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 : malcoame_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 93: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b4467 b4382 b4069 b4384 b3708 b3752 b2297 b2458 b2779 b2925 b2097 b2407 b3844 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b2797 b3117 b1814 b4471 b0261 b1701 b1805 b2799 b3945 b1602 b2913 b2406 b1727 b0114 b2366 b2492 b0904 b1533 b1380 b3662 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.385734 (mmol/gDw/h)
  Minimum Production Rate : 0.054465 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.761145
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.821632
  EX_pi_e : 0.535477
  EX_fe3_e : 0.411082
  EX_so4_e : 0.151601
  EX_k_e : 0.075293
  EX_mg2_e : 0.003346
  EX_ca2_e : 0.002008
  EX_cl_e : 0.002008
  EX_cu2_e : 0.000273
  EX_mn2_e : 0.000267
  EX_zn2_e : 0.000132
  EX_ni2_e : 0.000125

Product: (mmol/gDw/h)
  EX_h2o_e : 44.250514
  EX_co2_e : 32.577156
  EX_h_e : 9.369874
  EX_ac_e : 4.976637
  EX_fe2_e : 0.404887
  EX_ade_e : 0.054897
  Auxiliary production reaction : 0.054465
  DM_5drib_c : 0.000259
  DM_4crsol_c : 0.000086

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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