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 : dudp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4467 b3399 b4069 b2502 b2744 b3115 b1849 b2296 b2926 b1004 b3713 b1109 b0046 b3236 b1982 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b2913 b4381 b3915 b1727 b0114 b0529 b2492 b0904 b3927 b1380 b0606 b2285 b1007 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.454509 (mmol/gDw/h)
  Minimum Production Rate : 0.483036 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.976852
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.877272
  EX_pi_e : 1.404493
  EX_so4_e : 0.114454
  EX_k_e : 0.088717
  EX_fe3_e : 0.007300
  EX_mg2_e : 0.003943
  EX_ca2_e : 0.002366
  EX_cl_e : 0.002366
  EX_cu2_e : 0.000322
  EX_mn2_e : 0.000314
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.332447
  EX_co2_e : 36.464403
  EX_h_e : 4.933696
  Auxiliary production reaction : 0.483036
  EX_ac_e : 0.264609
  EX_ade_e : 0.000509
  DM_5drib_c : 0.000305
  DM_4crsol_c : 0.000101

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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