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 (37 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b2836 b4382 b4069 b4384 b3708 b3008 b2930 b4232 b3697 b3925 b2297 b2458 b2779 b0030 b2407 b0583 b2690 b1982 b2797 b3117 b1814 b4471 b0261 b3945 b2406 b0114 b1539 b2492 b0904 b2578 b1533 b3927 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.606254 (mmol/gDw/h)
  Minimum Production Rate : 0.116785 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.069348
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.781744
  EX_pi_e : 0.584797
  EX_so4_e : 0.152667
  EX_k_e : 0.118337
  EX_fe2_e : 0.009737
  EX_mg2_e : 0.005259
  EX_cl_e : 0.003156
  EX_ca2_e : 0.003156
  EX_cu2_e : 0.000430
  EX_mn2_e : 0.000419
  EX_zn2_e : 0.000207
  EX_ni2_e : 0.000196
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 45.599327
  EX_co2_e : 28.420617
  EX_h_e : 7.691977
  EX_ac_e : 1.536187
  DM_oxam_c : 0.234249
  DM_5drib_c : 0.233977
  DM_4crsol_c : 0.233706
  EX_glyc__R_e : 0.116785

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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