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 : 2dr5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (67 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b1478 b4269 b0493 b3588 b3003 b3011 b1241 b0871 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b0937 b1033 b2799 b3945 b1602 b2913 b4381 b0529 b2492 b0904 b1380 b1517 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.430887 (mmol/gDw/h)
  Minimum Production Rate : 1.105674 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.416531
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.653543
  EX_pi_e : 1.521310
  EX_so4_e : 0.108506
  EX_k_e : 0.084106
  EX_fe2_e : 0.006920
  EX_mg2_e : 0.003738
  EX_ca2_e : 0.002243
  EX_cl_e : 0.002243
  EX_cu2_e : 0.000305
  EX_mn2_e : 0.000298
  EX_zn2_e : 0.000147
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 47.752266
  EX_co2_e : 35.268058
  EX_h_e : 3.959162
  Auxiliary production reaction : 1.105674
  EX_acald_e : 0.758337
  DM_mththf_c : 0.000193
  DM_5drib_c : 0.000097
  DM_4crsol_c : 0.000096

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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