I am studying a gene, CAPN5, with two mutations. I have mapped their locations in the gene. I would like to know what motif the sequence relates to in the translated protein. Knowing what domain the mutation affects could help elucidate the impact of the mutation on the protein function.
Yes, UniProt.. or
InterPro (protein domains and families; includes Pfam): http://www.ebi.ac.uk/interpro/protein/O15484
Ensembl (gene overlaid on the genome): http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000149260;r=11:77066932-77126155
EBI summary: http://www.ebi.ac.uk/s4/summary/molecular?term=CAPN5&classification=9606&tid=nameOrgENSMUSG00000035547
You might want to try the Superfamily server too:
http://supfam.cs.bris.ac.uk/SUPERFAMILY/temp/hmm/329840159350172.html
pfam.sanger.ac.uk will give you the domains of the query sequences
In addition to pfam there are:
EMBL SMART:
http://smart.embl-heidelberg.de
and
PROSITE:
http://prosite.expasy.org/
FYI: InterPro summarises the results from Superfamily, Pfam, Smart, and Prosite (as well as CATH-Gene3D and ProDom, plus the family-centred databases Pather, HAMAP, PRINTS and TIGRFams) - so rather than visiting 11 sites, you could just go to one (all databases are part of the InterPro consortium) . The only resource not covered is NCBI's CDD.
- Badges
- Science topic
- Similar topics
- Mathematical Sciences
- Graphs