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 (70 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 54
  Gene deletion: b2836 b3399 b1241 b0351 b4069 b2744 b3708 b2930 b4232 b3697 b3925 b2297 b2458 b2926 b3617 b0160 b2690 b3962 b1982 b4139 b2797 b3117 b1814 b4471 b4267 b4374 b0675 b2361 b2291 b1415 b1014 b4014 b0261 b2976 b2799 b3945 b0507 b3709 b3161 b0112 b2975 b0114 b3603 b1539 b2492 b0904 b3035 b1533 b1380 b0508 b1473 b4266 b1813 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.265548 (mmol/gDw/h)
  Minimum Production Rate : 0.071554 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.261242
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.020581
  EX_so4_e : 0.789937
  EX_pi_e : 0.470810
  EX_k_e : 0.051833
  EX_fe2_e : 0.004265
  EX_mg2_e : 0.002304
  EX_ca2_e : 0.001382
  EX_cl_e : 0.001382
  EX_cu2_e : 0.000188
  EX_mn2_e : 0.000183
  EX_zn2_e : 0.000091
  EX_ni2_e : 0.000086

Product: (mmol/gDw/h)
  EX_h2o_e : 41.274867
  EX_co2_e : 31.527788
  EX_h_e : 8.337538
  EX_ac_e : 6.333658
  EX_met__L_e : 0.651513
  Auxiliary production reaction : 0.071554
  DM_oxam_c : 0.000297
  DM_5drib_c : 0.000178
  EX_dxylnt_e : 0.000178
  DM_4crsol_c : 0.000059

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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