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 : ahcys_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b2836 b4069 b2744 b3708 b3008 b2297 b2458 b1238 b2883 b2687 b2797 b3117 b1814 b4471 b4381 b2406 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b2366 b2492 b0904 b2947 b2578 b1533 b3927 b3662 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.724005 (mmol/gDw/h)
  Minimum Production Rate : 0.230660 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.318216
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.203155
  EX_pi_e : 0.698380
  EX_so4_e : 0.412979
  EX_k_e : 0.141321
  EX_mg2_e : 0.006281
  EX_fe2_e : 0.005975
  EX_fe3_e : 0.005653
  EX_ca2_e : 0.003768
  EX_cl_e : 0.003768
  EX_cu2_e : 0.000513
  EX_mn2_e : 0.000500
  EX_zn2_e : 0.000247
  EX_ni2_e : 0.000234
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 48.094730
  EX_co2_e : 25.749341
  EX_h_e : 8.232907
  EX_ac_e : 0.652166
  Auxiliary production reaction : 0.230660
  DM_5drib_c : 0.000163
  DM_4crsol_c : 0.000161

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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