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General Information
Manuscript title Metabolic flux analysis for a ppc mutant Escherichia coli based on 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements.
PubMed ID 15158257
Journal FEMS Microbiology Letters
Year 2004
Authors Lifeng Peng, Marcos J. Arauzo-Bravo, Kazuyuki Shimizu
Affiliations Department of Biochemical Engineering and Science, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
Keywords ppc mutant Escherichia coli, 2-Dimensional nuclear magnetic resonance, Gas chromatography-mass spectrometry, Metabolic flux analysis
Full text article Peng_2004.pdf
Project name not specified


Experiment Description
Organism Escherichia coli
Strain BW25113 and ppc mutant
Data type flux measurements
Data units (mmol/g-dry cell weight/h)
Execution date not specified


Experimental Details
Temperature (°C) 37
pH 7.0
Carbon source glucose,
Culture mode chemostat
Process condition aerobic
Dilution rate (h⁻¹) 0.2
Working volume (L) 1.0
Biomass concentration (g/L) see worksheet.
Medium composition

M9 minimal medium as described previously [3].

General protocol information Flux analysis method: 13C constrained MFA

Platform: NMR, GC-MS

Methods description - Notes

The fluxes of Pgi, Pyk, CS were chosen as the net free fluxes, and 11 exchange fluxes (Pgi, Eno, Rpi, Rpe, Tkt1, Tkt2, Tal, ICDH, Fum, Mdh, Ppc/Pck) were considered. In both cases, the free fluxes were obtained by minimizing the error criterion originating from the weighted ...

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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: 2018-07-21 14:36:12 UTC

Updated: 2020-04-24 16:10:36 UTC

Version: 2

Status: (reviewed) 2018-07-21 14:43:53 UTC

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Associated Models

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Model
EntryID
Model name Category Model Type Data used for Access Json
16 glycolysis Escherichia coli model Metabolism ordinary differential equations Model validation {"id":16,"organism_id":38,"comments":"","sbml_file_name":"Kadir_2010.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"21092096","dilution_rate":"—","name_of_model":"glycolysis Escherichia coli model","manuscript_title":"Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.","authors":"Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu","journal":"Microbial Cell Factories","affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan","project_name":"","biomodels_id":"","keywords":"Escherichia coli, single-gene knockouts, main central metabolism and TCA","software":"http://www.matlab.com (MATLAB)","control":"2018-07-21T20:34:09.507Z","main_organism":"Escherichia coli","year":2010,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys
41 Continuous kinetic model of Escherichia coli Metabolism ordinary differential equations Model building and Model validation {"id":41,"organism_id":null,"comments":"Kinetic model source: http://www.cadlive.jp/cadlive_main/Softwares/KineticModel/Ecolimetabolism.html.","sbml_file_name":"Kurata_2018.pdf","article_file_name":null,"category":"Metabolism","used_for":"---\n- Model building\n- Model validation\n","model_type":"ordinary differential equations","pubmed_id":"29054464","dilution_rate":"0.2, 0.4, 0.5 and 0.7","name_of_model":"Continuous kinetic model of Escherichia coli","manuscript_title":"Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures","authors":"Hiroyuki Kurata and Yurie Sugimoto","journal":"Journal of Bioscience and Bioengineering","affiliation":"Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680 -4 Kawazu, Iizuka, Fukuoka 820 -8502, Japan","project_name":"","biomodels_id":"","keywords":"Kinetic model, Synthetic biology, Central carbon metabolism, Dynamic simulation, Escherichia coli","software":"MATLAB (MathWorks)","control":"2018-07-24T15:46:04.831Z","main_organism":"Escherichia coli","year":2018,"combine_archive_file_name":null,"combine_archive_content_type":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"review_journal_id":null,"doi":null} Administrator KiMoSys



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