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 : ins_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (92 of 109: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b4384 b2744 b3926 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b2926 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b3946 b0825 b4374 b2361 b2291 b1602 b2913 b0114 b0529 b2492 b0904 b3927 b1380 b1771 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.369325 (mmol/gDw/h)
  Minimum Production Rate : 0.082502 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.132888
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.318689
  EX_pi_e : 0.356253
  EX_so4_e : 0.093003
  EX_k_e : 0.072090
  EX_fe2_e : 0.005932
  EX_mg2_e : 0.003204
  EX_ca2_e : 0.001922
  EX_cl_e : 0.001922
  EX_cu2_e : 0.000262
  EX_mn2_e : 0.000255
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_h2o_e : 43.952712
  EX_co2_e : 28.054725
  EX_h_e : 9.043625
  EX_pyr_e : 5.320109
  EX_ins_e : 0.082502
  DM_mththf_c : 0.000165
  DM_5drib_c : 0.000083
  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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