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 : ps141_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b4382 b4384 b2744 b3614 b0910 b4152 b2781 b3844 b1612 b1611 b4122 b1759 b4374 b0675 b4138 b4123 b0621 b2406 b3915 b2197 b3918 b4042 b1695 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.581081 (mmol/gDw/h)
  Minimum Production Rate : 0.306039 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.613709
  EX_o2_e : 267.970442
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.405814
  EX_pi_e : 0.866554
  EX_so4_e : 0.146328
  EX_k_e : 0.113423
  EX_mg2_e : 0.005041
  EX_ca2_e : 0.003025
  EX_cl_e : 0.003025
  EX_cu2_e : 0.000412
  EX_mn2_e : 0.000402
  EX_zn2_e : 0.000198
  EX_ni2_e : 0.000188
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990667
  EX_h2o_e : 541.504223
  EX_co2_e : 21.661589
  EX_succ_e : 0.605947
  EX_ura_e : 0.412073
  Auxiliary production reaction : 0.306039
  EX_hxa_e : 0.001712
  DM_5drib_c : 0.000131
  DM_4crsol_c : 0.000130

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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