Can I save results as a table?
Yes, there is save option "Table" on the right corner of the result page that allows you to do this. You may later on open the file using any spreadsheet program.
What does the iProClass value-added information represent?
The iProClass report provides an alternative view of UniProtKB proteins. On top of the information presented in the UniProtKB report, it contains thorough information regarding protein family classification (PIRSF), protein structure and function, and it also allows ID mapping to multiple databases.
In the past, I submitted protein sequences to PIR-PSD, where should I submit my sequence now?
PIR has recently joined forces with the European Bioinformatics Institute and the Swiss Institute of Bioinformatics to establish the Universal Protein Resource (UniProt), the central resource of protein sequence and function. Please submit your sequences directly to UniProtKB using SPIN, the new web-based tool for submitting directly sequenced proteins.
Classification
What does the PIRSF family level mean?
The primary PIRSF classification level is the homeomorphic family (HFam), whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). At a lower level are the subfamilies (SubFam) which are clusters representing functional specialization and/or domain architecture variation within the family. Above the homeomorphic level there may be parent superfamilies
(SuperFam) that connect distantly related families and orphan proteins based on common domains. They may be homeomorphic superfamilies, but are more likely to be domain superfamilies if the common domains do not extend over the full length of the proteins. Because proteins can belong to more than one domain superfamily, the PIRSF structure is formally a network.
What does curation status mean?
Curation status reflects the level PIRSFs are manually curated.
None: Computer-generated protein clusters, no manual curation. The clusters are computationally defined using both pairwise based parameters (% sequence identity, sequence length ratio and overlap length ratio) and cluster-based parameters (% matched members, distance to neighboring clusters and overall domain arrangement).
Preliminary: Computer-generated clusters are manually curated for membership (does this protein belong to the cluster?) and domain architecture (Pfam domains listed from N- to C- terminus).
Full: A name is assigned to the protein family, and accompanying references are listed when available. In many cases, brief descriptions are also provided.
PIRSF scan does not give a match to any PIRSF, however, I know my protein may belong to one PIRSF
It is possible that no PIRSF match is returned after a scan; the reason being that the query protein is analyzed versus a reduced set of PIRSFs. Only PIRSFs that are fully curated and have associated benchmarked HMM models are considered for the analysis.
On the other hand, if the query protein is related to a member that has been placed manually by a curator, it is possible that the algorithm fails to hit the relevant PIRSF.
