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 : pyr_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (104 of 114: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b1241 b0351 b2221 b0871 b2297 b2458 b2925 b2097 b2690 b3962 b1302 b2662 b4139 b4267 b4015 b0614 b0726 b3945 b4388 b2587 b4077 b0529 b1539 b0325 b0508 b4266 b4141 b1798 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.632112 (mmol/gDw/h)
  Minimum Production Rate : 0.174444 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.440502
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.826753
  EX_pi_e : 0.609739
  EX_so4_e : 0.159178
  EX_k_e : 0.123384
  EX_fe2_e : 0.010152
  EX_mg2_e : 0.005484
  EX_ca2_e : 0.003290
  EX_cl_e : 0.003290
  EX_cu2_e : 0.000448
  EX_mn2_e : 0.000437
  EX_zn2_e : 0.000216
  EX_ni2_e : 0.000204
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 46.568987
  EX_co2_e : 29.702219
  EX_h_e : 7.897122
  EX_ac_e : 1.914582
  EX_pyr_e : 0.174444
  DM_5drib_c : 0.000142
  DM_4crsol_c : 0.000141

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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