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 : prlp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3553 b4382 b1241 b0351 b4384 b3752 b0871 b2925 b2097 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b0207 b3012 b0937 b1982 b3946 b0825 b1033 b0261 b0411 b2799 b1602 b1727 b0529 b2492 b0904 b1781 b3001 b3927 b2835 b1380 b0325 b2660 b1771 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.378281 (mmol/gDw/h)
  Minimum Production Rate : 0.014487 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.390811
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.159947
  EX_pi_e : 0.393865
  EX_so4_e : 0.095259
  EX_k_e : 0.073838
  EX_fe2_e : 0.006076
  EX_mg2_e : 0.003282
  EX_ca2_e : 0.001969
  EX_cl_e : 0.001969
  EX_cu2_e : 0.000268
  EX_mn2_e : 0.000261
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_h2o_e : 43.961218
  EX_co2_e : 28.542443
  EX_h_e : 8.787215
  EX_pyr_e : 5.236873
  Auxiliary production reaction : 0.014487
  EX_ade_e : 0.000423
  DM_5drib_c : 0.000254
  DM_4crsol_c : 0.000084

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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