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 : aicar_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (19 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b3617 b0030 b2407 b1779 b1982 b0261 b0411 b0507 b4381 b0112 b0114 b0529 b2492 b0904 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.491768 (mmol/gDw/h)
  Minimum Production Rate : 0.580627 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.033017
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.665995
  EX_pi_e : 1.054990
  EX_so4_e : 0.123837
  EX_k_e : 0.095990
  EX_fe2_e : 0.007898
  EX_mg2_e : 0.004266
  EX_ca2_e : 0.002560
  EX_cl_e : 0.002560
  EX_cu2_e : 0.000349
  EX_mn2_e : 0.000340
  EX_zn2_e : 0.000168
  EX_ni2_e : 0.000159
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 48.724229
  EX_co2_e : 24.412863
  EX_h_e : 8.876792
  EX_thymd_e : 1.015255
  Auxiliary production reaction : 0.580627
  DM_oxam_c : 0.001920
  DM_5drib_c : 0.001700
  DM_4crsol_c : 0.001479
  EX_glyclt_e : 0.001370

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