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 : dgtp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (66 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4384 b3708 b3008 b0910 b3752 b0871 b2779 b2925 b2097 b2407 b3236 b3962 b2797 b3117 b1814 b4471 b3946 b2210 b0825 b4267 b3665 b2913 b4381 b0452 b0114 b0509 b3125 b1539 b2492 b0904 b1533 b3927 b0325 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.425514 (mmol/gDw/h)
  Minimum Production Rate : 0.073415 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.511186
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.964027
  EX_pi_e : 0.630699
  EX_so4_e : 0.107153
  EX_k_e : 0.083057
  EX_fe2_e : 0.006834
  EX_mg2_e : 0.003691
  EX_ca2_e : 0.002215
  EX_cl_e : 0.002215
  EX_cu2_e : 0.000302
  EX_mn2_e : 0.000294
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000137
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 44.814984
  EX_co2_e : 27.922186
  EX_h_e : 8.757080
  EX_pyr_e : 4.625464
  Auxiliary production reaction : 0.073415
  EX_ade_e : 0.000286
  EX_glyc__R_e : 0.000142
  DM_5drib_c : 0.000096
  DM_4crsol_c : 0.000095

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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