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 : prpncoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (13 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b2836 b3399 b1241 b0351 b4069 b2502 b2744 b3708 b2297 b2458 b3617 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b2291 b0261 b0507 b0112 b2975 b0114 b3603 b2366 b2492 b0904 b1533   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.504692 (mmol/gDw/h)
  Minimum Production Rate : 0.503396 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 991.170302
  EX_o2_e : 270.273322
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.974965
  EX_pi_e : 1.997017
  EX_so4_e : 0.630488
  EX_k_e : 0.098512
  EX_mg2_e : 0.004378
  EX_ca2_e : 0.002627
  EX_cl_e : 0.002627
  EX_cu2_e : 0.000358
  EX_mn2_e : 0.000349
  EX_zn2_e : 0.000172
  EX_ni2_e : 0.000163
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991894
  EX_h2o_e : 545.750940
  EX_co2_e : 21.855032
  EX_ac_e : 2.672965
  Auxiliary production reaction : 0.503396
  DM_oxam_c : 0.000565
  DM_5drib_c : 0.000339
  DM_4crsol_c : 0.000113

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