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 : dgtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b3708 b2930 b4232 b3697 b3925 b0871 b2926 b3617 b2797 b3117 b1814 b4471 b3946 b0825 b4374 b2361 b2291 b4381 b2868 b0114 b2366 b2492 b0904 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.333587 (mmol/gDw/h)
  Minimum Production Rate : 0.268302 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.643945
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.944215
  EX_pi_e : 1.126684
  EX_so4_e : 0.084004
  EX_k_e : 0.065114
  EX_fe2_e : 0.005358
  EX_mg2_e : 0.002894
  EX_ca2_e : 0.001736
  EX_cl_e : 0.001736
  EX_cu2_e : 0.000237
  EX_mn2_e : 0.000231
  EX_zn2_e : 0.000114
  EX_ni2_e : 0.000108

Product: (mmol/gDw/h)
  EX_h2o_e : 45.038188
  EX_co2_e : 27.739283
  EX_h_e : 8.603614
  EX_pyr_e : 4.733582
  EX_acald_e : 0.842004
  Auxiliary production reaction : 0.268302
  DM_mththf_c : 0.000149
  DM_5drib_c : 0.000075
  DM_4crsol_c : 0.000074

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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