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 : nad_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 50
  Gene deletion: b2836 b3553 b4069 b4384 b2744 b3708 b3008 b3752 b3115 b1849 b2296 b2779 b2925 b2097 b2883 b1779 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b1033 b0596 b4374 b2361 b2291 b0261 b0411 b3709 b4381 b3161 b0112 b2789 b3127 b2868 b4064 b4464 b0114 b2366 b2492 b0904 b2947 b2578 b1533 b3927 b3029 b1473 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.592916 (mmol/gDw/h)
  Minimum Production Rate : 0.228369 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.839047
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.005340
  EX_pi_e : 1.028668
  EX_so4_e : 0.149308
  EX_k_e : 0.115733
  EX_fe2_e : 0.009523
  EX_mg2_e : 0.005144
  EX_ca2_e : 0.003086
  EX_cl_e : 0.003086
  EX_cu2_e : 0.000420
  EX_mn2_e : 0.000410
  EX_zn2_e : 0.000202
  EX_ni2_e : 0.000192
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 47.877357
  EX_co2_e : 27.417708
  EX_h_e : 8.087458
  EX_ac_e : 1.722719
  Auxiliary production reaction : 0.228369
  EX_ade_e : 0.000663
  DM_5drib_c : 0.000398
  DM_4crsol_c : 0.000132

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 (2023).
[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: 09-Jul-2025
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