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 : preq1_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (89 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b4467 b1478 b4382 b1241 b4069 b4384 b2744 b3752 b2297 b2458 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b0937 b1982 b0477 b4139 b4014 b0261 b2976 b0411 b2799 b3945 b1602 b0507 b2975 b0114 b3603 b0529 b2492 b0904 b2954 b3029 b1380 b2660 b3662 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.404366 (mmol/gDw/h)
  Minimum Production Rate : 0.451385 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 39.014741
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.420617
  EX_pi_e : 0.390053
  EX_so4_e : 0.101827
  EX_k_e : 0.078929
  EX_mg2_e : 0.003508
  EX_fe2_e : 0.003337
  EX_fe3_e : 0.003157
  EX_ca2_e : 0.002105
  EX_cl_e : 0.002105
  EX_cu2_e : 0.000287
  EX_mn2_e : 0.000279
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 54.566772
  EX_co2_e : 38.577485
  EX_h_e : 6.953324
  EX_ac_e : 0.632575
  Auxiliary production reaction : 0.451385
  EX_urea_e : 0.397159
  EX_ade_e : 0.000452
  DM_5drib_c : 0.000271
  DM_4crsol_c : 0.000090

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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