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 : eig3p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4467 b3399 b3942 b1732 b4069 b2744 b2297 b2458 b2926 b0160 b3844 b1004 b3713 b1109 b0046 b3236 b0937 b1982 b0675 b2361 b3551 b0261 b2799 b3945 b1602 b4219 b1832 b1778 b4381 b2406 b1727 b0114 b0529 b2492 b0904 b1380 b1710 b2480 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.415866 (mmol/gDw/h)
  Minimum Production Rate : 0.913970 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.390140
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.375988
  EX_pi_e : 1.315117
  EX_so4_e : 0.104723
  EX_k_e : 0.081174
  EX_fe2_e : 0.006679
  EX_mg2_e : 0.003608
  EX_ca2_e : 0.002165
  EX_cl_e : 0.002165
  EX_cu2_e : 0.000295
  EX_mn2_e : 0.000287
  EX_zn2_e : 0.000142
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 51.457528
  EX_co2_e : 36.163204
  EX_h_e : 5.947926
  Auxiliary production reaction : 0.913970
  EX_etoh_e : 0.370858
  EX_ac_e : 0.242111
  EX_ade_e : 0.011347
  DM_5drib_c : 0.000279
  DM_4crsol_c : 0.000093

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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