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 : glyc__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (6 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1478 b1241 b1278 b3708 b3008 b0871 b2779 b2925 b2097 b3236 b2690 b2797 b3117 b1814 b4471 b0675 b0822 b4381 b2868 b0114 b1539 b2492 b0904 b1533 b3821   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.658564 (mmol/gDw/h)
  Minimum Production Rate : 1.795849 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.534823
  EX_o2_e : 276.767520
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.720037
  EX_pi_e : 0.635255
  EX_so4_e : 0.165840
  EX_k_e : 0.128547
  EX_mg2_e : 0.005713
  EX_ca2_e : 0.003428
  EX_cl_e : 0.003428
  EX_cu2_e : 0.000467
  EX_mn2_e : 0.000455
  EX_zn2_e : 0.000225
  EX_ni2_e : 0.000213
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989423
  EX_h2o_e : 545.574595
  EX_co2_e : 26.821926
  EX_glyc__R_e : 1.795849
  EX_xan_e : 0.151901
  DM_5drib_c : 0.000148
  DM_4crsol_c : 0.000147

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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