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 (56 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4382 b4384 b2744 b3708 b3008 b0910 b0871 b2926 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b2440 b0511 b0114 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b3447 b0516 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.692921 (mmol/gDw/h)
  Minimum Production Rate : 0.159462 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.822864
  EX_o2_e : 278.878856
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.282659
  EX_pi_e : 0.668395
  EX_so4_e : 0.174491
  EX_k_e : 0.135253
  EX_mg2_e : 0.006011
  EX_cl_e : 0.003607
  EX_ca2_e : 0.003607
  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 : 999.988871
  EX_h2o_e : 550.011122
  EX_co2_e : 29.960290
  EX_adn_e : 0.159462
  EX_xan_e : 0.000466
  DM_mththf_c : 0.000310
  DM_5drib_c : 0.000156
  DM_4crsol_c : 0.000155

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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