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 : dgdp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (37 of 41: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 43
  Gene deletion: b3942 b1732 b0474 b1241 b0351 b4069 b2744 b3708 b1479 b0871 b2297 b2458 b2779 b2925 b2097 b3617 b3236 b2690 b3962 b2797 b3117 b1814 b4471 b2210 b4267 b4374 b2361 b2291 b1415 b3945 b2913 b4381 b0511 b0114 b2366 b2492 b0904 b1533 b1380 b0325 b0508 b0515 b4266   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.326821 (mmol/gDw/h)
  Minimum Production Rate : 0.326235 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 29.974817
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.160818
  EX_pi_e : 0.967724
  EX_so4_e : 0.082300
  EX_k_e : 0.063793
  EX_fe2_e : 0.005249
  EX_mg2_e : 0.002835
  EX_ca2_e : 0.001701
  EX_cl_e : 0.001701
  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 : 44.989734
  EX_co2_e : 27.594898
  EX_h_e : 9.910029
  EX_pyr_e : 4.523332
  EX_ac_e : 1.078573
  Auxiliary production reaction : 0.326235
  EX_dxylnt_e : 0.000219
  DM_5drib_c : 0.000074
  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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