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0  structures 276  species 0  interactions 662  sequences 8  architectures

Family: Popeye (PF04831)

Summary: Popeye protein conserved region

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This is the Wikipedia entry entitled "Popeye protein conserved region". More...

Popeye protein conserved region Edit Wikipedia article

Popeye protein conserved region
Identifiers
Symbol Popeye
Pfam PF04831
InterPro IPR006916

Popeye protein conserved region is a family of evolutionarily related proteins.

The Popeye domain containing (POPDC) family of proteins, is found in many animal phyla (vertebrates, lower chordates, arthropodes, mollusca and some protostomia).[1] In vertebrates it is preferentially expressed in developing and adult striated muscle (heart and skeletal muscle). It is represented by a conserved region, the Popeye domain, which functions as a cAMP-binding domain.[1] All POPDC proteins also have three potential transmembrane domains.[2] The strong conservation of POPDC genes during evolution and their preferential expression in heart and skeletal muscle suggest that these proteins may have an important function in these tissues in vertebrates.[2]

References

  1. ^ a b Schindler RF, Scotton C, French V, Ferlini A, Brand T (June 2016). "The Popeye Domain Containing Genes and their Function in Striated Muscle". Journal of Cardiovascular Development and Disease. 3 (2): 22. doi:10.3390/jcdd3020022. PMID 27347491. 
  2. ^ a b Andrée B, Hillemann T, Kessler-Icekson G, Schmitt-John T, Jockusch H, Arnold HH, Brand T (July 2000). "Isolation and characterization of the novel popeye gene family expressed in skeletal muscle and heart". Developmental Biology. 223 (2): 371–82. doi:10.1006/dbio.2000.9751. PMID 10882522. 

This article incorporates text from the public domain Pfam and InterPro IPR006916

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.

Popeye protein conserved region Provide feedback

The function of Popeye proteins is not well understood. They are predominantly expressed in cardiac and skeletal muscle. This family represents a conserved region which includes three potential transmembrane domains [1].

Literature references

  1. Andree B, Hillemann T, Kessler-Icekson G, Schmitt-John T, Jockusch H, Arnold HH, Brand T; , Dev Biol 2000;223:371-382.: Isolation and characterization of the novel popeye gene family expressed in skeletal muscle and heart. PUBMED:10882522 EPMC:10882522


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006916

The Popeye (POP) family of proteins, is mainly restricted to vertebrates and is preferentially expressed in developing and adult striated muscle. It is represented by a conserved region which includes three potential transmembrane domains [PUBMED:10882522]. The strong conservation of POP genes during evolution and their preferential expression in heart and skeletal muscle suggest that these novel proteins may have an important function in these tissues in vertebrates.

A number of uncharacterized protein homologues are known from bacteria, invertebrates and apicomplexan protozoa.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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
(36)
Full
(662)
Representative proteomes UniProt
(1177)
NCBI
(2025)
Meta
(85)
RP15
(171)
RP35
(316)
RP55
(527)
RP75
(607)
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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
(36)
Full
(662)
Representative proteomes UniProt
(1177)
NCBI
(2025)
Meta
(85)
RP15
(171)
RP35
(316)
RP55
(527)
RP75
(607)
Alignment:
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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
(36)
Full
(662)
Representative proteomes UniProt
(1177)
NCBI
(2025)
Meta
(85)
RP15
(171)
RP35
(316)
RP55
(527)
RP75
(607)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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: Pfam-B_3905 (release 7.6)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Mifsud W
Number in seed: 36
Number in full: 662
Average length of the domain: 214.30 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 58.18 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.1 28.1
Trusted cut-off 28.4 28.1
Noise cut-off 27.9 28.0
Model length: 140
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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