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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 ... Read more
Data file	KIMODATAID105_v2.xlsx
Alternative format(s)	no file uploaded
Export metadata	RDF: metadataDataEntryID105.rdf XML: metadataDataEntryID105.xml Plain text: metadataDataEntryID105.txt

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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

Views: 412

Downloads: 76

Associated Models

Here we can find relevant models associated with Data EntryID 105:

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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APA	KiMoSys (https://kimosys.org). (2020, December 7). Data EntryID 105 (Escherichia coli). https://doi.org/10.34619/1yzf-1r95
MLA	KiMoSys (https://kimosys.org). "Data EntryID 105 (Escherichia coli)." 2025, https://doi.org/10.34619/1yzf-1r95
ISO-690	KiMoSys (https://kimosys.org). Data EntryID 105 (Escherichia coli). [online], [Accessed 7 December 2025]. Available from: https://doi.org/10.34619/1yzf-1r95
BibTeX	@misc{ KiMoSysDataEntryID105, author = "{KiMoSys (https://kimosys.org)}", title = "Data EntryID 105 (Escherichia coli)", url = https://doi.org/10.34619/1yzf-1r95", doi = "10.34619/1yzf-1r95", note = "[Online; accessed 7-December-2025]" }