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 : dhmpt_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (93 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 39
  Gene deletion: b3553 b1241 b0351 b3831 b4069 b4384 b3708 b3614 b0910 b3752 b3115 b1849 b2296 b2781 b2407 b1759 b1982 b2797 b3117 b1814 b4471 b3616 b3589 b1033 b0261 b1701 b1805 b0507 b4381 b2406 b0112 b0114 b2366 b2492 b0904 b1533 b3918 b1912 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.501156 (mmol/gDw/h)
  Minimum Production Rate : 1.408939 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.711100
  EX_nh4_e : 12.639120
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.483418
  EX_so4_e : 0.126201
  EX_k_e : 0.097822
  EX_fe2_e : 0.008049
  EX_mg2_e : 0.004348
  EX_ca2_e : 0.002609
  EX_cl_e : 0.002609
  EX_cu2_e : 0.000355
  EX_mn2_e : 0.000346
  EX_zn2_e : 0.000171
  EX_ni2_e : 0.000162
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 48.944834
  EX_co2_e : 21.166622
  EX_h_e : 14.395549
  EX_ac_e : 2.563154
  Auxiliary production reaction : 1.408939
  EX_thym_e : 0.090711
  DM_oxam_c : 0.000561
  DM_5drib_c : 0.000336
  EX_glyclt_e : 0.000335
  DM_4crsol_c : 0.000112

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