1. Today’s menu: -UniProt - SwissProt/TrEMBL -PROSITE -Pfam -Gene Onltology Protein and Function Databases Tutorial 7

2. Characterized proteins Hypothetical proteins

3. 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/

9. Pfam http://pfam.sanger.ac.uk/ Pfam is a database of multiple alignments of protein domains or conserved protein regions.

13. One more example

15. Description Structure info Gene Ontology Links

17. 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

18. 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)

19. 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

21. Search Results Domains architecture

23. http://www.expasy.ch/tools/pratt/ PRATT Make a pattern from FASTA format sequences inorder to query Prosite

25. Greed, Overlap and Include Search A-x(1,3)-A on ABACADAEAFA

27. 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/

28. Three principal branches http://www.geneontology.org/amigo/

29. GO structure is a Directed Acyclic Graph

30. Important: note what is the source of the GO entry

31. 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

32. http://www.ebi.ac.uk/interpro/ Interpro

33. Exercize 1. Find the accession number of the gene PRP in Human using Uniprot ? What is this gene?

34. 2. Use the accession number to search PFAM ? What domains did you find ?

35. 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:

36. 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?