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 : cdigmp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (55 of 79: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 29
  Gene deletion: b4382 b4069 b4384 b3708 b3752 b2297 b2458 b2407 b3124 b1982 b2797 b3117 b1814 b4471 b0261 b2239 b2406 b3453 b0114 b2366 b0755 b3612 b0529 b2492 b0904 b1533 b3927 b3825 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.664058 (mmol/gDw/h)
  Minimum Production Rate : 0.140647 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 28.582459
  EX_glc__D_e : 10.000000
  EX_nh4_e : 8.578238
  EX_pi_e : 0.921848
  EX_so4_e : 0.167223
  EX_k_e : 0.129619
  EX_fe2_e : 0.010665
  EX_mg2_e : 0.005761
  EX_ca2_e : 0.003456
  EX_cl_e : 0.003456
  EX_cu2_e : 0.000471
  EX_mn2_e : 0.000459
  EX_zn2_e : 0.000226
  EX_ni2_e : 0.000214
  EX_cobalt2_e : 0.000017

Product: (mmol/gDw/h)
  EX_h2o_e : 50.348592
  EX_co2_e : 29.155841
  EX_h_e : 7.613409
  EX_ac_e : 0.386605
  Auxiliary production reaction : 0.140647
  DM_5drib_c : 0.000446
  DM_4crsol_c : 0.000148

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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