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 : 5aprbu_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3553 b3399 b4069 b2744 b3708 b3926 b2297 b2458 b2779 b2925 b2097 b0160 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b2797 b3117 b1814 b4471 b1033 b0675 b2361 b0261 b1701 b1805 b3945 b1602 b2913 b4381 b2406 b0114 b0509 b3125 b0529 b1539 b2492 b0904 b1533 b3927 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.372047 (mmol/gDw/h)
  Minimum Production Rate : 0.221795 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.069944
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.956012
  EX_pi_e : 0.580674
  EX_so4_e : 0.093689
  EX_k_e : 0.072621
  EX_fe2_e : 0.005975
  EX_mg2_e : 0.003228
  EX_ca2_e : 0.001937
  EX_cl_e : 0.001937
  EX_cu2_e : 0.000264
  EX_mn2_e : 0.000257
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 44.095620
  EX_co2_e : 32.395015
  EX_h_e : 9.499664
  EX_ac_e : 5.143212
  Auxiliary production reaction : 0.221795
  EX_ade_e : 0.010151
  DM_5drib_c : 0.000250
  DM_4crsol_c : 0.000083

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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