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 : udpgal_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (90 of 119: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b3916 b4382 b3831 b4384 b3614 b0910 b3752 b4152 b2781 b1850 b2407 b1612 b1611 b4122 b1759 b1200 b4138 b4123 b0621 b2406 b1723 b3821 b3918 b4042 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.682437 (mmol/gDw/h)
  Minimum Production Rate : 0.360426 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.048210
  EX_o2_e : 272.864729
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.338159
  EX_pi_e : 1.379134
  EX_so4_e : 0.171851
  EX_k_e : 0.133207
  EX_mg2_e : 0.005920
  EX_cl_e : 0.003552
  EX_ca2_e : 0.003552
  EX_cu2_e : 0.000484
  EX_mn2_e : 0.000472
  EX_zn2_e : 0.000233
  EX_ni2_e : 0.000220
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989039
  EX_h2o_e : 545.830940
  EX_co2_e : 23.242061
  EX_succ_e : 0.711640
  Auxiliary production reaction : 0.360426
  EX_ura_e : 0.123523
  DM_5drib_c : 0.000154
  DM_4crsol_c : 0.000152

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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