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 (53 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b2836 b4384 b3708 b3008 b3752 b2930 b4232 b3697 b3925 b0512 b0871 b2779 b2926 b2407 b1238 b2690 b0120 b1982 b2797 b3117 b1814 b4471 b0596 b0261 b3945 b3709 b4381 b2406 b3161 b0112 b2789 b3127 b2975 b0114 b3603 b0886 b2366 b2492 b0904 b2578 b1533 b3927 b1473 b4141 b1798 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.615370 (mmol/gDw/h)
  Minimum Production Rate : 0.084720 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.338256
  EX_o2_e : 276.488359
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.241732
  EX_pi_e : 0.847748
  EX_so4_e : 0.239682
  EX_k_e : 0.120116
  EX_mg2_e : 0.005338
  EX_ca2_e : 0.003203
  EX_cl_e : 0.003203
  EX_cu2_e : 0.000436
  EX_mn2_e : 0.000425
  EX_zn2_e : 0.000210
  EX_ni2_e : 0.000199
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990117
  EX_h2o_e : 547.167617
  EX_co2_e : 27.058850
  EX_pyr_e : 1.655965
  Auxiliary production reaction : 0.084720
  EX_alltn_e : 0.000689
  DM_5drib_c : 0.000413
  DM_4crsol_c : 0.000137

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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