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 : glyc__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4384 b3708 b3008 b0871 b2779 b2926 b0030 b2407 b1238 b0121 b1982 b2797 b3117 b1814 b4471 b0596 b0261 b1701 b1805 b4381 b2406 b0112 b0114 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.680057 (mmol/gDw/h)
  Minimum Production Rate : 0.078049 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.174942
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.501418
  EX_pi_e : 0.655987
  EX_so4_e : 0.171252
  EX_k_e : 0.132742
  EX_fe2_e : 0.010922
  EX_mg2_e : 0.005899
  EX_cl_e : 0.003540
  EX_ca2_e : 0.003540
  EX_cu2_e : 0.000482
  EX_mn2_e : 0.000470
  EX_zn2_e : 0.000232
  EX_ni2_e : 0.000220
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 48.404670
  EX_co2_e : 29.664232
  EX_h_e : 6.640402
  DM_oxam_c : 0.156858
  DM_5drib_c : 0.156553
  DM_4crsol_c : 0.156249
  EX_glyc__R_e : 0.078049

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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