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 : adn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3553 b4269 b0493 b3588 b3003 b3011 b4384 b3752 b0512 b0871 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b4139 b1033 b1623 b0411 b1602 b2913 b4381 b1727 b0114 b0529 b2492 b0904 b3029 b1380 b1771 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.483785 (mmol/gDw/h)
  Minimum Production Rate : 0.129667 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.135082
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.874478
  EX_pi_e : 0.466662
  EX_so4_e : 0.121827
  EX_k_e : 0.094432
  EX_mg2_e : 0.004197
  EX_fe2_e : 0.003993
  EX_fe3_e : 0.003777
  EX_cl_e : 0.002518
  EX_ca2_e : 0.002518
  EX_cu2_e : 0.000343
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.046265
  EX_co2_e : 38.843453
  EX_h_e : 5.098628
  Auxiliary production reaction : 0.129667
  EX_hxan_e : 0.000326
  DM_mththf_c : 0.000217
  DM_5drib_c : 0.000109
  DM_4crsol_c : 0.000108

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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