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134  structures 1145  species 3  interactions 4424  sequences 96  architectures

Family: Vps4_C (PF09336)

Summary: Vps4 C terminal oligomerisation domain

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Vps4 C terminal oligomerisation domain Provide feedback

This domain is found at the C terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation [1].

Literature references

  1. Vajjhala PR, Wong JS, To HY, Munn AL; , FEBS J. 2006;273:2357-2373.: The beta domain is required for Vps4p oligomerization into a functionally active ATPase. PUBMED:16704411 EPMC:16704411


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015415

This domain is found at the C-terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation [PUBMED:16704411].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan AAA_lid (CL0671), which has the following description:

Many AAA+ proteins have a C-terminal alpha-helical bundle in addition to the AAA core [1]. The functional roles of the helical bundle are varied and include the formation of a lid over the nucleotide binding site and mediation of subunit interactions in oligomeric protein complexes [1].

The clan contains the following 22 members:

AAA_assoc_2 AAA_lid_1 AAA_lid_10 AAA_lid_11 AAA_lid_2 AAA_lid_3 AAA_lid_4 AAA_lid_5 AAA_lid_6 AAA_lid_7 AAA_lid_8 AAA_lid_9 CbbQ_C ClpB_D2-small Dpoe2NT MCM_lid Mg_chelatase_C ORC4_C PCP_red TIP49_C UVR Vps4_C

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...

View options

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
(142)
Full
(4424)
Representative proteomes UniProt
(6414)
NCBI
(9264)
Meta
(24)
RP15
(1220)
RP35
(2332)
RP55
(3400)
RP75
(4129)
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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
(142)
Full
(4424)
Representative proteomes UniProt
(6414)
NCBI
(9264)
Meta
(24)
RP15
(1220)
RP35
(2332)
RP55
(3400)
RP75
(4129)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(142)
Full
(4424)
Representative proteomes UniProt
(6414)
NCBI
(9264)
Meta
(24)
RP15
(1220)
RP35
(2332)
RP55
(3400)
RP75
(4129)
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_8681 (release 20.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mistry J , Wood V
Number in seed: 142
Number in full: 4424
Average length of the domain: 53.50 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 9.14 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.3 21.3
Trusted cut-off 21.3 21.3
Noise cut-off 21.2 21.2
Model length: 61
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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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Interactions

There are 3 interactions for this family. More...

Vta1 AAA Vps4_C

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 Vps4_C domain has been found. There are 134 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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