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 : adprib_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (81 of 97: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3708 b3614 b0910 b3115 b1849 b2296 b2781 b0030 b2407 b1759 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b4374 b0675 b0261 b4381 b2406 b0112 b0114 b2366 b2492 b0904 b1533 b3821 b3918 b4042 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.545188 (mmol/gDw/h)
  Minimum Production Rate : 0.766364 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.439508
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.917166
  EX_pi_e : 2.058620
  EX_so4_e : 0.137289
  EX_k_e : 0.106417
  EX_fe2_e : 0.008756
  EX_mg2_e : 0.004730
  EX_ca2_e : 0.002838
  EX_cl_e : 0.002838
  EX_cu2_e : 0.000387
  EX_mn2_e : 0.000377
  EX_zn2_e : 0.000186
  EX_ni2_e : 0.000176
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 47.207888
  EX_co2_e : 21.588480
  EX_h_e : 9.527847
  EX_ac_e : 2.021989
  Auxiliary production reaction : 0.766364
  EX_thym_e : 0.098681
  DM_5drib_c : 0.000366
  DM_4crsol_c : 0.000122

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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