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 : nadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3115 b1849 b2296 b2779 b3617 b0030 b2883 b0907 b1779 b1982 b0261 b4381 b2406 b0112 b2789 b3127 b2868 b4064 b4464 b2975 b0114 b3603 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.404173 (mmol/gDw/h)
  Minimum Production Rate : 0.774588 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.603881
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.789413
  EX_pi_e : 2.713631
  EX_so4_e : 0.101779
  EX_k_e : 0.078892
  EX_fe2_e : 0.006491
  EX_mg2_e : 0.003506
  EX_ca2_e : 0.002104
  EX_cl_e : 0.002104
  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 : 50.860052
  EX_co2_e : 23.141502
  EX_h_e : 8.813816
  EX_ac_e : 1.999317
  Auxiliary production reaction : 0.774588
  EX_ade_e : 0.000452
  DM_5drib_c : 0.000271
  EX_dxylnt_e : 0.000180
  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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