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 : ade_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (34 of 78: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 23
  Gene deletion: b3399 b1241 b0351 b4069 b2502 b4384 b2744 b3115 b1849 b2296 b3617 b3665 b0675 b2361 b4381 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b1518   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.648823 (mmol/gDw/h)
  Minimum Production Rate : 1.227347 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_fe2_e : 1000.000000
  EX_h_e : 985.698668
  EX_o2_e : 274.526697
  EX_nh4_e : 13.143973
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.625859
  EX_so4_e : 0.163387
  EX_k_e : 0.126646
  EX_mg2_e : 0.005629
  EX_ca2_e : 0.003377
  EX_cl_e : 0.003377
  EX_cu2_e : 0.000460
  EX_mn2_e : 0.000448
  EX_zn2_e : 0.000221
  EX_ni2_e : 0.000210
  EX_cobalt2_e : 0.000016

Product: (mmol/gDw/h)
  EX_fe3_e : 999.989579
  EX_h2o_e : 552.247430
  EX_co2_e : 22.845537
  EX_ac_e : 2.192527
  Auxiliary production reaction : 1.227347
  DM_mththf_c : 0.000291
  DM_5drib_c : 0.000146
  DM_4crsol_c : 0.000145

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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