A summary of genomic data relating to E. coli organized by metabolic pathways: An initial version

Price, M; Raju, M; Taylor, R

doi:10.2172/10133961

Title: A summary of genomic data relating to E. coli organized by metabolic pathways: An initial version

Full Record
Other Related Research

Abstract

This report summarizes the reactions that occur in some of the principal metabolic pathways of E. coli. These pathways have been encoded as objects in GenoBase, an integrated database under development at Argonne National Laboratory in collaboration with researchers at the National Institutes of Health and at Harvard University. The report lists the substrates, products, enzymes, and cofactors for each pathway as a whole, followed by a detailed description of each reaction in the pathway. In addition, for each enzyme, the report displays a description and activity as listed in the Enzyme Data Bank, followed by the corresponding Swiss Protein Data Bank entries. Separate summary lines are included for each of the E. coli genes associated with each enzyme.

Authors:: Price, M; Raju, M; Taylor, R

Publication Date:: Fri Jan 01 00:00:00 EST 1993

Research Org.:: Argonne National Lab., IL (United States). Mathematics and Computer Science Div.

Sponsoring Org.:: USDOE, Washington, DC (United States)

OSTI Identifier:: 10133961

Report Number(s):: ANL/MCS-TM-174
ON: DE93008116

DOE Contract Number:: W-31109-ENG-38

Resource Type:: Technical Report

Resource Relation:: Other Information: PBD: Jan 1993

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; BIOLOGICAL PATHWAYS; DATA BASE MANAGEMENT; GENES; METABOLIC ACTIVATION; ESCHERICHIA COLI; CHEMICAL REACTIONS; ENZYMES; COMPILED DATA; 550400; 990301; GENETICS; DATA HANDLING

Citation Formats


                    Price, M, Raju, M, and Taylor, R. A summary of genomic data relating to E. coli organized by metabolic pathways: An initial version.  United States: N. p., 1993. 
        Web.  doi:10.2172/10133961.

Copy to clipboard


                    Price, M, Raju, M, & Taylor, R. A summary of genomic data relating to E. coli organized by metabolic pathways: An initial version.  United States.  https://doi.org/10.2172/10133961

Copy to clipboard


                    Price, M, Raju, M, and Taylor, R. 1993.  
        "A summary of genomic data relating to E. coli organized by metabolic pathways: An initial version".  United States.  https://doi.org/10.2172/10133961.  https://www.osti.gov/servlets/purl/10133961.

Copy to clipboard


                    
@article{osti_10133961,

  title        = {A summary of genomic data relating to E. coli organized by metabolic pathways: An initial version},

  author       = {Price, M and Raju, M and Taylor, R},

  abstractNote = {This report summarizes the reactions that occur in some of the principal metabolic pathways of E. coli. These pathways have been encoded as objects in GenoBase, an integrated database under development at Argonne National Laboratory in collaboration with researchers at the National Institutes of Health and at Harvard University. The report lists the substrates, products, enzymes, and cofactors for each pathway as a whole, followed by a detailed description of each reaction in the pathway. In addition, for each enzyme, the report displays a description and activity as listed in the Enzyme Data Bank, followed by the corresponding Swiss Protein Data Bank entries. Separate summary lines are included for each of the E. coli genes associated with each enzyme.},

  doi          = {10.2172/10133961},

  url          = {https://www.osti.gov/biblio/10133961},
  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {Fri Jan 01 00:00:00 EST 1993},

  month        = {Fri Jan 01 00:00:00 EST 1993}

}

Copy to clipboard

Technical Report:

View Technical Report (5.80 MB)

https://doi.org/10.2172/10133961

Save / Share:

Export Metadata

Save to My Library

Similar records in OSTI.GOV collections:

A summary of genomic data relating to E. coli organized by metabolic pathways: An initial version

Technical Report Price, M.; Raju, M.; Taylor, R.

This report summarizes the reactions that occur in some of the principal metabolic pathways of E. coli. These pathways have been encoded as objects in GenoBase, an integrated database under development at Argonne National Laboratory in collaboration with researchers at the National Institutes of Health and at Harvard University. The report lists the substrates, products, enzymes, and cofactors for each pathway as a whole, followed by a detailed description of each reaction in the pathway. In addition, for each enzyme, the report displays a description and activity as listed in the Enzyme Data Bank, followed by the corresponding Swiss Proteinmore »« less
https://doi.org/10.2172/6697058

Full Text Available
Nutritional complementation of oxidative glucose metabolism in Escherichia coli via pyrroloquinoline quinone-dependent glucose dehydrogenase and the Entner-Doudoroff pathway

Journal Article Adamowicz, M; Conway, T; Nickerson, K - Applied and Environmental Microbiology; (United States)

Two glucose-negative Escherichia coli mutants (ZSC113 and DF214) were unable to grow on glucose as the sole carbon source unless supplemented with pyrroloquinoline quinone (PQQ). PQQ is the cofactor for the periplasmic enzyme glucose dehydrogenase, which converts glucose to gluconate. Aerobically, E. Coli ZSC113 grew on glucose plus PQQ with a generation time of 65 min, a generation time about the same as that for wild-type E. coli in a defined glucose-salts medium. Thus, for E. coli ZSC113 the Entner-Doudoroff pathway was fully able to replace the Embden-Meyerhof-Parnas pathway. In the presence of 5% sodium dodecyl sulfate, PQQ no longermore »« less
Light‐Driven Metabolic Pathways in Non‐Photosynthetic Biohybrid Bacteria

Journal Article Bassett, Shane; Ding, Yuchen; Roy, Micaela; ... - ChemBioChem: a European journal of chemical biology

Abstract Biomanufacturing via microorganisms relies on carbon substrates for molecular feedstocks and a source of energy to carry out enzymatic reactions. This creates metabolic bottlenecks and lowers the efficiency for substrate conversion. Nanoparticle biohybridization with proteins and whole cell surfaces can bypass the need for redox cofactor regeneration for improved secondary metabolite production in a non‐specific manner. Here we propose using nanobiohybrid organisms (Nanorgs), intracellular protein‐nanoparticle hybrids formed through the spontaneous coupling of core‐shell quantum dots (QDs) with histidine‐tagged enzymes in non‐photosynthetic bacteria, for light‐mediated control of bacterial metabolism. This proved to eliminate metabolic constrictions and replace glucose with lightmore »« less
https://doi.org/10.1002/cbic.202300572
Enhancing control of cell-free metabolism through pH modulation

Journal Article Karim, Ashty; Rasor, Blake; Jewett, Michael - Synthetic Biology

Engineering metabolism for the synthesis of bio-based products in non-model organisms can be challenging. One specific challenge is that biosynthetic pathways are often built from enzyme candidates sourced from diverse organisms, which can prove difficult to implement in recombinant hosts due to differences in their cellular environments (e.g. pH, cofactor balance). To address this problem, in this work we report a cell-free synthetic biology approach for understanding metabolism in a range of environmental conditions, specifically under varied pH. The key idea is to control the pH of Escherichia coli-based cell-free systems for assessing pathway performance using enzymes sourced from organismsmore »« less
https://doi.org/10.1093/synbio/ysz027

Full Text Available
Evaluating E. coli genome‐scale metabolic model accuracy with high‐throughput mutant fitness data

Journal Article Bernstein, David; Akkas, Batu; Price, Morgan; ... - Molecular Systems Biology

Abstract The Escherichia coli genome‐scale metabolic model (GEM) is an exemplar systems biology model for the simulation of cellular metabolism. Experimental validation of model predictions is essential to pinpoint uncertainty and ensure continued development of accurate models. Here, we quantified the accuracy of four subsequent E. coli GEMs using published mutant fitness data across thousands of genes and 25 different carbon sources. This evaluation demonstrated the utility of the area under a precision–recall curve relative to alternative accuracy metrics. An analysis of errors in the latest (iML1515) model identified several vitamins/cofactors that are likely available to mutants despite being absent frommore »« less
https://doi.org/10.15252/msb.202311566

Similar Records