EBI is an Outstation of the European Molecular Biology Laboratory. Proteins to Proteomes The InterPro Database

EBI is an Outstation of the European Molecular Biology Laboratory.

Proteins to Proteomes The InterPro Database

http://www.ebi.ac.uk/interpro

raw data

Origins of InterPro

UniProt

automated annotationInterPro

Swiss-Prot TrEMBL290K

annotated5M ???


Curated Annotation in InterPro

TrEMBL

uncharacterised sequence

Swiss-Prot

annotated sequence

TrEMBL

feed back common annotatio

n

groups of related proteins

(same family or share domains)

multiple signatures

InterPro


Finding Conserved Signatures

• Pattern

More information

Simplest (limited)• Fingerprint

• Sequence clustering

• HMM


Patterns

Pattern/motif in sequence regular expression

Can define important sites

Enzyme catalytic site Prosthetic group attachment Metal ion binding site Cysteines for disulphide bonds Protein or molecule binding

B chain xxxxxxCxxxxxxxxxxxxCxxxxxxxxx A chain xxxxxCCxxxCxxxxxxxxCx | |

EXAMPLE: Insulin


Patterns



MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN


EXAMPLE: PS00262 Insulin family signature


Patterns





MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQ CCTSICSLYQLENYC N


Patterns





C-C-{P}-x(2)-C-[STDNEKPI]-x(3)-[LIVMFS]-x(3)-C

Regular expression

MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQ CCTSICSLYQLENYC N


Patterns

Extract pattern sequencesxxxxxxxxxxxxxxxxxxxxxxxx

Sequence alignment

Insulin family motifDefine pattern

Pattern signature

C-C-{P}-x(2)-C-[STDNEKPI]-x(3)-[LIVMFS]-x(3)-CBuild regular expression

PS00000


Fingerprints

Several motifs characterise family

Different combinations of motifs describe subfamilies

Identify small conserved regions in divergent proteins

EXAMPLE: PR00107 Phosphocarrier HPr signature

PTHP_ENTFA: MEKKEFHIVAETGIHARPATLLVQTASKFNSDINLEYKGKSVNLK

SIMGVMSLGVGQGSDVTITVDGADEAEGMAAIVETLQKEGLAE


Fingerprints





PTHP_ENTFA: MEKKEFHIVAET GIHARPATLLVQTASKF NSDINLEYKGKSVNLK

SIMGVMSLGVGQGSDVTITVDGADEAEGMAAIVETLQKEGLAE

His phosphorylation site


Fingerprints





PTHP_ENTFA:


Ser phosphorylation site

MEKKEFHIVAET GIHARPATLLVQTASKF NSDINLEY KGKSVNLK

SIMGVMSL GVGQGSDVTITVDGADEAEGMAAIVETLQKEGLAE


Fingerprints





PTHP_ENTFA:


Ser phosphorylation siteConserved site

MEKKEFHIVAET GIHARPATLLVQTASK FNSDINLEY KGKSVNLK

SIMGVMSL GVGQGSDVTITVDGADE AEGMAAIVETLQKEGLAE


Fingerprints





PTHP_ENTFA: MEKKEFHIVAET GIHARPATLLVQTASK FNSDINLEY KGKSVNLK

SIMGVMSL GVGQGSDVTITVDGADE AEGMAAIVETLQKEGLAE

1) GIHARPATLLVQTASKF2) KGKSVNLKSIMGVMSL

3) LGVGQGSDVTITVDGADE 3-motif fingerprint


Fingerprints

Extract motif sequences

xxxxxxxxxxxxxxxxxxxxxxxx



Sequence alignment

Correct order

Correct spacing

Ser phosphorylation

site

Conserved site

His phosphorylation

siteDefine motifs

Fingerprint signature 1 2 3

PR00000


Sequence clustering

Automatic clustering of homologous domains

**Rarely covers entire domain (conserved core)

**Signature size can change with release

Known domain families

Recruit homologous domains

PSI-BLAST

MKDOM2

Automatic clustering

ProDomAlignAlign domain families


Hidden Markov Models (HMM)

Can characterise protein over entire length

Models conserved and divergent regions (position-specific scoring)

Models insertions and deletions

Outperform in sensitivity and specificity

More flexible (can use partial alignments)

Sequence 1:Sequence 2:Sequence 3:Sequence 4:Sequence 5:Sequence 6:Sequence 7:

Sequence alignment

Scoring matrix

(residue frequency at each position in

alignment)

Profile

Phe most conserved


Phe, Tyr and Leu found at position 1 of alignment

highest match value


Tyr and Leu found at equal frequency at position 1

Tyr closer to Phe than Leu

Scores: F > Y > L

Probability method gauges scoring

parameters



Sequence alignment

M1 M2 M3 M4Begin

End

M = match state



D3

I2 I3

M1 M2 M3 M4Begin

End

D1 D4

M = match state,

D2

D = delete state

I1

I = insert state,


SAM Profile HMMs

Homologous structural superfamilies

Start with single seed sequence

Proteins in superfamily may have low

sequence identity

Few proteins in family have PDB structures

Create 1 model for every protein in superfamily combine results


Specialisation of Databases

Describe sibling families

Identify binding and active sites

Describe conserved core of domains

PRINTS

PROSITE

PRODOM

Wide coverage of domains & familiesPFAM

Signalling, extracellular & nuclear domainsSMART

Functional classification of familiesTIGRFAM

Families conserved in domain compositionPIRSF

Functional classification of familiesPANTHER

Structural-based domain classificationSuperfam

Structural-based domain classificationGENE3D


Manual curation

Integration of signatures

InterProInterPro

Foundations of InterPro


InterPro Entry

Groups similar signature together

Adds extensive annotation

Linked to other databases

Structural information and viewers

Links related signatures


Assigning Type

Domain Biological units with defined boundaries

Full-length signatures grouping related proteins Family

Repeat

Site

Signature repeated as a series of short motifs

Protein feature described by a Prosite pattern

Region Any signature that doesn’t fit the above


Grouping Signatures Together

Same positions

Different protein hits2)

PFAM

PROSITE (100)

(50)

PROSITE

PFAM

3) (100)

(100)

Different positions

Same protein hits

PFAM

PROSITE1) (100)

(100)Same positionsSame protein hits

IPR000001

Different positions4)PFAM

PROSITE (100)

(100)

IPR000001

IPR000002

IPR000001

IPR000002

IPR000001

IPR000002


Link related signatures - relationships

1) Parent - Child (subgroup of more closely related proteins)

PFAM

(75)

(100)

SMART

Protein kinase

Serine kinase

PROSITE (25) Tyrosine kinase

*

PFAM (100) Protein kinase*

No proteins in common

SMART PROSITE

PFAM

Protein kinase

SMART PROSITE

Serine kinase Tyrosine kinase

Parent

Children

Applies to domains and families


2) Contains – Found in (Describes domain composition)

PROSITE C-terminal domainSMARTN-terminal domain

PFAM Receptor family

PFAM

Receptor Family

SMART PROSITE

N-terminal domain C-terminal domain

Both families and domains can contain domains

Found in(Pfam)

Contains (Smart and Prosite)



2) Contains – Found in


Coverage Signature must cover the entire (>90%) sequence of contained signature

PFAM

SMART

ContainsFound in

PFAM

SMART

Contains

Found in

Overlapping


Relationships – evolutionary context

GENE3D Grandparent

Parents

Children

InterPro Relationship

Criteria for Signature

Structural family

PFAM PFAMSequence families

TIGRFAM TIGRFAM TIGRFAM TIGRFAMFunctional families

Unique to InterPro


Extensive Annotation

Annotation Fields in InterPro

• Name and short name• Entry type (family, domain, site)

• Relationships (links related signatures)

• GO mapping ( large scale classification)

• Abstract • Taxonomy (search/download using taxonomy)

• Examples• Publications


Extensive Annotation


• Name and short name• Entry type (family, domain, site)

• Relationships (links related signatures)

• GO mapping ( large scale classification)

• Abstract • Taxonomy (search/download using taxonomy)

• Examples• Publications

Select species-specific protein sets


Links to Other Databases


• Blocks (family alignments)

• IntEnz (enzymes)

• Prosite documents• COME (bioinorganic motifs)

• CAZy (carbohydrate-active enzymes)

• IUPHAR (GPCR receptors)

• CluS-Tr (protein clusters)

• Pandit (phylogenetic trees of PFAMs)

• Merops (peptidases & inhibitors)


Structural information

PDB

Classification

Structures

CATH

SCOP

Homology Models

Swiss-Model

ModBase


Sequence-Structure Display

Signatures predictive of

protein annotation

Structural data for specific proteins

AstexViewer® for structure


Structure Viewer

Navigate between structure and sequence

Manipulate structures


Other Features – splice variants

Splice variants


Other Features – domain architecture

Select data set of these proteins

Each ‘balloon’ represents a

linked InterPro domain


Other Features – protein-protein interactions

Lists proteins in entry known to be involved in protein-protein interactions

IntAct database of interactions


Protein Sequence Coverage

InterPro signatures cover:

95% of UniProt/Swiss-Prot proteins

79% of UniProt/TrEMBL proteins

>4 million matches in InterPro

>16,000 InterPro entries

>50,000 signature methods


Searching InterPro

http://www.ebi.ac.uk/interpro/

Search tools include:

• Text Search

• InterProScan (sequence search)


InterPro Text Search

Text search box Search using:• text• protein ID• InterPro ID• GO term

Search results

Direct links to entry


InterProScan Search Use ftp site to run multiple sequences

simultaneously

Member database search engines

Paste in sequence (protein/nucleotide)


InterProScan Search Results

single InterPro entry

Direct links to entry

Direct links to signature databases

Documents

EBI is an Outstation of the European Molecular Biology Laboratory. Proteins to Proteomes The InterPro Database