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 : ckdo_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b2836 b4382 b3831 b4384 b3614 b0910 b3752 b4152 b0871 b2926 b2781 b2407 b1612 b1611 b4122 b1759 b4138 b4123 b0621 b2406 b0114 b2492 b0904 b3918 b4042 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.438847 (mmol/gDw/h)
  Minimum Production Rate : 0.231739 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.774385
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.593665
  EX_pi_e : 0.655054
  EX_so4_e : 0.110510
  EX_k_e : 0.085660
  EX_fe2_e : 0.007048
  EX_mg2_e : 0.003807
  EX_ca2_e : 0.002284
  EX_cl_e : 0.002284
  EX_cu2_e : 0.000311
  EX_mn2_e : 0.000303
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 50.660496
  EX_co2_e : 35.899400
  EX_h_e : 5.801708
  EX_succ_e : 0.457626
  Auxiliary production reaction : 0.231739
  EX_ura_e : 0.079468
  DM_5drib_c : 0.000099
  DM_4crsol_c : 0.000098

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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