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 : dhgly_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (87 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 54
  Gene deletion: b4467 b1478 b1241 b0351 b4069 b4384 b3752 b2930 b4232 b3697 b3925 b0871 b2297 b2458 b2926 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b3908 b1656 b0207 b3012 b1982 b0477 b4139 b3616 b3589 b0261 b2799 b1602 b0507 b2913 b4381 b2406 b2975 b0114 b3603 b0529 b2492 b0904 b1781 b3001 b1380 b0325 b1771 b3662 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.268023 (mmol/gDw/h)
  Minimum Production Rate : 0.513659 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.067596
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.464121
  EX_pi_e : 0.258537
  EX_so4_e : 0.067494
  EX_k_e : 0.052316
  EX_mg2_e : 0.002325
  EX_fe2_e : 0.002212
  EX_fe3_e : 0.002093
  EX_ca2_e : 0.001395
  EX_cl_e : 0.001395
  EX_cu2_e : 0.000190
  EX_mn2_e : 0.000185
  EX_zn2_e : 0.000091
  EX_ni2_e : 0.000087

Product: (mmol/gDw/h)
  EX_h2o_e : 46.282828
  EX_co2_e : 29.725613
  EX_h_e : 9.160482
  EX_pyr_e : 2.286588
  EX_ac_e : 1.325944
  EX_hxan_e : 0.513959
  DM_5drib_c : 0.513839
  DM_4crsol_c : 0.513719
  Auxiliary production reaction : 0.513659

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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