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 (16 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b2744 b3752 b2297 b2458 b2407 b0907 b3616 b3589 b3665 b0411 b0112 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.445238 (mmol/gDw/h)
  Minimum Production Rate : 0.853886 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.571877
  EX_nh4_e : 10.785735
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.137251
  EX_so4_e : 0.112120
  EX_k_e : 0.086907
  EX_fe2_e : 0.007151
  EX_mg2_e : 0.003862
  EX_ca2_e : 0.002317
  EX_cl_e : 0.002317
  EX_cu2_e : 0.000316
  EX_mn2_e : 0.000308
  EX_zn2_e : 0.000152
  EX_ni2_e : 0.000144
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 47.368651
  EX_co2_e : 19.387311
  EX_h_e : 10.563008
  EX_ac_e : 2.202553
  Auxiliary production reaction : 0.853886
  DM_mththf_c : 0.000199
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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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