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 : dhmpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (102 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b3553 b1478 b1241 b4069 b4384 b3752 b2297 b2458 b2779 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b4117 b3908 b1656 b1982 b4139 b1033 b1623 b4014 b0261 b2976 b2799 b3945 b1602 b2913 b4381 b2406 b2789 b3127 b3915 b0529 b2492 b0904 b2954 b2938 b1380 b1695 b3662 b1985 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.383631 (mmol/gDw/h)
  Minimum Production Rate : 0.647508 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 38.775991
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.382438
  EX_pi_e : 0.370053
  EX_so4_e : 0.096606
  EX_k_e : 0.074882
  EX_fe3_e : 0.006161
  EX_mg2_e : 0.003328
  EX_cl_e : 0.001997
  EX_ca2_e : 0.001997
  EX_cu2_e : 0.000272
  EX_mn2_e : 0.000265
  EX_zn2_e : 0.000131
  EX_ni2_e : 0.000124

Product: (mmol/gDw/h)
  EX_h2o_e : 54.582944
  EX_co2_e : 37.976451
  EX_h_e : 6.993717
  Auxiliary production reaction : 0.647508
  EX_ac_e : 0.223345
  EX_hxan_e : 0.000429
  DM_5drib_c : 0.000257
  DM_4crsol_c : 0.000086

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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