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 : adn_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (35 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b0030 b2883 b1982 b3616 b3589 b0411 b4381 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.604809 (mmol/gDw/h)
  Minimum Production Rate : 0.983450 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.717369
  EX_nh4_e : 11.451176
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.583403
  EX_so4_e : 0.152303
  EX_k_e : 0.118055
  EX_fe2_e : 0.009714
  EX_mg2_e : 0.005247
  EX_cl_e : 0.003148
  EX_ca2_e : 0.003148
  EX_cu2_e : 0.000429
  EX_mn2_e : 0.000418
  EX_zn2_e : 0.000206
  EX_ni2_e : 0.000195
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 49.099578
  EX_co2_e : 22.306214
  EX_h_e : 10.476516
  EX_acald_e : 1.515626
  Auxiliary production reaction : 0.983450
  EX_ade_e : 0.000407
  DM_mththf_c : 0.000271
  DM_5drib_c : 0.000136
  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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