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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (23 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b1241 b0351 b4069 b4384 b3708 b3752 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b3617 b2407 b2797 b3117 b1814 b4471 b3946 b0825 b3665 b4381 b2406 b0114 b1539 b2492 b0904 b1533 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.462427 (mmol/gDw/h)
  Minimum Production Rate : 0.894749 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.908491
  EX_o2_e : 276.993384
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.869730
  EX_pi_e : 0.446060
  EX_so4_e : 0.116448
  EX_k_e : 0.090262
  EX_mg2_e : 0.004012
  EX_cl_e : 0.002407
  EX_ca2_e : 0.002407
  EX_cu2_e : 0.000328
  EX_mn2_e : 0.000320
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992573
  EX_h2o_e : 544.834859
  EX_co2_e : 28.386413
  EX_ac_e : 1.064811
  Auxiliary production reaction : 0.894749
  EX_thym_e : 0.489627
  EX_ade_e : 0.000311
  DM_mththf_c : 0.000207
  DM_5drib_c : 0.000104
  DM_4crsol_c : 0.000103

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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