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 : nadp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b3553 b4382 b4069 b4384 b3752 b2297 b2458 b2779 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1982 b1033 b0261 b2799 b3945 b1602 b0507 b2913 b2406 b3915 b1727 b0114 b0529 b2492 b0904 b3927 b1380 b3662 b0606 b2285 b1007   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.388229 (mmol/gDw/h)
  Minimum Production Rate : 0.351113 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.913299
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.652800
  EX_pi_e : 1.427827
  EX_so4_e : 0.097764
  EX_k_e : 0.075780
  EX_fe3_e : 0.006235
  EX_mg2_e : 0.003368
  EX_ca2_e : 0.002021
  EX_cl_e : 0.002021
  EX_cu2_e : 0.000275
  EX_mn2_e : 0.000268
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_h2o_e : 52.666766
  EX_co2_e : 35.204852
  EX_h_e : 5.206081
  EX_etoh_e : 0.515845
  Auxiliary production reaction : 0.351113
  EX_ac_e : 0.226021
  EX_ade_e : 0.000434
  DM_5drib_c : 0.000261
  DM_4crsol_c : 0.000087

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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