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 : uri_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3831 b3614 b0910 b3752 b2930 b4232 b3697 b3925 b4152 b3115 b1849 b2296 b2781 b1612 b1611 b4122 b1779 b2690 b1759 b4014 b2976 b3945 b4138 b4123 b0621 b2492 b0904 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.425833 (mmol/gDw/h)
  Minimum Production Rate : 0.224901 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.643119
  EX_o2_e : 282.286927
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.202913
  EX_pi_e : 0.410761
  EX_so4_e : 0.107233
  EX_k_e : 0.083120
  EX_mg2_e : 0.003694
  EX_cl_e : 0.002216
  EX_ca2_e : 0.002216
  EX_cu2_e : 0.000302
  EX_mn2_e : 0.000294
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000138
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993161
  EX_h2o_e : 545.942868
  EX_co2_e : 32.522378
  EX_ac_e : 2.945255
  EX_succ_e : 0.444055
  EX_uri_e : 0.224901
  EX_ura_e : 0.077077
  DM_5drib_c : 0.000096
  DM_4crsol_c : 0.000095

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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