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Model repository

Models

+ Miyoshi et al. 2007
+ Plyusnina et al. (in prep.)
+ Hertel et al. 2013
+ Jablonsky et al. 2014
+ Clark et al. 2014 (in progress)
+ Fridlyand et al. 1995
o Grimaud et al. 2014
o E-cyano team 2017, clock & C-N metabolism
o Müller et al. 2019

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All quantitative parameters are managed under Parameters Tab. Constants are separated from assigned quantities.

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Experiments Tab
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Jablonsky et al. 2014

Jablonsky J, Schwarz D, Hagemann M (2014) Multi-Level Kinetic Model Explaining Diverse Roles of Isozymes in Prokaryotes. PLoS ONE 9(8): e105292.

Annotations
Components
Reactions
Parameters
Simulation
Analysis
Experiments
+publication: Jablonsky et al. 2014

Jablonsky J, Schwarz D, Hagemann M (2014) Multi-Level Kinetic Model Explaining Diverse Roles of Isozymes in Prokaryotes. PLoS ONE 9(8): e105292.


publication: Jablonsky et al. 2014
Contains:
+cytosol
Initial expression: 1
Simulation type: fixed
Details
+ADP
Initial expression: 0.3447986077
Simulation type: reaction
Details
+ATP
Initial expression: 1.15520132
Simulation type: reaction
Details
+Pi
Initial expression: 4.999999759
Simulation type: fixed
Details
+ATPr
Initial expression: ATP/(ATP+ADP)
Simulation type: assignment
+BPGA
Initial expression: 0.007482485571
Simulation type: reaction
Details
+CO2_cyt
Initial expression: 0.02
Simulation type: reaction
Details
+DHAP
Initial expression: 0.1
Simulation type: reaction
Details
+E4P
Initial expression: 0.2288202267
Simulation type: reaction
Details
+F6P
Initial expression: 0.4
Simulation type: reaction
Details
+FBP
Initial expression: 0.07617467533
Simulation type: reaction
Details
+G1P
Initial expression: 0.01359336237
Simulation type: reaction
Details
+G6P
Initial expression: 1.94057631
Simulation type: reaction
Details
+GAP
Initial expression: 0.3683626365
Simulation type: reaction
Details
+GCA
Initial expression: 0.01235938354
Simulation type: reaction
Details
+GCEA
Initial expression: 0.004000971532
Simulation type: reaction
Details
+GLY
Initial expression: 0.5
Simulation type: reaction
Details
+Glycogen
Initial expression: 20
Simulation type: reaction
Details
+GOA
Initial expression: 0.032736383
Simulation type: reaction
Details
+HPR
Initial expression: 0.1
Simulation type: reaction
Details
+Mass
Initial expression: Sink_PEP+Sink_DHAP+Sink_E4P+Sink_Ri5P+Sink1+Sink2+Sink3+Sink4
Simulation type: assignment
+NADPH
Initial expression: 0.1489955134
Simulation type: reaction
Details
+NADPHr
Initial expression: NADPH/(NADPH+NADPp)
Simulation type: assignment
+NADPp
Initial expression: 0.2710044663
Simulation type: reaction
Details
+O2
Initial expression: 0.02599999875
Simulation type: fixed
Details
+out
Initial expression: 0
Simulation type: reaction
+OXA
Initial expression: 0.1
Simulation type: reaction
Details
+PEP
Initial expression: 4.19091919
Simulation type: reaction
Details
+PGA
Initial expression: 2.07
Simulation type: reaction
Details
+PGCA
Initial expression: 0.01
Simulation type: reaction
+ppGA
Initial expression: 4.19091918
Simulation type: reaction
Details
+Ri5P
Initial expression: 0.0744045363
Simulation type: reaction
Details
+Ru5P
Initial expression: 0.02689822284
Simulation type: reaction
Details
+RuBP
Initial expression: 0.3105938683
Simulation type: reaction
Details
+S7P
Initial expression: 0.5113194231
Simulation type: reaction
Details
+SBP
Initial expression: 1.362618878
Simulation type: reaction
Details
+SER
Initial expression: 0.5
Simulation type: reaction
Details
+Sink1
Initial expression: 0
Simulation type: reaction
+Sink2
Initial expression: 0
Simulation type: reaction
+Sink3
Initial expression: 0
Simulation type: reaction
+Sink4
Initial expression: 0
Simulation type: reaction
+Sink_DHAP
Initial expression: 0
Simulation type: reaction
+Sink_E4P
Initial expression: 0
Simulation type: reaction
+Sink_GAP
Initial expression: 0
Simulation type: reaction
+Sink_PEP
Initial expression: 0
Simulation type: reaction
+Sink_Ri5P
Initial expression: 0
Simulation type: reaction
+Sucrose
Initial expression: 1.5
Simulation type: reaction
Details
+THR
Initial expression: 0.3
Simulation type: reaction
Details
+TSA
Initial expression: 0.03243314432
Simulation type: reaction
Details
+Xu5P
Initial expression: 0.05580778704
Simulation type: reaction
Details
+external
Initial expression: 1
Simulation type: fixed
Details
+CO2_ext
Initial expression: 0.1
Simulation type: fixed
Details
+CC_1 : RuBP + CO2 → 2*3PGA
Equation: RuBP + CO2_cyt -> PGA
Modifiers: FBP, SBP, Pi, NADPH, O2
Function: Function for CC_1 (irreversible)
Reaction rate: (RuBP*(cc_1*CO2_cyt/(CO2_cyt+0.0115*(1+O2/0.222))))/(RuBP+0.02*(1+PGA/0.84+FBP/0.04+SBP/0.075+Pi/0.9+NADPH/0.07))
Kinetic rate constant Value
cc_1 "V1"*"V1_LCgene"
k2 0.0115
k3 0.222
k4 0.02
k5 0.84
k6 0.04
k7 0.075
k8 0.9
k9 0.07
Details
+CC_10 : S7P + GAP ↔ Ri5P + Xu5P
Equation: GAP + S7P + -> Ri5P + Xu5P
Modifiers: F6P, E4P
Function: Function for CC_10 (reversible)
Reaction rate: (cc_10*(GAP*S7P-(Ri5P*Xu5P)/KE10))/((KM71a*KM101*(1+(1+GAP/0.27)*(F6P/0.54+S7P/0.09)+GAP/0.09+((Xu5P*(1+(E4P+Ri5P)/KM71a)+E4P+Ri5P))/KM101)))
Kinetic rate constant Value
cc_10 "V10"*"V10_LCgene"
KE10 1.54
KM71a 0.616
KM101 0.118
k5 0.27
k6 0.54
k7 0.09
k8 0.09
KM71a 0.616
KM101 0.118
Details
+CC_11 : Ri5P ↔ Ru5P
Equation: Ri5P -> Ru5P
Function: Function for CC_11_12_4 (reversible)
Reaction rate: (cc_11*(Ri5P-Ru5P/KE11))/(Ri5P+Ru5P)
Kinetic rate constant Value
cc_11 "V11"*"V11_LCgene"
KE11 2.35
Details
+CC_12 : Xu5P ↔ Ru5P
Equation: Xu5P -> Ru5P
Function: Function for CC_11_12_4 (reversible)
Reaction rate: (cc_12*(Xu5P-Ru5P/KE12))/(Xu5P+Ru5P)
Kinetic rate constant Value
cc_12 "V12"*"V12_LCgene"
KE12 0.32
Details
+CC_13 : Ru5P + ATP → RuBP + ADP
Equation: ATP + Ru5P -> ADP + RuBP
Modifiers: PGA, Pi
Function: Function for CC_13 (irreversible)
Reaction rate: (cc_13*ATP*Ru5P)/((ATP*(1+ADP/2.5)+KM132*(1+ADP/0.4))*(Ru5P+0.05*(1+PGA/2+RuBP/0.7+Pi/4)))
Kinetic rate constant Value
cc_13 "V13"*"V13_LCgene"
k2 2.5
KM132 0.05
k5 0.05
k6 2
k7 0.7
k8 4
k4 0.4
Details
+CC_2 : 3PGA + ATP → BPGA + ADP
Equation: PGA + ATP -> BPGA + ADP
Function: Function for CC_2 (irreversible)
Reaction rate: (cc_2*(PGA*ATP-(BPGA*ADP)/0.000619))/((PGA+0.24)*(ATP+0.39*(1+ADP/0.23)))
Kinetic rate constant Value
cc_2 "V2"*"V2_LCgene"
k2 0.000619
k3 0.24
k4 0.39
k5 0.23
+CC_3 : BPGA + NADPH ↔ GAP + NADPp + Pi
Equation: BPGA + NADPH -> GAP + NADPp + Pi
Function: Function for CC_3 (irreversible)
Reaction rate: (cc_3*BPGA*NADPH)/((BPGA+0.004)*(NADPH+0.1))
Kinetic rate constant Value
cc_3 "V3"*"V3_LCgene"
k2 0.004
k3 0.1
+CC_4 : GAP ↔ DHAP
Equation: GAP -> DHAP
Function: Function for CC_11_12_4 (reversible)
Reaction rate: (cc_4*(GAP-DHAP/KE4))/(GAP+DHAP)
Kinetic rate constant Value
cc_4 "V4"*"V4_LCgene"
KE4 0.1
+CC_5 : GAP + DHAP ↔ FBP
Equation: GAP + DHAP -> FBP
Function: Function for CC_5 (reversible)
Reaction rate: (cc_5*(GAP*DHAP-FBP/KE5))/(KM51*KM52*(1+GAP/KM51+DHAP/KM52+FBP/KM53+GAP*DHAP/(KM51*KM52)))
Kinetic rate constant Value
cc_5 "V5"*"V5_LCgene"
KE5 1.57
KM51 0.3
KM52 0.4
KM51 0.3
KM52 0.4
KM53 0.02
KM51 0.3
KM52 0.4
+CC_6 : FBP → F6P + Pi
Equation: FBP -> F6P + Pi
Function: Function for CC_6_PP_2a_2b (irreversible)
Reaction rate: (cc_6*FBP)/(FBP+KM61*(1+F6P/0.7+Pi/12))
Kinetic rate constant Value
cc_6 "V6"*"V6_LCgene"
KM61 0.033
k3 0.7
k4 12
+CC_7 : F6P + GAP ↔ E4P + Xu5P
Equation: F6P + GAP -> Xu5P + E4P
Function: Function for CC_7 (reversible)
Reaction rate: (cc_7*(F6P*GAP-(Xu5P*E4P)/KE7))/((F6P+KM73*(1+Xu5P/KM71+E4P/KM72))*(GAP+KM74))
Kinetic rate constant Value
cc_7 "V7"*"V7_LCgene"
KE7 0.3
KM73 0.1
KM71 0.1
KM72 0.1
KM74 0.1
Details
+CC_8 : DHAP + E4P ↔ SBP
Equation: DHAP + E4P -> SBP
Function: Function for CC_8 (reversible)
Reaction rate: (cc_8*(DHAP*E4P-SBP/KE8))/((E4P+KM82)*(DHAP+KM81))
Kinetic rate constant Value
cc_8 "V8"*"V8_LCgene"
KE8 0.83
KM82 0.2
KM81 0.4
+CC_9 : SBP → S7P + Pi
Equation: SBP -> S7P + Pi
Modifiers: Pi
Function: Function for CC_9 (irreversible)
Reaction rate: (cc_9*SBP)/(SBP+KM9*(1+Pi/12))
Kinetic rate constant Value
cc_9 "V9"*"V9_LCgene"
KM9 0.05
k3 12
+CO2 dif : CO2{external} -> CO2{cytosol}
Equation: CO2_ext -> CO2_cyt
Function: Mass Action (irreversible)
Reaction rate: co2_diff*CO2_ext
Kinetic rate constant Value
co2_diff "kf_CO2"*"kf_CO2_LCgene"
Details
+GC_1 : GOA -> TSA
Equation: GOA -> TSA
Function: Henri-Michaelis-Menten (irreversible)
Reaction rate: (V_TSA1*GOA)/(0.1 + GOA)
Kinetic rate constant Value
V_TSA1 0.01
k2 0.1
Details
+GC_2 : TSA -> GCEA
Equation: TSA -> GCEA
Function: Henri-Michaelis-Menten (irreversible)
Reaction rate: (V_TSA3*TSA)/(0.1 + TSA)
Kinetic rate constant Value
V_TSA3 0.1
k2 0.1
Details
+GL_1 : F6P → FBP
Equation: F6P -> FBP
Function: Henri-Michaelis-Menten (irreversible)
Reaction rate: (gl_1*F6P)/(KM_PFK + F6P)
Kinetic rate constant Value
gl_1 "V_PFK"*"V_PFK_LCgene"
KM_PFK 0.8
+GL_2a : GAP + NADPp + Pi ↔ BPGA + NADPH
Equation: GAP + NADPp -> PGA + NADPH
Function: Function for GL_2a_2b (reversible)
Reaction rate: (gl_2a*(GAP*NADPp-Keq_gap_dehyd*PGA*NADPH))/((1+GAP/Kgap+PGA/Kpga)*(1+NADPp/Knadpp+NADPH/knadph))
Kinetic rate constant Value
gl_2a "Vgap_dehyd"*"Vgap_dehyd_LCgene"
Keq_gap_dehyd 0.548
Kgap 1
Kpga 0.357
Knadpp 2
knadph 0.927
+GL_2b : GAP + NADPp + Pi ↔ BPGA + NADPH
Equation: GAP + NADPp -> PGA + NADPH
Function: Function for GL_2a_2b (reversible)
Reaction rate: (gl_2b*(GAP*NADPp-Keq_gap_dehyd*PGA*NADPH))/((1+GAP/Kgap_beta+PGA/Kpga_beta)*(1+NADPp/Knadpp_beta+NADPH/knadph_beta))
Kinetic rate constant Value
gl_2b "Vgap_dehyd_beta"*"Vgap_dehyd_beta_LCgene"
Keq_gap_dehyd 0.548
Kgap_beta 0.54
Kpga_beta 1.01
Knadpp_beta 1.3
knadph_beta 1.184
+GL_3a : 3PGA ↔ 2PGA
Equation: PGA -> ppGA
Function: Function for GL_3a_3b_3c_4 (reversible)
Reaction rate: (gl_3a*(PGA-ppGA/Keq_PGM))/(Kms_PGM_alpha*(1+PGA/Kms_PGM_alpha+ppGA/Kmp_PGM_alpha))
Kinetic rate constant Value
gl_3a "Vf_PGM_alpha"*"Vf_PGM_alpha_LCgene"
Keq_PGM 0.035
Kms_PGM_alpha 1.2
Kms_PGM_alpha 1.2
Kmp_PGM_alpha 0.32
+GL_3b : 3PGA ↔ 2PGA
Equation: PGA -> ppGA
Function: Function for GL_3a_3b_3c_4 (reversible)
Reaction rate: (gl_3b*(PGA-ppGA/Keq_PGM))/(Kms_PGM_beta*(1+PGA/Kms_PGM_beta+ppGA/Kmp_PGM_beta))
Kinetic rate constant Value
gl_3b "Vf_PGM_beta"*"Vf_PGM_beta_LCgene"
Keq_PGM 0.035
Kms_PGM_beta 0.57
Kms_PGM_beta 0.57
Kmp_PGM_beta 3.36
+GL_3c : 3PGA ↔ 2PGA
Equation: PGA -> ppGA
Function: Function for GL_3a_3b_3c_4 (reversible)
Reaction rate: (gl_3c*(PGA-ppGA/Keq_PGM))/(Kms_PGM_gama*(1+PGA/Kms_PGM_gama+ppGA/Kmp_PGM_gama))
Kinetic rate constant Value
gl_3c "Vf_PGM_gama"*"Vf_PGM_gama_LCgene"
Keq_PGM 0.035
Kms_PGM_gama 2.58
Kms_PGM_gama 2.58
Kmp_PGM_gama 0.6
+GL_4 : 2PGA ↔ PEP
Equation: ppGA -> PEP
Function: Function for GL_3a_3b_3c_4 (reversible)
Reaction rate: (gl_4*(ppGA-PEP/Keq_enol))/(Kms_enol*(1+ppGA/Kms_enol+PEP/Kmp_enol))
Kinetic rate constant Value
gl_4 "Vf_enol"*"Vf_enol_LCgene"
Keq_enol 1.56
Kms_enol 0.39
Kms_enol 0.39
Kmp_enol 0.95
+GSM_1 : GOA -> GLY
Equation: GOA -> GLY
Function: Henri-Michaelis-Menten (irreversible)
Reaction rate: (gsm_1*GOA)/(K_GOA + GOA)
Kinetic rate constant Value
gsm_1 "V_GLY_syn"*"V_GLY_syn_LCgene"
K_GOA 0.1
+GSM_2 : 3PGA -> SER
Equation: PGA -> SER
Function: Henri-Michaelis-Menten (irreversible)
Reaction rate: (V_synth_SER*PGA)/(2 + PGA)
Kinetic rate constant Value
V_synth_SER 0.0018
k2 2
+LIGHT_1 : ADP + Pi → ATP
Equation: Pi -> ATP
Function: Mass Action (irreversible)
Reaction rate: light_1*ADP * Pi
Kinetic rate constant Value
light_1 "kf_ATP"*"kf_ATP_LCgene"
+LIGHT_2 : NADPp → NADPH
Equation: NADPp -> NADPH
Function: Mass Action (irreversible)
Reaction rate: light_2*NADPp
Kinetic rate constant Value
light_2 "kf_NADPH"*"kf_NADPH_LCgene"
+OX_1 : GOA -> OXA
Equation: GOA -> OXA
Function: Henri-Michaelis-Menten (irreversible)
Reaction rate: (V_OXA1*GOA)/(2 + GOA)
Kinetic rate constant Value
V_OXA1 0.25
k2 2
+PP_1 : RuBP + O2 → 2PG + 3PGA
Equation: RuBP + CO2_cyt -> PGCA +
Modifiers: O2, FBP, SBP, Pi, NADPH, PGA
Function: Function for PP_1 (irreversible)
Reaction rate: (RuBP*(pp_1*CO2_cyt/(CO2_cyt+0.0115*(1+O2/0.222))))/(RuBP+0.02*(1+PGA/0.84+FBP/0.08+SBP/0.075+Pi/0.9+NADPH/0.07))
Kinetic rate constant Value
pp_1 "V_PP1"*"V_PP1_LCgene"
k2 0.0115
k3 0.222
k4 0.02
k5 0.84
k6 0.08
k7 0.075
k8 0.9
k9 0.07
Details
+PP_2a : 2PG -> GCA
Equation: PGCA -> GCA + Pi
Function: Function for CC_6_PP_2a_2b (irreversible)
Reaction rate: (pp_2a*PGCA)/(PGCA+Km112a*(1+GCA/94+Pi/2.55))
Kinetic rate constant Value
pp_2a "V_PP2a"*"V_PP2a_LCgene"
Km112a 0.8
k3 94
k4 2.55
+PP_2b : 2PG -> GCA
Equation: PGCA -> GCA + Pi
Function: Function for CC_6_PP_2a_2b (irreversible)
Reaction rate: (pp_2b*PGCA)/(PGCA+Km112b*(1+GCA/94+Pi/2.55))
Kinetic rate constant Value
pp_2b "V_PP2b"*"V_PP2b_LCgene"
Km112b 0.15
k3 94
k4 2.55
+PP_3 : GCA -> GOA
Equation: GCA -> GOA
Function: Henri-Michaelis-Menten (irreversible)
Reaction rate: (pp_3*GCA)/(0.1 + GCA)
Kinetic rate constant Value
pp_3 "V_PP3"*"V_PP3_LCgene"
k2 0.1
+PP_4 : GOA + SER <-> HPR + GLY
Equation: SER + GOA -> GLY + HPR
Function: Function for PP_4 (reversible)
Reaction rate: (pp_4*(GOA*SER-(HPR*GLY)/607))/((GOA+0.15)*(SER+1.7*(1+GLY/2)))
Kinetic rate constant Value
pp_4 "V_PP4"*"V_PP4_LCgene"
k2 607
k3 0.15
k4 1.7
k5 2
+PP_5 : 2*GLY -> SER
Equation: GLY -> SER
Function: Henri-Michaelis-Menten (irreversible)
Reaction rate: (pp_5*GLY)/(6 + GLY)
Kinetic rate constant Value
pp_5 "V_PP5"*"V_PP5_LCgene"
k2 6
+PP_6 : HPR -> GCEA
Equation: HPR -> GCEA
Function: Function for PP_6 (irreversible)
Reaction rate: (pp_6*(HPR-GCEA/250000))/(HPR+0.09*(1+HPR/12))
Kinetic rate constant Value
pp_6 "V_PP6"*"V_PP6_LCgene"
k2 250000
k3 0.09
k4 12
+PP_7 : GCEA + ATP -> 3PGA + ADP
Equation: ATP + GCEA -> ADP + PGA
Function: Function for PP_7 (irreversible)
Reaction rate: (V_PP7*(ATP*GCEA-(ADP*PGA)/300))/((GCEA+0.25)*(ATP+0.21*(1+PGA/0.36)))
Kinetic rate constant Value
V_PP7 0.05
k2 300
k3 0.25
k4 0.21
k5 0.36
+PP_8: GCEA + ATP -> ppGA + ADP
Equation: ATP + GCEA -> ADP + ppGA
Function: Function for PP_7 (irreversible)
Reaction rate: (V_PP7*(ATP*GCEA-(ADP*ppGA)/300))/((GCEA+0.25)*(ATP+0.21*(1+ppGA/0.36)))
Kinetic rate constant Value
V_PP7 0.05
k2 300
k3 0.25
k4 0.21
k5 0.36
+SS_1 : F6P ↔ G6P
Equation: F6P -> G6P
Function: Function for SS_1_SS_2 (reversible)
Reaction rate: (ss_1*(KE_SS1*F6P-G6P))/(F6P+G6P)
Kinetic rate constant Value
ss_1 "V_SS1"*"V_SS1_LCgene"
KE_SS1 1.24
+Sink Glycine : GLY → Sink2
Equation: GLY -> Sink2
Function: Henri-Michaelis-Menten (irreversible)
Reaction rate: (V_Sink_GLY*GLY)/(1 + GLY)
Kinetic rate constant Value
V_Sink_GLY 0.0004
k2 1
+Sink PEP : PEP -> 3 * Sink_PEP
Equation: PEP -> Sink_PEP
Function: Henri-Michaelis-Menten (irreversible)
Reaction rate: (V_Sink_PEP*PEP)/(K_Sink_PEP + PEP)
Kinetic rate constant Value
V_Sink_PEP 0.5
K_Sink_PEP 7.81
+Sink Serine : SER -> Sink2
Equation: SER -> Sink2
Function: Henri-Michaelis-Menten (irreversible)
Reaction rate: (V_Sink_SER*SER)/(1 + SER)
Kinetic rate constant Value
V_Sink_SER 0.0021
k2 1
+Sink Threonine : THR -> Sink2
Equation: THR -> Sink2
Function: Henri-Michaelis-Menten (irreversible)
Reaction rate: (V_Sink_THR*THR)/(1 + THR)
Kinetic rate constant Value
V_Sink_THR 0.001
k2 1
+Sink oxalate : OXA -> Sink4
Equation: OXA -> Sink4
Function: Henri-Michaelis-Menten (irreversible)
Reaction rate: (V_OXA2*OXA)/(5 + OXA)
Kinetic rate constant Value
V_OXA2 0.0002
k2 5
+Sink1_DHAP : DHAP -> 3 * Sink_DHAP
Equation: DHAP -> Sink_DHAP
Function: Henri-Michaelis-Menten (irreversible)
Reaction rate: (V_Sink_DHAP*DHAP)/(0.6 + DHAP)
Kinetic rate constant Value
V_Sink_DHAP 0
k2 0.6
+Sink1_E4P : E4P -> 4 * Sink_E4P
Equation: E4P -> Sink_E4P
Function: Henri-Michaelis-Menten (irreversible)
Reaction rate: (V_Sink_E4P*E4P)/(0.28 + E4P)
Kinetic rate constant Value
V_Sink_E4P 0.0009
k2 0.28
+Sink1_Ri5P : Ri5P -> 5 * Sink_Ri5P
Equation: Ri5P -> Sink_Ri5P
Function: Henri-Michaelis-Menten (irreversible)
Reaction rate: (V_Sink_Ri5P*Ri5P)/(0.61 + Ri5P)
Kinetic rate constant Value
V_Sink_Ri5P 0.006
k2 0.61

Constant quantities

+K_GOA
Initial expression: 0.1
Simulation type: fixed
+K_Sink_PEP
Initial expression: 7.81
Simulation type: fixed
+KE10
Initial expression: 1.54
Simulation type: fixed
+KE11
Initial expression: 2.35
Simulation type: fixed
+KE12
Initial expression: 0.32
Simulation type: fixed
+KE4
Initial expression: 0.1
Simulation type: fixed
+KE5
Initial expression: 1.57
Simulation type: fixed
+KE7
Initial expression: 0.3
Simulation type: fixed
+KE8
Initial expression: 0.83
Simulation type: fixed
+KE_SS1
Initial expression: 1.24
Simulation type: fixed
+KE_SS2
Initial expression: 0.0001
Simulation type: fixed
+Keq_enol
Initial expression: 1.56
Simulation type: fixed
+Keq_gap_dehyd
Initial expression: 0.548
Simulation type: fixed
+Keq_PGM
Initial expression: 0.035
Simulation type: fixed
+kf_CO2
Initial expression: 1.91
Simulation type: fixed
+kf_NADPH
Initial expression: 0.68
Simulation type: fixed
+Kgap
Initial expression: 1
Simulation type: fixed
+Kgap_beta
Initial expression: 0.54
Simulation type: fixed
+KM101
Initial expression: 0.118
Simulation type: fixed
+Km112a
Initial expression: 0.8
Simulation type: fixed
+Km112b
Initial expression: 0.15
Simulation type: fixed
+KM132
Initial expression: 0.05
Simulation type: fixed
+KM51
Initial expression: 0.3
Simulation type: fixed
+KM52
Initial expression: 0.4
Simulation type: fixed
+KM53
Initial expression: 0.02
Simulation type: fixed
+KM61
Initial expression: 0.033
Simulation type: fixed
+KM71
Initial expression: 0.1
Simulation type: fixed
+KM71a
Initial expression: 0.616
Simulation type: fixed
+KM72
Initial expression: 0.1
Simulation type: fixed
+KM73
Initial expression: 0.1
Simulation type: fixed
+KM74
Initial expression: 0.1
Simulation type: fixed
+KM81
Initial expression: 0.4
Simulation type: fixed
+KM82
Initial expression: 0.2
Simulation type: fixed
+KM9
Initial expression: 0.05
Simulation type: fixed
+KM_PFK
Initial expression: 0.8
Simulation type: fixed
+Kmp_enol
Initial expression: 0.95
Simulation type: fixed
+Kmp_PGM_alpha
Initial expression: 0.32
Simulation type: fixed
+Kmp_PGM_beta
Initial expression: 3.36
Simulation type: fixed
+Kmp_PGM_gama
Initial expression: 0.6
Simulation type: fixed
+Kms_enol
Initial expression: 0.39
Simulation type: fixed
+Kms_PGM_alpha
Initial expression: 1.2
Simulation type: fixed
+Kms_PGM_beta
Initial expression: 0.57
Simulation type: fixed
+Kms_PGM_gama
Initial expression: 2.58
Simulation type: fixed
+knadph
Initial expression: 0.927
Simulation type: fixed
+knadph_beta
Initial expression: 1.184
Simulation type: fixed
+Knadpp
Initial expression: 2
Simulation type: fixed
+Knadpp_beta
Initial expression: 1.3
Simulation type: fixed
+Kpga
Initial expression: 0.357
Simulation type: fixed
+Kpga_beta
Initial expression: 1.01
Simulation type: fixed
+V1
Initial expression: 0.991
Simulation type: fixed
+V10
Initial expression: 0.23
Simulation type: fixed
+V11
Initial expression: 1.3
Simulation type: fixed
+V12
Initial expression: 1.685
Simulation type: fixed
+V13
Initial expression: 0.43
Simulation type: fixed
+V2
Initial expression: 0.602
Simulation type: fixed
+V3
Initial expression: 0.536
Simulation type: fixed
+V4
Initial expression: 0.1
Simulation type: fixed
+V5
Initial expression: 1.613
Simulation type: fixed
+V6
Initial expression: 0.11
Simulation type: fixed
+V7
Initial expression: 0.3
Simulation type: fixed
+V8
Initial expression: 1.11
Simulation type: fixed
+V9
Initial expression: 0.159
Simulation type: fixed
+V_GLY_syn
Initial expression: 0.1
Simulation type: fixed
+V_OXA1
Initial expression: 0.25
Simulation type: fixed
+V_OXA2
Initial expression: 0.0002
Simulation type: fixed
+V_PFK
Initial expression: 0.0145
Simulation type: fixed
+V_PP1
Initial expression: 0.009
Simulation type: fixed
+V_PP2a
Initial expression: 0.001
Simulation type: fixed
+V_PP2b
Initial expression: 0.002
Simulation type: fixed
+V_PP3
Initial expression: 0.0042
Simulation type: fixed
+V_PP4
Initial expression: 0.43
Simulation type: fixed
+V_PP5
Initial expression: 0.002
Simulation type: fixed
+V_PP6
Initial expression: 0.004
Simulation type: fixed
+V_PP7
Initial expression: 0.05
Simulation type: fixed
+V_Sink_DHAP
Initial expression: 0
Simulation type: fixed
+V_Sink_E4P
Initial expression: 0.0009
Simulation type: fixed
+V_Sink_GLY
Initial expression: 0.0004
Simulation type: fixed
+V_Sink_PEP
Initial expression: 0.5
Simulation type: fixed
+V_Sink_Ri5P
Initial expression: 0.006
Simulation type: fixed
+V_Sink_SER
Initial expression: 0.0021
Simulation type: fixed
+V_Sink_THR
Initial expression: 0.001
Simulation type: fixed
+V_SS1
Initial expression: 0.052
Simulation type: fixed
+V_synth_SER
Initial expression: 0.0018
Simulation type: fixed
+V_synth_THR
Initial expression: 0.0005
Simulation type: fixed
+V_TSA1
Initial expression: 0.01
Simulation type: fixed
+V_TSA2
Initial expression: 0.023
Simulation type: fixed
+V_TSA3
Initial expression: 0.1
Simulation type: fixed
+Vf_enol
Initial expression: 1.69
Simulation type: fixed
+Vf_PGM_alpha
Initial expression: 0.64
Simulation type: fixed
+Vf_PGM_beta
Initial expression: 1.9
Simulation type: fixed
+Vf_PGM_gama
Initial expression: 1.59
Simulation type: fixed
+Vgap_dehyd
Initial expression: 0.824
Simulation type: fixed
+Vgap_dehyd_beta
Initial expression: 2.45
Simulation type: fixed
+kf_ATP_LCgene
Initial expression: 1
Simulation type: fixed
+kf_NADPH_LCgene
Initial expression: 1
Simulation type: fixed
+kf_CO2_LCgene
Initial expression: 1
Simulation type: fixed
+V1_LCgene
Initial expression: 1
Simulation type: fixed
+V2_LCgene
Initial expression: 1
Simulation type: fixed
+V3_LCgene
Initial expression: 1
Simulation type: fixed
+V4_LCgene
Initial expression: 1
Simulation type: fixed
+V5_LCgene
Initial expression: 1
Simulation type: fixed
+V6_LCgene
Initial expression: 1
Simulation type: fixed
+V7_LCgene
Initial expression: 1
Simulation type: fixed
+V8_LCgene
Initial expression: 1
Simulation type: fixed
+V9_LCgene
Initial expression: 1
Simulation type: fixed
+V10_LCgene
Initial expression: 1
Simulation type: fixed
+V11_LCgene
Initial expression: 1
Simulation type: fixed
+V12_LCgene
Initial expression: 1
Simulation type: fixed
+V13_LCgene
Initial expression: 1
Simulation type: fixed
+V_PFK_LCgene
Initial expression: 1
Simulation type: fixed
+Vgap_dehyd_LCgene
Initial expression: 1
Simulation type: fixed
+Vgap_dehyd_beta_LCgene
Initial expression: 1
Simulation type: fixed
+Vf_PGM_alpha_LCgene
Initial expression: 1
Simulation type: fixed
+Vf_PGM_beta_LCgene
Initial expression: 1
Simulation type: fixed
+Vf_PGM_gama_LCgene
Initial expression: 1
Simulation type: fixed
+Vf_enol_LCgene
Initial expression: 1
Simulation type: fixed
+V_PP1_LCgene
Initial expression: 1
Simulation type: fixed
+V_PP2a_LCgene
Initial expression: 1
Simulation type: fixed
+V_PP2b_LCgene
Initial expression: 1
Simulation type: fixed
+V_PP3_LCgene
Initial expression: 1
Simulation type: fixed
+V_PP4_LCgene
Initial expression: 1
Simulation type: fixed
+V_PP5_LCgene
Initial expression: 1
Simulation type: fixed
+V_PP6_LCgene
Initial expression: 1
Simulation type: fixed
+V_GLY_syn_LCgene
Initial expression: 1
Simulation type: fixed
+V_SS1_LCgene
Initial expression: 1
Simulation type: fixed
+kf_ATP
Initial expression: 0.19
Simulation type: fixed

Assigned quantities

+light_1
Initial expression: kf_ATP*kf_ATP_LCgene
Simulation type: assignment
+light_2
Initial expression: kf_NADPH*kf_NADPH_LCgene
Simulation type: assignment
+co2_diff
Initial expression: kf_CO2*kf_CO2_LCgene
Simulation type: assignment
+cc_1
Initial expression: V1*V1_LCgene
Simulation type: assignment
+cc_2
Initial expression: V2*V2_LCgene
Simulation type: assignment
+cc_3
Initial expression: V3*V3_LCgene
Simulation type: assignment
+cc_4
Initial expression: V4*V4_LCgene
Simulation type: assignment
+cc_5
Initial expression: V5*V5_LCgene
Simulation type: assignment
+cc_6
Initial expression: V6*V6_LCgene
Simulation type: assignment
+cc_7
Initial expression: V7*V7_LCgene
Simulation type: assignment
+cc_8
Initial expression: V8*V8_LCgene
Simulation type: assignment
+cc_9
Initial expression: V9*V9_LCgene
Simulation type: assignment
+cc_10
Initial expression: V10*V10_LCgene
Simulation type: assignment
+cc_11
Initial expression: V11*V11_LCgene
Simulation type: assignment
+cc_12
Initial expression: V12*V12_LCgene
Simulation type: assignment
+cc_13
Initial expression: V13*V13_LCgene
Simulation type: assignment
+gl_1
Initial expression: V_PFK*V_PFK_LCgene
Simulation type: assignment
+gl_2a
Initial expression: Vgap_dehyd*Vgap_dehyd_LCgene
Simulation type: assignment
+gl_2b
Initial expression: Vgap_dehyd_beta*Vgap_dehyd_beta_LCgene
Simulation type: assignment
+gl_3a
Initial expression: Vf_PGM_alpha*Vf_PGM_alpha_LCgene
Simulation type: assignment
+gl_3b
Initial expression: Vf_PGM_beta*Vf_PGM_beta_LCgene
Simulation type: assignment
+gl_3c
Initial expression: Vf_PGM_gama*Vf_PGM_gama_LCgene
Simulation type: assignment
+gl_4
Initial expression: Vf_enol*Vf_enol_LCgene
Simulation type: assignment
+pp_1
Initial expression: V_PP1*V_PP1_LCgene
Simulation type: assignment
+pp_2a
Initial expression: V_PP2a*V_PP2a_LCgene
Simulation type: assignment
+pp_2b
Initial expression: V_PP2b*V_PP2b_LCgene
Simulation type: assignment
+pp_3
Initial expression: V_PP3*V_PP3_LCgene
Simulation type: assignment
+pp_4
Initial expression: V_PP4*V_PP4_LCgene
Simulation type: assignment
+pp_5
Initial expression: V_PP5*V_PP5_LCgene
Simulation type: assignment
+pp_6
Initial expression: V_PP6*V_PP6_LCgene
Simulation type: assignment
+gsm_1
Initial expression: V_GLY_syn*V_GLY_syn_LCgene
Simulation type: assignment
+ss_1
Initial expression: V_SS1*V_SS1_LCgene
Simulation type: assignment
+Initial conditions
Name Value
cytosol 1
external 1
ADP 0.3447986077
ATP 1.15520132
Pi 4.999999759
ATPr ATP/(ATP+ADP)
BPGA 0.007482485571
CO2_cyt 0.02
DHAP 0.1
E4P 0.2288202267
F6P 0.4
FBP 0.07617467533
G1P 0.01359336237
G6P 1.94057631
GAP 0.3683626365
GCA 0.01235938354
GCEA 0.004000971532
GLY 0.5
Glycogen 20
GOA 0.032736383
HPR 0.1
Mass Sink_PEP+Sink_DHAP+Sink_E4P+Sink_Ri5P+Sink1+Sink2+Sink3+Sink4
NADPH 0.1489955134
NADPHr NADPH/(NADPH+NADPp)
NADPp 0.2710044663
O2 0.02599999875
out 0
OXA 0.1
PEP 4.19091919
PGA 2.07
PGCA 0.01
ppGA 4.19091918
Ri5P 0.0744045363
Ru5P 0.02689822284
RuBP 0.3105938683
S7P 0.5113194231
SBP 1.362618878
SER 0.5
Sink1 0
Sink2 0
Sink3 0
Sink4 0
Sink_DHAP 0
Sink_E4P 0
Sink_GAP 0
Sink_PEP 0
Sink_Ri5P 0
Sucrose 1.5
THR 0.3
TSA 0.03243314432
Xu5P 0.05580778704
CO2_ext 0.1
+Parameters

Constant quantities

Name Value
K_GOA 0.1
K_Sink_PEP 7.81
KE10 1.54
KE11 2.35
KE12 0.32
KE4 0.1
KE5 1.57
KE7 0.3
KE8 0.83
KE_SS1 1.24
KE_SS2 0.0001
Keq_enol 1.56
Keq_gap_dehyd 0.548
Keq_PGM 0.035
kf_CO2 1.91
kf_NADPH 0.68
Kgap 1
Kgap_beta 0.54
KM101 0.118
Km112a 0.8
Km112b 0.15
KM132 0.05
KM51 0.3
KM52 0.4
KM53 0.02
KM61 0.033
KM71 0.1
KM71a 0.616
KM72 0.1
KM73 0.1
KM74 0.1
KM81 0.4
KM82 0.2
KM9 0.05
KM_PFK 0.8
Kmp_enol 0.95
Kmp_PGM_alpha 0.32
Kmp_PGM_beta 3.36
Kmp_PGM_gama 0.6
Kms_enol 0.39
Kms_PGM_alpha 1.2
Kms_PGM_beta 0.57
Kms_PGM_gama 2.58
knadph 0.927
knadph_beta 1.184
Knadpp 2
Knadpp_beta 1.3
Kpga 0.357
Kpga_beta 1.01
V1 0.991
V10 0.23
V11 1.3
V12 1.685
V13 0.43
V2 0.602
V3 0.536
V4 0.1
V5 1.613
V6 0.11
V7 0.3
V8 1.11
V9 0.159
V_GLY_syn 0.1
V_OXA1 0.25
V_OXA2 0.0002
V_PFK 0.0145
V_PP1 0.009
V_PP2a 0.001
V_PP2b 0.002
V_PP3 0.0042
V_PP4 0.43
V_PP5 0.002
V_PP6 0.004
V_PP7 0.05
V_Sink_DHAP 0
V_Sink_E4P 0.0009
V_Sink_GLY 0.0004
V_Sink_PEP 0.5
V_Sink_Ri5P 0.006
V_Sink_SER 0.0021
V_Sink_THR 0.001
V_SS1 0.052
V_synth_SER 0.0018
V_synth_THR 0.0005
V_TSA1 0.01
V_TSA2 0.023
V_TSA3 0.1
Vf_enol 1.69
Vf_PGM_alpha 0.64
Vf_PGM_beta 1.9
Vf_PGM_gama 1.59
Vgap_dehyd 0.824
Vgap_dehyd_beta 2.45
kf_ATP_LCgene 1
kf_NADPH_LCgene 1
kf_CO2_LCgene 1
V1_LCgene 1
V2_LCgene 1
V3_LCgene 1
V4_LCgene 1
V5_LCgene 1
V6_LCgene 1
V7_LCgene 1
V8_LCgene 1
V9_LCgene 1
V10_LCgene 1
V11_LCgene 1
V12_LCgene 1
V13_LCgene 1
V_PFK_LCgene 1
Vgap_dehyd_LCgene 1
Vgap_dehyd_beta_LCgene 1
Vf_PGM_alpha_LCgene 1
Vf_PGM_beta_LCgene 1
Vf_PGM_gama_LCgene 1
Vf_enol_LCgene 1
V_PP1_LCgene 1
V_PP2a_LCgene 1
V_PP2b_LCgene 1
V_PP3_LCgene 1
V_PP4_LCgene 1
V_PP5_LCgene 1
V_PP6_LCgene 1
V_GLY_syn_LCgene 1
V_SS1_LCgene 1
kf_ATP 0.19

Assigned quantities

Name Value
light_1 kf_ATP*kf_ATP_LCgene
light_2 kf_NADPH*kf_NADPH_LCgene
co2_diff kf_CO2*kf_CO2_LCgene
cc_1 V1*V1_LCgene
cc_2 V2*V2_LCgene
cc_3 V3*V3_LCgene
cc_4 V4*V4_LCgene
cc_5 V5*V5_LCgene
cc_6 V6*V6_LCgene
cc_7 V7*V7_LCgene
cc_8 V8*V8_LCgene
cc_9 V9*V9_LCgene
cc_10 V10*V10_LCgene
cc_11 V11*V11_LCgene
cc_12 V12*V12_LCgene
cc_13 V13*V13_LCgene
gl_1 V_PFK*V_PFK_LCgene
gl_2a Vgap_dehyd*Vgap_dehyd_LCgene
gl_2b Vgap_dehyd_beta*Vgap_dehyd_beta_LCgene
gl_3a Vf_PGM_alpha*Vf_PGM_alpha_LCgene
gl_3b Vf_PGM_beta*Vf_PGM_beta_LCgene
gl_3c Vf_PGM_gama*Vf_PGM_gama_LCgene
gl_4 Vf_enol*Vf_enol_LCgene
pp_1 V_PP1*V_PP1_LCgene
pp_2a V_PP2a*V_PP2a_LCgene
pp_2b V_PP2b*V_PP2b_LCgene
pp_3 V_PP3*V_PP3_LCgene
pp_4 V_PP4*V_PP4_LCgene
pp_5 V_PP5*V_PP5_LCgene
pp_6 V_PP6*V_PP6_LCgene
gsm_1 V_GLY_syn*V_GLY_syn_LCgene
ss_1 V_SS1*V_SS1_LCgene
+Options
Name Value
start time 0  
end time 846000  
time offset 0  

Simulate   Export sbml

Conservation analysis

Conservation

Modes analysis

Modes

Matrix analysis

Matrix
Please use the following reference to cite this web site:
M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. In: Computational Methods in Systems Biology, CMSB 2016, Vol. 9859 of LNCS, pp. 316-322. Springer, 2016. DOI