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 : cdigmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b2744 b1479 b3752 b3115 b1849 b2296 b3617 b2407 b3236 b2463 b1982 b2210 b0511 b0114 b0529 b2492 b0904 b0515 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.569175 (mmol/gDw/h)
  Minimum Production Rate : 0.545595 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.936216
  EX_nh4_e : 11.604528
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.640220
  EX_so4_e : 0.143330
  EX_k_e : 0.111099
  EX_fe2_e : 0.009142
  EX_mg2_e : 0.004938
  EX_ca2_e : 0.002963
  EX_cl_e : 0.002963
  EX_cu2_e : 0.000404
  EX_mn2_e : 0.000393
  EX_zn2_e : 0.000194
  EX_ni2_e : 0.000184
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 51.095392
  EX_co2_e : 21.876127
  EX_h_e : 11.519479
  EX_ac_e : 1.923377
  Auxiliary production reaction : 0.545595
  EX_xan_e : 0.000383
  DM_mththf_c : 0.000255
  DM_5drib_c : 0.000128
  DM_4crsol_c : 0.000127

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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