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 : dcmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (39 of 117: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b3752 b0871 b3617 b2883 b1982 b0261 b4381 b2406 b0112 b2868 b4064 b4464 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.549633 (mmol/gDw/h)
  Minimum Production Rate : 1.786726 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 20.760781
  EX_nh4_e : 11.299246
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.316906
  EX_so4_e : 0.138409
  EX_k_e : 0.107285
  EX_fe2_e : 0.008828
  EX_mg2_e : 0.004768
  EX_ca2_e : 0.002861
  EX_cl_e : 0.002861
  EX_cu2_e : 0.000390
  EX_mn2_e : 0.000380
  EX_zn2_e : 0.000187
  EX_ni2_e : 0.000178
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 49.201757
  EX_co2_e : 20.387504
  EX_h_e : 10.413503
  Auxiliary production reaction : 1.786726
  EX_acald_e : 0.483871
  EX_ade_e : 0.000615
  DM_5drib_c : 0.000369
  DM_4crsol_c : 0.000123

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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