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 : hpyr_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 49
  Gene deletion: b4467 b4069 b4384 b3708 b3752 b2930 b4232 b3697 b3925 b3115 b1849 b2296 b2779 b2926 b2407 b1004 b3713 b1109 b0046 b3236 b2690 b1982 b2797 b3117 b1814 b4471 b2440 b0675 b0261 b0822 b1602 b4381 b2239 b2406 b2789 b3127 b1727 b2975 b0114 b3603 b2366 b0529 b2492 b0904 b1533 b3927 b1380 b3662 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.377139 (mmol/gDw/h)
  Minimum Production Rate : 0.079878 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 31.912907
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.233250
  EX_pi_e : 0.363791
  EX_so4_e : 0.094971
  EX_k_e : 0.073615
  EX_fe2_e : 0.006057
  EX_mg2_e : 0.003272
  EX_ca2_e : 0.001963
  EX_cl_e : 0.001963
  EX_cu2_e : 0.000267
  EX_mn2_e : 0.000261
  EX_zn2_e : 0.000129
  EX_ni2_e : 0.000122

Product: (mmol/gDw/h)
  EX_h2o_e : 43.555885
  EX_co2_e : 32.717181
  EX_h_e : 8.528084
  EX_ac_e : 4.662546
  DM_oxam_c : 0.160177
  DM_5drib_c : 0.160008
  DM_4crsol_c : 0.159839
  Auxiliary production reaction : 0.079878

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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