begin name
penkler2
end name

begin reactions
vPFvALD {1.0}f16bpPF = {1.0}dhapPF + {1.0}gapPF
vPFvATPASE {1.0}atpPF = {1.0}adpPF
vPFvENO {1.0}p2gPF = {1.0}pepPF
vPFvG3PDH {1.0}nadhPF + {1.0}dhapPF = {1.0}g3pPF + {1.0}nadPF
vPFvGAPDH {1.0}gapPF + {1.0}nadPF = {1.0}nadhPF + {1.0}b13pgPF
vPFvGLCtr {1.0}glcEX = {1.0}glcPF
vPFvGLYtr {1.0}g3pPF = {1.0}glyEX
vPFvHK {1.0}glcPF + {1.0}atpPF = {1.0}g6pPF + {1.0}adpPF
vPFvLACtr {1.0}lacPF = {1.0}lacEX
vPFvLDH {1.0}nadhPF + {1.0}pyrPF = {1.0}lacPF + {1.0}nadPF
vPFvPFK {1.0}atpPF + {1.0}f6pPF = {1.0}adpPF + {1.0}f16bpPF
vPFvPGI {1.0}g6pPF = {1.0}f6pPF
vPFvPGK {1.0}adpPF + {1.0}b13pgPF = {1.0}atpPF + {1.0}p3gPF
vPFvPGM {1.0}p3gPF = {1.0}p2gPF
vPFvPK {1.0}adpPF + {1.0}pepPF = {1.0}atpPF + {1.0}pyrPF
vPFvPYRtr {1.0}pyrPF = {1.0}pyrEX
vPFvTPI {1.0}dhapPF = {1.0}gapPF
end reactions

begin rate equations
vPFvALD = (VPFvALD*f16bpPF[t]*(1 - (dhapPF[t]*gapPF[t])/(KeqPFvALD*Vpf*f16bpPF[t])))/(Kf16bpPFvALD*(1 + dhapPF[t]/(KdhapPFvALD*Vpf) + f16bpPF[t]/(Kf16bpPFvALD*Vpf) + gapPF[t]/(KgapPFvALD*Vpf) + (dhapPF[t]*gapPF[t])/(KdhapPFvALD*KgapPFvALD*Vpf^2)))
vPFvATPASE = (VPFvATPASE*atpPF[t]^5)/(KmPFvATPASE^5*Vpf^4*(1 + atpPF[t]^5/(KmPFvATPASE^5*Vpf^5)))
vPFvENO = (VPFvENO*p2gPF[t]*(1 - pepPF[t]/(KeqPFvENO*p2gPF[t])))/(Kp2gPFvENO*(1 + p2gPF[t]/(Kp2gPFvENO*Vpf) + pepPF[t]/(KpepPFvENO*Vpf)))
vPFvG3PDH = (VfPFvG3PDH*dhapPF[t]*nadhPF[t]*(1 - (g3pPF[t]*nadPF[t])/(KeqPFvG3PDH*dhapPF[t]*nadhPF[t])))/(KdhapPFvG3PDH*KnadhPFvG3PDH*Vpf*(1 + dhapPF[t]/(KdhapPFvG3PDH*Vpf) + g3pPF[t]/(Kg3pPFvG3PDH*Vpf))*(1 + nadhPF[t]/(KnadhPFvG3PDH*Vpf) + nadPF[t]/(KnadPFvG3PDH*Vpf)))
vPFvGAPDH = (-((VrPFvGAPDH*b13pgPF[t]*nadhPF[t])/(Kb13pgPFvGAPDH*KnadhPFvGAPDH*Vpf)) + (VPFvGAPDH*gapPF[t]*nadPF[t])/(KgapPFvGAPDH*KnadPFvGAPDH*Vpf))/((1 + b13pgPF[t]/(Kb13pgPFvGAPDH*Vpf) + gapPF[t]/(KgapPFvGAPDH*Vpf))*(1 + nadhPF[t]/(KnadhPFvGAPDH*Vpf) + nadPF[t]/(KnadPFvGAPDH*Vpf)))
vPFvGLCtr = (Vpf*VPFvGLCtr*(glcEX[t]/Vex - glcPF[t]/Vpf))/(KmPFvGLCtr*(1 + glcEX[t]/(KmPFvGLCtr*Vex) + glcPF[t]/(KmPFvGLCtr*Vpf) + (alphaPFvGLCtr*glcEX[t]*glcPF[t])/(KmPFvGLCtr^2*Vex*Vpf)))
vPFvGLYtr = kPFvGLYtr*Vpf*(g3pPF[t]/Vpf - glyEX[t]/Vex)
vPFvHK = (VPFvHK*atpPF[t]*(1 - (adpPF[t]*g6pPF[t])/(KeqPFvHK*atpPF[t]*glcPF[t]))*glcPF[t])/(KatpPFvHK*KglcPFvHK*Vpf*(1 + adpPF[t]/(KadpPFvHK*Vpf) + atpPF[t]/(KatpPFvHK*Vpf))*(1 + atpPF[t]/(KiatpPFvHK*Vpf))*(1 + g6pPF[t]/(Kg6pPFvHK*Vpf) + glcPF[t]/(KglcPFvHK*Vpf)))
vPFvLACtr = KdPFvLACtr*(1 - (hEX*Vpf*lacEX[t])/(hPF*Vex*lacPF[t]))*lacPF[t] + (VPFvLACtr*(1 - (hEX*Vpf*lacEX[t])/(hPF*Vex*lacPF[t]))*lacPF[t])/(KlacPFvLACtr*(1 + lacEX[t]/(KlacPFvLACtr*Vex) + lacPF[t]/(KlacPFvLACtr*Vpf) + pyrEX[t]/(KipyrPFvLACtr*Vex) + pyrPF[t]/(KipyrPFvLACtr*Vpf)))
vPFvLDH = (-((VrPFvLDH*lacPF[t]*nadPF[t])/(KlacPFvLDH*KnadPFvLDH*Vpf)) + (VfPFvLDH*nadhPF[t]*pyrPF[t])/(KnadhPFvLDH*KpyrPFvLDH*Vpf))/((1 + nadhPF[t]/(KnadhPFvLDH*Vpf) + nadPF[t]/(KnadPFvLDH*Vpf))*(1 + lacPF[t]/(KlacPFvLDH*Vpf) + pyrPF[t]/(KpyrPFvLDH*Vpf)))
vPFvPFK = (VPFvPFK*atpPF[t]*f6pPF[t])/(KatpPFvPFK*Kf6pPFvPFK*Vpf*(1 + atpPF[t]/(KatpPFvPFK*Vpf))*(1 + adpPF[t]/(KadpPFvPFK*Vpf) + atpPF[t]/(KatpPFvPFK*Vpf))*(1 + f16bpPF[t]/(Kf16bpPFvPFK*Vpf) + f6pPF[t]/(Kf6pPFvPFK*Vpf)))
vPFvPGI = (VPFvPGI*(1 - f6pPF[t]/(KeqPFvPGI*g6pPF[t]))*g6pPF[t])/(Kg6pPFvPGI*(1 + f6pPF[t]/(Kf6pPFvPGI*Vpf) + g6pPF[t]/(Kg6pPFvPGI*Vpf)))
vPFvPGK = (KadpPFvPGK*Kb13pgPFvPGK*KeqPFvPGK*VrPFvPGK*atpPF[t]*(-1 + (KeqPFvPGK*adpPF[t]*b13pgPF[t])/(atpPF[t]*p3gPF[t]))*p3gPF[t])/(KatpPFvPGK^2*Kp3gPFvPGK^2*Vpf*(1 + adpPF[t]/(KadpPFvPGK*Vpf) + atpPF[t]/(KatpPFvPGK*Vpf))*(1 + b13pgPF[t]/(Kb13pgPFvPGK*Vpf) + p3gPF[t]/(Kp3gPFvPGK*Vpf)))
vPFvPGM = (VPFvPGM*(1 - p2gPF[t]/(KeqPFvPGM*p3gPF[t]))*p3gPF[t])/(Kp3gPFvPGM*(1 + p2gPF[t]/(Kp2gPFvPGM*Vpf) + p3gPF[t]/(Kp3gPFvPGM*Vpf)))
vPFvPK = (VPFvPK*adpPF[t]*pepPF[t])/(KadpPFvPK*KpepPFvPK*Vpf*(1 + adpPF[t]/(KadpPFvPK*Vpf))*(1 + pepPF[t]/(KpepPFvPK*Vpf))*(1 + LPFvPK*(1 + (adpPF[t]/(KiadpPFvPK*Vpf) + atpPF[t]/(KiatpPFvPK*Vpf))^h)*(1 + (pepPF[t]/(KipepPFvPK*Vpf) + pyrPF[t]/(KipyrPFvPK*Vpf))^h)))
vPFvPYRtr = KdPFvPYRtr*(1 - (hEX*Vpf*pyrEX[t])/(hPF*Vex*pyrPF[t]))*pyrPF[t] + (VPFvPYRtr*(1 - (hEX*Vpf*pyrEX[t])/(hPF*Vex*pyrPF[t]))*pyrPF[t])/(KpyrPFvPYRtr*(1 + lacEX[t]/(KilacPFvPYRtr*Vex) + lacPF[t]/(KilacPFvPYRtr*Vpf) + pyrEX[t]/(KpyrPFvPYRtr*Vex) + pyrPF[t]/(KpyrPFvPYRtr*Vpf)))
vPFvTPI = (VPFvTPI*dhapPF[t]*(1 - gapPF[t]/(KeqPFvTPI*dhapPF[t])))/(KdhapPFvTPI*(1 + dhapPF[t]/(KdhapPFvTPI*Vpf) + gapPF[t]/(KgapPFvTPI*Vpf) + pepPF[t]/(KipepPFvTPI*Vpf)))
end rate equations

begin parameters
ConcAdpPF = 0.0015
ConcAtpPF = 0.0015
ConcB13pgPF = 0.0001
ConcDhapPF = 0.0001
ConcF16bpPF = 0.0001
ConcF6pPF = 0.0001
ConcG6pPF = 0.0001
ConcGapPF = 0.0001
ConcGlcEX = 0.005
ConcGlcPF = 0.0001
ConcGly3pPF = 0.0001
ConcGlyEX = "3.79121e-11"
ConcLacEX = "3.79121e-11"
ConcLacPF = 0.0001
ConcNadPF = 0.0015
ConcNadhPF = 0.0015
ConcP2gPF = 0.0001
ConcP3gPF = 0.0001
ConcPepPF = "1e-05"
ConcPyrEX = "3.79121e-11"
ConcPyrPF = 0.0001
KadpPFvHK = 0.000846735
KadpPFvPFK = 0.00074176
KadpPFvPGK = 0.00015
KadpPFvPK = 0.000317
KatpPFvHK = 0.00069647
KatpPFvPFK = 0.0007862
KatpPFvPGK = 0.00077
Kb13pgPFvGAPDH = "2.359e-05"
Kb13pgPFvPGK = "1.34e-05"
KdPFvLACtr = 0.005
KdPFvPYRtr = 0.0007
KdhapPFvALD = 0.00011
KdhapPFvG3PDH = 0.00034
KdhapPFvTPI = 0.001954
KeqPFvALD = "9e-05"
KeqPFvENO = 4.6
KeqPFvG3PDH = 32600.0
KeqPFvHK = 1310.0
KeqPFvPGI = 0.33
KeqPFvPGK = 3200.0
KeqPFvPGM = 0.19
KeqPFvTPI = 0.04545
Kf16bpPFvALD = "6.84e-05"
Kf16bpPFvPFK = 0.003626
Kf6pPFvPFK = 0.00109454
Kf6pPFvPGI = "9.6651e-05"
Kg3pPFvG3PDH = 0.00398
Kg6pPFvHK = "4.3e-05"
Kg6pPFvPGI = 0.00100774
KgapPFvALD = "4.6e-05"
KgapPFvGAPDH = 0.000917
KgapPFvTPI = 0.000337
KglcPFvHK = 0.000168613
KiadpPFvPK = 0.002
KiatpPFvHK = 0.026
KiatpPFvPK = 0.00182
KilacPFvPYRtr = 0.000358
KipepPFvPK = 0.00292
KipepPFvTPI = "1.59e-05"
KipyrPFvLACtr = 0.00163
KipyrPFvPK = 0.105
KlacPFvLACtr = 0.0038
KlacPFvLDH = 0.003611
KmPFvATPASE = 0.0045
KmPFvGLCtr = 0.000213
KnadPFvG3PDH = 0.00051
KnadPFvGAPDH = 0.0005662
KnadPFvLDH = 0.000234
KnadhPFvG3PDH = "9e-05"
KnadhPFvGAPDH = "2.87e-05"
KnadhPFvLDH = "4.6e-05"
Kp2gPFvENO = 0.000521
Kp2gPFvPGM = 0.000318
Kp3gPFvPGK = 0.000267
Kp3gPFvPGM = 0.00173
KpepPFvENO = 0.00129
KpepPFvPK = 0.000406
KpyrPFvLDH = 0.000133
KpyrPFvPYRtr = 0.0157
LPFvPK = 0.255
VPFvALD = 0.0569593147718
VPFvATPASE = 0.345
VPFvENO = 0.286295503195
VPFvGAPDH = 0.656263383259
VPFvGLCtr = 0.0469
VPFvHK = 0.083
VPFvLACtr = 0.598
VPFvPFK = 0.41
VPFvPGI = 0.800428265477
VPFvPGM = 0.186937901488
VPFvPK = 0.762
VPFvPYRtr = 0.216
VPFvTPI = 1.50599571726
VfPFvG3PDH = 0.012
VfPFvLDH = 0.542612419668
VrPFvGAPDH = 0.243199143455
VrPFvLDH = 0.290792291203
VrPFvPGK = 0.353533190557
alphaPFvGLCtr = 0.91
h = 4.0
kPFvGLYtr = 2.0
pHConversionFactor = 1.0
phEX = 7.1
phPF = 7.2
Vex = 2637.68
Vpf = 28.0
end parameters

begin initial conditions
adpPF[0] = adpPFi
atpPF[0] = atpPFi
b13pgPF[0] = b13pgPFi
dhapPF[0] = dhapPFi
f16bpPF[0] = f16bpPFi
f6pPF[0] = f6pPFi
g3pPF[0] = g3pPFi
g6pPF[0] = g6pPFi
gapPF[0] = gapPFi
glcEX[0] = glcEXi
glcPF[0] = glcPFi
glyEX[0] = glyEXi
lacEX[0] = lacEXi
lacPF[0] = lacPFi
nadPF[0] = nadPFi
nadhPF[0] = nadhPFi
p2gPF[0] = p2gPFi
p3gPF[0] = p3gPFi
pepPF[0] = pepPFi
pyrEX[0] = pyrEXi
pyrPF[0] = pyrPFi
end initial conditions

begin initial values
adpPFi = 0.042
atpPFi = 0.042
b13pgPFi = 0.0028
dhapPFi = 0.0028
f16bpPFi = 0.0028
f6pPFi = 0.0028
g3pPFi = 0.0028
g6pPFi = 0.0028
gapPFi = 0.0028
glcEXi = 13.1884
glcPFi = 0.0028
glyEXi = 9.999998792799998*^-8
lacEXi = 9.999998792799998*^-8
lacPFi = 0.0028
nadPFi = 0.042
nadhPFi = 0.042
p2gPFi = 0.0028
p3gPFi = 0.0028
pepPFi = 7/25000
pyrEXi = 9.999998792799998*^-8
pyrPFi = 0.0028
end initial values

begin assignment rules
hPF := pHConversionFactor/10^phPF
hEX := pHConversionFactor/10^phEX
end assignment rules

begin function definitions
end function definitions

begin events
end events

begin process annotations
vPFvALD http://identifiers.org/ec-code/4.1.2.13
vPFvENO http://identifiers.org/ec-code/4.2.1.11
vPFvHK http://identifiers.org/ec-code/2.7.1.1
end process annotations

begin species annotations
adpPF http://identifiers.org/pubchem.substance/3310
adpPF http://identifiers.org/kegg.compound/C00008
adpPF http://identifiers.org/3dmet/B01130
atpPF http://identifiers.org/pubchem.substance/3304
atpPF http://identifiers.org/kegg.compound/C00002
atpPF http://identifiers.org/3dmet/B01125
atpPF http://identifiers.org/cas/56-65-5
dhapPF http://identifiers.org/pubchem.substance/3411
dhapPF http://identifiers.org/kegg.compound/C00111
dhapPF http://identifiers.org/3dmet/B00029
f16bpPF http://identifiers.org/pubchem.substance/3647
f16bpPF http://identifiers.org/kegg.compound/C00354
f16bpPF http://identifiers.org/3dmet/B04673
f16bpPF http://identifiers.org/cas/488-69-7
f6pPF http://identifiers.org/kegg.compound/C02976
f6pPF http://identifiers.org/pubchem.substance/5887
g3pPF http://identifiers.org/3dmet/B01157
g3pPF http://identifiers.org/obo.chebi/CHEBI%3A15978
g3pPF http://identifiers.org/kegg.compound/C00093
g3pPF http://identifiers.org/pubchem.substance/3393
g6pPF http://identifiers.org/cas/56-73-5
g6pPF http://identifiers.org/3dmet/B04630
g6pPF http://identifiers.org/obo.chebi/CHEBI%3A4170
g6pPF http://identifiers.org/kegg.compound/C00092
g6pPF http://identifiers.org/pubchem.substance/3392
gapPF http://identifiers.org/cas/591-57-1
gapPF http://identifiers.org/3dmet/B01163
gapPF http://identifiers.org/obo.chebi/CHEBI%3A29052
gapPF http://identifiers.org/kegg.compound/C00118
gapPF http://identifiers.org/pubchem.substance/3418
glcEX http://identifiers.org/obo.chebi/CHEBI%3A17634
glcPF http://identifiers.org/obo.chebi/CHEBI%3A17634
glyEX http://identifiers.org/cas/56-81-5
glyEX http://identifiers.org/3dmet/B00032
glyEX http://identifiers.org/obo.chebi/CHEBI%3A17754
glyEX http://identifiers.org/kegg.compound/C00116
glyEX http://identifiers.org/pubchem.substance/3416
lacEX http://identifiers.org/cas/50-21-5
lacEX http://identifiers.org/obo.chebi/CHEBI%3A28358
lacEX http://identifiers.org/pubchem.substance/4615
lacEX http://identifiers.org/kegg.compound/C01432
lacPF http://identifiers.org/cas/50-21-5
lacPF http://identifiers.org/obo.chebi/CHEBI%3A28358
lacPF http://identifiers.org/pubchem.substance/4615
lacPF http://identifiers.org/kegg.compound/C01432
nadPF http://identifiers.org/3dmet/B01126
nadPF http://identifiers.org/obo.chebi/CHEBI%3A15846
nadPF http://identifiers.org/kegg.compound/C00003
nadPF http://identifiers.org/pubchem.substance/3305
nadPF http://identifiers.org/cas/53-84-9
nadhPF http://identifiers.org/cas/58-68-4
nadhPF http://identifiers.org/3dmet/B01127
nadhPF http://identifiers.org/obo.chebi/CHEBI%3A16908
nadhPF http://identifiers.org/kegg.compound/C00004
nadhPF http://identifiers.org/pubchem.substance/3306
p2gPF http://identifiers.org/3dmet/B01295
p2gPF http://identifiers.org/kegg.compound/C00631
p2gPF http://identifiers.org/pubchem.substance/3904
p2gPF http://identifiers.org/obo.chebi/CHEBI%3A17835
p3gPF http://identifiers.org/3dmet/B01185
p3gPF http://identifiers.org/obo.chebi/CHEBI%3A17794
p3gPF http://identifiers.org/kegg.compound/C00197
p3gPF http://identifiers.org/pubchem.substance/3497
pepPF http://identifiers.org/cas/138-08-9
pepPF http://identifiers.org/3dmet/B00019
pepPF http://identifiers.org/obo.chebi/CHEBI%3A44897
pepPF http://identifiers.org/kegg.compound/C00074
pepPF http://identifiers.org/pubchem.substance/3374
pyrEX http://identifiers.org/cas/127-17-3
pyrEX http://identifiers.org/3dmet/B00006
pyrEX http://identifiers.org/obo.chebi/CHEBI%3A32816
pyrEX http://identifiers.org/kegg.compound/C00022
pyrEX http://identifiers.org/pubchem.substance/3324
pyrPF http://identifiers.org/cas/127-17-3
pyrPF http://identifiers.org/3dmet/B00006
pyrPF http://identifiers.org/obo.chebi/CHEBI%3A32816
pyrPF http://identifiers.org/kegg.compound/C00022
pyrPF http://identifiers.org/pubchem.substance/3324
end species annotations

begin units
end units