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 : xdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3399 b4384 b2744 b3708 b3008 b0871 b2926 b2407 b3236 b1982 b2797 b3117 b1814 b4471 b2210 b0675 b2361 b1701 b1805 b4381 b2868 b0114 b2366 b0529 b2492 b0904 b2578 b1533 b3927 b2413 b3447 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.493627 (mmol/gDw/h)
  Minimum Production Rate : 0.113599 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.888328
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.786857
  EX_pi_e : 0.703353
  EX_so4_e : 0.124305
  EX_k_e : 0.096353
  EX_fe2_e : 0.007928
  EX_mg2_e : 0.004282
  EX_cl_e : 0.002569
  EX_ca2_e : 0.002569
  EX_cu2_e : 0.000350
  EX_mn2_e : 0.000341
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 53.001620
  EX_co2_e : 38.600112
  EX_h_e : 4.877770
  Auxiliary production reaction : 0.113599
  EX_hxan_e : 0.000332
  DM_mththf_c : 0.000221
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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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