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 : trp__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (77 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3399 b4382 b4069 b2502 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b3236 b1779 b2690 b1982 b2797 b3117 b1814 b4471 b2210 b0675 b2361 b0261 b3945 b3709 b4381 b2406 b3161 b0112 b2868 b0114 b2366 b2492 b0904 b2947 b2578 b1533 b3927 b3821 b1473 b0594   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.595932 (mmol/gDw/h)
  Minimum Production Rate : 0.355263 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.417544
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.212252
  EX_pi_e : 0.574840
  EX_so4_e : 0.150068
  EX_k_e : 0.116322
  EX_fe2_e : 0.009571
  EX_mg2_e : 0.005170
  EX_ca2_e : 0.003102
  EX_cl_e : 0.003102
  EX_cu2_e : 0.000423
  EX_mn2_e : 0.000412
  EX_zn2_e : 0.000203
  EX_ni2_e : 0.000192
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.544632
  EX_co2_e : 27.818594
  EX_h_e : 8.117196
  EX_ac_e : 1.865299
  Auxiliary production reaction : 0.355263
  EX_xan_e : 0.015593
  EX_ade_e : 0.000667
  DM_5drib_c : 0.000400
  DM_4crsol_c : 0.000133

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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