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 : 2ombzl_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (77 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4382 b4384 b3708 b3008 b3752 b0871 b2925 b2097 b2407 b3236 b1982 b2797 b3117 b1814 b4471 b3449 b3946 b0825 b2239 b2406 b2868 b0114 b2366 b0755 b3612 b0529 b2492 b0904 b1533 b3927 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.712812 (mmol/gDw/h)
  Minimum Production Rate : 0.041010 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 25.456137
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.905758
  EX_pi_e : 0.687583
  EX_so4_e : 0.179500
  EX_k_e : 0.139136
  EX_fe2_e : 0.011448
  EX_mg2_e : 0.006184
  EX_ca2_e : 0.003710
  EX_cl_e : 0.003710
  EX_cu2_e : 0.000505
  EX_mn2_e : 0.000493
  EX_zn2_e : 0.000243
  EX_ni2_e : 0.000230
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.409743
  EX_co2_e : 27.380124
  EX_h_e : 7.097267
  EX_pyr_e : 0.340217
  EX_ade_e : 0.041490
  EX_mththf_e : 0.041329
  Auxiliary production reaction : 0.041010
  DM_5drib_c : 0.000160
  DM_4crsol_c : 0.000159

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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