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 : imp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4384 b2744 b3708 b3008 b3752 b0871 b2883 b1982 b2797 b3117 b1814 b4471 b4381 b2868 b4064 b4464 b0114 b0886 b2366 b0529 b2492 b0904 b1533 b3927 b3821 b2413 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.777845 (mmol/gDw/h)
  Minimum Production Rate : 0.179006 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.121717
  EX_o2_e : 275.064389
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.119299
  EX_pi_e : 0.929320
  EX_so4_e : 0.195877
  EX_k_e : 0.151830
  EX_mg2_e : 0.006748
  EX_ca2_e : 0.004049
  EX_cl_e : 0.004049
  EX_cu2_e : 0.000551
  EX_mn2_e : 0.000537
  EX_zn2_e : 0.000265
  EX_ni2_e : 0.000251
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_fe3_e : 999.987507
  EX_h2o_e : 548.787409
  EX_co2_e : 26.278625
  Auxiliary production reaction : 0.179006
  EX_ade_e : 0.000523
  DM_mththf_c : 0.000348
  DM_5drib_c : 0.000175
  DM_4crsol_c : 0.000173

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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