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 : dcmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3942 b1732 b1241 b0351 b4069 b4384 b2744 b1479 b3752 b0871 b2297 b2458 b2925 b2097 b3617 b3236 b2883 b0907 b2463 b1982 b3946 b2210 b0825 b4381 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b1511 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.386197 (mmol/gDw/h)
  Minimum Production Rate : 1.480791 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.549104
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.614571
  EX_pi_e : 1.853319
  EX_so4_e : 0.097252
  EX_k_e : 0.075383
  EX_fe2_e : 0.006203
  EX_mg2_e : 0.003350
  EX_cl_e : 0.002010
  EX_ca2_e : 0.002010
  EX_cu2_e : 0.000274
  EX_mn2_e : 0.000267
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_h2o_e : 48.456482
  EX_co2_e : 25.374396
  EX_h_e : 10.197135
  Auxiliary production reaction : 1.480791
  EX_ac_e : 1.170086
  EX_pyr_e : 1.034754
  EX_ade_e : 0.000260
  DM_mththf_c : 0.000173
  DM_5drib_c : 0.000087
  EX_glyc__R_e : 0.000086
  DM_4crsol_c : 0.000086

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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