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 : preq1_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3399 b1241 b0351 b4069 b2744 b2297 b2458 b2925 b2097 b3617 b0160 b1238 b1851 b1982 b1200 b0675 b2361 b0261 b4381 b0112 b0114 b0529 b2492 b0904 b0515   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.445883 (mmol/gDw/h)
  Minimum Production Rate : 0.658256 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.102111
  EX_nh4_e : 10.210350
  EX_glc__D_e : 10.000000
  EX_so4_e : 1.879216
  EX_pi_e : 0.430101
  EX_k_e : 0.087033
  EX_fe2_e : 0.007161
  EX_mg2_e : 0.003868
  EX_ca2_e : 0.002321
  EX_cl_e : 0.002321
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 49.409518
  EX_co2_e : 24.744199
  EX_h_e : 6.217521
  EX_h2s_e : 1.766934
  EX_thymd_e : 1.050790
  EX_ac_e : 0.917842
  Auxiliary production reaction : 0.658256
  EX_alltn_e : 0.000499
  DM_5drib_c : 0.000299
  DM_4crsol_c : 0.000099

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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