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 : gua_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (116 of 123: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b3399 b2744 b3926 b0871 b3115 b1849 b2296 b2779 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b2883 b1982 b3946 b0825 b0675 b2361 b0411 b3945 b1602 b2913 b4381 b2406 b0114 b0529 b2492 b0904 b3927 b1380 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.369774 (mmol/gDw/h)
  Minimum Production Rate : 0.089434 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.408441
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.440696
  EX_pi_e : 0.356686
  EX_so4_e : 0.093116
  EX_k_e : 0.072177
  EX_fe2_e : 0.005939
  EX_mg2_e : 0.003208
  EX_ca2_e : 0.001925
  EX_cl_e : 0.001925
  EX_cu2_e : 0.000262
  EX_mn2_e : 0.000256
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_h2o_e : 44.269398
  EX_co2_e : 28.238214
  EX_h_e : 9.226862
  EX_pyr_e : 5.372139
  Auxiliary production reaction : 0.089434
  EX_glyclt_e : 0.009924
  DM_mththf_c : 0.000166
  DM_5drib_c : 0.000083
  DM_4crsol_c : 0.000082

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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