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 : trp__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b4069 b4384 b3708 b3008 b0910 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b0030 b2407 b1238 b0583 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b2440 b3665 b0261 b4381 b2239 b2406 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.494912 (mmol/gDw/h)
  Minimum Production Rate : 0.314465 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.607490
  EX_o2_e : 277.139571
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.976712
  EX_pi_e : 0.477396
  EX_so4_e : 0.124629
  EX_k_e : 0.096603
  EX_mg2_e : 0.004293
  EX_ca2_e : 0.002576
  EX_cl_e : 0.002576
  EX_cu2_e : 0.000351
  EX_mn2_e : 0.000342
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992051
  EX_h2o_e : 545.398865
  EX_co2_e : 26.895031
  EX_pyr_e : 2.917277
  EX_trp__L_e : 0.314465
  EX_ac_e : 0.288131
  EX_ade_e : 0.000554
  DM_5drib_c : 0.000332
  DM_4crsol_c : 0.000110

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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