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 : unagamuf_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b1241 b0351 b3831 b4069 b2744 b0910 b3752 b4152 b3115 b1849 b2296 b3617 b1612 b1611 b2883 b4122 b0411 b4388 b4138 b4123 b0621 b4381 b2406 b0114 b0529 b2492 b0904 b1518 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.358274 (mmol/gDw/h)
  Minimum Production Rate : 0.058422 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 989.710761
  EX_o2_e : 277.741969
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.726646
  EX_pi_e : 0.462436
  EX_so4_e : 0.090220
  EX_k_e : 0.069933
  EX_mg2_e : 0.003108
  EX_cl_e : 0.001865
  EX_ca2_e : 0.001865
  EX_cu2_e : 0.000254
  EX_mn2_e : 0.000248
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994246
  EX_h2o_e : 547.024496
  EX_co2_e : 26.929044
  EX_ac_e : 1.538580
  EX_succ_e : 0.827022
  EX_ura_e : 0.707486
  EX_gsn_e : 0.453417
  Auxiliary production reaction : 0.058422
  DM_mththf_c : 0.000161
  DM_5drib_c : 0.000081
  DM_4crsol_c : 0.000080

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