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 : dump_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3942 b1732 b1241 b0351 b4069 b4384 b3708 b3752 b0871 b3115 b1849 b2296 b2925 b2097 b3617 b2407 b1238 b3236 b1982 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b4381 b2406 b0114 b1539 b2492 b0904 b1533 b0515 b1511 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.418770 (mmol/gDw/h)
  Minimum Production Rate : 1.250975 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.685093
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.031174
  EX_pi_e : 1.654923
  EX_so4_e : 0.105455
  EX_k_e : 0.081741
  EX_fe2_e : 0.006726
  EX_mg2_e : 0.003633
  EX_ca2_e : 0.002180
  EX_cl_e : 0.002180
  EX_cu2_e : 0.000297
  EX_mn2_e : 0.000289
  EX_zn2_e : 0.000143
  EX_ni2_e : 0.000135
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 46.806635
  EX_co2_e : 25.666145
  EX_h_e : 8.635611
  EX_pyr_e : 1.313654
  Auxiliary production reaction : 1.250975
  EX_ac_e : 0.965638
  EX_alltn_e : 0.001635
  DM_mththf_c : 0.001354
  DM_5drib_c : 0.000281
  DM_4crsol_c : 0.000093

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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