Annotation Of Protein Functions?

Question

[Cacau]

I find many tools that are talked about are BLAST2GO, PFAM and Interproscan. However, I wonder if there is any tool that can be used to annotate proteins without any names directly (not just focus on function or subcellular localization like GO) such as HAMAP (enter link description here)

[K]

I feel I should join you in your question. Regards from Spain.

Answer 1

[Hamish]

I am not entirely sure what your question actually is, but a brief overview of how some of these tools work may help...

There are a number of methods (HMMs, profiles and patterns) used to predict protein function based on databases of protein signatures describing functional features such as domains and sites and protein family information. For example:

• CATH/Gene3D
• HAMAP
• PANTHER
• Pfam
• PIRSF
• PRINTS
• ProDom
• PROSITE
• SMART
• SUPERFAMILY
• TIGRFAMs

Typically these databases focus on a specific aspect of protein classification/function.

While these databases are based on known proteins and their properties, the signatures (HMMs, profiles and patterns) described in the databases can be used to predict if an unknown protein shares features with known proteins and thus may have the same function.

The wide range of available signature databases and their variety of specialities has led to the development of an integrated signature database. InterPro uses the signatures from the databases listed above and identifies which signatures support a particular annotation choice, which are general and which are specific and which are unreliable. The result is the InterPro database, which describes the various protein families and features, and provides an analysis of the UniProtKB and UniParc databases based on the signature calls made by the InterProScan software which uses the signature methods of the member databases to scan the protein sequences, and using the InterPro data then makes decisions about which InterPro entries best describe the features of the protein.

The current version of InterProScan provides annotations that include signature database identifiers, InterPro identifiers, Gene Ontology (GO) terms and pathway terms. These are typically used to provide initial annotations for genes and proteins as a starting point for later manual annotation.

The Blast2GO software uses a combination of NCBI BLAST and InterProScan to annotate sequences with possible function, family and role information for the proteins.

As well as many genome and transcriptome projects which are using tools such as Blast2GO and InterProScan to provide automatic annotation, UniProt also use InterProScan results as part of their automatic annotation pipeline along with a collection of rules derived from the experience of the UniProt curators.