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 : hisp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b2744 b0910 b3115 b1849 b2296 b2883 b1982 b3616 b3589 b4374 b0675 b2361 b0261 b2913 b4381 b0112 b2868 b0114 b0755 b3612 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.483539 (mmol/gDw/h)
  Minimum Production Rate : 1.603467 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.124783
  EX_o2_e : 275.354440
  EX_nh4_e : 10.622640
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.069892
  EX_so4_e : 0.121765
  EX_k_e : 0.094383
  EX_mg2_e : 0.004195
  EX_ca2_e : 0.002517
  EX_cl_e : 0.002517
  EX_cu2_e : 0.000343
  EX_mn2_e : 0.000334
  EX_zn2_e : 0.000165
  EX_ni2_e : 0.000156
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992234
  EX_h2o_e : 549.802725
  EX_co2_e : 26.087019
  EX_ac_e : 1.627509
  Auxiliary production reaction : 1.603467
  EX_gua_e : 0.087522
  EX_thymd_e : 0.074870
  EX_ade_e : 0.000541
  DM_5drib_c : 0.000324
  DM_4crsol_c : 0.000108

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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