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 : aicar_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (22 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 26
  Gene deletion: b4382 b1241 b0351 b4069 b4384 b3115 b1849 b2296 b2926 b0030 b2407 b1982 b3616 b3589 b3665 b0261 b2406 b0112 b0114 b0509 b3125 b0529 b2492 b0904 b0508 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.425221 (mmol/gDw/h)
  Minimum Production Rate : 1.629848 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.724131
  EX_nh4_e : 11.114115
  EX_glc__D_e : 10.000000
  EX_pi_e : 2.040018
  EX_so4_e : 0.107079
  EX_k_e : 0.083000
  EX_fe2_e : 0.006829
  EX_mg2_e : 0.003689
  EX_ca2_e : 0.002213
  EX_cl_e : 0.002213
  EX_cu2_e : 0.000301
  EX_mn2_e : 0.000294
  EX_zn2_e : 0.000145
  EX_ni2_e : 0.000137
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 49.272914
  EX_co2_e : 23.370628
  EX_h_e : 12.680899
  EX_ac_e : 2.251749
  Auxiliary production reaction : 1.629848
  EX_ade_e : 0.000476
  DM_5drib_c : 0.000285
  EX_glyclt_e : 0.000284
  DM_4crsol_c : 0.000095

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