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 : gdpmann_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 108: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b0474 b2518 b4384 b3708 b3008 b0910 b3752 b2930 b4232 b3697 b3925 b0871 b2407 b0517 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b1033 b2440 b0261 b4381 b2406 b0114 b0886 b0755 b3612 b0529 b1539 b2492 b0904 b3035 b2578 b1533 b3927 b0508 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.612328 (mmol/gDw/h)
  Minimum Production Rate : 0.101901 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.858212
  EX_o2_e : 276.504451
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.307314
  EX_pi_e : 0.868346
  EX_so4_e : 0.154196
  EX_k_e : 0.119522
  EX_mg2_e : 0.005312
  EX_ca2_e : 0.003187
  EX_cl_e : 0.003187
  EX_cu2_e : 0.000434
  EX_mn2_e : 0.000423
  EX_zn2_e : 0.000209
  EX_ni2_e : 0.000198
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990165
  EX_h2o_e : 546.559109
  EX_co2_e : 26.356087
  EX_pyr_e : 2.089107
  Auxiliary production reaction : 0.138845
  DM_5drib_c : 0.002116
  DM_4crsol_c : 0.001842

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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