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5  structures 648  species 2  interactions 778  sequences 20  architectures

Family: Pex19 (PF04614)

Summary: Pex19 protein family

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.

Pex19 protein family Provide feedback

No Pfam abstract.

Literature references

  1. Hettema EH, Girzalsky W, van Den Berg M, Erdmann R, Distel B; , EMBO J 2000;19:223-233.: Saccharomyces cerevisiae pex3p and pex19p are required for proper localization and stability of peroxisomal membrane proteins. PUBMED:10637226 EPMC:10637226

  2. Snyder WB, Faber KN, Wenzel TJ, Koller A, Luers GH, Rangell L, Keller GA, Subramani S; , Mol Biol Cell 1999;10:1745-1761.: Pex19p interacts with Pex3p and Pex10p and is essential for peroxisome biogenesis in Pichia pastoris. PUBMED:10359594 EPMC:10359594

  3. Snyder WB, Koller A, Choy AJ, Johnson MA, Cregg JM, Rangell L, Keller GA, Subramani S; , Mol Biol Cell 1999;10:4005-4019.: Pex17p is required for import of both peroxisome membrane and lumenal proteins and interacts with Pex19p and the peroxisome targeting signal-receptor docking complex in Pichia pastoris. PUBMED:10588639 EPMC:10588639

  4. Gotte K, Girzalsky W, Linkert M, Baumgart E, Kammerer S, Kunau WH, Erdmann R; , Mol Cell Biol 1998;18:616-628.: Pex19p, a farnesylated protein essential for peroxisome biogenesis. PUBMED:9418908 EPMC:9418908


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006708

Peroxisome(s) form an intracellular compartment, bounded by a typical lipid bilayer membrane. Peroxisome functions are often specialised by organism and cell type; two widely distributed and well-conserved functions are H2O2-based respiration and fatty acid beta-oxidation. Other functions include ether lipid (plasmalogen) synthesis and cholesterol synthesis in animals, the glyoxylate cycle in germinating seeds ("glyoxysomes"), photorespiration in leaves, glycolysis in trypanosomes ("glycosomes"), and methanol and/or amine oxidation and assimilation in some yeasts.

PEX genes encode the machinery ("peroxins") required to assemble the peroxisome. Membrane assembly and maintenance requires three of these (peroxins 3, 16, and 19) and may occur without the import of the matrix (lumen) enzymes. Matrix protein import follows a branched pathway of soluble recycling receptors, with one branch for each class of peroxisome targeting sequence (two are well characterised), and a common trunk for all. At least one of these receptors, Pex5p, enters and exits peroxisomes as it functions. Proliferation of the organelle is regulated by Pex11p. Peroxisome biogenesis is remarkably conserved among eukaryotes. A group of fatal, inherited neuropathologies are recognised as peroxisome biogenesis diseases.

Gene Ontology

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

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 (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
(83)
Full
(778)
Representative proteomes UniProt
(1129)
NCBI
(1410)
Meta
(3)
RP15
(205)
RP35
(445)
RP55
(624)
RP75
(776)
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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
(83)
Full
(778)
Representative proteomes UniProt
(1129)
NCBI
(1410)
Meta
(3)
RP15
(205)
RP35
(445)
RP55
(624)
RP75
(776)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(83)
Full
(778)
Representative proteomes UniProt
(1129)
NCBI
(1410)
Meta
(3)
RP15
(205)
RP35
(445)
RP55
(624)
RP75
(776)
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: Wood V
Previous IDs: none
Type: Family
Author: Wood V, Bateman A
Number in seed: 83
Number in full: 778
Average length of the domain: 231.10 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 73.41 %

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 22.2 22.2
Trusted cut-off 22.3 22.4
Noise cut-off 22.0 22.0
Model length: 246
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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Interactions

There are 2 interactions for this family. More...

Pex14_N Pex19

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 Pex19 domain has been found. There are 5 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 seqence.

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