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 : sbzcoa_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (50 of 83: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 46
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b2744 b3708 b3614 b0910 b2297 b2458 b2781 b3617 b1759 b1982 b2797 b3117 b1814 b4471 b4374 b0675 b2361 b0261 b3709 b4381 b2406 b3161 b0112 b2975 b0114 b3603 b0509 b3125 b2366 b2492 b0904 b0591 b1533 b2835 b3918 b1912 b0508 b1473 b0494 b4141 b1798   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.454814 (mmol/gDw/h)
  Minimum Production Rate : 0.422251 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 19.796229
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.865462
  EX_pi_e : 1.705469
  EX_so4_e : 0.536782
  EX_k_e : 0.088776
  EX_fe2_e : 0.007305
  EX_mg2_e : 0.003946
  EX_ca2_e : 0.002367
  EX_cl_e : 0.002367
  EX_cu2_e : 0.000322
  EX_mn2_e : 0.000314
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 46.154956
  EX_co2_e : 20.677876
  EX_h_e : 9.204620
  EX_ac_e : 2.326441
  EX_thym_e : 0.492673
  Auxiliary production reaction : 0.422251
  DM_oxam_c : 0.012410
  DM_5drib_c : 0.000305
  DM_4crsol_c : 0.000101

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