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 : adp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (86 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b3752 b2297 b2458 b2925 b2097 b2926 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b1982 b0477 b1525 b4139 b4015 b2661 b0411 b2799 b3945 b1602 b4381 b3915 b2868 b2492 b0904 b2954 b3029 b1380 b2660 b1695 b1517 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.416364 (mmol/gDw/h)
  Minimum Production Rate : 0.012764 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.370031
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.561922
  EX_pi_e : 0.427156
  EX_so4_e : 0.104849
  EX_k_e : 0.081271
  EX_fe3_e : 0.006687
  EX_mg2_e : 0.003612
  EX_ca2_e : 0.002167
  EX_cl_e : 0.002167
  EX_cu2_e : 0.000295
  EX_mn2_e : 0.000288
  EX_zn2_e : 0.000142
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 44.388047
  EX_co2_e : 33.227622
  EX_h_e : 8.661145
  EX_ac_e : 4.776278
  Auxiliary production reaction : 0.012764
  EX_ade_e : 0.000280
  DM_mththf_c : 0.000187
  DM_5drib_c : 0.000094
  DM_4crsol_c : 0.000093

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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