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 : prpncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b1241 b0351 b3831 b4069 b4384 b3708 b3614 b0910 b3752 b2297 b2458 b2781 b3617 b2407 b1759 b1982 b2797 b3117 b1814 b4471 b0261 b1701 b1805 b0507 b4381 b2406 b0112 b0114 b1539 b2492 b0904 b1533 b3918 b1912 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.534715 (mmol/gDw/h)
  Minimum Production Rate : 0.375822 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.905234
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.351445
  EX_pi_e : 1.643255
  EX_so4_e : 0.510474
  EX_k_e : 0.104373
  EX_fe2_e : 0.008588
  EX_mg2_e : 0.004639
  EX_ca2_e : 0.002783
  EX_cl_e : 0.002783
  EX_cu2_e : 0.000379
  EX_mn2_e : 0.000369
  EX_zn2_e : 0.000182
  EX_ni2_e : 0.000173
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 46.325429
  EX_co2_e : 21.948585
  EX_h_e : 9.346383
  EX_ac_e : 2.358971
  EX_thym_e : 0.472607
  Auxiliary production reaction : 0.375822
  DM_oxam_c : 0.000598
  DM_5drib_c : 0.000359
  EX_glyclt_e : 0.000358
  DM_4crsol_c : 0.000119

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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