-
- SIFTS Mapping for UniProt sequences and PDB
- Structures
SIFTS (Structure Integration with Function,
- Taxonomy and Sequences) is a database of residue-level mappings
- between UniProt protein sequences, and protein structures found in
- the PDB. The database is updated for each PDB release, and is
- provided by the PDBe
- at EMBL-EBI.
-
When Jalview imports PDB data for a protein sequence found in - UniProt, either via the 'View 3D Structure...' option, or the 'Fetch - DB Refs' web services menu, Jalview will also download its SIFTS - record and use that information to construct a mapping between the - sequence and downloaded structure.
-If, for some reason, no SIFTS mapping data exists, then Jalview - will generate a mapping using the built-in Needleman and Wunsch - global alignment algorithm. This is how sequence-structure mappings - were created before version 2.10.
-
- Controlling and troubleshooting SIFTS mappings
- Configuration options controlling whether SIFTS mappings are used
- can be found in the Tools → Preferences →
- Structure tab, under 'Sequence ↔ Structure method'.
Note:
- Changing the configuration will only affect how new mappings are
- created. In order to recompute mappings for structures already
- loaded, please reload the sequence & structural data.
-
- Multi-Chain Mappings
SIFTS gives Jalview the
- ability to display multi-chain mappings between UniProt sequences
- and PDB structure data. This is important when working with
- multimeric proteins, when the biological assembly can contain
- several structures for the same protein sequence. Multi-chain
- mapping allows all residues in a structure to be located in the
- alignment, and also, when shading the structure by sequence colours,
- enables conservation patterns between oligomer interfaces to be
- explored.
-
To see this in action, Retrieve the UniProt sequence - FER1_MAIZE, and then view one of its structures: 3B2F. Mousing over - the sequence results to two positions being highlighted in the - structure, and colouring the alignment transfers the color to all - the mapped chains in the structure.
- -
- Viewing Mapping Output
The mapping provided
- by the SIFTS record is accessible via File →
- View mapping menu of the structure viewers. The screenshot below
- shows the mapping created between UniProt sequence FER1_MAIZE and
- proteins in PDB 3B2F, which reports mappings for two chains. The
- mapping method is also reported (highlighted with red border).
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- SIFTS Mapping integration was added in Jalview 2.10 -
- - -