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 : duri_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 50: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 48
  Gene deletion: b4467 b1478 b3846 b2341 b1241 b4069 b3708 b2297 b2458 b2779 b1238 b1004 b3713 b1109 b0046 b3236 b2797 b3117 b1814 b4471 b1701 b1805 b2799 b0505 b3945 b1602 b2913 b4381 b2406 b3915 b3654 b3714 b3664 b4064 b4464 b2366 b2492 b0904 b1533 b1380 b1511 b4141 b1798 b3662 b0606 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.443080 (mmol/gDw/h)
  Minimum Production Rate : 0.369879 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 35.911222
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.264610
  EX_pi_e : 0.427398
  EX_so4_e : 0.111577
  EX_k_e : 0.086486
  EX_fe3_e : 0.007118
  EX_mg2_e : 0.003844
  EX_ca2_e : 0.002306
  EX_cl_e : 0.002306
  EX_cu2_e : 0.000314
  EX_mn2_e : 0.000306
  EX_zn2_e : 0.000151
  EX_ni2_e : 0.000143
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 51.884117
  EX_co2_e : 36.118855
  EX_h_e : 5.815653
  Auxiliary production reaction : 0.369845
  EX_thym_e : 0.369845
  EX_ac_e : 0.257956
  EX_mththf_e : 0.000198
  DM_5drib_c : 0.000100
  DM_4crsol_c : 0.000099

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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