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 : btn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3708 b3008 b0910 b3752 b0871 b3617 b2407 b1982 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b0411 b0112 b0114 b2366 b2492 b0904 b1533 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.603672 (mmol/gDw/h)
  Minimum Production Rate : 0.181871 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.878167
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.792696
  EX_pi_e : 0.582305
  EX_so4_e : 0.515758
  EX_k_e : 0.117832
  EX_fe2_e : 0.009696
  EX_mg2_e : 0.005237
  EX_ca2_e : 0.003142
  EX_cl_e : 0.003142
  EX_cu2_e : 0.000428
  EX_mn2_e : 0.000417
  EX_zn2_e : 0.000206
  EX_ni2_e : 0.000195
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 45.083112
  EX_co2_e : 25.686272
  EX_h_e : 6.274258
  EX_acald_e : 1.948223
  DM_5drib_c : 0.182276
  EX_meoh_e : 0.181872
  DM_amob_c : 0.181872
  Auxiliary production reaction : 0.181871
  DM_4crsol_c : 0.000135

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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