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 : dhmpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (100 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b2744 b2297 b2458 b2779 b2926 b0160 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b0937 b1982 b4139 b1033 b0675 b2361 b4014 b0261 b2976 b2799 b3945 b1602 b2913 b4381 b2406 b2789 b3127 b0529 b2492 b0904 b2954 b3029 b1380 b1301 b1985 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.369275 (mmol/gDw/h)
  Minimum Production Rate : 0.736258 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.812436
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.719812
  EX_pi_e : 0.356205
  EX_so4_e : 0.092991
  EX_k_e : 0.072080
  EX_mg2_e : 0.003203
  EX_fe2_e : 0.003048
  EX_fe3_e : 0.002883
  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 : 54.948883
  EX_co2_e : 37.735445
  EX_h_e : 7.342589
  Auxiliary production reaction : 0.736258
  EX_ac_e : 0.214987
  EX_ade_e : 0.010076
  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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