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 : hdcea_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 28
  Gene deletion: b0474 b2518 b3831 b2744 b3752 b4152 b2781 b3844 b1612 b1611 b4122 b1759 b4374 b4161 b2361 b2291 b1852 b0411 b4138 b4123 b0621 b2913 b0452 b2197 b3918 b1912 b1206 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.430316 (mmol/gDw/h)
  Minimum Production Rate : 0.227200 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 985.741752
  EX_o2_e : 266.847130
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.257694
  EX_pi_e : 0.415086
  EX_so4_e : 0.108362
  EX_k_e : 0.083995
  EX_mg2_e : 0.003733
  EX_ca2_e : 0.002240
  EX_cl_e : 0.002240
  EX_cu2_e : 0.000305
  EX_mn2_e : 0.000297
  EX_zn2_e : 0.000147
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993089
  EX_h2o_e : 532.123583
  EX_co2_e : 18.561859
  EX_ac_e : 8.562444
  EX_succ_e : 0.448730
  EX_ura_e : 0.305158
  Auxiliary production reaction : 0.227200
  DM_5drib_c : 0.000097
  DM_4crsol_c : 0.000096

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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