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 : 2dr5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1241 b0351 b4069 b2744 b3115 b1849 b2296 b3617 b1779 b3962 b4139 b4267 b0261 b2799 b3945 b4381 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b0508 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.443660 (mmol/gDw/h)
  Minimum Production Rate : 0.559234 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 33.900366
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.647192
  EX_pi_e : 0.987191
  EX_so4_e : 0.111722
  EX_k_e : 0.086599
  EX_fe2_e : 0.007126
  EX_mg2_e : 0.003849
  EX_cl_e : 0.002309
  EX_ca2_e : 0.002309
  EX_cu2_e : 0.000315
  EX_mn2_e : 0.000307
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.685378
  EX_co2_e : 33.698908
  EX_h_e : 8.151742
  EX_ac_e : 1.219514
  EX_ade_e : 0.571141
  Auxiliary production reaction : 0.559234
  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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