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Below is displayed the model view of the selected project. Model view is shown in the form of the model overview page for the currently selected model. The central feature of the model view is the model scheme that shows individual model components of selected model. The navigation panel on the left allows you to browse the biological structure of the model. Manipulation with the navigation panel is realized by unfolding the items in the navigation tree and clicking on a requested system level.

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All the annotation terms relevant for the currently focused level of the project are displayed on the Annotation Tab below the scheme. Individual annotation data can be unfolded by clicking on the requested annotation item header.

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The Components Tab displays all the model species (state variables). More information for particular components are accessible after clicking on the requested component header.

Reactions Tab
Reactions Tab contains information regarding the modeled reactions. After clicking on the particular reaction header, the reacting components and relevant kinetic parameters are displayed.

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

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Simulation and SBML export are available by clicking on appropriate buttons at the bottom of the tab. All relevant settings of initial conditions, parameters, options and datasets are listed in respective folders.

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Conservation analysis, modes analysis and matrix analysis are available by clicking on appropriate buttons.

Experiments Tab
Experiments tab contains list of all experiments related to selected model.

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.

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:
Initial expression: 1
Simulation type: fixed
Details
Initial expression: 0.3447986077
Simulation type: reaction
Details
Initial expression: 1.15520132
Simulation type: reaction
Details
Initial expression: 4.999999759
Simulation type: fixed
Details
Initial expression: ATP/(ATP+ADP)
Simulation type: assignment
Initial expression: 0.007482485571
Simulation type: reaction
Details
Initial expression: 0.02
Simulation type: reaction
Details
Initial expression: 0.1
Simulation type: reaction
Details
Initial expression: 0.2288202267
Simulation type: reaction
Details
Initial expression: 0.4
Simulation type: reaction
Details
Initial expression: 0.07617467533
Simulation type: reaction
Details
Initial expression: 0.01359336237
Simulation type: reaction
Details
Initial expression: 1.94057631
Simulation type: reaction
Details
Initial expression: 0.3683626365
Simulation type: reaction
Details
Initial expression: 0.01235938354
Simulation type: reaction
Details
Initial expression: 0.004000971532
Simulation type: reaction
Details
Initial expression: 0.5
Simulation type: reaction
Details
Initial expression: 20
Simulation type: reaction
Details
Initial expression: 0.032736383
Simulation type: reaction
Details
Initial expression: 0.1
Simulation type: reaction
Details
Initial expression: Sink_PEP+Sink_DHAP+Sink_E4P+Sink_Ri5P+Sink1+Sink2+Sink3+Sink4
Simulation type: assignment
Initial expression: 0.1489955134
Simulation type: reaction
Details
Initial expression: NADPH/(NADPH+NADPp)
Simulation type: assignment
Initial expression: 0.2710044663
Simulation type: reaction
Details
Initial expression: 0.02599999875
Simulation type: fixed
Details
Initial expression: 0
Simulation type: reaction
Initial expression: 0.1
Simulation type: reaction
Details
Initial expression: 4.19091919
Simulation type: reaction
Details
Initial expression: 2.07
Simulation type: reaction
Details
Initial expression: 0.01
Simulation type: reaction
Initial expression: 4.19091918
Simulation type: reaction
Details
Initial expression: 0.0744045363
Simulation type: reaction
Details
Initial expression: 0.02689822284
Simulation type: reaction
Details
Initial expression: 0.3105938683
Simulation type: reaction
Details
Initial expression: 0.5113194231
Simulation type: reaction
Details
Initial expression: 1.362618878
Simulation type: reaction
Details
Initial expression: 0.5
Simulation type: reaction
Details
Initial expression: 0
Simulation type: reaction
Initial expression: 0
Simulation type: reaction
Initial expression: 0
Simulation type: reaction
Initial expression: 0
Simulation type: reaction
Initial expression: 0
Simulation type: reaction
Initial expression: 0
Simulation type: reaction
Initial expression: 0
Simulation type: reaction
Initial expression: 0
Simulation type: reaction
Initial expression: 0
Simulation type: reaction
Initial expression: 1.5
Simulation type: reaction
Details
Initial expression: 0.3
Simulation type: reaction
Details
Initial expression: 0.03243314432
Simulation type: reaction
Details
Initial expression: 0.05580778704
Simulation type: reaction
Details
Initial expression: 1
Simulation type: fixed
Details
Initial expression: 0.1
Simulation type: fixed
Details
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Equation: Pi -> ATP
Function: Mass Action (irreversible)
Reaction rate: light_1*ADP * Pi
Kinetic rate constant Value
light_1 "kf_ATP"*"kf_ATP_LCgene"
Equation: NADPp -> NADPH
Function: Mass Action (irreversible)
Reaction rate: light_2*NADPp
Kinetic rate constant Value
light_2 "kf_NADPH"*"kf_NADPH_LCgene"
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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

Initial expression: 0.1
Simulation type: fixed
Initial expression: 7.81
Simulation type: fixed
Initial expression: 1.54
Simulation type: fixed
Initial expression: 2.35
Simulation type: fixed
Initial expression: 0.32
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 1.57
Simulation type: fixed
Initial expression: 0.3
Simulation type: fixed
Initial expression: 0.83
Simulation type: fixed
Initial expression: 1.24
Simulation type: fixed
Initial expression: 0.0001
Simulation type: fixed
Initial expression: 1.56
Simulation type: fixed
Initial expression: 0.548
Simulation type: fixed
Initial expression: 0.035
Simulation type: fixed
Initial expression: 1.91
Simulation type: fixed
Initial expression: 0.68
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 0.54
Simulation type: fixed
Initial expression: 0.118
Simulation type: fixed
Initial expression: 0.8
Simulation type: fixed
Initial expression: 0.15
Simulation type: fixed
Initial expression: 0.05
Simulation type: fixed
Initial expression: 0.3
Simulation type: fixed
Initial expression: 0.4
Simulation type: fixed
Initial expression: 0.02
Simulation type: fixed
Initial expression: 0.033
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.616
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.4
Simulation type: fixed
Initial expression: 0.2
Simulation type: fixed
Initial expression: 0.05
Simulation type: fixed
Initial expression: 0.8
Simulation type: fixed
Initial expression: 0.95
Simulation type: fixed
Initial expression: 0.32
Simulation type: fixed
Initial expression: 3.36
Simulation type: fixed
Initial expression: 0.6
Simulation type: fixed
Initial expression: 0.39
Simulation type: fixed
Initial expression: 1.2
Simulation type: fixed
Initial expression: 0.57
Simulation type: fixed
Initial expression: 2.58
Simulation type: fixed
Initial expression: 0.927
Simulation type: fixed
Initial expression: 1.184
Simulation type: fixed
Initial expression: 2
Simulation type: fixed
Initial expression: 1.3
Simulation type: fixed
Initial expression: 0.357
Simulation type: fixed
Initial expression: 1.01
Simulation type: fixed
Initial expression: 0.991
Simulation type: fixed
Initial expression: 0.23
Simulation type: fixed
Initial expression: 1.3
Simulation type: fixed
Initial expression: 1.685
Simulation type: fixed
Initial expression: 0.43
Simulation type: fixed
Initial expression: 0.602
Simulation type: fixed
Initial expression: 0.536
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 1.613
Simulation type: fixed
Initial expression: 0.11
Simulation type: fixed
Initial expression: 0.3
Simulation type: fixed
Initial expression: 1.11
Simulation type: fixed
Initial expression: 0.159
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 0.25
Simulation type: fixed
Initial expression: 0.0002
Simulation type: fixed
Initial expression: 0.0145
Simulation type: fixed
Initial expression: 0.009
Simulation type: fixed
Initial expression: 0.001
Simulation type: fixed
Initial expression: 0.002
Simulation type: fixed
Initial expression: 0.0042
Simulation type: fixed
Initial expression: 0.43
Simulation type: fixed
Initial expression: 0.002
Simulation type: fixed
Initial expression: 0.004
Simulation type: fixed
Initial expression: 0.05
Simulation type: fixed
Initial expression: 0
Simulation type: fixed
Initial expression: 0.0009
Simulation type: fixed
Initial expression: 0.0004
Simulation type: fixed
Initial expression: 0.5
Simulation type: fixed
Initial expression: 0.006
Simulation type: fixed
Initial expression: 0.0021
Simulation type: fixed
Initial expression: 0.001
Simulation type: fixed
Initial expression: 0.052
Simulation type: fixed
Initial expression: 0.0018
Simulation type: fixed
Initial expression: 0.0005
Simulation type: fixed
Initial expression: 0.01
Simulation type: fixed
Initial expression: 0.023
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 1.69
Simulation type: fixed
Initial expression: 0.64
Simulation type: fixed
Initial expression: 1.9
Simulation type: fixed
Initial expression: 1.59
Simulation type: fixed
Initial expression: 0.824
Simulation type: fixed
Initial expression: 2.45
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 1
Simulation type: fixed
Initial expression: 0.19
Simulation type: fixed

Assigned quantities

Initial expression: kf_ATP*kf_ATP_LCgene
Simulation type: assignment
Initial expression: kf_NADPH*kf_NADPH_LCgene
Simulation type: assignment
Initial expression: kf_CO2*kf_CO2_LCgene
Simulation type: assignment
Initial expression: V1*V1_LCgene
Simulation type: assignment
Initial expression: V2*V2_LCgene
Simulation type: assignment
Initial expression: V3*V3_LCgene
Simulation type: assignment
Initial expression: V4*V4_LCgene
Simulation type: assignment
Initial expression: V5*V5_LCgene
Simulation type: assignment
Initial expression: V6*V6_LCgene
Simulation type: assignment
Initial expression: V7*V7_LCgene
Simulation type: assignment
Initial expression: V8*V8_LCgene
Simulation type: assignment
Initial expression: V9*V9_LCgene
Simulation type: assignment
Initial expression: V10*V10_LCgene
Simulation type: assignment
Initial expression: V11*V11_LCgene
Simulation type: assignment
Initial expression: V12*V12_LCgene
Simulation type: assignment
Initial expression: V13*V13_LCgene
Simulation type: assignment
Initial expression: V_PFK*V_PFK_LCgene
Simulation type: assignment
Initial expression: Vgap_dehyd*Vgap_dehyd_LCgene
Simulation type: assignment
Initial expression: Vgap_dehyd_beta*Vgap_dehyd_beta_LCgene
Simulation type: assignment
Initial expression: Vf_PGM_alpha*Vf_PGM_alpha_LCgene
Simulation type: assignment
Initial expression: Vf_PGM_beta*Vf_PGM_beta_LCgene
Simulation type: assignment
Initial expression: Vf_PGM_gama*Vf_PGM_gama_LCgene
Simulation type: assignment
Initial expression: Vf_enol*Vf_enol_LCgene
Simulation type: assignment
Initial expression: V_PP1*V_PP1_LCgene
Simulation type: assignment
Initial expression: V_PP2a*V_PP2a_LCgene
Simulation type: assignment
Initial expression: V_PP2b*V_PP2b_LCgene
Simulation type: assignment
Initial expression: V_PP3*V_PP3_LCgene
Simulation type: assignment
Initial expression: V_PP4*V_PP4_LCgene
Simulation type: assignment
Initial expression: V_PP5*V_PP5_LCgene
Simulation type: assignment
Initial expression: V_PP6*V_PP6_LCgene
Simulation type: assignment
Initial expression: V_GLY_syn*V_GLY_syn_LCgene
Simulation type: assignment
Initial expression: V_SS1*V_SS1_LCgene
Simulation type: assignment
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

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
Name Value
start time 0  
end time 846000  
time offset 0  

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Conservation analysis

Conservation

Modes analysis

Modes

Matrix analysis

Matrix