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 : aicar_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3553 b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b2502 b2744 b0871 b2779 b2926 b3617 b1982 b1033 b4374 b0675 b2361 b2291 b0261 b4388 b0112 b2789 b3127 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.430086 (mmol/gDw/h)
  Minimum Production Rate : 1.398107 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.513471
  EX_nh4_e : 10.237803
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.812971
  EX_so4_e : 0.108304
  EX_k_e : 0.083950
  EX_fe2_e : 0.006908
  EX_mg2_e : 0.003731
  EX_ca2_e : 0.002239
  EX_cl_e : 0.002239
  EX_cu2_e : 0.000305
  EX_mn2_e : 0.000297
  EX_zn2_e : 0.000147
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 48.801047
  EX_co2_e : 24.859735
  EX_h_e : 9.545482
  EX_acald_e : 2.450872
  Auxiliary production reaction : 1.398107
  DM_oxam_c : 0.000481
  DM_5drib_c : 0.000289
  EX_glyclt_e : 0.000288
  DM_4crsol_c : 0.000096

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