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 : datp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (51 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b0871 b0030 b2407 b2883 b3616 b3589 b4381 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b0529 b2492 b0904 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.649933 (mmol/gDw/h)
  Minimum Production Rate : 0.704841 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.903197
  EX_o2_e : 273.102775
  EX_nh4_e : 10.543422
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.741451
  EX_so4_e : 0.163666
  EX_k_e : 0.126862
  EX_mg2_e : 0.005638
  EX_ca2_e : 0.003383
  EX_cl_e : 0.003383
  EX_cu2_e : 0.000461
  EX_mn2_e : 0.000449
  EX_zn2_e : 0.000222
  EX_ni2_e : 0.000210
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989561
  EX_h2o_e : 550.746294
  EX_co2_e : 23.720815
  EX_acald_e : 1.276283
  Auxiliary production reaction : 0.704841
  DM_mththf_c : 0.000291
  DM_5drib_c : 0.000146
  DM_4crsol_c : 0.000145

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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