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 (61 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b3831 b1278 b3614 b0910 b3752 b4152 b2779 b2925 b2097 b2781 b1612 b1611 b4122 b1759 b3946 b0825 b0411 b4388 b4138 b4123 b0621 b4381 b0529 b2197 b3821 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.454305 (mmol/gDw/h)
  Minimum Production Rate : 0.239939 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.427966
  EX_o2_e : 279.441589
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.550800
  EX_pi_e : 0.918104
  EX_so4_e : 0.114403
  EX_k_e : 0.088677
  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 : 999.992703
  EX_h2o_e : 544.730438
  EX_co2_e : 29.452844
  EX_ac_e : 3.038505
  EX_succ_e : 0.473746
  Auxiliary production reaction : 0.239939
  EX_ura_e : 0.082231
  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.

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Last updated: 21-Sep-2023
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