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 : prfp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b0238 b0125 b4069 b4384 b2744 b3708 b3008 b3752 b2297 b2458 b2779 b2883 b1982 b0477 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b2406 b2868 b4064 b4464 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b3821 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.644311 (mmol/gDw/h)
  Minimum Production Rate : 0.272928 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.013808
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.326753
  EX_pi_e : 1.167363
  EX_so4_e : 0.162250
  EX_k_e : 0.125765
  EX_fe2_e : 0.010348
  EX_mg2_e : 0.005589
  EX_cl_e : 0.003354
  EX_ca2_e : 0.003354
  EX_cu2_e : 0.000457
  EX_mn2_e : 0.000445
  EX_zn2_e : 0.000220
  EX_ni2_e : 0.000208
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 49.274557
  EX_co2_e : 28.704802
  EX_h_e : 7.663544
  EX_ac_e : 0.375109
  Auxiliary production reaction : 0.272928
  EX_ade_e : 0.000721
  DM_5drib_c : 0.000432
  DM_4crsol_c : 0.000144

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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