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 (107 of 123: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3399 b4069 b4384 b2744 b3708 b2297 b2458 b2779 b3236 b2883 b0517 b1779 b1982 b2797 b3117 b1814 b4471 b2440 b1623 b0261 b0411 b4381 b2789 b3127 b0511 b0114 b1539 b2492 b0904 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.687805 (mmol/gDw/h)
  Minimum Production Rate : 0.017997 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.052952
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.518216
  EX_pi_e : 0.663460
  EX_so4_e : 0.173203
  EX_k_e : 0.134255
  EX_fe2_e : 0.011047
  EX_mg2_e : 0.005967
  EX_ca2_e : 0.003580
  EX_cl_e : 0.003580
  EX_cu2_e : 0.000488
  EX_mn2_e : 0.000475
  EX_zn2_e : 0.000235
  EX_ni2_e : 0.000222
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 48.672675
  EX_co2_e : 30.329688
  EX_h_e : 7.084363
  EX_ac_e : 0.400430
  EX_glyclt_e : 0.274125
  Auxiliary production reaction : 0.017997
  DM_5drib_c : 0.000155
  DM_4crsol_c : 0.000153

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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