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114  structures 384  species 0  interactions 2838  sequences 104  architectures

Family: PSI_integrin (PF17205)

Summary: Integrin plexin domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Integrin plexin domain Provide feedback

This short disulphide rich domain is found at the N-terminus of integrin beta chains.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR033760

This short disulphide rich domain is found at the N terminus of integrin beta chains.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan PSI (CL0630), which has the following description:

This superfamily includes a disulphide rich domain found in Plexins, semaphorins and some integrin protein. According to SCOP the common core is alpha+beta with two conserved disulfides.

The clan contains the following 3 members:

PSI PSI_integrin Trefoil

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(100)
Full
(2838)
Representative proteomes UniProt
(4662)
RP15
(249)
RP35
(774)
RP55
(2336)
RP75
(3085)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(100)
Full
(2838)
Representative proteomes UniProt
(4662)
RP15
(249)
RP35
(774)
RP55
(2336)
RP75
(3085)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(100)
Full
(2838)
Representative proteomes UniProt
(4662)
RP15
(249)
RP35
(774)
RP55
(2336)
RP75
(3085)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Bateman A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 100
Number in full: 2838
Average length of the domain: 49.50 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 5.82 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.5 21.5
Trusted cut-off 21.5 21.5
Noise cut-off 21.4 21.4
Model length: 46
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Tree controls

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The tree shows the occurrence of this domain across different species. More...

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the PSI_integrin domain has been found. There are 114 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2JVU1 View 3D Structure Click here
A0A2R8Q837 View 3D Structure Click here
A2A863 View 3D Structure Click here
B2RYB8 View 3D Structure Click here
B3DIP9 View 3D Structure Click here
B3DIV2 View 3D Structure Click here
B3DIV8 View 3D Structure Click here
E7F4H9 View 3D Structure Click here
E7FCN5 View 3D Structure Click here
F1QF91 View 3D Structure Click here
F1QGX0 View 3D Structure Click here
F1RA51 View 3D Structure Click here
G3V7M2 View 3D Structure Click here
O54890 View 3D Structure Click here
O70309 View 3D Structure Click here
P05106 View 3D Structure Click here
P05107 View 3D Structure Click here
P05556 View 3D Structure Click here
P09055 View 3D Structure Click here
P11835 View 3D Structure Click here
P16144 View 3D Structure Click here
P18084 View 3D Structure Click here
P18564 View 3D Structure Click here
P26010 View 3D Structure Click here
P26011 View 3D Structure Click here
P26012 View 3D Structure Click here
P49134 View 3D Structure Click here
Q0VBD0 View 3D Structure Click here
Q19U09 View 3D Structure Click here
Q27591 View 3D Structure Click here
Q27874 View 3D Structure Click here
Q3UV74 View 3D Structure Click here
Q64632 View 3D Structure Click here
Q6AYF4 View 3D Structure Click here
Q8R2H2 View 3D Structure Click here
Q9Z0T9 View 3D Structure Click here