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 : fprica_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b4384 b2744 b3752 b2297 b2458 b2883 b1982 b3616 b3589 b1623 b4381 b2406 b0511 b4064 b4464 b0114 b0529 b2492 b0904 b0515 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.585752 (mmol/gDw/h)
  Minimum Production Rate : 1.107644 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.408705
  EX_nh4_e : 10.819528
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.672663
  EX_so4_e : 0.147504
  EX_k_e : 0.114335
  EX_fe2_e : 0.009408
  EX_mg2_e : 0.005081
  EX_ca2_e : 0.003049
  EX_cl_e : 0.003049
  EX_cu2_e : 0.000415
  EX_mn2_e : 0.000405
  EX_zn2_e : 0.000200
  EX_ni2_e : 0.000189
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 47.528450
  EX_co2_e : 20.842439
  EX_h_e : 11.854973
  EX_ac_e : 1.979393
  Auxiliary production reaction : 1.107644
  EX_xan_e : 0.015721
  DM_mththf_c : 0.000262
  DM_5drib_c : 0.000132
  DM_4crsol_c : 0.000131

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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