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 (70 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b2836 b4382 b4069 b4384 b3708 b3008 b3115 b1849 b2296 b0030 b2407 b3124 b1982 b2797 b3117 b1814 b4471 b0596 b0261 b3709 b2406 b3161 b0112 b0653 b4077 b2663 b0114 b2366 b2492 b0904 b3653 b2578 b1533 b3927 b0514 b4141 b1798 b3662 b0221   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.709711 (mmol/gDw/h)
  Minimum Production Rate : 0.150316 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.791645
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.966241
  EX_pi_e : 0.684591
  EX_so4_e : 0.178719
  EX_k_e : 0.138531
  EX_fe2_e : 0.011399
  EX_mg2_e : 0.006157
  EX_ca2_e : 0.003694
  EX_cl_e : 0.003694
  EX_cu2_e : 0.000503
  EX_mn2_e : 0.000490
  EX_zn2_e : 0.000242
  EX_ni2_e : 0.000229
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 45.626551
  EX_co2_e : 25.380307
  EX_h_e : 7.687456
  EX_ac_e : 0.413184
  DM_oxam_c : 0.301426
  DM_5drib_c : 0.301108
  DM_4crsol_c : 0.300790
  EX_glyc__R_e : 0.150316

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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