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 (50 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b3708 b3008 b0871 b2779 b2925 b2097 b1612 b1611 b4122 b2797 b3117 b1814 b4471 b3946 b0825 b2440 b2913 b4381 b0114 b1539 b2492 b0904 b1533 b3927 b0515 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.370473 (mmol/gDw/h)
  Minimum Production Rate : 0.252263 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 29.589422
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.006864
  EX_pi_e : 0.609623
  EX_so4_e : 0.093293
  EX_k_e : 0.072314
  EX_fe2_e : 0.005950
  EX_mg2_e : 0.003214
  EX_ca2_e : 0.001928
  EX_cl_e : 0.001928
  EX_cu2_e : 0.000263
  EX_mn2_e : 0.000256
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000120

Product: (mmol/gDw/h)
  EX_h2o_e : 43.307330
  EX_co2_e : 27.741729
  EX_h_e : 8.930006
  EX_pyr_e : 4.744496
  EX_fum_e : 0.387773
  Auxiliary production reaction : 0.252263
  EX_alltn_e : 0.001446
  EX_glyc__R_e : 0.000124
  DM_5drib_c : 0.000083
  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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