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 : 5aizc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (16 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3115 b1849 b2296 b0030 b2407 b3236 b1982 b3616 b3589 b0261 b0507 b2406 b0112 b0511 b0114 b0529 b2492 b0904 b0515 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.475042 (mmol/gDw/h)
  Minimum Production Rate : 1.820812 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.708397
  EX_nh4_e : 10.594979
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.279041
  EX_so4_e : 0.119625
  EX_k_e : 0.092725
  EX_fe2_e : 0.007630
  EX_mg2_e : 0.004121
  EX_ca2_e : 0.002473
  EX_cl_e : 0.002473
  EX_cu2_e : 0.000337
  EX_mn2_e : 0.000328
  EX_zn2_e : 0.000162
  EX_ni2_e : 0.000153
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 46.194710
  EX_co2_e : 19.078876
  EX_h_e : 14.166150
  EX_ac_e : 2.515579
  Auxiliary production reaction : 1.820812
  EX_xan_e : 0.000532
  DM_5drib_c : 0.000319
  EX_glyclt_e : 0.000318
  DM_4crsol_c : 0.000106

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