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 (40 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b2836 b4382 b4069 b4384 b3708 b3008 b3752 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2407 b3124 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b2440 b0595 b0261 b2406 b2868 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b3447 b0514 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.714935 (mmol/gDw/h)
  Minimum Production Rate : 0.222848 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.532494
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.402350
  EX_pi_e : 0.689630
  EX_so4_e : 0.411396
  EX_k_e : 0.139550
  EX_fe2_e : 0.011483
  EX_mg2_e : 0.006202
  EX_ca2_e : 0.003721
  EX_cl_e : 0.003721
  EX_cu2_e : 0.000507
  EX_mn2_e : 0.000494
  EX_zn2_e : 0.000244
  EX_ni2_e : 0.000231
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 46.879152
  EX_co2_e : 25.746195
  EX_h_e : 7.435027
  EX_ac_e : 0.647586
  EX_met__L_e : 0.231361
  EX_trp__L_e : 0.222848
  EX_ade_e : 0.000800
  DM_5drib_c : 0.000480
  DM_4crsol_c : 0.000159
  EX_etha_e : 0.000058

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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