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 (103 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b2779 b2690 b1302 b2662 b4014 b2976 b0614 b0726 b3945 b0507 b2913 b2587 b0452 b2975 b0114 b3603   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.674069 (mmol/gDw/h)
  Minimum Production Rate : 1.170441 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.179592
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.279884
  EX_pi_e : 0.650211
  EX_so4_e : 0.169744
  EX_k_e : 0.131573
  EX_fe2_e : 0.010826
  EX_mg2_e : 0.005848
  EX_ca2_e : 0.003509
  EX_cl_e : 0.003509
  EX_cu2_e : 0.000478
  EX_mn2_e : 0.000466
  EX_zn2_e : 0.000230
  EX_ni2_e : 0.000218
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 47.003354
  EX_co2_e : 28.032623
  EX_h_e : 7.756937
  EX_pyr_e : 1.170441
  EX_ac_e : 0.392433
  EX_dxylnt_e : 0.000451
  EX_mththf_e : 0.000302
  DM_5drib_c : 0.000152
  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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