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 : pg141_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (54 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b0474 b2518 b3831 b2744 b4152 b2781 b0030 b1612 b1611 b4122 b0651 b2162 b1759 b4374 b4161 b2361 b2291 b4138 b4123 b0621 b2406 b2197 b3821 b3918 b4042 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.586229 (mmol/gDw/h)
  Minimum Production Rate : 0.309614 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 992.859613
  EX_o2_e : 267.263441
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.162673
  EX_pi_e : 0.875094
  EX_so4_e : 0.147624
  EX_k_e : 0.114428
  EX_mg2_e : 0.005086
  EX_ca2_e : 0.003051
  EX_cl_e : 0.003051
  EX_cu2_e : 0.000416
  EX_mn2_e : 0.000405
  EX_zn2_e : 0.000200
  EX_ni2_e : 0.000189
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_fe3_e : 999.990585
  EX_h2o_e : 540.707323
  EX_co2_e : 21.302947
  EX_succ_e : 0.611315
  EX_ura_e : 0.415723
  Auxiliary production reaction : 0.309614
  DM_5drib_c : 0.000132
  DM_4crsol_c : 0.000131

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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