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 : udpgalfur_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b2436 b4467 b2242 b0474 b2518 b3831 b3752 b2781 b1004 b3713 b1109 b0046 b3236 b1612 b1611 b4122 b1759 b4161 b4014 b2976 b4138 b4123 b0621 b4381 b2406 b0306 b3605 b3028 b3821 b3918 b0789 b1249 b1206 b2285 b3893 b1474   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.553668 (mmol/gDw/h)
  Minimum Production Rate : 0.292417 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.547273
  EX_o2_e : 279.869735
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.764834
  EX_pi_e : 1.118906
  EX_so4_e : 0.139425
  EX_k_e : 0.108072
  EX_mg2_e : 0.004803
  EX_ca2_e : 0.002882
  EX_cl_e : 0.002882
  EX_cu2_e : 0.000393
  EX_mn2_e : 0.000383
  EX_zn2_e : 0.000189
  EX_ni2_e : 0.000179
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991108
  EX_h2o_e : 548.501903
  EX_co2_e : 30.175313
  EX_succ_e : 0.577361
  Auxiliary production reaction : 0.292417
  EX_ura_e : 0.100216
  EX_for_e : 0.001358
  DM_5drib_c : 0.000372
  DM_4crsol_c : 0.000123

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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