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 (79 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b3553 b1478 b3399 b1241 b0351 b4069 b2502 b2744 b3115 b1849 b2296 b3617 b1238 b1004 b3713 b1109 b0046 b3236 b1638 b3908 b1656 b1982 b4139 b1033 b0675 b2361 b0261 b2799 b3945 b1602 b2913 b4381 b3915 b0114 b0509 b3125 b0755 b3612 b0529 b2492 b0904 b2954 b1380 b0221 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.333125 (mmol/gDw/h)
  Minimum Production Rate : 0.232468 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.000897
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.430135
  EX_pi_e : 0.321334
  EX_so4_e : 0.083888
  EX_k_e : 0.065024
  EX_fe3_e : 0.005350
  EX_mg2_e : 0.002890
  EX_ca2_e : 0.001734
  EX_cl_e : 0.001734
  EX_cu2_e : 0.000236
  EX_mn2_e : 0.000230
  EX_zn2_e : 0.000114
  EX_ni2_e : 0.000108

Product: (mmol/gDw/h)
  EX_h2o_e : 51.708123
  EX_co2_e : 34.551656
  EX_h_e : 8.373173
  EX_ac_e : 1.242055
  EX_his__L_e : 0.811913
  EX_ade_e : 0.232841
  DM_5drib_c : 0.232692
  DM_4crsol_c : 0.232543
  Auxiliary production reaction : 0.232468

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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