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 : acald_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (19 of 20: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4467 b4269 b0493 b3588 b3003 b3011 b2221 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2926 b3844 b1004 b3713 b1109 b0046 b3236 b3946 b0825 b1493 b3517 b4015 b0614 b0726 b1602 b2913 b1727 b1444 b1298 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.497338 (mmol/gDw/h)
  Minimum Production Rate : 0.096402 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.742602
  EX_o2_e : 280.923046
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.371212
  EX_pi_e : 0.479736
  EX_so4_e : 0.125240
  EX_k_e : 0.097077
  EX_mg2_e : 0.004314
  EX_ca2_e : 0.002589
  EX_cl_e : 0.002589
  EX_cu2_e : 0.000353
  EX_mn2_e : 0.000344
  EX_zn2_e : 0.000170
  EX_ni2_e : 0.000161
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992012
  EX_h2o_e : 545.163745
  EX_co2_e : 32.034408
  EX_ac_e : 3.679334
  EX_acald_e : 0.096402
  EX_glyclt_e : 0.000333
  DM_5drib_c : 0.000112
  DM_4crsol_c : 0.000111

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.

Last updated: 21-Sep-2023
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