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 : sbzcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 47
  Gene deletion: b4382 b3942 b1732 b4069 b4384 b3708 b3008 b3115 b1849 b2296 b2925 b2097 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b0596 b0261 b3709 b2406 b3161 b0112 b2975 b0114 b3603 b0886 b0509 b3125 b1539 b2492 b0904 b2578 b1533 b3927 b3821 b0508 b1473 b0515 b4141 b1798 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.491003 (mmol/gDw/h)
  Minimum Production Rate : 0.155307 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 28.381140
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.397607
  EX_pi_e : 0.939545
  EX_so4_e : 0.278951
  EX_k_e : 0.095840
  EX_fe2_e : 0.007886
  EX_mg2_e : 0.004259
  EX_ca2_e : 0.002556
  EX_cl_e : 0.002556
  EX_cu2_e : 0.000348
  EX_mn2_e : 0.000339
  EX_zn2_e : 0.000167
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 46.602886
  EX_co2_e : 29.581351
  EX_h_e : 7.775545
  EX_ac_e : 2.635117
  Auxiliary production reaction : 0.155307
  EX_alltn_e : 0.001917
  DM_5drib_c : 0.001697
  DM_4crsol_c : 0.001477

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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