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 : his__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 76: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4382 b3942 b1732 b4069 b4384 b3708 b3008 b3752 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2407 b1982 b2688 b2797 b3117 b1814 b4471 b3946 b0825 b0595 b0261 b0507 b2406 b0112 b0114 b2366 b0529 b2492 b0904 b2578 b1533 b3927 b3821 b0515 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.708368 (mmol/gDw/h)
  Minimum Production Rate : 0.615337 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.151592
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.646851
  EX_pi_e : 0.683296
  EX_so4_e : 0.317847
  EX_k_e : 0.138268
  EX_fe2_e : 0.011377
  EX_mg2_e : 0.006145
  EX_ca2_e : 0.003687
  EX_cl_e : 0.003687
  EX_cu2_e : 0.000502
  EX_mn2_e : 0.000489
  EX_zn2_e : 0.000242
  EX_ni2_e : 0.000229
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 48.093676
  EX_co2_e : 25.391411
  EX_h_e : 8.780213
  Auxiliary production reaction : 0.615337
  EX_ac_e : 0.551868
  EX_met__L_e : 0.139466
  EX_alltn_e : 0.002765
  DM_5drib_c : 0.002448
  DM_4crsol_c : 0.002131
  EX_glyclt_e : 0.001973

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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