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 : ametam_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (71 of 84: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 34
  Gene deletion: b4382 b4269 b0493 b3588 b3003 b3011 b1241 b0351 b4069 b4384 b3708 b3008 b0871 b3617 b0030 b2407 b1982 b2797 b3117 b1814 b4471 b0261 b0335 b2406 b0112 b0114 b0728 b1539 b2492 b0904 b1533 b3821 b2413 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.564749 (mmol/gDw/h)
  Minimum Production Rate : 0.552541 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 22.132543
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.414487
  EX_so4_e : 0.694756
  EX_pi_e : 0.544760
  EX_k_e : 0.110235
  EX_fe2_e : 0.009070
  EX_mg2_e : 0.004899
  EX_ca2_e : 0.002940
  EX_cl_e : 0.002940
  EX_cu2_e : 0.000400
  EX_mn2_e : 0.000390
  EX_zn2_e : 0.000193
  EX_ni2_e : 0.000182
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 47.025371
  EX_co2_e : 24.928880
  EX_h_e : 6.294220
  EX_acald_e : 2.076969
  Auxiliary production reaction : 0.552541
  DM_5drib_c : 0.000379
  DM_4crsol_c : 0.000126

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