1. Protein and Function Databases
Tutorial 9
Protein and Function Databases

2. UniProt - SwissProt/TrEMBL PROSITE Pfam Gene Onltology DAVID
Protein and Function Databases
UniProt - SwissProt/TrEMBL
PROSITE
Pfam
Gene Onltology
DAVID

3. Glossary
Domain
A structural unit which can be found in multiple protein contexts.

4. Glossary
Repeat
A short unit which is unstable in isolation but forms a stable structure when multiple copies are present.
Family
A collection of related proteins.

5. 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.

6. Protein search
Uniprot input
Reviewed protein

7. Uniprot output Sequence download Accession number Protein status
organism
length

8. Information for one protein
General information
annotations

9. GO annotation (MF, BP, CC)
General keywords
GO annotation (MF, BP, CC)

10. Alternative splicing isoforms Features in the sequence

11. Sequences
References

12. Alignment for two or more proteins

13. MSA

14. Blast

15. Pfam
Pfam is a database of multiple alignments of protein domains or conserved protein regions.

16. What kind of domains can we find in Pfam?
Trusted Domains
Repeats
Fragment Domains
Nested Domains
Disulfide bonds
Important residues
(e.g active sites)
Trans membrane domains

17. What kind of domains can we find in Pfam?
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)
Low complexity regions
Coiled Coils:
(two or three alpha helices that wind around each other)

19. Pfam input

20. Domains
Domain range and score

21. Description
Structure info
Gene Ontology
Links

23. Prosite
ProSite is a database of protein domains and motifs that can be searched by either regular expression patterns or sequence profiles.

25. Search Results
Domains architecture

27. Gene Ontology (GO) It is a database of biological processes,
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

28. Search by AmiGO

29. Three principal branches

30. Directed Acyclic Graph
GO structure is a
Directed Acyclic Graph

31. GO sources ISS Inferred from Sequence/Structural Similarity
IDA Inferred from Direct Assay
IPI Inferred from Physical Interaction
TAS Traceable Author Statement
NAS Non-traceable Author Statement
IMP Inferred from Mutant Phenotype
IGI Inferred from Genetic Interaction
IEP Inferred from Expression Pattern
IC Inferred by Curator
ND No Data available
IEA Inferred from electronic annotation

32. Results for alpha-synuclein

33. DAVID Functional Annotation Bioinformatics Microarray Analysis
DAVID 
Functional Annotation Bioinformatics Microarray Analysis
Identify enriched biological themes, particularly GO terms
Discover enriched functional-related gene/protein groups
Cluster redundant annotation terms
Explore gene names in batch 

34. annotation
classification
ID conversion

35. Functional annotation
Upload
Annotation options