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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3399 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4069 b4384 b2744 b3708 b0871 b3115 b1849 b2296 b2925 b2097 b3617 b2407 b1238 b3236 b1779 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b3665 b4381 b2406 b0114 b2366 b2492 b0904 b1533 b0515 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.305634 (mmol/gDw/h)
  Minimum Production Rate : 0.914982 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.665357
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.131813
  EX_pi_e : 2.124781
  EX_so4_e : 0.076965
  EX_k_e : 0.059658
  EX_fe2_e : 0.004909
  EX_mg2_e : 0.002651
  EX_ca2_e : 0.001591
  EX_cl_e : 0.001591
  EX_cu2_e : 0.000217
  EX_mn2_e : 0.000211
  EX_zn2_e : 0.000104
  EX_ni2_e : 0.000099

Product: (mmol/gDw/h)
  EX_h2o_e : 45.887074
  EX_co2_e : 26.835801
  EX_h_e : 7.560645
  EX_pyr_e : 3.658412
  Auxiliary production reaction : 0.914982
  EX_acald_e : 0.525835
  EX_ac_e : 0.177936
  EX_ade_e : 0.000206
  DM_mththf_c : 0.000137
  DM_5drib_c : 0.000069
  DM_4crsol_c : 0.000068

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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