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 : 2h3oppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (48 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b3115 b1849 b2296 b2779 b0160 b1779 b1982 b3616 b3589 b0675 b2361 b0261 b2913 b4381 b2406 b0112 b0114 b0529 b2492 b0904   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.426186 (mmol/gDw/h)
  Minimum Production Rate : 0.402954 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.886979
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.420029
  EX_pi_e : 0.411102
  EX_so4_e : 0.107322
  EX_k_e : 0.083189
  EX_fe2_e : 0.006845
  EX_mg2_e : 0.003697
  EX_ca2_e : 0.002218
  EX_cl_e : 0.002218
  EX_cu2_e : 0.000302
  EX_mn2_e : 0.000294
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000138
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 41.487713
  EX_co2_e : 25.778980
  EX_h_e : 8.061543
  EX_ac_e : 2.108114
  DM_oxam_c : 0.817252
  DM_5drib_c : 0.805909
  DM_4crsol_c : 0.805718
  Auxiliary production reaction : 0.402954

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