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 : mththf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b4384 b2744 b3708 b3115 b1849 b2296 b2926 b1850 b3617 b0030 b2883 b1982 b2797 b3117 b1814 b4471 b1623 b4374 b2361 b2291 b0411 b0114 b2366 b2492 b0904 b1380 b1601 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.540568 (mmol/gDw/h)
  Minimum Production Rate : 0.001748 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.888897
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.452898
  EX_pi_e : 0.521435
  EX_so4_e : 0.136126
  EX_k_e : 0.105515
  EX_fe2_e : 0.008682
  EX_mg2_e : 0.004689
  EX_ca2_e : 0.002814
  EX_cl_e : 0.002814
  EX_cu2_e : 0.000383
  EX_mn2_e : 0.000374
  EX_zn2_e : 0.000184
  EX_ni2_e : 0.000175
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 43.124900
  EX_co2_e : 27.235192
  EX_h_e : 9.443068
  EX_ac_e : 2.861304
  EX_ser__L_e : 1.614815
  DM_mththf_c : 0.001748
  DM_5drib_c : 0.000363
  DM_4crsol_c : 0.000121

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.

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Last updated: 21-Sep-2023
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