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 (60 of 89: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b3617 b1004 b3713 b1109 b0046 b3236 b2883 b1779 b0261 b0411 b1602 b4381 b3654 b2868 b3714 b3664 b1727 b4064 b4464 b0114 b0529 b2492 b0904 b1380 b2660 b1695 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.378273 (mmol/gDw/h)
  Minimum Production Rate : 1.045408 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.986615
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.189478
  EX_pi_e : 1.410292
  EX_so4_e : 0.095257
  EX_k_e : 0.073836
  EX_fe2_e : 0.006075
  EX_mg2_e : 0.003282
  EX_ca2_e : 0.001969
  EX_cl_e : 0.001969
  EX_cu2_e : 0.000268
  EX_mn2_e : 0.000261
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_h2o_e : 52.108563
  EX_co2_e : 34.663018
  EX_h_e : 7.335623
  Auxiliary production reaction : 1.045408
  EX_ac_e : 0.755485
  EX_gsn_e : 0.202670
  EX_glyclt_e : 0.000253
  DM_5drib_c : 0.000085
  DM_4crsol_c : 0.000084

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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