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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (65 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b2836 b0474 b2518 b1241 b0351 b3831 b4069 b2744 b1278 b3708 b2297 b2458 b2781 b0030 b2883 b0651 b2162 b1759 b2797 b3117 b1814 b4471 b3616 b3589 b4161 b0261 b4381 b2406 b0112 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b1539 b2492 b0904 b1533 b3918 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.548453 (mmol/gDw/h)
  Minimum Production Rate : 1.543048 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 17.965130
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.664926
  EX_pi_e : 0.529041
  EX_so4_e : 0.138111
  EX_k_e : 0.107054
  EX_fe2_e : 0.008809
  EX_mg2_e : 0.004758
  EX_ca2_e : 0.002855
  EX_cl_e : 0.002855
  EX_cu2_e : 0.000389
  EX_mn2_e : 0.000379
  EX_zn2_e : 0.000187
  EX_ni2_e : 0.000177
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 38.645077
  EX_co2_e : 20.579272
  EX_h_e : 9.586753
  Auxiliary production reaction : 1.543048
  EX_ac_e : 1.262620
  EX_thym_e : 0.099316
  DM_5drib_c : 0.000123
  DM_4crsol_c : 0.000122

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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