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 : u23ga_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b0474 b2518 b2744 b4152 b2926 b2781 b1612 b1611 b4122 b1759 b4374 b4161 b0675 b4138 b4123 b0621 b2913 b4381 b2406 b2197 b3821 b3918 b0789 b1249 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.492044 (mmol/gDw/h)
  Minimum Production Rate : 0.259870 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.092149
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.271762
  EX_pi_e : 0.994369
  EX_so4_e : 0.123906
  EX_k_e : 0.096043
  EX_fe2_e : 0.007903
  EX_mg2_e : 0.004268
  EX_ca2_e : 0.002561
  EX_cl_e : 0.002561
  EX_cu2_e : 0.000349
  EX_mn2_e : 0.000340
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 43.291166
  EX_co2_e : 26.220806
  EX_h_e : 5.985284
  EX_succ_e : 0.513099
  Auxiliary production reaction : 0.259870
  EX_ura_e : 0.089061
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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.

Last updated: 21-Sep-2023
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