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_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 87: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b4382 b4384 b3708 b3008 b3752 b0871 b2779 b2925 b2097 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b2440 b3665 b3945 b2406 b0114 b1539 b2492 b0904 b1533 b3927 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.651045 (mmol/gDw/h)
  Minimum Production Rate : 0.149825 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.414238
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.782546
  EX_pi_e : 0.628002
  EX_so4_e : 0.163946
  EX_k_e : 0.127079
  EX_fe2_e : 0.010456
  EX_mg2_e : 0.005648
  EX_ca2_e : 0.003389
  EX_cl_e : 0.003389
  EX_cu2_e : 0.000462
  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 : 45.403120
  EX_co2_e : 26.558366
  EX_h_e : 8.472488
  EX_glyc__R_e : 1.739111
  Auxiliary production reaction : 0.149825
  EX_ade_e : 0.000438
  DM_mththf_c : 0.000292
  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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