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 : dump_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 81: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 40
  Gene deletion: b4467 b1478 b3399 b1241 b4069 b2744 b2297 b2458 b0160 b1004 b3713 b1109 b0046 b3236 b1779 b0207 b3012 b1982 b4374 b0675 b2361 b2291 b0261 b2799 b1602 b2913 b3915 b0529 b2492 b0904 b1781 b3001 b1380 b0325 b1771 b0606 b0221 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.364514 (mmol/gDw/h)
  Minimum Production Rate : 1.144796 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 33.714130
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.228349
  EX_pi_e : 1.496408
  EX_so4_e : 0.091792
  EX_k_e : 0.071151
  EX_fe3_e : 0.005854
  EX_mg2_e : 0.003162
  EX_ca2_e : 0.001897
  EX_cl_e : 0.001897
  EX_cu2_e : 0.000258
  EX_mn2_e : 0.000252
  EX_zn2_e : 0.000124
  EX_ni2_e : 0.000118

Product: (mmol/gDw/h)
  EX_h2o_e : 50.668195
  EX_co2_e : 33.027672
  EX_h_e : 6.499132
  Auxiliary production reaction : 1.144796
  EX_glyclt_e : 0.640134
  EX_ac_e : 0.212215
  EX_ade_e : 0.000408
  DM_5drib_c : 0.000245
  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