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 (58 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b2836 b0474 b2518 b3831 b3752 b4152 b0871 b2781 b1612 b1611 b4122 b1779 b1759 b4161 b4138 b4123 b0621 b4381 b2406 b0114 b2492 b0904 b3918 b1912 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.435235 (mmol/gDw/h)
  Minimum Production Rate : 0.229832 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.239057
  EX_o2_e : 285.972045
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.547622
  EX_pi_e : 0.649662
  EX_so4_e : 0.109601
  EX_k_e : 0.084955
  EX_mg2_e : 0.003776
  EX_ca2_e : 0.002265
  EX_cl_e : 0.002265
  EX_cu2_e : 0.000309
  EX_mn2_e : 0.000301
  EX_zn2_e : 0.000148
  EX_ni2_e : 0.000141
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993010
  EX_h2o_e : 550.733877
  EX_co2_e : 36.097778
  EX_succ_e : 0.453859
  Auxiliary production reaction : 0.229832
  EX_ura_e : 0.078814
  DM_5drib_c : 0.000098
  DM_4crsol_c : 0.000097

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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