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 : dcamp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b4382 b4069 b4384 b3708 b3752 b2297 b2458 b2779 b2925 b2097 b2407 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b0261 b2406 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b2835 b0494 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.613096 (mmol/gDw/h)
  Minimum Production Rate : 0.259706 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.112941
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.920596
  EX_pi_e : 0.851101
  EX_so4_e : 0.154390
  EX_k_e : 0.119672
  EX_fe2_e : 0.009847
  EX_mg2_e : 0.005319
  EX_ca2_e : 0.003191
  EX_cl_e : 0.003191
  EX_cu2_e : 0.000435
  EX_mn2_e : 0.000424
  EX_zn2_e : 0.000209
  EX_ni2_e : 0.000198
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 47.338851
  EX_co2_e : 27.511438
  EX_h_e : 9.295271
  EX_ac_e : 1.842591
  Auxiliary production reaction : 0.259706
  DM_oxam_c : 0.000686
  DM_5drib_c : 0.000411
  DM_4crsol_c : 0.000137

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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