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 : pg120_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (72 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b2744 b3614 b0910 b3926 b2930 b4232 b3697 b3925 b4152 b2297 b2458 b2781 b1612 b1611 b4122 b0907 b1759 b3449 b3946 b0825 b4374 b0675 b3945 b4138 b4123 b0621 b4381 b2406 b0452 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 : 0.636586 (mmol/gDw/h)
  Minimum Production Rate : 0.016238 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.092877
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.777937
  EX_fe3_e : 6.403369
  EX_pi_e : 0.630293
  EX_so4_e : 0.160305
  EX_k_e : 0.124257
  EX_mg2_e : 0.005522
  EX_ca2_e : 0.003313
  EX_cl_e : 0.003313
  EX_cu2_e : 0.000451
  EX_mn2_e : 0.000440
  EX_zn2_e : 0.000217
  EX_ni2_e : 0.000206
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 43.784014
  EX_co2_e : 27.221763
  EX_h_e : 14.837463
  EX_fe2_e : 6.393144
  EX_succ_e : 0.663826
  EX_ura_e : 0.451433
  EX_ac_e : 0.370611
  EX_glyald_e : 0.319971
  Auxiliary production reaction : 0.016238
  DM_5drib_c : 0.000143
  DM_4crsol_c : 0.000142

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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