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 : 5pg35pg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (58 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3708 b3115 b1849 b2296 b0160 b1238 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0675 b2361 b4381 b2406 b2868 b0114 b2366 b2492 b0904 b1533 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.599521 (mmol/gDw/h)
  Minimum Production Rate : 0.448699 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.273125
  EX_nh4_e : 10.963781
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.475700
  EX_so4_e : 0.150971
  EX_k_e : 0.117022
  EX_fe2_e : 0.009629
  EX_mg2_e : 0.005201
  EX_ca2_e : 0.003121
  EX_cl_e : 0.003121
  EX_cu2_e : 0.000425
  EX_mn2_e : 0.000414
  EX_zn2_e : 0.000204
  EX_ni2_e : 0.000194
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 48.912506
  EX_co2_e : 21.859310
  EX_h_e : 11.826834
  EX_ac_e : 2.277890
  Auxiliary production reaction : 0.448699
  EX_ade_e : 0.000403
  DM_mththf_c : 0.000269
  DM_5drib_c : 0.000135
  DM_4crsol_c : 0.000134

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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