 5pmev_c --> adp_c + 5dpmev_c h2o_c + ppmi12346p_c --> h_c + pi_c + minohp_c minohp_c + atp_c --> adp_c + ppmi12346p_c h2o_c + ppmi1346p_c --> pi_c + mi13456p_c + h_c mi13456p_c + atp_c --> ppmi1346p_c + adp_c atp_c + 4ampm_c --> 2mahmp_c + adp_c pi_c + rnam_c <=> r1p_c + ncam_c + h_c pnto_R_c + atp_c --> 4ppan_c + adp_c + h_c pnto_R_e + h_e <=> h_c + pnto_R_c h2o_c + o2_c + N1aspmd_c --> aprut_c + h2o2_c + aproa_c h2o_c + o2_c + N1sprm_c --> h2o2_c + N1aspmd_c + aproa_c h2o_c + o2_c + sprm_c --> h2o2_c + spmd_c + aproa_c h2o_c + ppi_c --> h_c + 2.0 pi_c h2o_m + ppi_m --> 2.0 pi_m + h_m 2.0 5aop_c --> 2.0 h2o_c + ppbng_c + h_c h_c + 4ppcys_c --> co2_c + pan4p_c atp_c + oaa_c --> pep_c + adp_c + co2_c r1p_c <=> r5p_c ctp_c + cys_L_c + 4ppan_c --> ppi_c + h_c + cmp_c + 4ppcys_c nad_c + pphn_c --> nadh_c + co2_c + 34hpp_c nadp_c + pphn_c --> 34hpp_c + nadph_c + co2_c pphn_c + h_c --> h2o_c + co2_c + phpyr_c pppg9_c <=> pppg9_m 3.0 o2_m + 2.0 pppg9_m --> 2.0 ppp9_m + 6.0 h2o_m ipdp_m + pendp_m --> hexdp_m + ppi_m h_c + phpyr_c --> pacald_c + co2_c pram_c + gly_c + atp_c <=> pi_c + gar_c + adp_c + h_c atp_c + fpram_c --> air_c + adp_c + 2.0 h_c + pi_c pran_c --> 2cpr5p_c h2o_c + prbamp_c --> prfp_c atp_c + asp_L_c + 5aizc_c <=> adp_c + 25aics_c + h_c + pi_c h2o_c + prbatp_c --> prbamp_c + ppi_c + h_c h2o_c + gln_L_c + fgam_c + atp_c --> glu_L_c + fpram_c + adp_c + h_c + pi_c prfp_c --> prlp_c pro_L_m + nad_m --> nadh_m + 2.0 h_m + 1pyr5c_m atp_c + trnapro_c + pro_L_c --> ppi_c + protrna_c + amp_c pro_L_e + h_e <=> h_c + pro_L_c pro_L_c <=> pro_L_m r5p_c + atp_c <=> h_c + amp_c + prpp_c prpp_c <=> prpp_m pep_c + skm5p_c --> 3psme_c + pi_c h_g + 0.01 ps_SC_g --> co2_g + 0.01 pe_SC_g 0.01 ps_SC_m + h_m --> 0.01 pe_SC_m + co2_m h_v + 0.01 ps_SC_v --> co2_v + 0.01 pe_SC_v ser_L_c + 0.01 cdpdag_SC_c <=> cmp_c + 0.01 ps_SC_c + h_c 0.01 cdpdag_SC_m + ser_L_m <=> cmp_m + 0.01 ps_SC_m + h_m glu_L_c + 3php_c --> pser_L_c + akg_c psph1p_c --> psph1p_r psph1p_c --> 2hhxdal_c + ethamp_c o2_c + nadph_c + h_c + sphgn_c --> h2o_c + psphings_c + nadp_c pser_L_c + h2o_c --> pi_c + ser_L_c ps_SC_c <=> ps_SC_g ps_SC_c <=> ps_SC_m ps_SC_c <=> ps_SC_v ptd1ino_SC_c <=> ptd1ino_SC_n ptd4ino_SC_c <=> ptd4ino_SC_n dcacoa_x + h2o_x --> h_x + coa_x + dca_x h2o_x + ddcacoa_x --> h_x + coa_x + ddca_x ttccoa_x + h2o_x --> ttc_x + h_x + coa_x h2o_x + pmtcoa_x --> hdca_x + h_x + coa_x h2o_x + tdcoa_x --> coa_x + ttdca_x + h_x stcoa_x + h2o_x --> coa_x + h_x + ocdca_x h2o_x + occoa_x --> coa_x + h_x + octa_x h_c + pan4p_c + atp_c --> ppi_c + dpcoa_c atp_m + h_m + pan4p_m --> dpcoa_m + ppi_m h_c + ptrc_e --> ptrc_c + h_e ptrc_c --> ptrc_e pi_c + adn_c <=> r1p_c + ade_c pi_m + adn_m <=> ade_m + r1p_m pi_c + dad_2_c <=> 2dr1p_c + ade_c gsn_c + pi_c <=> gua_c + r1p_c pi_m + gsn_m <=> gua_m + r1p_m pi_c + dgsn_c <=> 2dr1p_c + gua_c pi_c + ins_c <=> hxan_c + r1p_c pi_c + din_c <=> hxan_c + 2dr1p_c xtsn_c + pi_c <=> r1p_c + xan_c h2o_c + o2_c + pyam5p_c --> h2o2_c + pydx5p_c + nh4_c pydam_c + atp_c --> adp_c + pyam5p_c + h_c pydx_c + atp_c --> h_c + adp_c + pydx5p_c pydxn_c + atp_c --> h_c + adp_c + pdx5p_c o2_c + pydxn_c <=> h2o2_c + pydx_c 2.0 h2o_c + 0.5 o2_c + pydx_c + nh4_c <=> 2.0 h2o2_c + pydam_c pep_c + h_c + adp_c --> atp_c + pyr_c pi_c + uri_c <=> r1p_c + ura_c glu5sa_m + h2o_m + nadp_m --> 2.0 h_m + nadph_m + glu_L_m h_c + pyr_c --> acald_c + co2_c h_c + pyr_c + acald_c --> co2_c + actn_R_c pyr_c --> pyr_e pyr_e + h_e --> h_c + pyr_c h_c + pyr_c <=> h_m + pyr_m h_c + pyr_c <=> pyr_x + h_x cmusa_c --> h2o_c + h_c + quln_c dhap_c + iasp_c --> 2.0 h2o_c + quln_c + pi_c quln_c <=> quln_m raffin_c + h2o_c --> sucr_c + gal_c atp_c + ribflv_c --> fmn_c + adp_c + h_c ribflv_m + atp_m --> adp_m + h_m + fmn_m db4p_c + 4r5au_c --> 2.0 h2o_c + dmlz_c + pi_c 2.0 dmlz_c --> 4r5au_c + ribflv_c rib_D_c + atp_c --> adp_c + r5p_c + h_c h_e + ribflv_e --> h_c + ribflv_c ribflv_c <=> ribflv_m h_e + rib_D_e --> rib_D_c + h_c adp_c + trdrd_c --> trdox_c + h2o_c + dadp_c adp_n + trdrd_n --> trdox_n + dadp_n + h2o_n gdp_c + trdrd_c --> trdox_c + h2o_c + dgdp_c trdrd_n + gdp_n --> trdox_n + h2o_n + dgdp_n trdrd_c + cdp_c --> trdox_c + h2o_c + dcdp_c trdrd_n + cdp_n --> trdox_n + dcdp_n + h2o_n udp_c + trdrd_c --> trdox_c + h2o_c + dudp_c trdrd_n + udp_n --> trdox_n + dudp_n + h2o_n rnam_c + atp_c --> adp_c + h_c + nmn_c atp_c + trdrd_c --> trdox_c + h2o_c + datp_c trdrd_c + gtp_c --> trdox_c + h2o_c + dgtp_c ctp_c + trdrd_c --> trdox_c + h2o_c + dctp_c utp_c + trdrd_c --> trdox_c + h2o_c + dutp_c ru5p_D_c <=> xu5p_D_c r5p_c <=> ru5p_D_c glu_L_c + L2aadp6sa_c + h_c + nadph_c <=> h2o_c + saccrp_L_c + nadp_c h2o_c + saccrp_L_c + nad_c <=> lys_L_c + nadh_c + akg_c + h_c atp_c + so4_c + h_c --> aps_c + ppi_c amet_c + zymst_c --> ahcys_c + fecost_c + h_c sph1p_r + h2o_r --> pi_r + sphgn_r psph1p_r + h2o_r --> pi_r + psphings_r sbt_D_c + nad_c --> fru_c + h_c + nadh_c sbt_L_c + nad_c --> h_c + srb_L_c + nadh_c h_c + nadph_c + glc_D_c --> sbt_D_c + nadp_c sbt_D_e <=> sbt_D_c sbt_L_e <=> sbt_L_c accoa_c + ser_L_c --> coa_c + acser_c ser_L_c --> pyr_c + nh4_c pmtcoa_c + h_c + ser_L_c --> 3dsphgn_c + co2_c + coa_c atp_c + ser_L_c + trnaser_c --> ppi_c + amp_c + sertrna_c h_c + ser_L_c <=> h_m + ser_L_m h_e + ser_L_e <=> h_c + ser_L_c h2o_c + Sfglutth_c <=> h_c + gthrd_c + for_c dscl_c + nadp_c --> nadph_c + scl_c + h_c fe2_c + scl_c --> 3.0 h_c + sheme_c 3dhsk_c + nadph_c + h_c --> skm_c + nadp_c atp_c + skm_c --> h_c + skm5p_c + adp_c suchms_c + cys_L_c --> cyst_L_c + h_c + succ_c h2o_c + suchms_c <=> succ_c + h_c + nh4_c + 2obut_c sphgn_c + atp_c --> h_c + adp_c + sph1p_c psphings_c + atp_c --> h_c + adp_c + psph1p_c adp_c + so4_c + h_c <=> aps_c + pi_c so3_c --> so3_e so4_e --> so4_c sph1p_c --> sph1p_r sph1p_c --> ethamp_c + hxdcal_c spmd_c + accoa_c --> N1aspmd_c + h_c + coa_c h_c + spmd_e --> h_e + spmd_c spmd_c --> spmd_e ptrc_c + ametam_c --> 5mta_c + h_c + spmd_c spmd_c + ametam_c --> 5mta_c + sprm_c + h_c h_c + sprm_e --> sprm_c + h_e Ssq23epx_r <=> Ssq23epx_c h_r + nadph_r + sql_r + o2_r --> Ssq23epx_r + nadp_r + h2o_r h_r + nadh_r + sql_r + o2_r --> Ssq23epx_r + h2o_r + nad_r 2.0 frdp_c + h_c + nadph_c --> nadp_c + 2.0 ppi_c + sql_c sql_c <=> sql_r srb_L_e <=> srb_L_c h2o_c + nadp_c + sucsal_c --> nadph_c + 2.0 h_c + succ_c succ_e + h_e <=> h_c + succ_c pi_m + succ_c --> succ_m + pi_c fad_m + succ_m <=> fadh2_m + fum_m q6_m + succ_m <=> fum_m + q6h2_m fadh2_m + q6_m <=> q6h2_m + fad_m succ_c + fum_m --> fum_c + succ_m succ_m + coa_m + atp_m <=> pi_m + succoa_m + adp_m h2o_e + sucr_e --> glc_D_e + fru_e h_e + sucr_e --> sucr_c + h_c 3.0 h2o_c + 3.0 nadp_c + h2s_c <=> 5.0 h_c + so3_c + 3.0 nadph_c 34hpl_m --> h2o_m + T4hcinnm_m h2o_c + 0.01 triglyc_SC_c --> 0.24 ocdcea_c + 0.27 hdca_c + h_c + 0.01 12dgr_SC_c + 0.06 ddca_c + 0.17 hdcea_c + 0.02 dca_c + 0.1 ttdca_c + 0.09 ocdcya_c + 0.05 ocdca_c g3p_c + s7p_c <=> e4p_c + f6p_c o2_c + akg_c + taur_c --> h_c + so3_c + aacald_c + co2_c + succ_c taur_c <=> taur_e atp_v + tchola_c + h2o_v --> h_v + adp_v + pi_v + tchola_v methf_m + h2o_m --> 5fthf_m + h_m glu_L_c + thf_c + atp_c <=> pi_c + thfglu_c + adp_c + h_c h2o2_c + trdrd_c --> 2.0 h2o_c + trdox_c trdrd_m + h2o2_m <=> 2.0 h2o_m + trdox_m trdrd_n + h2o2_n --> trdox_n + 2.0 h2o_n h2o2_x + trdrd_x <=> trdox_x + 2.0 h2o_x thmpp_e + 2.0 h2o_e --> thm_e + h_e + 2.0 pi_e thymd_e + h_e --> h_c + thymd_c h2o_c + thmmp_c --> pi_c + thm_c thmpp_c --> thmpp_m thmmp_e + h2o_e --> thm_e + pi_e thm_e + h_e --> h_c + thm_c athr_L_c --> acald_c + gly_c thr_L_c --> gly_c + acald_c thr_L_c --> 2obut_c + nh4_c thr_L_m --> 2obut_m + nh4_m h2o_c + phom_c --> pi_c + thr_L_c atp_c + thr_L_c + trnathr_c --> ppi_c + amp_c + thrtrna_c thr_L_m + trnathr_m + atp_m --> amp_m + thrtrna_m + ppi_m thr_L_c + h_c <=> thr_L_m + h_m thr_L_e + h_e <=> h_c + thr_L_c thym_c + h_e <=> h_c + thym_e achms_c + h_c + cys_L_c + gly_c + xu5p_D_c --> 4mpetz_c + 4abut_c + 3.0 h2o_c + pyr_c + nh4_c + ac_c + co2_c achms_c + h_c + cys_L_c + gly_c + r5p_c --> 3.0 h2o_c + 4abut_c + 4mpetz_c + ac_c + nh4_c + co2_c + pyr_c xu5p_D_c + r5p_c <=> g3p_c + s7p_c e4p_c + xu5p_D_c <=> f6p_c + g3p_c thymd_c + atp_c --> dtmp_c + adp_c + h_c atp_c + thm_c --> thmpp_c + amp_c + h_c thymd_c + pi_c <=> 2dr1p_c + thym_c thmpp_c + atp_c --> adp_c + thmtp_c mlthf_c + dump_c --> dhf_c + dtmp_c thm_c + h2o_c --> 4mhetz_c + h_c + 4ahmmp_c thmmp_c + atp_c <=> adp_c + thmpp_c 4mpetz_c + 2mahmp_c + h_c --> ppi_c + thmmp_c dhap_c <=> g3p_c trdox_c <=> trdox_x trdox_c + nadph_c + h_c --> trdrd_c + nadp_c trdrd_c <=> trdrd_x h_m + nadph_m + trdox_m --> nadp_m + trdrd_m h2o_c + tre6p_c --> pi_c + tre_c g6p_c + udpg_c --> tre6p_c + udp_c + h_c h2o_c + tre_c --> 2.0 glc_D_c h2o_v + tre_v --> 2.0 glc_D_v tre_e + h_e --> h_c + tre_c h_c + tre_c <=> tre_v + h_v 0.01 12dgr_SC_c + 0.02 dcacoa_c + 0.1 tdcoa_c + 0.06 ddcacoa_c + 0.24 odecoa_c + 0.17 hdcoa_c + 0.05 stcoa_c + 0.09 ocdycacoa_c + 0.27 pmtcoa_c --> 0.01 triglyc_SC_c + coa_c o2_c + trp_L_c --> Lfmkynr_c ser_L_c + 3ig3p_c --> h2o_c + g3p_c + trp_L_c trp_L_c + akg_c <=> glu_L_c + indpyr_c atp_c + trnatrp_c + trp_L_c --> trptrna_c + ppi_c + amp_c trp_L_m + trnatrp_m + atp_m --> amp_m + trptrna_m + ppi_m h_c + trp_L_c <=> trp_L_m + h_m trp_L_e + h_e <=> h_c + trp_L_c ttccoa_c <=> ttccoa_x ttdca_e <=> ttdca_c tyr_L_c + 10fthf_c --> thf_c + Nfortyr_c + h_c glu_L_c + 34hpp_c --> tyr_L_c + akg_c glu_L_m + 34hpp_m --> tyr_L_m + akg_m glu_L_x + 34hpp_x --> akg_x + tyr_L_x atp_c + trnatyr_c + tyr_L_c --> ppi_c + tyrtrna_c + amp_c tyr_L_m + trnatyr_m + atp_m --> amp_m + ppi_m + tyrtrna_m h_c + tyr_L_c <=> h_m + tyr_L_m h_c + tyr_L_c <=> tyr_L_x + h_x tyr_L_e + h_e <=> h_c + tyr_L_c tyr_L_c + h_v --> tyr_L_v + h_c h_v + tyr_L_v --> h_c + tyr_L_c acgam1p_c + h_c + utp_c <=> ppi_c + udpacgal_c udpg_c <=> udpgal_c udpgal_c --> udpgal_g gal1p_c + udpg_c <=> udpgal_c + g1p_c h2o_c + urdglyc_c + 2.0 h_c <=> glx_c + co2_c + 2.0 nh4_c atp_c + ump_c <=> adp_c + udp_c ump_n + atp_n <=> udp_n + adp_n ump_c <=> ump_n glu_L_c + 2kmb_c --> akg_c + met_L_c 2.0 amet_c + uppg3_c --> 2.0 ahcys_c + dscl_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 ura_e + h_e --> h_c + ura_c urea_e + 2.0 h_e <=> 2.0 h_c + urea_c urea_c + hco3_c + atp_c <=> pi_c + allphn_c + adp_c + h_c dump_c + atp_c <=> dudp_c + adp_c dump_n + atp_n <=> dudp_n + adp_n uri_c + atp_c --> h_c + adp_c + ump_c gtp_c + uri_c --> gdp_c + ump_c + h_c uri_e + h_e --> h_c + uri_c 2.0 h2o_c + utp_c --> 2.0 h_c + 2.0 pi_c + ump_c ump_m + utp_c + 2.0 h_c --> ump_c + utp_m + 2.0 h_m val_L_c + akg_c <=> 3mob_c + glu_L_c val_L_m + akg_m --> 3mob_m + glu_L_m trnaval_c + atp_c + val_L_c --> ppi_c + amp_c + valtrna_c val_L_m + trnaval_m + atp_m --> valtrna_m + amp_m + ppi_m h_c + val_L_c <=> h_m + val_L_m val_L_e + h_e <=> h_c + val_L_c xan_e <=> xan_c prpp_c + xan_c --> ppi_c + xmp_c xtsn_e + h_e --> h_c + xtsn_c atp_c + xylu_D_c --> h_c + adp_c + xu5p_D_c h_c + nadph_c + xyl_D_c --> nadp_c + xylt_c nad_c + xylt_c --> h_c + xylu_D_c + nadh_c xylt_e <=> xylt_c xyl_D_e <=> xyl_D_c ura_c + r5p_c <=> h2o_c + psd5p_c 0.01 zymst_c + 0.015 tdcoa_c + 0.03 stcoa_c + 0.27 odecoa_c + 0.02 pmtcoa_c + 0.01 hexccoa_c + 0.655 hdcoa_c --> 0.01 zymstest_SC_c + coa_c h2o_c + 0.01 zymstest_SC_c --> 0.27 ocdcea_c + 0.02 hdca_c + 0.01 zymst_c + h_c + 0.01 hexc_c + 0.655 hdcea_c + 0.015 ttdca_c + 0.03 ocdca_c h2o_e + 0.01 zymstest_SC_e --> 0.03 ocdca_e + 0.02 hdca_e + 0.01 zymst_e + 0.27 ocdcea_e + 0.015 ttdca_e + h_e + 0.01 hexc_e + 0.655 hdcea_e zymst_e <=> zymst_c 59.276 h2o_c + 0.2862 lys_L_c + 0.3018 glu_L_c + 0.0024 dcmp_c + 0.0066 cys_L_c + 0.2904 gly_c + 0.046 amp_c + 0.0447 cmp_c + 6e-06 pa_SC_c + 6e-05 pc_SC_c + 0.0507 met_L_c + 0.5185 glycogen_c + 0.0015 zymst_c + 1.1348 13BDglcn_c + 0.0036 damp_c + 6.6e-05 triglyc_SC_c + 0.4588 ala_L_c + 0.02 so4_c + 0.1927 ile_L_c + 0.2646 val_L_c + 0.8079 mannan_c + 0.0007 ergst_c + 0.0599 ump_c + 0.1607 arg_L_c + 0.046 gmp_c + 0.102 tyr_L_c + 0.1339 phe_L_c + 0.0036 dtmp_c + 0.2975 asp_L_c + 0.1854 ser_L_c + 0.00099 ribflv_c + 0.1054 gln_L_c + 0.0234 tre_c + 0.1647 pro_L_c + 59.276 atp_c + 0.0284 trp_L_c + 1.7e-05 ps_SC_c + 0.1017 asn_L_c + 0.2964 leu_L_c + 0.0024 dgmp_c + 0.1914 thr_L_c + 0.0663 his_L_c + 5.3e-05 ptd1ino_SC_c + 4.5e-05 pe_SC_c --> 59.305 pi_c + 58.70001 h_c + 59.276 adp_c |
Strain-design¶
All strain-design methods have been coded as python classes t
Predicting heterologous pathways¶
from cameo.strain_design.pathway_prediction import PathwayPredictor
PathwayPredictor(model)
pathway_predictor = PathwayPredictor(model)
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-4-9e8d88b43feb> in <module>()
----> 1 pathway_predictor = PathwayPredictor(model)
NameError: name 'model' is not defined
Deterministic methods¶
Heuristic methods¶
Avoid copies at all costs¶
Copying models is expensive!
%time model_copy = model.copy()
CPU times: user 3.17 s, sys: 84.7 ms, total: 3.26 s
Wall time: 3.25 s
To avoid excessive copying of models, we suggest the following utility included in cameo. For example, temporary reaction deletion, solve the model and magically returns to it original state.
from functools import partial
from cameo.util import TimeMachine
with TimeMachine() as tm:
tm
TimeMachine performs do steps immediately and stores all corresponding undo actions in order. Running all undo steps can be achieved with TimeMachine.reset() (wich is run) We recommend using TimeMachine in conjunction with with, as in case of an unforseen exception all undo steps will be run and manipulated models will return to their original states. This is more elegant than using explicit try-except-else-finally statements.