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 : glyc_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (70 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b3553 b2066 b0474 b2518 b1241 b0351 b4384 b3926 b0871 b2926 b2407 b1004 b3713 b1109 b0046 b3236 b2498 b1033 b0261 b1602 b2913 b3915 b0529 b2492 b0904 b2835 b1380 b0494 b1695 b1771 b0606 b2285 b1010 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.499492 (mmol/gDw/h)
  Minimum Production Rate : 0.131736 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 37.969150
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.394469
  EX_pi_e : 0.481813
  EX_so4_e : 0.125782
  EX_k_e : 0.097497
  EX_fe3_e : 0.008022
  EX_mg2_e : 0.004333
  EX_cl_e : 0.002600
  EX_ca2_e : 0.002600
  EX_cu2_e : 0.000354
  EX_mn2_e : 0.000345
  EX_zn2_e : 0.000170
  EX_ni2_e : 0.000161
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 52.157400
  EX_co2_e : 39.102949
  EX_h_e : 4.597552
  EX_glyc_e : 0.131736
  DM_5drib_c : 0.000112
  DM_4crsol_c : 0.000111

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