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 : dutp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (38 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2502 b2744 b2930 b4232 b3697 b3925 b0871 b3617 b1238 b3236 b0907 b1982 b3946 b2210 b0825 b0675 b2361 b4381 b0114 b0529 b2492 b0904 b0516 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.400966 (mmol/gDw/h)
  Minimum Production Rate : 1.303982 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.319228
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.939443
  EX_pi_e : 4.298721
  EX_so4_e : 0.100971
  EX_k_e : 0.078266
  EX_fe2_e : 0.006440
  EX_mg2_e : 0.003478
  EX_ca2_e : 0.002087
  EX_cl_e : 0.002087
  EX_cu2_e : 0.000284
  EX_mn2_e : 0.000277
  EX_zn2_e : 0.000137
  EX_ni2_e : 0.000130
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 49.383092
  EX_co2_e : 25.664649
  EX_h_e : 5.077625
  EX_pyr_e : 1.392310
  Auxiliary production reaction : 1.303982
  EX_acald_e : 0.981395
  EX_alltn_e : 0.000270
  DM_mththf_c : 0.000180
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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