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 : gdptp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (64 of 70: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 32
  Gene deletion: b3942 b1732 b4069 b4384 b3708 b3008 b1479 b2297 b2458 b0030 b2407 b3236 b2463 b1982 b2797 b3117 b1814 b4471 b2210 b3665 b1701 b1805 b4381 b2406 b0114 b2366 b2492 b0904 b1533 b3927 b3662 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.732003 (mmol/gDw/h)
  Minimum Production Rate : 0.310510 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.363742
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.460591
  EX_pi_e : 2.258647
  EX_so4_e : 0.184333
  EX_k_e : 0.142882
  EX_fe2_e : 0.011757
  EX_mg2_e : 0.006350
  EX_ca2_e : 0.003810
  EX_cl_e : 0.003810
  EX_cu2_e : 0.000519
  EX_mn2_e : 0.000506
  EX_zn2_e : 0.000250
  EX_ni2_e : 0.000236
  EX_cobalt2_e : 0.000018

Product: (mmol/gDw/h)
  EX_h2o_e : 50.296371
  EX_co2_e : 25.993089
  EX_h_e : 7.775586
  EX_ac_e : 0.426162
  Auxiliary production reaction : 0.310510
  EX_ade_e : 0.000493
  DM_mththf_c : 0.000328
  DM_5drib_c : 0.000165
  DM_4crsol_c : 0.000163

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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