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 : fgam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4382 b3942 b1732 b4069 b4384 b3708 b3008 b1479 b3752 b3115 b1849 b2296 b2926 b2407 b3236 b2463 b2797 b3117 b1814 b4471 b2210 b3665 b3551 b4219 b1832 b1778 b0114 b2366 b2492 b0904 b1533 b3927 b3825 b1710 b2480 b0494 b1511 b0606 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.633409 (mmol/gDw/h)
  Minimum Production Rate : 0.403031 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.670117
  EX_o2_e : 277.101868
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.648963
  EX_pi_e : 1.014022
  EX_so4_e : 0.159505
  EX_k_e : 0.123637
  EX_mg2_e : 0.005495
  EX_ca2_e : 0.003297
  EX_cl_e : 0.003297
  EX_cu2_e : 0.000449
  EX_mn2_e : 0.000438
  EX_zn2_e : 0.000216
  EX_ni2_e : 0.000205
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989827
  EX_h2o_e : 547.454317
  EX_co2_e : 27.390656
  EX_fum_e : 0.661367
  Auxiliary production reaction : 0.403031
  EX_ac_e : 0.368762
  EX_ade_e : 0.000426
  EX_mththf_e : 0.000284
  DM_5drib_c : 0.000143
  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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