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 (73 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3553 b1241 b0351 b3831 b4069 b3708 b3752 b3115 b1849 b2296 b3617 b2407 b3236 b2883 b3962 b2797 b3117 b1814 b4471 b2210 b4267 b1033 b4381 b2943 b2868 b0837 b0124 b4064 b4464 b0114 b0755 b3612 b1539 b2492 b0904 b1533 b0325 b4266 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.455714 (mmol/gDw/h)
  Minimum Production Rate : 0.454760 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.901800
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.197010
  EX_pi_e : 1.803866
  EX_so4_e : 0.114758
  EX_k_e : 0.088952
  EX_fe2_e : 0.007319
  EX_mg2_e : 0.003953
  EX_ca2_e : 0.002372
  EX_cl_e : 0.002372
  EX_cu2_e : 0.000323
  EX_mn2_e : 0.000315
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.140501
  EX_co2_e : 33.736636
  EX_h_e : 7.057214
  EX_ac_e : 1.504115
  Auxiliary production reaction : 0.454760
  EX_ade_e : 0.000307
  DM_mththf_c : 0.000204
  DM_5drib_c : 0.000103
  DM_4crsol_c : 0.000102

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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