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0  structures 81  species 0  interactions 1059  sequences 23  architectures

Family: HS1_rep (PF02218)

Summary: Repeat in HS1/Cortactin

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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.

Repeat in HS1/Cortactin Provide feedback

The function of this repeat is unknown. Seven copies are found in cortactin Q14247 and four copies are found in HS1 P14317. The repeats are always found amino terminal to an SH3 domain PF00018.

Literature references

  1. Wu H, Reynolds AB, Kanner SB, Vines RR, Parsons JT; , Mol Cell Biol 1991;11:5113-5124.: Identification and characterization of a novel cytoskeleton-associated pp60src substrate. PUBMED:1922035 EPMC:1922035


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003134

The cortactin or HS1 repeat is a tandem repeat of 37-amino acid actin-binding domains. The repeat is named after human cortactin and HS1, proteins involved in cytoskeletal rearrangements implicated in cell migration and apoptosis, respectively. Cortactin contains 6.5 tandem copies of the repeat and is conserved among metazoans, although e.g. insect cortactin and splice variants contain fewer copies. Hematopoietic lineage cell specific protein 1 (HS1) contains 3.5 tandem copies of the cortactin repeat and is mainly expressed in hematopoietic cells. Both cortactin and HS1 contain a C-terminal SH3 domain (INTERPRO). The cortactin repeat domain binds filamentous actin (F-actin) in proteins that modulate the assembly of the actin cytoskeleton. Secondary structure predictions indicate that the cortactin repeat could exhibit a helix-turn-helix structure [PUBMED:12534372, PUBMED:15186216].

Domain organisation

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

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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(18)
Full
(1059)
Representative proteomes NCBI
(857)
Meta
(0)
RP15
(125)
RP35
(164)
RP55
(293)
RP75
(511)
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PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(18)
Full
(1059)
Representative proteomes NCBI
(857)
Meta
(0)
RP15
(125)
RP35
(164)
RP55
(293)
RP75
(511)
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
(18)
Full
(1059)
Representative proteomes NCBI
(857)
Meta
(0)
RP15
(125)
RP35
(164)
RP55
(293)
RP75
(511)
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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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: Pfam-B_5631 (Release 5.2)
Previous IDs: none
Type: Repeat
Author: Bateman A
Number in seed: 18
Number in full: 1059
Average length of the domain: 34.90 aa
Average identity of full alignment: 59 %
Average coverage of the sequence by the domain: 36.89 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.5 22.0
Noise cut-off 20.8 20.9
Model length: 37
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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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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