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 : dgtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b0474 b2518 b1241 b0351 b4069 b3708 b3752 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2779 b2407 b2883 b2797 b3117 b1814 b4471 b3616 b3589 b3946 b0825 b0261 b2913 b4381 b2868 b4064 b4464 b0114 b2366 b2492 b0904 b1380   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.523164 (mmol/gDw/h)
  Minimum Production Rate : 0.521991 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.573288
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.261840
  EX_pi_e : 2.070619
  EX_so4_e : 0.131743
  EX_k_e : 0.102118
  EX_fe2_e : 0.008403
  EX_mg2_e : 0.004538
  EX_ca2_e : 0.002723
  EX_cl_e : 0.002723
  EX_cu2_e : 0.000371
  EX_mn2_e : 0.000362
  EX_zn2_e : 0.000178
  EX_ni2_e : 0.000169
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 48.510490
  EX_co2_e : 27.383786
  EX_h_e : 9.335219
  EX_ac_e : 2.960272
  Auxiliary production reaction : 0.521991
  EX_ade_e : 0.000352
  EX_glyc__R_e : 0.000175
  DM_5drib_c : 0.000118
  DM_4crsol_c : 0.000117

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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