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 : ins_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (31 of 37: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b1478 b1241 b4069 b4384 b3752 b3115 b1849 b2296 b2925 b2097 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b2690 b1982 b4139 b0411 b1602 b4381 b0114 b0529 b2492 b0904 b3029 b1380 b2660 b1771 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.400209 (mmol/gDw/h)
  Minimum Production Rate : 0.184932 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 995.343297
  EX_o2_e : 290.863308
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.061953
  EX_pi_e : 0.386044
  EX_so4_e : 0.100781
  EX_k_e : 0.078118
  EX_mg2_e : 0.003472
  EX_ca2_e : 0.002083
  EX_cl_e : 0.002083
  EX_cu2_e : 0.000284
  EX_mn2_e : 0.000277
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993572
  EX_h2o_e : 553.671028
  EX_co2_e : 41.256505
  EX_ac_e : 0.232996
  Auxiliary production reaction : 0.184932
  EX_glyclt_e : 0.000269
  DM_mththf_c : 0.000179
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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