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 : pg120_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b0474 b2518 b2744 b2930 b4232 b3697 b3925 b4152 b2781 b3236 b1612 b1611 b4122 b1638 b1759 b3449 b3946 b0825 b4374 b4161 b0675 b4015 b4138 b4123 b0621 b2913 b4381 b2406 b3915 b0452 b2197 b3029 b3918 b0789 b1249 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.619305 (mmol/gDw/h)
  Minimum Production Rate : 0.083165 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.488212
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.566805
  EX_pi_e : 0.680551
  EX_so4_e : 0.155953
  EX_k_e : 0.120884
  EX_fe3_e : 0.009947
  EX_mg2_e : 0.005372
  EX_ca2_e : 0.003223
  EX_cl_e : 0.003223
  EX_cu2_e : 0.000439
  EX_mn2_e : 0.000428
  EX_zn2_e : 0.000211
  EX_ni2_e : 0.000200
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 47.102660
  EX_co2_e : 27.745455
  EX_h_e : 7.787179
  EX_succ_e : 0.645807
  EX_ura_e : 0.439179
  Auxiliary production reaction : 0.083165
  DM_5drib_c : 0.000139
  DM_4crsol_c : 0.000138

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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