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 : 5aizc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b2836 b4384 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b0030 b2407 b1779 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b3665 b4374 b2361 b2291 b0261 b0411 b0114 b0529 b1539 b2492 b0904 b2947 b2578 b1533 b3927 b2413 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.614749 (mmol/gDw/h)
  Minimum Production Rate : 0.211586 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.646488
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.277435
  EX_pi_e : 0.804576
  EX_so4_e : 0.154806
  EX_k_e : 0.119995
  EX_fe2_e : 0.009873
  EX_mg2_e : 0.005333
  EX_ca2_e : 0.003200
  EX_cl_e : 0.003200
  EX_cu2_e : 0.000436
  EX_mn2_e : 0.000425
  EX_zn2_e : 0.000210
  EX_ni2_e : 0.000199
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.531945
  EX_co2_e : 26.468688
  EX_h_e : 8.628210
  EX_pyr_e : 2.129867
  Auxiliary production reaction : 0.211586
  EX_ade_e : 0.000688
  DM_5drib_c : 0.000412
  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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