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 : prbatp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (40 of 47: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b2836 b3399 b2502 b2744 b1278 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b1779 b2690 b1982 b2797 b3117 b1814 b4471 b0595 b1623 b3665 b0675 b2361 b0261 b0822 b4381 b2406 b1727 b0114 b0886 b2366 b0529 b2492 b0904 b2578 b1533 b3927 b2413   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.615022 (mmol/gDw/h)
  Minimum Production Rate : 0.125027 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.649593
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.286851
  EX_pi_e : 1.093362
  EX_so4_e : 0.154875
  EX_k_e : 0.120048
  EX_fe2_e : 0.009878
  EX_mg2_e : 0.005335
  EX_ca2_e : 0.003201
  EX_cl_e : 0.003201
  EX_cu2_e : 0.000436
  EX_mn2_e : 0.000425
  EX_zn2_e : 0.000210
  EX_ni2_e : 0.000199
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 46.948297
  EX_co2_e : 26.579771
  EX_h_e : 8.149776
  EX_pyr_e : 2.088003
  Auxiliary production reaction : 0.125027
  DM_oxam_c : 0.016093
  EX_ade_e : 0.000688
  DM_5drib_c : 0.000413
  DM_4crsol_c : 0.000137

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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