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 : pnto__R_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (7 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b3752 b2297 b2458 b2779 b2925 b2097 b3617 b2407 b3236 b2690 b1982 b2797 b3117 b1814 b4471 b0261 b3945 b2406 b0114 b1539 b2492 b0904 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.523939 (mmol/gDw/h)
  Minimum Production Rate : 0.348931 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.682169
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.445802
  EX_pi_e : 0.505395
  EX_so4_e : 0.131938
  EX_k_e : 0.102269
  EX_fe2_e : 0.008415
  EX_mg2_e : 0.004545
  EX_ca2_e : 0.002727
  EX_cl_e : 0.002727
  EX_cu2_e : 0.000371
  EX_mn2_e : 0.000362
  EX_zn2_e : 0.000179
  EX_ni2_e : 0.000169
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 46.254014
  EX_co2_e : 25.624728
  EX_h_e : 9.767292
  EX_ac_e : 1.816134
  EX_ins_e : 0.609447
  Auxiliary production reaction : 0.348931
  DM_oxam_c : 0.000586
  DM_5drib_c : 0.000352
  EX_glyc__R_e : 0.000175
  DM_4crsol_c : 0.000117

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