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 : fmnh2_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (12 of 15: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3916 b3426 b2242 b3553 b2744 b3114 b3952 b0903 b1638 b1779 b3962 b0477 b4139 b4267 b1033 b2361 b2291 b4015 b1014 b2799 b4265 b1723 b0529 b0306 b1539 b3605 b3028 b4321 b3415 b4476 b4266 b2285 b1378   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.396782 (mmol/gDw/h)
  Minimum Production Rate : 0.392147 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.779251
  EX_o2_e : 286.395178
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.853796
  EX_pi_e : 0.774885
  EX_so4_e : 0.099918
  EX_k_e : 0.077449
  EX_mg2_e : 0.003442
  EX_ca2_e : 0.002065
  EX_cl_e : 0.002065
  EX_cu2_e : 0.000281
  EX_mn2_e : 0.000274
  EX_zn2_e : 0.000135
  EX_ni2_e : 0.000128

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993627
  EX_h2o_e : 552.620068
  EX_co2_e : 37.047438
  Auxiliary production reaction : 0.392147
  DM_5drib_c : 0.000089
  DM_4crsol_c : 0.000088

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