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 : gua_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (110 of 123: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3399 b4384 b2744 b3708 b3008 b0910 b2930 b4232 b3697 b3925 b0512 b0871 b2926 b2883 b2690 b1982 b0477 b2797 b3117 b1814 b4471 b1623 b3945 b4381 b4064 b4464 b0114 b2366 b2492 b0904 b2954 b1533 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.379344 (mmol/gDw/h)
  Minimum Production Rate : 0.009926 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.337275
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.457140
  EX_pi_e : 0.365918
  EX_so4_e : 0.095526
  EX_k_e : 0.074045
  EX_fe2_e : 0.006093
  EX_mg2_e : 0.003291
  EX_ca2_e : 0.001974
  EX_cl_e : 0.001974
  EX_cu2_e : 0.000269
  EX_mn2_e : 0.000262
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000123

Product: (mmol/gDw/h)
  EX_h2o_e : 44.181413
  EX_co2_e : 28.246988
  EX_h_e : 9.119960
  EX_pyr_e : 5.274139
  EX_alltn_e : 0.077656
  Auxiliary production reaction : 0.009926
  DM_5drib_c : 0.000085
  DM_4crsol_c : 0.000085

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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