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 : quln_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (100 of 106: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3553 b1241 b0351 b3831 b3752 b2930 b4232 b3697 b3925 b4152 b1612 b1611 b4122 b1779 b2690 b3962 b4267 b1033 b0675 b0822 b2799 b4138 b4123 b0621 b1727 b0755 b3612 b4266 b1206 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.479754 (mmol/gDw/h)
  Minimum Production Rate : 0.340217 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 990.747816
  EX_o2_e : 280.030209
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.521518
  EX_pi_e : 0.462774
  EX_so4_e : 0.120812
  EX_k_e : 0.093645
  EX_mg2_e : 0.004162
  EX_ca2_e : 0.002497
  EX_cl_e : 0.002497
  EX_cu2_e : 0.000340
  EX_mn2_e : 0.000332
  EX_zn2_e : 0.000164
  EX_ni2_e : 0.000155
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992295
  EX_h2o_e : 545.502178
  EX_co2_e : 30.295473
  EX_ac_e : 2.815091
  EX_succ_e : 0.500284
  Auxiliary production reaction : 0.340217
  DM_5drib_c : 0.000108
  DM_4crsol_c : 0.000107

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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