bakker1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000071) Biomodels notes: The paper refers to the model equations present in Bakker et al's " Glycolysis in bloodstream from Trypanosoma brucei can be understood in terms of the kinetics of glycolytic enzymes" (Pubmed ID: 9013556), also, the authors claim that some of the modifications in these equations were made based on the experimental results from the paper "Contribution of glucose transport in the control of glycolytic flux in Trypanosoma brucei" (Pubmed ID: 10468568). The model reproduces the various flux values in Fig 3 for 100% TPI activity. It also matches with the values provided in Table 2 of the paper. The model was successfully tested with Copasi and SBML ODE Solver. The volumes are set to the values containing 1 mg of total protein per microlitre total cell volume. To change the protein concentration use Vt , the total cell volume in micro litre per mg protein. To change the TPI activity use the global parameter TPIact. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.
None
None
None
None
None
None
Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.
| Name | Definition |
|---|
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| default_compartment | — | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| BPGA13 | — | 0.0 | default_compartment | ✘ | |
| DHAP | — | 1.0 | default_compartment | ✘ | |
| Fru16BP | — | 10.0 | default_compartment | ✘ | |
| Fru6P | — | 1.0 | default_compartment | ✘ | |
| GAP | — | 0.0 | default_compartment | ✘ | |
| Glc6P | — | 1.0 | default_compartment | ✘ | |
| GlcE | — | 5.0 | default_compartment | ✔ | |
| GlcI | — | 0.0 | default_compartment | ✘ | |
| Gly | — | 0.0 | default_compartment | ✔ | |
| Gly3P | — | 0.0 | default_compartment | ✔ | |
| NAD | — | 4.0 | default_compartment | ✘ | |
| NADH | — | 0.0 | default_compartment | ✘ | |
| Nb | — | 1.0 | default_compartment | ✘ | |
| Pc | — | 1.0 | default_compartment | ✘ | |
| Pg | — | 1.0 | default_compartment | ✘ | |
| Pyr | — | 1.0 | default_compartment | ✘ | |
| PyrE | — | 0.0 | default_compartment | ✔ | |
| X | — | 0.0 | default_compartment | ✔ |
Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.
| Definition |
|---|
| Id | Name | Objective coefficient | Reaction Equation and Kinetic Law | Flux bounds | |
|---|---|---|---|---|---|
| v_1 | — | GlcE = {0.175439}GlcI Vm1*(GlcE - GlcI)/(K1Glc + GlcE + GlcI + afac*GlcE*GlcI/K1Glc) | |||
| v_10 | — | {0.183306}Pyr = PyrE Vm10*Pyr/K10Pyr/(1 + Pyr/K10Pyr) | |||
| v_11 | — | {4.087719}BPGA13 = {0.175439}Nb + {4.087719}Pg (Vm11*(Vm11f*(BPGA13*ADPg/K11BPGA13/K11ADPg - Vm11r/Vm11f*PGA3*ATPg/K11PGA3/K11ATPg)/((1 + BPGA13/K11BPGA13 + PGA3/K11PGA3)*(1 + ADPg/K11ADPg + ATPg/K11ATPg)))) | |||
| v_12 | — | {0.175439}Nb = {0.183306}Pc + {0.183306}Pyr (Vm12*((PEP/K12PEP)^n12 * ADPc/K12ADP/(1+(PEP/K12PEP)^n12)/(1+ADPc/K12ADP))) | |||
| v_13 | — | {0.183306}Pc = X (K13*ATPc/ADPc) | |||
| v_14 | — | X = Gly + {4.087719}Pg (Vm14*(Vm14f*(Gly3Pg*ADPg/K14Gly3Pg/K14ADPg) - (Vm14r*(Gly*ATPg/K14Gly/K14ATPg)))/((1 + Gly3Pg/K14Gly3Pg + Gly/K14Gly)*(1+ADPg/K14ADPg+ATPg/K14ATPg))) | |||
| v_2 | — | {0.175439}GlcI + {4.087719}Pg = {4.087719}Glc6P (Vm2*ATPg*GlcI/K2GlcI/K2ATPg/(1 + ATPg/K2ATPg + ADPg/K2ADPg)/(1 + GlcI/K2GlcI + Glc6P/K2Glc6P)) | |||
| v_3 | — | {4.087719}Glc6P = {4.087719}Fru6P Vm3*(Glc6P/K3Glc6P - Fru6P/K3Fru6P)/(1 + Glc6P/K3Glc6P + Fru6P/K3Fru6P) | |||
| v_4 | — | {4.087719}Fru6P + {4.087719}Pg = {4.087719}Fru16BP (Vm4*(K4i1Fru16BP/(K4i1Fru16BP + Fru16BP)*Fru6P/K4Fru6P*ATPg/K4ATPg/(1 + Fru6P/K4Fru6P + Fru16BP/K4i2Fru16BP)/(1 + ATPg/K4ATPg))) | |||
| v_5 | — | {4.087719}Fru16BP = {0.175439}DHAP + {4.087719}GAP (Vm5*(Vm5f*Fru16BP/K5Fru16BP - Vm5r*GAP*DHAPg/K5GAP/K5DHAP)/(1+Fru16BP/K5Fru16BP+GAP/K5GAP+DHAPg/K5DHAP+Fru16BP/K5Fru16BP*GAP/K5i+GAP*DHAPg/K5GAP/K5DHAP)) | |||
| v_6 | — | {0.175439}DHAP = {4.087719}GAP (Vm6*(DHAPg/K6DHAPg - 5.7*GAP/K6GAP)/(1 + DHAPg/K6DHAPg + GAP/K6GAP)) | |||
| v_7 | — | {4.087719}GAP + {4.087719}NAD = {4.087719}BPGA13 + {4.087719}NADH Vm7*(Vm7f*(GAP*(NAD/K7GAP/K7NAD) - (Vm7r/Vm7f)*(BPGA13*NADH/K7BPGA13/K7NADH))/((1 + GAP/K7GAP + BPGA13/K7BPGA13)*(1 + NAD/K7NAD + NADH/K7NADH))) | |||
| v_8 | — | {0.175439}DHAP + {4.087719}NADH = Gly3P + {4.087719}NAD (Vm8*(Vm8f*((DHAPg*NADH/K8DHAPg/K8NADH) - (Vm8r/Vm8f)*(NAD*Gly3Pg/K8NAD/K8Gly3Pg))/((1 + DHAPg/K8DHAPg + Gly3Pg/K8Gly3Pg)*(1 + NADH/K8NADH + NAD/K8NAD)))) | |||
| v_9 | — | Gly3P = {0.175439}DHAP (Vm9*(Gly3Pc/K9Gly3Pc)/(1+Gly3Pc/K9Gly3Pc)) |
| Id | Value | |
|---|---|---|
| ADPc | 0.0 | |
| ADPg | 0.0 | |
| AMPg | 0.0 | |
| ATPc | 0.0 | |
| ATPg | 0.0 | |
| DHAPc | 0.0 | |
| DHAPct0 | 4.01536 | |
| DHAPg | 0.0 | |
| Gly3Pc | 0.0 | |
| Gly3Pg | 0.0 | |
| K10Pyr | 1.96 | |
| K11ADPg | 0.1 | |
| K11ATPg | 0.29 | |
| K11BPGA13 | 0.05 | |
| K11PGA3 | 1.62 | |
| K12ADP | 0.114 | |
| K12PEP | 0.0 | |
| K13 | 50.0 | |
| K14ADPg | 0.12 | |
| K14ATPg | 0.19 | |
| K14Gly | 0.12 | |
| K14Gly3Pg | 5.1 | |
| K1Glc | 2.0 | |
| K2ADPg | 0.126 | |
| K2ATPg | 0.116 | |
| K2Glc6P | 12.0 | |
| K2GlcI | 0.1 | |
| K3Fru6P | 0.12 | |
| K3Glc6P | 0.4 | |
| K4ATPg | 0.026 | |
| K4Fru6P | 0.82 | |
| K4i1Fru16BP | 15.8 | |
| K4i2Fru16BP | 10.7 | |
| K5DHAP | 0.015 | |
| K5Fru16BP | 0.0 | |
| K5GAP | 0.067 | |
| K5i | 0.098 | |
| K6DHAPg | 1.2 | |
| K6GAP | 0.25 | |
| K7BPGA13 | 0.1 | |
| K7GAP | 0.15 | |
| K7NAD | 0.45 | |
| K7NADH | 0.02 | |
| K8DHAPg | 0.1 | |
| K8Gly3Pg | 2.0 | |
| K8NAD | 0.4 | |
| K8NADH | 0.01 | |
| K9Gly3Pc | 1.7 | |
| KeqAK | 0.442 | |
| KeqENO | 6.7 | |
| KeqPGM | 0.187 | |
| PEP | 0.0 | |
| PGA3 | 0.0 | |
| Vc | 5.4549 | |
| Vg | 0.2451 | |
| Vm1 | 106.2 | |
| Vm10 | 200.0 | |
| Vm11 | 1.0 | |
| Vm11f | 640.0 | |
| Vm11r | 18.56 | |
| Vm12 | 2600.0 | |
| Vm14 | 1.0 | |
| Vm14f | 200.0 | |
| Vm14r | 33400.0 | |
| Vm2 | 625.0 | |
| Vm3 | 848.0 | |
| Vm4 | 780.0 | |
| Vm5 | 1.0 | |
| Vm5f | 184.5 | |
| Vm5r | 219.555 | |
| Vm6 | 842.0 | |
| Vm7 | 1.0 | |
| Vm7f | 1470.0 | |
| Vm7r | 984.9 | |
| Vm8 | 1.0 | |
| Vm8f | 533.0 | |
| Vm8r | 149.24 | |
| Vm9 | 368.0 | |
| Vt | 5.7 | |
| ac | 0.0 | |
| afac | 0.75 | |
| ag | 0.0 | |
| n12 | 2.5 | |
| rsum | 0.0 | |
| sumAc | 3.9 | |
| sumAg | 6.0 | |
| sumc4 | 45.0 | |
| sumc5 | 5.0 |
| Id | Value | Reaction |
|---|
| Definition | |
|---|---|
| ADPg = Pg-2*ATPg | |
| Gly3Pc = sumc5 - DHAPc | |
| Gly3Pg = sumc4 - DHAPg - Glc6P - Fru6P - 2*Fru16BP - GAP - BPGA13 - Pg | |
| AMPg = sumAg-ATPg-ADPg | |
| ag = 1-4*KeqAK | |
| ADPc = Pc-2*ATPc | |
| PEP = PGA3*KeqPGM*KeqENO | |
| ac = 1-4*KeqAK | |
| DHAPg = (DHAP*Vt - DHAPc*Vc)/Vg | |
| K12PEP = 0.34*(1 + ATPc/0.57 + ADPc/0.64) | |
| K5Fru16BP = 0.009*(1+ATPg/0.68+ADPg/1.51+AMPg/3.65) | |
| PGA3 = Nb*(1 + Vc/Vg)/(1 + Vc/Vg*(1 + KeqPGM + KeqPGM*KeqENO)) | |
| ATPg = (-(sumAg-Pg*ag)+((sumAg-Pg*ag)*(sumAg-Pg*ag)-4*ag*(-KeqAK*Pg*Pg))^0.5)/2/ag | |
| DHAPc = sumc5*DHAP*(Vc/Vg+1)/(sumc5*Vc/Vg + rsum) | |
| rsum = sumc4 - Glc6P - Fru6P - 2*Fru16BP - GAP - BPGA13 - Pg | |
| ATPc = (-(sumAc-Pc*ac)+((sumAc-Pc*ac)*(sumAc-Pc*ac)-4*ac*(-KeqAK*Pc*Pc))^0.5)/2/ac |
| Definition |
|---|
| Definition |
|---|
| Definition |
|---|
| Trigger | Assignments |
|---|