Table 3. Major Protein Domain Collections and Servers
Domain and Motif Collections (Sequence Profiles and Signatures)
Name Website Domains Generation PTP Domain Accession #
PROSITE 1676 Semi-manual PS50055
PRINTS 1700 Semi-manual PR00700
SMART 639 Semi-manual SM00194
PfamA 7255 Semi-manual PF00102
PfamB 88000 Automatic ---
PRODOM1 579477 Automatic PD000167
BLOCKs1 2101 Automatic PB000242
1)Provides ungapped alignments (i.e. motifs). Rarely encompassses the full-length sequence of conseved domains.
Domain Servers (Useful for Annotation of Sequences)
Name Website Comments
InterProScan Searches many domain databases simultaneously
CD server Output includes E-values and alignments
ProfileScan Graphical summary of hits at the amino acid level
ScanProsite Graphical summary of hits. Searches only Prosite
Motif Search Tools
Name Website Comments
PATTINPROT Scans a protein database for a sequence pattern
SIRW Motif search combined with keyword search