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 : udpg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (82 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b0474 b2518 b3831 b3614 b0910 b3752 b4152 b2297 b2458 b2779 b2925 b2097 b2781 b1612 b1611 b4122 b1759 b3946 b0825 b4014 b2976 b0411 b0614 b4138 b4123 b0621 b2913 b4381 b0452 b0529 b2197 b3918 b1912 b1206 b2285 b3924   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.368959 (mmol/gDw/h)
  Minimum Production Rate : 0.194864 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.354446
  EX_o2_e : 281.229941
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.508016
  EX_pi_e : 0.745627
  EX_so4_e : 0.092911
  EX_k_e : 0.072018
  EX_mg2_e : 0.003201
  EX_ca2_e : 0.001920
  EX_cl_e : 0.001920
  EX_cu2_e : 0.000262
  EX_mn2_e : 0.000255
  EX_zn2_e : 0.000126
  EX_ni2_e : 0.000119

Product: (mmol/gDw/h)
  EX_fe3_e : 999.994074
  EX_h2o_e : 543.646535
  EX_co2_e : 31.433883
  EX_ac_e : 4.346305
  EX_succ_e : 0.384747
  Auxiliary production reaction : 0.194864
  EX_ura_e : 0.066783
  EX_glyc__R_e : 0.000123
  DM_5drib_c : 0.000083
  DM_4crsol_c : 0.000082

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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