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 : mnl1p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 60
  Gene deletion: b4467 b1478 b4269 b0493 b3846 b3588 b2341 b3003 b3011 b1241 b0351 b4069 b4384 b2744 b3752 b3115 b1849 b2296 b2925 b2097 b2926 b3617 b2407 b1004 b3713 b1109 b0046 b3236 b1638 b2690 b3908 b1656 b0207 b3012 b1982 b1525 b4139 b1623 b4374 b2361 b2291 b4015 b2661 b0261 b2799 b1602 b2406 b3915 b1539 b2492 b0904 b2954 b1781 b3001 b1380 b0325 b2660 b1771 b2285 b1008   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.400063 (mmol/gDw/h)
  Minimum Production Rate : 0.270644 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.184866
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.320647
  EX_pi_e : 0.656548
  EX_so4_e : 0.100744
  EX_k_e : 0.078090
  EX_fe3_e : 0.006425
  EX_mg2_e : 0.003471
  EX_ca2_e : 0.002082
  EX_cl_e : 0.002082
  EX_cu2_e : 0.000284
  EX_mn2_e : 0.000276
  EX_zn2_e : 0.000136
  EX_ni2_e : 0.000129
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 43.069750
  EX_co2_e : 32.508405
  EX_h_e : 7.739405
  EX_ac_e : 4.056593
  EX_acald_e : 0.666003
  Auxiliary production reaction : 0.270644
  EX_glyclt_e : 0.000448
  DM_5drib_c : 0.000268
  DM_4crsol_c : 0.000089

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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