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 : dcyt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b2836 b3553 b4382 b4269 b0493 b3588 b3003 b3011 b4384 b3752 b2930 b4232 b3697 b3925 b0871 b2926 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b3908 b1656 b1982 b4139 b1033 b1623 b0261 b2799 b3945 b1602 b0507 b2406 b3915 b1727 b0114 b0529 b2492 b0904 b2954 b1380 b2660 b3662 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.337522 (mmol/gDw/h)
  Minimum Production Rate : 0.367488 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.122306
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.942952
  EX_pi_e : 0.325575
  EX_so4_e : 0.084995
  EX_k_e : 0.065882
  EX_fe3_e : 0.005421
  EX_mg2_e : 0.002928
  EX_ca2_e : 0.001757
  EX_cl_e : 0.001757
  EX_cu2_e : 0.000239
  EX_mn2_e : 0.000233
  EX_zn2_e : 0.000115
  EX_ni2_e : 0.000109

Product: (mmol/gDw/h)
  EX_h2o_e : 44.530911
  EX_co2_e : 27.906752
  EX_h_e : 9.348719
  EX_pyr_e : 4.944267
  Auxiliary production reaction : 0.367488
  EX_urea_e : 0.096697
  EX_ade_e : 0.000378
  DM_5drib_c : 0.000226
  DM_4crsol_c : 0.000075

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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