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 : dctp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (44 of 73: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 37
  Gene deletion: b3399 b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b2744 b2930 b4232 b3697 b3925 b0871 b2779 b3617 b0160 b1238 b3236 b1982 b3946 b2210 b0825 b0675 b2361 b2913 b4381 b0112 b2868 b0114 b0529 b2492 b0904 b1517 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.278688 (mmol/gDw/h)
  Minimum Production Rate : 0.906321 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.966304
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.729518
  EX_pi_e : 2.987787
  EX_so4_e : 0.070179
  EX_k_e : 0.054398
  EX_fe2_e : 0.004476
  EX_mg2_e : 0.002418
  EX_cl_e : 0.001451
  EX_ca2_e : 0.001451
  EX_cu2_e : 0.000198
  EX_mn2_e : 0.000193
  EX_zn2_e : 0.000095
  EX_ni2_e : 0.000090

Product: (mmol/gDw/h)
  EX_h2o_e : 47.428111
  EX_co2_e : 26.986597
  EX_h_e : 7.485100
  EX_pyr_e : 4.017240
  Auxiliary production reaction : 0.906321
  EX_acald_e : 0.682048
  EX_hxan_e : 0.000188
  DM_mththf_c : 0.000125
  EX_glyc__R_e : 0.000093
  DM_5drib_c : 0.000063
  DM_4crsol_c : 0.000062

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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