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 : accoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 55
  Gene deletion: b2836 b1478 b3399 b1241 b0351 b4069 b2502 b2744 b3708 b1479 b3115 b1849 b2296 b2926 b3236 b3962 b1982 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b4374 b0675 b2361 b2291 b1415 b1014 b4014 b0261 b2976 b3945 b0507 b3709 b2913 b3161 b0112 b2975 b0114 b3603 b1539 b2492 b0904 b1533 b1380 b0325 b0508 b1473 b0494 b0594 b4266 b2842   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.300274 (mmol/gDw/h)
  Minimum Production Rate : 0.318719 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.085235
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.735399
  EX_pi_e : 1.245804
  EX_so4_e : 0.655430
  EX_k_e : 0.058611
  EX_fe2_e : 0.004823
  EX_mg2_e : 0.002605
  EX_ca2_e : 0.001563
  EX_cl_e : 0.001563
  EX_cu2_e : 0.000213
  EX_mn2_e : 0.000207
  EX_zn2_e : 0.000102
  EX_ni2_e : 0.000097

Product: (mmol/gDw/h)
  EX_h2o_e : 49.523598
  EX_co2_e : 34.696946
  EX_h_e : 5.624883
  EX_ac_e : 2.169911
  Auxiliary production reaction : 0.318719
  EX_met__L_e : 0.261095
  DM_oxam_c : 0.000336
  DM_5drib_c : 0.000201
  EX_dxylnt_e : 0.000201
  DM_4crsol_c : 0.000067

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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