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 : 5caiz_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 54
  Gene deletion: b3553 b1478 b4382 b4269 b0493 b3588 b3003 b3011 b0238 b0125 b1241 b0351 b4384 b2744 b3752 b0871 b2779 b3617 b3844 b1004 b3713 b1109 b0046 b3236 b2883 b1638 b1779 b1982 b0477 b4139 b1033 b0261 b0411 b2799 b3945 b1602 b0153 b2913 b2789 b3127 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b2954 b0591 b3029 b1380 b3662 b2285 b1011   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.346410 (mmol/gDw/h)
  Minimum Production Rate : 0.525252 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.925168
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.121426
  EX_pi_e : 0.859401
  EX_so4_e : 0.087233
  EX_k_e : 0.067617
  EX_mg2_e : 0.003005
  EX_fe2_e : 0.002859
  EX_fe3_e : 0.002705
  EX_ca2_e : 0.001803
  EX_cl_e : 0.001803
  EX_cu2_e : 0.000246
  EX_mn2_e : 0.000239
  EX_zn2_e : 0.000118
  EX_ni2_e : 0.000112

Product: (mmol/gDw/h)
  EX_h2o_e : 51.656900
  EX_co2_e : 34.699564
  EX_h_e : 7.091137
  EX_acald_e : 1.373426
  EX_his__L_e : 0.600845
  Auxiliary production reaction : 0.525252
  EX_ade_e : 0.000388
  DM_5drib_c : 0.000232
  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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