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 : adprib_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (77 of 97: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4382 b0238 b0125 b4384 b2744 b3708 b3008 b0871 b2926 b0030 b2883 b1982 b0477 b2797 b3117 b1814 b4471 b0261 b2406 b2868 b4064 b4464 b0114 b0886 b2366 b0529 b2492 b0904 b2578 b1533 b3927 b3821 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.680246 (mmol/gDw/h)
  Minimum Production Rate : 0.156140 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.672041
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.131107
  EX_pi_e : 0.968450
  EX_so4_e : 0.171300
  EX_k_e : 0.132779
  EX_fe2_e : 0.010925
  EX_mg2_e : 0.005901
  EX_ca2_e : 0.003541
  EX_cl_e : 0.003541
  EX_cu2_e : 0.000482
  EX_mn2_e : 0.000470
  EX_zn2_e : 0.000232
  EX_ni2_e : 0.000220
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 49.888591
  EX_co2_e : 29.731597
  EX_h_e : 6.722599
  Auxiliary production reaction : 0.156140
  EX_ade_e : 0.000761
  DM_5drib_c : 0.000456
  DM_4crsol_c : 0.000152

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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