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 (83 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b2242 b3553 b4382 b0474 b2518 b3831 b4384 b3752 b2781 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1759 b1033 b2440 b4161 b4015 b0411 b4138 b4123 b0621 b0306 b3605 b3028 b3918 b1912 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.567870 (mmol/gDw/h)
  Minimum Production Rate : 0.299158 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 30.307416
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.936842
  EX_pi_e : 0.547771
  EX_so4_e : 0.143001
  EX_k_e : 0.110844
  EX_fe2_e : 0.009121
  EX_mg2_e : 0.004926
  EX_ca2_e : 0.002956
  EX_cl_e : 0.002956
  EX_cu2_e : 0.000403
  EX_mn2_e : 0.000392
  EX_zn2_e : 0.000194
  EX_ni2_e : 0.000183
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 48.815663
  EX_co2_e : 30.918723
  EX_h_e : 7.207444
  EX_succ_e : 0.592171
  EX_thymd_e : 0.299158
  EX_ura_e : 0.102786
  EX_for_e : 0.001393
  DM_5drib_c : 0.000128
  DM_4crsol_c : 0.000127

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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