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 : pant__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 93: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4467 b1478 b1241 b4069 b2297 b2458 b2779 b2925 b2097 b3844 b1004 b3713 b1109 b0046 b3236 b3946 b0825 b2799 b3945 b1602 b2913 b4381 b3915 b0114 b2492 b0904 b1380 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.401163 (mmol/gDw/h)
  Minimum Production Rate : 0.630749 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.995606
  EX_o2_e : 280.898857
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.332522
  EX_pi_e : 0.386964
  EX_so4_e : 0.101021
  EX_k_e : 0.078304
  EX_mg2_e : 0.003480
  EX_ca2_e : 0.002088
  EX_cl_e : 0.002088
  EX_cu2_e : 0.000284
  EX_mn2_e : 0.000277
  EX_zn2_e : 0.000137
  EX_ni2_e : 0.000130
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993557
  EX_h2o_e : 542.977679
  EX_co2_e : 32.387305
  EX_ac_e : 3.681160
  Auxiliary production reaction : 0.630749
  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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