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 : ugmd_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 75: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b3831 b2744 b1278 b3614 b0910 b3752 b4152 b2781 b3844 b1612 b1611 b4122 b1759 b4374 b2361 b2291 b0411 b4138 b4123 b0621 b3915 b2197 b3918 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.622664 (mmol/gDw/h)
  Minimum Production Rate : 0.328307 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 19.721384
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.249374
  EX_pi_e : 1.257239
  EX_so4_e : 0.156799
  EX_k_e : 0.121540
  EX_fe3_e : 0.010001
  EX_mg2_e : 0.005402
  EX_ca2_e : 0.003241
  EX_cl_e : 0.003241
  EX_cu2_e : 0.000441
  EX_mn2_e : 0.000430
  EX_zn2_e : 0.000212
  EX_ni2_e : 0.000201
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_h2o_e : 44.449370
  EX_co2_e : 19.901513
  EX_h_e : 9.554560
  EX_succ_e : 0.649309
  Auxiliary production reaction : 0.328307
  EX_ura_e : 0.113254
  DM_5drib_c : 0.000140
  DM_4crsol_c : 0.000139

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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