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 : pgp140_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (79 of 96: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b2836 b2744 b1278 b3614 b0910 b4152 b2781 b3844 b1612 b1611 b4122 b1759 b4374 b0675 b4138 b4123 b0621 b0153 b2223 b4381 b2406 b3035 b2197 b3918 b1206   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.573938 (mmol/gDw/h)
  Minimum Production Rate : 0.303076 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 17.860816
  EX_glc__D_e : 10.000000
  EX_nh4_e : 7.012500
  EX_pi_e : 1.159777
  EX_so4_e : 0.144529
  EX_k_e : 0.112029
  EX_fe2_e : 0.009218
  EX_mg2_e : 0.004979
  EX_ca2_e : 0.002987
  EX_cl_e : 0.002987
  EX_cu2_e : 0.000407
  EX_mn2_e : 0.000397
  EX_zn2_e : 0.000196
  EX_ni2_e : 0.000185
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 40.814735
  EX_co2_e : 22.115846
  EX_h_e : 6.981510
  EX_succ_e : 0.598498
  EX_ura_e : 0.407007
  Auxiliary production reaction : 0.303076
  DM_5drib_c : 0.000129
  DM_4crsol_c : 0.000128

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