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 : air_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3708 b3115 b1849 b2296 b2779 b3617 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b0261 b2406 b0112 b0114 b0509 b3125 b1539 b2492 b0904 b1533 b3821 b0508 b0515 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.464051 (mmol/gDw/h)
  Minimum Production Rate : 1.388617 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 989.103044
  EX_o2_e : 275.323476
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.179643
  EX_pi_e : 1.836244
  EX_so4_e : 0.116857
  EX_k_e : 0.090580
  EX_mg2_e : 0.004026
  EX_ca2_e : 0.002415
  EX_cl_e : 0.002415
  EX_cu2_e : 0.000329
  EX_mn2_e : 0.000321
  EX_zn2_e : 0.000158
  EX_ni2_e : 0.000150
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_fe3_e : 999.992547
  EX_h2o_e : 546.899946
  EX_co2_e : 24.925407
  EX_ac_e : 2.457376
  Auxiliary production reaction : 1.388617
  EX_alltn_e : 0.000519
  DM_5drib_c : 0.000311
  EX_glyclt_e : 0.000310
  DM_4crsol_c : 0.000103

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