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 : pant__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 93: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3553 b3831 b4384 b0871 b2925 b2097 b2407 b1004 b3713 b1109 b0046 b3236 b2498 b3946 b0825 b1033 b1602 b2913 b0114 b0755 b3612 b2492 b0904 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.388054 (mmol/gDw/h)
  Minimum Production Rate : 1.086051 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.143804
  EX_o2_e : 280.144336
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.190955
  EX_pi_e : 0.374320
  EX_so4_e : 0.097720
  EX_k_e : 0.075746
  EX_mg2_e : 0.003366
  EX_ca2_e : 0.002020
  EX_cl_e : 0.002020
  EX_cu2_e : 0.000275
  EX_mn2_e : 0.000268
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993767
  EX_h2o_e : 543.403545
  EX_co2_e : 30.960904
  EX_pyr_e : 2.198314
  Auxiliary production reaction : 1.086051
  DM_5drib_c : 0.000087
  DM_4crsol_c : 0.000087

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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