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 : prpncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (53 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b2836 b4069 b4384 b2744 b3708 b3008 b3752 b2297 b2458 b2925 b2097 b2407 b1982 b2797 b3117 b1814 b4471 b3946 b0825 b3665 b4374 b2361 b2291 b0261 b2406 b0114 b2366 b2492 b0904 b2578 b1533 b3927 b0594 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.722063 (mmol/gDw/h)
  Minimum Production Rate : 0.035844 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.056618
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.791364
  EX_pi_e : 0.804038
  EX_so4_e : 0.586773
  EX_k_e : 0.140942
  EX_fe2_e : 0.011597
  EX_mg2_e : 0.006264
  EX_ca2_e : 0.003758
  EX_cl_e : 0.003758
  EX_cu2_e : 0.000512
  EX_mn2_e : 0.000499
  EX_zn2_e : 0.000246
  EX_ni2_e : 0.000233
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 47.305482
  EX_co2_e : 26.000599
  EX_h_e : 7.571492
  EX_ac_e : 0.825318
  EX_cgly_e : 0.369099
  Auxiliary production reaction : 0.035844
  EX_ade_e : 0.000808
  DM_5drib_c : 0.000485
  DM_4crsol_c : 0.000161

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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