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 : ser__D_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b3708 b2930 b4232 b3697 b3925 b0871 b3236 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b2913 b0114 b2366 b0755 b3612 b2492 b0904 b1533 b0516   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.648663 (mmol/gDw/h)
  Minimum Production Rate : 1.184130 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.845278
  EX_o2_e : 279.028177
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.189634
  EX_pi_e : 0.625704
  EX_so4_e : 0.163346
  EX_k_e : 0.126614
  EX_mg2_e : 0.005627
  EX_ca2_e : 0.003376
  EX_cl_e : 0.003376
  EX_cu2_e : 0.000460
  EX_mn2_e : 0.000448
  EX_zn2_e : 0.000221
  EX_ni2_e : 0.000210
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989582
  EX_h2o_e : 548.131292
  EX_co2_e : 29.822977
  Auxiliary production reaction : 1.184130
  DM_5drib_c : 0.000146
  DM_4crsol_c : 0.000145

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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