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 : gsn_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (43 of 49: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b4467 b3399 b4069 b4384 b2744 b3115 b1849 b2296 b2925 b2097 b0030 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b1779 b2690 b3908 b1656 b1982 b4139 b1623 b0261 b3945 b1602 b2913 b4381 b2406 b1727 b0114 b0529 b2492 b0904 b3927 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.391974 (mmol/gDw/h)
  Minimum Production Rate : 0.067272 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 32.205432
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.569639
  EX_pi_e : 0.378100
  EX_so4_e : 0.098707
  EX_k_e : 0.076510
  EX_fe3_e : 0.006295
  EX_mg2_e : 0.003400
  EX_cl_e : 0.002040
  EX_ca2_e : 0.002040
  EX_cu2_e : 0.000278
  EX_mn2_e : 0.000271
  EX_zn2_e : 0.000134
  EX_ni2_e : 0.000127

Product: (mmol/gDw/h)
  EX_h2o_e : 43.929317
  EX_co2_e : 32.841539
  EX_h_e : 9.142341
  EX_ac_e : 5.197640
  EX_gsn_e : 0.067272
  EX_glyclt_e : 0.000439
  DM_5drib_c : 0.000263
  DM_4crsol_c : 0.000087

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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