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 : pg141_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (87 of 95: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 33
  Gene deletion: b2836 b2744 b3614 b0910 b4152 b2297 b2458 b2925 b2097 b2781 b1612 b1611 b4122 b1759 b3449 b3946 b0825 b4374 b0675 b4138 b4123 b0621 b2913 b2223 b4381 b2239 b2406 b2197 b3918 b0789 b1249 b1206 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.622871 (mmol/gDw/h)
  Minimum Production Rate : 0.006635 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.050684
  EX_o2_e : 276.437915
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.610368
  EX_pi_e : 0.929791
  EX_so4_e : 0.156851
  EX_k_e : 0.121580
  EX_mg2_e : 0.005403
  EX_ca2_e : 0.003242
  EX_cl_e : 0.003242
  EX_cu2_e : 0.000442
  EX_mn2_e : 0.000430
  EX_zn2_e : 0.000212
  EX_ni2_e : 0.000201
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989996
  EX_h2o_e : 546.512157
  EX_co2_e : 27.184259
  EX_succ_e : 0.649525
  EX_ura_e : 0.441708
  EX_ac_e : 0.362627
  EX_g3pg_e : 0.322331
  Auxiliary production reaction : 0.006635
  DM_5drib_c : 0.000140
  DM_4crsol_c : 0.000139

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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