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 : thymd_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b2242 b3553 b3831 b3614 b0910 b2781 b0030 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b0651 b2162 b1759 b1033 b4015 b0411 b4138 b4123 b0621 b4381 b0452 b0306 b3605 b3028 b3918 b4042 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.562841 (mmol/gDw/h)
  Minimum Production Rate : 0.296418 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.571012
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.875408
  EX_pi_e : 0.542920
  EX_so4_e : 0.141735
  EX_k_e : 0.109863
  EX_fe2_e : 0.009040
  EX_mg2_e : 0.004883
  EX_ca2_e : 0.002930
  EX_cl_e : 0.002930
  EX_cu2_e : 0.000399
  EX_mn2_e : 0.000389
  EX_zn2_e : 0.000192
  EX_ni2_e : 0.000182
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 48.915167
  EX_co2_e : 31.176815
  EX_h_e : 7.143614
  EX_succ_e : 0.586926
  EX_thymd_e : 0.296418
  EX_ura_e : 0.101967
  EX_for_e : 0.001381
  DM_5drib_c : 0.000127
  DM_4crsol_c : 0.000126

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
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