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 (79 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 44
  Gene deletion: b3399 b4069 b2502 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b3115 b1849 b2296 b1982 b2797 b3117 b1814 b4471 b3449 b3946 b0825 b1623 b3665 b4374 b0675 b2361 b2291 b0261 b3709 b3161 b0112 b0114 b2366 b2492 b0904 b3035 b2578 b1533 b3927 b1473 b0494 b3447 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.496202 (mmol/gDw/h)
  Minimum Production Rate : 0.315285 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.121077
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.992289
  EX_pi_e : 0.478640
  EX_so4_e : 0.124954
  EX_k_e : 0.096855
  EX_fe2_e : 0.007970
  EX_mg2_e : 0.004305
  EX_ca2_e : 0.002583
  EX_cl_e : 0.002583
  EX_cu2_e : 0.000352
  EX_mn2_e : 0.000343
  EX_zn2_e : 0.000169
  EX_ni2_e : 0.000160
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 45.416921
  EX_co2_e : 26.886939
  EX_h_e : 8.380351
  EX_pyr_e : 2.898818
  Auxiliary production reaction : 0.315285
  EX_ac_e : 0.288882
  EX_ade_e : 0.000555
  DM_5drib_c : 0.000333
  DM_4crsol_c : 0.000111

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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