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 (61 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 51
  Gene deletion: b2836 b0474 b2518 b1241 b0351 b4069 b4384 b2744 b3708 b2297 b2458 b2779 b2926 b2781 b3617 b0030 b2407 b3844 b1759 b1982 b2797 b3117 b1814 b4471 b4374 b4161 b0675 b0261 b3709 b2913 b4381 b2406 b3161 b0112 b2789 b3127 b2975 b0114 b3603 b2366 b2492 b0904 b0591 b1533 b3918 b1912 b1473 b4141 b1798 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.295903 (mmol/gDw/h)
  Minimum Production Rate : 0.277282 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.991264
  EX_o2_e : 283.720055
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.798763
  EX_pi_e : 1.117276
  EX_so4_e : 0.351796
  EX_k_e : 0.057758
  EX_mg2_e : 0.002567
  EX_ca2_e : 0.001540
  EX_cl_e : 0.001540
  EX_cu2_e : 0.000210
  EX_mn2_e : 0.000204
  EX_zn2_e : 0.000101
  EX_ni2_e : 0.000096

Product: (mmol/gDw/h)
  EX_fe3_e : 999.995248
  EX_h2o_e : 550.974619
  EX_co2_e : 34.298692
  EX_ac_e : 1.513588
  EX_thym_e : 0.330865
  Auxiliary production reaction : 0.277282
  DM_oxam_c : 0.000331
  DM_5drib_c : 0.000199
  DM_4crsol_c : 0.000066

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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