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 : 6hmhptpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (93 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b3399 b0586 b1241 b0351 b4069 b2502 b2744 b3708 b3115 b1849 b2296 b2779 b3962 b1982 b4139 b0104 b2797 b3117 b1814 b4471 b3616 b3589 b4267 b4374 b0675 b2361 b2291 b1014 b4014 b0261 b2976 b0822 b0507 b2913 b0112 b2975 b0114 b3603 b2366 b0306 b3605 b2492 b0904 b1533 b3821 b1380 b0325 b0508 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.320806 (mmol/gDw/h)
  Minimum Production Rate : 0.115258 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.686080
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.886041
  EX_so4_e : 0.925501
  EX_pi_e : 0.539967
  EX_k_e : 0.062619
  EX_fe2_e : 0.005152
  EX_mg2_e : 0.002783
  EX_ca2_e : 0.001670
  EX_cl_e : 0.001670
  EX_cu2_e : 0.000227
  EX_mn2_e : 0.000222
  EX_zn2_e : 0.000109
  EX_ni2_e : 0.000104

Product: (mmol/gDw/h)
  EX_h2o_e : 47.680971
  EX_co2_e : 36.136129
  EX_h_e : 5.223739
  EX_ac_e : 2.543539
  EX_met__L_e : 0.844716
  EX_dxylnt_e : 0.115472
  Auxiliary production reaction : 0.115258
  DM_oxam_c : 0.000359
  DM_5drib_c : 0.000215
  DM_4crsol_c : 0.000072

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