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13  structures 1339  species 0  interactions 3103  sequences 60  architectures

Family: Vta1 (PF04652)

Summary: Vta1 like

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.

Vta1 like Provide feedback

Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4. Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT). Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region [1].

Literature references

  1. Azmi I, Davies B, Dimaano C, Payne J, Eckert D, Babst M, Katzmann DJ; , J Cell Biol. 2006;172:705-717.: Recycling of ESCRTs by the AAA-ATPase Vps4 is regulated by a conserved VSL region in Vta1. PUBMED:16505166 EPMC:16505166


This tab holds annotation information from the InterPro database.

InterPro entry IPR039431

This domain can be found in the N terminus of the Vta1 protein, which is a class E vacuolar protein sorting (VPS) protein required for the formation of the multivesicular body (MVB) [ PUBMED:14701806 ]. Proteins containing this domain also include Vta1 homologues, such as SBP1 from humans and LIP5 from Arabidopsis thaliana [ PUBMED:16505166 ]. This domain can also be found in plant callose synthase, which is involved in callose synthesis at the forming cell plate during cytokinesis [ PUBMED:11283334 ].

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 and the UniProtKB 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
(134)
Full
(3103)
Representative proteomes UniProt
(5018)
RP15
(446)
RP35
(1409)
RP55
(2470)
RP75
(3322)
Jalview View  View  View  View  View  View  View 
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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
(134)
Full
(3103)
Representative proteomes UniProt
(5018)
RP15
(446)
RP35
(1409)
RP55
(2470)
RP75
(3322)
Alignment:
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Sequence:
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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
(134)
Full
(3103)
Representative proteomes UniProt
(5018)
RP15
(446)
RP35
(1409)
RP55
(2470)
RP75
(3322)
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.

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_5537 (release 7.5)
Previous IDs: DUF605;
Type: Family
Sequence Ontology: SO:0100021
Author: Mifsud W , Mistry J , Wood V
Number in seed: 134
Number in full: 3103
Average length of the domain: 137.60 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 15.59 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.8 26.8
Trusted cut-off 27.2 27.0
Noise cut-off 26.7 26.6
Model length: 145
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Selections

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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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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 Vta1 domain has been found. There are 13 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A096MKH2 View 3D Structure Click here
A0A0P0V3M1 View 3D Structure Click here
A0A0P0VH06 View 3D Structure Click here
A0A0P0VRQ2 View 3D Structure Click here
A0A0P0VSN8 View 3D Structure Click here
A0A0P0X1F9 View 3D Structure Click here
A0A0R0EGR0 View 3D Structure Click here
A0A0R0F7F5 View 3D Structure Click here
A0A0R0IMN2 View 3D Structure Click here
A0A0R0ISM0 View 3D Structure Click here
A0A0R0IV27 View 3D Structure Click here
A0A0R0K4H8 View 3D Structure Click here
A0A0R0KAY0 View 3D Structure Click here
A0A1D6GWW8 View 3D Structure Click here
A0A1D6HQB0 View 3D Structure Click here
A0A1D6JMD5 View 3D Structure Click here
A0A1D6LIZ6 View 3D Structure Click here
A0A1D6LMB0 View 3D Structure Click here
A0A1D6LXR8 View 3D Structure Click here
A0A1D6LXS2 View 3D Structure Click here
A0A1D6NNC6 View 3D Structure Click here
A0A1D6NNZ3 View 3D Structure Click here
A0A1D6NZK8 View 3D Structure Click here
A0A1R3LAC8 View 3D Structure Click here
A0A2R8RJY3 View 3D Structure Click here
A0A368UHV8 View 3D Structure Click here
A4HSJ6 View 3D Structure Click here
B9ZSH9 View 3D Structure Click here
I1JJE3 View 3D Structure Click here
I1KZH4 View 3D Structure Click here
I1M2S4 View 3D Structure Click here
I1M6L7 View 3D Structure Click here
I1N0X8 View 3D Structure Click here
K7MDN8 View 3D Structure Click here
K7ME49 View 3D Structure Click here
K7MVL3 View 3D Structure Click here
O13703 View 3D Structure Click here
Q06263 View 3D Structure Click here
Q3B724 View 3D Structure Click here
Q4CXG7 View 3D Structure Click here
Q4DBY8 View 3D Structure Click here
Q55B11 View 3D Structure Click here
Q5A3J5 View 3D Structure Click here
Q5Z4L5 View 3D Structure Click here
Q8GW77 View 3D Structure Click here
Q9AUE0 View 3D Structure Click here
Q9CR26 View 3D Structure Click here
Q9LUD7 View 3D Structure Click here
Q9LXT9 View 3D Structure Click here
Q9LYS6 View 3D Structure Click here
Q9NP79 View 3D Structure Click here
Q9SHJ3 View 3D Structure Click here
Q9SL03 View 3D Structure Click here
Q9SZ15 View 3D Structure Click here
Q9W0B3 View 3D Structure Click here