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The Proteome Browser provides a wealth of protein information presented
in the form of graphical images and links to external internet sites.
SwissProt information: The top line of the page shows the
SwissProt accession number, entry name,
and protein name for the current selection. Click on the accession
number to open the record for this protein in the SwissProt database.
Proteome browser tracks: The tracks image displays a set of
aligned tracks showing information about the protein's amino acid
sequence and anomalies, the corresponding DNA sequence and exon make-up,
and protein traits such as hydrophobicity, glycosylation potential,
polarity, cysteine content, and SuperFamily domain composition.
To display a description of a track from the Protein Browser web page,
click on the track's label. For more information about
the individual tracks, see the Protein Tracks
section.
The navigation buttons permit scrolling and resizing of the tracks
image:
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Scrolling left or right: To shift the browser tracks image
sideways to the left or right by 2%, 47.5%, or 95% of the displayed size,
click the corresponding move arrow.
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Rescaling the image: The Rescale to buttons control the size
of the tracks image. At the default "Full" setting, the
image is displayed at its full size. The "1/2" and "1/6" buttons shrink
the image size by the equivalent amount. The image
retains its scrolled settings when it is rescaled. The amino acid
sequence of the protein is displayed only in the full-sized image.
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Displaying the Genomic sequence: To view the codons that
correspond to the Amino Acid Sequence track and their reverse
complements, click the DNA rescale button. The Genomic Sequence
track is hidden by default.
Protein property histograms: The Protein Browser's histogram
section provides a graphical comparison of several protein traits
relative to those of proteins genome-wide. The
pictured traits include amino acid frequencies and anomalies,
molecular weight, exon count, cysteine abundance, hydrophobicity,
isoelectric point, and predicted domains. To display a brief description
of a histogram from the Protein Browser web page, click on the graph's
label. For detailed information on the
histograms, see the Protein Property Histograms
section.
UCSC links: These links display additional information
about the gene and mRNA associated with the selected protein.
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Genome Browser link: Click on the accession number to open up a
Genome Browser window displaying this mRNA.
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Gene Details Page link: Click on the accession number to display
the Genome Browser Known Genes details page for the gene associated with
this protein.
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Gene Sorter link: Click on the accession number to open
up a Gene Sorter window displaying the gene associated with this mRNA,
along with a set of related genes.
Domain information: The browser provides 3 primary sources of
detailed domain information about the selected protein.
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SuperFamily/SCOP track: See the
Protein Tracks section for a description
of this track. Click on a yellow domain box in the track to display
Superfamily information about that domain.
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EMBL-EBI InterPro website link: Click on the Graphical view of domain
structure
link to open a page showing protein matches from the UniProt-SwissProt
database. Click on an ID number to display the InterPro
information page for that domain.
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Sanger Institute
Pfam (Protein families database of alignments and
HMMs) website link: Click on the Pfam accession number to display the Pfam
database record for the domain.
Comparative 3-D structures:
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Protein Data Bank (PDB):
When available, this section displays one or more 3-D structures of the protein from
the PDB. Click on a structure number to display the associated PDB record.
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ModBase: This section displays front, top,
and Side views of the predicted comparative 3-D structure of the protein
obtained from UCSF's ModBase. Click on the protein accession number or
one of the images to display the ModBase database record for the
protein. If no images are displayed, no ModBase structure exists for
the protein.
Pathways:
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BioCarta:
Provides information about gene interactions
within pathways for human cellular processes, displayed on NCI's
Cancer Genome Anatomy Project (CGAP) website.
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KEGG: Displays the associated pathway record in the Kyoto
Encyclopedia of Genes and Genomes
(KEGG).
Fasta format: This section shows the Fasta record for the
protein containing the complete amino acid sequence.
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