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 : glyc__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (9 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3708 b0871 b2297 b2458 b2779 b2925 b2097 b2407 b2797 b3117 b1814 b4471 b3946 b0825 b2789 b3127 b2868 b0114 b2366 b2492 b0904 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.642528 (mmol/gDw/h)
  Minimum Production Rate : 1.621552 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.998689
  EX_o2_e : 276.769192
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.030812
  EX_pi_e : 0.619786
  EX_so4_e : 0.161801
  EX_k_e : 0.125417
  EX_mg2_e : 0.005574
  EX_ca2_e : 0.003344
  EX_cl_e : 0.003344
  EX_cu2_e : 0.000456
  EX_mn2_e : 0.000444
  EX_zn2_e : 0.000219
  EX_ni2_e : 0.000208
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989680
  EX_h2o_e : 546.068181
  EX_co2_e : 26.649933
  Auxiliary production reaction : 1.621552
  EX_ac_e : 0.374071
  EX_hxan_e : 0.272892
  DM_5drib_c : 0.000145
  DM_4crsol_c : 0.000143

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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