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 : dgdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3942 b1732 b4069 b2744 b3708 b3115 b1849 b2296 b2925 b2097 b3236 b2883 b1779 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b4381 b0452 b2868 b4064 b4464 b0114 b1539 b2492 b0904 b1533 b3927 b1380   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.588342 (mmol/gDw/h)
  Minimum Production Rate : 0.175495 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.249555
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.310465
  EX_pi_e : 0.918507
  EX_so4_e : 0.148156
  EX_k_e : 0.114840
  EX_fe2_e : 0.009449
  EX_mg2_e : 0.005104
  EX_cl_e : 0.003062
  EX_ca2_e : 0.003062
  EX_cu2_e : 0.000417
  EX_mn2_e : 0.000407
  EX_zn2_e : 0.000201
  EX_ni2_e : 0.000190
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 47.002684
  EX_co2_e : 29.026875
  EX_h_e : 8.682102
  EX_ac_e : 2.495254
  Auxiliary production reaction : 0.175495
  EX_ade_e : 0.015790
  DM_5drib_c : 0.000132
  DM_4crsol_c : 0.000131

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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