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 : succoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (17 of 28: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b2836 b0238 b0125 b4384 b2744 b3708 b3008 b0871 b0030 b2883 b1982 b0477 b2797 b3117 b1814 b4471 b4374 b2361 b2291 b0261 b0411 b2342 b3845 b2868 b4064 b4464 b0114 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.766742 (mmol/gDw/h)
  Minimum Production Rate : 0.087997 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.644580
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.901015
  EX_pi_e : 1.003595
  EX_so4_e : 0.281078
  EX_k_e : 0.149663
  EX_fe2_e : 0.012315
  EX_mg2_e : 0.006651
  EX_ca2_e : 0.003991
  EX_cl_e : 0.003991
  EX_cu2_e : 0.000544
  EX_mn2_e : 0.000530
  EX_zn2_e : 0.000261
  EX_ni2_e : 0.000248
  EX_cobalt2_e : 0.000019

Product: (mmol/gDw/h)
  EX_h2o_e : 48.426895
  EX_co2_e : 26.322847
  EX_h_e : 7.401407
  Auxiliary production reaction : 0.087997
  EX_ade_e : 0.000858
  DM_5drib_c : 0.000514
  DM_4crsol_c : 0.000171

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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