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 : pyr_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (95 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3553 b1241 b0351 b2221 b0871 b2297 b2458 b2925 b2097 b2926 b3617 b0907 b1525 b3946 b0825 b1033 b2661 b4014 b2976 b0614 b0726 b2587 b1444 b0509 b3125 b1380   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.652250 (mmol/gDw/h)
  Minimum Production Rate : 0.372011 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.975203
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.044247
  EX_pi_e : 0.629164
  EX_so4_e : 0.164250
  EX_k_e : 0.127315
  EX_fe2_e : 0.010476
  EX_mg2_e : 0.005658
  EX_ca2_e : 0.003395
  EX_cl_e : 0.003395
  EX_cu2_e : 0.000462
  EX_mn2_e : 0.000451
  EX_zn2_e : 0.000222
  EX_ni2_e : 0.000211
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 46.777104
  EX_co2_e : 29.180967
  EX_h_e : 7.829978
  EX_ac_e : 1.464541
  EX_pyr_e : 0.372011
  DM_mththf_c : 0.000292
  EX_glyclt_e : 0.000291
  DM_5drib_c : 0.000147
  DM_4crsol_c : 0.000145

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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