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3  structures 1374  species 0  interactions 2991  sequences 86  architectures

Family: Vps39_2 (PF10367)

Summary: Vacuolar sorting protein 39 domain 2

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Vacuolar sorting protein 39 domain 2 Provide feedback

This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex [2]. Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [3]. In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange [1]. This domain is involved in localisation and in mediating the interactions of Vps39 with Vps11 [1].

Literature references

  1. Wurmser AE, Sato TK, Emr SD; , J Cell Biol. 2000;151:551-562.: New component of the vacuolar class C-Vps complex couples nucleotide exchange on the Ypt7 GTPase to SNARE-dependent docking and fusion. PUBMED:11062257 EPMC:11062257

  2. Nakamura N, Hirata A, Ohsumi Y, Wada Y; , J Biol Chem. 1997;272:11344-11349.: Vam2/Vps41p and Vam6/Vps39p are components of a protein complex on the vacuolar membranes and involved in the vacuolar assembly in the yeast Saccharomyces cerevisiae. PUBMED:9111041 EPMC:9111041

  3. Raymond CK, Howald-Stevenson I, Vater CA, Stevens TH; , Mol Biol Cell. 1992;3:1389-1402.: Morphological classification of the yeast vacuolar protein sorting mutants: evidence for a prevacuolar compartment in class E vps mutants. PUBMED:1493335 EPMC:1493335


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR019453

This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [ PUBMED:9111041 , PUBMED:1493335 ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange [ PUBMED:11062257 ]. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [ PUBMED:9545258 , PUBMED:11278302 ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [ PUBMED:11062257 ].

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
(18)
Full
(2991)
Representative proteomes UniProt
(4944)
RP15
(596)
RP35
(1409)
RP55
(2407)
RP75
(3154)
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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
(18)
Full
(2991)
Representative proteomes UniProt
(4944)
RP15
(596)
RP35
(1409)
RP55
(2407)
RP75
(3154)
Alignment:
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Sequence:
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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
(18)
Full
(2991)
Representative proteomes UniProt
(4944)
RP15
(596)
RP35
(1409)
RP55
(2407)
RP75
(3154)
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: Manual
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mistry J , Wood V
Number in seed: 18
Number in full: 2991
Average length of the domain: 103.20 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 10.68 %

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 24.7 24.7
Trusted cut-off 24.7 24.7
Noise cut-off 24.6 24.6
Model length: 109
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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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 Vps39_2 domain has been found. There are 3 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
A0A0G2JV19 View 3D Structure Click here
A0A0G2KA50 View 3D Structure Click here
A0A0R0LJG6 View 3D Structure Click here
A0A1D6L259 View 3D Structure Click here
A0A1D6LIJ2 View 3D Structure Click here
A0A1D8PGN0 View 3D Structure Click here
A0A1D8PPZ6 View 3D Structure Click here
A4I2P5 View 3D Structure Click here
A4IG72 View 3D Structure Click here
B0G127 View 3D Structure Click here
E7FDE3 View 3D Structure Click here
E9AGJ5 View 3D Structure Click here
F1RCV6 View 3D Structure Click here
F4I312 View 3D Structure Click here
I1JMK1 View 3D Structure Click here
I1LHS2 View 3D Structure Click here
K7KPC4 View 3D Structure Click here
K7L130 View 3D Structure Click here
O13955 View 3D Structure Click here
O74925 View 3D Structure Click here
Q07468 View 3D Structure Click here
Q10DX1 View 3D Structure Click here
Q1ZXS5 View 3D Structure Click here
Q3UR70 View 3D Structure Click here
Q4D5R9 View 3D Structure Click here
Q4D6I2 View 3D Structure Click here
Q4DMW3 View 3D Structure Click here
Q54LI4 View 3D Structure Click here
Q54ZD6 View 3D Structure Click here
Q75M25 View 3D Structure Click here
Q8ILL4 View 3D Structure Click here
Q8L5Y0 View 3D Structure Click here
Q8R5L3 View 3D Structure Click here
Q8WUH2 View 3D Structure Click here
Q96JC1 View 3D Structure Click here
Q9VEA2 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;