MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : gua_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b4069 b2744 b3708 b3115 b1849 b2296 b2926 b2883 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b0411 b4381 b2239 b3453 b0114 b2366 b2492 b0904 b1533 b2835   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.688599 (mmol/gDw/h)
  Minimum Production Rate : 0.273978 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.916964
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.806696
  EX_pi_e : 0.664226
  EX_so4_e : 0.173403
  EX_k_e : 0.134410
  EX_fe2_e : 0.011060
  EX_mg2_e : 0.005974
  EX_ca2_e : 0.003584
  EX_cl_e : 0.003584
  EX_cu2_e : 0.000488
  EX_mn2_e : 0.000476
  EX_zn2_e : 0.000235
  EX_ni2_e : 0.000222
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 50.488279
  EX_co2_e : 29.564514
  EX_h_e : 8.097901
  EX_ac_e : 0.400892
  Auxiliary production reaction : 0.273978
  DM_5drib_c : 0.000155
  DM_4crsol_c : 0.000154

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] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[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: 21-Sep-2023
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