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 : 2h3oppan_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b0871 b2925 b2097 b0030 b2407 b1982 b3616 b3589 b3946 b0825 b3665 b0261 b2913 b2406 b0112 b0114 b0755 b3612 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.435872 (mmol/gDw/h)
  Minimum Production Rate : 0.289955 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 24.469062
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.252113
  EX_pi_e : 0.420445
  EX_so4_e : 0.109761
  EX_k_e : 0.085079
  EX_fe2_e : 0.007001
  EX_mg2_e : 0.003781
  EX_cl_e : 0.002269
  EX_ca2_e : 0.002269
  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 : 46.656579
  EX_co2_e : 25.641609
  EX_h_e : 7.839653
  EX_acald_e : 1.775386
  EX_ade_e : 0.708946
  DM_5drib_c : 0.708751
  DM_4crsol_c : 0.708555
  Auxiliary production reaction : 0.289955

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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