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 (66 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3553 b0469 b4382 b0238 b0125 b4384 b0871 b3115 b1849 b2296 b1004 b3713 b1109 b0046 b3236 b0477 b1033 b1602 b2913 b1727 b0114 b0529 b2492 b0904 b1380 b0515 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.524470 (mmol/gDw/h)
  Minimum Production Rate : 0.084296 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 37.142065
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.003180
  EX_pi_e : 0.505907
  EX_so4_e : 0.132072
  EX_k_e : 0.102373
  EX_fe2_e : 0.008424
  EX_mg2_e : 0.004550
  EX_ca2_e : 0.002730
  EX_cl_e : 0.002730
  EX_cu2_e : 0.000372
  EX_mn2_e : 0.000362
  EX_zn2_e : 0.000179
  EX_ni2_e : 0.000169
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.661668
  EX_co2_e : 38.049672
  EX_h_e : 5.157988
  EX_hxan_e : 0.084296
  EX_ade_e : 0.000353
  DM_5drib_c : 0.000118
  DM_4crsol_c : 0.000117

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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