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 : dhgly_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 88: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b3399 b2502 b2744 b3708 b3008 b2930 b4232 b3697 b3925 b0871 b1779 b1982 b2688 b2797 b3117 b1814 b4471 b3946 b0825 b4374 b0675 b2361 b2291 b0261 b0507 b0114 b0529 b1539 b2492 b0904 b1533 b3927 b3821   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.623110 (mmol/gDw/h)
  Minimum Production Rate : 0.001735 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.536231
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.945636
  EX_pi_e : 0.601055
  EX_so4_e : 0.368847
  EX_k_e : 0.121627
  EX_fe2_e : 0.010008
  EX_mg2_e : 0.005405
  EX_ca2_e : 0.003243
  EX_cl_e : 0.003243
  EX_cu2_e : 0.000442
  EX_mn2_e : 0.000431
  EX_zn2_e : 0.000212
  EX_ni2_e : 0.000201
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 46.189260
  EX_co2_e : 27.066936
  EX_h_e : 7.752086
  EX_pyr_e : 2.230305
  EX_cys__L_e : 0.211936
  DM_oxam_c : 0.002433
  DM_5drib_c : 0.002153
  DM_4crsol_c : 0.001874
  Auxiliary production reaction : 0.001735

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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