begin name
machado1
end name

begin reactions
ACCOAC {1.0}accoa = {1.0}malcoa
CURS {1.0}fercoa + {1.0}ferdicoa = {1.0}cur
CURt {1.0}cur = {1.0}curext
DCS {1.0}fercoa + {1.0}malcoa = {1.0}ferdicoa
EXCUR {1.0}curext = {1.0}$EXTERNAL
EXFER {1.0}$EXTERNAL = {1.0}ferext
FERt {1.0}ferext = {1.0}fer
R4CL {1.0}fer = {1.0}fercoa
Synth3 {1.0}accoa = {1.0}$EXTERNAL
Synth4 {1.0}malcoa = {1.0}$EXTERNAL
vACCOA {1.0}accoa = {1.0}$EXTERNAL
vALDO {1.0}cfdp = {1.0}cdhap + {1.0}cgap
vCUR {1.0}cur = {1.0}$EXTERNAL
vDAHPS {1.0}ce4p + {1.0}cpep = {1.0}$EXTERNAL
vDHAP {1.0}cdhap = {1.0}$EXTERNAL
vE4P {1.0}ce4p = {1.0}$EXTERNAL
vENO {1.0}cpg2 = {1.0}cpep
vEXTER {1.0}$EXTERNAL = {1.0}cglcex
vFER {1.0}fer = {1.0}$EXTERNAL
vFERCOA {1.0}fercoa = {1.0}$EXTERNAL
vFERDICOA {1.0}ferdicoa = {1.0}$EXTERNAL
vG1PAT {1.0}cg1p = {1.0}$EXTERNAL
vG3PDH {1.0}cdhap = {1.0}$EXTERNAL
vG6P {1.0}cg6p = {1.0}$EXTERNAL
vG6PDH {1.0}cg6p = {1.0}cpg
vGAP {1.0}cgap = {1.0}$EXTERNAL
vGAPDH {1.0}cgap = {1.0}cpgp
vGLP {1.0}cg1p = {1.0}$EXTERNAL
vMALCOA {1.0}malcoa = {1.0}$EXTERNAL
vMURSyNTH {2.0}cf6p = {1.0}$EXTERNAL
vMethSynth {1.0}$EXTERNAL = {1.0}cpyr
vPDH {1.0}cpyr = {1.0}accoa
vPEP {1.0}cpep = {1.0}$EXTERNAL
vPFK {1.0}cf6p = {1.0}cfdp
vPG {1.0}cpg = {1.0}$EXTERNAL
vPG3 {1.0}cpg3 = {1.0}$EXTERNAL
vPGDH {1.0}cpg = {1.0}cribu5p
vPGI {1.0}cg6p = {1.0}cf6p
vPGK {1.0}cpgp = {1.0}cpg3
vPGM {1.0}cg6p = {1.0}cg1p
vPGP {1.0}cpgp = {1.0}$EXTERNAL
vPK {1.0}cpep = {1.0}cpyr
vPPK {1.0}crib5p = {1.0}$EXTERNAL
vPTS {1.0}cglcex + {1.0}cpep = {1.0}cg6p + {1.0}cpyr
vR5PI {1.0}cribu5p = {1.0}crib5p
vRIB5P {1.0}crib5p = {1.0}$EXTERNAL
vRibu5p {1.0}cribu5p = {1.0}$EXTERNAL
vRu5P {1.0}cribu5p = {1.0}cxyl5p
vSED7P {1.0}csed7p = {1.0}$EXTERNAL
vSynth1 {1.0}cpep = {1.0}$EXTERNAL
vSynth2 {1.0}cpyr = {1.0}$EXTERNAL
vTA {1.0}cgap + {1.0}csed7p = {1.0}cf6p + {1.0}ce4p
vTIS {1.0}cdhap = {1.0}cgap
vTKA {1.0}crib5p + {1.0}cxyl5p = {1.0}cgap + {1.0}csed7p
vTKB {1.0}ce4p + {1.0}cxyl5p = {1.0}cgap + {1.0}cf6p
vTRPSYNTH {1.0}$EXTERNAL = {1.0}cpyr + {1.0}cgap
vXYL5P {1.0}cxyl5p = {1.0}$EXTERNAL
vf6P {1.0}cf6p = {1.0}$EXTERNAL
vfdP {1.0}cfdp = {1.0}$EXTERNAL
vpepCxylase {1.0}cpep = {1.0}$EXTERNAL
vpg2 {1.0}cpg2 = {1.0}$EXTERNAL
vpyr {1.0}cpyr = {1.0}$EXTERNAL
vrpGluMu {1.0}cpg3 = {1.0}cpg2
vsersynth {1.0}cpg3 = {1.0}$EXTERNAL
end reactions

begin rate equations
ACCOAC = (ACCOACrmaxACCOAC*cytosol*accoa[t])/(accoa[t] + ACCOACKACCOACaccoa*(1 + malcoa[t]/ACCOACKiACCOACmalcoa))
CURS = (CURSECURS*CURSkcatCURS*fercoa[t]*ferdicoa[t])/((CURSKmCURSfercoa + fercoa[t])*(CURSKmCURSferdicoa + ferdicoa[t]))
CURt = CURtkCURt*cytosol*(cur[t] - curext[t]/CURtKeqCURt)
DCS = (DCSEDCS*DCSkcatDCS*fercoa[t]^DCSnDCSfercoa*malcoa[t])/((DCSKmDCSfercoa^DCSnDCSfercoa + fercoa[t]^DCSnDCSfercoa)*(DCSKmDCSmalcoa + malcoa[t]))
EXCUR = Dil*extracellular*curext[t]
EXFER = Dil*extracellular*(EXFERcfeedfer - ferext[t])
FERt = extracellular*FERtkFERt*(-(fer[t]/FERtKeqFERt) + ferext[t])
R4CL = (R4CLE4CL*R4CLkcat4CL*fer[t])/(R4CLKm4CL + fer[t])
Synth3 = (cytosol*Synth3rmaxSynth3*accoa[t])/(Synth3KSynth3accoa + accoa[t])
Synth4 = (cytosol*Synth4rmaxSynth4*malcoa[t])/(Synth4KSynth4malcoa + malcoa[t])
vACCOA = cytosol*Dil*accoa[t]
vALDO = (cytosol*vALDOrmaxALDO*(cfdp[t] - (cdhap[t]*cgap[t])/vALDOkALDOeq))/(vALDOkALDOfdp + (vALDOkALDOgap*cdhap[t])/(vALDOkALDOeq*vALDOVALDOblf) + cfdp[t] + (vALDOkALDOdhap*cgap[t])/(vALDOkALDOeq*vALDOVALDOblf) + (cdhap[t]*cgap[t])/(vALDOkALDOeq*vALDOVALDOblf) + (cfdp[t]*cgap[t])/vALDOkALDOgapinh)
vCUR = cytosol*Dil*cur[t]
vDAHPS = (cytosol*vDAHPSrmaxDAHPS*ce4p[t]^vDAHPSnDAHPSe4p*cpep[t]^vDAHPSnDAHPSpep)/((vDAHPSKDAHPSe4p + ce4p[t]^vDAHPSnDAHPSe4p)*(vDAHPSKDAHPSpep + cpep[t]^vDAHPSnDAHPSpep))
vDHAP = cytosol*Dil*cdhap[t]
vE4P = cytosol*Dil*ce4p[t]
vENO = (cytosol*vENOrmaxENO*(-(cpep[t]/vENOKENOeq) + cpg2[t]))/(vENOKENOpg2*(1 + cpep[t]/vENOKENOpep) + cpg2[t])
vEXTER = Dil*extracellular*(vEXTERcfeedglc - cglcex[t])
vFER = cytosol*Dil*fer[t]
vFERCOA = cytosol*Dil*fercoa[t]
vFERDICOA = cytosol*Dil*ferdicoa[t]
vG1PAT = (catp*cytosol*vG1PATrmaxG1PAT*(1 + (cfdp[t]/vG1PATKG1PATfdp)^vG1PATnG1PATfdp)*cg1p[t])/((catp + vG1PATKG1PATatp)*(vG1PATKG1PATg1p + cg1p[t]))
vG3PDH = (cytosol*vG3PDHrmaxG3PDH*cdhap[t])/(vG3PDHKG3PDHdhap + cdhap[t])
vG6P = cytosol*Dil*cg6p[t]
vG6PDH = (cnadp*cytosol*vG6PDHrmaxG6PDH*cg6p[t])/((1 + cnadph/vG6PDHKG6PDHnadphg6pinh)*(cnadp + vG6PDHKG6PDHnadp*(1 + cnadph/vG6PDHKG6PDHnadphnadpinh))*(vG6PDHKG6PDHg6p + cg6p[t]))
vGAP = cytosol*Dil*cgap[t]
vGAPDH = (cytosol*vGAPDHrmaxGAPDH*(cnad*cgap[t] - (cnadh*cpgp[t])/vGAPDHKGAPDHeq))/((cnad + vGAPDHKGAPDHnad*(1 + cnadh/vGAPDHKGAPDHnadh))*(cgap[t] + vGAPDHKGAPDHgap*(1 + cpgp[t]/vGAPDHKGAPDHpgp)))
vGLP = cytosol*Dil*cg1p[t]
vMALCOA = cytosol*Dil*malcoa[t]
vMURSyNTH = cytosol*vMURSyNTHrmaxMurSynth
vMethSynth = cytosol*vMethSynthrmaxMetSynth
vPDH = (cytosol*vPDHrmaxPDH*cpyr[t]^vPDHnPDH)/(vPDHKPDHpyr*(1 + accoa[t]/vPDHKiPDHaccoa) + cpyr[t]^vPDHnPDH)
vPEP = cytosol*Dil*cpep[t]
vPFK = (catp*cytosol*vPFKrmaxPFK*cf6p[t])/((catp + (1 + cadp/vPFKKPFKadpc)*vPFKKPFKatps)*(cf6p[t] + (vPFKKPFKf6ps*(1 + cadp/vPFKKPFKadpb + camp/vPFKKPFKampb + cpep[t]/vPFKKPFKpep))/(1 + cadp/vPFKKPFKadpa + camp/vPFKKPFKampa))*(1 + vPFKLPFK/(1 + ((1 + cadp/vPFKKPFKadpa + camp/vPFKKPFKampa)*cf6p[t])/(vPFKKPFKf6ps*(1 + cadp/vPFKKPFKadpb + camp/vPFKKPFKampb + cpep[t]/vPFKKPFKpep)))^vPFKnPFK))
vPG = cytosol*Dil*cpg[t]
vPG3 = cytosol*Dil*cpg3[t]
vPGDH = (cnadp*cytosol*vPGDHrmaxPGDH*cpg[t])/((cnadp + (1 + catp/vPGDHKPGDHatpinh)*vPGDHKPGDHnadp*(1 + cnadph/vPGDHKPGDHnadphinh))*(vPGDHKPGDHpg + cpg[t]))
vPGI = (cytosol*vPGIrmaxPGI*(-(cf6p[t]/vPGIKPGIeq) + cg6p[t]))/(cg6p[t] + vPGIKPGIg6p*(1 + cpg[t]/vPGIKPGIg6ppginh + cf6p[t]/(vPGIKPGIf6p*(1 + cpg[t]/vPGIKPGIf6ppginh))))
vPGK = (cytosol*vPGKrmaxPGK*(-((catp*cpg3[t])/vPGKKPGKeq) + cadp*cpgp[t]))/((cadp + vPGKKPGKadp*(1 + catp/vPGKKPGKatp))*(vPGKKPGKpgp*(1 + cpg3[t]/vPGKKPGKpg3) + cpgp[t]))
vPGM = (cytosol*vPGMrmaxPGM*(-(cg1p[t]/vPGMKPGMeq) + cg6p[t]))/(vPGMKPGMg6p*(1 + cg1p[t]/vPGMKPGMg1p) + cg6p[t])
vPGP = cytosol*Dil*cpgp[t]
vPK = (cadp*cytosol*vPKrmaxPK*cpep[t]*(1 + cpep[t]/vPKKPKpep)^(-1 + vPKnPK))/((cadp + vPKKPKadp)*vPKKPKpep*(vPKLPK*((1 + catp/vPKKPKatp)/(1 + camp/vPKKPKamp + cfdp[t]/vPKKPKfdp))^vPKnPK + (1 + cpep[t]/vPKKPKpep)^vPKnPK))
vPPK = (cytosol*vPPKrmaxRPPK*crib5p[t])/(vPPKKRPPKrib5p + crib5p[t])
vPTS = (extracellular*vPTSrmaxPTS*cglcex[t]*cpep[t])/((1 + cg6p[t]^vPTSnPTSg6p/vPTSKPTSg6p)*(vPTSKPTSa1 + vPTSKPTSa3*cglcex[t] + (vPTSKPTSa2*cpep[t])/cpyr[t] + (cglcex[t]*cpep[t])/cpyr[t])*cpyr[t])
vR5PI = cytosol*vR5PIrmaxR5PI*(-(crib5p[t]/vR5PIKR5PIeq) + cribu5p[t])
vRIB5P = cytosol*Dil*crib5p[t]
vRibu5p = cytosol*Dil*cribu5p[t]
vRu5P = cytosol*vRu5PrmaxRu5P*(cribu5p[t] - cxyl5p[t]/vRu5PKRu5Peq)
vSED7P = cytosol*Dil*csed7p[t]
vSynth1 = (cytosol*vSynth1rmaxSynth1*cpep[t])/(vSynth1KSynth1pep + cpep[t])
vSynth2 = (cytosol*vSynth2rmaxSynth2*cpyr[t])/(vSynth2KSynth2pyr + cpyr[t])
vTA = cytosol*vTArmaxTA*(-((ce4p[t]*cf6p[t])/vTAKTAeq) + cgap[t]*csed7p[t])
vTIS = (cytosol*vTISrmaxTIS*(cdhap[t] - cgap[t]/vTISkTISeq))/(cdhap[t] + vTISkTISdhap*(1 + cgap[t]/vTISkTISgap))
vTKA = cytosol*vTKArmaxTKa*(-((cgap[t]*csed7p[t])/vTKAKTKaeq) + crib5p[t]*cxyl5p[t])
vTKB = cytosol*vTKBrmaxTKb*(-((cf6p[t]*cgap[t])/vTKBKTKbeq) + ce4p[t]*cxyl5p[t])
vTRPSYNTH = cytosol*vTRPSYNTHrmaxTrpSynth
vXYL5P = cytosol*Dil*cxyl5p[t]
vf6P = cytosol*Dil*cf6p[t]
vfdP = cytosol*Dil*cfdp[t]
vpepCxylase = (cytosol*vpepCxylasermaxpepCxylase*(1 + (cfdp[t]/vpepCxylaseKpepCxylasefdp)^vpepCxylasenpepCxylasefdp)*cpep[t])/(vpepCxylaseKpepCxylasepep + cpep[t])
vpg2 = cytosol*Dil*cpg2[t]
vpyr = cytosol*Dil*cpyr[t]
vrpGluMu = (cytosol*vrpGluMurmaxPGluMu*(-(cpg2[t]/vrpGluMuKPGluMueq) + cpg3[t]))/(vrpGluMuKPGluMupg3*(1 + cpg2[t]/vrpGluMuKPGluMupg2) + cpg3[t])
vsersynth = (cytosol*vsersynthrmaxSerSynth*cpg3[t])/(vsersynthKSerSynthpg3 + cpg3[t])
end rate equations

begin 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
vPTSrmaxPTS = 7829.78
vPTSKPTSa1 = 3082.3
vPTSKPTSa2 = 0.01
vPTSKPTSa3 = 245.3
vPTSnPTSg6p = 3.66
vPTSKPTSg6p = 2.15
vPGIrmaxPGI = 650.9878687
vPGIKPGIeq = 0.1725
vPGIKPGIg6p = 2.9
vPGIKPGIf6p = 0.266
vPGIKPGIf6ppginh = 0.2
vPGIKPGIg6ppginh = 0.2
vPGMrmaxPGM = 0.8398242773
vPGMKPGMeq = 0.196
vPGMKPGMg6p = 1.038
vPGMKPGMg1p = 0.0136
vG6PDHrmaxG6PDH = 1.380196955
vG6PDHKG6PDHg6p = 14.4
vG6PDHKG6PDHnadphg6pinh = 6.43
vG6PDHKG6PDHnadp = 0.0246
vG6PDHKG6PDHnadphnadpinh = 0.01
vPFKrmaxPFK = 1840.584747
vPFKKPFKatps = 0.123
vPFKKPFKadpc = 4.14
vPFKKPFKf6ps = 0.325
vPFKKPFKpep = 3.26
vPFKKPFKadpb = 3.89
vPFKKPFKampb = 3.2
vPFKKPFKadpa = 128.0
vPFKKPFKampa = 19.1
vPFKLPFK = 5629067.0
vPFKnPFK = 11.1
vTArmaxTA = 10.87164108
vTAKTAeq = 1.05
vTKArmaxTKa = 9.473384783
vTKAKTKaeq = 1.2
vTKBrmaxTKb = 86.55855855
vTKBKTKbeq = 10.0
vMURSyNTHrmaxMurSynth = 0.0
vALDOrmaxALDO = 17.41464425
vALDOkALDOeq = 0.144
vALDOkALDOfdp = 1.75
vALDOkALDOgap = 0.088
vALDOVALDOblf = 2.0
vALDOkALDOdhap = 0.088
vALDOkALDOgapinh = 0.6
vGAPDHrmaxGAPDH = 921.5942861
vGAPDHKGAPDHeq = 0.63
vGAPDHKGAPDHgap = 0.683
vGAPDHKGAPDHpgp = "1.04e-05"
vGAPDHKGAPDHnad = 0.252
vGAPDHKGAPDHnadh = 1.09
vTISrmaxTIS = 68.67474392
vTISkTISeq = 1.39
vTISkTISdhap = 2.8
vTISkTISgap = 0.3
vTRPSYNTHrmaxTrpSynth = 0.001037
vG3PDHrmaxG3PDH = 0.01162042696
vG3PDHKG3PDHdhap = 1.0
vPGKrmaxPGK = 3021.773771
vPGKKPGKeq = 1934.4
vPGKKPGKadp = 0.185
vPGKKPGKatp = 0.653
vPGKKPGKpgp = 0.0468
vPGKKPGKpg3 = 0.473
vsersynthrmaxSerSynth = 0.025712107
vsersynthKSerSynthpg3 = 1.0
vrpGluMurmaxPGluMu = 89.04965407
vrpGluMuKPGluMueq = 0.188
vrpGluMuKPGluMupg3 = 0.2
vrpGluMuKPGluMupg2 = 0.369
vENOrmaxENO = 330.4476151
vENOKENOeq = 6.73
vENOKENOpg2 = 0.1
vENOKENOpep = 0.135
vPKrmaxPK = 0.06113150238
vPKKPKpep = 0.31
vPKnPK = 4.0
vPKLPK = 1000.0
vPKKPKatp = 22.5
vPKKPKfdp = 0.19
vPKKPKamp = 0.2
vPKKPKadp = 0.26
vpepCxylasermaxpepCxylase = 0.1070205858
vpepCxylaseKpepCxylasefdp = 0.7
vpepCxylasenpepCxylasefdp = 4.21
vpepCxylaseKpepCxylasepep = 4.07
vSynth1rmaxSynth1 = 0.01953897003
vSynth1KSynth1pep = 1.0
vSynth2rmaxSynth2 = 0.07361855055
vSynth2KSynth2pyr = 1.0
vDAHPSrmaxDAHPS = 0.1079531227
vDAHPSnDAHPSe4p = 2.6
vDAHPSnDAHPSpep = 2.2
vDAHPSKDAHPSe4p = 0.035
vDAHPSKDAHPSpep = 0.0053
vPDHrmaxPDH = 270.27734
vPDHnPDH = 3.68
vPDHKPDHpyr = 1159.0
vPDHKiPDHaccoa = 0.0222222
vMethSynthrmaxMetSynth = 0.0022627
vPGDHrmaxPGDH = 16.23235977
vPGDHKPGDHpg = 37.5
vPGDHKPGDHnadp = 0.0506
vPGDHKPGDHnadphinh = 0.0138
vPGDHKPGDHatpinh = 208.0
vR5PIrmaxR5PI = 4.83841193
vR5PIKR5PIeq = 4.0
vRu5PrmaxRu5P = 6.739029475
vRu5PKRu5Peq = 1.4
vPPKrmaxRPPK = 0.01290045226
vPPKKRPPKrib5p = 0.1
vG1PATrmaxG1PAT = 0.007525458026
vG1PATKG1PATfdp = 0.119
vG1PATnG1PATfdp = 1.2
vG1PATKG1PATatp = 4.42
vG1PATKG1PATg1p = 3.2
vEXTERcfeedglc = 110.96
ACCOACrmaxACCOAC = 0.04634
ACCOACKACCOACaccoa = 0.0003
ACCOACKiACCOACmalcoa = 0.1
Synth3rmaxSynth3 = 0.284
Synth3KSynth3accoa = 1.0
Synth4rmaxSynth4 = 0.092372
Synth4KSynth4malcoa = 1.0
R4CLE4CL = 100.0
R4CLkcat4CL = 9.572
R4CLKm4CL = 0.026
DCSEDCS = 100.0
DCSkcatDCS = 0.01343
DCSKmDCSfercoa = 0.046
DCSKmDCSmalcoa = 0.0084
DCSnDCSfercoa = 1.8
CURSECURS = 100.0
CURSkcatCURS = 0.02163
CURSKmCURSfercoa = 0.018
CURSKmCURSferdicoa = 0.018
FERtkFERt = 1000.0
FERtKeqFERt = 1.0
CURtkCURt = 1000.0
CURtKeqCURt = 1.0
EXFERcfeedfer = 500.0
cytosol = 1.0
extracellular = 65.0
end parameters

begin initial conditions
accoa[0] = accoai
cdhap[0] = cdhapi
ce4p[0] = ce4pi
cf6p[0] = cf6pi
cfdp[0] = cfdpi
cg1p[0] = cg1pi
cg6p[0] = cg6pi
cgap[0] = cgapi
cglcex[0] = cglcexi
cpep[0] = cpepi
cpg[0] = cpgi
cpg2[0] = cpg2i
cpg3[0] = cpg3i
cpgp[0] = cpgpi
cpyr[0] = cpyri
crib5p[0] = crib5pi
cribu5p[0] = cribu5pi
csed7p[0] = csed7pi
cur[0] = curi
curext[0] = curexti
cxyl5p[0] = cxyl5pi
fer[0] = feri
ferext[0] = ferexti
fercoa[0] = fercoai
ferdicoa[0] = ferdicoai
malcoa[0] = malcoai
end initial conditions

begin initial values
accoai = 1.0
cdhapi = 0.167
ce4pi = 0.098
cf6pi = 0.6
cfdpi = 0.272
cg1pi = 0.653
cg6pi = 3.48
cgapi = 0.218
cglcexi = 55.5
cpepi = 2.67
cpgi = 0.808
cpg2i = 0.399
cpg3i = 2.13
cpgpi = 0.008
cpyri = 2.67
crib5pi = 0.398
cribu5pi = 0.111
csed7pi = 0.276
curi = 0.0
curexti = 0.0
cxyl5pi = 0.138
feri = 0.0
ferexti = 271.5
fercoai = 0.0
ferdicoai = 0.0
malcoai = 1.0
end initial values

begin assignment rules
end assignment rules

begin function definitions
end function definitions

begin events
end events

begin process annotations
end process annotations

begin species annotations
end species annotations

begin units
end units