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 : cph4_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 43: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b2926 b3617 b0030 b2883 b1982 b1033 b0261 b0411 b4381 b0112 b2868 b4064 b4464 b0114 b0509 b3125 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.486553 (mmol/gDw/h)
  Minimum Production Rate : 0.576501 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.692064
  EX_nh4_e : 10.150285
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.469331
  EX_so4_e : 0.122524
  EX_k_e : 0.094972
  EX_fe2_e : 0.007815
  EX_mg2_e : 0.004221
  EX_ca2_e : 0.002533
  EX_cl_e : 0.002533
  EX_cu2_e : 0.000345
  EX_mn2_e : 0.000336
  EX_zn2_e : 0.000166
  EX_ni2_e : 0.000157
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 49.435242
  EX_co2_e : 24.785288
  EX_h_e : 9.942699
  EX_thymd_e : 1.005164
  Auxiliary production reaction : 0.576501
  EX_acald_e : 0.576501
  EX_ade_e : 0.000544
  DM_5drib_c : 0.000326
  DM_4crsol_c : 0.000109

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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