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 (74 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b4467 b1478 b3399 b0474 b2518 b1241 b4069 b2744 b0871 b3115 b1849 b2296 b2779 b2925 b2097 b0160 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b1982 b4139 b0675 b2361 b0261 b2799 b3945 b1602 b0507 b2913 b4381 b2406 b3915 b2975 b0114 b3603 b0529 b2492 b0904 b3927 b3029 b1380 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.353161 (mmol/gDw/h)
  Minimum Production Rate : 0.046089 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.104191
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.083101
  EX_pi_e : 0.432840
  EX_so4_e : 0.088933
  EX_k_e : 0.068935
  EX_fe3_e : 0.005672
  EX_mg2_e : 0.003064
  EX_ca2_e : 0.001838
  EX_cl_e : 0.001838
  EX_cu2_e : 0.000250
  EX_mn2_e : 0.000244
  EX_zn2_e : 0.000120
  EX_ni2_e : 0.000114

Product: (mmol/gDw/h)
  EX_h2o_e : 43.520173
  EX_co2_e : 27.975030
  EX_h_e : 9.076982
  EX_pyr_e : 5.443907
  EX_ac_e : 0.205605
  Auxiliary production reaction : 0.046089
  EX_hxan_e : 0.009636
  DM_5drib_c : 0.000237
  DM_4crsol_c : 0.000079

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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