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 : coa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b2836 b3399 b4382 b1241 b0351 b4069 b4384 b2744 b3708 b3115 b1849 b2296 b3617 b0160 b2883 b2797 b3117 b1814 b4471 b1623 b3665 b2361 b2291 b0411 b2406 b0112 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b1533 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.518571 (mmol/gDw/h)
  Minimum Production Rate : 0.517704 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.926785
  EX_o2_e : 270.721799
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.224449
  EX_pi_e : 2.053329
  EX_so4_e : 0.648291
  EX_k_e : 0.101221
  EX_mg2_e : 0.004499
  EX_ca2_e : 0.002699
  EX_cl_e : 0.002699
  EX_cu2_e : 0.000368
  EX_mn2_e : 0.000358
  EX_zn2_e : 0.000177
  EX_ni2_e : 0.000167
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991671
  EX_h2o_e : 545.874460
  EX_co2_e : 22.348226
  EX_ac_e : 2.746938
  Auxiliary production reaction : 0.517704
  EX_mththf_e : 0.000232
  DM_5drib_c : 0.000117
  DM_4crsol_c : 0.000116

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