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 (96 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b3399 b4382 b4069 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b2779 b0583 b2883 b2690 b1982 b2797 b3117 b1814 b4471 b0675 b2361 b0261 b0411 b3945 b0507 b3709 b4381 b2406 b3161 b0112 b2975 b0114 b3603 b2366 b2492 b0904 b2578 b1533 b3927 b3825 b1380 b1473 b0494 b3662 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.556101 (mmol/gDw/h)
  Minimum Production Rate : 0.331518 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.305825
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.684048
  EX_pi_e : 0.536418
  EX_so4_e : 0.140037
  EX_k_e : 0.108547
  EX_fe2_e : 0.008932
  EX_mg2_e : 0.004824
  EX_ca2_e : 0.002895
  EX_cl_e : 0.002895
  EX_cu2_e : 0.000394
  EX_mn2_e : 0.000384
  EX_zn2_e : 0.000190
  EX_ni2_e : 0.000180
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 46.045878
  EX_co2_e : 26.593048
  EX_h_e : 8.212072
  EX_pyr_e : 2.085262
  Auxiliary production reaction : 0.331518
  EX_ac_e : 0.323754
  DM_oxam_c : 0.015173
  DM_5drib_c : 0.000373
  DM_4crsol_c : 0.000124

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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