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 : histd_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (41 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b4467 b4069 b4384 b2297 b2458 b0030 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b1779 b0937 b1982 b0261 b2799 b3945 b1602 b2913 b4381 b2406 b1727 b0114 b0529 b2492 b0904 b1380 b3662 b0606 b2285 b1009   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.411974 (mmol/gDw/h)
  Minimum Production Rate : 0.933125 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.042332
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.250502
  EX_pi_e : 0.397392
  EX_so4_e : 0.103743
  EX_k_e : 0.080414
  EX_fe2_e : 0.006617
  EX_mg2_e : 0.003574
  EX_cl_e : 0.002144
  EX_ca2_e : 0.002144
  EX_cu2_e : 0.000292
  EX_mn2_e : 0.000285
  EX_zn2_e : 0.000140
  EX_ni2_e : 0.000133
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 51.469297
  EX_co2_e : 36.283189
  EX_h_e : 5.893320
  Auxiliary production reaction : 0.933125
  EX_etoh_e : 0.362756
  EX_ac_e : 0.239845
  EX_hxan_e : 0.000461
  DM_5drib_c : 0.000276
  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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