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 : glyclt_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b0238 b0125 b4384 b2744 b3708 b3008 b3752 b0871 b2883 b0593 b1982 b0477 b2797 b3117 b1814 b4471 b2265 b4374 b2361 b2291 b0261 b1701 b1805 b3709 b2406 b3161 b0112 b2868 b4064 b4464 b0114 b0886 b0509 b3125 b2366 b2492 b0904 b2578 b1533 b3927 b0508 b1473 b1600 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.756535 (mmol/gDw/h)
  Minimum Production Rate : 0.173651 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.203568
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.043000
  EX_pi_e : 0.729758
  EX_so4_e : 0.190511
  EX_k_e : 0.147670
  EX_fe2_e : 0.012151
  EX_mg2_e : 0.006563
  EX_cl_e : 0.003938
  EX_ca2_e : 0.003938
  EX_cu2_e : 0.000536
  EX_mn2_e : 0.000523
  EX_zn2_e : 0.000258
  EX_ni2_e : 0.000244
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 47.886353
  EX_co2_e : 25.642429
  EX_h_e : 7.997484
  EX_ade_e : 0.174498
  DM_5drib_c : 0.174159
  DM_4crsol_c : 0.173820
  EX_glyclt_e : 0.173651

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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