InterPro, progress and status in 2005

Article (PDF Available)inNucleic Acids Research 33(Database issue):D201-5 · February 2005with29 Reads
DOI: 10.1093/nar/gki106 · Source: PubMed
Abstract
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIRSF and SUPERFAMILY. Signatures are manually integrated into InterPro entries that are curated to provide biological and functional information. Annotation is provided in an abstract, Gene Ontology mapping and links to specialized databases. New features of InterPro include extended protein match views, taxonomic range information and protein 3D structure data. One of the new match views is the InterPro Domain Architecture view, which shows the domain composition of protein matches. Two new entry types were introduced to better describe InterPro entries: these are active site and binding site. PIRSF and the structure-based SUPERFAMILY are the latest member databases to join InterPro, and CATH and PANTHER are soon to be integrated. InterPro release 8.0 contains 11 007 entries, representing 2573 domains, 8166 families, 201 repeats, 26 active sites, 21 binding sites and 20 post-translational modification sites. InterPro covers over 78% of all proteins in the Swiss-Prot and TrEMBL components of UniProt. The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro).

Figures

InterPro, progress and status in 2005
Nicola J. Mulder
1,
*, Rolf Apweiler
1
, Teresa K. Attwood
3
, Amos Bairoch
4
, Alex Bateman
2
,
David Binns
1
, Paul Bradley
1,3
, Peer Bork
5
, Phillip Bucher
6
, Lorenzo Cerutti
6
,
Richard Copley
7
, Emmanuel Courcelle
8
, Ujjwal Das
1
, Richard Durbin
2
,
Wolfgang Fleischmann
1
, Julian Gough
9
, Daniel Haft
10
, Nicola Harte
1
, Nicolas Hulo
4
,
Daniel Kahn
8
, Alexander Kanapin
1
, Maria Krestyaninova
1
, David Lonsdale
1
,
Rodrigo Lopez
1
, Ivica Letunic
5
, Martin Madera
11
, John Maslen
1
, Jennifer McDowall
1
,
Alex Mitchell
1,3
, Anastasia N. Nikolskaya
12
, Sandra Orchard
1
, Marco Pagni
6
,
Chris P. Ponting
13
, Emmanuel Quevillon
1
, Jeremy Selengut
10
, Christian J. A. Sigrist
4
,
Ville Silventoinen
1
, David J. Studholme
2
, Robert Vaughan
1
and Cathy H. Wu
12
1
EMBL Outstation—European Bioinformatics Institute and
2
Wellcome Trust Sanger Institute, Wellcome Trust Genome
Campus, Hinxton, Cambridge, UK,
3
School of Biological Sciences and Department of Computer Science,
The University of Manchester, Manchester, UK,
4
Swiss Institute for Bioinformatics, Geneva, Switzerland,
5
Biocomputing Unit EMBL, Heidelberg, Germany,
6
Swiss Institute for Experimental Cancer Research, Lausanne,
Switzerland,
7
Wellcome Trust Centre for Human Genetics, Oxford, UK,
8
CNRS/INRA, Toulouse, France,
9
Genomic Sciences Centre, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Japan,
10
The Institute for Genomic Research, MD, USA,
11
MRC Laboratory of Molecular Biology, Cambridge, UK,
12
Protein Information Resource, Georgetown University Medical Center, Washington, DC, USA and
13
MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford, UK
Received September 20, 2004; Revised and Accepted October 18, 2004
ABSTRACT
InterPro, an integrated documentation resource of
protein families, domains and functional sites, was
created to integrate the major protein signature
databases. Currently, it includes PROSITE, Pfam,
PRINTS, ProDom, SMART, TIGRFAMs, PIRSF and
SUPERFAMILY. Signatures are manually integrated
into InterPro entries that are curated to provide biolo-
gical and functional information. Annotation is pro-
vided in an abstract, Gene Ontology mapping and
links to specialized databases. New features of
InterPro include extended protein match views, taxo-
nomic range information and protein 3D structure
data. One of the new match views is the InterPro
Domain Architecture view, which shows the domain
composition of protein matches. Two new entry types
were introduced to better describe InterPro entries:
these are active site and binding site. PIRSF and the
structure-based SUPERFAMILY are the latest member
databases to join InterPro, and CATH and PANTHER
are soon to be integrated. InterPro release 8.0
contains 11 007 entries, representing 2573 domains,
8166 families, 201 repeats, 26 active sites, 21 binding
sites and 20 post-translational modification sites.
InterPro covers over 78% of all proteins in the
Swiss-Prot and TrEMBL components of UniProt.
The database is available for text- and sequence-
based searches via a webserver (http://www.ebi.
ac.uk/interpro), and for download by anonymous
FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro).
INTRODUCTION
The genome sequencing centres are generating raw sequence
data at an alarming rate, and the result is a need for automated
sequence analysis methods. The automatic analysis of protein
sequences is possible through the use of ‘protein signatures’,
which are methods for diagnosing a domain or characteristic
region of a protein family in a protein sequence. A number of
protein signature databases have been developed, each using a
variation on the handful of signature methods available, which
include patterns, profiles and hidden Markov models (HMMs).
These databases are most effective when used together, rather
*To whom correspondence should be addressed. Tel: +44 0 1223 494 602; Fax: +44 0 1223 494 468; Email: mulder@ebi.ac.uk
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ª 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue ª Oxford University Press 2005; all rights reserved
Nucleic Acids Research, 2005, Vol. 33, Database issue D201–D205
doi:10.1093/nar/gki106
than in isolation. InterPro (1) integrates into one resource the
major protein signatures databases: PROSITE (2), which uses
regular expressions and profiles, PRINTS (3), which uses
position-specific scoring matrix-based (PSSM-based) finger-
prints, ProDom (4), which uses automatic sequence clustering,
and Pfam (5), SMART (6), TIGRFAMs (7), PIRSF (also
known as PIR SuperFamily) (8) and SUPERFAMILY (9),
all of which use HMMs.
Signatures from the member databases are integrated manu-
ally as they are developed. A team of biologists have this
responsibility, as well as that of annotating the new or existing
entries. Each InterPro entry is described by one or more sig-
natures, and corresponds to a biologically meaningful family,
domain, repeat or site, e.g. post-translational modification
(PTM). Not every entry will contain a signature from each
member database, only those that correspond to each other are
united. Entries are assigned a type to describe what they repre-
sent, which may be family, domain, repeat, PTM, active site or
binding site. The last two are new entry types, which were
introduced to better describe the signatures in some of the
entries. Entries may be related to each other through two
different relationships: the parent/child and contains/found
in relationship. Parent/child relationships are used to describe
a common ancestry between entries, whereas the contains/
found in relationship generally refers to the presence of geneti-
cally mobile domains. InterPro entries are annotated with a
name, an abstract, mapping to Gene Ontology (GO) terms and
links to specialized databases. InterPro groups all protein
sequences matching related signatures into entries. All hits
of the protein signatures in InterPro against a composite of
the Swiss-Prot and TrEMBL components of UniProt (10) are
precomputed. The matches are available for viewing in each
InterPro entry in different formats.
The number of entries and coverage of protein space by
InterPro is continuing to grow. The beta release of InterPro in
1999 contained 2423 entries, while the latest release of the
database contains 11 007 entries, representing nearly a 5-fold
increase in 5 years. In its infancy, InterPro covered 66% of
all proteins in Swiss-Prot and TrEMBL, and this has increased
to over 90% for Swiss-Prot, 76% for TrEMBL and 78% for
UniProt (Swiss-Prot and TrEMBL). A number of new features
have been added to the InterPro database since its publication
in Nucleic Acids Research in 2003. These include additional
protein match views, the InterPro Domain Architectures
Viewer, taxonomic range information, additional database
links and protein 3D structural information. New members
databases that have been integrated are the full-length
sequence-based PIRSF database and the structure-based
SUPERFAMILY. These are described in more detail below.
NEW FEATURES OF INTERPRO
Protein match views
For each protein signature, a list of proteins in UniProt that it
matches is precomputed. This list gets updated when new
proteins enter UniProt or if the signatures themselves change.
The match lists may be viewed in a number of different for-
mats including a table view, a detailed view and an overview.
There are new options for the ordering of proteins within these
views. For example, the views can all be displayed either
ordered by Swiss-Prot ID or for only those proteins of
known structure. The overview and detailed view can also
be ordered by UniProt accession number, and the former
can be ordered by taxonomy too. In the overview, clicking
on the protein accession number takes the user to the detailed
view for that protein. Searching for a protein accession number
in the InterPro text search with the ‘find protein matches’
option returns the overview of matches for the protein. Simi-
larly, the detailed view is retrieved through the accession
number link (see Figure 1). For the graphical views, a
mouse-over displays the actual positions of the matches on
the sequence.
Where structures are available for proteins, there is a link
from the graphical views to the corresponding Protein Data
Bank (PDB) structures and a separate line in the display, below
the InterPro matches, showing the hyperlinked SCOP (11),
CATH (12) and PDB (13) matches on the sequence as
white striped bars (see Figure 1). This shows where the protein
signatures correspond with structural chains. An Astex icon is
available for structures, and clicking on which, loads the
AstexViewer
TM
Java applet page displaying the PDB struc-
ture, with the residues included in the CATH or SCOP domain
definition highlighted on the PDB chain.
InterPro Domain Architecture viewer
The InterPro Domain Architecture (IDA) viewer is a graphical
representation of protein domain architecture, where the
domain architecture of a protein sequence is displayed as a
series of non-overlapping domains (see Figure 1). These
domains are calculated by a method that identifies a subset
of InterPro entries/methods, representing non-overlapping
domains within proteins. If two domains overlap slightly,
their centres are used to order the domains, and domain bound-
aries are discarded to enhance a comparison of various archi-
tectures. If a parent/child hierarchy exists between InterPro
domains, matches with the children are represented as those
from the parent entry. For each InterPro entry, a graphical
representation of unique IDA(s) is provided and each
kind of IDA is displayed with an example protein and
total number of proteins, sharing this architecture, next to
it. Clicking on the count of proteins retrieves all proteins
sharing a common architecture. Although domains should
not overlap, inserted domains (e.g. nested domains) are still
shown in the IDA viewer, as this provides more accurate
comparison between IDAs.
Taxonomy viewer
A new feature in InterPro is the ‘Taxonomy’ field, which aims
to provide an ‘at a glance’ view of the taxonomic range of the
sequences associated with each InterPro entry. This is repre-
sented as a circular display with the taxonomy-tree root as its
centre. The lineages populating the nodes were selected to
provide a view of the major groups of organisms with the
model organisms on the outer most circle. Nodes of the tax-
onomy-tree are placed on the inner circles and radial lines lead
to the description for each node. No significance is attached to
the position of the node on a particular inner-circle, although
some attempt has been made to group nodes. The nodes them-
selves are either true taxonomy nodes or artificial nodes, of
which there are three: ‘Unclassified’, ‘Other Eukaryota
D202 Nucleic Acids Research, 2005, Vol. 33, Database issue
(Non-Metazoa)’ and the ‘Plastid Group’. The number of
sequences associated with each lineage is displayed, and click-
ing the number retrieves the graphical overview for proteins
within that taxonomic group.
Database cross-references
In addition to cross-referencing the member database signa-
tures and GO (14) terms, there is a separate field in InterPro
entries, ‘Database Links’, to provide cross-references to other
databases. These included cross-references to corresponding
Blocks accession numbers, PROSITE documentation, the
CArbohydrate-Active EnZymes (CAZy) website and the
Enzyme Commission (EC) Database. New links have been
produced to the IUPHAR Receptor Database, the MEROPS
Peptidase Database (15) and COMe. The bioinorganic motif
database, COMe, is an attempt to classify metalloproteins and
some other complex proteins using the concept of bioinorganic
motifs.
3D Structural information
A separate field, called ‘Structural links’, provides informa-
tion on curated structure links. Structural domains from
SCOP (11) and CATH (12) are made up of one or more
protein chains in a PDB entry. These may include the full
chain or region(s) of chain(s). The links to the curated struc-
tural domains in this field of InterPro entries are based on the
correspondence between the proteins matching the InterPro
entry and those proteins of known structure belonging to
SCOP or CATH superfamilies. In addition, they include
only those links where the structural domains overlap con-
siderably with one or more of the InterPro signatures on the
protein sequence. The structural domains are also displayed
at the protein level in the graphical views, as described
above. Here, all the representative domains at the SCOP/
CATH family level are displayed, showing the location of
the structural domain(s) in the protein. This enables the user
to directly access the SCOP/CATH classification for that
particular domain from the protein’s detailed graphical
view. Mapping between UniProt and PDB entries can be
many-to-many, so the ‘Structure link displays all the PDB
entries associated with that particular protein. The user
is able to view the residue-by-residue mapping between
UniProt and a PDB chain of interest. This is a useful tool,
quite unique in its nature, to show such relationships in a
compact way.
Figure 1. Illustration of the detailed view for protein Q06124, the human protein-tyrosine phosphatase, non-receptor type 11. From an InterPro entry page, clicking on
a protein accession number in the ‘Examples’ field takes you to this view for that protein. The oval shapes at the top of the figure display the InterPro Domain
Architecture (IDA) view for this protein, which represents its domain composition. Each oval shape contains the domain name and the number of its iterations of the
domain if greater than one. The InterPro detailed view represents the protein sequence as a series of different lines for each protein signature hit. The bars are colour
coded according to the member database. A separate view below the signature matches displays the structural domains from the SCOP and CATH as white-striped
bars. This view provides a complete picture of the protein domain composition and where sequence-based domains correspond to known structures.
Nucleic Acids Research, 2005, Vol. 33, Database issue D203
New member databases
Two of the newest member databases to join the InterPro
Consortium are PIRSF (8) and the structure-based SUPER-
FAMILY (9). PIRSF is a network classification system that
accommodates a flexible number of levels from superfamily to
subfamily to reflect varying degrees of sequence conservation.
Members of a PIRSF homeomorphic family share full-length
sequence similarity with a common domain architecture
(homeomorphic) and have common evolutionary origin
(monophyletic). PIRSF HMMs are designed to cover the
full length of a protein sequence, and thus to include all
domains within the sequence. In this way, PIRSF homeo-
morphic families tend to encompass one or more of the exist-
ing InterPro domain entries and show the domain composition
of UniProt sequences. Classification based on full-length pro-
teins allows annotation of both generic biochemical and spe-
cific biological functions, identification of domain and family
relationships, and classification of multidomain proteins.
SUPERFAMILY is the first member database that is based
solely on structural protein families rather than sequence-
based protein families. SUPERFAMILY is a collection of
HMMs built from members of SCOP structural superfamilies.
This facilitates comparison of protein families based on struc-
ture and sequence and adds a new dimension to InterPro
entries. Many of the SUPERFAMILY HMMs actually corre-
spond to Pfam HMMs, but also, unsurprisingly, to the struc-
tural links in InterPro generated from the SCOP and CATH
links to proteins in the PDB.
DISCUSSION
The amalgamation of PROSITE, PRINTS, Pfam, ProDom,
SMART, TIGRFAMs, PIRSF and SUPERFAMILY into
InterPro has provided a useful tool for protein sequence ana-
lysis and characterization. InterPro has a number of applica-
tions and databases dependent on its continued success. It is
the tool of choice for the annotation of new genomes and is
used extensively for the automatic annotation of TrEMBL
entries. The mappings of InterPro to GO terms (14) provide
a means of large-scale mapping of proteins onto GO terms.
This accounts for the bulk of the UniProt proteins that are
mapped to GO terms. In addition, InterPro is used for the
Proteome Analysis Database (16), to provide statistical ana-
lyses of whole proteomes for the completely sequenced gen-
omes. For each proteome, the database provides tables of all
the InterPro matches ordered by the number of proteins match-
ing the entries, the top 30 InterPro hits, the top 200 hits, the 15
most common families, etc. A tool is also available to perform
proteome comparisons between two or more organisms of
choice through InterPro analyses.
The InterPro database is available via a webserver (http://
www.ebi.ac.uk/interpro) and anonymous FTP (ftp://ftp.ebi.
ac.uk/pub/databases/interpro). The webserver facilitates text
and sequence searches, and the FTP site provides regular
releases of an XML file for downloading. Future plans for
InterPro involve the integration of the next two member data-
bases, CATH HMMs and the PANTHER database. In addi-
tion, SWISS-MODEL 3D structure homology models (17)
will be displayed in protein graphical views to provide pre-
dicted structural information where proteins do not have their
structures solved. InterPro is growing along with its member
databases, and has increased coverage of the UniProt protein
sequence database. The resource continues to expand and
provide up-to-date data and new features and thus increases
its use to the scientific community as a powerful protein clas-
sification tool.
ACKNOWLEDGEMENTS
The InterPro project is supported by the ProFuSe grant (number
QLG2-CT-2000-00517) and the Integr8 grant (number QLRI-
CT-2001000015) of the European Commission.
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Nucleic Acids Research, 2005, Vol. 33, Database issue D205
    • "The analysis was performed with a set of parameters as follows: number of repetitions, any; minimum width for each motif, 6; maximum width for each motif, 100; and maximum number of motifs to be found, 5. All obtained motifs were searched in the InterPro database with InterProScan [32]. The exon/intron structures of HMGR genes were obtained by comparing the genomic sequences and their predicted coding sequences (CDS) using GSDS (http://gsds.cbi.pku.edu.cn/) "
    [Show abstract] [Hide abstract] ABSTRACT: The terpene compounds represent the largest and most diverse class of plant secondary metabolites which are important in plant growth and development. The 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR; EC 1.1.1.34) is one of the key enzymes contributed to terpene biosynthesis. To better understand the basic characteristics and evolutionary history of the HMGR gene family in plants, a genome-wide analysis of HMGR genes from 20 representative species was carried out. A total of 56 HMGR genes in the 14 land plant genomes were identified, but no genes were found in all 6 algal genomes. The gene structure and protein architecture of all plant HMGR genes were highly conserved. The phylogenetic analysis revealed that the plant HMGRs were derived from one ancestor gene and finally developed into four distinct groups, two in the monocot plants and two in dicot plants. Species-specific gene duplications, caused mainly by segmental duplication, led to the limited expansion of HMGR genes in Zea mays, Gossypium raimondii, Populus trichocarpa and Glycine max after the species diverged. The analysis of Ka/Ks ratios and expression profiles indicated that functional divergence after the gene duplications was restricted. The results suggested that the function and evolution of HMGR gene family were dramatically conserved throughout the plant kingdom.
    Full-text · Article · Apr 2014
    • "Annotation was performed by using the GenDB, version 2.2 system (Meyer et al., 2003), supplemented by the tool JCoast, version 1.6 (Richter et al., 2008). For each predicted ORF observations have been collected from similarity searches against sequence databases NCBI-nr, Swiss-Prot, KEGG and genomesDB (Richter et al., 2008) and for protein family databases from Pfam (Bateman et al., 2004) and InterPro (Mulder et al., 2005). SignalP has been used for signal peptide predictions (Bendtsen et al., 2004) and TMHMM for transmembrane helix-analysis (Krogh et al., 2001). "
    [Show abstract] [Hide abstract] ABSTRACT: The majority of strains belonging to the genus Pseudovibrio have been isolated from marine invertebrates such as tunicates, corals and particularly sponges, but the physiology of these bacteria is poorly understood. In this study, we analyse for the first time the genomes of two Pseudovibrio strains - FO-BEG1 and JE062. The strain FO-BEG1 is a required symbiont of a cultivated Beggiatoa strain, a sulfide-oxidizing, autotrophic bacterium, which was initially isolated from a coral. Strain JE062 was isolated from a sponge. The presented data show that both strains are generalistic bacteria capable of importing and oxidizing a wide range of organic and inorganic compounds to meet their carbon, nitrogen, phosphorous and energy requirements under both, oxic and anoxic conditions. Several physiological traits encoded in the analysed genomes were verified in laboratory experiments with both isolates. Besides the versatile metabolic abilities of both Pseudovibrio strains, our study reveals a number of open reading frames and gene clusters in the genomes that seem to be involved in symbiont-host interactions. Both Pseudovibrio strains have the genomic potential to attach to host cells, interact with the eukaryotic cell machinery, produce secondary metabolites and supply the host with cofactors.
    Full-text · Article · Mar 2013
    • "Annotation was performed with GenDB, version 2.2 [40], supplemented with the tool JCoast, version 1.6 [41]. For each predicted ORF, observations were collected from similarity searches against the NCBI-nr, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG) and genomesDB sequence databases [41] and against protein family databases from Pfam [42] and InterPro [43]. SignalP was used for signal peptide predictions [44] and TMHMM was used for transmembrane helix analysis [45]. "
    [Show abstract] [Hide abstract] ABSTRACT: Recent studies have indicated the existence of an extensive trans-genomic trans-mural co-metabolism between gut microbes and animal hosts that is diet-, host phylogeny- and provenance-influenced. Here, we analyzed the biodiversity at the level of small subunit rRNA gene sequence and the metabolic composition of 18 Mbp of consensus metagenome sequences and activity characteristics of bacterial intra-cellular extracts, in wild Iberian lynx (Lynx pardinus) fecal samples. Bacterial signatures (14.43% of all of the Firmicutes reads and 6.36% of total reads) related to the uncultured anaerobic commensals Anaeroplasma spp., which are typically found in ovine and bovine rumen, were first identified. The lynx gut was further characterized by an over-representation of 'presumptive' aquaporin aqpZ genes and genes encoding 'active' lysosomal-like digestive enzymes that are possibly needed to acquire glycerol, sugars and amino acids from glycoproteins, glyco(amino)lipids, glyco(amino)glycans and nucleoside diphosphate sugars. Lynx gut was highly enriched (28% of the total glycosidases) in genes encoding α-amylase and related enzymes, although it exhibited low rate of enzymatic activity indicative of starch degradation. The preponderance of β-xylosidase activity in protein extracts further suggests lynx gut microbes being most active for the metabolism of β-xylose containing plant N-glycans, although β-xylosidases sequences constituted only 1.5% of total glycosidases. These collective and unique bacterial, genetic and enzymatic activity signatures suggest that the wild lynx gut microbiota not only harbors gene sets underpinning sugar uptake from primary animal tissues (with the monotypic dietary profile of the wild lynx consisting of 80-100% wild rabbits) but also for the hydrolysis of prey-derived plant biomass. Although, the present investigation corresponds to a single sample and some of the statements should be considered qualitative, the data most likely suggests a tighter, more coordinated and complex evolutionary and nutritional ecology scenario of carnivore gut microbial communities than has been previously assumed.
    Full-text · Article · Dec 2012
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