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 : dutp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (24 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 25
  Gene deletion: b1241 b0351 b4069 b4384 b2744 b3115 b1849 b2296 b0030 b2407 b3616 b3589 b3665 b0411 b4381 b0112 b3654 b3714 b3664 b0114 b0529 b2492 b0904 b1511 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.524622 (mmol/gDw/h)
  Minimum Production Rate : 1.550992 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 19.945138
  EX_glc__D_e : 10.000000
  EX_nh4_e : 9.690387
  EX_pi_e : 5.159031
  EX_so4_e : 0.132110
  EX_k_e : 0.102403
  EX_fe2_e : 0.008426
  EX_mg2_e : 0.004551
  EX_ca2_e : 0.002731
  EX_cl_e : 0.002731
  EX_cu2_e : 0.000372
  EX_mn2_e : 0.000363
  EX_zn2_e : 0.000179
  EX_ni2_e : 0.000169
  EX_cobalt2_e : 0.000013

Product: (mmol/gDw/h)
  EX_h2o_e : 49.863404
  EX_co2_e : 19.283067
  EX_h_e : 6.048393
  Auxiliary production reaction : 1.550992
  EX_thymd_e : 0.461265
  EX_ac_e : 0.305428
  DM_mththf_c : 0.000235
  DM_5drib_c : 0.000118
  DM_4crsol_c : 0.000117

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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