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 : adn_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4384 b2744 b3708 b3008 b0871 b3115 b1849 b2296 b2779 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b4381 b2868 b0114 b0529 b1539 b2492 b0904 b2947 b1533 b3927 b3821 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.692819 (mmol/gDw/h)
  Minimum Production Rate : 0.159439 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.823451
  EX_o2_e : 278.883187
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.281911
  EX_pi_e : 0.668297
  EX_so4_e : 0.174466
  EX_k_e : 0.135233
  EX_mg2_e : 0.006010
  EX_cl_e : 0.003606
  EX_ca2_e : 0.003606
  EX_cu2_e : 0.000491
  EX_mn2_e : 0.000479
  EX_zn2_e : 0.000236
  EX_ni2_e : 0.000224
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.988873
  EX_h2o_e : 550.013053
  EX_co2_e : 29.964695
  EX_adn_e : 0.159439
  EX_ade_e : 0.000466
  DM_mththf_c : 0.000310
  DM_5drib_c : 0.000156
  DM_4crsol_c : 0.000154

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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