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 : 2p4c2me_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (90 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b2836 b3831 b3614 b0910 b3752 b4152 b2925 b2097 b2781 b1850 b1612 b1611 b4122 b1759 b1200 b4138 b4123 b0621 b4381 b2406 b0755 b3612 b3918 b0789 b1249 b1517 b1206 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.650293 (mmol/gDw/h)
  Minimum Production Rate : 0.343396 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.614351
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.288808
  EX_pi_e : 1.657465
  EX_so4_e : 0.163757
  EX_k_e : 0.126933
  EX_mg2_e : 0.005641
  EX_fe2_e : 0.005367
  EX_fe3_e : 0.005077
  EX_cl_e : 0.003385
  EX_ca2_e : 0.003385
  EX_cu2_e : 0.000461
  EX_mn2_e : 0.000449
  EX_zn2_e : 0.000222
  EX_ni2_e : 0.000210
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 47.186723
  EX_co2_e : 25.315964
  EX_h_e : 7.915376
  EX_succ_e : 0.678120
  Auxiliary production reaction : 0.343396
  EX_ura_e : 0.117757
  EX_mththf_e : 0.000291
  DM_5drib_c : 0.000146
  DM_4crsol_c : 0.000145

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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