examples/sbtab/jiang_model.multi.tsv
!!ObjTables objTablesVersion='0.0.8' schema='SBtab' document='BIOMD0000000239' type='Data' class='Compartment'
!ID !Name !Size
CYTOPLASM cytoplasm 1
MT_IMS mitochondrial intermembrane space 1
MT_IM mitochondrial inner membrane 1
MATRIX mitochondrial matrix 1
!!ObjTables objTablesVersion='0.0.8' schema='SBtab' document='BIOMD0000000239' type='Data' class='Compound'
!ID !Name !Location !Charge !IsConstant !InitialConcentration !hasOnlySubstanceUnits !Identifiers:kegg.compound
GLC glucose CYTOPLASM 0 FALSE 0 FALSE C00267
F6P fructose-6-phosphate CYTOPLASM 0 FALSE 0 FALSE C00085
FBP "fructose-1,6-bisphosphate" CYTOPLASM 0 FALSE 0 FALSE C00354
GAP glyceraldehyde 3-phosphate CYTOPLASM 0 FALSE 0 FALSE C00118
DPG "1,2-bisphospho-D-glycerate" CYTOPLASM 0 FALSE 0 FALSE C00236
PEP phosphoenolpyruvate CYTOPLASM 0 FALSE 0 FALSE C00074
PYR_cyt pyruvate CYTOPLASM 0 FALSE 0 FALSE C00022
AMP adenine monophosphate CYTOPLASM 0 FALSE 0 FALSE C00020
LAC lactate CYTOPLASM 0 FALSE 0 FALSE C00186
G3P glycerol-3-phosphate CYTOPLASM 0 FALSE 0 FALSE C00093
DHAP dihydrohxyacetone-phosphate CYTOPLASM 0 FALSE 0 FALSE C00111
OXA_cyt oxaloacetate CYTOPLASM 0 FALSE 0 FALSE C00036
Asp_cyt aspartate CYTOPLASM 0 FALSE 0 FALSE C00049
Glu_cyt glutamate CYTOPLASM 0 FALSE 0 FALSE C00025
OG_cyt oxoglutarate CYTOPLASM 0 FALSE 0 FALSE C00026
Mal_cyt malate CYTOPLASM 0 FALSE 0 FALSE C00149
Acetyl_CoA_cyt acetyl CoA CYTOPLASM 0 FALSE 0 FALSE C00024
CoA_cyt coenzyme A CYTOPLASM 0 FALSE 0 FALSE C00010
IsoCitcyt isocitrate CYTOPLASM 0 FALSE 0 FALSE C00311
Cit_cyt citrate CYTOPLASM 0 FALSE 0 FALSE C00158
ATP_cyt adenine triphosphate CYTOPLASM 0 FALSE 0 FALSE C0002
ADP_cyt adenine diphosphate CYTOPLASM 0 FALSE 0 FALSE C0008
NAD NAD CYTOPLASM 0 FALSE 0 FALSE C00003
NADH_cyt NADH CYTOPLASM 0 FALSE 0 FALSE C00004
NADP_cyt NADP CYTOPLASM 0 FALSE 0 FALSE C00006
NADPH_cyt NADPH CYTOPLASM 0 FALSE 0 FALSE C00005
Pyr pyruvate MATRIX 0 FALSE 0 FALSE C00022
CO2 carbon dioxide MATRIX 0 FALSE 0 FALSE C00011
CoA coenzyme A MATRIX 0 FALSE 0 FALSE C00010
Acetyl_CoA acetyl CoA MATRIX 0 FALSE 0 FALSE C00024
Pi phosphate MATRIX 0 FALSE 0 FALSE C00009
Fum fumarate MATRIX 0 FALSE 0 FALSE C00122
SCoA succinyl-CoA MATRIX 0 FALSE 0 FALSE C00091
Suc succinate MATRIX 0 FALSE 0 FALSE C00042
GTP guanosine triphosphate MATRIX 0 FALSE 0 FALSE C00044
GDP guanosine diphosphate MATRIX 0 FALSE 0 FALSE C00035
Ala slanine MATRIX 0 FALSE 0 FALSE C00041
Asp aspartate MATRIX 0 FALSE 0 FALSE C00049
Glu glutamate MATRIX 0 FALSE 0 FALSE C00025
H2O water MATRIX 0 FALSE 0 FALSE C00001
ETFred electron transfer flavoprotein (reduced form) MATRIX 0 FALSE 0 FALSE C04570
ETFox electron transfer flavoprotein (oxidised form) MATRIX 0 FALSE 0 FALSE C04253
FADH2 FADH2 MATRIX 0 FALSE 0 FALSE C01352
FAD FAD MATRIX 0 FALSE 0 FALSE C00016
OG oxoglutarate MATRIX 0 FALSE 0 FALSE C00026
Mal malate MATRIX 0 FALSE 0 FALSE C00149
OXA oxaloacetate MATRIX 0 FALSE 0 FALSE C00036
Cit citrate MATRIX 0 FALSE 0 FALSE C00158
IsoCit isocitrate MATRIX 0 FALSE 0 FALSE C00311
ATP adenine triphosphate MATRIX 0 FALSE 0 FALSE C0002
ADP adenine diphosphate MATRIX 0 FALSE 0 FALSE C0008
NADP_p NADP+ MATRIX 0 FALSE 0 FALSE C00006
NADPH NADPH MATRIX 0 FALSE 0 FALSE C00005
NAD_p NAD+ MATRIX 0 FALSE 0 FALSE C00003
NADH NADH MATRIX 0 FALSE 0 FALSE C00004
Q ubiquinone MT_IMS 0 FALSE 0 FALSE C00399
QH2 ubiquinol MT_IMS 0 FALSE 0 FALSE C00390
Cytc3p ferrocytochrome c MT_IMS 0 FALSE 0 FALSE C00126
Cytc2p ferricytochrome c MT_IMS 0 FALSE 0 FALSE C00125
!!ObjTables objTablesVersion='0.0.8' schema='SBtab' document='BIOMD0000000239' type='Data' class='Reaction'
!ID !Name !ReactionFormula !Regulator !KineticLaw !IsReversible !Identifiers:ec-code
GLCflow <=> GLC "CYTOPLASM * (Glc_F * pow(10, -3) - GLC) * flow" TRUE
LACflow LAC <=> CYTOPLASM * LAC * flow FALSE
GAPflow GAP <=> CYTOPLASM * GAP * flow FALSE
v1 glucokinase GLC + ATP_cyt <=> F6P + ADP_cyt CYTOPLASM * (V1 * ATP_cyt * GLC / ((K1GLC + GLC) * (K1ATP + ATP_cyt))) FALSE 2.7.1.2
v2 6-phosphofructokinase F6P + ATP_cyt <=> FBP + ADP_cyt AMP "CYTOPLASM * (V2 * ATP_cyt * pow(F6P, 2) / ((K2 * (1 + k2 * pow(ATP_cyt / AMP, 2)) + pow(F6P, 2)) * (K2ATP + ATP_cyt)))" FALSE 2.7.1.11
v3 fructose-bisphosphate aldolase FBP <=> 2.0 GAP "CYTOPLASM * (k3f * FBP - k3b * pow(GAP, 2))" TRUE 4.1.2.13
v4 glyceraldehyde 3-phosphate dehydrogenase GAP + NAD <=> DPG + NADH_cyt CYTOPLASM * (V4 * NAD * GAP / ((K4GAP + GAP) * (K4NAD + NAD))) FALSE 1.2.1.12
v5 bisphosphoglycerate phosphotase (1/2) DPG + ADP_cyt <=> PEP + ATP_cyt CYTOPLASM * (k5f * DPG * ADP_cyt - k5b * PEP * ATP_cyt) TRUE 5.4.2.4
v6 pyruvate kinase PEP + ADP_cyt <=> PYR_cyt + ATP_cyt CYTOPLASM * (V6 * ADP_cyt * PEP / ((K6PEP + PEP) * (K6ADP + ADP_cyt))) FALSE 2.7.1.40
v7 lactate dehydrogenase PYR_cyt + NADH_cyt <=> LAC + NAD CYTOPLASM * (k8f * NADH_cyt * PYR_cyt - k8b * NAD * LAC) TRUE 1.1.1.27
hidden_1 AMP + ATP_cyt <=> 2.0 ADP_cyt "CYTOPLASM * (k9f * AMP * ATP_cyt - k9b * pow(ADP_cyt, 2))" TRUE
v8 pyruvate carrier PYR_cyt <=> Pyr MATRIX * (V * PYR_cyt * v8_PYC / (K + PYR_cyt)) TRUE
v9 pyruvate dehydrogenase complex Pyr + CoA + NAD_p <=> CO2 + Acetyl_CoA + NADH MATRIX * (KcF * v9_PDC * Pyr * CoA * NAD_p / (KmC * Pyr * CoA + KmB * Pyr * NAD_p + KmA * CoA * NAD_p + Pyr * CoA * NAD_p + KmA * KmP * Kib * Kic / KmR / Kip / Kiq * Acetyl_CoA * NADH + KmC / Kir * Pyr * CoA * NADH + KmB / Kiq * Pyr * NAD_p * Acetyl_CoA + KmA * KmP * Kib * Kic / KmR / Kip / Kia / Kiq * Pyr * Acetyl_CoA * NADH)) FALSE 1.2.4.1
v10 citrate synthase OXA + Acetyl_CoA <=> Cit + CoA MATRIX * (V * Acetyl_CoA * OXA * v10_CS / (Acetyl_CoA * OXA + Ka * OXA + Kb * Acetyl_CoA + Kia * Kib)) TRUE 2.3.3.3
v11 aconitase Cit <=> IsoCit MATRIX * ((KcF * Kp * Cit - KcR * Ks * IsoCit) * v11_ACO / (Ks * IsoCit + Kp * Cit + Ks * Kp)) TRUE 4.2.1.3
v12 isocitrate dehydrogenase (NAD+) (alpha/beta/gamma) IsoCit + NAD_p <=> OG + NADH ADP MATRIX * (KcF * v12_IDHa * (IsoCit * IsoCit + b * ADP * IsoCit) / (IsoCit * IsoCit + c * IsoCit + d * ADP + e * ADP * IsoCit + f)) FALSE 1.1.1.41
v14 oxoglutarate dehydrogenase complex OG + CoA + NAD_p <=> CO2 + SCoA + NADH MATRIX * (KcF * v14_OGDC * OG * CoA * NAD_p / (KmC * OG * CoA + KmB * OG * NAD_p + KmA * CoA * NAD_p + OG * CoA * NAD_p + KmA * KmP * Kib * Kic / KmR / Kip / Kiq * SCoA * NADH + KmC / Kir * OG * CoA * NADH + KmB / Kiq * OG * NAD_p * SCoA + KmA * KmP * Kib * Kic / KmR / Kip / Kia / Kiq * OG * SCoA * NADH)) FALSE 1.2.4.2
v15 succinyl-CoA synthetase GDP + SCoA + Pi <=> Suc + GTP + CoA MATRIX * ((GDP * SCoA * pi - Suc * GTP * CoA / Keq) * (Kc1 * v15_SCS + Kc2 * v15_SCS * (KmC * Suc / KmC2 * Kip + pi / KmC2)) / (Kia * KmB * pi + KmB * GDP * pi + KmA * SCoA * pi + KmC * GDP * SCoA + GDP * SCoA * pi + GDP * SCoA * pi * pi / KmC2 + Kia * KmB * KmC * Suc / Kip + Kia * KmB * KmC * Suc * GTP / Kip / Kiq + Kia * KmB * KmC * Suc * CoA / Kip / Kir + Kia * KmB * Kic * GTP * CoA / KmQ / Kir + Kia * KmB * KmC * Suc * GTP * CoA / Kip / KmQ / Kir + Kia * KmB * KmC * Suc * Suc * GTP * CoA / Kip / KmP2 / KmQ / Kir + Kia * KmB * pi * GTP / Kiq + Kia * KmB * pi * CoA / Kir + Kia * KmB * pi * GTP * CoA / KmQ / Kir + Kia * KmB * pi * Suc * GTP * CoA / KmP2 / KmQ / Kir + KmB * KmC * GDP * Suc / Kip + KmA * KmC * SCoA * Suc / Kip + KmC * GDP * SCoA * Suc / Kip + KmC * GDP * SCoA * pi * Suc / KmC2 / Kip + KmA * SCoA * pi * GTP / Kiq + KmB * GDP * pi * CoA / Kir + KmA * KmC * SCoA * Suc * GTP / Kip / Kiq + KmB * KmC * GDP * Suc * CoA / Kip / Kir)) TRUE 6.2.1.4
v16 succinate dehydrogenase Suc + Q <=> Fum + QH2 MATRIX * (KcF * KcR * v16_SDH * (Suc * Q - Fum * QH2 / Keq) / (KcR * KmS2 * Suc + KcR * KmS1 * Q + KcF * KmP2 * Fum / Keq + KcF * KmP1 * QH2 / Keq + KcR * Suc * Q + KcF * KmP2 * Suc * Fum / (Keq * KiS1) + KcF * Fum * QH2 / Keq + KcR * KmS1 * Q * QH2 / KiP2)) TRUE 1.3.5.1
v17 fumarase Fum <=> Mal MATRIX * ((KcF * Kp * Fum - KcR * Ks * Mal) * v17_FM / (Ks * Mal + Kp * Fum + Ks * Kp)) TRUE 4.2.1.2
v18 malate dehydrogenase (mitochondrion) Mal + NAD_p <=> NADH + OXA MATRIX * ((KcF * Mal * NAD_p / KiS1 / KmS2 - KcR * OXA * NADH / KmP1 / KiP2) * v18_MDH / (1 + Mal / KiS1 + KmS1 * NAD_p / KiS1 / KmS2 + KmP2 * OXA / KmP1 / KiP2 + NADH / KiP2 + Mal * NAD_p / KiS1 / KmS2 + KmP2 * Mal * OXA / KiS1 / KmP1 / KiP2 + KmS1 * NAD_p * NADH / KiS1 / KmS2 / KiP2 + OXA * NADH / KmP1 * KiP2 + Mal * NAD_p * OXA / KiS1 / KmS2 / KiP1 + NAD_p * OXA * NADH / KiS2 / KmP1 / KiP2)) TRUE 1.1.1.37
v20 alanine transaminase Ala + OG <=> Glu + Pyr MATRIX * (KcF * KcR * v20_AlaTA * (Ala * OG - Glu * Pyr / Keq) / (KcR * KmS2 * Ala + KcR * KmS1 * OG + KcF * KmP2 * Glu / Keq + KcF * KmP1 * Pyr / Keq + KcR * Ala * OG + KcF * KmP2 * Ala * Glu / (Keq * KiS1) + KcF * Glu * Pyr / Keq + KcR * KmS1 * OG * Pyr / KiP2)) TRUE 2.6.1.2
v21 aspartate transaminase OXA + Glu <=> Asp + OG MATRIX * (KcF * KcR * v21_AspTA * (OXA * Glu - Asp * OG / Keq) / (KcR * KmS2 * OXA + KcR * KmS1 * Glu + KcF * KmP2 * Asp / Keq + KcF * KmP1 * OG / Keq + KcR * OXA * Glu + KcF * KmP2 * OXA * Asp / (Keq * KiS1) + KcF * Asp * OG / Keq + KcR * KmS1 * Glu * OG / KiP2)) TRUE 2.6.1.1
v22 aspartate/glutamate carrier Glu_cyt + Asp <=> Asp_cyt + Glu MATRIX * ((Asp * Glu_cyt / alpha / KiS1 / KiS2 * KcF - Glu * Asp_cyt / beta / KiP1 / KiP2 * KcR) * v22_AGC / (1 + Asp / KiS1 + Glu_cyt / KiS2 + Glu / KiP1 + Asp_cyt / KiP2 + Asp * Glu_cyt / alpha / KiS1 / KiS2 + Glu * Asp_cyt / beta / KiP1 / KiP2 + Glu_cyt * Asp_cyt / gamma / KiS2 / KiP2 + Asp * Glu / delta / KiS1 / KiP1)) TRUE
v24 NADH:ubiquinone oxidoreductase NADH + Q <=> NAD_p + QH2 MATRIX * (KcF * KcR * v24_Complex_I * (NADH * Q - NAD_p * QH2 / Keq) / (KcR * KmS2 * NADH + KcR * KmS1 * Q + KcF * KmP2 * NAD_p / Keq + KcF * KmP1 * QH2 / Keq + KcR * NADH * Q + KcF * KmP2 * NADH * NAD_p / (Keq * KiS1) + KcF * NAD_p * QH2 / Keq + KcR * KmS1 * Q * QH2 / KiP2)) TRUE 2.7.4.6
v25 ubiquinol:cytochrome c oxidoreductase QH2 + 2.0 Cytc3p <=> Q + 2.0 Cytc2p MT_IMS * (KcF * v25_Complex_III * QH2 * Cytc3p / ((KmA * Kq2 * Kb2 + KmA * Kq2 * Cytc3p + KcF / k8 * Kq1 * QH2 * Kb1 + KcF / k8 * Kq1 * QH2 * Cytc3p) * Cytc2p + KmA * Cytc3p + KmB * QH2 + QH2 * Cytc3p)) FALSE 1.10.2.2
v26 cytochrome c oxidase Cytc2p <=> Cytc3p MT_IMS * (KcF * v26_Complex_IV * Cytc2p / (Ks + Cytc2p)) FALSE 1.9.3.1
v27 citrate synthase Cit_cyt + CoA_cyt <=> OXA_cyt + Acetyl_CoA_cyt CYTOPLASM * Kid * Kc * (V * Acetyl_CoA_cyt * OXA_cyt * v10_CS / (Acetyl_CoA_cyt * OXA_cyt + Ka * OXA_cyt + Kb * Acetyl_CoA_cyt + Kia * Kib)) / (Keq * Kia * Kb) TRUE 2.3.3.3
v28 ATPase complex ADP + Pi <=> ATP + H2O MATRIX * v28_Complex_V * V * ADP / (Km + ADP + ADP * ADP / Ki) TRUE 3.6.1.5
v29 aconitase Cit_cyt <=> IsoCitcyt CYTOPLASM * ((KcF * Kp * Cit_cyt - KcR * Ks * IsoCitcyt) * v29_ACO / (Ks * IsoCitcyt + Kp * Cit_cyt + Ks * Kp)) TRUE 4.2.1.3
v30 oxoglutarate carrier Mal_cyt + OG <=> OG_cyt + Mal MATRIX * ((OG * Mal_cyt / alpha / KiS1 / KiS2 * KcF - Mal * OG_cyt / beta / KiP1 / KiP2 * KcR) * v30_OGC / (1 + OG / KiS1 + Mal_cyt / KiS2 + Mal / KiP1 + OG_cyt / KiP2 + OG * Mal_cyt / alpha / KiS1 / KiS2 + Mal * OG_cyt / beta / KiP1 / KiP2 + Mal_cyt * OG_cyt / gamma / KiS2 / KiP2 + OG * Mal / delta / KiS1 / KiP1)) TRUE
v31 malate dehydrogenase (cytosol) NADH_cyt + OXA_cyt <=> Mal_cyt + NAD CYTOPLASM * (v31_MDH * (k1 * k2 * k3 * k4 * NADH_cyt * OXA_cyt - kminus1 * kminus2 * kminus3 * kminus4 * Mal_cyt * NAD) / (kminus1 * (kminus2 + k3) * k4 + k1 * (kminus2 + k3) * k4 * NADH_cyt + kminus1 * (kminus2 + k3) * kminus4 * NAD + k2 * k3 * k4 * OXA_cyt + kminus1 * kminus2 * kminus3 * Mal_cyt + k1 * k2 * (k3 + k4) * NADH_cyt * OXA_cyt + (kminus1 + kminus2) * kminus3 * kminus4 * Mal_cyt * NAD + k1 + kminus2 + kminus3 * NADH_cyt * Mal_cyt + k1 * k2 * kminus3 * NADH_cyt * OXA_cyt * Mal_cyt + k2 * k3 * kminus4 * OXA_cyt * NAD + k2 * kminus3 * kminus4 * OXA_cyt * Mal_cyt * NAD)) FALSE 1.1.1.37
v32 aspartate transaminase Asp_cyt + OG_cyt <=> OXA_cyt + Glu_cyt CYTOPLASM * (KcF * KcR * v32_AspTA * (Asp_cyt * OG_cyt - OXA_cyt * Glu_cyt / Keq) / (KcR * KmS2 * Asp_cyt + KcR * KmS1 * OG_cyt + KcF * KmP2 * OXA_cyt / Keq + KcF * KmP1 * Glu_cyt / Keq + KcR * Asp_cyt * OG_cyt + KcF * KmP2 * Asp_cyt * OXA_cyt / (Keq * KiS1) + KcF * OXA_cyt * Glu_cyt / Keq + KcR * KmS1 * OG_cyt * Glu_cyt / KiP2)) TRUE 2.6.1.1
v33 citrate carrier Cit_cyt + Mal <=> Mal_cyt + Cit MATRIX * ((Cit_cyt * Mal / alpha / KiS1 / KiS2 * KcF - Mal_cyt * Cit / beta / KiP1 / KiP2 * KcR) * v33_CIC / (1 + Cit_cyt / KiS1 + Mal / KiS2 + Mal_cyt / KiP1 + Cit / KiP2 + Cit_cyt * Mal / alpha / KiS1 / KiS2 + Mal_cyt * Cit / beta / KiP1 / KiP2 + Mal * Cit / gamma / KiS2 / KiP2 + Cit_cyt * Mal_cyt / delta / KiS1 / KiP1)) TRUE
v34 ETF:Q oxidoreductase ETFred + Q <=> ETFox + QH2 MATRIX * (KcF * KcR * v34_ETF_QO * (ETFred * Q - ETFox * QH2 / Keq) / (KcR * KmS2 * ETFred + KcR * KmS1 * Q + KcF * KmP2 * ETFox / Keq + KcF * KmP1 * QH2 / Keq + KcR * ETFred * Q + KcF * KmP2 * ETFred * ETFox / (Keq * KiS1) + KcF * ETFox * QH2 / Keq + KcR * KmS1 * Q * QH2 / KiP2)) TRUE 1.5.5.1
v35 glutathione reductase FADH2 + ETFox <=> ETFred + FAD MATRIX * (KcF * KcR * v35_ACD * (FADH2 * ETFox - ETFred * FAD / Keq) / (KcR * KiS1 * KmS2 + KcR * KmS2 * FADH2 + KcR * KmS1 * ETFox + KcF * KmP2 * ETFred / Keq + KcF * KmP1 * FAD / Keq + KcR * FADH2 * ETFox + KcF * KmP2 * FADH2 * ETFred / (Keq * KiS1) + KcF * ETFred * FAD / Keq + KcR * KmS1 * ETFox * FAD / KiP2 + KcR * FADH2 * ETFox * ETFred / KiP1 + KcF * ETFox * ETFred * FAD / (KiS2 * Keq))) TRUE 1.8.1.7
v36 pyruvate decarboxylase ATP + CO2 + Pyr <=> Pi + ADP + OXA MATRIX * (KcF * KcR * v36_PC * (ATP * CO2 * Pyr - pi * ADP * OXA / Keq) / (Kia * KmB * KcR * Pyr + KmC * KcR * ATP * CO2 + KmA * KcR * CO2 * Pyr + KmB * KcR * ATP * Pyr + KcR * ATP * CO2 * Pyr + Kip * KmQ * KcF * OXA / Keq + KmQ * KcF * pi * OXA / Keq + KmP * KcF * ADP * OXA / Keq + KmR * KcF * pi * ADP / Keq + KcF * pi * ADP * OXA / Keq + Kia * KmB * KcR * Pyr * pi / Kip + Kia * KmB * KcR * Pyr * ADP / Kia + Kiq * KmP * KcF * CO2 * OXA / Kib / Keq + Kia * KmP * KcF * ATP * OXA / Kia / Keq + KmA * KcR * ATP * CO2 * OXA / Kir + KmR * KcF * Pyr * pi * ADP / Kic / Keq + KmA * KcR * CO2 * Pyr * ADP / Kiq + KmA * KcR * CO2 * Pyr * pi / Kip + KmP * KcF * CO2 * ADP * OXA / Kib / Keq + KmQ * KcF * CO2 * pi * OXA / Kib / Keq)) TRUE 6.4.1.1
v37 glycerol-3-phosphate dehydrogenase (FAD dependent) G3P + FAD <=> FADH2 + DHAP CYTOPLASM * (V * v37_GUT2P * G3P / (K + G3P)) FALSE 1.1.99.5
v38 glycerol-3-phosphate dehydrogenase (NAD+ dependent) NADH_cyt + DHAP <=> G3P + NAD CYTOPLASM * (V * v38_GUT2P * NADH_cyt / (K + NADH_cyt)) FALSE 1.1.1.8
v40 ATP/ADP carrier ADP_cyt <=> ADP MATRIX * (V * v40_AAC * ADP_cyt / (K + ADP_cyt)) FALSE
v41 cytosolic isocitrate dehydrogenase IsoCitcyt + NADP_cyt <=> OG_cyt + NADPH_cyt CO2 CYTOPLASM * v41_IDHc * (IsoCitcyt * NADP_cyt / (phi0 * IsoCitcyt * NADP_cyt + phi1 * NADP_cyt + phi2 * IsoCitcyt + phi12) - OG_cyt * NADPH_cyt * CO2 / (phir0 * OG_cyt * NADPH_cyt * CO2 + phir1 * NADPH_cyt * CO2 + phir2 * OG_cyt * CO2 + phir3 * OG_cyt * NADPH_cyt + phir12 * CO2 + phir13 * NADPH_cyt + phir23 * OG_cyt + phir123)) TRUE 1.1.1.42
v42 citrate carrier IsoCitcyt + Mal <=> Mal_cyt + IsoCit MATRIX * ((IsoCitcyt * Mal / alpha / KiS1 / KiS2 * KcF - Mal_cyt * IsoCit / beta / KiP1 / KiP2 * KcR) * v42_CIC / (1 + IsoCitcyt / KiS1 + Mal / KiS2 + Mal_cyt / KiP1 + IsoCit / KiP2 + IsoCitcyt * Mal / alpha / KiS1 / KiS2 + Mal_cyt * IsoCit / beta / KiP1 / KiP2 + Mal * IsoCit / gamma / KiS2 / KiP2 + IsoCitcyt * Mal_cyt / delta / KiS1 / KiP1)) TRUE
v43 ATP/ADP carrier ATP <=> ATP_cyt MATRIX * (V * v43_AAC * ATP / (K + ATP)) FALSE
v39 malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) Mal_cyt + NADP_cyt <=> NADPH_cyt + PYR_cyt CYTOPLASM * (v39_MDH * Kcat * Mal_cyt * NADP_cyt / ((Kmal + Mal_cyt) * (Knadp + NADP_cyt))) TRUE 1.1.1.40
v44 malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) Mal + NADP_p <=> NADPH + Pyr MATRIX * (v44_MDH * Kcat * Mal / (Km + Mal)) TRUE 1.1.1.40
!!ObjTables objTablesVersion='0.0.8' schema='SBtab' document='BIOMD0000000239' type='Data' class='Quantity' description='Parameter prior'
!QuantityType !Unit !BiologicalElement !MathematicalType !PriorMedian !PriorStd !PriorGeometricStd !LowerBound !UpperBound !DataStd !Symbol !PhysicalType !Dependence !UseAsPriorInformation !SBMLElement !Abbreviation !MatrixInfo
standard chemical potential kJ/mol Species Additive -880 1500 -3000 2000 10 mu0 Thermodynamic Basic 1 Global parameter scp "[I_species, 0, 0, 0, 0, 0, 0, 0]"
catalytic rate constant geometric mean 1/s Reaction Multiplicative 10 100 0.0000001 10000 100 KV Kinetic Basic 1 Local parameter kcrg "[0, I_reaction, 0, 0, 0, 0, 0, 0]"
Michaelis constant mM Reaction/Species Multiplicative 0.1 10 0.000001 1000 1 KM Kinetic Basic 1 Local parameter kmc "[0, 0, I_KM, 0, 0, 0, 0, 0]"
activation constant mM Reaction/Species Multiplicative 0.1 10 0.0001 100 1 KA Kinetic Basic 1 Local parameter kac "[0, 0, 0, I_KA, 0, 0, 0, 0]"
inhibitory constant mM Reaction/Species Multiplicative 0.1 10 0.0001 100 1 KI Kinetic Basic 1 Local parameter kic "[0, 0, 0, 0, I_KI, 0, 0, 0]"
concentration mM Species Multiplicative 0.1 10 0.000001 1000 1 c Dynamic Basic 1 Species (conc.) c "[0, 0, 0, 0, 0, I_species, 0, 0]"
concentration of enzyme mM Reaction Multiplicative 0.001 100 0.000001 0.5 0.05 u Dynamic Basic 1 Local parameter eco "[0, 0, 0, 0, 0, 0, I_reaction, 0]"
pH dimensionless None Additive 7 1 0 14 1 pH Dynamic Basic 1 Global parameter ph "[0, 0, 0, 0, 0, 0, 0, 1]"
standard Gibbs energy of reaction kJ/mol Reaction Additive 0 1500 -1000 1000 10 dmu0 Thermodynamic Derived 0 Global parameter dscp "[Nt, 0, 0, 0, 0, 0, 0, 0]"
equilibrium constant dimensionless Reaction Multiplicative 1 100 1.00E-10 100000000 100 Keq Thermodynamic Derived 1 Local parameter keq "[[-1/RT * Nt], 0, 0, 0, 0, 0, 0, 0]"
substrate catalytic rate constant 1/s Reaction Multiplicative 10 100 0.01 10000000 100 Kcatf Kinetic Derived 1 Local parameter kcrf "[[-0.5/RT * Nt], I_reaction, [-0.5 * Nkm], 0, 0, 0, 0, 0]"
product catalytic rate constant 1/s Reaction Multiplicative 10 100 0.000000001 10000000 100 Kcatr Kinetic Derived 1 Local parameter kcrr "[[0.5/RT * Nt], I_reaction, [0.5 * Nkm], 0, 0, 0, 0, 0]"
chemical potential kJ/mol Species Additive -880 1500 -3000 2000 20 mu Dynamic Derived 0 cp "[I_species, 0, 0, 0, 0, [RT * I_species], 0, 0]"
reaction affinity kJ/mol Reaction Additive 0 10 -60 60 10 A Dynamic Derived 0 raf "[[-1 * Nt], 0, 0, 0, 0, [-RT * Nt], 0, 0]"
forward maximal velocity mM/s Reaction Multiplicative 0.01 100 0.00000001 1000000 0.1 Vmaxf Dynamic Derived 0 Local parameter vmaf "[[-0.5/RT * Nt], I_reaction, [-0.5 * Nkm], 0, 0, 0, I_reaction, 0]"
reverse maximal velocity mM/s Reaction Multiplicative 0.01 100 0.00000001 1000000 0.1 Vmaxr Dynamic Derived 0 Local parameter vmar "[[0.5/RT * Nt], I_reaction, [0.5 * Nkm], 0, 0, 0, I_reaction, 0]"
forward mass action term 1/s Reaction Multiplicative 1 1000 0.0000001 10000000 1 thetaf Dynamic Derived 0 thtf "[[-1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nft, 0, 0]"
reverse mass action term 1/s Reaction Multiplicative 1 1000 0.0000001 10000000 1 thetar Dynamic Derived 0 thtr "[[ 1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nrt, 0, 0]"
forward enzyme mass action term mM/s Reaction Multiplicative 1 1000 0.0000001 10000000 1 tauf Dynamic Derived 0 tauf "[[-1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nft, I_reaction, 0]"
reverse enzyme mass action term mM/s Reaction Multiplicative 1 1000 0.0000001 10000000 1 taur Dynamic Derived 0 taur "[[ 1/(2*RT) * h * Nt], I_reaction, - 1/2 * h * abs(Nkm), 0, 0, h * Nrt, I_reaction, 0]"
Michaelis constant product mM Reaction Multiplicative 1 1000 0.001 1000 1 KMprod Kinetic Derived 0 Local parameter kmprod "[0, 0, Nkm, 0, 0, 0, 0, 0]"
!!ObjTables objTablesVersion='0.0.8' schema='SBtab' document='BIOMD0000000239' type='Data' class='PbConfig' description='Parameter balancing configuration file'
!Option !Value
use_pseudo_values TRUE
ph 7
temperature 298.15
overwrite_kinetics TRUE
cell_volume 43
parametrisation hal
enzyme_prefactor TRUE
default_inhibition complete
default_activation complete
model_name outputname
boundary_values ignore