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 : hxan_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (61 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3553 b0512 b0871 b3115 b1849 b2296 b2925 b2097 b1004 b3713 b1109 b0046 b3236 b3946 b0825 b1033 b1602 b2913 b4381 b1727 b0114 b0529 b2492 b0904 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.413656 (mmol/gDw/h)
  Minimum Production Rate : 0.099985 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 25.152651
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.911793
  EX_pi_e : 0.399015
  EX_so4_e : 0.104167
  EX_k_e : 0.080743
  EX_fe2_e : 0.006644
  EX_mg2_e : 0.003588
  EX_ca2_e : 0.002153
  EX_cl_e : 0.002153
  EX_cu2_e : 0.000293
  EX_mn2_e : 0.000286
  EX_zn2_e : 0.000141
  EX_ni2_e : 0.000134
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 38.542647
  EX_co2_e : 27.995958
  EX_h_e : 5.968541
  EX_12ppd__R_e : 3.099955
  EX_pyr_e : 1.723360
  EX_hxan_e : 0.111087
  DM_5drib_c : 0.000093
  DM_4crsol_c : 0.000092

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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