CGD Help: Domains/Motifs Page

Contents

Page Description and Navigation
Page Organization

Proteome Browser
Shared Domains/Motifs
Unique Domains/Motifs
Transmembrane Domains
Signal Peptides
External Links

Related CGD Help Documents

Page Description and Navigation

The CGD Domains/Motifs Page displays information on conserved sequence features for a subject CGD protein, predicted using the InterProScan program from the InterPro database. The page lists other proteins in the same organism that share domains in common with the subject protein, and conversely lists the domains that are unique to the subject. Additionally, links are provided to search external databases directly with the subject protein sequence.

The top of the page provides a site-wide quick search, links to the major CGD informational resources, and a bar with links to popular tools, such as a local BLAST search. Beneath this is a series of tabs linking to other locus-specific information pages, including Locus Summary, Locus History, Literature, Gene Ontology, and Phenotype.

Page Organization

Proteome Browser

The CGD Proteome Browser interactively displays conserved domains identified using the protein sequence to query the InterPro database. The Domains/Motifs page displays a thumbnail image of the browser; clicking on that brings up the browser itself.
Shared Domains/Motifs

Table providing information about other proteins (in the same organism) that also contain features identified in the query protein sequence. The table has three columns:
1. Protein. The name of the protein sharing features with the query, with a link to its Locus Summary page.
2. Features in common with query protein. List of InterPro domains or motifs identified in both query protein and this protein. Includes the source database, the feature accession number (linked to a description of the feature), and a brief description of the feature.
3. Other features in this protein (but not in query protein). List of InterPro domains or motifs identified in this protein but absent in query. Includes the source database, the feature accession number (linked to a description of the feature), and a brief description of the feature.
Unique Domains/Motifs

Table listing features found in the query protein, but which are found in no other other proteins in the organism. The table has three columns:
1. Database source. InterPro member database where the feature was defined.
2. Accession number. Feature identifier, linked to a description of the feature at the source database.
3. Description Brief description of the name and function of the feature, if known.
Transmembrane Domains

Table showing transmembrane domains (if any) identified in the query protein using the TMHMM program. The table has two columns:
1. Predicted Transmembrane Domain(s). A Proteome Browser thumbnail image showing the relative position in the protein of transmembrane domains. Clicking on the image opens a browser session.
2. Amino Acid Coordinates. A table listing the start and end positions of each transmembrane domain.
Signal Peptides

Table showing signal peptides (if any) identified in the query protein using the SignalP program. The table has two columns:
1. Predicted Signal Peptide(s). A Proteome Browser thumbnail image showing the relative position in the protein of signal peptides. Clicking on the image opens a browser session.
2. Amino Acid Coordinates. A table listing the start and end positions of each signal peptide.
External Links

For your convenience, we also provide several links for searching external resources with the query sequence. Depending on your specific problem or interest, one or the other of these may produce the best results for you. For specific help with any of these other resources, you will be best served at the original source. Currently we support searches of the following resources: