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 (60 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3916 b3399 b4069 b2502 b2744 b3708 b3008 b3115 b1849 b2296 b1850 b1238 b1982 b1200 b2688 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b4381 b0114 b2366 b1723 b2492 b0904 b1533 b3927 b3821   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.727325 (mmol/gDw/h)
  Minimum Production Rate : 0.408391 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.607569
  EX_nh4_e : 10.004503
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.109973
  EX_so4_e : 0.183155
  EX_k_e : 0.141969
  EX_fe2_e : 0.011682
  EX_mg2_e : 0.006310
  EX_ca2_e : 0.003786
  EX_cl_e : 0.003786
  EX_cu2_e : 0.000516
  EX_mn2_e : 0.000503
  EX_zn2_e : 0.000248
  EX_ni2_e : 0.000235
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 48.590686
  EX_co2_e : 25.085133
  EX_h_e : 9.255845
  EX_ac_e : 0.423439
  Auxiliary production reaction : 0.408391
  EX_acser_e : 0.107498
  DM_5drib_c : 0.000488
  DM_4crsol_c : 0.000162

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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