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 : ditp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b2836 b3399 b2744 b3708 b3008 b0871 b2925 b2097 b2883 b2797 b3117 b1814 b4471 b3946 b0825 b1623 b3665 b0411 b2913 b4381 b3654 b3714 b3664 b0114 b2366 b0755 b3612 b2492 b0904 b2954 b1533 b1380   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.597441 (mmol/gDw/h)
  Minimum Production Rate : 0.103452 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.241116
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.866118
  EX_pi_e : 0.886650
  EX_so4_e : 0.150448
  EX_k_e : 0.116616
  EX_fe2_e : 0.009595
  EX_mg2_e : 0.005183
  EX_ca2_e : 0.003110
  EX_cl_e : 0.003110
  EX_cu2_e : 0.000424
  EX_mn2_e : 0.000413
  EX_zn2_e : 0.000204
  EX_ni2_e : 0.000193
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.657621
  EX_co2_e : 27.082341
  EX_h_e : 8.150075
  EX_pyr_e : 2.453646
  Auxiliary production reaction : 0.103452
  DM_5drib_c : 0.000134
  DM_4crsol_c : 0.000133

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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