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 (55 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b4384 b2744 b3708 b3752 b2930 b4232 b3697 b3925 b2297 b2458 b1238 b2883 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b3946 b0825 b1033 b1623 b0261 b0411 b0507 b4381 b2406 b0112 b0114 b2366 b2492 b0904 b3035 b1533 b3821 b2413 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.367941 (mmol/gDw/h)
  Minimum Production Rate : 1.101019 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.021578
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.176178
  EX_pi_e : 0.354918
  EX_so4_e : 0.092655
  EX_k_e : 0.071819
  EX_fe2_e : 0.005909
  EX_mg2_e : 0.003192
  EX_ca2_e : 0.001915
  EX_cl_e : 0.001915
  EX_cu2_e : 0.000261
  EX_mn2_e : 0.000254
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_h2o_e : 44.881892
  EX_co2_e : 26.356621
  EX_h_e : 8.797773
  EX_ac_e : 3.213880
  EX_trp__L_e : 1.101019
  DM_oxam_c : 0.000412
  DM_5drib_c : 0.000247
  EX_glyclt_e : 0.000246
  DM_4crsol_c : 0.000082

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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