Pfam Relationships and Multiple Alignments
This application can be used to investigate relationships between closely-related and distantly-related Pfam families, and to retrieve pile-up alignments between them. We have used the Global Trace Graph to create an all-against-all database of Pfam alignments. Enter your query Pfam identifier below to begin a search.
Quick Help
  • By default, you will be shown a list of families containing alignments to your query family, with descriptions, mean scores and links to Pfam - you may then select families to align. To skip this stage and align all hits, select 'fetch alignment using all hits'.
  • Alignments can be displayed in two forms: with gap expansion (all indels shown) and without (insertions in hit sequences omitted). The latter is a quick way to see conserved motifs; use 'expand gaps: yes' to retrieve the full, gapped alignment.
  • Alignments are coloured using the default Clustal Colour Scheme.
  • Depending on input parameters, neighbourhood size and alignment length, it can take a while to retrieve the alignment. Please be patient and do not re-click 'search' - this will only make it slower!
  • The full help page can be found here - right-click the link and open in new tab/page/window.
  • You can use the comments page if you need to contact us.
  • Pfam Version: v19.0
(eg:PF00001)
Expand Gaps?
Score Thresholds
Reference