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

Gene deletion strategy (110 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b3752 b2297 b2458 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b0207 b3012 b0937 b1982 b4139 b1623 b4014 b0261 b2976 b2799 b1602 b0507 b2913 b4381 b2406 b2975 b0114 b3603 b0529 b2492 b0904 b2954 b1781 b3001 b3029 b1380 b0325 b1771 b3662 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.392034 (mmol/gDw/h)
  Minimum Production Rate : 0.547024 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.505963
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.975068
  EX_pi_e : 0.925182
  EX_so4_e : 0.098722
  EX_k_e : 0.076522
  EX_mg2_e : 0.003401
  EX_fe2_e : 0.003235
  EX_fe3_e : 0.003061
  EX_ca2_e : 0.002041
  EX_cl_e : 0.002041
  EX_cu2_e : 0.000278
  EX_mn2_e : 0.000271
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 53.528574
  EX_co2_e : 37.699126
  EX_h_e : 6.850239
  Auxiliary production reaction : 0.547024
  EX_ac_e : 0.503879
  EX_urea_e : 0.275643
  EX_hxan_e : 0.000439
  DM_5drib_c : 0.000263
  DM_4crsol_c : 0.000087

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, in press.
[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: 21-Sep-2023
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