SMART 5: domains in the context of genomes
EMBL, Meyerhofstrasse 1, 69012 Heidelberg, Germany,1Wellcome Trust Centre for Human Genetics,
5 Roosevelt Drive, Oxford OX3 7BN, UK and2Bioinformatik, Biozentrum, Am Hubland, University of Wuerzburg,
97074 Wuerzburg, Germany
Received September 13, 2005; Revised and Accepted October 11, 2005
The Simple Modular Architecture Research Tool
10 (SMART) is an online resource (http://smart.embl.
de/) used for protein domain identification and the
analysis of protein domain architectures. Many new
features were implemented to make SMART more
accessible to scientists from different fields. The
15 new ‘Genomic’ mode in SMART makes it easy to ana-
lyze domain architectures in completely sequenced
genomes. Domain annotation has been updated
of the catalytic activity for 50 SMART domains is now
20 available, based on the presence of essential amino
acids. Furthermore, intrinsically disordered protein
regions can be identified and displayed. The network
context is now displayed in the results page for more
than 350000 proteins, enabling easy analyses of
25 domain interactions.
When the Simple Modular Architecture Research Tool
(SMART) database was first made public 8 years ago (1),
the current extent of completely sequenced genomes was little
30 more than a dream. In the last few years, the astonishing
successes of whole organism approaches to biology are not
only limited to sequencing efforts but also include techniques,
such as the high-throughput identification of protein–protein
interactions, which have created new opportunities and higher
35 expectations for computational approaches to interpreting bio-
logical sequences. In the last 2 years, we have been developing
new ways of meeting these challenges.
The basic data of SMART are high-quality manually
derived alignments of protein domain families. As hidden
40 Markov models (2) these allow us to identify protein domains
in sequence databases; these results are stored in a database
accessible via a simple web interface (http://smart.embl.de).
The data provide a framework for understanding the evolution
Whereas the SMART philosophy has been to include essen-
tially all available protein sequences, we recognize that many
users are interested primarily in the biology of a particular
organism. Accordingly, we have developed new views more
tightly integrated with genome data. These new genome views
allow further cross-referencing with protein–protein inter-
action maps, making SMART an invaluable tool for systems
biologists to interpret pathways and networks.
REDUCED PROTEIN DATABASE REDUNDANCY
AND ‘GENOMIC’ MODE
Owing to the nature of our source databases (Swiss-Prot,
SP-TrEMBL and Ensembl) (3,4) the protein database in
SMART has significant redundancy, even though identical
proteins are removed. Different proteins and fragments in
the source databases often correspond to the same gene. Users
exploring the various domain architectures or interested in
domain counts in various genomes are particularly vulnerable
to this problem, as the numbers they get are often inflated and
unrealistic. To overcome this problem, we extended SMART
with a new operating mode, namely ‘Genomic’ mode. The
main difference between normal and genomic mode in
SMART is the underlying protein database. In genomic mode,
only the proteins from 170 completely sequenced genomes are
included (a full list is available at http://smart.embl.de/smart/
list_genomes.pl). Swiss-Prot (3) is our main source database
of genomic data, together with Ensembl (4) for metazoan
genomes. This database has minimal redundancy, and is there-
fore particularly useful for whole genome studies of domain
architectures or single domain distributions.
PREDICTION OF CATALYTIC ACTIVITY
To improve the function prediction for single domains, we
annotated essential catalytic sites for all enzymatic domains
in SMART. These were extracted from structural reports in the
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Nucleic Acids Research, 2006, Vol. 34, Database issueD257–D260
primary literature, wherever the catalytic mechanism was
known (5). Now, protein sequences can be scanned for the
presence of important catalytic amino acids (Figure 1).
Absence of one of these amino acids very likely results in
5 loss of catalytic activity. Recently, it turned out that many
domains homologous to signaling enzymes seem to have
lost their catalytic ability, although they are evolutionarily
conserved. Instead of a catalytic function these domains
appear to play a role in regulatory processes. This trend is
10 especially obvious in the protein tyrosine phosphatase family
(5). The inclusion of catalytic amino acid residues in the
database will allow a more rapid identification of inactive
enzyme homologs in the future.
DOMAIN ARCHITECTURE INVENTION DATING
15 As a further step from the single domain to the understanding
ofmulti domain proteins, SMART nowpredicts the taxonomic
class, where the concept of a protein, that is its domain archi-
linear order of all SMART domains in the protein sequence.
20 To derive the point of its invention, all proteins with the same
domain architecture are mapped onto NCBIs taxonomy (6).
The last common ancestor of all organisms containing at least
one protein with the domain architecture is defined as the point
of its origin. From the knowledge on the origin of domain
25 architectures one might infer the distribution and presence
of these architectures in not yet or incompletely sequenced
genomes. In addition, conclusions on the general function of
domain architectures can be drawn.
PROTEIN INTERACTION DATA
30 The latest version of SMART provides information about
putative interaction partners for more than 350000 proteins
(Figure 2). This information is imported from the STRING
database (7), in which known and predicted protein–protein
associations are integrated from a variety of sources. The
interactors are shown in SMART in the form of a summary
graphic (network); the various types of interaction evidence
are depicted as lines of different colors in the network. Click-
ing on the graphic will launch the STRING website, where the
underlying evidence can be studied in detail. The interactions
in STRING include physical binding interactions, as well
as functional associations, such as membership in a common
pathway or process. The data are derived from a variety of
sources, including knowledge bases, such as BIND (8), KEGG
(9), HPRD (10) and Reactome (11), as well as in silico pre-
diction approaches and automated text-mining. STRING aims
to improve usability of the interactome by scoring and ranking
interaction data (making a confidence estimate on each
prediction), as well as by transferring interaction knowledge
between model organisms where applicable. SMART and
STRING are both cross-referenced through a common set
of proteins and genomes, and STRING in turn uses domain
information from the SMART server in its pages as well.
NEW DATABASE FEATURES
The core of SMART is a relational database management
system (RDBMS) which stores information on SMART
domains (1,12). Owing to the exponentially increasing amount
of data, many parts of the database access code have been
updated or completely rewritten, resulting in greatly improved
response times, most noticeably in the domain architecture
SMART database includes the information on domain pres-
ence in all proteins in a non-redundant database, now with the
added data on the catalytic activity for 50 catalytic domains.
All domain architecture analysis results include this infor-
mation, and domains with missing essential amino acids
are overlaid with the word ‘inactive’ (Figure 1). The domain
Figure 1. PredictionofcatalyticactivityinSMART.FirstguanylylcyclasedomaininhumanadenylatecyclasetypeIII(ENSP00000260600)ismarkedas‘inactive’
because the two amino acids required for its activity are not present. Domain annotation page shows which amino acids are not detected and gives pointers to the
D258 Nucleic Acids Research, 2006, Vol. 34, Database issue
annotation page provides detailed information on which of the
required amino acids are missing, and gives pointers to the
NEW ANALYSIS METHODS
5 DisEMBL [http://dis.embl.de, (13)] predictions of intrinsic
protein disorder were included into SMART’s analysis
methods. DisEMBL is a computational tool for the prediction
of disordered/unstructured regions within a protein sequence.
Predictions included in SMART are based on missing coordin-
ates in X-ray structure as defined by REMARK465 entries
in PDB and the ‘Hot loops’ method. Hot loops constitute a
refined subset of the standard loops/coils as defined by DSSP
(14), namely, those loops with a high degree of mobility as
determined from C-a temperature factors (B-factors).
Figure 2. InteractionnetworksinSMART.Around350000proteinannotationpagesincludeaninteractionnetworkinapop-upwindow.Networksarelinkedtothe
STRING database (http://string.embl.de) which provides the data.
Nucleic Acids Research, 2006, Vol. 34, Database issueD259
USER INTERFACE IMPROVEMENTS AND Download full-text
SMART’s user interface was completely rewritten and is
now fully compliant with the latest web standards, such as
5 XHTML1.0 and CSS2. Users with standards-compliant web
browsers can fully enjoy the extra speed and features. Owing
to increasing server load, the queuing system was completely
rewritten and the hardware greatly expanded resulting in a
more stable operation and faster response times.
An important new feature is the introduction of taxonomic
trees into SMART. Two primary uses for taxonomic trees in
SMART are the grouping of domain architecture query results
and the detailed taxonomicdistributionofdomainsnowshown
on domain annotation pages (Figure 3). The grouping of
15 architecture query results allows users to easily display only
proteins from certain species or taxonomic nodes. Taxonomic
distribution of proteins on domain annotation pages gives
a detailed overview of domain presence in different species
We would like to thankChristian von Mering for providing the
interaction network data and STRING links. We are grateful to
Rune Linding for helping with the integration of DisEMBL
predictions into SMART. Funding to pay the Open Access
25 publication charges for this article was provided by EMBL.
Conflict of interest statement. None declared.
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Figure 3. TaxonomictreesinSMART.(a)Domainarchitecturequeryresultsgroupedintoatree.Userscanselectindividualproteinsortaxonomicnodestodisplay.
(b) Domain annotation pages show detailed domain and protein counts in various taxonomic nodes.
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