Please visit the new BioModels platform to access the latest content. This website is no longer updated and will be retired on 31 May 2019.
BioModels Database logo

BioModels Database

spacer

BIOMD0000000572 - Costa2014 - Computational Model of L. lactis Metabolism

 

 |   |   |  Send feedback
Reference Publication
Publication ID: 24413179
Costa RS, Hartmann A, Gaspar P, Neves AR, Vinga S.
An extended dynamic model of Lactococcus lactis metabolism for mannitol and 2,3-butanediol production.
Mol Biosyst 2014 Mar; 10(3): 628-639
Instituto de Engenharia de Sistemas e Computadores, Investigac√£o e Desenvolvimento (INESC-ID), R Alves Redol 9, 1000-029 Lisboa, Portugal. rcosta@kdbio.inesc-id.pt.  [more]
Model
Original Model: BIOMD0000000572.origin
Submitter: Rafael Costa
Submission ID: MODEL1503180000
Submission Date: 18 Mar 2015 10:08:38 UTC
Last Modification Date: 26 Mar 2015 16:41:43 UTC
Creation Date: 26 Mar 2015 15:31:31 UTC
Encoders:  Audald Lloret i Villas
   Rafael Costa
set #1
bqmodel:isDerivedFrom PubMed 15345435
PubMed 873604
PubMed 21841021
PubMed 15006767
PubMed 22325620
PubMed 11932446
set #2
bqbiol:isVersionOf Gene Ontology butanediol biosynthetic process
set #3
bqbiol:hasTaxon Taxonomy Lactococcus lactis
Notes
Costa2014 - Computational Model of L. lactis Metabolism

This model is described in the article:

Costa RS, Hartmann A, Gaspar P, Neves AR, Vinga S.
Mol Biosyst 2014 Mar; 10(3): 628-639

Abstract:

Biomedical research and biotechnological production are greatly benefiting from the results provided by the development of dynamic models of microbial metabolism. Although several kinetic models of Lactococcus lactis (a Lactic Acid Bacterium (LAB) commonly used in the dairy industry) have been developed so far, most of them are simplified and focus only on specific metabolic pathways. Therefore, the application of mathematical models in the design of an engineering strategy for the production of industrially important products by L. lactis has been very limited. In this work, we extend the existing kinetic model of L. lactis central metabolism to include industrially relevant production pathways such as mannitol and 2,3-butanediol. In this way, we expect to study the dynamics of metabolite production and make predictive simulations in L. lactis. We used a system of ordinary differential equations (ODEs) with approximate Michaelis-Menten-like kinetics for each reaction, where the parameters were estimated from multivariate time-series metabolite concentrations obtained by our team through in vivo Nuclear Magnetic Resonance (NMR). The results show that the model captures observed transient dynamics when validated under a wide range of experimental conditions. Furthermore, we analyzed the model using global perturbations, which corroborate experimental evidence about metabolic responses upon enzymatic changes. These include that mannitol production is very sensitive to lactate dehydrogenase (LDH) in the wild type (W.T.) strain, and to mannitol phosphoenolpyruvate: a phosphotransferase system (PTS(Mtl)) in a LDH mutant strain. LDH reduction has also a positive control on 2,3-butanediol levels. Furthermore, it was found that overproduction of mannitol-1-phosphate dehydrogenase (MPD) in a LDH/PTS(Mtl) deficient strain can increase the mannitol levels. The results show that this model has prediction capability over new experimental conditions and offers promising possibilities to elucidate the effect of alterations in the main metabolism of L. lactis, with application in strain optimization.

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Model
Publication ID: 24413179 Submission Date: 18 Mar 2015 10:08:38 UTC Last Modification Date: 26 Mar 2015 16:41:43 UTC Creation Date: 26 Mar 2015 15:31:31 UTC
Mathematical expressions
Reactions
PTS_Glc ATPase P_transp PGI
PFK FBA GAPDH ENO
PYK LDH PDH AE
AC PA AB MPD
MP PTS_Man Acetoin_transp Mannitol_transp
FBPase      
Physical entities
Compartments Species
Intracellular G6P ATP ADP
Pint F6P FBP
G3P BPG PEP
NAD NADH PYR
AcetCoA Acetoin Mannitol
Mannitol1Phosphate CoA  
Extracellular Pext Lactate Ethanol
Acetate Butanediol Glucose
Acetoin_Ext Mannitol_Ext Formate
Reactions (21)
 
 PTS_Glc [Glucose] + [PEP] → [G6P] + [PYR];   {FBP} , {Pint} , {FBP} , {G6P} , {Glucose} , {PEP} , {PYR} , {Pint}
 
 ATPase [ATP] → [ADP] + [Pint];   {ATP}
 
 P_transp [Pext] + [ATP] → 2.0 × [Pint] + [ADP];   {Pint} , {ADP} , {ATP} , {Pext} , {Pint}
 
 PGI [G6P] ↔ [F6P];   {F6P} , {G6P}
 
 PFK [F6P] + [ATP] → [FBP] + [ADP];   {ADP} , {ATP} , {F6P} , {FBP}
 
 FBA [FBP] ↔ 2.0 × [G3P];   {FBP} , {G3P}
 
 GAPDH [G3P] + [Pint] + [NAD] ↔ [BPG] + [NADH];   {BPG} , {G3P} , {NAD} , {NADH} , {Pint}
 
 ENO [BPG] + [ADP] ↔ [PEP] + [ATP];   {ADP} , {ATP} , {BPG} , {PEP}
 
 PYK [PEP] + [ADP] → [PYR] + [ATP];   {FBP} , {Pint} , {ADP} , {ATP} , {FBP} , {PEP} , {PYR} , {Pint}
 
 LDH [PYR] + [NADH] → [Lactate] + [NAD];   {FBP} , {Pint} , {FBP} , {Lactate} , {NAD} , {NADH} , {PYR} , {Pint}
 
 PDH [PYR] + [CoA] ↔ [AcetCoA] + [Formate];   {G3P} , {AcetCoA} , {CoA} , {Formate} , {G3P} , {PYR}
 
 AE [AcetCoA] + 2.0 × [NADH] → [Ethanol] + 2.0 × [NAD] + [CoA];   {ATP} , {ATP} , {AcetCoA} , {CoA} , {Ethanol} , {NAD} , {NADH}
 
 AC [AcetCoA] + [ADP] → [Acetate] + [ATP] + [CoA];   {ADP} , {ATP} , {AcetCoA} , {Acetate} , {CoA}
 
 PA 2.0 × [PYR] ↔ [Acetoin];   {Acetoin} , {PYR}
 
 AB [Acetoin] + [NADH] ↔ [Butanediol] + [NAD];   {Acetoin} , {Butanediol} , {NAD} , {NADH}
 
 MPD [F6P] + [NADH] ↔ [Mannitol1Phosphate] + [NAD];   {F6P} , {F6P} , {Mannitol1Phosphate} , {NAD} , {NADH}
 
 MP [Mannitol1Phosphate] → [Mannitol];   {Mannitol} , {Mannitol1Phosphate}
 
 PTS_Man [Mannitol_Ext] + [PEP] → [Mannitol1Phosphate] + [PYR];   {Mannitol1Phosphate} , {Mannitol_Ext} , {PEP} , {PYR}
 
 Acetoin_transp [Acetoin] → [Acetoin_Ext];   {Acetoin} , {Acetoin_Ext}
 
 Mannitol_transp [Mannitol] → [Mannitol_Ext];   {Mannitol} , {Mannitol_Ext}
 
 FBPase [FBP] → [F6P] + [Pint];   {F6P} , {FBP} , {Pint}
 
Functions (21)
 
 function_4_PTS_Glc lambda(FBP, G6P, Glucose, PEP, PYR, Pint, Vmax_PTS_Glc, kaPint_PTS_Glc, kiFBP_PTS_Glc, kmG6P_PTS_Glc, kmGlucose_PTS_Glc, kmPEP_PTS_Glc, kmPYR_PTS_Glc, Pint/(Pint+kaPint_PTS_Glc)*kiFBP_PTS_Glc/(FBP+kiFBP_PTS_Glc)*Vmax_PTS_Glc*Glucose/kmGlucose_PTS_Glc*PEP/kmPEP_PTS_Glc/(((1+Glucose/kmGlucose_PTS_Glc)*(1+PEP/kmPEP_PTS_Glc)+(1+G6P/kmG6P_PTS_Glc)*(1+PYR/kmPYR_PTS_Glc))-1))
 
 function_4_ATPase lambda(ATP, Vmax_ATPase, kmATP_ATPase, nATPase, Vmax_ATPase*(ATP/kmATP_ATPase)^nATPase/((ATP/kmATP_ATPase)^nATPase+1))
 
 function_4_P_transp lambda(ADP, ATP, Pext, Pint, Vmax_Ptransport, kiPint_Ptransport, kmADP_Ptransport, kmATP_Ptransport, kmPext_Ptransport, kmPint_Ptransport, kiPint_Ptransport/(Pint+kiPint_Ptransport)*Vmax_Ptransport*ATP/kmATP_Ptransport*Pext/kmPext_Ptransport/(((1+Pext/kmPext_Ptransport)*(1+ATP/kmATP_Ptransport)+(1+Pint/kmPint_Ptransport+(Pint/kmPint_Ptransport)^2)*(1+ADP/kmADP_Ptransport))-1))
 
 function_4_PGI lambda(F6P, G6P, Keq_PGI, Vmax_PGI, kmF6P_PGI, kmG6P_PGI, (Vmax_PGI*G6P/kmG6P_PGI-Vmax_PGI/Keq_PGI*F6P/kmG6P_PGI)/(1+G6P/kmG6P_PGI+F6P/kmF6P_PGI))
 
 function_4_PFK lambda(ADP, ATP, F6P, FBP, Vmax_PFK, kmADP_PFK, kmATP_PFK, kmF6P_PFK, kmFBP_PFK, Vmax_PFK*F6P/kmF6P_PFK*ATP/kmATP_PFK/(((1+F6P/kmF6P_PFK)*(1+ATP/kmATP_PFK)+(1+FBP/kmFBP_PFK)*(1+ADP/kmADP_PFK))-1))
 
 function_4_FBA lambda(FBP, G3P, Keq_FBA, Vmax_FBA, kmFBP_FBA, kmG3P_FBA, (Vmax_FBA*FBP/kmFBP_FBA-Vmax_FBA/Keq_FBA*G3P^2/kmFBP_FBA)/(1+FBP/kmFBP_FBA+G3P/kmG3P_FBA+(G3P/kmG3P_FBA)^2))
 
 function_4_GAPDH lambda(BPG, G3P, Keq_GAPDH, NAD, NADH, Pint, Vmax_GAPDH, kmBPG_GAPDH, kmG3P_GAPDH, kmNADH_GAPDH, kmNAD_GAPDH, kmPint_GAPDH, (Vmax_GAPDH*G3P/kmG3P_GAPDH*NAD/kmNAD_GAPDH*Pint/kmPint_GAPDH-Vmax_GAPDH/Keq_GAPDH*BPG/kmG3P_GAPDH*NADH/kmNAD_GAPDH*1/kmPint_GAPDH)/(((1+G3P/kmG3P_GAPDH)*(1+Pint/kmPint_GAPDH)*(1+NAD/kmNAD_GAPDH)+(1+BPG/kmBPG_GAPDH)*(1+NADH/kmNADH_GAPDH))-1))
 
 function_4_ENO lambda(ADP, ATP, BPG, Keq_ENO, PEP, Vmax_ENO, kmADP_ENO, kmATP_ENO, kmBPG_ENO, kmPEP_ENO, (Vmax_ENO*BPG/kmBPG_ENO*ADP/kmADP_ENO-Vmax_ENO/Keq_ENO*PEP/kmBPG_ENO*ATP/kmADP_ENO)/(((1+BPG/kmBPG_ENO)*(1+ADP/kmADP_ENO)+(1+PEP/kmPEP_ENO)*(1+ATP/kmATP_ENO))-1))
 
 function_4_PYK lambda(ADP, ATP, FBP, PEP, PYR, Pint, Vmax_PYK, kaFBP_PYK, kiPint_PYK, kmADP_PYK, kmATP_PYK, kmPEP_PYK, kmPYR_PYK, nPYK, FBP/(FBP+kaFBP_PYK)*kiPint_PYK^nPYK/(Pint^nPYK+kiPint_PYK^nPYK)*Vmax_PYK*ADP/kmADP_PYK*PEP/kmPEP_PYK/(((1+ADP/kmADP_PYK)*(1+PEP/kmPEP_PYK)+(1+ATP/kmATP_PYK)*(1+PYR/kmPYR_PYK))-1))
 
 function_4_LDH lambda(FBP, Lactate, NAD, NADH, PYR, Pint, Vmax_LDH, kaFBP_LDH, kiPint_LDH, kmLactate_LDH, kmNADH_LDH, kmNAD_LDH, kmPYR_LDH, FBP/(FBP+kaFBP_LDH)*kiPint_LDH/(Pint+kiPint_LDH)*Vmax_LDH*PYR/kmPYR_LDH*NADH/kmNADH_LDH/(((1+PYR/kmPYR_LDH)*(1+NADH/kmNADH_LDH)+(1+Lactate/kmLactate_LDH)*(1+NAD/kmNAD_LDH))-1))
 
 function_4_PFL lambda(AcetCoA, CoA, Formate, G3P, Keq_PFL, KmCoA_PFL, PYR, Vmax_PFL, kiG3P_PFL, kmAcetCoA_PFL, kmFormate_PFL, kmPYR_PFL, kiG3P_PFL/(G3P+kiG3P_PFL)*(Vmax_PFL*PYR/kmPYR_PFL*CoA/KmCoA_PFL-Vmax_PFL/Keq_PFL*AcetCoA/kmPYR_PFL*Formate/KmCoA_PFL)/(((1+PYR/kmPYR_PFL)*(1+CoA/KmCoA_PFL)+(1+AcetCoA/kmAcetCoA_PFL)*(1+Formate/kmFormate_PFL))-1))
 
 function_4_AE lambda(ATP, AcetCoA, CoA, Ethanol, NAD, NADH, Vmax_AE, kiATP_AE, kmAcetCoA_AE, kmCoA_AE, kmEthanol_AE, kmNADH_AE, kmNAD_AE, kiATP_AE/(ATP+kiATP_AE)*Vmax_AE*AcetCoA/kmAcetCoA_AE*(NADH/kmNADH_AE)^2/(((1+NADH/kmNADH_AE+(NADH/kmNADH_AE)^2)*(1+AcetCoA/kmAcetCoA_AE)+(1+Ethanol/kmEthanol_AE)*(1+CoA/kmCoA_AE)*(1+NAD/kmNAD_AE+(NAD/kmNAD_AE)^2))-1))
 
 function_4_ACK lambda(ADP, ATP, AcetCoA, Acetate, CoA, Vmax_ACK, kmADP_ACK, kmATP_ACK, kmAcetCoA_ACK, kmAcetate_ACK, kmCoA_ACK, Vmax_ACK*AcetCoA/kmAcetCoA_ACK*ADP/kmADP_ACK/(((1+AcetCoA/kmAcetCoA_ACK)*(1+ADP/kmADP_ACK)+(1+Acetate/kmAcetate_ACK)*(1+ATP/kmATP_ACK)*(1+CoA/kmCoA_ACK))-1))
 
 function_4_ALS lambda(Acetoin, Keq_ALS, PYR, Vmax_ALS, kmAcetoin_ALS, kmPYR_ALS, (Vmax_ALS*(PYR/kmPYR_ALS)^2-Vmax_ALS/Keq_ALS*Acetoin/kmPYR_ALS)/((1+PYR/kmPYR_ALS+(PYR/kmPYR_ALS)^2+1+Acetoin/kmAcetoin_ALS)-1))
 
 function_4_BDH lambda(Acetoin, Butanediol, Keq_BDH, NAD, NADH, Vmax_BDH, kmAcetoin_BDH, kmButanediol_BDH, kmNADH_BDH, kmNAD_BDH, (Vmax_BDH*Acetoin/kmAcetoin_BDH*NADH/kmNADH_BDH-Vmax_BDH/Keq_BDH*Butanediol/kmAcetoin_BDH*NAD/kmNADH_BDH)/(((1+Acetoin/kmAcetoin_BDH)*(1+NADH/kmNADH_BDH)+(1+Butanediol/kmButanediol_BDH)*(1+NAD/kmNAD_BDH))-1))
 
 function_4_MPD lambda(F6P, Keq_MPD, Mannitol1Phosphate, NAD, NADH, Vmax_MPD, kiF6P_MPD, kmF6P_MPD, kmMannitol1Phoshate_MPD, kmNADH_MPD, kmNAD_MPD, kiF6P_MPD/(F6P+kiF6P_MPD)*(Vmax_MPD*F6P/kmF6P_MPD*NADH/kmNADH_MPD-Vmax_MPD/Keq_MPD*Mannitol1Phosphate/kmF6P_MPD*NAD/kmNADH_MPD)/(((1+F6P/kmF6P_MPD)*(1+NADH/kmNADH_MPD)+(1+Mannitol1Phosphate/kmMannitol1Phoshate_MPD)*(1+NAD/kmNAD_MPD))-1))
 
 function_4_MP lambda(Mannitol, Mannitol1Phosphate, Vmax_MP, kmMannitol1Phosphate_MP, kmMannitol_MP, Vmax_MP*Mannitol1Phosphate/kmMannitol1Phosphate_MP/((1+Mannitol1Phosphate/kmMannitol1Phosphate_MP+1+Mannitol/kmMannitol_MP)-1))
 
 function_4_PTS_Man lambda(Mannitol1Phosphate, Mannitol_Ext, PEP, PYR, Vmax_PTS_Man, kmMannitol1Phosphate_PTS_Man, kmMannitolExt_PTS_Man, kmPEP_PTS_Man, kmPYR_PTS_Man, Vmax_PTS_Man*Mannitol_Ext/kmMannitolExt_PTS_Man*PEP/kmPEP_PTS_Man/(((1+Mannitol_Ext/kmMannitolExt_PTS_Man)*(1+PEP/kmPEP_PTS_Man)+(1+Mannitol1Phosphate/kmMannitol1Phosphate_PTS_Man)*(1+PYR/kmPYR_PTS_Man))-1))
 
 function_4_Acetoin_transp lambda(Acetoin, Acetoin_Ext, Vmax_Acetoin_transp, kmAcetoin_Acetoin_transp, kmAcetoin_Ext_Acetoin_transp, Vmax_Acetoin_transp*Acetoin/kmAcetoin_Acetoin_transp/(1+Acetoin/kmAcetoin_Acetoin_transp+Acetoin_Ext/kmAcetoin_Ext_Acetoin_transp))
 
 function_4_Mannitol_transp lambda(Mannitol, Mannitol_Ext, Vmax_Mannitol_transp, kmMannitol_Ext_Mannitol_transp, kmMannitol_Mannitol_transp, Vmax_Mannitol_transp*Mannitol/kmMannitol_Mannitol_transp/(1+Mannitol/kmMannitol_Mannitol_transp+Mannitol_Ext/kmMannitol_Ext_Mannitol_transp))
 
 function_4_FBPase lambda(F6P, FBP, Pint, Vmax_FBPase, kmF6P_FBPase, kmFBP_FBPase, kmPint_FBPase, Vmax_FBPase*FBP/kmFBP_FBPase/(FBP/kmFBP_FBPase+(1+F6P/kmF6P_FBPase)*(1+Pint/kmPint_FBPase)))
 
 Intracellular Spatial dimensions: 3.0  Compartment size: 0.047
 
 G6P
Compartment: Intracellular
Initial concentration: 0.0
 
 ATP
Compartment: Intracellular
Initial concentration: 4.88632508879394
 
 ADP
Compartment: Intracellular
Initial concentration: 20.3856905308319
 
 Pint
Compartment: Intracellular
Initial concentration: 38.26
 
 F6P
Compartment: Intracellular
Initial concentration: 0.0
 
 FBP
Compartment: Intracellular
Initial concentration: 15.3
 
 G3P
Compartment: Intracellular
Initial concentration: 0.0
 
 BPG
Compartment: Intracellular
Initial concentration: 1.26348531244692
 
 PEP
Compartment: Intracellular
Initial concentration: 2.4790177588998
 
 NAD
Compartment: Intracellular
Initial concentration: 4.67
 
 NADH
Compartment: Intracellular
Initial concentration: 2.03337939283534E-6
 
 PYR
Compartment: Intracellular
Initial concentration: 0.0
 
 AcetCoA
Compartment: Intracellular
Initial concentration: 0.0
 
 Acetoin
Compartment: Intracellular
Initial concentration: 0.0
 
 Mannitol
Compartment: Intracellular
Initial concentration: 0.0
 
 Mannitol1Phosphate
Compartment: Intracellular
Initial concentration: 0.0
 
 CoA
Compartment: Intracellular
Initial concentration: 1.0
 
 Extracellular Spatial dimensions: 3.0  Compartment size: 1.0
 
 Pext
Compartment: Extracellular
Initial concentration: 50.0
 
 Lactate
Compartment: Extracellular
Initial concentration: 0.0
 
 Ethanol
Compartment: Extracellular
Initial concentration: 0.0
 
 Acetate
Compartment: Extracellular
Initial concentration: 0.0
 
 Butanediol
Compartment: Extracellular
Initial concentration: 0.0
 
 Glucose
Compartment: Extracellular
Initial concentration: 80.0
 
 Acetoin_Ext
Compartment: Extracellular
Initial concentration: 0.0
 
 Mannitol_Ext
Compartment: Extracellular
Initial concentration: 0.0
 
 Formate
Compartment: Extracellular
Initial concentration: 0.0
 
PTS_Glc (7)
 
   Vmax_PTS_Glc
Value: 3.71082
Constant
 
   kaPint_PTS_Glc
Value: 0.070909
Constant
 
   kiFBP_PTS_Glc
Value: 1.16937
Constant
 
   kmG6P_PTS_Glc
Value: 0.284871
Constant
 
   kmGlucose_PTS_Glc
Value: 0.0485045
Constant
 
   kmPEP_PTS_Glc
Value: 0.305604
Constant
 
   kmPYR_PTS_Glc
Value: 1.95993
Constant
 
ATPase (3)
 
   Vmax_ATPase
Value: 3.2901
Constant
 
   kmATP_ATPase
Value: 4.34159
Constant
 
   nATPase
Value: 3.0
Constant
 
P_transp (6)
 
   Vmax_Ptransport
Value: 3.59588
Constant
 
   kiPint_Ptransport
Value: 0.561093
Constant
 
   kmADP_Ptransport
Value: 0.192278
Constant
 
   kmATP_Ptransport
Value: 0.523288
Constant
 
   kmPext_Ptransport
Value: 0.749898
Constant
 
   kmPint_Ptransport
Value: 0.30336
Constant
 
PGI (4)
 
   Keq_PGI
Value: 0.43
Constant
 
   Vmax_PGI
Value: 21.681
Constant
 
   kmF6P_PGI
Value: 3.13894
Constant
 
   kmG6P_PGI
Value: 0.199409
Constant
 
PFK (5)
 
   Vmax_PFK
Value: 18.3577
Constant
 
   kmADP_PFK
Value: 10.7357
Constant
 
   kmATP_PFK
Value: 0.0616607
Constant
 
   kmF6P_PFK
Value: 1.01973
Constant
 
   kmFBP_PFK
Value: 86.8048
Constant
 
FBA (4)
 
   Keq_FBA
Value: 0.056
Constant
 
   Vmax_FBA
Value: 56.1311
Constant
 
   kmFBP_FBA
Value: 0.300745
Constant
 
   kmG3P_FBA
Value: 10.1058
Constant
 
GAPDH (7)
 
   Keq_GAPDH
Value: 7.0E-4
Constant
 
   Vmax_GAPDH
Value: 30.0058
Constant
 
   kmBPG_GAPDH
Value: 0.0481603
Constant
 
   kmG3P_GAPDH
Value: 0.181788
Constant
 
   kmNADH_GAPDH
Value: 0.643019
Constant
 
   kmNAD_GAPDH
Value: 0.0477445
Constant
 
   kmPint_GAPDH
Value: 6.75302
Constant
 
ENO (6)
 
   Keq_ENO
Value: 27.55
Constant
 
   Vmax_ENO
Value: 29.132
Constant
 
   kmADP_ENO
Value: 0.413195
Constant
 
   kmATP_ENO
Value: 0.748238
Constant
 
   kmBPG_ENO
Value: 0.0241572
Constant
 
   kmPEP_ENO
Value: 1.38899
Constant
 
PYK (8)
 
   Vmax_PYK
Value: 2.22404
Constant
 
   kaFBP_PYK
Value: 0.0388651
Constant
 
   kiPint_PYK
Value: 3.70071
Constant
 
   kmADP_PYK
Value: 3.07711
Constant
 
   kmATP_PYK
Value: 29.6028
Constant
 
   kmPEP_PYK
Value: 0.330583
Constant
 
   kmPYR_PYK
Value: 96.4227
Constant
 
   nPYK
Value: 3.0
Constant
 
LDH (7)
 
   Vmax_LDH
Value: 566.598
Constant
 
   kaFBP_LDH
Value: 0.0184011
Constant
 
   kiPint_LDH
Value: 0.0676829
Constant
 
   kmLactate_LDH
Value: 94.1203
Constant
 
   kmNADH_LDH
Value: 0.144443
Constant
 
   kmNAD_LDH
Value: 3.08447
Constant
 
   kmPYR_LDH
Value: 0.01
Constant
 
PDH (7)
 
   Keq_PFL
Value: 650.0
Constant
 
   KmCoA_PFL
Value: 0.124066
Constant
 
   Vmax_PFL
Value: 0.00230934
Constant
 
   kiG3P_PFL
Value: 0.511288
Constant
 
   kmAcetCoA_PFL
Value: 7.34319
Constant
 
   kmFormate_PFL
Value: 54.2693
Constant
 
   kmPYR_PFL
Value: 5.77662
Constant
 
AE (7)
 
   Vmax_AE
Value: 2.11844
Constant
 
   kiATP_AE
Value: 6.28119
Constant
 
   kmAcetCoA_AE
Value: 7.38021
Constant
 
   kmCoA_AE
Value: 0.091813
Constant
 
   kmEthanol_AE
Value: 2.28106
Constant
 
   kmNADH_AE
Value: 0.43127
Constant
 
   kmNAD_AE
Value: 1.31442
Constant
 
AC (6)
 
   Vmax_ACK
Value: 3.83918
Constant
 
   kmADP_ACK
Value: 1.17242
Constant
 
   kmATP_ACK
Value: 14.1556
Constant
 
   kmAcetCoA_ACK
Value: 0.55824
Constant
 
   kmAcetate_ACK
Value: 0.552221
Constant
 
   kmCoA_ACK
Value: 0.173388
Constant
 
PA (4)
 
   Keq_ALS
Value: 900000.0
Constant
 
   Vmax_ALS
Value: 0.354581
Constant
 
   kmAcetoin_ALS
Value: 0.0495418
Constant
 
   kmPYR_ALS
Value: 0.262819
Constant
 
AB (6)
 
   Keq_BDH
Value: 1400.0
Constant
 
   Vmax_BDH
Value: 2.28578
Constant
 
   kmAcetoin_BDH
Value: 5.62373
Constant
 
   kmButanediol_BDH
Value: 1.80684
Constant
 
   kmNADH_BDH
Value: 3.54858
Constant
 
   kmNAD_BDH
Value: 1.29567
Constant
 
MPD (7)
 
   Keq_MPD
Value: 200.0
Constant
 
   Vmax_MPD
Value: 1.32695
Constant
 
   kiF6P_MPD
Value: 22.0284
Constant
 
   kmF6P_MPD
Value: 0.321372
Constant
 
   kmMannitol1Phoshate_MPD
Value: 0.0891203
Constant
 
   kmNADH_MPD
Value: 0.0303446
Constant
 
   kmNAD_MPD
Value: 0.373149
Constant
 
MP (3)
 
   Vmax_MP
Value: 3.48563
Constant
 
   kmMannitol1Phosphate_MP
Value: 3.51571
Constant
 
   kmMannitol_MP
Value: 0.238849
Constant
 
PTS_Man (5)
 
   Vmax_PTS_Man
Value: 4.44903
Constant
 
   kmMannitol1Phosphate_PTS_Man
Value: 0.362571
Constant
 
   kmMannitolExt_PTS_Man
Value: 0.0127321
Constant
 
   kmPEP_PTS_Man
Value: 2.20816
Constant
 
   kmPYR_PTS_Man
Value: 0.344134
Constant
 
Acetoin_transp (3)
 
   Vmax_Acetoin_transp
Value: 1.60066
Constant
 
   kmAcetoin_Acetoin_transp
Value: 1.89255
Constant
 
   kmAcetoin_Ext_Acetoin_transp
Value: 7.05248
Constant
 
Mannitol_transp (3)
 
   Vmax_Mannitol_transp
Value: 1.62459
Constant
 
   kmMannitol_Ext_Mannitol_transp
Value: 0.940662
Constant
 
   kmMannitol_Mannitol_transp
Value: 0.0223502
Constant
 
FBPase (4)
 
   Vmax_FBPase
Value: 0.0970486
Constant
 
   kmF6P_FBPase
Value: 1.90796
Constant
 
   kmFBP_FBPase
Value: 0.412307
Constant
 
   kmPint_FBPase
Value: 0.0109675
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000572

Curator's comment: (updated: 26 Mar 2015 16:41:04 GMT)

Figure 2 of the reference publication has been reproduced here: time course simulation for main metabolites for 120 minutes.

The simulation was done using Copasi v4.14 (Build 89) and the plot was generated using Gnuplot. The Copasi file of the model with simulation settings for the whole Figure 3 can be downloaded from the below link:

Additional file(s)
  • Costa2014 - Computational Model of L. lactis Metabolism:
    Copasi file of the model
spacer
spacer