PRINTS–a protein motif fingerprint database

Abstract

The PRINTS database of protein 'fingerprints' is described. Fingerprints comprise sets of motifs excised from conserved regions of sequence alignments, their diagnostic power or potency being refined by iterative database scanning (in this case the OWL composite sequence database). Generally, the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3-D space. The use of groups of independent, linearly or spatially separate motifs allows particular protein folds and functionalities to be characterized more flexibly and powerfully than conventional single-component patterns or regular expressions. The current version of the database (4.0) contains 150 entries (encoding > 700 motifs), covering a wide range of globular and membrane proteins, modular polypeptides and so on. The growth of the database is influenced by a number of factors, e.g. the use of multiple motifs, the maximization of sequence information through iterative database scanning and the fact that the database searched is a large composite. The information contained within PRINTS is distinct from but complementary to the single consensus expressions stored in the widely used PROSITE dictionary of patterns.

Alignment and structure prediction of divergent protein families: periplasmic and outer membrane proteins of bacterial efflux pumps

“…Tandem sequence similarity has been observed for three closely related OEPs in prior studies (Gross, 1995), but could not be detected in TolC with the same method, and has not been observed previously to be a general feature of OEPs. There are also no PROSITE, PRINTS (Attwood et al, 1994), or Pfam (2.1) motifs which represent the OEP family as a whole, although the Pfam database contains an entry (B 1036) which aligns C-terminal fragments of 11 OEPs closely related to TolC.…”

Embedding strategies for effective use of information from multiple sequence alignments

“…bPSU00707-1, the member from among the eight intein-containing sequences documented in PRINTS (Attwood & Beck, 1994) closest to the consensus computed as in Table 2 from the six blocks in PRINTS for this group. Because this is a DNA polymerase I1 homologue, all DNA polymerases in the results list were ignored.…”

“…Either a single sequence query is used to search for homologues in a database of multiple sequence alignments (Henikoff & Henikoff, 1991;Attwood & Beck, 1994;Sonnhammer & Kahn, 1994) or patterns (Smith & Smith, 1990;Bairoch, 1992), or an alignment or pattern query is used to search a sequence database (Gribskov et al, 1987;Henikoff et al, 1990;Krogh et al, 1994;Neuwald & Green, 1994;Tatusov et al, 1994;Thompson et al, 1994b (Gribskov et al, 1990; Krogh et ah., 1994;Eddy, 1996). In either case, position-specific scoring matrices (PSSMs) can represent all available information in a multiple sequence alignment, and several improvements in constructing PSSMs have been introduced recently (Brown et al, 1993;Tatusov et al, 1994;Bailey & Gribskov, 1996;Henikoff & Henikoff, 1996;Sjolander et al, 1996).…”

Classifying a Protein in the CATH Database of Domain Structures

“…There are also links from CATH entries to SWISS-PROT (Bairoch & Boeckman, 1992) and PRINTS (Attwood et al, 1994). For each fold family, there are two-dimensional matrices giving the pairwise SSAP scores and sequence identities between all non-identical relatives.…”