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 : dgsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3399 b4069 b2744 b3708 b2297 b2458 b2925 b2097 b2926 b2797 b3117 b1814 b4471 b3946 b0825 b4381 b0452 b2868 b0114 b2366 b2492 b0904 b1533 b3927 b1511 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.400715 (mmol/gDw/h)
  Minimum Production Rate : 0.119640 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 32.001583
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.969172
  EX_pi_e : 0.386532
  EX_so4_e : 0.100908
  EX_k_e : 0.078217
  EX_fe2_e : 0.006436
  EX_mg2_e : 0.003476
  EX_ca2_e : 0.002086
  EX_cl_e : 0.002086
  EX_cu2_e : 0.000284
  EX_mn2_e : 0.000277
  EX_zn2_e : 0.000137
  EX_ni2_e : 0.000129
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 44.520354
  EX_co2_e : 32.525487
  EX_h_e : 9.211388
  EX_ac_e : 4.887974
  Auxiliary production reaction : 0.119640
  EX_xan_e : 0.010485
  EX_ade_e : 0.000270
  DM_mththf_c : 0.000180
  DM_5drib_c : 0.000090
  DM_4crsol_c : 0.000089

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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