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 : hxan_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (63 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4467 b3942 b1732 b0871 b2297 b2458 b2925 b2097 b1004 b3713 b1109 b0046 b3946 b2210 b0825 b1602 b4381 b1727 b0114 b0529 b2492 b0904 b1380 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.430615 (mmol/gDw/h)
  Minimum Production Rate : 0.115641 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.115099
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.113167
  EX_pi_e : 0.415373
  EX_so4_e : 0.108437
  EX_k_e : 0.084053
  EX_mg2_e : 0.003736
  EX_fe2_e : 0.003554
  EX_fe3_e : 0.003362
  EX_cl_e : 0.002241
  EX_ca2_e : 0.002241
  EX_cu2_e : 0.000305
  EX_mn2_e : 0.000298
  EX_zn2_e : 0.000147
  EX_ni2_e : 0.000139
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 41.637231
  EX_co2_e : 27.913796
  EX_h_e : 7.384628
  EX_pyr_e : 2.962041
  EX_12ppd__R_e : 1.649040
  EX_hxan_e : 0.115641
  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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