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 : thmnp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3553 b1478 b3399 b1241 b4069 b2744 b2297 b2458 b0160 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b1982 b4139 b1033 b0675 b2361 b4014 b0261 b2976 b2799 b3945 b1602 b0507 b4381 b2406 b3915 b0529 b2492 b0904 b2954 b3029 b1380 b1301 b2660 b1985 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.377367 (mmol/gDw/h)
  Minimum Production Rate : 0.750834 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.982098
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.881184
  EX_pi_e : 0.364010
  EX_so4_e : 0.095029
  EX_k_e : 0.073659
  EX_fe3_e : 0.006061
  EX_mg2_e : 0.003274
  EX_ca2_e : 0.001964
  EX_cl_e : 0.001964
  EX_cu2_e : 0.000268
  EX_mn2_e : 0.000261
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_h2o_e : 54.084254
  EX_co2_e : 37.261596
  EX_h_e : 7.498809
  Auxiliary production reaction : 0.750834
  EX_ac_e : 0.219698
  EX_ade_e : 0.010296
  DM_5drib_c : 0.000253
  DM_4crsol_c : 0.000084

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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