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 : 5mthf_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (32 of 120: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b2836 b4382 b4069 b4384 b3708 b3008 b0910 b3115 b1849 b2296 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b2440 b0596 b0261 b0507 b3709 b2406 b3161 b0112 b2975 b0114 b3603 b0886 b1539 b2492 b0904 b2578 b1533 b3927 b1473 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.690467 (mmol/gDw/h)
  Minimum Production Rate : 0.249033 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.734499
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.266151
  EX_pi_e : 0.666028
  EX_so4_e : 0.173873
  EX_k_e : 0.134774
  EX_fe2_e : 0.011090
  EX_mg2_e : 0.005990
  EX_ca2_e : 0.003594
  EX_cl_e : 0.003594
  EX_cu2_e : 0.000490
  EX_mn2_e : 0.000477
  EX_zn2_e : 0.000235
  EX_ni2_e : 0.000223
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 48.458927
  EX_co2_e : 25.741484
  EX_h_e : 8.740067
  EX_ac_e : 0.401980
  Auxiliary production reaction : 0.249033
  EX_etha_e : 0.065171
  DM_oxam_c : 0.000773
  DM_5drib_c : 0.000463
  DM_4crsol_c : 0.000154

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