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 : gdpddman_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b4382 b0474 b2518 b1241 b0351 b4384 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b2926 b0030 b2407 b3844 b2688 b2797 b3117 b1814 b4471 b3616 b3589 b3946 b0825 b2406 b0452 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b2413 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.597802 (mmol/gDw/h)
  Minimum Production Rate : 0.137878 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.701989
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.145601
  EX_pi_e : 0.852400
  EX_so4_e : 0.150538
  EX_k_e : 0.116687
  EX_fe2_e : 0.009601
  EX_mg2_e : 0.005186
  EX_ca2_e : 0.003112
  EX_cl_e : 0.003112
  EX_cu2_e : 0.000424
  EX_mn2_e : 0.000413
  EX_zn2_e : 0.000204
  EX_ni2_e : 0.000193
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.556846
  EX_co2_e : 26.425772
  EX_h_e : 8.183082
  EX_pyr_e : 2.276606
  Auxiliary production reaction : 0.137878
  DM_mththf_c : 0.000268
  DM_5drib_c : 0.000135
  DM_4crsol_c : 0.000133

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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