MetNetComp Database [1] / Core Genes

A set of core genes for simulation-based growth-coupled production. You can also see minimal gene deletions.

Model : e_coli_core [2].
Target metabolite : pep_c
Core genes for growth-coupled production (at least stoichioemetrically feasible)
  #Remaining genes : 68
  Remaining genes: s0001 b1276 b0116 b2587 b3734 b3733 b3736 b3737 b3738 b3735 b3731 b3732 b0720 b0733 b0734 b0979 b0978 b2779 b1773 b4152 b4153 b4151 b1819 b1817 b2416 b2415 b1779 b2417 b1621 b3870 b1761 b3212 b0875 b1136 b2281 b2277 b2280 b2286 b2287 b2284 b2276 b2282 b2279 b2283 b2285 b2288 b2278 b1603 b0451 b0114 b0115 b3916 b3951 b0902 b4025 b2926 b3612 b3493 b3956 b4301 b4090 b0721 b0722 b0723 b0728 b0008 b2465 b3919   (List of alternative genes)
  Computed by: AddGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.403135 (mmol/gDw/h)
  Minimum Production Rate : 0.048578 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 14.608133
  EX_glc__D_e : 10.000000
  EX_nh4_e : 2.198213
  EX_pi_e : 1.531590

Product: (mmol/gDw/h)
  EX_h2o_e : 24.995848
  EX_h_e : 21.959840
  EX_co2_e : 8.137719
  EX_akg_e : 6.912189
  Auxiliary production reaction : 0.048578

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Orth, J. D., Fleming, R. M., Palsson, B. Ø. (2010). Reconstruction and use of microbial metabolic networks: the core Escherichia coli metabolic model as an educational guide. EcoSal plus, 4(1).
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 27-Sep-2023
Contact