Pfam database

A variety of databases and online tools exist to facilitate searches for protein motifs (Table 6). The most comprehensive resource for the detection of large protein motifs is the Conserved Domain Database (CDD) provided by NCBI. The CDD includes all data present in the SMART and PFAM databases, along with some manually curated entries. All protein-protein BLAST... 

PFAM Database and search tools www.sanger.ac.uk/Pfam... 

Figure 1. Schematic domain structures are shown for homologous villidin proteins from D. d/sco/deum (XP 636652,1704aa) and E. histolytica ("ABPH", AF118397,1602aa). Both contain typical coronin domains at their amino termini in addition to 3 pleckstrin homology (PH), 3-5 gelsolin (C) and a villin headpiece (VHP) domains at the C-termini, all detected by matches to the corresponding hidden Markov models (HMM) from the PFAM database (http //www. sanger.ac.uk/Software/Pfam/).

PFAM Database or protein domains based on sequence alignment via HMM http //www.sanger.ac.uk/Software/Pfam/ Sanger Centre, Cambridge, UK, A. Bateman of q1 [22, 24, 73]... 

Chukkapalli, G., C. Guda, and S. Subramaniam. 2004. SledgeHMMER A web server for batch searching the Pfam database. Nucleic Acids Res 32 W542 1. 

Fig. 10.3 Human parvulins. Protein nomenclature is according to Fischer [3], The gene name and the molecular mass of the unprocessed proteins are shown in the brackets. In the second row, the accession number ofthe SWISS-PROT/ TREM BL database and an example of an alternative name ofthe protein is given. The amino acid residues that border the protein domains or functional modules are designated according to SWISS-PROT or Pfam databases. The parvulin domain is depicted in yellow. Signal sequence regions are shown as colorless boxes. WW, WW domain.

However, other perspectives suggest that there are likely to be as yet unidentified protein folds. As of 2004, the Pfam database (version 10.0) contained 6190 domains only about a third were associated with a protein of known structure. Some of these may be cases in which highly divergent or completely unrelated sequences adopt an already discovered fold. Some may not be amenable to structural characterization, either because they are too large for characterization by nuclear magnetic resonance spectroscopy (NMR), or contain disordered regions that interfere with crystallization. However, there may indeed be unidentified protein domain structures remaining to be discovered. 

The PROSITE database is used to determine the domain and the family of the protein sequences that, in turn, are based on biologically significant sites, patterns, and profiles.This database is similar to the HOMologous STRucture Alignment Database " (HOMSTRAD) and the Protein family (Pfam) database, both of which contain domain and family information for proteins. HOMSTRAD uses sequence and structure to group proteins into domains and families. Pfam classifies protein domains and families, based... 

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