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 : pant__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (73 of 93: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3942 b1732 b4069 b3708 b3115 b1849 b2296 b2925 b2097 b3236 b1779 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b2440 b4381 b0511 b0114 b1539 b2492 b0904 b1533 b3927 b0515 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.399710 (mmol/gDw/h)
  Minimum Production Rate : 0.509558 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 31.171226
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.316836
  EX_pi_e : 0.385563
  EX_so4_e : 0.100655
  EX_k_e : 0.078021
  EX_fe2_e : 0.006420
  EX_mg2_e : 0.003467
  EX_ca2_e : 0.002080
  EX_cl_e : 0.002080
  EX_cu2_e : 0.000283
  EX_mn2_e : 0.000276
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129

Product: (mmol/gDw/h)
  EX_h2o_e : 43.089016
  EX_co2_e : 32.533774
  EX_h_e : 8.183560
  EX_ac_e : 4.001305
  Auxiliary production reaction : 0.509558
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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