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 : grdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (45 of 51: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b4382 b3831 b3708 b3008 b0910 b3752 b2930 b4232 b3697 b3925 b4152 b0871 b1612 b1611 b4122 b2797 b3117 b1814 b4471 b3946 b0825 b4138 b4123 b0621 b4381 b2406 b0452 b0114 b1539 b2492 b0904 b1533 b3927 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.492034 (mmol/gDw/h)
  Minimum Production Rate : 0.129893 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.388046
  EX_o2_e : 277.882481
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.092222
  EX_pi_e : 0.734405
  EX_so4_e : 0.123904
  EX_k_e : 0.096042
  EX_mg2_e : 0.004268
  EX_ca2_e : 0.002561
  EX_cl_e : 0.002561
  EX_cu2_e : 0.000349
  EX_mn2_e : 0.000340
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992097
  EX_h2o_e : 545.635709
  EX_co2_e : 27.429652
  EX_pyr_e : 2.408465
  EX_succ_e : 0.513089
  EX_ura_e : 0.348925
  Auxiliary production reaction : 0.129893
  EX_acser_e : 0.080445
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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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