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 : coa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (25 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b2779 b2407 b1779 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0261 b2406 b0112 b2868 b0114 b1539 b2492 b0904 b1533 b3821 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.461524 (mmol/gDw/h)
  Minimum Production Rate : 0.460352 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.053125
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.209464
  EX_pi_e : 1.826244
  EX_so4_e : 0.576573
  EX_k_e : 0.090086
  EX_fe2_e : 0.007413
  EX_mg2_e : 0.004004
  EX_ca2_e : 0.002402
  EX_cl_e : 0.002402
  EX_cu2_e : 0.000327
  EX_mn2_e : 0.000319
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 47.436533
  EX_co2_e : 26.497113
  EX_h_e : 8.068452
  EX_ac_e : 2.443993
  Auxiliary production reaction : 0.460352
  EX_ade_e : 0.000516
  DM_5drib_c : 0.000310
  EX_glyc__R_e : 0.000154
  DM_4crsol_c : 0.000103

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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