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 : aps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3708 b3008 b0871 b3617 b0160 b2797 b3117 b1814 b4471 b3665 b4374 b0675 b2361 b2291 b0112 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b1533 b4141 b1798 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.618898 (mmol/gDw/h)
  Minimum Production Rate : 0.746664 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 23.147347
  EX_nh4_e : 10.417368
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.343657
  EX_so4_e : 0.902515
  EX_k_e : 0.120805
  EX_fe2_e : 0.009940
  EX_mg2_e : 0.005369
  EX_ca2_e : 0.003221
  EX_cl_e : 0.003221
  EX_cu2_e : 0.000439
  EX_mn2_e : 0.000428
  EX_zn2_e : 0.000211
  EX_ni2_e : 0.000200
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 49.556975
  EX_co2_e : 23.506952
  EX_h_e : 7.926676
  EX_acald_e : 1.811045
  Auxiliary production reaction : 0.746664
  DM_mththf_c : 0.000277
  DM_5drib_c : 0.000139
  DM_4crsol_c : 0.000138

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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