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 : adn_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4069 b4384 b2744 b3708 b3752 b2297 b2458 b2407 b1779 b1982 b2797 b3117 b1814 b4471 b3665 b0411 b1701 b1805 b4381 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.479894 (mmol/gDw/h)
  Minimum Production Rate : 0.203567 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.191050
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.202264
  EX_pi_e : 0.462908
  EX_so4_e : 0.120847
  EX_k_e : 0.093672
  EX_fe2_e : 0.007708
  EX_mg2_e : 0.004163
  EX_ca2_e : 0.002498
  EX_cl_e : 0.002498
  EX_cu2_e : 0.000340
  EX_mn2_e : 0.000332
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.620566
  EX_co2_e : 37.705427
  EX_h_e : 5.708295
  EX_ac_e : 0.279387
  Auxiliary production reaction : 0.203567
  EX_ade_e : 0.000323
  DM_mththf_c : 0.000215
  DM_5drib_c : 0.000108
  DM_4crsol_c : 0.000107

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.

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Last updated: 21-Sep-2023
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