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 : dhpmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (56 of 116: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 27
  Gene deletion: b3399 b4382 b1241 b0351 b4069 b2502 b4384 b2744 b3115 b1849 b2296 b2926 b2407 b3616 b3589 b3665 b0675 b2361 b0112 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b1511   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.454545 (mmol/gDw/h)
  Minimum Production Rate : 0.671908 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 25.295529
  EX_nh4_e : 10.411703
  EX_glc__D_e : 10.000000
  EX_pi_e : 1.110365
  EX_so4_e : 0.114463
  EX_k_e : 0.088724
  EX_fe2_e : 0.007300
  EX_mg2_e : 0.003943
  EX_ca2_e : 0.002366
  EX_cl_e : 0.002366
  EX_cu2_e : 0.000322
  EX_mn2_e : 0.000314
  EX_zn2_e : 0.000155
  EX_ni2_e : 0.000147
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 49.873599
  EX_co2_e : 24.049987
  EX_h_e : 9.943826
  EX_thymd_e : 1.071559
  Auxiliary production reaction : 0.671908
  EX_ac_e : 0.264630
  DM_mththf_c : 0.000204
  DM_5drib_c : 0.000102
  DM_4crsol_c : 0.000101

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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