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General Information
| Manuscript title | Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli. |
| PubMed ID | 19690571 |
| Journal | Molecular Systems Biology |
| Year | 2009 |
| Authors | Jie Yuan, Christopher D Doucette, William U Fowler, Xiao-Jiang Feng, Matthew Piazza, Herschel A Rabitz, Ned S Wingreen and Joshua D Rabinowitz |
| Affiliations | Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA and Department of Chemistry, Princeton University, Princeton, NJ, USA |
| Keywords | E. coli, ammonia assimilation, nitrogen upshift, differential equations, sensitivity analysis |
| Full text article |
Yuan_2009.pdf
|
| Project name | not specified |
| Data used for | Model building and Model validation |
Model Information
| Model name | Nitrogen assimilation model | ||||||||||||||||||||
| Organism | Escherichia coli | ||||||||||||||||||||
| Model type | ordinary differential equations | ||||||||||||||||||||
| Category | Metabolism | ||||||||||||||||||||
| Number of reactions | 14 | ||||||||||||||||||||
| Number of species | 6 | ||||||||||||||||||||
| Number of regulators | 7 | ||||||||||||||||||||
| Number of parameters | 45 | ||||||||||||||||||||
| Number of compartments | 1 | ||||||||||||||||||||
| Dilution rate (h-1) | — | ||||||||||||||||||||
| Model file(s) and history |
LATEST KIMOMODELID25.xml
(2014-04-11 17:38:32 UTC
by Administrator KiMoSys
)
Preview
Preview file KIMOMODELID25.xml<?xml version='1.0' encoding='UTF-8'?>
<sbml level='2' version='1' xmlns='http://www.sbml.org/sbml/level2'>
<model name='N-assimilation model'>
<notes>
<html xmlns='http://www.w3.org/1999/xhtml'>
<body>
<p>This is only for the WT. Parameter values can be different for mutants</p>
<p>MAL,KG,NH3out concentrations are constant. This is for sbml output only.</p>
</body>
</html>
</notes>
<listOfReactions>
<reaction id='vgs' name='vgs' reversible='false'>
<listOfReactants>
<speciesReference species='GLU'/>
<speciesReference species='NH3int'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='GLN'/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species='GS'/>
</listOfModifiers>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<divide/>
<apply>
<times/>
<apply>
<divide/>
<apply>
<plus/>
<apply>
<times/>
<ci> V_GS </ci>
<ci> GS </ci>
</apply>
<apply>
<times/>
<ci> V_GSAMP </ci>
<apply>
<minus/>
<ci> GStot </ci>
<ci> GS </ci>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci> K_GS_GLU </ci>
<ci> K_GS_NH3 </ci>
</apply>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci> GLU </ci>
<ci> NH3int </ci>
</apply>
<apply>
<divide/>
<ci> GLN </ci>
<apply>
<times/>
<ci> KeqGS </ci>
<ci> ATPtoADPPi </ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<times/>
<apply>
<plus/>
<cn type='integer'> 1 </cn>
<apply>
<divide/>
<ci> NH3int </ci>
<ci> K_GS_NH3 </ci>
</apply>
</apply>
<apply>
<plus/>
<cn type='integer'> 1 </cn>
<apply>
<divide/>
<ci> GLU </ci>
<ci> K_GS_GLU </ci>
</apply>
<apply>
<divide/>
<ci> GLN </ci>
<ci> K_GS_GLN </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='vgog' name='vgog' reversible='false'>
<listOfReactants>
<speciesReference species='GLN'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='GLU' stoichiometry='2'/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species='ASP'/>
</listOfModifiers>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<divide/>
<apply>
<times/>
<apply>
<divide/>
<ci> V_GOG </ci>
<apply>
<times/>
<ci> K_GOG_GLN </ci>
<ci> K_GOG_KG </ci>
</apply>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci> GLN </ci>
<ci> KG </ci>
</apply>
<apply>
<divide/>
<apply>
<power/>
<ci> GLU </ci>
<cn type='integer'> 2 </cn>
</apply>
<apply>
<times/>
<ci> KeqGOG </ci>
<ci> NADPHtoNADP </ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<times/>
<apply>
<plus/>
<cn type='integer'> 1 </cn>
<apply>
<divide/>
<ci> GLN </ci>
<ci> K_GOG_GLN </ci>
</apply>
<apply>
<divide/>
<ci> ASP </ci>
<ci> K_GOG_ASP </ci>
</apply>
<apply>
<divide/>
<ci> GLU </ci>
<ci> K_GOG_GLU </ci>
</apply>
</apply>
<apply>
<plus/>
<cn type='integer'> 1 </cn>
<apply>
<divide/>
<ci> KG </ci>
<ci> K_GOG_KG </ci>
</apply>
<apply>
<divide/>
<ci> GLU </ci>
<ci> K_GOG_GLU </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='vgdh' name='vgdh' reversible='false'>
<listOfReactants>
<speciesReference species='NH3int'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='GLU'/>
</listOfProducts>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<divide/>
<apply>
<times/>
<apply>
<divide/>
<ci> V_GDH </ci>
<apply>
<times/>
<ci> K_GDH_KG </ci>
<ci> K_GDH_NH3 </ci>
</apply>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci> KG </ci>
<ci> NH3int </ci>
</apply>
<apply>
<divide/>
<ci> GLU </ci>
<apply>
<times/>
<ci> KeqGDH </ci>
<ci> NADPHtoNADP </ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<times/>
<apply>
<plus/>
<cn type='integer'> 1 </cn>
<apply>
<divide/>
<ci> NH3int </ci>
<ci> K_GDH_NH3 </ci>
</apply>
</apply>
<apply>
<plus/>
<cn type='integer'> 1 </cn>
<apply>
<divide/>
<ci> KG </ci>
<ci> K_GDH_KG </ci>
</apply>
<apply>
<divide/>
<ci> GLU </ci>
<ci> K_GDH_GLU </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='vast' name='vast' reversible='false'>
<listOfReactants>
<speciesReference species='GLU'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='ASP'/>
</listOfProducts>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<divide/>
<apply>
<times/>
<apply>
<divide/>
<ci> V_AST </ci>
<apply>
<times/>
<ci> K_AST_OA </ci>
<ci> K_AST_GLU </ci>
</apply>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci> MAL </ci>
<ci> KeqMDH </ci>
<ci> NADtoNADH </ci>
<ci> GLU </ci>
</apply>
<apply>
<divide/>
<apply>
<times/>
<ci> ASP </ci>
<ci> KG </ci>
</apply>
<ci> KeqAST </ci>
</apply>
</apply>
</apply>
<apply>
<times/>
<apply>
<plus/>
<cn type='integer'> 1 </cn>
<apply>
<divide/>
<apply>
<times/>
<ci> MAL </ci>
<ci> KeqMDH </ci>
<ci> NADtoNADH </ci>
</apply>
<ci> K_AST_OA </ci>
</apply>
<apply>
<divide/>
<ci> ASP </ci>
<ci> K_AST_ASP </ci>
</apply>
</apply>
<apply>
<plus/>
<cn type='integer'> 1 </cn>
<apply>
<divide/>
<ci> KG </ci>
<ci> K_AST_KG </ci>
</apply>
<apply>
<divide/>
<ci> GLU </ci>
<ci> K_AST_GLU </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='vnh3diff' name='vnh3diff' reversible='false'>
<listOfProducts>
<speciesReference species='NH3int'/>
</listOfProducts>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<times/>
<ci> K_DIFF </ci>
<apply>
<minus/>
<ci> NH3out </ci>
<ci> NH3int </ci>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='vat' name='vat' reversible='false'>
<listOfReactants>
<speciesReference species='GS'/>
</listOfReactants>
<listOfModifiers>
<modifierSpeciesReference species='GLN'/>
<modifierSpeciesReference species='PII'/>
</listOfModifiers>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<times/>
<ci> V_AT </ci>
<apply>
<divide/>
<ci> GS </ci>
<apply>
<plus/>
<ci> GS </ci>
<ci> K_AT_GS </ci>
</apply>
</apply>
<apply>
<divide/>
<ci> PII </ci>
<apply>
<plus/>
<ci> PII </ci>
<apply>
<times/>
<ci> K_AT_PII </ci>
<apply>
<plus/>
<cn type='integer'> 1 </cn>
<apply>
<divide/>
<ci> KG </ci>
<ci> K_AT_KG </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<divide/>
<ci> GLN </ci>
<apply>
<plus/>
<ci> GLN </ci>
<ci> K_ATAR_GLN </ci>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='var' name='var' reversible='false'>
<listOfProducts>
<speciesReference species='GS'/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species='GLN'/>
<modifierSpeciesReference species='PII'/>
</listOfModifiers>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<divide/>
<apply>
<times/>
<ci> V_AR </ci>
<apply>
<divide/>
<apply>
<minus/>
<ci> GStot </ci>
<ci> GS </ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<ci> GStot </ci>
<ci> GS </ci>
</apply>
<ci> K_AR_GSAMP </ci>
</apply>
</apply>
<apply>
<divide/>
<apply>
<minus/>
<cn type='integer'> 1 </cn>
<ci> PII </ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<cn type='integer'> 1 </cn>
<ci> PII </ci>
</apply>
<ci> K_AR_PIIUMP </ci>
</apply>
</apply>
</apply>
<apply>
<plus/>
<cn type='integer'> 1 </cn>
<apply>
<divide/>
<ci> GLN </ci>
<ci> K_ATAR_GLN </ci>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='vut' name='vut' reversible='false'>
<listOfReactants>
<speciesReference species='PII'/>
</listOfReactants>
<listOfModifiers>
<modifierSpeciesReference species='GLN'/>
</listOfModifiers>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<divide/>
<apply>
<times/>
<ci> V_UT </ci>
<apply>
<divide/>
<ci> PII </ci>
<apply>
<plus/>
<ci> PII </ci>
<ci> K_UT_PII </ci>
</apply>
</apply>
</apply>
<apply>
<plus/>
<cn type='integer'> 1 </cn>
<apply>
<divide/>
<ci> GLN </ci>
<ci> K_UTUR_GLN </ci>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='vur' name='vur' reversible='false'>
<listOfProducts>
<speciesReference species='PII'/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species='GLN'/>
</listOfModifiers>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<times/>
<ci> V_UR </ci>
<apply>
<divide/>
<apply>
<minus/>
<cn type='integer'> 1 </cn>
<ci> PII </ci>
</apply>
<apply>
<plus/>
<apply>
<minus/>
<cn type='integer'> 1 </cn>
<ci> PII </ci>
</apply>
<ci> K_UR_PIIUMP </ci>
</apply>
</apply>
<apply>
<divide/>
<ci> GLN </ci>
<apply>
<plus/>
<ci> GLN </ci>
<ci> K_UTUR_GLN </ci>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='vgluf' name='vgluf' reversible='false'>
<listOfReactants>
<speciesReference species='GLU'/>
</listOfReactants>
<listOfModifiers>
<modifierSpeciesReference species='GLN'/>
</listOfModifiers>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<divide/>
<cn> 347 </cn>
<apply>
<times/>
<ci> tau </ci>
<apply>
<plus/>
<cn type='integer'> 1 </cn>
<apply>
<divide/>
<apply>
<power/>
<ci> KgrowthGLU </ci>
<cn type='integer'> 2 </cn>
</apply>
<apply>
<power/>
<ci> GLU </ci>
<cn type='integer'> 2 </cn>
</apply>
</apply>
<apply>
<divide/>
<apply>
<power/>
<ci> KgrowthGLN </ci>
<cn type='integer'> 2 </cn>
</apply>
<apply>
<power/>
<ci> GLN </ci>
<cn type='integer'> 2 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='vglnf' name='vglnf' reversible='false'>
<listOfReactants>
<speciesReference species='GLN'/>
</listOfReactants>
<listOfModifiers>
<modifierSpeciesReference species='GLU'/>
</listOfModifiers>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<divide/>
<cn> 107.9 </cn>
<apply>
<times/>
<ci> tau </ci>
<apply>
<plus/>
<cn type='integer'> 1 </cn>
<apply>
<divide/>
<apply>
<power/>
<ci> KgrowthGLU </ci>
<cn type='integer'> 2 </cn>
</apply>
<apply>
<power/>
<ci> GLU </ci>
<cn type='integer'> 2 </cn>
</apply>
</apply>
<apply>
<divide/>
<apply>
<power/>
<ci> KgrowthGLN </ci>
<cn type='integer'> 2 </cn>
</apply>
<apply>
<power/>
<ci> GLN </ci>
<cn type='integer'> 2 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='vglnn' name='vglnn' reversible='false'>
<listOfReactants>
<speciesReference species='GLN'/>
</listOfReactants>
<listOfProducts>
<speciesReference species='GLU'/>
</listOfProducts>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<divide/>
<cn> 882 </cn>
<apply>
<times/>
<ci> tau </ci>
<apply>
<plus/>
<cn type='integer'> 1 </cn>
<apply>
<divide/>
<apply>
<power/>
<ci> KgrowthGLU </ci>
<cn type='integer'> 2 </cn>
</apply>
<apply>
<power/>
<ci> GLU </ci>
<cn type='integer'> 2 </cn>
</apply>
</apply>
<apply>
<divide/>
<apply>
<power/>
<ci> KgrowthGLN </ci>
<cn type='integer'> 2 </cn>
</apply>
<apply>
<power/>
<ci> GLN </ci>
<cn type='integer'> 2 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='vasp' name='vasp' reversible='false'>
<listOfReactants>
<speciesReference species='ASP'/>
</listOfReactants>
<listOfModifiers>
<modifierSpeciesReference species='GLN'/>
<modifierSpeciesReference species='GLU'/>
</listOfModifiers>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<divide/>
<cn> 658 </cn>
<apply>
<times/>
<ci> tau </ci>
<apply>
<plus/>
<cn type='integer'> 1 </cn>
<apply>
<divide/>
<apply>
<power/>
<ci> KgrowthGLU </ci>
<cn type='integer'> 2 </cn>
</apply>
<apply>
<power/>
<ci> GLU </ci>
<cn type='integer'> 2 </cn>
</apply>
</apply>
<apply>
<divide/>
<apply>
<power/>
<ci> KgrowthGLN </ci>
<cn type='integer'> 2 </cn>
</apply>
<apply>
<power/>
<ci> GLN </ci>
<cn type='integer'> 2 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id='vglun' name='vglun' reversible='false'>
<listOfReactants>
<speciesReference species='GLU'/>
</listOfReactants>
<listOfModifiers>
<modifierSpeciesReference species='GLN'/>
</listOfModifiers>
<kineticLaw>
<math xmlns='http://www.w3.org/1998/Math/MathML'>
<apply>
<divide/>
<cn> 2388 </cn>
<apply>
<times/>
<ci> tau </ci>
<apply>
<plus/>
<cn type='integer'> 1 </cn>
<apply>
<divide/>
<apply>
<power/>
<ci> KgrowthGLU </ci>
<cn type='integer'> 2 </cn>
</apply>
<apply>
<power/>
<ci> GLU </ci>
<cn type='integer'> 2 </cn>
</apply>
</apply>
<apply>
<divide/>
<apply>
<power/>
<ci> KgrowthGLN </ci>
<cn type='integer'> 2 </cn>
</apply>
<apply>
<power/>
<ci> GLN </ci>
<cn type='integer'> 2 </cn>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
Simulation of KIMOMODELID25.xml |
||||||||||||||||||||
| Notes |
not specified
|
||||||||||||||||||||
| Software | written in C++ | ||||||||||||||||||||
| BioModels or JWS Online ID | — | ||||||||||||||||||||
| Export metadata |
RDF:
metadataModelEntryID25.rdf
XML: metadataModelEntryID25.xml Plain text: metadataModelEntryID25.txt |
||||||||||||||||||||
GLN
Share
|
Cite Model EntryID 25
Cite Model EntryID 25
| APA |
KiMoSys (https://kimosys.org). (2014, October 27). Model EntryID 25 (Escherichia coli). https://kimosys.org/repository/63/associated_models/25
|
|
| MLA |
KiMoSys (https://kimosys.org). "Model EntryID 25 (Escherichia coli)." 2025, kimosys.org/repository/63/associated_models/25.
|
|
| ISO-690 |
KiMoSys (https://kimosys.org). Model EntryID 25 (Escherichia coli). [online], [Accessed 27 October 2025]. Available from: https://kimosys.org/repository/63/associated_models/25
|
|
| BibTeX |
@misc{ KiMoSysModelEntryID25,
author = "{KiMoSys (https://kimosys.org)}",
title = "Model EntryID 25 (Escherichia coli)",
url = "https://kimosys.org/repository/63/associated_models/25",
note = "[Online; accessed 27-October-2025]"
}
|
|
Related Model(s): AccessID 13 | AccessID 16 | AccessID 36 | AccessID 38 | AccessID 40 | AccessID 42 | AccessID 43 | AccessID 44 | AccessID 45
Submission and curation
Entered by:
Administrator KiMoSysFirst name: Administrator
Affiliation: INESC-ID/IST
Homepage: http://kdbio.inesc-id.pt/kimosys
Interests: mathematical modeling, accessible data, use of data
Created: 2013-06-12 13:43:10 UTC
Updated: 2014-06-30 17:56:44 UTC
Version: 0
Status: (reviewed) 2013-12-06 18:05:51 UTC
Views: 219
Downloads: 81