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 : q8h2_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b4382 b4384 b2744 b3708 b3008 b0871 b2779 b2925 b2097 b0160 b2797 b3117 b1814 b4471 b3946 b0825 b3665 b0675 b2361 b2291 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b1533 b3927 b3821   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.650589 (mmol/gDw/h)
  Minimum Production Rate : 0.032156 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.253500
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.026307
  EX_pi_e : 0.627562
  EX_so4_e : 0.163831
  EX_k_e : 0.126990
  EX_fe2_e : 0.010449
  EX_mg2_e : 0.005644
  EX_cl_e : 0.003386
  EX_ca2_e : 0.003386
  EX_cu2_e : 0.000461
  EX_mn2_e : 0.000450
  EX_zn2_e : 0.000222
  EX_ni2_e : 0.000210
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 45.016067
  EX_co2_e : 27.482093
  EX_h_e : 7.390729
  EX_glyc__R_e : 1.412857
  Auxiliary production reaction : 0.032156
  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.

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Last updated: 21-Sep-2023
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