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 : duri_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (36 of 50: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b2836 b3553 b4384 b3708 b3008 b3752 b0871 b2925 b2097 b2407 b1238 b2690 b0120 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b3945 b4381 b2406 b0114 b0886 b0509 b3125 b2366 b2492 b0904 b0591 b2578 b1533 b3927 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.758369 (mmol/gDw/h)
  Minimum Production Rate : 0.198069 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.225653
  EX_o2_e : 274.871923
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.983441
  EX_pi_e : 0.731527
  EX_so4_e : 0.190972
  EX_k_e : 0.148028
  EX_mg2_e : 0.006579
  EX_ca2_e : 0.003947
  EX_cl_e : 0.003947
  EX_cu2_e : 0.000538
  EX_mn2_e : 0.000524
  EX_zn2_e : 0.000259
  EX_ni2_e : 0.000245
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987820
  EX_h2o_e : 548.296883
  EX_co2_e : 26.096099
  Auxiliary production reaction : 0.198069
  EX_thym_e : 0.198069
  DM_oxam_c : 0.000849
  DM_5drib_c : 0.000509
  DM_4crsol_c : 0.000169

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