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 : q8h2_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b1478 b4382 b1241 b4384 b3708 b3008 b3752 b0871 b2779 b2925 b2097 b2407 b1612 b1611 b4122 b2690 b2797 b3117 b1814 b4471 b0675 b0822 b0114 b2366 b2492 b0904 b1533 b3927 b3821 b1912 b1813 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.369644 (mmol/gDw/h)
  Minimum Production Rate : 0.011088 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.849325
  EX_o2_e : 279.990709
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.025635
  EX_pi_e : 0.356561
  EX_so4_e : 0.093084
  EX_k_e : 0.072152
  EX_mg2_e : 0.003207
  EX_ca2_e : 0.001924
  EX_cl_e : 0.001924
  EX_cu2_e : 0.000262
  EX_mn2_e : 0.000255
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994063
  EX_h2o_e : 543.707192
  EX_co2_e : 28.078615
  EX_pyr_e : 4.776296
  EX_fum_e : 0.452490
  DM_oxam_c : 0.033514
  Auxiliary production reaction : 0.011088
  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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