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InterPro

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InterPro
InterPro logo.png
Content
DescriptionInterPro functionally analyzes protein sequences and classifies them into protein families while predicting the presence of domains and functional sites.
Contact
Research centerEMBL
LaboratoryEuropean Bioinformatics Institute
Primary citationThe InterPro protein families and domains database: 20 years on[1]
Release date1999
Access
Websitewww.ebi.ac.uk/interpro/
Download URLftp.ebi.ac.uk/pub/databases/interpro/
Miscellaneous
Data release
frequency
8-weekly
Version91.0 (13 October 2022; 43 days ago (2022-10-13))

InterPro is a database of protein families, protein domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences[2] in order to functionally characterise them.[3][4]

The contents of InterPro consist of diagnostic signatures and the proteins that they significantly match. The signatures consist of models (simple types, such as regular expressions or more complex ones, such as Hidden Markov models) which describe protein families, domains or sites. Models are built from the amino acid sequences of known families or domains and they are subsequently used to search unknown sequences (such as those arising from novel genome sequencing) in order to classify them. Each of the member databases of InterPro contributes towards a different niche, from very high-level, structure-based classifications (SUPERFAMILY and CATH-Gene3D) through to quite specific sub-family classifications (PRINTS and PANTHER).

InterPro's intention is to provide a one-stop-shop for protein classification, where all the signatures produced by the different member databases are placed into entries within the InterPro database. Signatures which represent equivalent domains, sites or families are put into the same entry and entries can also be related to one another. Additional information such as a description, consistent names and Gene Ontology (GO) terms are associated with each entry, where possible.

Discover more about InterPro related topics

Protein family

Protein family

A protein family is a group of evolutionarily related proteins. In many cases, a protein family has a corresponding gene family, in which each gene encodes a corresponding protein with a 1:1 relationship. The term "protein family" should not be confused with family as it is used in taxonomy.

Protein domain

Protein domain

A protein domain is a region of the protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. Each domain forms a compact folded three-dimensional structure. Many proteins consist of several domains. One domain may appear in a variety of different proteins. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions. In general, domains vary in length from between about 50 amino acids up to 250 amino acids in length. The shortest domains, such as zinc fingers, are stabilized by metal ions or disulfide bridges. Domains often form functional units, such as the calcium-binding EF hand domain of calmodulin. Because they are independently stable, domains can be "swapped" by genetic engineering between one protein and another to make chimeric proteins.

PRINTS

PRINTS

In molecular biology, the PRINTS database is a collection of so-called "fingerprints": it provides both a detailed annotation resource for protein families, and a diagnostic tool for newly determined sequences. A fingerprint is a group of conserved motifs taken from a multiple sequence alignment - together, the motifs form a characteristic signature for the aligned protein family. The motifs themselves are not necessarily contiguous in sequence, but may come together in 3D space to define molecular binding sites or interaction surfaces. The particular diagnostic strength of fingerprints lies in their ability to distinguish sequence differences at the clan, superfamily, family and subfamily levels. This allows fine-grained functional diagnoses of uncharacterised sequences, allowing, for example, discrimination between family members on the basis of the ligands they bind or the proteins with which they interact, and highlighting potential oligomerisation or allosteric sites.

PANTHER

PANTHER

In bioinformatics, the PANTHER classification system is a large curated biological database of gene/protein families and their functionally related subfamilies that can be used to classify and identify the function of gene products. PANTHER is part of the Gene Ontology Reference Genome Project designed to classify proteins and their genes for high-throughput analysis.

Gene Ontology

Gene Ontology

The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and gene product attributes; 2) annotate genes and gene products, and assimilate and disseminate annotation data; and 3) provide tools for easy access to all aspects of the data provided by the project, and to enable functional interpretation of experimental data using the GO, for example via enrichment analysis. GO is part of a larger classification effort, the Open Biomedical Ontologies, being one of the Initial Candidate Members of the OBO Foundry.

Data contained in InterPro

InterPro contains three main entities: proteins, signatures (also referred to as "methods" or "models") and entries. The proteins in UniProtKB are also the central protein entities in InterPro. Information regarding which signatures significantly match these proteins are calculated as the sequences are released by UniProtKB and these results are made available to the public (see below). The matches of signatures to proteins are what determine how signatures are integrated together into InterPro entries: comparative overlap of matched protein sets and the location of the signatures' matches on the sequences are used as indicators of relatedness. Only signatures deemed to be of sufficient quality are integrated into InterPro. As of version 81.0 (released 21 August 2020) InterPro entries annotated 73.9% of residues found in UniProtKB with another 9.2% annotated by signatures that are pending integration.[5]

The coverage of UniProtKB residues by InterPro entries as of InterPro version 81.0.[5]
The coverage of UniProtKB residues by InterPro entries as of InterPro version 81.0.[5]

InterPro also includes data for splice variants and the proteins contained in the UniParc and UniMES databases.

InterPro consortium member databases

The signatures from InterPro come from 13 "member databases", which are listed below.

CATH-Gene3D
Describes protein families and domain architectures in complete genomes. Protein families are formed using a Markov clustering algorithm, followed by multi-linkage clustering according to sequence identity. Mapping of predicted structure and sequence domains is undertaken using hidden Markov models libraries representing CATH and Pfam domains. Functional annotation is provided to proteins from multiple resources. Functional prediction and analysis of domain architectures is available from the Gene3D website.
CDD
Conserved Domain Database is a protein annotation resource that consists of a collection of annotated multiple sequence alignment models for ancient domains and full-length proteins. These are available as position-specific score matrices (PSSMs) for fast identification of conserved domains in protein sequences via RPS-BLAST.
HAMAP
Stands for High-quality Automated and Manual Annotation of microbial Proteomes. HAMAP profiles are manually created by expert curators they identify proteins that are part of well-conserved bacterial, archaeal and plastid-encoded (i.e. chloroplasts, cyanelles, apicoplasts, non-photosynthetic plastids) proteins families or subfamilies.
MobiDB
MobiDB is database annotating intrinsic disorder in proteins.
PANTHER
PANTHER is a large collection of protein families that have been subdivided into functionally related subfamilies, using human expertise. These subfamilies model the divergence of specific functions within protein families, allowing more accurate association with function (human-curated molecular function and biological process classifications and pathway diagrams), as well as inference of amino acids important for functional specificity. Hidden Markov models (HMMs) are built for each family and subfamily for classifying additional protein sequences.
Pfam
Is large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families.
The 13 member databases of the InterPro consortium grouped by their signature construction method and the biological entity they focus on.[6]
The 13 member databases of the InterPro consortium grouped by their signature construction method and the biological entity they focus on.[6]
PIRSF
Protein classification system is a network with multiple levels of sequence diversity from superfamilies to subfamilies that reflects the evolutionary relationship of full-length proteins and domains. The primary PIRSF classification unit is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture).
PRINTS
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 UniProt. 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.
PROSITE
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.
SMART
Simple Modular Architecture Research Tool Allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. More than 800 domain families found in signaling, 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.
SUPERFAMILY
SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain and aims to represent the entire SCOP superfamily that the domain belongs to. SUPERFAMILY has been used to carry out structural assignments to all completely sequenced genomes.
SFLD
A hierarchical classification of enzymes that relates specific sequence-structure features to specific chemical capabilities.
TIGRFAMs
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.

Data types

InterPro consists of seven types of data provided by different members of the consortium:

Data Types of InterPro
Data Type Description Contributing Databases
InterPro Entries Structural and/or functional domains of proteins predicted using one or more signatures All 13 member databases
Member Database signatures Signatures from member databases. These include signatures that are integrated into InterPro, and those that are not All 13 member databases
Protein Protein sequences UniProtKB (Swiss-Prot and TrEMBL)
Proteome Collection of proteins that belong to a single organism UniProtKB
Structure 3-dimensional structures of proteins PDBe
Taxonomy Protein taxonomic information UniProtKB
Set Groups of evolutionary related families Pfam, CDD
Icons that identify the five entry types found in InterPro (Homologous Superfamily, Family, Domain, Repeat, or Site).[7]
Icons that identify the five entry types found in InterPro (Homologous Superfamily, Family, Domain, Repeat, or Site).[7]

InterPro entry types

InterPro entries can be further broken down into five types:

  • Homologous Superfamily: A group of proteins that share a common evolutionary origin as seen in their structural similarities, even if their sequences are not highly similar. These entries are specifically only provided by two member databases: CATH-Gene3D and SUPERFAMILY.
  • Family: A group of proteins that have a common evolutionary origin determined through structural similarities, related functions, or sequence homology.
  • Domain: A distinct unit in a protein with a particular function, structure, or sequence.
  • Repeat: A sequence of amino acids, usually no longer than 50 amino acids, that tend to repeat many times in a protein.
  • Site: A short sequence of amino acids where at least one amino acid is conserved. These include post-translation modification sites, conserved sites, binding sites, and active sites.

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Alternative splicing

Alternative splicing

Alternative splicing, or alternative RNA splicing, or differential splicing, is an alternative splicing process during gene expression that allows a single gene to code for multiple proteins. In this process, particular exons of a gene may be included within or excluded from the final, processed messenger RNA (mRNA) produced from that gene. This means the exons are joined in different combinations, leading to different (alternative) mRNA strands. Consequently, the proteins translated from alternatively spliced mRNAs will contain differences in their amino acid sequence and, often, in their biological functions.

Pfam

Pfam

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 35.0, was released in November 2021 and contains 19,632 families.

Conserved Domain Database

Conserved Domain Database

The Conserved Domain Database (CDD) is a database of well-annotated multiple sequence alignment models and derived database search models, for ancient domains and full-length proteins.

MobiDB

MobiDB

In molecular biology, MobiDB is a curated biological database designed to offer a centralized resource for annotations of intrinsic protein disorder. Protein disorder is a structural feature characterizing a large number of proteins with prominent members known as intrinsically unstructured proteins. The database features three levels of annotation: manually curated, indirect and predicted. By combining different data sources of protein disorder into a consensus annotation, MobiDB aims at giving the best possible picture of the "disorder landscape" of a given protein of interest.

PANTHER

PANTHER

In bioinformatics, the PANTHER classification system is a large curated biological database of gene/protein families and their functionally related subfamilies that can be used to classify and identify the function of gene products. PANTHER is part of the Gene Ontology Reference Genome Project designed to classify proteins and their genes for high-throughput analysis.

PRINTS

PRINTS

In molecular biology, the PRINTS database is a collection of so-called "fingerprints": it provides both a detailed annotation resource for protein families, and a diagnostic tool for newly determined sequences. A fingerprint is a group of conserved motifs taken from a multiple sequence alignment - together, the motifs form a characteristic signature for the aligned protein family. The motifs themselves are not necessarily contiguous in sequence, but may come together in 3D space to define molecular binding sites or interaction surfaces. The particular diagnostic strength of fingerprints lies in their ability to distinguish sequence differences at the clan, superfamily, family and subfamily levels. This allows fine-grained functional diagnoses of uncharacterised sequences, allowing, for example, discrimination between family members on the basis of the ligands they bind or the proteins with which they interact, and highlighting potential oligomerisation or allosteric sites.

PROSITE

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. These are manually curated by a team of the Swiss Institute of Bioinformatics and tightly integrated into Swiss-Prot protein annotation. 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.

Protein superfamily

Protein superfamily

A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred. Usually this common ancestry is inferred from structural alignment and mechanistic similarity, even if no sequence similarity is evident. Sequence homology can then be deduced even if not apparent. Superfamilies typically contain several protein families which show sequence similarity within each family. The term protein clan is commonly used for protease and glycosyl hydrolases superfamilies based on the MEROPS and CAZy classification systems.

PDBe-KB

PDBe-KB

Protein Data Bank in Europe – Knowledge Base (PDBe-KB) is a community-driven, open-access, integrated resource whose mission is to place macromolecular structure data in their biological context and to make them accessible to the scientific community in order to support fundamental and translational research and education. It is part of the European Bioinformatics Institute (EMBL-EBI), based at the Wellcome Genome Campus, Hinxton, Cambridgeshire, England.

Sequence homology

Sequence homology

Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speciation event (orthologs), or a duplication event (paralogs), or else a horizontal gene transfer event (xenologs).

Post-translational modification

Post-translational modification

Post-translational modification (PTM) is the covalent and generally enzymatic modification of proteins following protein biosynthesis. This process occurs in the endoplasmic reticulum and the golgi apparatus. Proteins are synthesized by ribosomes translating mRNA into polypeptide chains, which may then undergo PTM to form the mature protein product. PTMs are important components in cell signaling, as for example when prohormones are converted to hormones.

Binding site

Binding site

In biochemistry and molecular biology, a binding site is a region on a macromolecule such as a protein that binds to another molecule with specificity. The binding partner of the macromolecule is often referred to as a ligand. Ligands may include other proteins, enzyme substrates, second messengers, hormones, or allosteric modulators. The binding event is often, but not always, accompanied by a conformational change that alters the protein's function. Binding to protein binding sites is most often reversible, but can also be covalent reversible or irreversible.

Access

The database is available for text- and sequence-based searches via a webserver, and for download via anonymous FTP. Like other EBI databases, it is in the public domain, since its content can be used "by any individual and for any purpose".[8] InterPro aims to release data to the public every 8 weeks, typically within a day of the UniProtKB release of the same proteins.

InterPro application programming interface (API)

InterPro provides an API for programmatic access to all InterPro entries and their related entries in Json format.[9] There are six main endpoints for the API corresponding to the different InterPro data types: entry, protein, structure, taxonomy, proteome and set.

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European Bioinformatics Institute

European Bioinformatics Institute

The European Bioinformatics Institute (EMBL-EBI) is an Intergovernmental Organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wellcome Genome Campus in Hinxton near Cambridge, and employs over 600 full-time equivalent (FTE) staff. Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics.

Public domain

Public domain

The public domain (PD) consists of all the creative work to which no exclusive intellectual property rights apply. Those rights may have expired, been forfeited, expressly waived, or may be inapplicable. Because those rights have expired, anyone can legally use or reference those works without permission.

API

API

An application programming interface (API) is a way for two or more computer programs to communicate with each other. It is a type of software interface, offering a service to other pieces of software.A document or standard that describes how to build or use such a connection or interface is called an API specification. A computer system that meets this standard is said to implement or expose an API. The term API may refer either to the specification or to the implementation.

JSON

JSON

JSON is an open standard file format and data interchange format that uses human-readable text to store and transmit data objects consisting of attribute–value pairs and arrays. It is a common data format with diverse uses in electronic data interchange, including that of web applications with servers.

InterProScan

InterProScan is a software package that allows users to scan sequences against member database signatures. Users can use this signature scanning software to functionally characterize novel nucleotide or protein sequences.[10] InterProScan is frequently used in genome projects in order to obtain a "first-pass" characterisation of the genome of interest.[11][12] As of December 2020, the public version of InterProScan (v5.x) uses a Java-based architecture.[13] The software package is currently only supported on a 64-bit Linux operating system.

InterProScan, along with many other EMBL-EBI bioinformatics tools, can also be accessed programmatically using RESTful and SOAP Web Services APIs.[14]

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Java (programming language)

Java (programming language)

Java is a high-level, class-based, object-oriented programming language that is designed to have as few implementation dependencies as possible. It is a general-purpose programming language intended to let programmers write once, run anywhere (WORA), meaning that compiled Java code can run on all platforms that support Java without the need to recompile. Java applications are typically compiled to bytecode that can run on any Java virtual machine (JVM) regardless of the underlying computer architecture. The syntax of Java is similar to C and C++, but has fewer low-level facilities than either of them. The Java runtime provides dynamic capabilities that are typically not available in traditional compiled languages. As of 2019, Java was one of the most popular programming languages in use according to GitHub, particularly for client–server web applications, with a reported 9 million developers.

Linux

Linux

Linux is an open-source Unix-like operating system based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution.

Representational state transfer

Representational state transfer

Representational state transfer (REST) is a software architectural style that describes a uniform interface between physically separate components, often across the Internet in a client-server architecture. REST defines four interface constraints:Identification of resources Manipulation of resources Self-descriptive messages and Hypermedia as the engine of application state

SOAP

SOAP

SOAP is a messaging protocol specification for exchanging structured information in the implementation of web services in computer networks. It uses XML Information Set for its message format, and relies on application layer protocols, most often Hypertext Transfer Protocol (HTTP), although some legacy systems communicate over Simple Mail Transfer Protocol (SMTP), for message negotiation and transmission.

Source: "InterPro", Wikipedia, Wikimedia Foundation, (2022, November 25th), https://en.wikipedia.org/wiki/InterPro.

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References
  1. ^ Blum M, Chang HY, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, et al. (November 2020). "The InterPro protein families and domains database: 20 years on". Nucleic Acids Research. 49 (D1): D344–D354. doi:10.1093/nar/gkaa977. PMC 7778928. PMID 33156333.
  2. ^ Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, et al. (January 2012). "InterPro in 2011: new developments in the family and domain prediction database". Nucleic Acids Research. 40 (Database issue): D306-12. doi:10.1093/nar/gkr948. PMC 3245097. PMID 22096229.
  3. ^ Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, et al. (January 2001). "The InterPro database, an integrated documentation resource for protein families, domains and functional sites". Nucleic Acids Research. 29 (1): 37–40. doi:10.1093/nar/29.1.37. PMC 29841. PMID 11125043.
  4. ^ Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, et al. (December 2000). "InterPro--an integrated documentation resource for protein families, domains and functional sites". Bioinformatics. 16 (12): 1145–50. doi:10.1093/bioinformatics/16.12.1145. PMID 11159333.
  5. ^ a b Blum, Matthias; Chang, Hsin-Yu; Chuguransky, Sara; Grego, Tiago; Kandasaamy, Swaathi; Mitchell, Alex; Nuka, Gift; Paysan-Lafosse, Typhaine; Qureshi, Matloob; Raj, Shriya; Richardson, Lorna (2020-11-06). "The InterPro protein families and domains database: 20 years on". Nucleic Acids Research. 49 (D1): D344–D354. doi:10.1093/nar/gkaa977. ISSN 0305-1048. PMC 7778928. PMID 33156333.
  6. ^ EMBL-EBI. "Where does the data come from? | InterPro". Retrieved 2020-12-04.
  7. ^ EMBL-EBI. "InterPro entry types | InterPro". Retrieved 2020-12-04.
  8. ^ "Terms of Use for EMBL-EBI Services | European Bioinformatics Institute".
  9. ^ "How to download InterPro data? — InterPro Documentation". interpro-documentation.readthedocs.io. Retrieved 2020-12-04.
  10. ^ Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (July 2005). "InterProScan: protein domains identifier" (Free full text). Nucleic Acids Research. 33 (Web Server issue): W116-20. doi:10.1093/nar/gki442. PMC 1160203. PMID 15980438.
  11. ^ Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. (February 2001). "Initial sequencing and analysis of the human genome" (PDF). Nature. 409 (6822): 860–921. Bibcode:2001Natur.409..860L. doi:10.1038/35057062. PMID 11237011.
  12. ^ Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, et al. (October 2002). "The genome sequence of the malaria mosquito Anopheles gambiae". Science. 298 (5591): 129–49. Bibcode:2002Sci...298..129H. CiteSeerX 10.1.1.149.9058. doi:10.1126/science.1076181. PMID 12364791. S2CID 4512225.
  13. ^ Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, et al. (May 2014). "InterProScan 5: genome-scale protein function classification". Bioinformatics. 30 (9): 1236–40. doi:10.1093/bioinformatics/btu031. PMC 3998142. PMID 24451626.
  14. ^ Madeira F, Park YM, Lee J, Buso N, Gur T, Madhusoodanan N, et al. (July 2019). "The EMBL-EBI search and sequence analysis tools APIs in 2019". Nucleic Acids Research. 47 (W1): W636–W641. doi:10.1093/nar/gkz268. PMC 6602479. PMID 30976793.
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