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 : q8h2_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (76 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b0474 b2518 b1241 b0351 b2502 b2744 b2930 b4232 b3697 b3925 b0871 b3617 b1779 b1982 b3946 b0825 b4374 b0675 b2361 b4381 b0114 b2492 b0904 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.562013 (mmol/gDw/h)
  Minimum Production Rate : 0.020607 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.431152
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.902243
  EX_pi_e : 0.542121
  EX_so4_e : 0.141526
  EX_k_e : 0.109701
  EX_fe2_e : 0.009026
  EX_mg2_e : 0.004875
  EX_ca2_e : 0.002925
  EX_cl_e : 0.002925
  EX_cu2_e : 0.000398
  EX_mn2_e : 0.000388
  EX_zn2_e : 0.000192
  EX_ni2_e : 0.000182
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 45.613204
  EX_co2_e : 27.610354
  EX_h_e : 7.091432
  EX_acald_e : 1.263391
  EX_pyr_e : 0.766096
  DM_oxam_c : 0.328787
  EX_thymd_e : 0.251880
  DM_mththf_c : 0.062074
  Auxiliary production reaction : 0.020607
  DM_5drib_c : 0.000126
  DM_4crsol_c : 0.000125

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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