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 (31 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b2836 b4382 b1241 b0351 b4069 b4384 b3708 b2297 b2458 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b0261 b0507 b2406 b0112 b0114 b1539 b2492 b0904 b1533 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.524949 (mmol/gDw/h)
  Minimum Production Rate : 0.261801 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.084491
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.026193
  EX_so4_e : 0.655794
  EX_pi_e : 0.506369
  EX_k_e : 0.102466
  EX_fe2_e : 0.008431
  EX_mg2_e : 0.004554
  EX_ca2_e : 0.002732
  EX_cl_e : 0.002732
  EX_cu2_e : 0.000372
  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 : 43.088832
  EX_co2_e : 23.203803
  EX_h_e : 9.961068
  EX_ac_e : 3.041700
  DM_oxam_c : 0.524189
  DM_5drib_c : 0.262153
  EX_meoh_e : 0.261802
  DM_amob_c : 0.261802
  Auxiliary production reaction : 0.261801
  EX_glyclt_e : 0.000351
  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