Note_Reactions – Reactions

WID Note_Reactions
Name Reactions
Comments Chemical reactions were compiled from a variety of sources including the Feist et al E. coli [PUB_0558] and Suthers et M. genitalium [PUB_0610] FBA models, the database BioCyc [PUB_0006], KEGG [PUB_0113] and UniProt [PUB_0096], and the primary literature. Every chemical reaction (except FBA exchange reactions) satifies mass balance. See Note_ReactionCatalysis for more information about the reconstruction of reaction catalysis and kinetics. Note_Metabolites for more information about the reconstruction of small molecules and their structures.
  1. Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3, 121 (2007). WholeCell: PUB_0558, PubMed: 17593909

  2. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. KEGG for linking genomes to life and the environment. Nucleic Acids Res 36, D480-4 (2008). WholeCell: PUB_0113, PubMed: 18077471, URL:

  3. Keseler IM, Bonavides-Martínez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, Johnson DA, Krummenacker M, Nolan LM, Paley S, Paulsen IT, Peralta-Gil M, Santos-Zavaleta A, Shearer AG, Karp PD. EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res 37, D464-70 (2009). WholeCell: PUB_0006, PubMed: 18974181

  4. Suthers PF, Dasika MS, Kumar VS, Denisov G, Glass JI, Maranas CD. A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189. PLoS Comput Biol 5, e1000285 (2009). WholeCell: PUB_0610, PubMed: 19214212

  5. UniProt Consortium. The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res 37, D169-74 (2009). WholeCell: PUB_0096, PubMed: 18836194, URL:

Created 2012-10-01 15:07:34
Last updated 2012-10-01 15:13:58