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 : dimp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (78 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3942 b1732 b3708 b3008 b0910 b3752 b0871 b2925 b2097 b2926 b2407 b3236 b2883 b2690 b2797 b3117 b1814 b4471 b2210 b0675 b0822 b4381 b2406 b0452 b2868 b1727 b4064 b4464 b0114 b1539 b2492 b0904 b1533 b3927 b1518 b0221 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.366731 (mmol/gDw/h)
  Minimum Production Rate : 0.056100 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.253119
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.234272
  EX_pi_e : 0.409851
  EX_so4_e : 0.092350
  EX_k_e : 0.071583
  EX_fe2_e : 0.005890
  EX_mg2_e : 0.003181
  EX_ca2_e : 0.001909
  EX_cl_e : 0.001909
  EX_cu2_e : 0.000260
  EX_mn2_e : 0.000253
  EX_zn2_e : 0.000125
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 43.986277
  EX_co2_e : 28.211436
  EX_h_e : 9.018255
  EX_pyr_e : 5.374975
  Auxiliary production reaction : 0.056100
  EX_ade_e : 0.009843
  DM_mththf_c : 0.000164
  DM_5drib_c : 0.000083
  DM_4crsol_c : 0.000082

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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