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 : gdpofuc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b2836 b3399 b4069 b2744 b3708 b3008 b2297 b2458 b2926 b1850 b0160 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b0114 b2366 b2492 b0904 b1533 b3927 b1380 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.628580 (mmol/gDw/h)
  Minimum Production Rate : 0.265955 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.664908
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.118382
  EX_pi_e : 1.138241
  EX_so4_e : 0.158289
  EX_k_e : 0.122694
  EX_fe3_e : 0.010096
  EX_mg2_e : 0.005453
  EX_ca2_e : 0.003272
  EX_cl_e : 0.003272
  EX_cu2_e : 0.000446
  EX_mn2_e : 0.000434
  EX_zn2_e : 0.000214
  EX_ni2_e : 0.000203
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 49.794437
  EX_co2_e : 29.211111
  EX_h_e : 6.949552
  EX_ac_e : 0.365950
  Auxiliary production reaction : 0.265955
  DM_5drib_c : 0.000422
  DM_4crsol_c : 0.000140

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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