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 : dgmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (74 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3399 b4384 b2744 b3708 b3008 b0871 b2925 b2097 b2407 b3236 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b2440 b3665 b4374 b0675 b2361 b2291 b0114 b2366 b0755 b3612 b2492 b0904 b1533 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.638908 (mmol/gDw/h)
  Minimum Production Rate : 0.110203 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.635521
  EX_o2_e : 276.755873
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.453318
  EX_pi_e : 0.726497
  EX_so4_e : 0.160890
  EX_k_e : 0.124710
  EX_mg2_e : 0.005543
  EX_cl_e : 0.003326
  EX_ca2_e : 0.003326
  EX_cu2_e : 0.000453
  EX_mn2_e : 0.000441
  EX_zn2_e : 0.000218
  EX_ni2_e : 0.000206
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989738
  EX_h2o_e : 547.003957
  EX_co2_e : 26.880045
  EX_pyr_e : 1.930509
  Auxiliary production reaction : 0.110203
  EX_ade_e : 0.000430
  DM_5drib_c : 0.000144
  DM_4crsol_c : 0.000142

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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