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 : nadhx__S_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (24 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3553 b4382 b1241 b0351 b4069 b4384 b3115 b1849 b2296 b2779 b3617 b0030 b2407 b1779 b1982 b1033 b0261 b4388 b2406 b0112 b2789 b3127 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.402958 (mmol/gDw/h)
  Minimum Production Rate : 0.772259 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.325656
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.758177
  EX_pi_e : 1.933213
  EX_so4_e : 0.101473
  EX_k_e : 0.078655
  EX_fe2_e : 0.006472
  EX_mg2_e : 0.003496
  EX_ca2_e : 0.002097
  EX_cl_e : 0.002097
  EX_cu2_e : 0.000286
  EX_mn2_e : 0.000278
  EX_zn2_e : 0.000137
  EX_ni2_e : 0.000130
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 48.569040
  EX_co2_e : 23.254209
  EX_h_e : 9.558223
  EX_ac_e : 1.993217
  Auxiliary production reaction : 0.772259
  DM_oxam_c : 0.000451
  DM_5drib_c : 0.000270
  EX_glyclt_e : 0.000270
  DM_4crsol_c : 0.000090

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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