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 : dctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b2836 b3553 b4069 b4384 b3708 b3752 b3926 b3115 b1849 b2296 b2779 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1982 b4139 b2797 b3117 b1814 b4471 b1033 b1623 b0261 b1602 b0507 b4381 b2406 b3915 b0114 b2366 b0529 b2492 b0904 b2954 b1533 b3927 b3029 b1380 b2660 b1771 b3662 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.420381 (mmol/gDw/h)
  Minimum Production Rate : 0.534217 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 35.565597
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.145083
  EX_pi_e : 2.008153
  EX_so4_e : 0.105860
  EX_k_e : 0.082055
  EX_fe3_e : 0.006752
  EX_mg2_e : 0.003647
  EX_ca2_e : 0.002188
  EX_cl_e : 0.002188
  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 : 52.157190
  EX_co2_e : 36.145585
  EX_h_e : 4.650690
  Auxiliary production reaction : 0.534217
  EX_glyc_e : 0.432994
  EX_ac_e : 0.244740
  EX_ade_e : 0.000470
  DM_5drib_c : 0.000282
  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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