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 : dcmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (96 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b3553 b3399 b4269 b0493 b3588 b3003 b3011 b4384 b2744 b3752 b0871 b3844 b1238 b1004 b3713 b1109 b0046 b3236 b2883 b1779 b0937 b1982 b1033 b1623 b0261 b0411 b2799 b3945 b1602 b2913 b4381 b1727 b0114 b0529 b2492 b0904 b3927 b1380 b3662 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.421273 (mmol/gDw/h)
  Minimum Production Rate : 0.708929 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.023186
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.678859
  EX_pi_e : 1.115291
  EX_so4_e : 0.106085
  EX_k_e : 0.082230
  EX_fe2_e : 0.006766
  EX_mg2_e : 0.003655
  EX_ca2_e : 0.002193
  EX_cl_e : 0.002193
  EX_cu2_e : 0.000299
  EX_mn2_e : 0.000291
  EX_zn2_e : 0.000144
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 52.012985
  EX_co2_e : 35.583123
  EX_h_e : 5.999970
  Auxiliary production reaction : 0.708929
  EX_etoh_e : 0.370945
  EX_ade_e : 0.000471
  DM_5drib_c : 0.000283
  DM_4crsol_c : 0.000094

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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