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 : adn_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (42 of 82: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b4269 b3942 b1732 b0493 b3588 b3003 b3011 b1241 b0351 b4384 b2744 b0871 b3617 b0030 b2407 b1982 b4374 b2361 b2291 b0114 b0529 b2492 b0904 b0515 b3662 b1518 b2285   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.461721 (mmol/gDw/h)
  Minimum Production Rate : 0.749290 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 31.540430
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.740212
  EX_pi_e : 0.445379
  EX_so4_e : 0.116271
  EX_k_e : 0.090125
  EX_fe2_e : 0.007416
  EX_mg2_e : 0.004005
  EX_cl_e : 0.002403
  EX_ca2_e : 0.002403
  EX_cu2_e : 0.000327
  EX_mn2_e : 0.000319
  EX_zn2_e : 0.000157
  EX_ni2_e : 0.000149
  EX_cobalt2_e : 0.000012

Product: (mmol/gDw/h)
  EX_h2o_e : 51.673343
  EX_co2_e : 31.225749
  EX_h_e : 7.996141
  EX_acald_e : 1.157053
  EX_adn_e : 0.749290
  EX_alltn_e : 0.001803
  DM_mththf_c : 0.001493
  DM_5drib_c : 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
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