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 Protein Homology/analogY Recognition Engine V 2.0


 

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BackPhyre

What it is

Instead of predicting the 3D structure of a protein sequence, often users have a solved structure and they are interested in determining if there is a related structure in a genome of interest. I have received frequent requests for this functionality and have called it "BackPhyre" to indicate how Phyre is being used in reverse.

IMPORTANT: For this procedure to work, only single protein chains must be submitted. There are currently no checks performed on your uploaded structure, so please be sure to only submit one chain.

The following genomes are currently available to search

  • Arabidopsis_thaliana
  • Drosophila_melanogaster
  • Homo_sapiens
  • Mus_musculus
  • Plasmodium_falciparum
  • Saccharomyces_cerevisiae
  • Sulfolobus_solfataricus_P2
  • Thermoplasma_acidophilum
  • Agrobacterium_tumefaciens_C58_Cereon
  • Bacillus_subtilis
  • Bartonella_henselae_Houston-1
  • Corynebacterium_diphtheriae
  • Desulfitobacterium_hafniense_Y51
  • Escherichia_coli_K12
  • Lactobacillus_casei_ATCC_334
  • Neisseria_meningitidis_MC58
  • Pseudomonas_aeruginosa
  • Staphylococcus_aureus_COL
  • Streptococcus_pneumoniae_D39
  • Streptomyces_coelicolor
  • Synechococcus_CC9311
  • Yersinia_pestis_CO92

    If you want to search a genome not on this list please let me know. It takes considerable computation to process a large genome for use by BackPhyre so it may take a while between you asking for a genome and getting it up and running. I will maintain a list here and on the Phyre Google Group of requests and and genomes currently being processed

    Results and interpretation

    Unlike ordinary Phyre results, BackPhyre does not produce a 3D model. Instead it displays a ranked list of hits from the genomes searched, and links to the alignments. See figures below.

  • If you find an interesting hit simple retrieve the sequence using the links in the main page and submit that sequence for a normal Phyre modelling run.



    Phyre is for non-commercial use only

    Commercial users please contact Michael Sternberg

    Please cite: The Phyre2 web portal for protein modeling, prediction and analysis
    Kelley LA et al. Nature Protocols 10, 845-858 (2015) [paper] [Citation link]
     
    © Structural Bioinformatics Group, Imperial College, London
    Lawrence Kelley, Michael Sternberg 
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    Phyre2 is part of Genome3D