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 : udpglcur_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4382 b4384 b2744 b1278 b3614 b0910 b4152 b2925 b2097 b2781 b1612 b1611 b4122 b0907 b1779 b1759 b3946 b0825 b4374 b0675 b4138 b4123 b0621 b0529 b2197 b3918 b0418 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.454299 (mmol/gDw/h)
  Minimum Production Rate : 0.239936 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.427843
  EX_o2_e : 279.441548
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.550715
  EX_pi_e : 0.918090
  EX_so4_e : 0.114401
  EX_k_e : 0.088676
  EX_mg2_e : 0.003941
  EX_ca2_e : 0.002365
  EX_cl_e : 0.002365
  EX_cu2_e : 0.000322
  EX_mn2_e : 0.000314
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992704
  EX_h2o_e : 544.730163
  EX_co2_e : 29.452802
  EX_ac_e : 3.038712
  EX_succ_e : 0.473739
  Auxiliary production reaction : 0.239936
  EX_ura_e : 0.082229
  DM_5drib_c : 0.000102
  DM_4crsol_c : 0.000101

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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