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 : adpglc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (30 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b4384 b2744 b3752 b3115 b1849 b2296 b1238 b2883 b1982 b3616 b3589 b1623 b0261 b0411 b4381 b0112 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.527099 (mmol/gDw/h)
  Minimum Production Rate : 0.518770 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.285138
  EX_nh4_e : 10.252074
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.545982
  EX_so4_e : 0.132734
  EX_k_e : 0.102886
  EX_fe2_e : 0.008466
  EX_mg2_e : 0.004573
  EX_ca2_e : 0.002744
  EX_cl_e : 0.002744
  EX_cu2_e : 0.000374
  EX_mn2_e : 0.000364
  EX_zn2_e : 0.000180
  EX_ni2_e : 0.000170
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 46.700577
  EX_co2_e : 19.621770
  EX_h_e : 8.671976
  EX_thymd_e : 0.982802
  Auxiliary production reaction : 0.518770
  EX_ac_e : 0.306869
  DM_5drib_c : 0.000354
  DM_4crsol_c : 0.000118

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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