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 : accoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 51
  Gene deletion: b2836 b3553 b1478 b3399 b1241 b4069 b2744 b3708 b2297 b2458 b2926 b0160 b3844 b1004 b3713 b1109 b0046 b3236 b0121 b1982 b2797 b3117 b1814 b4471 b1033 b4374 b0675 b2361 b2291 b0261 b2799 b3945 b1602 b3709 b2913 b3161 b0112 b3915 b0509 b3125 b1539 b2492 b0904 b1533 b1380 b1473 b4141 b1798 b0606 b2285 b1010   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.363960 (mmol/gDw/h)
  Minimum Production Rate : 0.302737 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 34.489067
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.051931
  EX_pi_e : 1.259287
  EX_so4_e : 0.394389
  EX_k_e : 0.071043
  EX_fe3_e : 0.005847
  EX_mg2_e : 0.003157
  EX_ca2_e : 0.001894
  EX_cl_e : 0.001894
  EX_cu2_e : 0.000258
  EX_mn2_e : 0.000251
  EX_zn2_e : 0.000124
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 51.236088
  EX_co2_e : 35.569028
  EX_h_e : 5.523450
  EX_ac_e : 1.263145
  Auxiliary production reaction : 0.302736
  EX_ade_e : 0.000407
  DM_5drib_c : 0.000244
  DM_4crsol_c : 0.000081

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
Contact