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 : udpLa4o_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (77 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3831 b1278 b3614 b0910 b3752 b3926 b2930 b4232 b3697 b3925 b4152 b3115 b1849 b2296 b2781 b1612 b1611 b4122 b1779 b2690 b1759 b0411 b3945 b4138 b4123 b0621 b2913 b4381 b0529 b2197 b3927 b3825 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.444491 (mmol/gDw/h)
  Minimum Production Rate : 0.234756 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.631872
  EX_o2_e : 279.787067
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.430882
  EX_pi_e : 0.898270
  EX_so4_e : 0.111932
  EX_k_e : 0.086761
  EX_mg2_e : 0.003856
  EX_ca2_e : 0.002314
  EX_cl_e : 0.002314
  EX_cu2_e : 0.000315
  EX_mn2_e : 0.000307
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992861
  EX_h2o_e : 544.862999
  EX_co2_e : 29.915457
  EX_ac_e : 3.188898
  EX_succ_e : 0.463511
  Auxiliary production reaction : 0.234756
  EX_ura_e : 0.080454
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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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