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 : 2dr5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (47 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b0871 b2779 b3617 b0030 b2407 b3236 b0907 b3962 b4267 b0261 b4381 b2868 b0114 b0529 b2492 b0904 b0325 b0508 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.439546 (mmol/gDw/h)
  Minimum Production Rate : 0.468947 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 994.032421
  EX_o2_e : 283.588834
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.668856
  EX_pi_e : 0.892936
  EX_so4_e : 0.110687
  EX_k_e : 0.085796
  EX_mg2_e : 0.003813
  EX_ca2_e : 0.002288
  EX_cl_e : 0.002288
  EX_cu2_e : 0.000312
  EX_mn2_e : 0.000304
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992940
  EX_h2o_e : 550.496370
  EX_co2_e : 34.099716
  EX_acald_e : 1.555976
  EX_xan_e : 0.480448
  Auxiliary production reaction : 0.468947
  DM_5drib_c : 0.000099
  DM_4crsol_c : 0.000098

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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