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 : 5aizc_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (52 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4382 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b0474 b2518 b1241 b0351 b4384 b3752 b0871 b2926 b1850 b3617 b2407 b3236 b1982 b2210 b3665 b0261 b2406 b0112 b0114 b0529 b2492 b0904 b1380 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.436221 (mmol/gDw/h)
  Minimum Production Rate : 1.418050 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 26.730395
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.967740
  EX_pi_e : 1.838831
  EX_so4_e : 0.109849
  EX_k_e : 0.085147
  EX_fe2_e : 0.007006
  EX_mg2_e : 0.003784
  EX_ca2_e : 0.002271
  EX_cl_e : 0.002271
  EX_cu2_e : 0.000309
  EX_mn2_e : 0.000301
  EX_zn2_e : 0.000149
  EX_ni2_e : 0.000141
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 48.593785
  EX_co2_e : 25.725115
  EX_h_e : 9.682813
  EX_acald_e : 1.802078
  Auxiliary production reaction : 1.418050
  EX_ade_e : 0.000488
  DM_5drib_c : 0.000293
  DM_4crsol_c : 0.000097

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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