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BIOMD0000000393 - Arnold2011_Zhu2007_CalvinCycle_Starch_Sucrose_Photorespiration

 

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Reference Publication
Publication ID: 22001849
Arnold A, Nikoloski Z.
A quantitative comparison of Calvin-Benson cycle models.
Trends Plant Sci. 2011 Dec; 16(12): 676-683
Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.  [more]
Model
Original Model: BIOMD0000000393.xml.origin
Submitter: Anne Arnold
Submission ID: MODEL1109270009
Submission Date: 27 Sep 2011 11:20:58 UTC
Last Modification Date: 20 Apr 2012 19:50:41 UTC
Creation Date: 24 Oct 2011 11:17:58 UTC
Encoders:  Vijayalakshmi Chelliah
   Anne Arnold
   Zoran Nikoloski
set #1
bqbiol:encodes Gene Ontology reductive pentose-phosphate cycle
set #2
bqbiol:occursIn Taxonomy Viridiplantae
Notes

This model is from the article:
A quantitative comparison of Calvin–Benson cycle models
Anne Arnold, Zoran Nikoloski Trends in Plant Science 2011 Oct 14. 22001849 ,
Abstract:
The Calvin-Benson cycle (CBC) provides the precursors for biomass synthesis necessary for plant growth. The dynamic behavior and yield of the CBC depend on the environmental conditions and regulation of the cellular state. Accurate quantitative models hold the promise of identifying the key determinants of the tightly regulated CBC function and their effects on the responses in future climates. We provide an integrative analysis of the largest compendium of existing models for photosynthetic processes. Based on the proposed ranking, our framework facilitates the discovery of best-performing models with regard to metabolomics data and of candidates for metabolic engineering.

Note: Model of the Calvin cycle and the related end-product pathways to starch and sucrose synthesis and photorespiration by Zhu et al. (2007, DOI:10.1104/pp.107.103713 ) and the personally provided implementation.

The parameter values are partly taken from Pettersson and Ryde-Pettersson (1988, DOI:10.1111/j.1432-1033.1988.tb14242.x ). The initial metabolite values are chosen from the data set of Zhu et al. (2007, DOI:10.1104/pp.107.103713 ). A detailed description of all modifications is given in the model described by Arnold and Nikoloski (2011, PMID:22001849 .
Model
Publication ID: 22001849 Submission Date: 27 Sep 2011 11:20:58 UTC Last Modification Date: 20 Apr 2012 19:50:41 UTC Creation Date: 24 Oct 2011 11:17:58 UTC
Mathematical expressions
Reactions
RuBisCO - CO2 PGA kinase GAP dehydrogenase FBP aldolase
FBPase F6P transketolase SBP aldolase SBPase
S7P transketolase Ru5P kinase ATP synthetase AGPase
TPT - PGA TPT - GAP TPT - DHAP FBPc aldolase
FBPcase UGPase SucPc synthase SucPc phosphatase
F6Pc kinase F26BPc phosphatase Succ degradation PGAc degradation
GPT - GCEAc GPT - GCEA GPT - GCA GPT - GCAc
RuBisC0 - O2 PGCA phosphatase GCEA kinase GCAc oxidase
SERc:GOAc aminotransferase GCEA dehydrogenase GLUc:GOAc aminotransferase GLYc decarboxylase
Rules
Assignment Rule (variable: K52a) Assignment Rule (variable: R5P) Assignment Rule (variable: G6P) Assignment Rule (variable: DHAP)
Assignment Rule (variable: GAP) Assignment Rule (variable: G1P) Assignment Rule (variable: X5P) Assignment Rule (variable: Pi)
Assignment Rule (variable: Ru5P) Assignment Rule (variable: F6P) Assignment Rule (variable: ADP) Assignment Rule (variable: G6Pc)
Assignment Rule (variable: GAPc) Assignment Rule (variable: PiTc) Assignment Rule (variable: F6Pc) Assignment Rule (variable: Pic)
Assignment Rule (variable: PiPic) Assignment Rule (variable: Wc*min) Assignment Rule (variable: G1Pc) Assignment Rule (variable: DHAPc)
Assignment Rule (variable: UDPc) Assignment Rule (variable: Wo*min) Assignment Rule (variable: ADPc)  
Physical entities
Compartments Species
chloroplast PGA DPGA GAP
DHAP TP FBP
F6P G6P G1P
HeP E4P SBP
S7P X5P R5P
Ru5P PeP RuBP
ATP ADP NADPH
Pi PGCA GCA
GCEA CO2 O2
NADP HPRc  
cytosol GCAc GOAc GLYc
SERc GCEAc PGAc
GAPc DHAPc TPc
FBPc F6Pc G6Pc
G1Pc HePc F26BPc
UDPGc SucPc Succ
UTPc UDPc NAD
NADH GLUc KGc
Pic PiTc ATPc
ADPc PiPic  
Global parameters
cA cP cAc cPc
cNc cUc E Wc*min
Wo*min K52a    
Reactions (36)
 
 RuBisCO - CO2 [RuBP] → 2.0 × [PGA];   {PGA} , {FBP} , {SBP} , {Pi} , {NADPH}
 
 PGA kinase [PGA] + [ATP] → [DPGA] + [ADP];   {ADP}
 
 GAP dehydrogenase [DPGA] + [NADPH] → [TP] + [NADP];   {GAP}
 
 FBP aldolase 2.0 × [TP] ↔ [FBP];   {GAP} , {DHAP}
 
 FBPase [FBP] ↔ [HeP] + [Pi];   {F6P} , {Pi}
 
 F6P transketolase [HeP] + [TP] ↔ [E4P] + [PeP];   {F6P} , {GAP} , {X5P} , {E4P}
 
 SBP aldolase [TP] + [E4P] ↔ [SBP];   {DHAP}
 
 SBPase [SBP] ↔ [S7P] + [Pi];   {Pi}
 
 S7P transketolase [TP] + [S7P] ↔ 2.0 × [PeP];   {GAP} , {X5P} , {R5P}
 
 Ru5P kinase [PeP] + [ATP] ↔ [RuBP] + [ADP];   {Ru5P} , {PGA} , {RuBP} , {Pi} , {ADP}
 
 ATP synthetase [ADP] + [Pi] ↔ [ATP];  
 
 AGPase [HeP] + [ATP] → ;   {G1P} , {ADP} , {Pi} , {PGA} , {F6P} , {FBP}
 
 TPT - PGA [PGA] → [PGAc];   {Pic} , {Pi} , {GAP} , {DHAP}
 
 TPT - GAP [TP] → [TPc];   {GAP} , {GAPc} , {Pic} , {Pi} , {PGA} , {DHAP}
 
 TPT - DHAP [TP] → [TPc];   {DHAP} , {DHAPc} , {Pic} , {Pi} , {PGA} , {GAP}
 
 FBPc aldolase 2.0 × [TPc] ↔ [FBPc];   {GAPc} , {DHAPc}
 
 FBPcase [FBPc] ↔ [HePc] + [Pic];   {F6Pc}
 
 UGPase [HePc] + [UTPc] ↔ [UDPGc] + [PiPic];   {G1Pc}
 
 SucPc synthase [HePc] + [UDPGc] ↔ [SucPc] + [UDPc];   {F6Pc} , {FBPc} , {UDPc} , {SucPc} , {Succ} , {Pic}
 
 SucPc phosphatase [SucPc] ↔ [Succ] + [Pic];   {Succ}
 
 F6Pc kinase [HePc] + [ATPc] ↔ [F26BPc] + [ADPc];   {F6Pc} , {F26BPc} , {DHAPc} , {ADPc}
 
 F26BPc phosphatase [F26BPc] → [HePc] + [Pic];   {Pic} , {F6Pc}
 
 Succ degradation [Succ] → ;  
 
 PGAc degradation [PGAc] → ;  
 
 GPT - GCEAc [GCEAc] → [GCEA];   {GCAc}
 
 GPT - GCEA [GCEA] → [GCEAc];   {GCA}
 
 GPT - GCA [GCA] → [GCAc];   {GCEA}
 
 GPT - GCAc [GCAc] → [GCA];   {GCEAc}
 
 RuBisC0 - O2 [RuBP] → [PGA] + [PGCA];   {PGA} , {FBP} , {SBP} , {Pi} , {NADPH}
 
 PGCA phosphatase [PGCA] → [GCA];   {GCA} , {Pi}
 
 GCEA kinase [ATP] + [GCEA] ↔ [PGA] + [ADP];   {PGA}
 
 GCAc oxidase [GCAc] → [GOAc];  
 
 SERc:GOAc aminotransferase [SERc] + [GOAc] ↔ [HPRc] + [GLYc];   {GLYc}
 
 GCEA dehydrogenase [HPRc] + [NADH] ↔ [GCEAc] + [NAD];   {HPRc}
 
 GLUc:GOAc aminotransferase [GLUc] + [GOAc] ↔ [KGc] + [GLYc];   {GLYc}
 
 GLYc decarboxylase 2.0 × [GLYc] → [SERc];   {SERc}
 
Rules (23)
 
 Assignment Rule (name: K52a) K52a = 0.0025*(1+F26BPc/7E-5)
 
 Assignment Rule (name: R5P) R5P = PeP/0.4/(1+1/0.4+1/0.67)
 
 Assignment Rule (name: G6P) G6P = HeP/(1+1/2.3+0.058)
 
 Assignment Rule (name: DHAP) DHAP = TP/(1+0.05)
 
 Assignment Rule (name: GAP) GAP = 0.05*TP/(1+0.05)
 
 Assignment Rule (name: G1P) G1P = HeP*0.058/(1+1/2.3+0.058)
 
 Assignment Rule (name: X5P) X5P = PeP/0.67/(1+1/0.4+1/0.67)
 
 Assignment Rule (name: Pi) Pi = cP-2*(RuBP+DPGA+FBP+SBP)-(PGA+TP+HeP+E4P+S7P+PeP+ATP+PGCA)
 
 Assignment Rule (name: Ru5P) Ru5P = PeP/(1+1/0.4+1/0.67)
 
 Assignment Rule (name: F6P) F6P = HeP/2.3/(1+1/2.3+0.058)
 
 Assignment Rule (name: ADP) ADP = cA-ATP
 
 Assignment Rule (name: G6Pc) G6Pc = HePc/(1+1/2.3+0.0584)
 
 Assignment Rule (name: GAPc) GAPc = 0.05*TPc/(1+0.05)
 
 Assignment Rule (name: PiTc) PiTc = cPc-2*(FBPc+F26BPc)-(PGAc+TPc+HePc+SucPc+ATPc+UTPc)
 
 Assignment Rule (name: F6Pc) F6Pc = HePc/2.3/(1+1/2.3+0.0584)
 
 Assignment Rule (name: Pic) Pic = 12000000/2*((1+4*PiTc/12000000)^(0.5)-1)
 
 Assignment Rule (name: PiPic) PiPic = PiTc-Pic
 
 Assignment Rule (name: Wc_min) Wc*min = 2.913930914*CO2/(CO2+0.0115*(1+O2/0.222))*(1+RuBP/E-abs(1-RuBP/E))/2
 
 Assignment Rule (name: G1Pc) G1Pc = HePc*0.0584/(1+1/2.3+0.0584)
 
 Assignment Rule (name: DHAPc) DHAPc = TPc/(1+0.05)
 
 Assignment Rule (name: UDPc) UDPc = cUc-UTPc-UDPGc
 
 Assignment Rule (name: Wo_min) Wo*min = 0.24*2.913930914*O2/(O2+0.222*(1+CO2/0.0115))*(1+RuBP/E-abs(1-RuBP/E))/2
 
 Assignment Rule (name: ADPc) ADPc = cAc-ATPc
 
Functions (22)
 
 MMlike s2p2 + reg 3*c-s1,1*m-s2 lambda(Vm, s1, s2, p1, p2, q, Ks1, r1, Kr1, r2, Kr2, r3, Kr3, r4, Kr41, Ks2, Kr42, Vm*(s1*s2-p1*p2/q)/((s1+Ks1*(1+r1/Kr1+r2/Kr2+r3/Kr3))*(s2*(1+r4/Kr41)+Ks2*(1+r4/Kr42))))
 
 Competitive inhibition (irr) lambda(substrate, Inhibitor, Km, V, Ki, V*substrate/(Km+substrate+Km*Inhibitor/Ki))
 
 Henri-Michaelis-Menten (irreversible) lambda(substrate, Km, V, V*substrate/(Km+substrate))
 
 MMlike s1p2 + reg 2*c lambda(Vm, s1, p1, p2, q, Ks1, r1, Kr1, r2, Kr2, Vm*(s1-p1*p2/q)/(s1+Ks1*(1+r1/Kr1+r2/Kr2)))
 
 MMlike s2p2 + reg 1*c-s1,4*c-s2 lambda(Vm, s1, s2, p1, p2, q, Ks1, r1, Kr1, Ks2, r2, Kr2, r3, Kr3, r4, Kr4, r5, Kr5, Vm*(s1*s2-p1*p2/q)/((s1+Ks1*(1+r1/Kr1))*(s2+Ks2*(1+r2/Kr2)*(1+r3/Kr3)*(1+r4/Kr4)*(1+r5/Kr5))))
 
 MMlike s2p2 -s2 + reg 1*c lambda(Vm, s1, s2, p1, p2, q, Ks1, r1, Kr1, Vm*(s1*s2-p1*p2/q)/(s1+Ks1*(1+r1/Kr1)))
 
 MMlike s2p2 + reg 2*c-s1,1*c-s2 lambda(Vm, s1, s2, p1, p2, q, Ks1, r1, Kr1, r2, Kr2, Ks2, r3, Kr3, Vm*(s1*s2-p1*p2/q)/((s1+Ks1*(1+r1/Kr1)*(1+r2/Kr2))*(s2+Ks2*(1+r3/Kr3))))
 
 MM s2p1 - reg lambda(s1, s2, p1, q, Ks1, Ks2, Kp1, Vm, Vm*(s1*s2-p1/q)/(Ks1*Ks2*((1+s1/Ks1)*(1+s2/Ks2)+p1/Kp1)))
 
 MMlike s1p2 + reg 1*c lambda(Vm, s1, p1, p2, q, Ks1, r1, Kr1, Vm*(s1-p1*p2/q)/(s1+Ks1*(1+r1/Kr1)))
 
 MM s1p2 - reg lambda(s1, p1, p2, q, Ks1, Kp1, Kp2, Vm, Vm*(s1-p1*p2/q)/(Ks1*(s1/Ks1+(1+p1/Kp1)*(1+p2/Kp2))))
 
 MM s2p2 - reg lambda(s1, s2, p1, p2, q, Ks1, Ks2, Kp1, Kp2, Vm, Vm*(s1*s2-p1*p2/q)/(Ks1*Ks2*((1+s1/Ks1)*(1+s2/Ks2)+(1+p1/Kp1)*(1+p2/Kp2)-1)))
 
 MM s2 + reg 1*c lambda(Vm, s1, s2, Ks1, Ks2, r1, Kr1, Vm*s1*s2/((s1+Ks1)*(s2+Ks2*(1+r1/Kr1))))
 
 starch synthase - Pettersson lambda(Vm, S1, S2, K1, K2, R1, KR1, R2, KA1, A1, KA2, A2, KA3, A3, Vm*S1*S2/((S1+K1)*(1+R1/KR1)*(S2+K2*(1+K2*R2/(KA1*A1+KA2*A2+KA3*A3)))))
 
 MM s1 + reg 2*s lambda(Vm, s1, Ks1, r1, Kr1, r2, Kr2, Vm*s1/(s1+Ks1*(1+r1/Kr1)*(1+r2/Kr2)))
 
 MMlike s2p2 + reg 1*c lambda(Vm, s1, s2, p1, p2, q, Ks1, r1, Kr1, Ks2, Vm*(s1*s2-p1*p2/q)/((s1+Ks1*(1+r1/Kr1))*(s2+Ks2)))
 
 MM s1 + reg 5*c lambda(Vm, S, K, R1, KR1, R2, KR2, R3, KR3, R4, KR4, R5, KR5, Vm*S/(S+K*(1+R1/KR1+R2/KR2+R3/KR3+R4/KR4+R5/KR5)))
 
 MM s2 - reg lambda(Vm, s1, s2, K1, K2, Vm*s1*s2/((s1+K1)*(s2+K2)))
 
 MMlike s1 - reg lambda(Vm, s1, Ks1, r1, Kr1, Vm*s1/(s1+Ks1*(1+r1/Kr1)))
 
 MM s1 + reg 2*n lambda(Vm, s1, r1, Kr1, r2, Kr2, Ks1, Vm*s1/((s1+Ks1)*(1+r1/Kr1)*(1+r2/Kr2)))
 
 MMlike s2p2 + reg 2*c lambda(Vm, s1, s2, p1, p2, Ks1, Ks2, r1, Kr1, r2, Kr2, q, Vm*(s1*s2-p1*p2/q)/((s1+Ks1*(1+r1/Kr1+r2/Kr2))*(s2+Ks2)))
 
 MMlike s2p1 - reg lambda(Vm, s1, s2, p1, q, Ks1, Ks2, Vm*(s1*s2-p1/q)/((s1+Ks1)*(s2+Ks2)))
 
 MM s1 + reg A,3*c lambda(Vm, S, KA, A, K, R1, KR1, R2, KR2, R3, KR3, Vm*S/(S*(1+KA/A)+K*(1+(1+KA/A)*(R1/KR1+R2/KR2+R3/KR3))))
 
   chloroplast Spatial dimensions: 3.0  Compartment size: 1.0
 
 PGA
Compartment: chloroplast
Initial concentration: 2.4
 
 DPGA
Compartment: chloroplast
Initial concentration: 0.0011
 
  GAP
Compartment: chloroplast
Initial concentration: 0.0238095238095238
 
  DHAP
Compartment: chloroplast
Initial concentration: 0.476190476190476
 
 TP
Compartment: chloroplast
Initial concentration: 0.5
 
 FBP
Compartment: chloroplast
Initial concentration: 0.669999999999999
 
  F6P
Compartment: chloroplast
Initial concentration: 0.640764257004718
 
  G6P
Compartment: chloroplast
Initial concentration: 1.47375779111085
 
  G1P
Compartment: chloroplast
Initial concentration: 0.0854779518844294
 
 HeP
Compartment: chloroplast
Initial concentration: 2.2
 
 E4P
Compartment: chloroplast
Initial concentration: 0.05
 
 SBP
Compartment: chloroplast
Initial concentration: 0.3
 
 S7P
Compartment: chloroplast
Initial concentration: 2.0
 
  X5P
Compartment: chloroplast
Initial concentration: 0.0747384155455904
 
  R5P
Compartment: chloroplast
Initial concentration: 0.125186846038864
 
  Ru5P
Compartment: chloroplast
Initial concentration: 0.0500747384155456
 
 PeP
Compartment: chloroplast
Initial concentration: 0.25
 
 RuBP
Compartment: chloroplast
Initial concentration: 2.0
 
 ATP
Compartment: chloroplast
Initial concentration: 0.68
 
  ADP
Compartment: chloroplast
Initial concentration: 0.82
 
 NADPH
Compartment: chloroplast
Initial concentration: 0.21
Constant
 
  Pi
Compartment: chloroplast
Initial concentration: 1.4749
 
 PGCA
Compartment: chloroplast
Initial concentration: 0.0029
 
 GCA
Compartment: chloroplast
Initial concentration: 0.36
 
 GCEA
Compartment: chloroplast
Initial concentration: 0.1812
 
 CO2
Compartment: chloroplast
Initial concentration: 0.0090
Constant
 
 O2
Compartment: chloroplast
Initial concentration: 0.2646
Constant
 
 NADP
Compartment: chloroplast
Initial concentration: 0.29
Constant
 
 HPRc
Compartment: chloroplast
Initial concentration: 0.0035
 
   cytosol Spatial dimensions: 3.0  Compartment size: 1.0
 
 GCAc
Compartment: cytosol
Initial concentration: 0.36
 
 GOAc
Compartment: cytosol
Initial concentration: 0.028
 
 GLYc
Compartment: cytosol
Initial concentration: 1.8
 
 SERc
Compartment: cytosol
Initial concentration: 7.5
 
 GCEAc
Compartment: cytosol
Initial concentration: 0.1812
 
 PGAc
Compartment: cytosol
Initial concentration: 0.0
 
  GAPc
Compartment: cytosol
Initial concentration: 0.109523809523809
 
  DHAPc
Compartment: cytosol
Initial concentration: 2.19047619047619
 
 TPc
Compartment: cytosol
Initial concentration: 2.3
 
 FBPc
Compartment: cytosol
Initial concentration: 2.0
 
  F6Pc
Compartment: cytosol
Initial concentration: 1.68883505322742
 
  G6Pc
Compartment: cytosol
Initial concentration: 3.88432062242307
 
  G1Pc
Compartment: cytosol
Initial concentration: 0.226844324349507
 
 HePc
Compartment: cytosol
Initial concentration: 5.8
 
 F26BPc
Compartment: cytosol
Initial concentration: 7.8E-6
 
 UDPGc
Compartment: cytosol
Initial concentration: 0.57
 
 SucPc
Compartment: cytosol
Initial concentration: 0.0
 
 Succ
Compartment: cytosol
Initial concentration: 0.0
 
 UTPc
Compartment: cytosol
Initial concentration: 0.75
Constant
 
  UDPc
Compartment: cytosol
Initial concentration: 0.18
 
 NAD
Compartment: cytosol
Initial concentration: 0.4
Constant
 
 NADH
Compartment: cytosol
Initial concentration: 0.47
Constant
 
 GLUc
Compartment: cytosol
Initial concentration: 24.0
Constant
 
   KGc
Compartment: cytosol
Initial concentration: 0.4
Constant
 
  Pic
Compartment: cytosol
Initial concentration: 4.09998299977232
 
  PiTc
Compartment: cytosol
Initial concentration: 4.0999844
 
 ATPc
Compartment: cytosol
Initial concentration: 0.35
Constant
 
  ADPc
Compartment: cytosol
Initial concentration: 0.65
 
  PiPic
Compartment: cytosol
Initial concentration: 1.40022767958214E-6
 
Global Parameters (10)
 
 cA
Value: 1.5
Constant
 
 cP
Value: 15.0
Constant
 
 cAc
Value: 1.0
Constant
 
 cPc
Value: 15.0
Constant
 
 cNc
Value: 0.87
Constant
 
 cUc
Value: 1.5
Constant
 
 E
Value: 1.456965457
Constant
 
  Wc*min
Value: 0.76667245633627
 
  Wo*min
Value: 0.280229143229506
 
  K52a
Value: 0.00277857142857143
 
RuBisCO - CO2 (6)
 
 K
Value: 0.02
Constant
 
 KR1
Value: 0.84
Constant
 
 KR2
Value: 0.04
Constant
 
 KR3
Value: 0.075
Constant
 
 KR4
Value: 0.9
Constant
 
 KR5
Value: 0.07
Constant
 
PGA kinase (4)
 
 Vm
Value: 30.1408
Constant
 
 Ks1
Value: 0.24
Constant
 
 Ks2
Value: 0.39
Constant
 
 Kr1
Value: 0.23
Constant
 
GAP dehydrogenase (3)
 
 Vm
Value: 4.03948
Constant
 
 K1
Value: 0.0040
Constant
 
 K2
Value: 0.1
Constant
 
FBP aldolase (5)
 
 q
Value: 7.1
Constant
 
 Ks1
Value: 0.3
Constant
 
 Ks2
Value: 0.4
Constant
 
 Kp1
Value: 0.02
Constant
 
 Vm
Value: 1.21889
Constant
 
FBPase (5)
 
 Vm
Value: 0.72626
Constant
 
 q
Value: 666000.0
Constant
 
 Ks1
Value: 0.033
Constant
 
 Kr1
Value: 0.7
Constant
 
 Kr2
Value: 12.0
Constant
 
F6P transketolase (6)
 
 Vm
Value: 3.12207
Constant
 
 Ks1
Value: 0.1
Constant
 
 Ks2
Value: 0.1
Constant
 
 Kr1
Value: 0.1
Constant
 
 Kr2
Value: 0.1
Constant
 
 q
Value: 10.0
Constant
 
SBP aldolase (4)
 
 Vm
Value: 1.21889
Constant
 
 q
Value: 1.017
Constant
 
 Ks1
Value: 0.4
Constant
 
 Ks2
Value: 0.2
Constant
 
SBPase (4)
 
 Vm
Value: 0.324191
Constant
 
 q
Value: 666000.0
Constant
 
 Ks1
Value: 0.05
Constant
 
 Kr1
Value: 12.0
Constant
 
S7P transketolase (6)
 
 Vm
Value: 3.12207
Constant
 
 Ks1
Value: 0.072
Constant
 
 Ks2
Value: 0.46
Constant
 
 Kr1
Value: 0.1
Constant
 
 Kr2
Value: 1.5
Constant
 
 q
Value: 1.17647
Constant
 
Ru5P kinase (9)
 
 Vm
Value: 10.8348
Constant
 
 q
Value: 6846.0
Constant
 
 Ks1
Value: 0.05
Constant
 
 Kr1
Value: 2.0
Constant
 
 Kr2
Value: 0.7
Constant
 
 Kr3
Value: 4.0
Constant
 
 Kr41
Value: 2.5
Constant
 
 Ks2
Value: 0.059
Constant
 
 Kr42
Value: 0.4
Constant
 
ATP synthetase (5)
 
 q
Value: 5.734
Constant
 
 Ks1
Value: 0.014
Constant
 
 Ks2
Value: 0.3
Constant
 
 Kp1
Value: 0.3
Constant
 
 Vm
Value: 15.0
Constant
 
AGPase (7)
 
 Vm
Value: 0.266843
Constant
 
 K1
Value: 0.08
Constant
 
 K2
Value: 0.08
Constant
 
 KR1
Value: 10.0
Constant
 
 KA1
Value: 0.1
Constant
 
 KA2
Value: 0.02
Constant
 
 KA3
Value: 0.02
Constant
 
TPT - PGA (6)
 
 Vm
Value: 1.24333
Constant
 
 KA
Value: 0.74
Constant
 
 K
Value: 0.25
Constant
 
 KR1
Value: 0.63
Constant
 
 KR2
Value: 0.075
Constant
 
 KR3
Value: 0.077
Constant
 
TPT - GAP (6)
 
 Vm
Value: 1.24333
Constant
 
 KA
Value: 0.74
Constant
 
 K
Value: 0.075
Constant
 
 KR1
Value: 0.63
Constant
 
 KR2
Value: 0.25
Constant
 
 KR3
Value: 0.077
Constant
 
TPT - DHAP (6)
 
 Vm
Value: 1.24333
Constant
 
 KA
Value: 0.74
Constant
 
 K
Value: 0.077
Constant
 
 KR1
Value: 0.63
Constant
 
 KR2
Value: 0.25
Constant
 
 KR3
Value: 0.075
Constant
 
FBPc aldolase (5)
 
 q
Value: 12.0
Constant
 
 Ks1
Value: 0.3
Constant
 
 Ks2
Value: 0.4
Constant
 
 Kp1
Value: 0.02
Constant
 
 Vm
Value: 0.107377
Constant
 
FBPcase (4)
 
 q
Value: 6663.0
Constant
 
 Kp1
Value: 0.7
Constant
 
 Kp2
Value: 12.0
Constant
 
 Vm
Value: 0.063979
Constant
 
UGPase (6)
 
 q
Value: 0.31
Constant
 
 Ks1
Value: 0.14
Constant
 
 Ks2
Value: 0.1
Constant
 
 Kp1
Value: 0.12
Constant
 
 Kp2
Value: 0.11
Constant
 
 Vm
Value: 0.115403
Constant
 
SucPc synthase (9)
 
 Vm
Value: 0.0555034
Constant
 
 q
Value: 10.0
Constant
 
 Ks1
Value: 0.8
Constant
 
 Kr1
Value: 0.8
Constant
 
 Ks2
Value: 2.4
Constant
 
 Kr2
Value: 0.7
Constant
 
 Kr3
Value: 0.4
Constant
 
 Kr4
Value: 50.0
Constant
 
 Kr5
Value: 11.0
Constant
 
SucPc phosphatase (4)
 
 Vm
Value: 0.555034
Constant
 
 q
Value: 780.0
Constant
 
 Ks1
Value: 0.35
Constant
 
 Kr1
Value: 80.0
Constant
 
F6Pc kinase (7)
 
 Vm
Value: 0.100915
Constant
 
 q
Value: 590.0
Constant
 
 Ks1
Value: 0.5
Constant
 
 Kr1
Value: 0.021
Constant
 
 Kr2
Value: 0.7
Constant
 
 Ks2
Value: 0.5
Constant
 
 Kr3
Value: 0.16
Constant
 
F26BPc phosphatase (4)
 
 Vm
Value: 0.0168192
Constant
 
 Kr1
Value: 0.5
Constant
 
 Kr2
Value: 0.1
Constant
 
 Ks1
Value: 0.032
Constant
 
Succ degradation (2)
 
 Km
Value: 5.0
Constant
 
 V
Value: 2.0
Constant
 
PGAc degradation (2)
 
 Km
Value: 1.0
Constant
 
 V
Value: 0.5
Constant
 
GPT - GCEAc (3)
 
 Km
Value: 0.39
Constant
 
 V
Value: 5.0
Constant
 
 Ki
Value: 0.28
Constant
 
GPT - GCEA (3)
 
 Km
Value: 0.39
Constant
 
 V
Value: 5.0
Constant
 
 Ki
Value: 0.28
Constant
 
GPT - GCA (3)
 
 Km
Value: 0.2
Constant
 
 V
Value: 6.0
Constant
 
 Ki
Value: 0.22
Constant
 
GPT - GCAc (3)
 
 Km
Value: 0.2
Constant
 
 V
Value: 6.0
Constant
 
 Ki
Value: 0.22
Constant
 
RuBisC0 - O2 (6)
 
 K
Value: 0.02
Constant
 
 KR1
Value: 0.84
Constant
 
 KR2
Value: 0.04
Constant
 
 KR3
Value: 0.075
Constant
 
 KR4
Value: 0.9
Constant
 
 KR5
Value: 0.07
Constant
 
PGCA phosphatase (4)
 
 Vm
Value: 52.4199
Constant
 
 Ks1
Value: 0.026
Constant
 
 Kr1
Value: 94.0
Constant
 
 Kr2
Value: 2.55
Constant
 
GCEA kinase (5)
 
 Vm
Value: 5.71579
Constant
 
 q
Value: 300.0
Constant
 
 Ks1
Value: 0.21
Constant
 
 Kr1
Value: 0.36
Constant
 
 Ks2
Value: 0.25
Constant
 
GCAc oxidase (2)
 
 Km
Value: 0.1
Constant
 
 V
Value: 1.45611
Constant
 
SERc:GOAc aminotransferase (5)
 
 Vm
Value: 3.30619
Constant
 
 q
Value: 0.24
Constant
 
 Ks1
Value: 2.7
Constant
 
 Kr1
Value: 33.0
Constant
 
 Ks2
Value: 0.15
Constant
 
GCEA dehydrogenase (4)
 
 Vm
Value: 10.0098
Constant
 
 q
Value: 250000.0
Constant
 
 Ks1
Value: 0.09
Constant
 
 Kr1
Value: 12.0
Constant
 
GLUc:GOAc aminotransferase (5)
 
 Vm
Value: 2.74582
Constant
 
 q
Value: 607.0
Constant
 
 Ks1
Value: 1.7
Constant
 
 Kr1
Value: 2.0
Constant
 
 Ks2
Value: 0.15
Constant
 
GLYc decarboxylase (3)
 
 Vm
Value: 2.49475
Constant
 
 Ks1
Value: 6.0
Constant
 
 Kr1
Value: 4.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000393

Curator's comment: (updated: 19 Oct 2011 15:48:08 BST)

The steady state concentration of the metabolites involved are reproduced here. This is the reproduction of the Table S7 (referring Zhu 2007) of the reference (supp. material) publication. The simulation was done using Copasi v4.7 (Build 34).

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