This help document answers the following questions about the Protein Superfamily Browser:
See also:
Protein families are clustered into homeomorphic superfamilies. PIRSF uses this concept to represent protein clusters with 80% sequence similarity. Currently there are about 36,000 PIRSF superfamilies, and 1786 are represented in mouse.
PIRSF is a curated protein classification system based on sequence analysis which clusters all known protein sequences into a network structure representing domain superfamilies, homeomorphic superfamilies, subfamilies and families. At one level there is a computationally-derived homeomorphic clustering with aims to divide all proteins into groups called superfamilies, with 80 percent sequence similarity. These homeomorphic superfamilies contain protein sequences which are homologous from end-to-end and contain the same domain architecture.
A PIRSF ID identifies a data record in the PIRSF database. PIRSF IDs have an alphanumeric format of PIRSFnnnnnn; PIRSF005574, for example, is the ID for DNA mismatch repair protein.
The Protein Superfamily Vocabulary is a catalog of Protein Information Resource SuperFamily (PIRSF) classification names annotated to MGI genes.
See Protein Superfamily Terms and Concepts.
The Vocabulary has a flat structure and is organized alphanumerically (A-Z; 0-9). When you click any letter of the alphabet, a list of all protein superfamilies beginning with that letter appears, arranged alphabetically. When you click 0-9, one list appears, containing all protein superfamilies beginning with a number (e.g., 1 alpha,25-dihydroxyvitamin D3-inducible protein). The number of mouse genes in MGI appears in parentheses next to each protein superfamily name. The absence of this text, e.g., (3 genes), means that MGI currently contains no annotations for this gene.
Back to TopYou can either browse or search from the Protein Superfamily Browser entry page.
You can use the Browser to search for new gene clusters according to the PIRSF superfamilies they derive from. The tool integrates MGI associations between mouse genes and their representative polypeptide sequences with the PIRSF protein clustering data. MGI genes (mouse, human and rat) appear on the Protein Superfamily Detail page, grouped and classified by structural and functional relationships, based on PIRSF homeomorphic superfamilies combined with MGI orthology data.
Back to TopSee What Boolean operators are allowed? How do they work? Is there a default operator?.
Yes, you can. However, the tool interprets any spaces in your query as ANDs. Therefore, if you do not use a Boolean operator, make sure any family names and IDs are from the same term. See What Boolean operators are allowed? How do they work? Is there a default operator? and Examples for sample entries and results.
Back to TopThere are several ways to use the Protein Superfamily Browser to find protein superfamilies with MGI gene annotations in MGI.
Once a superfamily list appears, click an item to view its Protein Superfamily Detail page. On the Protein Superfamily Detail page, there are links to additional MGI resources. (See Interpreting a Protein Superfamily Detail page.)
Clicking the PIRSF ID number takes you to the PIR iProClass report (for an example, see the IProClass tutorial).
Back to TopSee Interpreting a Protein Superfamily Detail Page .
If your query returns no results, a Protein Superfamily Browser summary displays your input text and reports that there were zero matching human gene protein superfamily names for that term (or ID), e.g.:
You searched for... Protein Superfamily Vocabulary:contains PIRSF0000894 searching Protein Superfamily vocabulary terms and accessionIDs. 0 matching Protein Superfamily terms
The probable cause is that something in the search box is incorrect. For example:
See the sample query entries below for additional help.
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The number of matches in the examples is representative and may not be the same as what you get when you query. The point is to show how structuring a query in various ways yields different (or zero) results. Sometimes getting zero (0) results, just means that MGI has no records for to the superfamily or PIRSF ID at this time. See also Using Full-Text Searches on MGI Query Forms for detailed explanations on using Boolean operators. If your results are not as expected, this document provides additional examples of queries and returns. Back to Top
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