Interpreting a Protein Superfamily Detail Page
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This help document answers the following questions:

What information is in a Protein Superfamily Detail report?

The Protein Superfamily Detail report displays protein classification sets obtained from the Protein Information Resource SuperFamily (PIRSF) site for a homeomorphic superfamily with mouse, human, and rat relationships from HomoloGene Class data. You can select representative protein sequences for mouse, human and rat by row and download them in FASTA format or forward them to MouseBLAST.

How do I interpret the Protein Superfamily Detail report resulting from my query?

Mouse superfamily members are shown with links to their corresponding Homology Classes. Note that pseudogenes are included in PIRSF families but not in orthology sets used here. You can select a given mouse superfamily member and download (or forward to MouseBLAST) FASTA formatted protein sequences of that mouse gene and its mouse, human and rat homologs, as defined in the corresponding Homology Class.

The numbers of mouse, human and rat genes in the Homology Class are shown. You can also "Select all" mouse superfamily members to obtain their protein sequences and the protein sequences for all mouse, human and rat homologs of the mouse superfamily members. The number of protein sequences returned does not always match the numbers of homologs shown, because the same protein sequence can be associated with multiple homologs. For mouse superfamily members not included in any Homology Class, only the mouse protein sequence is returned.

See How do the buttons work? What does Invert do? for additional viewing options.

FIELD DESCRIPTION
Mouse PIRSF MembersThe official gene symbol for the mouse genetic marker, linked to the MGI Gene Detail page.
Chr Chromosomal assignment of the mouse marker.
Homology Class The Homology Class ID from HomoloGene, linked to the MGI Vertebrate Homology Class page.
Mouse : Human : Rat Homology Class Shows the number of members in this Homology Class for mouse, human and rat.
Select Proteins (mouse, human, rat)A check box is provided to allow you to select homology classes for downloading representative protein sequences in FASTA format or to be forwarded to MouseBLAST.

How do I use a Protein Superfamily Detail report?

There are several ways to use the detail reports. You can:

  1. view Vertebrate Homology Class pages for the different PIRSF members of this Superfamily.
  2. download mouse, human and rat protein sequences for one or more homology classes in FASTA format.
  3. forward one or more sets of protein sequences to MouseBLAST.

How do I download sequences in FASTA format?

To download sequences in FASTA format:

  1. Click to put a check mark in the Select Proteins column for one or more Homology Classes.
  2. Just above the table, For the selected sequences, toggle download in FASTA format (this is the default).
  3. Click GO.

How do I forward sequences to MouseBLAST?

To forward sequences to MouseBLAST:

  1. Click to put a check mark in the Select Proteins column for one or more Homology Classes.
  2. Just above the table, For the selected sequences, toggle download in FASTA format (this is the default) to forward to MouseBLAST.
  3. Click GO.

For additional information, see:

How do the buttons work? What does Invert do?

ButtonActionUse this when...
Select allSelects all the Homology Classes on the list.You want to examine every protein sequence.
InvertToggles to remove check marks from selected boxes and put them in boxes not selected.You don't want the action of Reset (which removes all check marks) or when the list of sequences you want to see is longer than the list you do not want to see.
To use it, click Select all, click boxes beside any undesired sequences, then click Invert. Only the desired sequences remain.
ResetRemoves any check marks from boxes. You want to start over and make all new selections.
GoActivates your choice (or the default action) from the selection menu.You are ready to download a sequence in FASTA format or forward it to MouseBLAST. See How do I download sequences in FASTA format? or How do I forward sequences to MouseBLAST? for details.

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