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 : hpyr_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 85: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b3553 b4382 b1241 b0351 b4069 b4384 b3926 b2297 b2458 b2779 b2407 b1004 b3713 b1109 b0046 b3236 b3616 b3589 b1033 b0261 b1602 b2913 b0114 b0509 b3125 b0529 b2492 b0904 b1380 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.403884 (mmol/gDw/h)
  Minimum Production Rate : 0.195530 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.321750
  EX_o2_e : 287.980405
  EX_glc__D_e : 10.000000
  EX_nh4_e : 4.745607
  EX_pi_e : 0.389589
  EX_so4_e : 0.101706
  EX_k_e : 0.078835
  EX_mg2_e : 0.003504
  EX_ca2_e : 0.002102
  EX_cl_e : 0.002102
  EX_cu2_e : 0.000286
  EX_mn2_e : 0.000279
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000130
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_fe3_e : 999.993513
  EX_h2o_e : 549.697985
  EX_co2_e : 38.072850
  EX_ac_e : 1.997795
  DM_oxam_c : 0.383696
  Auxiliary production reaction : 0.195530
  DM_5drib_c : 0.000091
  DM_4crsol_c : 0.000090

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