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 : hxan_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3399 b4382 b4069 b2502 b4384 b2744 b3708 b2930 b4232 b3697 b3925 b2297 b2458 b2690 b2797 b3117 b1814 b4471 b2440 b0675 b2361 b2291 b0822 b3654 b2868 b3714 b3664 b1727 b0114 b2366 b2492 b0904 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.775869 (mmol/gDw/h)
  Minimum Production Rate : 0.290458 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.868864
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.541155
  EX_pi_e : 0.748408
  EX_so4_e : 0.195379
  EX_k_e : 0.151444
  EX_fe2_e : 0.012461
  EX_mg2_e : 0.006731
  EX_cl_e : 0.004038
  EX_ca2_e : 0.004038
  EX_cu2_e : 0.000550
  EX_mn2_e : 0.000536
  EX_zn2_e : 0.000265
  EX_ni2_e : 0.000251
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.901125
  EX_co2_e : 25.798440
  EX_h_e : 8.742529
  EX_ac_e : 0.451700
  EX_hxan_e : 0.290458
  DM_5drib_c : 0.000175
  DM_4crsol_c : 0.000173

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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