Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
0  structures 248  species 0  interactions 2734  sequences 38  architectures

Family: Calponin (PF00402)

Summary: Calponin family repeat

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

This is the Wikipedia entry entitled "Calponin family repeat". More...

Calponin family repeat Edit Wikipedia article

Calponin
Identifiers
Symbol Calponin
Pfam PF00402
InterPro IPR000557
PROSITE PDOC00808

In molecular biology, the calponin family repeat is a 26 amino acid protein domain. Calponin 1 (CNN1) contains three copies of this domain. This domain is also found in vertebrate smooth muscle protein (SM22 or transgelin), and a number of other proteins whose physiological role is not yet established, including Drosophila synchronous flight muscle protein SM20, Caenorhabditis elegans unc-87 protein,[1] rat neuronal protein NP25,[2] and an Onchocerca volvulus antigen.[3]

References

  1. ^ Goetinck S, Waterston RH (October 1994). "The Caenorhabditis elegans muscle-affecting gene unc-87 encodes a novel thin filament-associated protein". J. Cell Biol. 127 (1): 79–93. doi:10.1083/jcb.127.1.79. PMC 2120179Freely accessible. PMID 7929573. 
  2. ^ Ren WZ, Ng GY, Wang RX, Wu PH, O'Dowd BF, Osmond DH, George SR, Liew CC (March 1994). "The identification of NP25: a novel protein that is differentially expressed by neuronal subpopulations". Brain Res. Mol. Brain Res. 22 (1-4): 173–85. doi:10.1016/0169-328X(94)90045-0. PMID 8015377. 
  3. ^ Irvine M, Huima T, Prince AM, Lustigman S (May 1994). "Identification and characterization of an Onchocerca volvulus cDNA clone encoding a highly immunogenic calponin-like protein". Mol. Biochem. Parasitol. 65 (1): 135–46. doi:10.1016/0166-6851(94)90122-8. PMID 7935620. 

This article incorporates text from the public domain Pfam and InterPro IPR000557

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Calponin family repeat Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000557

Calponin [PUBMED:8130072, PUBMED:8144658] is a thin filament-associated protein that is implicated in the regulation and modulation of smooth muscle contraction. It is capable of binding to actin, calmodulin, troponin C and tropomyosin. The interaction of calponin with actin inhibits the actomyosin MgATPase activity. Calponin is a basic protein of approximately 34 Kd. Multiple isoforms are found in smooth muscles. Calponin contains three repeats of a well conserved 26 amino acid domain. Such a domain is also found in vertebrate smooth muscle protein (SM22 or transgelin), and a number of other proteins whose physiological role is not yet established, including Drosophila synchronous flight muscle protein SM20, Caenorhabditis elegans unc-87 protein [PUBMED:7929573], rat neuronal protein NP25 [PUBMED:8015377], and an Onchocerca volvulus antigen [PUBMED:7935620].

Domain organisation

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

Loading domain graphics...

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...

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
(71)
Full
(2734)
Representative proteomes UniProt
(4021)
NCBI
(4812)
Meta
(0)
RP15
(813)
RP35
(1413)
RP55
(2126)
RP75
(2518)
Jalview View  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
(71)
Full
(2734)
Representative proteomes UniProt
(4021)
NCBI
(4812)
Meta
(0)
RP15
(813)
RP35
(1413)
RP55
(2126)
RP75
(2518)
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
(71)
Full
(2734)
Representative proteomes UniProt
(4021)
NCBI
(4812)
Meta
(0)
RP15
(813)
RP35
(1413)
RP55
(2126)
RP75
(2518)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   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: Prosite
Previous IDs: calponin;
Type: Repeat
Author: Finn RD
Number in seed: 71
Number in full: 2734
Average length of the domain: 24.10 aa
Average identity of full alignment: 56 %
Average coverage of the sequence by the domain: 19.98 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 20.9 21.0
Model length: 25
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

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

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

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

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.