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 : hisp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3752 b0871 b3617 b1238 b2883 b1982 b1623 b0261 b0411 b4381 b0112 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.581044 (mmol/gDw/h)
  Minimum Production Rate : 1.377313 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.786064
  EX_nh4_e : 11.430215
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.937792
  EX_so4_e : 0.146319
  EX_k_e : 0.113416
  EX_fe2_e : 0.009332
  EX_mg2_e : 0.005041
  EX_ca2_e : 0.003024
  EX_cl_e : 0.003024
  EX_cu2_e : 0.000412
  EX_mn2_e : 0.000402
  EX_zn2_e : 0.000198
  EX_ni2_e : 0.000188
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 49.447184
  EX_co2_e : 22.770392
  EX_h_e : 9.116540
  Auxiliary production reaction : 1.377313
  EX_thymd_e : 0.511524
  DM_5drib_c : 0.000390
  DM_4crsol_c : 0.000130

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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