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 : mal__L_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (7 of 29: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 31
  Gene deletion: b3553 b3942 b1732 b1479 b0871 b2925 b2097 b3617 b3236 b2463 b3962 b1525 b3946 b2210 b0825 b4267 b1033 b3551 b2799 b0726 b4219 b1832 b1778 b0114 b2492 b0904 b1710 b2480 b4266 b1206 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.607540 (mmol/gDw/h)
  Minimum Production Rate : 0.633538 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 26.844605
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.561381
  EX_pi_e : 0.586037
  EX_so4_e : 0.152991
  EX_k_e : 0.118588
  EX_mg2_e : 0.005270
  EX_fe2_e : 0.005014
  EX_fe3_e : 0.004744
  EX_cl_e : 0.003162
  EX_ca2_e : 0.003162
  EX_cu2_e : 0.000431
  EX_mn2_e : 0.000420
  EX_zn2_e : 0.000207
  EX_ni2_e : 0.000196
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 45.187448
  EX_co2_e : 26.504683
  EX_h_e : 8.862285
  EX_pyr_e : 2.008145
  Auxiliary production reaction : 0.633538
  DM_5drib_c : 0.000137
  DM_4crsol_c : 0.000135

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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