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 : forcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b3708 b3008 b3752 b0871 b2407 b1238 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b3665 b4381 b2406 b0114 b1539 b2492 b0904 b1533 b1511 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.625560 (mmol/gDw/h)
  Minimum Production Rate : 0.301712 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 21.998489
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.870085
  EX_pi_e : 1.508555
  EX_so4_e : 0.459241
  EX_k_e : 0.122105
  EX_fe2_e : 0.010047
  EX_mg2_e : 0.005427
  EX_cl_e : 0.003256
  EX_ca2_e : 0.003256
  EX_cu2_e : 0.000444
  EX_mn2_e : 0.000432
  EX_zn2_e : 0.000213
  EX_ni2_e : 0.000202
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 46.880856
  EX_co2_e : 24.323093
  EX_h_e : 6.655137
  EX_acald_e : 1.679683
  Auxiliary production reaction : 0.301712
  EX_ade_e : 0.000421
  DM_mththf_c : 0.000280
  DM_5drib_c : 0.000141
  DM_4crsol_c : 0.000139

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.

Last updated: 21-Sep-2023
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