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General Information
Manuscript title Metabolic flux analysis of pykF gene knockout Escherichia coli based on 13C-labeling experiments together with measurements of enzyme activities and intracellular metabolite concentrations.
PubMed ID 12802531
Journal Appl Micriobiol Biotechnology
Year 2004
Authors Al Zaid Siddiquee K, Arauzo-Bravo MJ, Shimizu K.
Affiliations Department of Biochemical Engineering and Science, Kyushu Institute of Technology,Iizuka, 820–8502 Fukuoka, Japan
Keywords Dilution Ratem Intracellular Metabolite, Metabolic Flux Analysis, Oxidative Pentose Phosphate Pathway, Proteinogenic Amino Acid
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Experiment Description
Organism Escherichia coli
Strain BW25113 and pyk 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) 0.1
Working volume (L) 0.5
Biomass concentration (g/L) see worksheet.
Medium composition

Minimal medium consisting of 5 g glucose per liter, 48 mM Na2HPO4,22mMKH2PO4, 10 mM NaCl, and40 mM (NH4)SO4, was used. For minimal medium, the following components were filter-sterilized separately and then added (per liter of final volume): 1 ml 1 M MgSO4, 1 ml 0.1 mM CaCl2, 1ml vitamin B1 (1 mg/l stock) and 10 ml trace element solution containing (per liter): 0.55 g CaCl2, 1 g FeCl3, 0.1 g MnCl2·4H2O, 0.17 g ZnCl2, 0.043 g CuCl2·2H2O, 0.06 g CoCl2·2H2O, and 0.06 g Na2MoO4·2H2O.

General protocol information Flux analysis method: 13C constrained MFA

Platform: NMR, GC-MS

Methods description - Notes

The isotopomer balance systems were described using isotopomer mapping matrices [1] and solved through an iterative scheme, based on the approach of [1]. The isotopomers of the proteinogenic amino acids were used to generate NMR synthetic patterns. For the representation of ...

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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 20:09:18 UTC

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

Version: 1

Status: (reviewed) 2018-07-21 20:19:41 UTC

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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



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