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 : xmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4384 b3708 b3008 b3752 b0871 b2925 b2097 b2407 b0517 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b4381 b2406 b0114 b1539 b2492 b0904 b1533 b3927 b3821 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.784641 (mmol/gDw/h)
  Minimum Production Rate : 0.178035 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.745092
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.186191
  EX_pi_e : 0.934904
  EX_so4_e : 0.197588
  EX_k_e : 0.153156
  EX_fe2_e : 0.012602
  EX_mg2_e : 0.006807
  EX_ca2_e : 0.004084
  EX_cl_e : 0.004084
  EX_cu2_e : 0.000556
  EX_mn2_e : 0.000542
  EX_zn2_e : 0.000268
  EX_ni2_e : 0.000253
  EX_cobalt2_e : 0.000020

Product: (mmol/gDw/h)
  EX_h2o_e : 48.586918
  EX_co2_e : 25.862857
  EX_h_e : 7.967220
  Auxiliary production reaction : 0.178035
  EX_pyr_e : 0.045490
  DM_mththf_c : 0.002537
  DM_5drib_c : 0.000526
  DM_4crsol_c : 0.000175

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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