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 : udpLa4n_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b0474 b2518 b3831 b3752 b4152 b2925 b2097 b2781 b1850 b1612 b1611 b4122 b1759 b1200 b4161 b1701 b1805 b4138 b4123 b0621 b4381 b2406 b3918 b0789 b1249 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.684925 (mmol/gDw/h)
  Minimum Production Rate : 0.361740 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.093821
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.730300
  EX_pi_e : 1.384163
  EX_so4_e : 0.172478
  EX_k_e : 0.133693
  EX_fe2_e : 0.011001
  EX_mg2_e : 0.005942
  EX_cl_e : 0.003565
  EX_ca2_e : 0.003565
  EX_cu2_e : 0.000486
  EX_mn2_e : 0.000473
  EX_zn2_e : 0.000234
  EX_ni2_e : 0.000221
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 46.508259
  EX_co2_e : 23.469778
  EX_h_e : 7.969782
  EX_succ_e : 0.714235
  Auxiliary production reaction : 0.361740
  EX_ura_e : 0.123974
  DM_5drib_c : 0.000154
  DM_4crsol_c : 0.000153

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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