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 : gdpmann_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 108: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b3617 b0030 b2883 b1982 b1623 b0261 b0411 b4381 b0112 b0114 b0529 b2492 b0904 b2954 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.563321 (mmol/gDw/h)
  Minimum Production Rate : 0.445100 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 20.948754
  EX_nh4_e : 10.191358
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.433583
  EX_so4_e : 0.141855
  EX_k_e : 0.109956
  EX_fe2_e : 0.009047
  EX_mg2_e : 0.004887
  EX_ca2_e : 0.002932
  EX_cl_e : 0.002932
  EX_cu2_e : 0.000399
  EX_mn2_e : 0.000389
  EX_zn2_e : 0.000192
  EX_ni2_e : 0.000182
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 47.098476
  EX_co2_e : 20.345206
  EX_h_e : 8.393357
  EX_thymd_e : 0.941021
  Auxiliary production reaction : 0.445100
  DM_5drib_c : 0.000378
  DM_4crsol_c : 0.000126

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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