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 : frdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (68 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3399 b4382 b4384 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b2926 b2407 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b0675 b2361 b0452 b0114 b2366 b2492 b0904 b1533 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.376087 (mmol/gDw/h)
  Minimum Production Rate : 0.086633 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.829864
  EX_o2_e : 279.952552
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.061958
  EX_pi_e : 0.536041
  EX_so4_e : 0.094706
  EX_k_e : 0.073409
  EX_mg2_e : 0.003263
  EX_ca2_e : 0.001958
  EX_cl_e : 0.001958
  EX_cu2_e : 0.000267
  EX_mn2_e : 0.000260
  EX_zn2_e : 0.000128
  EX_ni2_e : 0.000121

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993960
  EX_h2o_e : 543.948779
  EX_co2_e : 28.878763
  EX_pyr_e : 4.794587
  Auxiliary production reaction : 0.086633
  DM_oxam_c : 0.000253
  EX_mththf_e : 0.000168
  DM_5drib_c : 0.000085
  DM_4crsol_c : 0.000084

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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