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

Gene deletion strategy (100 of 109: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3399 b4069 b2744 b3708 b3008 b3115 b1849 b2296 b0160 b2883 b2797 b3117 b1814 b4471 b1623 b3665 b4374 b2361 b2291 b0411 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b1533 b3927 b3821 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.562508 (mmol/gDw/h)
  Minimum Production Rate : 0.716971 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.394678
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.075040
  EX_pi_e : 0.542599
  EX_so4_e : 0.141651
  EX_k_e : 0.109798
  EX_fe2_e : 0.009034
  EX_mg2_e : 0.004880
  EX_ca2_e : 0.002928
  EX_cl_e : 0.002928
  EX_cu2_e : 0.000399
  EX_mn2_e : 0.000389
  EX_zn2_e : 0.000192
  EX_ni2_e : 0.000182
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 47.524824
  EX_co2_e : 31.953568
  EX_h_e : 6.213005
  Auxiliary production reaction : 0.716971
  EX_ac_e : 0.327484
  DM_mththf_c : 0.000252
  DM_5drib_c : 0.000127
  DM_4crsol_c : 0.000125

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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