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 : pgp160_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (83 of 98: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b2836 b2744 b3614 b0910 b4152 b2781 b1612 b1611 b4122 b1759 b4374 b0675 b2361 b2291 b4138 b4123 b0621 b2913 b2943 b0529 b2492 b0904 b2197 b3918 b3437 b4268 b0789 b1249 b0494 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.420820 (mmol/gDw/h)
  Minimum Production Rate : 0.220349 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.870521
  EX_o2_e : 277.775344
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.143572
  EX_pi_e : 0.848528
  EX_so4_e : 0.105971
  EX_k_e : 0.082141
  EX_mg2_e : 0.003651
  EX_ca2_e : 0.002190
  EX_cl_e : 0.002190
  EX_cu2_e : 0.000298
  EX_mn2_e : 0.000291
  EX_zn2_e : 0.000143
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993241
  EX_h2o_e : 545.045992
  EX_co2_e : 31.333893
  EX_succ_e : 0.438828
  EX_ura_e : 0.298424
  Auxiliary production reaction : 0.220349
  EX_enlipa_e : 0.000635
  DM_5drib_c : 0.000095
  DM_4crsol_c : 0.000094

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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