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 : gdpddman_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4382 b0474 b2518 b1241 b0351 b4384 b3708 b3008 b3752 b2930 b4232 b3697 b3925 b0871 b2407 b1779 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b3449 b3946 b0825 b0261 b2406 b0114 b2366 b0529 b2492 b0904 b1533 b3927 b1380 b0494 b3447 b0515 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.565270 (mmol/gDw/h)
  Minimum Production Rate : 0.128175 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 27.160154
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.754575
  EX_pi_e : 0.801614
  EX_so4_e : 0.142346
  EX_k_e : 0.110337
  EX_fe2_e : 0.009079
  EX_mg2_e : 0.004904
  EX_cl_e : 0.002942
  EX_ca2_e : 0.002942
  EX_cu2_e : 0.000401
  EX_mn2_e : 0.000391
  EX_zn2_e : 0.000193
  EX_ni2_e : 0.000183
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 46.196584
  EX_co2_e : 26.630604
  EX_h_e : 8.283237
  EX_pyr_e : 2.695954
  Auxiliary production reaction : 0.128175
  EX_alltn_e : 0.002207
  DM_5drib_c : 0.001954
  DM_4crsol_c : 0.001700

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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