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 : glyc__R_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (7 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3399 b2502 b2744 b3708 b3008 b0871 b2925 b2097 b3124 b3236 b2690 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b3945 b0114 b0755 b3612 b1539 b2492 b0904 b1380   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.630821 (mmol/gDw/h)
  Minimum Production Rate : 2.141247 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.833709
  EX_o2_e : 276.861074
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.031066
  EX_pi_e : 0.608494
  EX_so4_e : 0.158853
  EX_k_e : 0.123132
  EX_mg2_e : 0.005472
  EX_ca2_e : 0.003283
  EX_cl_e : 0.003283
  EX_cu2_e : 0.000447
  EX_mn2_e : 0.000436
  EX_zn2_e : 0.000215
  EX_ni2_e : 0.000204
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989868
  EX_h2o_e : 543.901472
  EX_co2_e : 27.029618
  EX_glyc__R_e : 2.141247
  EX_ser__L_e : 0.217827
  DM_oxam_c : 0.000425
  DM_5drib_c : 0.000142
  DM_4crsol_c : 0.000141

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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