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 : ac_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (17 of 18: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3942 b1732 b1479 b0871 b2925 b2097 b2926 b1232 b3236 b3962 b1525 b3946 b2210 b0825 b4267 b2661 b0726 b0114 b0509 b3125 b1539 b0325 b4266 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.488566 (mmol/gDw/h)
  Minimum Production Rate : 3.045819 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.252631
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.276466
  EX_pi_e : 0.471273
  EX_so4_e : 0.123031
  EX_k_e : 0.095365
  EX_fe2_e : 0.007847
  EX_mg2_e : 0.004238
  EX_ca2_e : 0.002543
  EX_cl_e : 0.002543
  EX_cu2_e : 0.000346
  EX_mn2_e : 0.000338
  EX_zn2_e : 0.000167
  EX_ni2_e : 0.000158
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 41.637151
  EX_co2_e : 28.735487
  EX_h_e : 12.654460
  EX_for_e : 5.119506
  EX_ac_e : 3.045819
  DM_5drib_c : 0.000110
  DM_4crsol_c : 0.000109

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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