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 : adphep_LD_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b2836 b1241 b0351 b4069 b4384 b2744 b3708 b3752 b3115 b1849 b2296 b3617 b2407 b1982 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b0411 b0112 b2868 b0114 b2366 b2492 b0904 b1533 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.532404 (mmol/gDw/h)
  Minimum Production Rate : 0.796557 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.412568
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.735684
  EX_pi_e : 2.106674
  EX_so4_e : 0.134070
  EX_k_e : 0.103922
  EX_fe2_e : 0.008551
  EX_mg2_e : 0.004619
  EX_ca2_e : 0.002771
  EX_cl_e : 0.002771
  EX_cu2_e : 0.000377
  EX_mn2_e : 0.000368
  EX_zn2_e : 0.000182
  EX_ni2_e : 0.000172
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 45.773045
  EX_co2_e : 20.555967
  EX_h_e : 9.307418
  EX_ac_e : 2.022826
  Auxiliary production reaction : 0.796557
  EX_ade_e : 0.000596
  DM_5drib_c : 0.000357
  DM_4crsol_c : 0.000119

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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