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 : adpglc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b2407 b2797 b3117 b1814 b4471 b3616 b3589 b3449 b3665 b2239 b2406 b0112 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b1533 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.544383 (mmol/gDw/h)
  Minimum Production Rate : 0.815232 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.475159
  EX_o2_e : 271.348030
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.955449
  EX_pi_e : 2.155578
  EX_so4_e : 0.137087
  EX_k_e : 0.106260
  EX_mg2_e : 0.004723
  EX_ca2_e : 0.002834
  EX_cl_e : 0.002834
  EX_cu2_e : 0.000386
  EX_mn2_e : 0.000376
  EX_zn2_e : 0.000186
  EX_ni2_e : 0.000176
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991257
  EX_h2o_e : 546.258385
  EX_co2_e : 20.473861
  EX_ac_e : 2.068394
  Auxiliary production reaction : 0.815232
  EX_mththf_e : 0.000244
  DM_5drib_c : 0.000122
  DM_4crsol_c : 0.000121

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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