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 : dump_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b4467 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2930 b4232 b3697 b3925 b0871 b3617 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1982 b3946 b0825 b1602 b4381 b2406 b0114 b0529 b2492 b0904 b1380 b0516 b3662 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.380661 (mmol/gDw/h)
  Minimum Production Rate : 1.237948 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.892592
  EX_o2_e : 277.503170
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.588030
  EX_pi_e : 1.605136
  EX_so4_e : 0.095858
  EX_k_e : 0.074302
  EX_mg2_e : 0.003302
  EX_ca2_e : 0.001981
  EX_cl_e : 0.001981
  EX_cu2_e : 0.000270
  EX_mn2_e : 0.000263
  EX_zn2_e : 0.000130
  EX_ni2_e : 0.000123

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993886
  EX_h2o_e : 547.025475
  EX_co2_e : 26.182440
  EX_pyr_e : 2.126452
  Auxiliary production reaction : 1.237948
  EX_acald_e : 0.334946
  EX_alltn_e : 0.000256
  EX_glyclt_e : 0.000255
  EX_mththf_e : 0.000171
  DM_5drib_c : 0.000086
  DM_4crsol_c : 0.000085

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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