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 : malcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b2836 b3399 b4382 b1241 b0351 b4069 b2744 b3708 b3115 b1849 b2296 b3617 b2883 b1982 b2797 b3117 b1814 b4471 b2440 b0675 b2361 b0261 b0411 b3709 b4381 b2239 b2406 b3161 b0112 b2975 b0114 b3603 b0509 b3125 b2366 b2492 b0904 b0591 b1533 b0508 b1473 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.438337 (mmol/gDw/h)
  Minimum Production Rate : 0.643836 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 19.699661
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.253871
  EX_pi_e : 2.355390
  EX_so4_e : 0.754218
  EX_k_e : 0.085560
  EX_fe2_e : 0.007040
  EX_mg2_e : 0.003803
  EX_ca2_e : 0.002282
  EX_cl_e : 0.002282
  EX_cu2_e : 0.000311
  EX_mn2_e : 0.000303
  EX_zn2_e : 0.000149
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 45.739093
  EX_co2_e : 20.618299
  EX_h_e : 9.579682
  EX_ac_e : 2.953866
  Auxiliary production reaction : 0.643836
  DM_oxam_c : 0.011960
  EX_g3pe_e : 0.001060
  DM_5drib_c : 0.000294
  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
Contact