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 : dhnpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (85 of 90: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b2744 b3115 b1849 b2296 b2779 b0160 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b1638 b0907 b1779 b1982 b4139 b1033 b0675 b2361 b4014 b0261 b2976 b2799 b3945 b1602 b0153 b4381 b2789 b3127 b0529 b2492 b0904 b2954 b0591 b3927 b3029 b1380 b2660 b1985 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.364921 (mmol/gDw/h)
  Minimum Production Rate : 0.766096 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.835047
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.773633
  EX_pi_e : 0.352005
  EX_so4_e : 0.091894
  EX_k_e : 0.071230
  EX_mg2_e : 0.003166
  EX_fe2_e : 0.003012
  EX_fe3_e : 0.002849
  EX_cl_e : 0.001899
  EX_ca2_e : 0.001899
  EX_cu2_e : 0.000259
  EX_mn2_e : 0.000252
  EX_zn2_e : 0.000124
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 54.998411
  EX_co2_e : 37.698247
  EX_h_e : 7.401022
  Auxiliary production reaction : 0.766096
  EX_ac_e : 0.212452
  EX_ade_e : 0.000408
  DM_5drib_c : 0.000245
  EX_dxylnt_e : 0.000163
  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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