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 (56 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3831 b3614 b0910 b3752 b4152 b0871 b2781 b1612 b1611 b4122 b1779 b1759 b4138 b4123 b0621 b4381 b2406 b0114 b0529 b2492 b0904 b3821 b3918 b1912 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.596175 (mmol/gDw/h)
  Minimum Production Rate : 0.314867 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.108741
  EX_o2_e : 277.086442
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.599057
  EX_pi_e : 0.889941
  EX_so4_e : 0.150129
  EX_k_e : 0.116369
  EX_mg2_e : 0.005172
  EX_cl_e : 0.003103
  EX_ca2_e : 0.003103
  EX_cu2_e : 0.000423
  EX_mn2_e : 0.000412
  EX_zn2_e : 0.000203
  EX_ni2_e : 0.000193
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990425
  EX_h2o_e : 547.307086
  EX_co2_e : 27.258644
  EX_succ_e : 0.621686
  Auxiliary production reaction : 0.314867
  EX_ura_e : 0.107909
  DM_5drib_c : 0.000134
  DM_4crsol_c : 0.000133

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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