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 : nicrnt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b3831 b3614 b0910 b3752 b3926 b2930 b4232 b3697 b3925 b4152 b0871 b2297 b2458 b2781 b1612 b1611 b4122 b1779 b1759 b3946 b0825 b4015 b0411 b0614 b0726 b4138 b4123 b0621 b0452 b0755 b3612 b3918 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.438707 (mmol/gDw/h)
  Minimum Production Rate : 0.231701 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.379330
  EX_o2_e : 281.022748
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.128513
  EX_pi_e : 0.654880
  EX_so4_e : 0.110475
  EX_k_e : 0.085633
  EX_mg2_e : 0.003806
  EX_cl_e : 0.002283
  EX_ca2_e : 0.002283
  EX_cu2_e : 0.000311
  EX_mn2_e : 0.000303
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992954
  EX_h2o_e : 546.310385
  EX_co2_e : 30.741586
  EX_succ_e : 1.968342
  EX_ac_e : 0.255409
  Auxiliary production reaction : 0.231701
  EX_ura_e : 0.079407
  DM_mththf_c : 0.000197
  DM_5drib_c : 0.000099
  DM_4crsol_c : 0.000098

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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