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 : gdpofuc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 45
  Gene deletion: b3553 b3399 b0474 b2518 b4069 b2502 b2744 b0871 b2297 b2458 b2925 b2097 b3844 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b4139 b3946 b0825 b1033 b4374 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b0507 b1727 b0114 b0755 b3612 b0529 b2492 b0904 b3927 b3029 b1380 b2660 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.327185 (mmol/gDw/h)
  Minimum Production Rate : 0.150993 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.831335
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.289998
  EX_pi_e : 0.617591
  EX_fe3_e : 0.534862
  EX_so4_e : 0.082392
  EX_k_e : 0.063864
  EX_mg2_e : 0.002838
  EX_ca2_e : 0.001703
  EX_cl_e : 0.001703
  EX_cu2_e : 0.000232
  EX_mn2_e : 0.000226
  EX_zn2_e : 0.000112
  EX_ni2_e : 0.000106

Product: (mmol/gDw/h)
  EX_h2o_e : 43.527062
  EX_co2_e : 27.532638
  EX_h_e : 9.598930
  EX_pyr_e : 5.353617
  EX_fe2_e : 0.529607
  EX_ac_e : 0.190482
  Auxiliary production reaction : 0.150993
  EX_3hpp_e : 0.059221
  EX_hxan_e : 0.000366
  DM_5drib_c : 0.000220
  DM_4crsol_c : 0.000073

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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