#kerkhovenC

FIX: CO2_c CO2_g Glc_e Gly_e Pi_g Pyr_e Rib5P_c Rib_g

#reactions
AK_c:
 {2.0}ADP_c = {1.0}AMP_c + {1.0}ATP_c
  vAK(ADP_c, AMP_c, ATP_c, AK_c_k1, AK_c_k2)
AK_g:
 {2.0}ADP_g = {1.0}AMP_g + {1.0}ATP_g
  vAK(ADP_g, AMP_g, ATP_g, AK_g_k1, AK_g_k2)
ALD_g:
 {1.0}Fru16BP_g = {1.0}GA3P_g + {1.0}DHAP_g
  ALD_g_Vmax * Fru16BP_g * (1 - GA3P_g * DHAP_g / (Fru16BP_g * ALD_g_Keq)) / (ALD_g_KmFru16BP * (1 + ATP_g / ALD_g_KiATP + ADP_g / ALD_g_KiADP + AMP_g / ALD_g_KiAMP) * (1 + GA3P_g / ALD_g_KmGA3P + DHAP_g / ALD_g_KmDHAP + Fru16BP_g / (ALD_g_KmFru16BP * (1 + ATP_g / ALD_g_KiATP + ADP_g / ALD_g_KiADP + AMP_g / ALD_g_KiAMP)) + GA3P_g * DHAP_g / (ALD_g_KmGA3P * ALD_g_KmDHAP) + Fru16BP_g * GA3P_g / (ALD_g_KmFru16BP * ALD_g_KiGA3P * (1 + ATP_g / ALD_g_KiATP + ADP_g / ALD_g_KiADP + AMP_g / ALD_g_KiAMP))))
ATPu_c:
 {1.0}ATP_c = {1.0}ADP_c
  ATPu_c_k * ATP_c / ADP_c
ENO_c:
 {1.0}_2PGA_c = {1.0}PEP_c
  v1sub1prod(ENO_c_Vmax, ENO_c_Keq, _2PGA_c, ENO_c_Km2PGA, PEP_c, ENO_c_KmPEP)
G3PDH_g:
 {1.0}NADH_g + {1.0}DHAP_g = {1.0}Gly3P_g + {1.0}NAD_g
  v2sub2prod(G3PDH_g_Vmax, G3PDH_g_Keq, DHAP_g, G3PDH_g_KmDHAP, NADH_g, G3PDH_g_KmNADH, Gly3P_g, G3PDH_g_KmGly3P, NAD_g, G3PDH_g_KmNAD)
G6PDH_c:
 {1.0}Glc6P_c + {1.0}NADP_c = {1.0}NADPH_c + {1.0}_6PGL_c
  v2sub2prod(G6PDH_c_Vmax, G6PDH_c_Keq, Glc6P_c, G6PDH_c_KmGlc6P, NADP_c, G6PDH_c_KmNADP, _6PGL_c, G6PDH_c_Km6PGL, NADPH_c, G6PDH_c_KmNADPH)
G6PDH_g:
 {1.0}Glc6P_g + {1.0}NADP_g = {1.0}_6PGL_g + {1.0}NADPH_g
  v2sub2prod(G6PDH_g_Vmax, G6PDH_g_Keq, Glc6P_g, G6PDH_g_KmGlc6P, NADP_g, G6PDH_g_KmNADP, _6PGL_g, G6PDH_g_Km6PGL, NADPH_g, G6PDH_g_KmNADPH)
G6PP_c:
 {1.0}Glc6P_c = {1.0}Glc_c
  v1sub1prod(G6PP_c_Vmax, G6PP_c_Keq, Glc6P_c, G6PP_c_KmGlc6P, Glc_c, G6PP_c_KmGlc)
GAPDH_g:
 {1.0}GA3P_g + {1.0}NAD_g + {1.0}Pi_g = {1.0}NADH_g + {1.0}_13BPGA_g
  v2sub2prod(GAPDH_g_Vmax, GAPDH_g_Keq, GA3P_g, GAPDH_g_KmGA3P, NAD_g, GAPDH_g_KmNAD, _13BPGA_g, GAPDH_g_Km13BPGA, NADH_g, GAPDH_g_KmNADH)
GDA_g:
 {1.0}Gly3P_g + {1.0}DHAP_c = {1.0}Gly3P_c + {1.0}DHAP_g
  Gly3P_g * GDA_g_k * DHAP_c - Gly3P_c * GDA_g_k * DHAP_g
GK_g:
 {1.0}Gly3P_g + {1.0}ADP_g = {1.0}Gly_e + {1.0}ATP_g
  v2sub2prod(GK_g_Vmax, GK_g_Keq, Gly3P_g, GK_g_KmGly3P, ADP_g, GK_g_KmADP, Gly_e, GK_g_KmGly, ATP_g, GK_g_KmATP)
GPO_c:
 {1.0}Gly3P_c = {1.0}DHAP_c
  v1sub(GPO_c_Vmax, Gly3P_c, GPO_c_KmGly3P)
GlcT_c:
 {1.0}Glc_e = {1.0}Glc_c
  GlcT_c_Vmax * (Glc_e - Glc_c) / (GlcT_c_KmGlc + Glc_e + Glc_c + GlcT_c_alpha * Glc_e * Glc_c / GlcT_c_KmGlc)
GlcT_g:
 {1.0}Glc_c = {1.0}Glc_g
  mass_action_rev(GlcT_g_k1, Glc_c, GlcT_g_k2, Glc_g)
HXK_c:
 {1.0}Glc_c + {1.0}ATP_c = {1.0}Glc6P_c + {1.0}ADP_c
  v2sub2prod(HXK_c_Vmax, HXK_c_Keq, Glc_c, HXK_c_KmGlc, ATP_c, HXK_c_KmATP, Glc6P_c, HXK_c_KmGlc6P, ADP_c, HXK_c_KmADP)
HXK_g:
 {1.0}ATP_g + {1.0}Glc_g = {1.0}Glc6P_g + {1.0}ADP_g
  v2sub2prod(HXK_g_Vmax, HXK_g_Keq, Glc_g, HXK_g_KmGlc, ATP_g, HXK_g_KmATP, Glc6P_g, HXK_g_KmGlc6P, ADP_g, HXK_g_KmADP)
NADPHu_c:
 {1.0}NADPH_c = {1.0}NADP_c
  mass_action_irrev(NADPHu_c_k, NADPH_c)
NADPHu_g:
 {1.0}NADPH_g = {1.0}NADP_g
  mass_action_irrev(NADPHu_g_k, NADPH_g)
PFK_g:
 {1.0}ATP_g + {1.0}Fru6P_g = {1.0}Fru16BP_g + {1.0}ADP_g
  PFK_g_Vmax * PFK_g_Ki1 * Fru6P_g * ATP_g * (1 - Fru16BP_g * ADP_g / (PFK_g_Keq * Fru6P_g * ATP_g)) / (PFK_g_KmFru6P * PFK_g_KmATP * (Fru16BP_g + PFK_g_Ki1) * (PFK_g_KsATP / PFK_g_KmATP + Fru6P_g / PFK_g_KmFru6P + ATP_g / PFK_g_KmATP + ADP_g / PFK_g_KmADP + Fru16BP_g * ADP_g / (PFK_g_KmADP * PFK_g_Ki2) + Fru6P_g * ATP_g / (PFK_g_KmFru6P * PFK_g_KmATP)))
PGAM_c:
 {1.0}_3PGA_c = {1.0}_2PGA_c
  v1sub1prod(PGAM_c_Vmax, PGAM_c_Keq, _3PGA_c, PGAM_c_Km3PGA, _2PGA_c, PGAM_c_Km2PGA)
PGI_g:
 {1.0}Glc6P_g = {1.0}Fru6P_g
  PGI_g_Vmax * Glc6P_g * (1 - Fru6P_g / (PGI_g_Keq * Glc6P_g)) / (PGI_g_KmGlc6P * (1 + Glc6P_g / PGI_g_KmGlc6P + Fru6P_g / PGI_g_KmFru6P + _6PG_g / PGI_g_Ki6PG))
PGK_g:
 {1.0}_13BPGA_g + {1.0}ADP_g = {1.0}_3PGA_g + {1.0}ATP_g
  v2sub2prod(PGK_g_Vmax, PGK_g_Keq, _13BPGA_g, PGK_g_Km13BPGA, ADP_g, PGK_g_KmADP, _3PGA_g, PGK_g_Km3PGA, ATP_g, PGK_g_KmATP)
PGL_c:
 {1.0}_6PGL_c = {1.0}_6PG_c
  PGL_c_k * cytosol * (_6PGL_c - _6PG_c / PGL_c_Keq) + v1sub1prod(PGL_c_Vmax, PGL_c_Keq, _6PGL_c, PGL_c_Km6PGL, _6PG_c, PGL_c_Km6PG)
PGL_g:
 {1.0}_6PGL_g = {1.0}_6PG_g
  glycosome * PGL_g_k * (_6PGL_g - _6PG_g / PGL_g_Keq) + v1sub1prod(PGL_g_Vmax, PGL_g_Keq, _6PGL_g, PGL_g_Km6PGL, _6PG_g, PGL_g_Km6PG)
PPI_c:
 {1.0}Rul5P_c = {1.0}Rib5P_c
  v1sub1prod(PPI_c_Vmax, PPI_c_Keq, Rul5P_c, PPI_c_KmRul5P, Rib5P_c, PPI_c_KmRib5P)
PPI_g:
 {1.0}Rul5P_g = {1.0}Rib5P_g
  v1sub1prod(PPI_g_Vmax, PPI_g_Keq, Rul5P_g, PPI_g_KmRul5P, Rib5P_g, PPI_g_KmRib5P)
PYK_c:
 {1.0}PEP_c + {1.0}ADP_c = {1.0}Pyr_c + {1.0}ATP_c
  PYK_c_Vmax * ADP_c * (1 - Pyr_c * ATP_c / (PYK_c_Keq * PEP_c * ADP_c)) * pow(PEP_c / (PYK_c_KmPEP * (1 + ADP_c / PYK_c_KiADP + ATP_c / PYK_c_KiATP)), PYK_c_n) / (PYK_c_KmADP * (1 + pow(PEP_c / (PYK_c_KmPEP * (1 + ADP_c / PYK_c_KiADP + ATP_c / PYK_c_KiATP)), PYK_c_n) + Pyr_c / PYK_c_KmPyr) * (1 + ADP_c / PYK_c_KmADP + ATP_c / PYK_c_KmATP))
PyrT_c:
 {1.0}Pyr_c = {1.0}Pyr_e
  v1sub(PyrT_c_Vmax, Pyr_c, PyrT_c_KmPyr)
RK_g:
 {1.0}ADP_g + {1.0}Rib5P_g = {1.0}ATP_g + {1.0}Rib_g
  v2sub2prod(RK_g_Vmax, RK_g_Keq, Rib5P_g, RK_g_KmRib5P, ADP_g, RK_g_KmADP, Rib_g, RK_g_KmRib, ATP_g, RK_g_KmATP)
TOX_c:
 {1.0}TSH2_c = {1.0}TS2_c
  mass_action_irrev(TOX_c_k, TSH2_c)
TPI_g:
 {1.0}DHAP_g = {1.0}GA3P_g
  v1sub1prod(TPI_g_Vmax, TPI_g_Keq, DHAP_g, TPI_g_KmDHAP, GA3P_g, TPI_g_KmGA3P)
TR_c:
 {1.0}TS2_c + {1.0}NADPH_c = {1.0}NADP_c + {1.0}TSH2_c
  v2sub2prod(TR_c_Vmax, TR_c_Keq, TS2_c, TR_c_KmTS2, NADPH_c, TR_c_KmNADPH, TSH2_c, TR_c_KmTSH2, NADP_c, TR_c_KmNADP)
_3PGAT_g:
 {1.0}_3PGA_g = {1.0}_3PGA_c
  mass_action_rev(_3PGAT_g_k, _3PGA_g, _3PGAT_g_k, _3PGA_c)
_6PGDH_c:
 {1.0}NADP_c + {1.0}_6PG_c = {1.0}CO2_c + {1.0}NADPH_c + {1.0}Rul5P_c
  v2sub2prod(_6PGDH_c_Vmax, _6PGDH_c_Keq, _6PG_c, _6PGDH_c_Km6PG, NADP_c, _6PGDH_c_KmNADP, Rul5P_c, _6PGDH_c_KmRul5P, NADPH_c, _6PGDH_c_KmNADPH)
_6PGDH_g:
 {1.0}_6PG_g + {1.0}NADP_g = {1.0}Rul5P_g + {1.0}CO2_g + {1.0}NADPH_g
  v2sub2prod(_6PGDH_g_Vmax, _6PGDH_g_Keq, _6PG_g, _6PGDH_g_Km6PG, NADP_g, _6PGDH_g_KmNADP, Rul5P_g, _6PGDH_g_KmRul5P, NADPH_g, _6PGDH_g_KmNADPH)


#parameters
CO2_c = 0.0
CO2_g = 0.0
Glc_e = 5.0
Gly_e = 0.0
Pi_g = 0.0
Pyr_e = 0.0
Rib5P_c = 0.01
Rib_g = 0.01
TPI_g_TPI_g_Vmax = 999.3
TPI_g_TPI_g_Keq = 0.046
TPI_g_TPI_g_KmDHAP = 1.2
TPI_g_TPI_g_KmGA3P = 0.25
PYK_c_PYK_c_Vmax = 1020.0
PYK_c_PYK_c_KmPEP = 0.34
PYK_c_PYK_c_KiATP = 0.57
PYK_c_PYK_c_KiADP = 0.64
PYK_c_PYK_c_n = 2.5
PYK_c_PYK_c_KmADP = 0.114
PYK_c_PYK_c_Keq = 10800.0
PYK_c_PYK_c_KmPyr = 50.0
PYK_c_PYK_c_KmATP = 15.0
PFK_g_PFK_g_Vmax = 1708.0
PFK_g_PFK_g_Ki1 = 15.8
PFK_g_PFK_g_KmFru6P = 0.999
PFK_g_PFK_g_KmATP = 0.0648
PFK_g_PFK_g_Keq = 1035.0
PFK_g_PFK_g_KsATP = 0.0393
PFK_g_PFK_g_KmADP = 1.0
PFK_g_PFK_g_Ki2 = 10.7
G6PDH_g_G6PDH_g_Vmax = 8.4
G6PDH_g_G6PDH_g_Keq = 5.02
G6PDH_g_G6PDH_g_KmGlc6P = 0.058
G6PDH_g_G6PDH_g_KmNADP = 0.0094
G6PDH_g_G6PDH_g_Km6PGL = 0.04
G6PDH_g_G6PDH_g_KmNADPH = 0.0001
PGAM_c_PGAM_c_Vmax = 225.0
PGAM_c_PGAM_c_Keq = 0.17
PGAM_c_PGAM_c_Km3PGA = 0.15
PGAM_c_PGAM_c_Km2PGA = 0.16
PyrT_c_PyrT_c_Vmax = 230.0
PyrT_c_PyrT_c_KmPyr = 1.96
G6PDH_c_G6PDH_c_Vmax = 8.4
G6PDH_c_G6PDH_c_Keq = 5.02
G6PDH_c_G6PDH_c_KmGlc6P = 0.058
G6PDH_c_G6PDH_c_KmNADP = 0.0094
G6PDH_c_G6PDH_c_Km6PGL = 0.04
G6PDH_c_G6PDH_c_KmNADPH = 0.0001
ENO_c_ENO_c_Vmax = 598.0
ENO_c_ENO_c_Keq = 4.17
ENO_c_ENO_c_Km2PGA = 0.054
ENO_c_ENO_c_KmPEP = 0.24
HXK_g_HXK_g_Vmax = 1774.68
HXK_g_HXK_g_Keq = 759.0
HXK_g_HXK_g_KmGlc = 0.1
HXK_g_HXK_g_KmATP = 0.116
HXK_g_HXK_g_KmGlc6P = 2.7
HXK_g_HXK_g_KmADP = 0.126
RK_g_RK_g_Vmax = 10.0
RK_g_RK_g_Keq = 0.0036
RK_g_RK_g_KmRib5P = 0.39
RK_g_RK_g_KmADP = 0.25
RK_g_RK_g_KmRib = 0.51
RK_g_RK_g_KmATP = 0.24
_3PGAT_g__3PGAT_g_k = 250.0
NADPHu_c_NADPHu_c_k = 2.0
HXK_c_HXK_c_Vmax = 154.32
HXK_c_HXK_c_Keq = 759.0
HXK_c_HXK_c_KmGlc = 0.1
HXK_c_HXK_c_KmATP = 0.116
HXK_c_HXK_c_KmGlc6P = 2.7
HXK_c_HXK_c_KmADP = 0.126
NADPHu_g_NADPHu_g_k = 2.0
AK_c_AK_c_k1 = 480.0
AK_c_AK_c_k2 = 1000.0
G6PP_c_G6PP_c_Vmax = 28.0
G6PP_c_G6PP_c_Keq = 263.0
G6PP_c_G6PP_c_KmGlc6P = 5.6
G6PP_c_G6PP_c_KmGlc = 5.6
_6PGDH_g__6PGDH_g_Vmax = 10.6
_6PGDH_g__6PGDH_g_Keq = 47.0
_6PGDH_g__6PGDH_g_Km6PG = 0.0035
_6PGDH_g__6PGDH_g_KmNADP = 0.001
_6PGDH_g__6PGDH_g_KmRul5P = 0.03
_6PGDH_g__6PGDH_g_KmNADPH = 0.0006
PGI_g_PGI_g_Vmax = 1305.0
PGI_g_PGI_g_KmGlc6P = 0.4
PGI_g_PGI_g_Keq = 0.457
PGI_g_PGI_g_KmFru6P = 0.12
PGI_g_PGI_g_Ki6PG = 0.14
AK_g_AK_g_k1 = 480.0
AK_g_AK_g_k2 = 1000.0
TOX_c_TOX_c_k = 2.0
GDA_g_GDA_g_k = 600.0
PGL_c_PGL_c_Vmax = 28.0
PGL_c_PGL_c_Keq = 20000.0
PGL_c_PGL_c_Km6PGL = 0.05
PGL_c_PGL_c_Km6PG = 0.05
PGL_c_PGL_c_k = 0.055
_6PGDH_c__6PGDH_c_Vmax = 10.6
_6PGDH_c__6PGDH_c_Keq = 47.0
_6PGDH_c__6PGDH_c_Km6PG = 0.0035
_6PGDH_c__6PGDH_c_KmNADP = 0.001
_6PGDH_c__6PGDH_c_KmRul5P = 0.03
_6PGDH_c__6PGDH_c_KmNADPH = 0.0006
PPI_c_PPI_c_Vmax = 72.0
PPI_c_PPI_c_Keq = 5.6
PPI_c_PPI_c_KmRul5P = 1.4
PPI_c_PPI_c_KmRib5P = 4.0
PPI_g_PPI_g_Vmax = 72.0
PPI_g_PPI_g_Keq = 5.6
PPI_g_PPI_g_KmRul5P = 1.4
PPI_g_PPI_g_KmRib5P = 4.0
GlcT_g_GlcT_g_k1 = 250000.0
GlcT_g_GlcT_g_k2 = 250000.0
GlcT_c_GlcT_c_Vmax = 111.7
GlcT_c_GlcT_c_KmGlc = 1.0
GlcT_c_GlcT_c_alpha = 0.75
PGL_g_PGL_g_Vmax = 5.0
PGL_g_PGL_g_Keq = 20000.0
PGL_g_PGL_g_Km6PGL = 0.05
PGL_g_PGL_g_Km6PG = 0.05
PGL_g_PGL_g_k = 0.055
TR_c_TR_c_Vmax = 252.0
TR_c_TR_c_Keq = 434.0
TR_c_TR_c_KmTS2 = 0.0069
TR_c_TR_c_KmNADPH = 0.00077
TR_c_TR_c_KmTSH2 = 0.0018
TR_c_TR_c_KmNADP = 0.081
PGK_g_PGK_g_Vmax = 2862.0
PGK_g_PGK_g_Keq = 3377.0
PGK_g_PGK_g_Km13BPGA = 0.003
PGK_g_PGK_g_KmADP = 0.1
PGK_g_PGK_g_Km3PGA = 1.62
PGK_g_PGK_g_KmATP = 0.29
G3PDH_g_G3PDH_g_Vmax = 465.0
G3PDH_g_G3PDH_g_Keq = 17085.0
G3PDH_g_G3PDH_g_KmDHAP = 0.1
G3PDH_g_G3PDH_g_KmNADH = 0.01
G3PDH_g_G3PDH_g_KmGly3P = 2.0
G3PDH_g_G3PDH_g_KmNAD = 0.4
ATPu_c_ATPu_c_k = 50.0
GK_g_GK_g_Vmax = 200.0
GK_g_GK_g_Keq = 0.000837
GK_g_GK_g_KmGly3P = 3.83
GK_g_GK_g_KmADP = 0.56
GK_g_GK_g_KmGly = 0.44
GK_g_GK_g_KmATP = 0.24
ALD_g_ALD_g_Vmax = 560.0
ALD_g_ALD_g_KmFru16BP = 0.009
ALD_g_ALD_g_KiATP = 0.68
ALD_g_ALD_g_KiADP = 1.51
ALD_g_ALD_g_KiAMP = 3.65
ALD_g_ALD_g_Keq = 0.084
ALD_g_ALD_g_KmGA3P = 0.067
ALD_g_ALD_g_KmDHAP = 0.015
ALD_g_ALD_g_KiGA3P = 0.098
GAPDH_g_GAPDH_g_Vmax = 720.9
GAPDH_g_GAPDH_g_Keq = 0.066
GAPDH_g_GAPDH_g_KmGA3P = 0.15
GAPDH_g_GAPDH_g_KmNAD = 0.45
GAPDH_g_GAPDH_g_Km13BPGA = 0.1
GAPDH_g_GAPDH_g_KmNADH = 0.02
GPO_c_GPO_c_Vmax = 368.0
GPO_c_GPO_c_KmGly3P = 1.7
cytosol = 5.4549
default = 1.0
glycosome = 0.2451


#initial values
ADP_c = 1.3165
ADP_g = 1.519
AMP_c = 2.2418
AMP_g = 4.2405
ATP_c = 0.3417
ATP_g = 0.2405
DHAP_c = 2.23132912
DHAP_g = 8.483130623
Fru16BP_g = 10.0
Fru6P_g = 0.5
GA3P_g = 2.5
Glc6P_c = 0.5
Glc6P_g = 0.5
Glc_c = 0.1
Glc_g = 0.1
Gly3P_c = 2.76867088
Gly3P_g = 10.51686938
NADH_g = 2.0
NADPH_c = 3.9
NADPH_g = 3.9
NADP_c = 0.1
NADP_g = 0.1
NAD_g = 2.0
PEP_c = 1.0
Pyr_c = 10.0
Rib5P_g = 0.01
Rul5P_c = 0.41282
Rul5P_g = 0.41282
TS2_c = 0.37
TSH2_c = 0.01
_13BPGA_g = 0.5
_2PGA_c = 0.1
_3PGA_c = 0.1
_3PGA_g = 0.1
_6PGL_c = 0.0795278
_6PGL_g = 0.0795278
_6PG_c = 0.0841958
_6PG_g = 0.0841958


#assignment rules