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 : 4r5au_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (94 of 111: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 35
  Gene deletion: b3553 b1241 b0351 b4069 b4384 b3708 b3752 b3115 b1849 b2296 b3617 b2407 b1238 b1982 b2797 b3117 b1814 b4471 b1033 b0261 b4381 b2406 b0112 b0452 b0114 b0509 b3125 b0755 b3612 b1539 b2492 b0904 b1533 b2835 b3662   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.439888 (mmol/gDw/h)
  Minimum Production Rate : 1.316278 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.131240
  EX_nh4_e : 10.016362
  EX_glc__D_e : 10.000000
  EX_pi_e : 0.424319
  EX_so4_e : 0.110773
  EX_k_e : 0.085863
  EX_fe2_e : 0.007065
  EX_mg2_e : 0.003816
  EX_ca2_e : 0.002290
  EX_cl_e : 0.002290
  EX_cu2_e : 0.000312
  EX_mn2_e : 0.000304
  EX_zn2_e : 0.000150
  EX_ni2_e : 0.000142
  EX_cobalt2_e : 0.000011

Product: (mmol/gDw/h)
  EX_h2o_e : 46.267796
  EX_co2_e : 25.436628
  EX_h_e : 11.637719
  EX_ac_e : 2.329458
  Auxiliary production reaction : 1.316278
  DM_oxam_c : 0.000492
  DM_5drib_c : 0.000295
  EX_glyclt_e : 0.000294
  DM_4crsol_c : 0.000098

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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