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 : dgsn_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (69 of 77: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 38
  Gene deletion: b2836 b4382 b3942 b1732 b1241 b0351 b4384 b3708 b3008 b1479 b0871 b2297 b2458 b2926 b3617 b0030 b2407 b3236 b3962 b2797 b3117 b1814 b4471 b2210 b4267 b3665 b0114 b0509 b3125 b1539 b2492 b0904 b1533 b3927 b0325 b4266 b1517 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.522493 (mmol/gDw/h)
  Minimum Production Rate : 0.090150 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 36.759870
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.095384
  EX_pi_e : 0.504000
  EX_so4_e : 0.131574
  EX_k_e : 0.101987
  EX_mg2_e : 0.004533
  EX_fe2_e : 0.004312
  EX_fe3_e : 0.004080
  EX_ca2_e : 0.002720
  EX_cl_e : 0.002720
  EX_cu2_e : 0.000370
  EX_mn2_e : 0.000361
  EX_zn2_e : 0.000178
  EX_ni2_e : 0.000169
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 52.440359
  EX_co2_e : 37.649647
  EX_h_e : 5.257458
  Auxiliary production reaction : 0.090150
  EX_ade_e : 0.000352
  EX_mththf_e : 0.000234
  DM_5drib_c : 0.000118
  DM_4crsol_c : 0.000117

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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