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 : adphep_DD_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (97 of 99: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b4382 b4384 b3708 b3008 b3752 b3926 b0871 b2297 b2458 b2925 b2097 b2926 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b0261 b1602 b2406 b0452 b2868 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b1380 b2660 b1771 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.346959 (mmol/gDw/h)
  Minimum Production Rate : 0.079640 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.066225
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.147265
  EX_pi_e : 0.493957
  EX_so4_e : 0.087372
  EX_k_e : 0.067724
  EX_fe2_e : 0.005574
  EX_mg2_e : 0.003010
  EX_cl_e : 0.001806
  EX_ca2_e : 0.001806
  EX_cu2_e : 0.000246
  EX_mn2_e : 0.000240
  EX_zn2_e : 0.000118
  EX_ni2_e : 0.000112

Product: (mmol/gDw/h)
  EX_h2o_e : 43.646850
  EX_co2_e : 27.847515
  EX_h_e : 8.947134
  EX_pyr_e : 5.518277
  Auxiliary production reaction : 0.079639
  EX_ade_e : 0.000388
  DM_5drib_c : 0.000233
  DM_4crsol_c : 0.000077

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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