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 : eig3p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (83 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b3617 b0030 b2883 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b4374 b2361 b2291 b0261 b0411 b4381 b0112 b2868 b4064 b4464 b0114 b2366 b0755 b3612 b2492 b0904 b1533 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.584353 (mmol/gDw/h)
  Minimum Production Rate : 1.408405 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.739969
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.131047
  EX_pi_e : 1.972076
  EX_so4_e : 0.147152
  EX_k_e : 0.114062
  EX_fe2_e : 0.009385
  EX_mg2_e : 0.005069
  EX_ca2_e : 0.003042
  EX_cl_e : 0.003042
  EX_cu2_e : 0.000414
  EX_mn2_e : 0.000404
  EX_zn2_e : 0.000199
  EX_ni2_e : 0.000189
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 47.416745
  EX_co2_e : 24.631172
  EX_h_e : 8.495203
  Auxiliary production reaction : 1.408405
  EX_acald_e : 1.005625
  EX_pyr_e : 0.305850
  EX_ade_e : 0.000654
  DM_5drib_c : 0.000392
  DM_4crsol_c : 0.000130

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.

Last updated: 09-Jul-2025
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