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 : ditp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3399 b0474 b2518 b1241 b0351 b3831 b4069 b4384 b2744 b3115 b1849 b2296 b2407 b3962 b1982 b4139 b2498 b3616 b3589 b4267 b2913 b2868 b0114 b0755 b3612 b0529 b2492 b0904 b0325 b0508 b4266 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.420137 (mmol/gDw/h)
  Minimum Production Rate : 0.536976 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.941664
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.686763
  EX_pi_e : 2.016194
  EX_so4_e : 0.105799
  EX_k_e : 0.082008
  EX_fe2_e : 0.006748
  EX_mg2_e : 0.003645
  EX_ca2_e : 0.002187
  EX_cl_e : 0.002187
  EX_cu2_e : 0.000298
  EX_mn2_e : 0.000290
  EX_zn2_e : 0.000143
  EX_ni2_e : 0.000136
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.841762
  EX_co2_e : 33.763588
  EX_h_e : 6.745552
  EX_ac_e : 1.809798
  Auxiliary production reaction : 0.536976
  EX_ade_e : 0.000283
  DM_mththf_c : 0.000188
  DM_5drib_c : 0.000095
  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.

Last updated: 21-Sep-2023
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