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 : adphep_DD_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b2836 b4382 b4069 b4384 b3708 b3008 b0910 b3752 b2297 b2458 b2407 b1779 b1982 b2688 b2797 b3117 b1814 b4471 b0261 b2406 b0114 b1539 b2492 b0904 b0591 b2578 b1533 b3927 b3662 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.640058 (mmol/gDw/h)
  Minimum Production Rate : 0.270811 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.686501
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.266626
  EX_pi_e : 1.159026
  EX_so4_e : 0.161179
  EX_k_e : 0.124935
  EX_fe3_e : 0.010280
  EX_mg2_e : 0.005553
  EX_cl_e : 0.003332
  EX_ca2_e : 0.003332
  EX_cu2_e : 0.000454
  EX_mn2_e : 0.000442
  EX_zn2_e : 0.000218
  EX_ni2_e : 0.000207
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 49.066457
  EX_co2_e : 28.378083
  EX_h_e : 7.076453
  EX_ac_e : 0.372633
  Auxiliary production reaction : 0.270811
  DM_5drib_c : 0.000429
  DM_4crsol_c : 0.000143

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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