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 : 25drapp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b2744 b2297 b2458 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b1779 b0937 b1982 b4139 b1033 b0675 b2361 b4014 b0261 b2976 b0411 b2799 b3945 b1602 b0507 b2913 b4381 b0529 b2492 b0904 b2954 b3927 b3029 b1380 b3662 b1985 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.364291 (mmol/gDw/h)
  Minimum Production Rate : 0.764449 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.874415
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.758593
  EX_pi_e : 1.115846
  EX_so4_e : 0.091736
  EX_k_e : 0.071107
  EX_mg2_e : 0.003160
  EX_fe2_e : 0.003006
  EX_fe3_e : 0.002844
  EX_ca2_e : 0.001896
  EX_cl_e : 0.001896
  EX_cu2_e : 0.000258
  EX_mn2_e : 0.000252
  EX_zn2_e : 0.000124
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 55.007530
  EX_co2_e : 37.740471
  EX_h_e : 7.386462
  Auxiliary production reaction : 0.764449
  EX_ac_e : 0.212085
  EX_ade_e : 0.000408
  DM_5drib_c : 0.000244
  DM_4crsol_c : 0.000081

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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