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 : ipdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4384 b3708 b3008 b3752 b2930 b4232 b3697 b3925 b0871 b2926 b2407 b3124 b3236 b0517 b1982 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b4381 b0452 b0114 b2366 b2492 b0904 b1533 b3927 b0514 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.373038 (mmol/gDw/h)
  Minimum Production Rate : 0.257625 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.995119
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.028774
  EX_pi_e : 0.875083
  EX_so4_e : 0.093938
  EX_k_e : 0.072814
  EX_fe2_e : 0.005991
  EX_mg2_e : 0.003236
  EX_ca2_e : 0.001942
  EX_cl_e : 0.001942
  EX_cu2_e : 0.000264
  EX_mn2_e : 0.000258
  EX_zn2_e : 0.000127
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 44.091119
  EX_co2_e : 28.887645
  EX_h_e : 8.007578
  EX_pyr_e : 4.837335
  Auxiliary production reaction : 0.257625
  EX_glyc__R_e : 0.000250
  DM_5drib_c : 0.000084
  DM_4crsol_c : 0.000083

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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