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 : pg161_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b2744 b3614 b0910 b4152 b2781 b3844 b1612 b1611 b4122 b1759 b4374 b0675 b2361 b2291 b4138 b4123 b0621 b0153 b2223 b0591 b2197 b3918 b4042 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.559775 (mmol/gDw/h)
  Minimum Production Rate : 0.295597 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 993.181785
  EX_o2_e : 267.420463
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.839451
  EX_pi_e : 0.835560
  EX_so4_e : 0.140963
  EX_k_e : 0.109264
  EX_mg2_e : 0.004856
  EX_ca2_e : 0.002914
  EX_cl_e : 0.002914
  EX_cu2_e : 0.000397
  EX_mn2_e : 0.000387
  EX_zn2_e : 0.000191
  EX_ni2_e : 0.000181
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_fe3_e : 999.991009
  EX_h2o_e : 540.396888
  EX_co2_e : 21.868335
  EX_succ_e : 0.583729
  EX_ura_e : 0.396963
  Auxiliary production reaction : 0.295597
  DM_5drib_c : 0.000126
  DM_4crsol_c : 0.000125

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