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 : dtdp4d6dg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b0474 b2518 b2744 b4152 b2781 b3844 b1612 b1611 b4122 b1759 b4374 b4161 b0675 b2361 b2291 b4138 b4123 b0621 b3915 b0452 b2197 b3918 b0789 b1249 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.691573 (mmol/gDw/h)
  Minimum Production Rate : 0.364028 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 21.652994
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.449780
  EX_pi_e : 1.395152
  EX_so4_e : 0.174152
  EX_k_e : 0.134990
  EX_fe3_e : 0.011107
  EX_mg2_e : 0.005999
  EX_ca2_e : 0.003600
  EX_cl_e : 0.003600
  EX_cu2_e : 0.000490
  EX_mn2_e : 0.000478
  EX_zn2_e : 0.000236
  EX_ni2_e : 0.000223
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 45.649817
  EX_co2_e : 22.399405
  EX_h_e : 8.060683
  EX_succ_e : 0.721166
  Auxiliary production reaction : 0.364028
  EX_ura_e : 0.126399
  DM_5drib_c : 0.000156
  DM_4crsol_c : 0.000154

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.

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Last updated: 21-Sep-2023
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