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 : dgtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (48 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3399 b4382 b4384 b2744 b3708 b3008 b0871 b2925 b2097 b0160 b2797 b3117 b1814 b4471 b3946 b0825 b2440 b3665 b0675 b2361 b2291 b3654 b3714 b3664 b0114 b1539 b2492 b0904 b1533 b3927   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.789018 (mmol/gDw/h)
  Minimum Production Rate : 0.136493 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.821447
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.203787
  EX_pi_e : 1.170569
  EX_so4_e : 0.198690
  EX_k_e : 0.154011
  EX_fe2_e : 0.012672
  EX_mg2_e : 0.006845
  EX_ca2_e : 0.004107
  EX_cl_e : 0.004107
  EX_cu2_e : 0.000559
  EX_mn2_e : 0.000545
  EX_zn2_e : 0.000269
  EX_ni2_e : 0.000255
  EX_cobalt2_e : 0.000020

Product: (mmol/gDw/h)
  EX_h2o_e : 48.927774
  EX_co2_e : 26.146890
  EX_h_e : 7.693498
  Auxiliary production reaction : 0.136493
  EX_pyr_e : 0.034211
  DM_5drib_c : 0.000178
  DM_4crsol_c : 0.000176

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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