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 : cph4_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (32 of 43: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3553 b3399 b1241 b0351 b4069 b4384 b2744 b2297 b2458 b2779 b2926 b3617 b2407 b0907 b1982 b1033 b4374 b0675 b2361 b2291 b0261 b0112 b2789 b3127 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.405008 (mmol/gDw/h)
  Minimum Production Rate : 1.552373 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 982.624792
  EX_o2_e : 277.635379
  EX_nh4_e : 12.136368
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.390673
  EX_so4_e : 0.101989
  EX_k_e : 0.079055
  EX_mg2_e : 0.003513
  EX_cl_e : 0.002108
  EX_ca2_e : 0.002108
  EX_cu2_e : 0.000287
  EX_mn2_e : 0.000280
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000131
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993495
  EX_h2o_e : 550.060021
  EX_co2_e : 23.843501
  EX_ac_e : 4.332004
  Auxiliary production reaction : 1.552373
  DM_oxam_c : 0.000453
  DM_5drib_c : 0.000272
  EX_glyclt_e : 0.000181
  DM_4crsol_c : 0.000090

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