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 : fgam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3942 b1732 b4384 b2744 b3708 b3008 b3752 b2930 b4232 b3697 b3925 b0871 b2926 b2407 b3844 b3236 b0517 b1982 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b4374 b2361 b2291 b0507 b0452 b0114 b2366 b2492 b0904 b2578 b1533 b3927 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.622835 (mmol/gDw/h)
  Minimum Production Rate : 0.211831 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.542888
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.159949
  EX_pi_e : 0.812621
  EX_so4_e : 0.156842
  EX_k_e : 0.121573
  EX_fe2_e : 0.010003
  EX_mg2_e : 0.005403
  EX_cl_e : 0.003242
  EX_ca2_e : 0.003242
  EX_cu2_e : 0.000442
  EX_mn2_e : 0.000430
  EX_zn2_e : 0.000212
  EX_ni2_e : 0.000201
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 46.189884
  EX_co2_e : 26.639717
  EX_h_e : 8.182892
  EX_pyr_e : 2.026651
  Auxiliary production reaction : 0.211831
  EX_alltn_e : 0.002432
  DM_mththf_c : 0.002014
  DM_5drib_c : 0.000418
  DM_4crsol_c : 0.000139

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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