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 : dhpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (115 of 115: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 51
  Gene deletion: b4467 b2836 b3399 b4069 b2502 b4384 b2744 b3708 b3752 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b1004 b3713 b1109 b0046 b3236 b2883 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b1623 b4374 b2361 b2291 b0261 b0411 b1602 b0507 b1727 b2975 b0114 b3603 b0529 b1539 b2492 b0904 b1533 b3927 b1380 b2660 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.374859 (mmol/gDw/h)
  Minimum Production Rate : 0.158789 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.960958
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.002864
  EX_pi_e : 0.361592
  EX_so4_e : 0.094397
  EX_k_e : 0.073170
  EX_fe2_e : 0.006021
  EX_mg2_e : 0.003252
  EX_ca2_e : 0.001951
  EX_cl_e : 0.001951
  EX_cu2_e : 0.000266
  EX_mn2_e : 0.000259
  EX_zn2_e : 0.000128
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_h2o_e : 44.806382
  EX_co2_e : 32.362977
  EX_h_e : 9.569953
  EX_ac_e : 5.012392
  Auxiliary production reaction : 0.158789
  EX_hxan_e : 0.000419
  DM_5drib_c : 0.000252
  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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