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 : 2h3oppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4382 b4384 b3708 b3008 b0871 b2779 b2926 b0030 b2407 b0120 b1982 b2797 b3117 b1814 b4471 b0261 b2406 b0112 b3915 b0452 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b0594 b4141 b1798 b3662 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.676634 (mmol/gDw/h)
  Minimum Production Rate : 0.077322 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.381583
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.462994
  EX_pi_e : 0.652685
  EX_so4_e : 0.170390
  EX_k_e : 0.132074
  EX_fe3_e : 0.010867
  EX_mg2_e : 0.005870
  EX_cl_e : 0.003522
  EX_ca2_e : 0.003522
  EX_cu2_e : 0.000480
  EX_mn2_e : 0.000468
  EX_zn2_e : 0.000231
  EX_ni2_e : 0.000219
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 48.541929
  EX_co2_e : 29.827266
  EX_h_e : 6.616177
  DM_oxam_c : 0.155401
  DM_5drib_c : 0.155098
  DM_4crsol_c : 0.154795
  Auxiliary production reaction : 0.077322

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.

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Last updated: 21-Sep-2023
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