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 : dgdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (33 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3399 b3942 b1732 b1241 b0351 b4069 b2744 b3708 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2779 b3617 b0517 b2797 b3117 b1814 b4471 b3946 b0825 b4381 b2406 b0114 b1539 b2492 b0904 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.356592 (mmol/gDw/h)
  Minimum Production Rate : 0.349625 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 31.552263
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.599292
  EX_pi_e : 1.043222
  EX_so4_e : 0.089797
  EX_k_e : 0.069604
  EX_fe2_e : 0.005727
  EX_mg2_e : 0.003093
  EX_ca2_e : 0.001856
  EX_cl_e : 0.001856
  EX_cu2_e : 0.000253
  EX_mn2_e : 0.000246
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000115

Product: (mmol/gDw/h)
  EX_h2o_e : 45.398466
  EX_co2_e : 31.436723
  EX_h_e : 9.887437
  EX_ac_e : 5.207520
  Auxiliary production reaction : 0.349625
  EX_glyc__R_e : 0.004905
  EX_mththf_e : 0.000160
  DM_5drib_c : 0.000080
  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
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