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 : ppgpp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (49 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 30
  Gene deletion: b1241 b0351 b4069 b4384 b3708 b2297 b2458 b3617 b0030 b2407 b1238 b2797 b3117 b1814 b4471 b3449 b3665 b4381 b2406 b0112 b3654 b3714 b3664 b0114 b2366 b2492 b0904 b1533 b3662 b1517   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.595828 (mmol/gDw/h)
  Minimum Production Rate : 0.892272 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 23.497522
  EX_nh4_e : 10.896255
  EX_glc__D_e : 10.000000
  EX_pi_e : 4.143829
  EX_so4_e : 0.150041
  EX_k_e : 0.116301
  EX_fe2_e : 0.009570
  EX_mg2_e : 0.005169
  EX_ca2_e : 0.003101
  EX_cl_e : 0.003101
  EX_cu2_e : 0.000422
  EX_mn2_e : 0.000412
  EX_zn2_e : 0.000203
  EX_ni2_e : 0.000192
  EX_cobalt2_e : 0.000015

Product: (mmol/gDw/h)
  EX_h2o_e : 51.210472
  EX_co2_e : 22.092215
  EX_h_e : 10.415384
  EX_ac_e : 2.263860
  Auxiliary production reaction : 0.892272
  EX_mththf_e : 0.000267
  DM_5drib_c : 0.000134
  DM_4crsol_c : 0.000133

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
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