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 : dtdp4addg_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (80 of 107: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3916 b4382 b3831 b4384 b3614 b0910 b3752 b4152 b2926 b2781 b2407 b1851 b1612 b1611 b4122 b1759 b3946 b0825 b4138 b4123 b0621 b2406 b1723 b3821 b3918 b1912 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.612921 (mmol/gDw/h)
  Minimum Production Rate : 0.063059 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.076262
  EX_o2_e : 276.728783
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.378087
  EX_pi_e : 0.717346
  EX_so4_e : 0.154346
  EX_k_e : 0.119638
  EX_mg2_e : 0.005317
  EX_ca2_e : 0.003190
  EX_cl_e : 0.003190
  EX_cu2_e : 0.000435
  EX_mn2_e : 0.000424
  EX_zn2_e : 0.000209
  EX_ni2_e : 0.000198
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.903272
  EX_h2o_e : 547.839012
  EX_co2_e : 27.879059
  EX_succ_e : 0.639149
  EX_ura_e : 0.110940
  EX_pheme_e : 0.086884
  Auxiliary production reaction : 0.063059
  DM_5drib_c : 0.000138
  DM_4crsol_c : 0.000137

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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