PRINTS and PRINTS-S shed light on protein ancestry - PubMed (original) (raw)

PRINTS and PRINTS-S shed light on protein ancestry

T K Attwood et al. Nucleic Acids Res. 2002.

Abstract

The PRINTS database houses a collection of protein fingerprints. These may be used to make family and tentative functional assignments for uncharacterised sequences. The September 2001 release (version 32.0) includes 1600 fingerprints, encoding approximately 10 000 motifs, covering a range of globular and membrane proteins, modular polypeptides and so on. In addition to its continued steady growth, we report here its use as a source of annotation in the InterPro resource, and the use of its relational cousin, PRINTS-S, to model relationships between families, including those beyond the reach of conventional sequence analysis approaches. The database is accessible for BLAST, fingerprint and text searches at http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/.

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Figures

Figure 1

The rhodopsin family hierarchy depicted by PRINTS-S. The different levels of the hierarchy are colour-coded as follows: red, children; green, siblings; purple, parents; brown, grandparents (or great-grandparents).

Figure 2

Result of searching PRINTS-S with the sequence of ovine rhodopsin using FingerPRINTScan. The table shows the top 10 matches (significant matches are highlighted, the best is coloured purple), and traces the relationships between each matched fingerprint from its position in the familial hierarchy back to its most distant ancestor. Here, each rhodopsin-like GPCR match can be traced back through its parent super-family, through the ancestral GPCR clan, ultimately to a presumed ‘7TM’ architectural predecessor.

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