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 : 2dr5p_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4069 b2744 b3708 b3008 b2297 b2458 b2926 b2883 b2797 b3117 b1814 b4471 b0261 b0411 b4381 b3654 b2868 b3714 b3664 b4064 b4464 b0114 b1539 b2492 b0904 b1533 b3927 b3821 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.653553 (mmol/gDw/h)
  Minimum Production Rate : 0.832724 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.603907
  EX_o2_e : 276.436366
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.058318
  EX_pi_e : 1.463145
  EX_so4_e : 0.164578
  EX_k_e : 0.127569
  EX_mg2_e : 0.005670
  EX_ca2_e : 0.003402
  EX_cl_e : 0.003402
  EX_cu2_e : 0.000463
  EX_mn2_e : 0.000452
  EX_zn2_e : 0.000223
  EX_ni2_e : 0.000211
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989503
  EX_h2o_e : 546.336054
  EX_co2_e : 28.250048
  Auxiliary production reaction : 0.832724
  EX_ac_e : 0.380489
  DM_5drib_c : 0.000147
  DM_4crsol_c : 0.000146

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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