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 : aps_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b2836 b3399 b2744 b3708 b3008 b0871 b2779 b2925 b2097 b0160 b2797 b3117 b1814 b4471 b3946 b0825 b1623 b3665 b0675 b2361 b2913 b4381 b2406 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b2578 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.633086 (mmol/gDw/h)
  Minimum Production Rate : 0.129408 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.767545
  EX_o2_e : 276.722606
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.500882
  EX_pi_e : 0.740087
  EX_so4_e : 0.288832
  EX_k_e : 0.123574
  EX_mg2_e : 0.005492
  EX_ca2_e : 0.003295
  EX_cl_e : 0.003295
  EX_cu2_e : 0.000449
  EX_mn2_e : 0.000437
  EX_zn2_e : 0.000216
  EX_ni2_e : 0.000204
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989832
  EX_h2o_e : 547.148147
  EX_co2_e : 26.735858
  EX_pyr_e : 1.983883
  Auxiliary production reaction : 0.129408
  DM_oxam_c : 0.016565
  DM_5drib_c : 0.000142
  DM_4crsol_c : 0.000141

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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