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 : dadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (95 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b4382 b0238 b0125 b4069 b4384 b2744 b3708 b3752 b3115 b1849 b2296 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1982 b0477 b2797 b3117 b1814 b4471 b1602 b2868 b1727 b4064 b4464 b0114 b2366 b2492 b0904 b1533 b2835 b1380 b0494 b2660 b3662 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.488957 (mmol/gDw/h)
  Minimum Production Rate : 0.155559 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.590875
  EX_o2_e : 287.069459
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.060128
  EX_pi_e : 0.782768
  EX_so4_e : 0.123129
  EX_k_e : 0.095441
  EX_mg2_e : 0.004242
  EX_ca2_e : 0.002545
  EX_cl_e : 0.002545
  EX_cu2_e : 0.000347
  EX_mn2_e : 0.000338
  EX_zn2_e : 0.000167
  EX_ni2_e : 0.000158
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992147
  EX_h2o_e : 552.736544
  EX_co2_e : 37.802926
  EX_ac_e : 0.284664
  Auxiliary production reaction : 0.155559
  EX_ade_e : 0.000329
  DM_mththf_c : 0.000219
  DM_5drib_c : 0.000110
  DM_4crsol_c : 0.000109

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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