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 : fpram_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (46 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 42
  Gene deletion: b3553 b1478 b1241 b0351 b2930 b4232 b3697 b3925 b0871 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b0937 b3946 b2210 b0825 b1033 b0411 b2799 b3945 b1602 b2913 b4381 b3654 b3714 b3664 b4064 b4464 b0529 b1539 b2492 b0904 b3927 b1380 b1518 b0606 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.375991 (mmol/gDw/h)
  Minimum Production Rate : 0.022314 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 30.427849
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.127607
  EX_pi_e : 0.384996
  EX_so4_e : 0.094682
  EX_k_e : 0.073391
  EX_fe2_e : 0.006039
  EX_mg2_e : 0.003262
  EX_ca2_e : 0.001957
  EX_cl_e : 0.001957
  EX_cu2_e : 0.000267
  EX_mn2_e : 0.000260
  EX_zn2_e : 0.000128
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_h2o_e : 43.906671
  EX_co2_e : 28.571896
  EX_h_e : 8.771401
  EX_pyr_e : 5.272022
  Auxiliary production reaction : 0.022314
  DM_mththf_c : 0.000168
  DM_5drib_c : 0.000085
  DM_4crsol_c : 0.000084

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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