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_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4382 b3942 b1732 b4384 b2744 b3708 b3008 b0871 b0030 b2407 b3844 b1982 b2797 b3117 b1814 b4471 b0411 b0452 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b0516 b4141 b1798 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.577901 (mmol/gDw/h)
  Minimum Production Rate : 0.131032 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.016547
  EX_o2_e : 284.048616
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.905468
  EX_pi_e : 0.557447
  EX_so4_e : 0.145527
  EX_k_e : 0.112802
  EX_mg2_e : 0.005013
  EX_ca2_e : 0.003008
  EX_cl_e : 0.003008
  EX_cu2_e : 0.000410
  EX_mn2_e : 0.000399
  EX_zn2_e : 0.000197
  EX_ni2_e : 0.000187
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990718
  EX_h2o_e : 551.663116
  EX_co2_e : 34.949840
  Auxiliary production reaction : 0.131032
  EX_alltn_e : 0.002256
  DM_mththf_c : 0.002126
  DM_5drib_c : 0.000130
  DM_4crsol_c : 0.000129

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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