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 : 5aizc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (19 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1241 b0351 b4069 b4384 b3752 b2297 b2458 b2926 b3617 b2407 b3236 b0517 b1982 b0261 b4381 b2406 b0112 b0114 b0509 b3125 b0529 b2492 b0904 b0508 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.428139 (mmol/gDw/h)
  Minimum Production Rate : 1.638651 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.488968
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.546508
  EX_pi_e : 2.051637
  EX_so4_e : 0.107814
  EX_k_e : 0.083570
  EX_fe2_e : 0.006876
  EX_mg2_e : 0.003714
  EX_cl_e : 0.002228
  EX_ca2_e : 0.002228
  EX_cu2_e : 0.000304
  EX_mn2_e : 0.000296
  EX_zn2_e : 0.000146
  EX_ni2_e : 0.000138
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 47.552515
  EX_co2_e : 23.122051
  EX_h_e : 12.762698
  EX_ac_e : 2.266014
  Auxiliary production reaction : 1.638651
  EX_alltn_e : 0.001671
  DM_5drib_c : 0.001480
  EX_glyclt_e : 0.001479
  DM_4crsol_c : 0.001288

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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