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 : nmn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b2744 b1278 b3614 b0910 b4152 b2781 b2235 b3844 b1612 b1611 b4122 b1759 b4374 b0675 b4138 b4123 b0621 b2913 b4381 b1654 b3610 b0849 b1064 b0452 b0755 b3612 b3918 b1206 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.626826 (mmol/gDw/h)
  Minimum Production Rate : 0.078034 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.140270
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.658687
  EX_pi_e : 0.682673
  EX_so4_e : 0.157847
  EX_k_e : 0.122352
  EX_fe2_e : 0.010067
  EX_mg2_e : 0.005438
  EX_ca2_e : 0.003263
  EX_cl_e : 0.003263
  EX_cu2_e : 0.000444
  EX_mn2_e : 0.000433
  EX_zn2_e : 0.000214
  EX_ni2_e : 0.000202
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 47.731251
  EX_co2_e : 27.815290
  EX_h_e : 7.877811
  EX_succ_e : 0.653649
  EX_thymd_e : 0.252920
  EX_ura_e : 0.113558
  Auxiliary production reaction : 0.078034
  DM_5drib_c : 0.000141
  DM_4crsol_c : 0.000140

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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