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 : u23ga_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4382 b0474 b2518 b3831 b4384 b1278 b3752 b4152 b2926 b2781 b1612 b1611 b4122 b1759 b4161 b4138 b4123 b0621 b2406 b2197 b3825 b3918 b0494 b1695 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.492293 (mmol/gDw/h)
  Minimum Production Rate : 0.260002 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.073445
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.274941
  EX_pi_e : 0.994873
  EX_so4_e : 0.123969
  EX_k_e : 0.096092
  EX_fe2_e : 0.007907
  EX_mg2_e : 0.004271
  EX_ca2_e : 0.002562
  EX_cl_e : 0.002562
  EX_cu2_e : 0.000349
  EX_mn2_e : 0.000340
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 43.282698
  EX_co2_e : 26.203688
  EX_h_e : 5.988317
  EX_succ_e : 0.513359
  Auxiliary production reaction : 0.260002
  EX_ura_e : 0.089106
  DM_5drib_c : 0.000111
  DM_4crsol_c : 0.000110

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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