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0  structures 283  species 0  interactions 612  sequences 31  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


External 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

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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(24)
Full
(612)
Representative proteomes NCBI
(603)
Meta
(4)
RP15
(180)
RP35
(269)
RP55
(381)
RP75
(445)
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Format an alignment

  Seed
(24)
Full
(612)
Representative proteomes NCBI
(603)
Meta
(4)
RP15
(180)
RP35
(269)
RP55
(381)
RP75
(445)
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
(24)
Full
(612)
Representative proteomes NCBI
(603)
Meta
(4)
RP15
(180)
RP35
(269)
RP55
(381)
RP75
(445)
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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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
Author: Mistry J, Wood V
Number in seed: 24
Number in full: 612
Average length of the domain: 104.40 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 11.03 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.2 21.2
Trusted cut-off 21.2 21.2
Noise cut-off 21.1 21.1
Model length: 109
Family (HMM) version: 4
Download: download the raw HMM for this family

Species distribution

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