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 : dcdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (62 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 41
  Gene deletion: b3553 b3942 b1732 b1241 b0351 b4069 b4384 b0871 b3115 b1849 b2296 b2925 b2097 b0030 b2407 b1004 b3713 b1109 b0046 b2463 b1982 b3616 b3589 b3946 b2210 b0825 b1033 b0411 b1602 b4381 b2406 b1727 b0114 b0529 b2492 b0904 b1380 b1517 b0606 b2285 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.326666 (mmol/gDw/h)
  Minimum Production Rate : 1.252532 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 24.410867
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.286443
  EX_pi_e : 2.820168
  EX_so4_e : 0.082261
  EX_k_e : 0.063763
  EX_mg2_e : 0.002834
  EX_fe2_e : 0.002696
  EX_fe3_e : 0.002551
  EX_ca2_e : 0.001700
  EX_cl_e : 0.001700
  EX_cu2_e : 0.000232
  EX_mn2_e : 0.000226
  EX_zn2_e : 0.000111
  EX_ni2_e : 0.000106

Product: (mmol/gDw/h)
  EX_h2o_e : 43.817014
  EX_co2_e : 26.343471
  EX_h_e : 6.110922
  EX_12ppd__R_e : 2.549571
  Auxiliary production reaction : 1.252532
  EX_ac_e : 0.477616
  EX_pyr_e : 0.123273
  EX_hxan_e : 0.000220
  DM_mththf_c : 0.000146
  DM_5drib_c : 0.000073
  DM_4crsol_c : 0.000073

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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