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 : gtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3752 b3115 b1849 b2296 b2926 b2407 b3236 b1982 b3616 b3589 b2210 b2406 b0112 b0511 b0114 b0529 b2492 b0904 b0516 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.509745 (mmol/gDw/h)
  Minimum Production Rate : 0.977254 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.701821
  EX_nh4_e : 10.392839
  EX_glc__D_e : 10.000000
  EX_pi_e : 3.423464
  EX_so4_e : 0.128364
  EX_k_e : 0.099499
  EX_fe2_e : 0.008187
  EX_mg2_e : 0.004422
  EX_ca2_e : 0.002653
  EX_cl_e : 0.002653
  EX_cu2_e : 0.000361
  EX_mn2_e : 0.000352
  EX_zn2_e : 0.000174
  EX_ni2_e : 0.000165
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 53.002421
  EX_co2_e : 25.856837
  EX_h_e : 9.339417
  EX_ac_e : 1.722547
  Auxiliary production reaction : 0.977254
  EX_xan_e : 0.000343
  DM_mththf_c : 0.000228
  DM_5drib_c : 0.000115
  DM_4crsol_c : 0.000114

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
Contact