- Course overview
- Search within this course
- What is CATH database?
- Functional families and structural clusters in CATH
- Summary
- Quiz: Check your learning
- Your feedback
- Get help and support
- References
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Search by sequence in CATH
The search by sequence uses FunFHMMer function prediction server, which takes a protein sequence in FASTA format or a UniProt/GenBank sequence identifier as input. The server identifies the functional family (FunFam) for a query sequence by scanning input against a library of FunFam HMMs in CATH. The output of the web server provides matched FunFam assignments within the query sequence and also highlights the multi-domain architecture of the sequence, where appropriate. Watch the demonstration about how to use the CATH sequence search tool (Video 1).
Let’s do it together: locate the position of structural domains on a protein sequence
- Download the FASTA sequence of Alanine Racemase from E. coli, using UniProt ID: P0A6B4 (359 amino acids) from UniProt database.
- Go to http://www.cathdb.info/search/by_sequence and paste the sequence in the text area and click on ‘Search’ button (Figure 6).
- The search can take some time to be processed as shown in the ‘Progress’ tab (Figure 6).
- Click on ‘Matching Domains’ or ‘Matching FunFams’ to view the search results (explained on the next page).
