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 : pyr_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 20
  Gene deletion: b0871 b2297 b2458 b2779 b2925 b2097 b1779 b1525 b3946 b0825 b2661 b4014 b2976 b0726 b0507 b2975 b0114 b3603 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.672052 (mmol/gDw/h)
  Minimum Production Rate : 1.197464 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.736420
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.258101
  EX_pi_e : 0.648265
  EX_so4_e : 0.169236
  EX_k_e : 0.131180
  EX_fe2_e : 0.010794
  EX_mg2_e : 0.005830
  EX_ca2_e : 0.003498
  EX_cl_e : 0.003498
  EX_cu2_e : 0.000476
  EX_mn2_e : 0.000464
  EX_zn2_e : 0.000229
  EX_ni2_e : 0.000217
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 46.049552
  EX_co2_e : 27.105062
  EX_h_e : 8.697398
  EX_pyr_e : 1.197464
  EX_for_e : 0.933146
  EX_ac_e : 0.391259
  EX_dxylnt_e : 0.000450
  DM_5drib_c : 0.000151
  DM_4crsol_c : 0.000150

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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