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 : ipdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b1478 b3399 b1241 b0351 b2744 b2930 b4232 b3697 b3925 b0871 b3617 b1779 b2690 b1623 b3665 b0675 b2361 b0822 b4381 b0114 b0529 b2492 b0904 b1912 b0515 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.366954 (mmol/gDw/h)
  Minimum Production Rate : 0.267077 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.092280
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.001484
  EX_pi_e : 0.888120
  EX_so4_e : 0.092406
  EX_k_e : 0.071627
  EX_fe2_e : 0.005894
  EX_mg2_e : 0.003183
  EX_cl_e : 0.001910
  EX_ca2_e : 0.001910
  EX_cu2_e : 0.000260
  EX_mn2_e : 0.000254
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_h2o_e : 44.109075
  EX_co2_e : 28.943977
  EX_h_e : 8.016533
  EX_pyr_e : 4.873479
  Auxiliary production reaction : 0.267077
  EX_alltn_e : 0.009602
  DM_5drib_c : 0.000083
  DM_4crsol_c : 0.000082

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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