UniProt The Universal Protein Resource (UniProt) is a central Repository of protein sequence, function,classification,and cross reference. It was created by Joining the information contained in Swiss-Prot and TrEMBL. http://www.uniprot.org/
What kind of domains can we find in Pfam? Trusted Domains Repeats and Motifs Fragment Domains Nested Domains Disulfide bonds Important residues (e.g active sites) Trans membrane domains
What kind of domains can we find in Pfam? Low complexity regions Coiled Coils: (two or three alpha helices that wind around each other) Context domains: are those that despite not scoring above the family threshold are expected to be real, based on the other domains found in the protein. Signal peptides: (indicate a protein that will be secreted)
http://www.expasy.org/tools/scanprosite ProSite is a database of protein domains and motifs that can be searched by either regular expression patterns or sequence profiles.http://www.expasy.org/tools/scanprosite
Gene Ontology (GO) It is a database of biological processes, molecular functions and cellular components. GO does not contain sequence information nor gene or protein description. GO is linked to gene and protein databases. The GO database is structured as a tree http://www.geneontology.org/
Three principal branches http://www.geneontology.org/amigo/
Important: note what is the source of the GO entry
GO sources ISSInferred from Sequence/Structural Similarity IDAInferred from Direct Assay IPIInferred from Physical Interaction TASTraceable Author Statement NASNon-traceable Author Statement IMPInferred from Mutant Phenotype IGIInferred from Genetic Interaction IEPInferred from Expression Pattern ICInferred by Curator NDNo Data available IEAInferred from electronic annotation
Exercize 1. Find the accession number of the gene PRP in Human using Uniprot ? What is this gene?
2. Use the accession number to search PFAM ? What domains did you find ?
3. a. Double Click on the Prion domain? b. Choose the “Alignments” option from the left tool bar. c. Press the “View” bottom to see the alignments. d. Copy the alignments using the following manuals:
4. Use the alignments as input for PRATT http://www.expasy.ch/tools/pratt/ To find a motif to scan PROSITE. How many results did you find using PROSITE?