Summary: Repeat in HS1/Cortactin
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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
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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
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
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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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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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 (72) |
Full (3459) |
Representative proteomes | UniProt (6139) |
NCBI (10276) |
Meta (0) |
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RP15 (577) |
RP35 (1242) |
RP55 (2526) |
RP75 (3668) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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not generated,
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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 (72) |
Full (3459) |
Representative proteomes | UniProt (6139) |
NCBI (10276) |
Meta (0) |
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RP15 (577) |
RP35 (1242) |
RP55 (2526) |
RP75 (3668) |
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Raw Stockholm | |||||||||
Gzipped |
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
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Curation
Seed source: | Pfam-B_5631 (Release 5.2) |
Previous IDs: | none |
Type: | Repeat |
Sequence Ontology: | SO:0001068 |
Author: |
Bateman A |
Number in seed: | 72 |
Number in full: | 3459 |
Average length of the domain: | 34.30 aa |
Average identity of full alignment: | 59 % |
Average coverage of the sequence by the domain: | 32.19 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 36 | ||||||||||||
Family (HMM) version: | 16 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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