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 : btn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (30 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b3617 b2407 b1982 b2797 b3117 b1814 b4471 b0261 b0507 b2406 b0112 b0452 b0114 b2366 b2492 b0904 b1533 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.525731 (mmol/gDw/h)
  Minimum Production Rate : 0.245843 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.436694
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.891021
  EX_so4_e : 0.624075
  EX_pi_e : 0.507123
  EX_k_e : 0.102619
  EX_fe2_e : 0.008444
  EX_mg2_e : 0.004561
  EX_ca2_e : 0.002736
  EX_cl_e : 0.002736
  EX_cu2_e : 0.000373
  EX_mn2_e : 0.000363
  EX_zn2_e : 0.000179
  EX_ni2_e : 0.000170
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 43.096331
  EX_co2_e : 23.557673
  EX_h_e : 9.926866
  EX_ac_e : 3.127971
  DM_oxam_c : 0.492274
  DM_5drib_c : 0.246196
  EX_meoh_e : 0.245844
  DM_amob_c : 0.245844
  Auxiliary production reaction : 0.245843
  EX_glyclt_e : 0.000352
  DM_4crsol_c : 0.000117

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