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 : 2tpr3dpcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (3 of 106: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4069 b4384 b3708 b3008 b3752 b3115 b1849 b2296 b2407 b1982 b2797 b3117 b1814 b4471 b0261 b4381 b2406 b0114 b2366 b2492 b0904 b1533 b3927 b3821 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.735564 (mmol/gDw/h)
  Minimum Production Rate : 0.002049 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.188484
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.876724
  EX_pi_e : 0.719772
  EX_so4_e : 0.187278
  EX_k_e : 0.143577
  EX_fe2_e : 0.011814
  EX_mg2_e : 0.006381
  EX_ca2_e : 0.003829
  EX_cl_e : 0.003829
  EX_cu2_e : 0.000522
  EX_mn2_e : 0.000508
  EX_zn2_e : 0.000251
  EX_ni2_e : 0.000238
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 45.607213
  EX_co2_e : 24.301224
  EX_h_e : 8.109344
  EX_acser_e : 0.918360
  EX_ac_e : 0.430283
  Auxiliary production reaction : 0.002049
  DM_5drib_c : 0.000494
  DM_4crsol_c : 0.000164

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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