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 : trp__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (33 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b2836 b3553 b3399 b1241 b0351 b4069 b2744 b3708 b2297 b2458 b2925 b2097 b3617 b0160 b1779 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b1033 b4374 b0675 b2361 b2291 b0261 b0507 b0112 b0114 b1539 b2492 b0904 b0591 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.409427 (mmol/gDw/h)
  Minimum Production Rate : 1.225129 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.332898
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.872494
  EX_pi_e : 0.394936
  EX_so4_e : 0.103102
  EX_k_e : 0.079917
  EX_fe2_e : 0.006576
  EX_mg2_e : 0.003552
  EX_ca2_e : 0.002131
  EX_cl_e : 0.002131
  EX_cu2_e : 0.000290
  EX_mn2_e : 0.000283
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000132
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 45.432241
  EX_co2_e : 24.818456
  EX_h_e : 8.662251
  EX_ac_e : 2.448824
  EX_trp__L_e : 1.225129
  DM_oxam_c : 0.000458
  DM_5drib_c : 0.000275
  EX_glyclt_e : 0.000274
  DM_4crsol_c : 0.000091

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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