examples/sbtab/jiang_model.csv/Reaction.csv from KarrLab/obj_tables

examples/sbtab/jiang_model.csv/Reaction.csv
Summary

Maintainability

Test Coverage

Issues
!!ObjTables schema='SBtab' type='Data' tableFormat='row' class='Reaction' name='Reaction' date='2020-07-18 12:19:10' objTablesVersion='1.0.5' document='BIOMD0000000239',,,,,,,,,,,,,
!Name,!ID,!ReactionFormula,!IsComplete,!IsReversible,!IsInEquilibrium,!IsExchangeReaction,!IsNonEnzymatic,!KineticLaw,!BuildReaction,!BuildEnzyme,!BuildEnzymeProduction,!Identifiers:ec-code,!Regulator
,GLCflow, <=> GLC,False,True,False,False,False,"CYTOPLASM * (Glc_F * pow(10, -3) - GLC) * flow",False,False,False,,
,LACflow,LAC <=>,False,False,False,False,False,CYTOPLASM * LAC * flow,False,False,False,,
,GAPflow,GAP <=>,False,False,False,False,False,CYTOPLASM * GAP * flow,False,False,False,,
glucokinase,v1,GLC + ATP_cyt <=> F6P + ADP_cyt,False,False,False,False,False,CYTOPLASM * (V1 * ATP_cyt * GLC / ((K1GLC + GLC) * (K1ATP + ATP_cyt))),False,False,False,2.7.1.2,
6-phosphofructokinase,v2,F6P + ATP_cyt <=> FBP + ADP_cyt,False,False,False,False,False,"CYTOPLASM * (V2 * ATP_cyt * pow(F6P, 2) / ((K2 * (1 + k2 * pow(ATP_cyt / AMP, 2)) + pow(F6P, 2)) * (K2ATP + ATP_cyt)))",False,False,False,2.7.1.11,AMP
fructose-bisphosphate aldolase,v3,FBP <=> 2.0 GAP,False,True,False,False,False,"CYTOPLASM * (k3f * FBP - k3b * pow(GAP, 2))",False,False,False,4.1.2.13,
glyceraldehyde 3-phosphate dehydrogenase,v4,GAP + NAD <=> DPG + NADH_cyt,False,False,False,False,False,CYTOPLASM * (V4 * NAD * GAP / ((K4GAP + GAP) * (K4NAD + NAD))),False,False,False,1.2.1.12,
bisphosphoglycerate phosphotase (1/2),v5,DPG + ADP_cyt <=> PEP + ATP_cyt,False,True,False,False,False,CYTOPLASM * (k5f * DPG * ADP_cyt - k5b * PEP * ATP_cyt),False,False,False,5.4.2.4,
pyruvate kinase,v6,PEP + ADP_cyt <=> PYR_cyt + ATP_cyt,False,False,False,False,False,CYTOPLASM * (V6 * ADP_cyt * PEP / ((K6PEP + PEP) * (K6ADP + ADP_cyt))),False,False,False,2.7.1.40,
lactate dehydrogenase,v7,PYR_cyt + NADH_cyt <=> LAC + NAD,False,True,False,False,False,CYTOPLASM * (k8f * NADH_cyt * PYR_cyt - k8b * NAD * LAC),False,False,False,1.1.1.27,
,hidden_1,AMP + ATP_cyt <=> 2.0 ADP_cyt,False,True,False,False,False,"CYTOPLASM * (k9f * AMP * ATP_cyt - k9b * pow(ADP_cyt, 2))",False,False,False,,
pyruvate carrier,v8,PYR_cyt <=> Pyr,False,True,False,False,False,MATRIX * (V * PYR_cyt * v8_PYC / (K + PYR_cyt)),False,False,False,,
pyruvate dehydrogenase complex,v9,Pyr + CoA + NAD_p <=> CO2 + Acetyl_CoA + NADH,False,False,False,False,False,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,False,False,1.2.4.1,
citrate synthase,v10,OXA + Acetyl_CoA <=> Cit + CoA,False,True,False,False,False,MATRIX * (V * Acetyl_CoA * OXA * v10_CS / (Acetyl_CoA * OXA + Ka * OXA + Kb * Acetyl_CoA + Kia * Kib)),False,False,False,2.3.3.3,
aconitase,v11,Cit <=> IsoCit,False,True,False,False,False,MATRIX * ((KcF * Kp * Cit - KcR * Ks * IsoCit) * v11_ACO / (Ks * IsoCit + Kp * Cit + Ks * Kp)),False,False,False,4.2.1.3,
isocitrate dehydrogenase (NAD+) (alpha/beta/gamma),v12,IsoCit + NAD_p <=> OG + NADH,False,False,False,False,False,MATRIX * (KcF * v12_IDHa * (IsoCit * IsoCit + b * ADP * IsoCit) / (IsoCit * IsoCit + c * IsoCit + d * ADP + e * ADP * IsoCit + f)),False,False,False,1.1.1.41,ADP
oxoglutarate dehydrogenase complex,v14,OG + CoA + NAD_p <=> CO2 + SCoA + NADH,False,False,False,False,False,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,False,False,1.2.4.2,
succinyl-CoA synthetase,v15,GDP + SCoA + Pi <=> Suc + GTP + CoA,False,True,False,False,False,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)),False,False,False,6.2.1.4,
succinate dehydrogenase,v16,Suc + Q <=> Fum + QH2,False,True,False,False,False,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)),False,False,False,1.3.5.1,
fumarase,v17,Fum <=> Mal,False,True,False,False,False,MATRIX * ((KcF * Kp * Fum - KcR * Ks * Mal) * v17_FM / (Ks * Mal + Kp * Fum + Ks * Kp)),False,False,False,4.2.1.2,
malate dehydrogenase (mitochondrion),v18,Mal + NAD_p <=> NADH + OXA,False,True,False,False,False,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)),False,False,False,1.1.1.37,
alanine transaminase,v20,Ala + OG <=> Glu + Pyr,False,True,False,False,False,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)),False,False,False,2.6.1.2,
aspartate transaminase,v21,OXA + Glu <=> Asp + OG,False,True,False,False,False,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)),False,False,False,2.6.1.1,
aspartate/glutamate carrier,v22,Glu_cyt + Asp <=> Asp_cyt + Glu,False,True,False,False,False,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)),False,False,False,,
NADH:ubiquinone oxidoreductase,v24,NADH + Q <=> NAD_p + QH2,False,True,False,False,False,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)),False,False,False,2.7.4.6,
ubiquinol:cytochrome c oxidoreductase,v25,QH2 + 2.0 Cytc3p <=> Q + 2.0 Cytc2p,False,False,False,False,False,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,False,False,1.10.2.2,
cytochrome c oxidase,v26,Cytc2p <=> Cytc3p,False,False,False,False,False,MT_IMS * (KcF * v26_Complex_IV * Cytc2p / (Ks + Cytc2p)),False,False,False,1.9.3.1,
citrate synthase,v27,Cit_cyt + CoA_cyt <=> OXA_cyt + Acetyl_CoA_cyt,False,True,False,False,False,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),False,False,False,2.3.3.3,
ATPase complex,v28,ADP + Pi <=> ATP + H2O,False,True,False,False,False,MATRIX * v28_Complex_V * V * ADP / (Km + ADP + ADP * ADP / Ki),False,False,False,3.6.1.5,
aconitase,v29,Cit_cyt <=> IsoCitcyt,False,True,False,False,False,CYTOPLASM * ((KcF * Kp * Cit_cyt - KcR * Ks * IsoCitcyt) * v29_ACO / (Ks * IsoCitcyt + Kp * Cit_cyt + Ks * Kp)),False,False,False,4.2.1.3,
oxoglutarate carrier,v30,Mal_cyt + OG <=> OG_cyt + Mal,False,True,False,False,False,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)),False,False,False,,
malate dehydrogenase (cytosol),v31,NADH_cyt + OXA_cyt <=> Mal_cyt + NAD,False,False,False,False,False,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,False,False,1.1.1.37,
aspartate transaminase,v32,Asp_cyt + OG_cyt <=> OXA_cyt + Glu_cyt,False,True,False,False,False,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)),False,False,False,2.6.1.1,
citrate carrier,v33,Cit_cyt + Mal <=> Mal_cyt + Cit,False,True,False,False,False,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)),False,False,False,,
ETF:Q oxidoreductase,v34,ETFred + Q <=> ETFox + QH2,False,True,False,False,False,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)),False,False,False,1.5.5.1,
glutathione reductase,v35,FADH2 + ETFox <=> ETFred + FAD,False,True,False,False,False,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))),False,False,False,1.8.1.7,
pyruvate decarboxylase,v36,ATP + CO2 + Pyr <=> Pi + ADP + OXA,False,True,False,False,False,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)),False,False,False,6.4.1.1,
glycerol-3-phosphate dehydrogenase (FAD dependent),v37,G3P + FAD <=> FADH2 + DHAP,False,False,False,False,False,CYTOPLASM * (V * v37_GUT2P * G3P / (K + G3P)),False,False,False,1.1.99.5,
glycerol-3-phosphate dehydrogenase (NAD+ dependent),v38,NADH_cyt + DHAP <=> G3P + NAD,False,False,False,False,False,CYTOPLASM * (V * v38_GUT2P * NADH_cyt / (K + NADH_cyt)),False,False,False,1.1.1.8,
ATP/ADP carrier,v40,ADP_cyt <=> ADP,False,False,False,False,False,MATRIX * (V * v40_AAC * ADP_cyt / (K + ADP_cyt)),False,False,False,,
cytosolic isocitrate dehydrogenase,v41,IsoCitcyt + NADP_cyt <=> OG_cyt + NADPH_cyt,False,True,False,False,False,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)),False,False,False,1.1.1.42,CO2
citrate carrier,v42,IsoCitcyt + Mal <=> Mal_cyt + IsoCit,False,True,False,False,False,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)),False,False,False,,
ATP/ADP carrier,v43,ATP <=> ATP_cyt,False,False,False,False,False,MATRIX * (V * v43_AAC * ATP / (K + ATP)),False,False,False,,
malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+),v39,Mal_cyt + NADP_cyt <=> NADPH_cyt + PYR_cyt,False,True,False,False,False,CYTOPLASM * (v39_MDH * Kcat * Mal_cyt * NADP_cyt / ((Kmal + Mal_cyt) * (Knadp + NADP_cyt))),False,False,False,1.1.1.40,
malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+),v44,Mal + NADP_p <=> NADPH + Pyr,False,True,False,False,False,MATRIX * (v44_MDH * Kcat * Mal / (Km + Mal)),False,False,False,1.1.1.40,