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 : gdpddman_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (60 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b4384 b3708 b3008 b3752 b2930 b4232 b3697 b3925 b0871 b2779 b2407 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b0261 b4381 b2406 b0114 b0886 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b2835 b0494 b0594 b0516 b3662 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.619561 (mmol/gDw/h)
  Minimum Production Rate : 0.140486 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.407186
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.403309
  EX_pi_e : 0.878604
  EX_so4_e : 0.156018
  EX_k_e : 0.120934
  EX_fe2_e : 0.009951
  EX_mg2_e : 0.005375
  EX_ca2_e : 0.003225
  EX_cl_e : 0.003225
  EX_cu2_e : 0.000439
  EX_mn2_e : 0.000428
  EX_zn2_e : 0.000211
  EX_ni2_e : 0.000200
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.790864
  EX_co2_e : 26.306995
  EX_h_e : 8.118352
  EX_pyr_e : 1.993584
  Auxiliary production reaction : 0.140486
  EX_alltn_e : 0.002419
  DM_5drib_c : 0.002141
  DM_4crsol_c : 0.001864
  EX_glyc__R_e : 0.000863

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.

Last updated: 21-Sep-2023
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