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 (60 of 86: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b2436 b3500 b2836 b3831 b1278 b3614 b0910 b3752 b4152 b2779 b2781 b2235 b1612 b1611 b4122 b0907 b1759 b0411 b4138 b4123 b0621 b4381 b0529 b3918 b1206 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.617167 (mmol/gDw/h)
  Minimum Production Rate : 0.077019 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.310869
  EX_o2_e : 277.411012
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.540677
  EX_pi_e : 0.749360
  EX_so4_e : 0.155415
  EX_k_e : 0.120467
  EX_mg2_e : 0.005354
  EX_ca2_e : 0.003212
  EX_cl_e : 0.003212
  EX_cu2_e : 0.000438
  EX_mn2_e : 0.000426
  EX_zn2_e : 0.000210
  EX_ni2_e : 0.000199
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990088
  EX_h2o_e : 547.682846
  EX_co2_e : 28.001277
  EX_succ_e : 0.643577
  EX_thymd_e : 0.248885
  EX_ura_e : 0.111759
  Auxiliary production reaction : 0.077019
  DM_5drib_c : 0.000414
  DM_4crsol_c : 0.000138

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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