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 : nadhx__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b3399 b1241 b0351 b4069 b2502 b2744 b2297 b2458 b2926 b3617 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b4374 b0675 b2361 b2291 b0261 b1602 b0153 b2913 b1727 b0114 b0529 b2492 b0904 b0591 b1380 b1771 b0606 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.334703 (mmol/gDw/h)
  Minimum Production Rate : 0.252702 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.377123
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.718041
  EX_pi_e : 0.828261
  EX_so4_e : 0.084285
  EX_k_e : 0.065332
  EX_fe2_e : 0.005376
  EX_mg2_e : 0.002904
  EX_ca2_e : 0.001742
  EX_cl_e : 0.001742
  EX_cu2_e : 0.000237
  EX_mn2_e : 0.000231
  EX_zn2_e : 0.000114
  EX_ni2_e : 0.000108

Product: (mmol/gDw/h)
  EX_h2o_e : 50.989921
  EX_co2_e : 33.753487
  EX_h_e : 6.868117
  EX_etoh_e : 1.072213
  EX_his__L_e : 0.777496
  Auxiliary production reaction : 0.252702
  EX_ac_e : 0.194860
  EX_ade_e : 0.000375
  DM_5drib_c : 0.000225
  DM_4crsol_c : 0.000075

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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