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 : quln_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (94 of 106: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b2242 b3553 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1779 b3946 b0825 b1033 b1415 b4015 b4138 b4123 b0621 b3028 b1380 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.441166 (mmol/gDw/h)
  Minimum Production Rate : 0.312852 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.348987
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.077408
  EX_pi_e : 0.425551
  EX_so4_e : 0.111094
  EX_k_e : 0.086113
  EX_fe2_e : 0.007086
  EX_mg2_e : 0.003827
  EX_ca2_e : 0.002296
  EX_cl_e : 0.002296
  EX_cu2_e : 0.000313
  EX_mn2_e : 0.000305
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 46.578276
  EX_co2_e : 32.591144
  EX_h_e : 8.547692
  EX_ac_e : 2.635437
  EX_succ_e : 0.460044
  Auxiliary production reaction : 0.312852
  DM_5drib_c : 0.000099
  DM_4crsol_c : 0.000098

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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