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 : 4c2me_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (75 of 96: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b0474 b2518 b2744 b4152 b2781 b1850 b1612 b1611 b4122 b1759 b4374 b4161 b0675 b4138 b4123 b0621 b2913 b4381 b2406 b0114 b0755 b3612 b3821 b3918 b4042 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.609942 (mmol/gDw/h)
  Minimum Production Rate : 0.073523 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.073555
  EX_o2_e : 277.037483
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.360181
  EX_pi_e : 0.735399
  EX_so4_e : 0.153596
  EX_k_e : 0.119056
  EX_mg2_e : 0.005291
  EX_ca2_e : 0.003175
  EX_cl_e : 0.003175
  EX_cu2_e : 0.000432
  EX_mn2_e : 0.000421
  EX_zn2_e : 0.000208
  EX_ni2_e : 0.000197
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.907332
  EX_h2o_e : 547.948300
  EX_co2_e : 28.131945
  EX_succ_e : 0.636043
  EX_ura_e : 0.110401
  EX_pheme_e : 0.082872
  Auxiliary production reaction : 0.073523
  DM_5drib_c : 0.000137
  DM_4crsol_c : 0.000136

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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