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 : dgsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b2744 b3708 b3008 b0871 b2925 b2097 b2926 b2883 b2797 b3117 b1814 b4471 b3946 b0825 b4381 b0452 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b1539 b2492 b0904 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.641655 (mmol/gDw/h)
  Minimum Production Rate : 0.490100 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.643410
  EX_o2_e : 278.615362
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.380323
  EX_pi_e : 0.618945
  EX_so4_e : 0.161582
  EX_k_e : 0.125247
  EX_mg2_e : 0.005566
  EX_ca2_e : 0.003340
  EX_cl_e : 0.003340
  EX_cu2_e : 0.000455
  EX_mn2_e : 0.000443
  EX_zn2_e : 0.000219
  EX_ni2_e : 0.000207
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989694
  EX_h2o_e : 551.092284
  EX_co2_e : 28.761995
  Auxiliary production reaction : 0.490100
  DM_5drib_c : 0.000144
  DM_4crsol_c : 0.000143

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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