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By InterPro Accession
Select proteins having a match to an InterPro entry. This is restricted to true matches for the compact view. If 'Splice variants' is checked then proteins are selected which have alternative splice forms where any of the splice forms have a true match to the entry. In this case proteins without alternative splice forms are not shown.
By UniProtKB Accession
Select a protein using a UniProtKB accession.
By InterPro Architecture Code
Selects proteins using the Architecture code.
Proteins having Splice Variants Displays splice variants of proteins where they exist. Splice variants associated with a UniProtKB accession that are cross referenced and have a different UniProtKB accession are not displayed. Only available with compact and detailed displays.
Proteins of known structure Restrict the selection by only showing proteins of known structure.
Taxonomy - NCBI tax ID(s) Restrict the selection of proteins to the taxonomy defined by the tax ID(s).
Proteins are sorted by database category - UniProtKB/Swiss-Prot followed by UniProtKB/TrEMBL, and then by alphabetically by UniProtKB accession or ID.
Key to symbols which may appear in the protein label on the left hand side of the match display.
Accession: Proteins are linked (click on the accession) to the detailed view.
Scale: The scale indicates how many amino-acids per vertical line in the match line.
ID: The UniProtKB protein is ID is shown.
Structure links to the known protein structure when available.
Fragment indicates that a protein is a fragment*.
Variants links to the protein splice variants when existing.
GO! links to GO annotation for the protein.
* UniProtKB fragments with FT NON_CONS and FT NON_TER features.
NON_CONS fragments are not indicated as non-consecutive in InterPro and being non-consecutive the match to methods may be incorrect if the method spans the 'break'.
Each protein is represented as a scaled horizontal line, the protein match line, along which vertical lines are drawn at 10, 20, 50, 100, 200 or 500 aa intervals, depending on the length of the protein. The scale is shown to the left of the match graphics.
Coloured bars are displayed along the protein match line to indicate where in a protein matches were found among the InterPro entries. The bar is coloured according to which InterPro entry matched that region of the protein. If multiple InterPro entries match at the same point on an protein match line their match lines boxes will be displayed one above the other - the vertical position of a match line box and its colour has no significance. In addition to matches to InterPro entries, matches to curated structural data, CATH, SCOP, and PDB and to non-curated predicted structural elements defined by SWISS-MODEL and MODBASE are also displayed. The matches to these structural models have fixed colours with white striped lines.
See the key near the bottom of the page to identify which colours correspond to which InterPro entries or structural features.
Each protein is represented as a scaled horizontal line, the protein match line, along which vertical lines are drawn at 10, 20, 50, 100, 200 or 500 aa intervals, depending on the length of the protein. The scale is shown to the left of the match graphics.
For single protein views, the InterPro Architecture is also shown (coloured lozenges)
The key table near the bottom of the page identifies which colours correspond to which member database method or structural feature.
The matches against the UniProtKB proteins are flagged as T for a TRUE hit, N for a FALSE NEGATIVE, P for a PARTIAL, F for a FALSE POSITIVE, and ? for a hit of UNKNOWN status. All PRINTS, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D, PANTHER and PROSITE prefile (preliminary profile) hits against UniProtKB are considered to be TRUE if the score is above the individual threshold(s) given by the member databases and are thus flagged as T.
Member databases provide lists of protein sequences in UniProtKB that match their signatures. An exception to this is the PROSITE pattern hits to protein sequences in UniProtKB/TrEMBL. This list is not provided by PROSITE but is derived by the UniProtKB/TrEMBL group in the following way:
All protein sequences in UniProtKB/TrEMBL are scanned for PROSITE patterns.
If a matching pattern is found, the significance of the PROSITE pattern match is verified using a set of secondary patterns derived from the PROSITE pattern.
These secondary patterns are computed with the eMotif algorithm (
Nevill-Manning C.G., et al.). The PROSITE database contains a list of all UniProtKB/Swiss-Prot proteins that are TRUE members of the relevant protein family. For each pattern, sequences that have TRUE hits to that pattern are aligned and fed into eMotif which computes a nearly optimal set of regular expressions, based on statistical rather than biological evidence.
InterPro uses a stringency of e-9, so that each eMotif pattern is expected to produce random false positive hit in e-9 matches.
All PROSITE hits confirmed by eMotif are considered as TRUE, the others are flagged as UNKNOWN.
In this way, pattern matches against protein sequences in UniProtKB/TrEMBL may be flagged as T or U and in UniProtKB/Swiss-Prot section of UniProtKB, the status may be manually curated as F, N, P or T.
Each member database method with a match to the protein sequence is displayed on a horizontal line. The position of the match reflects its position on the sequence. Hovering the mouse over a coloured bar will show the method database, accession number and the residues corresponding to the position of the match on the protein.
The member database accession number is linked to the member database summary page for that signature and the name of the signature is given in the far right column. Each member database signature is identified by a specific colour:
Fainter bands of a particular colour indicate that the hit is either false positive (F) or unknown (?). For hits with false negative (N) and partial (P) status the positions are undefined and cannot be shown in the graphical view.
Structural information is presented for those proteins with a structure in the PDB and for those whose structure is predicted from automated homology-modelling. It is represented on sequences as coloured white striped bars:
In the Detailed Graphical View the structural matches are listed at the bottom of the view. Entries are sorted by UniProtKB accession number. The UniProtKB accession number links to the UniProtKB entry record, The GO! link returns the associated GO terms for the protein based on mappings to GO via all sources (see QuickGo). The 'Structure' link returns the MSD protein entry page for that PDB entry. The links for the SCOP and CATH classification hierarchies, and the domain ID is a link to the domain itself (this ID contains the PDB identifier). For proteins with a predicted structure feature based on either SWISS-MODEL or MODBASE a link to the SWISS-MODEL Repository or MODBASE is provided through the protein accession number.
WARNING: SWISS-MODEL and MODBASE models are theoretically calculated structures, not experimentally determined structures. Therefore the models may contain significant errors.
For those proteins with a known structure clicking on the Astex icon, [
] second column, loads the AstexViewer(tm) Java
applet page displaying the PDB structure, with the residues included in the CATH or SCOP domain definition
highlighted on the PDB chain. The view can be rotated by clicking on the left mouse button and moving the cursor over the image, clicking the right mouse button over the image opens a menu to perform various functions, such as adding a ligand to the view. This viewer will require your browser to be java enabled.
The software should run on most operating systems and in most Internet browsers (so far we are aware that the viewer does not work on Internet Explorer 4).
However, the license agreement must be read and accepted before using the viewer. Should any problems occur with the display, please contact us at: EBI Support.
| InterPro 12.1 | Please contact EBI Support with any problems or suggestions regarding this site. Terms of Use |
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