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| InterPro |
Member
Databases |
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| InterPro Member Databases |
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The SWISS-PROT
database consists of sequence entries. It contains
high-quality annotation, is non-redundant and
cross-referenced to many other databases. |
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The TrEMBL database is a computer-annotated
supplement to SWISS-PROT. TrEMBL contains the
translations of all coding sequences (CDS) present in
the EMBL Nucleotide Sequence Database, which are not yet
integrated into SWISS-PROT. |
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PROSITE
is a database of protein families and domains. It
consists of biologically significant sites, patterns and
profiles that help to reliably identify to which known
protein family (if any) a new sequence belongs. |
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Pfam
is a large collection of multiple sequence alignments
and hidden Markov models covering many common protein
domains. |
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PRINTS
is a compendium of protein fingerprints. A fingerprint
is a group of conserved motifs used to characterise a
protein family; its diagnostic power is refined by
iterative scanning of a composite of SWISS-PROT +
SP-TrEMBL. Usually the motifs do not overlap, but are
separated along a sequence, though they may be
contiguous in 3D-space. Fingerprints can encode protein
folds and functionalities more flexibly and powerfully
than can single motifs, their full diagnostic potency
deriving from the mutual context afforded by motif
neighbours. |
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The ProDom
protein domain database consists of an automatic
compilation of homologous domains. Current versions of
ProDom are built using a novel procedure based on
recursive PSI-BLAST searches (Altschul SF, Madden TL,
Schaffer AA, Zhang J, Zhang Z, Miller W & Lipman DJ,
1997, Nucleic Acids Res., 25:3389-3402; Gouzy J., Corpet
F. & Kahn D., 1999, Computers and Chemistry
23:333-340.) Large families are much better processed
with this new procedure than with the former DOMAINER
program (Sonnhammer, E.L.L. & Kahn, D., 1994,
Protein Sci., 3:482-492). |
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SMART
(a Simple Modular Architecture Research Tool) allows the
identification and annotation of genetically mobile
domains and the analysis of domain architectures. More
than 500 domain families found in signalling,
extracellular and chromatin-associated proteins are
detectable. These domains are extensively annotated with
respect to phyletic distributions, functional class,
tertiary structures and functionally important residues.
Each domain found in a non-redundant protein database as
well as search parameters and taxonomic information are
stored in a relational database system. User interfaces
to this database allow searches for proteins containing
specific combinations of domains in defined taxa. |
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TIGRFAMs
is a collection of protein families, featuring curated
multiple sequence alignments, Hidden Markov Models
(HMMs) and annotation, which provides a tool for
identifying functionally related proteins based on
sequence homology. Those entries which are "equivalogs"
group homologous proteins which are conserved with
respect to function. |
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