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 (38 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3399 b4382 b3942 b1732 b1241 b0351 b4069 b2502 b4384 b2744 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b3617 b3236 b1779 b1982 b3946 b2210 b0825 b0675 b2361 b2291 b0261 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.494126 (mmol/gDw/h)
  Minimum Production Rate : 0.376992 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.528824
  EX_nh4_e : 10.206942
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.230620
  EX_so4_e : 0.124431
  EX_k_e : 0.096450
  EX_fe2_e : 0.007936
  EX_mg2_e : 0.004287
  EX_cl_e : 0.002572
  EX_ca2_e : 0.002572
  EX_cu2_e : 0.000350
  EX_mn2_e : 0.000341
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 50.073448
  EX_co2_e : 24.906124
  EX_h_e : 9.321885
  EX_his__L_e : 1.081961
  EX_thymd_e : 0.435004
  Auxiliary production reaction : 0.376992
  EX_ac_e : 0.287673
  DM_oxam_c : 0.000553
  DM_5drib_c : 0.000332
  DM_4crsol_c : 0.000110

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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