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 : ipdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (48 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b2066 b1241 b0351 b4069 b4384 b3752 b2297 b2458 b2779 b3617 b2407 b0517 b1982 b2498 b2913 b0114 b0529 b2492 b0904 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.369328 (mmol/gDw/h)
  Minimum Production Rate : 1.413722 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.457010
  EX_glc__D_e : 10.000000
  EX_nh4_e : 3.988707
  EX_pi_e : 3.183699
  EX_so4_e : 0.093004
  EX_k_e : 0.072090
  EX_fe2_e : 0.005932
  EX_mg2_e : 0.003204
  EX_ca2_e : 0.001922
  EX_cl_e : 0.001922
  EX_cu2_e : 0.000262
  EX_mn2_e : 0.000255
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_h2o_e : 48.105588
  EX_co2_e : 35.525223
  EX_h_e : 2.194826
  Auxiliary production reaction : 1.413722
  EX_acald_e : 0.905069
  EX_ac_e : 0.215017
  DM_mththf_c : 0.001194
  DM_5drib_c : 0.000248
  DM_4crsol_c : 0.000082

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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