#machado1



#reactions
ACCOAC:
 {1.0}accoa = {1.0}malcoa
  cytosol * rmaxACCOAC * accoa / (K_ACCOAC_accoa * (1 + malcoa / Ki_ACCOAC_malcoa) + accoa)
CURS:
 {1.0}fercoa + {1.0}ferdicoa = {1.0}cur
  E_CURS * kcat_CURS * (fercoa / (Km_CURS_fercoa + fercoa)) * (ferdicoa / (Km_CURS_ferdicoa + ferdicoa))
CUR_t:
 {1.0}cur = {1.0}cur_ext
  cytosol * k_CUR_t * (cur - cur_ext / Keq_CUR_t)
DCS:
 {1.0}fercoa + {1.0}malcoa = {1.0}ferdicoa
  E_DCS * kcat_DCS * (pow(fercoa, n_DCS_fercoa) / (pow(Km_DCS_fercoa, n_DCS_fercoa) + pow(fercoa, n_DCS_fercoa))) * (malcoa / (Km_DCS_malcoa + malcoa))
EX_CUR:
 {1.0}cur_ext = $pool
  extracellular * Dil * cur_ext
EX_FER:
 $pool = {1.0}fer_ext
  extracellular * Dil * (cfeed_fer - fer_ext)
FER_t:
 {1.0}fer_ext = {1.0}fer
  extracellular * k_FER_t * (fer_ext - fer / Keq_FER_t)
R4CL:
 {1.0}fer = {1.0}fercoa
  E_4CL * kcat_4CL * fer / (Km_4CL + fer)
Synth3:
 {1.0}accoa = $pool
  cytosol * rmaxSynth3 * accoa / (KSynth3accoa + accoa)
Synth4:
 {1.0}malcoa = $pool
  cytosol * rmaxSynth4 * malcoa / (KSynth4malcoa + malcoa)
vACCOA:
 {1.0}accoa = $pool
  cytosol * Dil * accoa
vALDO:
 {1.0}cfdp = {1.0}cdhap + {1.0}cgap
  cytosol * rmaxALDO * (cfdp - cgap * cdhap / kALDOeq) / (kALDOfdp + cfdp + kALDOgap * cdhap / (kALDOeq * VALDOblf) + kALDOdhap * cgap / (kALDOeq * VALDOblf) + cfdp * cgap / kALDOgapinh + cgap * cdhap / (VALDOblf * kALDOeq))
vCUR:
 {1.0}cur = $pool
  cytosol * Dil * cur
vDAHPS:
 {1.0}ce4p + {1.0}cpep = $pool
  cytosol * rmaxDAHPS * pow(ce4p, nDAHPSe4p) * pow(cpep, nDAHPSpep) / ((KDAHPSe4p + pow(ce4p, nDAHPSe4p)) * (KDAHPSpep + pow(cpep, nDAHPSpep)))
vDHAP:
 {1.0}cdhap = $pool
  cytosol * Dil * cdhap
vE4P:
 {1.0}ce4p = $pool
  cytosol * Dil * ce4p
vENO:
 {1.0}cpg2 = {1.0}cpep
  cytosol * rmaxENO * (cpg2 - cpep / KENOeq) / (KENOpg2 * (1 + cpep / KENOpep) + cpg2)
vEXTER:
 $pool = {1.0}cglcex
  extracellular * Dil * (cfeed_glc - cglcex)
vFER:
 {1.0}fer = $pool
  cytosol * Dil * fer
vFERCOA:
 {1.0}fercoa = $pool
  cytosol * Dil * fercoa
vFERDICOA:
 {1.0}ferdicoa = $pool
  cytosol * Dil * ferdicoa
vG1PAT:
 {1.0}cg1p = $pool
  cytosol * rmaxG1PAT * cg1p * catp * (1 + pow(cfdp / KG1PATfdp, nG1PATfdp)) / ((KG1PATatp + catp) * (KG1PATg1p + cg1p))
vG3PDH:
 {1.0}cdhap = $pool
  cytosol * rmaxG3PDH * cdhap / (KG3PDHdhap + cdhap)
vG6P:
 {1.0}cg6p = $pool
  cytosol * Dil * cg6p
vG6PDH:
 {1.0}cg6p = {1.0}cpg
  cytosol * rmaxG6PDH * cg6p * cnadp / ((cg6p + KG6PDHg6p) * (1 + cnadph / KG6PDHnadphg6pinh) * (KG6PDHnadp * (1 + cnadph / KG6PDHnadphnadpinh) + cnadp))
vGAP:
 {1.0}cgap = $pool
  cytosol * Dil * cgap
vGAPDH:
 {1.0}cgap = {1.0}cpgp
  cytosol * rmaxGAPDH * (cgap * cnad - cpgp * cnadh / KGAPDHeq) / ((KGAPDHgap * (1 + cpgp / KGAPDHpgp) + cgap) * (KGAPDHnad * (1 + cnadh / KGAPDHnadh) + cnad))
vGLP:
 {1.0}cg1p = $pool
  cytosol * Dil * cg1p
vMALCOA:
 {1.0}malcoa = $pool
  cytosol * Dil * malcoa
vMURSyNTH:
 {2.0}cf6p = $pool
  cytosol * rmaxMurSynth
vMethSynth:
 $pool = {1.0}cpyr
  cytosol * rmaxMetSynth
vPDH:
 {1.0}cpyr = {1.0}accoa
  cytosol * rmaxPDH * pow(cpyr, nPDH) / (KPDHpyr * (1 + accoa / Ki_PDH_accoa) + pow(cpyr, nPDH))
vPEP:
 {1.0}cpep = $pool
  cytosol * Dil * cpep
vPFK:
 {1.0}cf6p = {1.0}cfdp
  cytosol * rmaxPFK * catp * cf6p / ((catp + KPFKatps * (1 + cadp / KPFKadpc)) * (cf6p + KPFKf6ps * (1 + cpep / KPFKpep + cadp / KPFKadpb + camp / KPFKampb) / (1 + cadp / KPFKadpa + camp / KPFKampa)) * (1 + LPFK / pow(1 + cf6p * (1 + cadp / KPFKadpa + camp / KPFKampa) / (KPFKf6ps * (1 + cpep / KPFKpep + cadp / KPFKadpb + camp / KPFKampb)), nPFK)))
vPG:
 {1.0}cpg = $pool
  cytosol * Dil * cpg
vPG3:
 {1.0}cpg3 = $pool
  cytosol * Dil * cpg3
vPGDH:
 {1.0}cpg = {1.0}cribu5p
  cytosol * rmaxPGDH * cpg * cnadp / ((cpg + KPGDHpg) * (cnadp + KPGDHnadp * (1 + cnadph / KPGDHnadphinh) * (1 + catp / KPGDHatpinh)))
vPGI:
 {1.0}cg6p = {1.0}cf6p
  cytosol * rmaxPGI * (cg6p - cf6p / KPGIeq) / (KPGIg6p * (1 + cf6p / (KPGIf6p * (1 + cpg / KPGIf6ppginh)) + cpg / KPGIg6ppginh) + cg6p)
vPGK:
 {1.0}cpgp = {1.0}cpg3
  cytosol * rmaxPGK * (cadp * cpgp - catp * cpg3 / KPGKeq) / ((KPGKadp * (1 + catp / KPGKatp) + cadp) * (KPGKpgp * (1 + cpg3 / KPGKpg3) + cpgp))
vPGM:
 {1.0}cg6p = {1.0}cg1p
  cytosol * rmaxPGM * (cg6p - cg1p / KPGMeq) / (KPGMg6p * (1 + cg1p / KPGMg1p) + cg6p)
vPGP:
 {1.0}cpgp = $pool
  cytosol * Dil * cpgp
vPK:
 {1.0}cpep = {1.0}cpyr
  cytosol * rmaxPK * cpep * pow(cpep / KPKpep + 1, nPK - 1) * cadp / (KPKpep * (LPK * pow((1 + catp / KPKatp) / (cfdp / KPKfdp + camp / KPKamp + 1), nPK) + pow(cpep / KPKpep + 1, nPK)) * (cadp + KPKadp))
vPPK:
 {1.0}crib5p = $pool
  cytosol * rmaxRPPK * crib5p / (KRPPKrib5p + crib5p)
vPTS:
 {1.0}cglcex + {1.0}cpep = {1.0}cg6p + {1.0}cpyr
  extracellular * rmaxPTS * cglcex * (cpep / cpyr) / ((KPTSa1 + KPTSa2 * (cpep / cpyr) + KPTSa3 * cglcex + cglcex * (cpep / cpyr)) * (1 + pow(cg6p, nPTSg6p) / KPTSg6p))
vR5PI:
 {1.0}cribu5p = {1.0}crib5p
  cytosol * rmaxR5PI * (cribu5p - crib5p / KR5PIeq)
vRIB5P:
 {1.0}crib5p = $pool
  cytosol * Dil * crib5p
vRibu5p:
 {1.0}cribu5p = $pool
  cytosol * Dil * cribu5p
vRu5P:
 {1.0}cribu5p = {1.0}cxyl5p
  cytosol * rmaxRu5P * (cribu5p - cxyl5p / KRu5Peq)
vSED7P:
 {1.0}csed7p = $pool
  cytosol * Dil * csed7p
vSynth1:
 {1.0}cpep = $pool
  cytosol * rmaxSynth1 * cpep / (KSynth1pep + cpep)
vSynth2:
 {1.0}cpyr = $pool
  cytosol * rmaxSynth2 * cpyr / (KSynth2pyr + cpyr)
vTA:
 {1.0}cgap + {1.0}csed7p = {1.0}cf6p + {1.0}ce4p
  cytosol * rmaxTA * (cgap * csed7p - ce4p * cf6p / KTAeq)
vTIS:
 {1.0}cdhap = {1.0}cgap
  cytosol * rmaxTIS * (cdhap - cgap / kTISeq) / (kTISdhap * (1 + cgap / kTISgap) + cdhap)
vTKA:
 {1.0}crib5p + {1.0}cxyl5p = {1.0}cgap + {1.0}csed7p
  cytosol * rmaxTKa * (crib5p * cxyl5p - csed7p * cgap / KTKaeq)
vTKB:
 {1.0}ce4p + {1.0}cxyl5p = {1.0}cgap + {1.0}cf6p
  cytosol * rmaxTKb * (cxyl5p * ce4p - cf6p * cgap / KTKbeq)
vTRPSYNTH:
 $pool = {1.0}cpyr + {1.0}cgap
  cytosol * rmaxTrpSynth
vXYL5P:
 {1.0}cxyl5p = $pool
  cytosol * Dil * cxyl5p
vf6P:
 {1.0}cf6p = $pool
  cytosol * Dil * cf6p
vfdP:
 {1.0}cfdp = $pool
  cytosol * Dil * cfdp
vpepCxylase:
 {1.0}cpep = $pool
  cytosol * rmaxpepCxylase * cpep * (1 + pow(cfdp / KpepCxylasefdp, npepCxylasefdp)) / (KpepCxylasepep + cpep)
vpg2:
 {1.0}cpg2 = $pool
  cytosol * Dil * cpg2
vpyr:
 {1.0}cpyr = $pool
  cytosol * Dil * cpyr
vrpGluMu:
 {1.0}cpg3 = {1.0}cpg2
  cytosol * rmaxPGluMu * (cpg3 - cpg2 / KPGluMueq) / (KPGluMupg3 * (1 + cpg2 / KPGluMupg2) + cpg3)
vsersynth:
 {1.0}cpg3 = $pool
  cytosol * rmaxSerSynth * cpg3 / (KSerSynthpg3 + cpg3)


#parameters
Dil = 0.0
cadp = 0.595
camp = 0.955
catp = 4.27
cnad = 1.47
cnadh = 0.1
cnadp = 0.195
cnadph = 0.062
vPTS_rmaxPTS = 7829.78
vPTS_KPTSa1 = 3082.3
vPTS_KPTSa2 = 0.01
vPTS_KPTSa3 = 245.3
vPTS_nPTSg6p = 3.66
vPTS_KPTSg6p = 2.15
vPGI_rmaxPGI = 650.9878687
vPGI_KPGIeq = 0.1725
vPGI_KPGIg6p = 2.9
vPGI_KPGIf6p = 0.266
vPGI_KPGIf6ppginh = 0.2
vPGI_KPGIg6ppginh = 0.2
vPGM_rmaxPGM = 0.8398242773
vPGM_KPGMeq = 0.196
vPGM_KPGMg6p = 1.038
vPGM_KPGMg1p = 0.0136
vG6PDH_rmaxG6PDH = 1.380196955
vG6PDH_KG6PDHg6p = 14.4
vG6PDH_KG6PDHnadphg6pinh = 6.43
vG6PDH_KG6PDHnadp = 0.0246
vG6PDH_KG6PDHnadphnadpinh = 0.01
vPFK_rmaxPFK = 1840.584747
vPFK_KPFKatps = 0.123
vPFK_KPFKadpc = 4.14
vPFK_KPFKf6ps = 0.325
vPFK_KPFKpep = 3.26
vPFK_KPFKadpb = 3.89
vPFK_KPFKampb = 3.2
vPFK_KPFKadpa = 128.0
vPFK_KPFKampa = 19.1
vPFK_LPFK = 5629067.0
vPFK_nPFK = 11.1
vTA_rmaxTA = 10.87164108
vTA_KTAeq = 1.05
vTKA_rmaxTKa = 9.473384783
vTKA_KTKaeq = 1.2
vTKB_rmaxTKb = 86.55855855
vTKB_KTKbeq = 10.0
vMURSyNTH_rmaxMurSynth = 0.0
vALDO_rmaxALDO = 17.41464425
vALDO_kALDOeq = 0.144
vALDO_kALDOfdp = 1.75
vALDO_kALDOgap = 0.088
vALDO_VALDOblf = 2.0
vALDO_kALDOdhap = 0.088
vALDO_kALDOgapinh = 0.6
vGAPDH_rmaxGAPDH = 921.5942861
vGAPDH_KGAPDHeq = 0.63
vGAPDH_KGAPDHgap = 0.683
vGAPDH_KGAPDHpgp = 1.04e-05
vGAPDH_KGAPDHnad = 0.252
vGAPDH_KGAPDHnadh = 1.09
vTIS_rmaxTIS = 68.67474392
vTIS_kTISeq = 1.39
vTIS_kTISdhap = 2.8
vTIS_kTISgap = 0.3
vTRPSYNTH_rmaxTrpSynth = 0.001037
vG3PDH_rmaxG3PDH = 0.01162042696
vG3PDH_KG3PDHdhap = 1.0
vPGK_rmaxPGK = 3021.773771
vPGK_KPGKeq = 1934.4
vPGK_KPGKadp = 0.185
vPGK_KPGKatp = 0.653
vPGK_KPGKpgp = 0.0468
vPGK_KPGKpg3 = 0.473
vsersynth_rmaxSerSynth = 0.025712107
vsersynth_KSerSynthpg3 = 1.0
vrpGluMu_rmaxPGluMu = 89.04965407
vrpGluMu_KPGluMueq = 0.188
vrpGluMu_KPGluMupg3 = 0.2
vrpGluMu_KPGluMupg2 = 0.369
vENO_rmaxENO = 330.4476151
vENO_KENOeq = 6.73
vENO_KENOpg2 = 0.1
vENO_KENOpep = 0.135
vPK_rmaxPK = 0.06113150238
vPK_KPKpep = 0.31
vPK_nPK = 4.0
vPK_LPK = 1000.0
vPK_KPKatp = 22.5
vPK_KPKfdp = 0.19
vPK_KPKamp = 0.2
vPK_KPKadp = 0.26
vpepCxylase_rmaxpepCxylase = 0.1070205858
vpepCxylase_KpepCxylasefdp = 0.7
vpepCxylase_npepCxylasefdp = 4.21
vpepCxylase_KpepCxylasepep = 4.07
vSynth1_rmaxSynth1 = 0.01953897003
vSynth1_KSynth1pep = 1.0
vSynth2_rmaxSynth2 = 0.07361855055
vSynth2_KSynth2pyr = 1.0
vDAHPS_rmaxDAHPS = 0.1079531227
vDAHPS_nDAHPSe4p = 2.6
vDAHPS_nDAHPSpep = 2.2
vDAHPS_KDAHPSe4p = 0.035
vDAHPS_KDAHPSpep = 0.0053
vPDH_rmaxPDH = 270.27734
vPDH_nPDH = 3.68
vPDH_KPDHpyr = 1159.0
vPDH_Ki_PDH_accoa = 0.0222222
vMethSynth_rmaxMetSynth = 0.0022627
vPGDH_rmaxPGDH = 16.23235977
vPGDH_KPGDHpg = 37.5
vPGDH_KPGDHnadp = 0.0506
vPGDH_KPGDHnadphinh = 0.0138
vPGDH_KPGDHatpinh = 208.0
vR5PI_rmaxR5PI = 4.83841193
vR5PI_KR5PIeq = 4.0
vRu5P_rmaxRu5P = 6.739029475
vRu5P_KRu5Peq = 1.4
vPPK_rmaxRPPK = 0.01290045226
vPPK_KRPPKrib5p = 0.1
vG1PAT_rmaxG1PAT = 0.007525458026
vG1PAT_KG1PATfdp = 0.119
vG1PAT_nG1PATfdp = 1.2
vG1PAT_KG1PATatp = 4.42
vG1PAT_KG1PATg1p = 3.2
vEXTER_cfeed_glc = 110.96
ACCOAC_rmaxACCOAC = 0.04634
ACCOAC_K_ACCOAC_accoa = 0.0003
ACCOAC_Ki_ACCOAC_malcoa = 0.1
Synth3_rmaxSynth3 = 0.284
Synth3_KSynth3accoa = 1.0
Synth4_rmaxSynth4 = 0.092372
Synth4_KSynth4malcoa = 1.0
R4CL_E_4CL = 100.0
R4CL_kcat_4CL = 9.572
R4CL_Km_4CL = 0.026
DCS_E_DCS = 100.0
DCS_kcat_DCS = 0.01343
DCS_Km_DCS_fercoa = 0.046
DCS_Km_DCS_malcoa = 0.0084
DCS_n_DCS_fercoa = 1.8
CURS_E_CURS = 100.0
CURS_kcat_CURS = 0.02163
CURS_Km_CURS_fercoa = 0.018
CURS_Km_CURS_ferdicoa = 0.018
FER_t_k_FER_t = 1000.0
FER_t_Keq_FER_t = 1.0
CUR_t_k_CUR_t = 1000.0
CUR_t_Keq_CUR_t = 1.0
EX_FER_cfeed_fer = 500.0
cytosol = 1.0
extracellular = 65.0


#initial values
accoa = 1.0
cdhap = 0.167
ce4p = 0.098
cf6p = 0.6
cfdp = 0.272
cg1p = 0.653
cg6p = 3.48
cgap = 0.218
cglcex = 55.5
cpep = 2.67
cpg = 0.808
cpg2 = 0.399
cpg3 = 2.13
cpgp = 0.008
cpyr = 2.67
crib5p = 0.398
cribu5p = 0.111
csed7p = 0.276
cur = 0.0
cur_ext = 0.0
cxyl5p = 0.138
fer = 0.0
fer_ext = 271.5
fercoa = 0.0
ferdicoa = 0.0
malcoa = 1.0


#assignment rules