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 : gua_p
List of minimal gene deletion strategies (Download)

Gene deletion strategy (57 of 74: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b4269 b0493 b3588 b3003 b3011 b2066 b0238 b0125 b1241 b0351 b2744 b0871 b3617 b2883 b0477 b2498 b2361 b2291 b0411 b2868 b0114 b0529 b2492 b0904 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.684816 (mmol/gDw/h)
  Minimum Production Rate : 0.742671 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 989.983285
  EX_o2_e : 273.721780
  EX_nh4_e : 11.109308
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.660578
  EX_so4_e : 0.172450
  EX_k_e : 0.133671
  EX_mg2_e : 0.005941
  EX_ca2_e : 0.003564
  EX_cl_e : 0.003564
  EX_cu2_e : 0.000486
  EX_mn2_e : 0.000473
  EX_zn2_e : 0.000234
  EX_ni2_e : 0.000221
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989001
  EX_h2o_e : 549.506959
  EX_co2_e : 24.001655
  EX_acald_e : 2.087454
  Auxiliary production reaction : 0.742671
  DM_mththf_c : 0.000307
  DM_5drib_c : 0.000154
  DM_4crsol_c : 0.000153

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