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 : dhnpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (84 of 90: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b4467 b1478 b1241 b4069 b2744 b2297 b2458 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b0937 b1302 b2662 b4139 b1623 b3665 b4015 b2799 b3945 b1602 b4381 b2406 b3654 b2868 b3714 b3664 b4064 b4464 b0755 b3612 b0529 b2492 b0904 b2954 b3029 b1380 b2660 b3662 b1985 b1517 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.357636 (mmol/gDw/h)
  Minimum Production Rate : 0.752245 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.233979
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.623667
  EX_pi_e : 0.344978
  EX_so4_e : 0.090060
  EX_k_e : 0.069808
  EX_mg2_e : 0.003102
  EX_fe2_e : 0.002952
  EX_fe3_e : 0.002792
  EX_ca2_e : 0.001861
  EX_cl_e : 0.001861
  EX_cu2_e : 0.000254
  EX_mn2_e : 0.000247
  EX_zn2_e : 0.000122
  EX_ni2_e : 0.000116

Product: (mmol/gDw/h)
  EX_h2o_e : 53.082506
  EX_co2_e : 36.117267
  EX_h_e : 8.266323
  EX_ac_e : 1.216201
  Auxiliary production reaction : 0.752245
  DM_mththf_c : 0.000160
  DM_5drib_c : 0.000080
  DM_4crsol_c : 0.000080

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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