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 : trp__L_e
List of minimal gene deletion strategies (Download)

Gene deletion strategy (77 of 80: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 60
  Gene deletion: b4467 b1478 b4382 b3942 b1732 b1241 b3831 b4069 b4384 b3708 b0910 b3752 b3115 b1849 b2296 b2779 b2407 b1004 b3713 b1109 b0046 b3124 b3236 b2463 b1982 b2143 b2797 b3117 b1814 b4471 b2498 b3449 b2210 b3551 b0261 b0411 b2799 b3945 b1602 b4219 b1832 b1778 b2239 b2406 b3915 b1539 b2492 b0904 b1533 b1380 b1710 b2480 b0514 b1695 b4141 b1798 b0606 b2285 b1009 b4209   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.403309 (mmol/gDw/h)
  Minimum Production Rate : 0.391948 (mmol/gDw/h)

Substrate: (mmol/gDw/h)
  EX_o2_e : 34.914044
  EX_glc__D_e : 10.000000
  EX_nh4_e : 5.455622
  EX_pi_e : 0.445106
  EX_so4_e : 0.101561
  EX_k_e : 0.078723
  EX_fe3_e : 0.006478
  EX_mg2_e : 0.003499
  EX_ca2_e : 0.002099
  EX_cl_e : 0.002099
  EX_cu2_e : 0.000286
  EX_mn2_e : 0.000279
  EX_zn2_e : 0.000138
  EX_ni2_e : 0.000130
  EX_cobalt2_e : 0.000010

Product: (mmol/gDw/h)
  EX_h2o_e : 50.321853
  EX_co2_e : 35.412263
  EX_h_e : 6.161275
  EX_ac_e : 0.618317
  EX_mal__L_e : 0.421470
  EX_trp__L_e : 0.391948
  EX_ura_e : 0.129071
  EX_g3pe_e : 0.056071
  EX_hxan_e : 0.000451
  DM_5drib_c : 0.000271
  DM_4crsol_c : 0.000090

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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