3. Sequence motif :
In genetics, a sequence motif is a nucleotide or
amino-acid sequence pattern that is widespread and
has, or is conjectured to have, a biological
significance.
For proteins, a sequence motif is distinguished
from a structural motif, a motif formed by the
three-dimensional arrangement of amino acids
which may not be adjacent.
4. There are mainly two types of sequence
motif databases such as:
P fam
Prosite
5. Pfam is a database of protein families that
includes their annotations and multiple sequence
alignments generated using hidden Markov
models. The most recent version, Pfam 31.0, was
released in March 2017 and contains 16,712
families.
Uses:
The general purpose of the Pfam database is to
provide a complete and accurate classification of
protein families and domains.
6. It is used by experimental biologists researching
specific proteins, by structural biologists to identify
new targets for structure determination, by
computational biologists to organise sequences and
by evolutionary biologists tracing the origins of
proteins.
Pfam has also been used in the creation of other
resources such as iPfam, which catalogs domain-
domain interactions within and between proteins,
based on information in structure databases and
mapping of Pfam domains onto these structures
7. Features :
For each family in Pfam one can:
View a description of the family
Look at multiple alignments
View protein domain architectures
Examine species distribution
Follow links to other databases
View known protein structures
8.
9. The Pfam database is licensed under the GNU
General Public License, which basically makes
it available to anyone.
But imposes the restriction that derivative
works (new databases, modifications) must be
made available in source form.
10. PROSITE :
(www.expasy.ch/prosite/)
PROSITE is a protein database. It consists of
entries describing the protein families, domains
and functional sites as well as amino acid patterns
and profiles in them.
PROSITE was created in 1988 by Amos
Bairoch, who directed the group for more than 20
years. Since July 2018, the director of PROSITE
and Swiss-Prot is Alan Bridge
11. PROSITE's uses include identifying possible
functions of newly discovered proteins and
analysis of known proteins for previously
undetermined activity.
PROSITE offers tools for protein sequence
analysis and motif detection (see sequence motif,
PROSITE patterns). It provides additional
information about functionally or structurally
critical amino acids.
