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 : imacp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 103: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3752 b3115 b1849 b2296 b2779 b2407 b0907 b1982 b3616 b3589 b3665 b0411 b4381 b0112 b0114 b0529 b2492 b0904 b3662 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.365000 (mmol/gDw/h)
  Minimum Production Rate : 1.399516 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.328995
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.742233
  EX_pi_e : 1.751598
  EX_so4_e : 0.091914
  EX_k_e : 0.071246
  EX_fe2_e : 0.005862
  EX_mg2_e : 0.003166
  EX_ca2_e : 0.001900
  EX_cl_e : 0.001900
  EX_cu2_e : 0.000259
  EX_mn2_e : 0.000252
  EX_zn2_e : 0.000124
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 52.445744
  EX_co2_e : 34.407541
  EX_h_e : 7.259894
  Auxiliary production reaction : 1.399516
  EX_ac_e : 1.105865
  EX_ade_e : 0.000246
  DM_mththf_c : 0.000164
  DM_5drib_c : 0.000082
  DM_4crsol_c : 0.000081

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