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 : ump_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 92: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b3831 b3614 b0910 b3752 b2930 b4232 b3697 b3925 b4152 b2779 b2781 b1612 b1611 b4122 b1759 b3946 b0825 b0411 b4388 b4138 b4123 b0621 b4381 b0114 b3918 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.390264 (mmol/gDw/h)
  Minimum Production Rate : 0.206116 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.814440
  EX_o2_e : 279.435334
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.768328
  EX_pi_e : 0.582567
  EX_so4_e : 0.098276
  EX_k_e : 0.076177
  EX_mg2_e : 0.003386
  EX_cl_e : 0.002031
  EX_ca2_e : 0.002031
  EX_cu2_e : 0.000277
  EX_mn2_e : 0.000270
  EX_zn2_e : 0.000133
  EX_ni2_e : 0.000126

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993732
  EX_h2o_e : 540.043773
  EX_co2_e : 27.538142
  EX_glyc__R_e : 4.225952
  EX_succ_e : 0.406964
  Auxiliary production reaction : 0.206116
  EX_ura_e : 0.070639
  DM_5drib_c : 0.000088
  DM_4crsol_c : 0.000087

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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