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76  structures 467  species 0  interactions 12823  sequences 739  architectures

Family: PSI (PF01437)

Summary: Plexin repeat

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.

Plexin repeat Provide feedback

A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin (P70206) [1]. Two copies of the repeat are found in mahogany protein. A related C. elegans protein (Q19981) contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas [1] shows 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman).

Literature references

  1. Ohta K, Mizutani A, Kawakami A, Murakami Y, Kasuya Y, Takagi S, Tanaka H, Fujisawa H; , Neuron 1995;14:1189-1199.: Plexin: a novel neuronal cell surface molecule that mediates cell adhesion via a homophilic binding mechanism in the presence of calcium ions. PUBMED:7605632 EPMC:7605632

  2. Bork P, Doerks T, Springer TA, Snel B; , Trends Biochem Sci 1999;24:261-263.: Domains in plexins: links to integrins and transcription factors. PUBMED:10390613 EPMC:10390613


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002165

This is a cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found in plexin ( SWISSPROT ) [ PUBMED:7605632 ]. Two copies of the repeat are found in mahogany protein. A related Caenorhabditis elegans protein ( SWISSPROT ) contains four copies of the repeat, while the Met receptor contains a single copy of the repeat.

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
(95)
Full
(12823)
Representative proteomes UniProt
(21436)
RP15
(1129)
RP35
(3598)
RP55
(10735)
RP75
(14463)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(95)
Full
(12823)
Representative proteomes UniProt
(21436)
RP15
(1129)
RP35
(3598)
RP55
(10735)
RP75
(14463)
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
(95)
Full
(12823)
Representative proteomes UniProt
(21436)
RP15
(1129)
RP35
(3598)
RP55
(10735)
RP75
(14463)
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: Plexin_repeat;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 95
Number in full: 12823
Average length of the domain: 54.70 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 5.70 %

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 23.1 23.1
Trusted cut-off 23.1 23.1
Noise cut-off 23.0 23.0
Model length: 51
Family (HMM) version: 27
Download: download the raw HMM for this family

Species distribution

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Selections

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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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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 domain has been found. There are 76 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
A0A0G2JZC4 View 3D Structure Click here
A0A0R4IRZ9 View 3D Structure Click here
A0A140LGG1 View 3D Structure Click here
A0A140LGG1 View 3D Structure Click here
A0A2R8Q3J7 View 3D Structure Click here
A0A2R8Q3J7 View 3D Structure Click here
A0A2R8Q662 View 3D Structure Click here
A0A2R8QAH3 View 3D Structure Click here
A0A2R8QPJ6 View 3D Structure Click here
A0A2R8QPJ6 View 3D Structure Click here
A3KPS4 View 3D Structure Click here
B0S5N4 View 3D Structure Click here
B0S5N4 View 3D Structure Click here
B2RXS4 View 3D Structure Click here
B2RXS4 View 3D Structure Click here
B5DEZ8 View 3D Structure Click here
C0SQ71 View 3D Structure Click here
C0SQ73 View 3D Structure Click here
D3Z981 View 3D Structure Click here
D3Z981 View 3D Structure Click here
D3ZAG0 View 3D Structure Click here
D3ZDX5 View 3D Structure Click here
D3ZES7 View 3D Structure Click here
D3ZES7 View 3D Structure Click here
D3ZES7 View 3D Structure Click here
D3ZLH5 View 3D Structure Click here
D3ZPX4 View 3D Structure Click here
D3ZPX4 View 3D Structure Click here
D3ZQ57 View 3D Structure Click here
D3ZQ57 View 3D Structure Click here
D3ZQP6 View 3D Structure Click here
D3ZWP6 View 3D Structure Click here
D3ZYR4 View 3D Structure Click here
D4A6G2 View 3D Structure Click here
D4A7M0 View 3D Structure Click here
D4A9J3 View 3D Structure Click here
D4AA77 View 3D Structure Click here
E7EYX4 View 3D Structure Click here
E7F6C7 View 3D Structure Click here
E7F6C7 View 3D Structure Click here
E7F898 View 3D Structure Click here
E7FGY1 View 3D Structure Click here
F1LSV0 View 3D Structure Click here
F1M3T8 View 3D Structure Click here
F1M3T8 View 3D Structure Click here
F1Q4X2 View 3D Structure Click here
F1Q4X2 View 3D Structure Click here
F1Q4X2 View 3D Structure Click here
F1Q6L2 View 3D Structure Click here
F1Q7U0 View 3D Structure Click here
F1QBC0 View 3D Structure Click here
F1QF70 View 3D Structure Click here
F1QJZ8 View 3D Structure Click here
F1QLR7 View 3D Structure Click here
F1QR50 View 3D Structure Click here
F1QU86 View 3D Structure Click here
F1R501 View 3D Structure Click here
F1R5J7 View 3D Structure Click here
F7F3I7 View 3D Structure Click here
F8W238 View 3D Structure Click here
F8W2K2 View 3D Structure Click here
M9MMA2 View 3D Structure Click here
O09126 View 3D Structure Click here
O15031 View 3D Structure Click here
O35464 View 3D Structure Click here
O43157 View 3D Structure Click here
O45657 View 3D Structure Click here
O45657 View 3D Structure Click here
O60486 View 3D Structure Click here
O75051 View 3D Structure Click here
O75051 View 3D Structure Click here
O75326 View 3D Structure Click here
O75882 View 3D Structure Click here
O75882 View 3D Structure Click here
O95754 View 3D Structure Click here
P08581 View 3D Structure Click here
P16056 View 3D Structure Click here
P51805 View 3D Structure Click here
P51805 View 3D Structure Click here
P70206 View 3D Structure Click here
P70206 View 3D Structure Click here
P70207 View 3D Structure Click here
P70208 View 3D Structure Click here
P70208 View 3D Structure Click here
Q17330 View 3D Structure Click here
Q19981 View 3D Structure Click here
Q24322 View 3D Structure Click here
Q3UH93 View 3D Structure Click here
Q55EQ1 View 3D Structure Click here
Q5RH90 View 3D Structure Click here
Q5RHX7 View 3D Structure Click here
Q5VV63 View 3D Structure Click here
Q5VV63 View 3D Structure Click here
Q62178 View 3D Structure Click here
Q62179 View 3D Structure Click here
Q64151 View 3D Structure Click here
Q6A051 View 3D Structure Click here
Q6A051 View 3D Structure Click here
Q6BEA0 View 3D Structure Click here
Q6BEA0 View 3D Structure Click here
Q6UX71 View 3D Structure Click here
Q76KF0 View 3D Structure Click here
Q80UG2 View 3D Structure Click here
Q80UG2 View 3D Structure Click here
Q80UG2 View 3D Structure Click here
Q8CJH3 View 3D Structure Click here
Q8IUK5 View 3D Structure Click here
Q8NFY4 View 3D Structure Click here
Q91ZV7 View 3D Structure Click here
Q92854 View 3D Structure Click here
Q99J86 View 3D Structure Click here
Q99J86 View 3D Structure Click here
Q9C0C4 View 3D Structure Click here
Q9DC11 View 3D Structure Click here
Q9H2E6 View 3D Structure Click here
Q9H3S1 View 3D Structure Click here
Q9H3T3 View 3D Structure Click here
Q9HCM2 View 3D Structure Click here
Q9HCM2 View 3D Structure Click here
Q9NPR2 View 3D Structure Click here
Q9NTN9 View 3D Structure Click here
Q9P283 View 3D Structure Click here
Q9QUR8 View 3D Structure Click here
Q9QY40 View 3D Structure Click here
Q9QZC2 View 3D Structure Click here
Q9UIW2 View 3D Structure Click here
Q9UIW2 View 3D Structure Click here
Q9ULL4 View 3D Structure Click here
Q9V491 View 3D Structure Click here
Q9V491 View 3D Structure Click here
Q9V491 View 3D Structure Click here
Q9V4A7 View 3D Structure Click here
Q9VTT0 View 3D Structure Click here
Q9W2V9 View 3D Structure Click here
Q9WU60 View 3D Structure Click here
Q9WU60 View 3D Structure Click here
Q9WUH7 View 3D Structure Click here
Q9Y4D7 View 3D Structure Click here
Q9Y4D7 View 3D Structure Click here
Q9YHX4 View 3D Structure Click here
Q9Z123 View 3D Structure Click here
Q9Z143 View 3D Structure Click here
U4PRY7 View 3D Structure Click here
U4PRY7 View 3D Structure Click here