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 : dcdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4382 b3942 b1732 b1241 b0351 b4069 b4384 b0871 b3115 b1849 b2296 b2925 b2097 b2926 b0030 b2407 b3236 b3962 b1982 b3616 b3589 b3946 b2210 b0825 b4267 b3665 b1415 b2799 b2406 b0112 b0114 b0509 b3125 b0529 b2492 b0904 b1380 b4266 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.287085 (mmol/gDw/h)
  Minimum Production Rate : 1.100766 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.055312
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.403755
  EX_pi_e : 2.478455
  EX_so4_e : 0.072294
  EX_k_e : 0.056037
  EX_fe2_e : 0.004611
  EX_mg2_e : 0.002490
  EX_ca2_e : 0.001494
  EX_cl_e : 0.001494
  EX_cu2_e : 0.000204
  EX_mn2_e : 0.000198
  EX_zn2_e : 0.000098
  EX_ni2_e : 0.000093

Product: (mmol/gDw/h)
  EX_h2o_e : 47.836738
  EX_co2_e : 26.786427
  EX_h_e : 8.820654
  EX_pyr_e : 3.560369
  Auxiliary production reaction : 1.100766
  EX_ac_e : 0.419744
  EX_ade_e : 0.000193
  EX_dxylnt_e : 0.000192
  DM_mththf_c : 0.000129
  DM_5drib_c : 0.000065
  DM_4crsol_c : 0.000064

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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