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203  structures 1508  species 0  interactions 7181  sequences 145  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 and the UniProtKB 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
(124)
Full
(7181)
Representative proteomes UniProt
(12557)
RP15
(1376)
RP35
(3188)
RP55
(5795)
RP75
(7732)
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HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(124)
Full
(7181)
Representative proteomes UniProt
(12557)
RP15
(1376)
RP35
(3188)
RP55
(5795)
RP75
(7732)
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
(124)
Full
(7181)
Representative proteomes UniProt
(12557)
RP15
(1376)
RP35
(3188)
RP55
(5795)
RP75
(7732)
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_8681 (release 20.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mistry J , Wood V
Number in seed: 124
Number in full: 7181
Average length of the domain: 53.70 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 9.17 %

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 21.3 21.3
Trusted cut-off 21.3 21.3
Noise cut-off 21.2 21.2
Model length: 61
Family (HMM) version: 12
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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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 203 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
A0A0B4KFL3 View 3D Structure Click here
A0A0R0H530 View 3D Structure Click here
A0A0R4IPK7 View 3D Structure Click here
A0A1D6FE31 View 3D Structure Click here
A0A1D6KUI9 View 3D Structure Click here
A0A1D6MTY9 View 3D Structure Click here
A0A1D6NFE4 View 3D Structure Click here
A0A1D8PU31 View 3D Structure Click here
A4HVM4 View 3D Structure Click here
A4HWQ5 View 3D Structure Click here
A4I4W4 View 3D Structure Click here
B2RYN7 View 3D Structure Click here
B3DGU1 View 3D Structure Click here
B7E390 View 3D Structure Click here
B8A2W9 View 3D Structure Click here
C0P882 View 3D Structure Click here
D3ZYS4 View 3D Structure Click here
F4JEX5 View 3D Structure Click here
I1KH58 View 3D Structure Click here
I1KV99 View 3D Structure Click here
I1L8Z3 View 3D Structure Click here
I1LKT2 View 3D Structure Click here
I1LRE7 View 3D Structure Click here
I1LTU5 View 3D Structure Click here
I1LZ82 View 3D Structure Click here
I1MCK1 View 3D Structure Click here
I1N3G3 View 3D Structure Click here
K7KP02 View 3D Structure Click here
K7MX18 View 3D Structure Click here
O13764 View 3D Structure Click here
O16299 View 3D Structure Click here
O43078 View 3D Structure Click here
O75351 View 3D Structure Click here
O75449 View 3D Structure Click here
P25694 View 3D Structure Click here
P39955 View 3D Structure Click here
P40328 View 3D Structure Click here
P46462 View 3D Structure Click here
P46467 View 3D Structure Click here
P52917 View 3D Structure Click here
P54811 View 3D Structure Click here
P54812 View 3D Structure Click here
P55072 View 3D Structure Click here
P90532 View 3D Structure Click here
Q01853 View 3D Structure Click here
Q07844 View 3D Structure Click here
Q08BZ6 View 3D Structure Click here
Q09803 View 3D Structure Click here
Q29RA2 View 3D Structure Click here
Q4CSI8 View 3D Structure Click here
Q4CXI9 View 3D Structure Click here
Q4D4Y6 View 3D Structure Click here
Q4D5V3 View 3D Structure Click here
Q4D731 View 3D Structure Click here
Q4DFV8 View 3D Structure Click here
Q4DIH8 View 3D Structure Click here
Q4DLN7 View 3D Structure Click here
Q4DNT6 View 3D Structure Click here
Q4DTR4 View 3D Structure Click here
Q4E658 View 3D Structure Click here
Q4KLL7 View 3D Structure Click here
Q4QPP5 View 3D Structure Click here
Q503S1 View 3D Structure Click here
Q54KQ7 View 3D Structure Click here
Q54PT2 View 3D Structure Click here
Q55GC3 View 3D Structure Click here
Q58556 View 3D Structure Click here
Q59WG3 View 3D Structure Click here
Q5AG40 View 3D Structure Click here
Q5HY92 View 3D Structure Click here
Q5XIK7 View 3D Structure Click here
Q5ZEN9 View 3D Structure Click here
Q658G8 View 3D Structure Click here
Q6E0V2 View 3D Structure Click here
Q6ETH5 View 3D Structure Click here
Q6GX84 View 3D Structure Click here
Q6NW58 View 3D Structure Click here
Q6PIW4 View 3D Structure Click here
Q793F9 View 3D Structure Click here
Q7KN62 View 3D Structure Click here
Q7ZU99 View 3D Structure Click here
Q8BPY9 View 3D Structure Click here
Q8IKQ5 View 3D Structure Click here
Q8K0T4 View 3D Structure Click here
Q8S118 View 3D Structure Click here
Q8VEJ9 View 3D Structure Click here
Q9BL83 View 3D Structure Click here
Q9BW62 View 3D Structure Click here
Q9ERZ6 View 3D Structure Click here
Q9P3U2 View 3D Structure Click here
Q9QYY8 View 3D Structure Click here
Q9SEX2 View 3D Structure Click here
Q9UBP0 View 3D Structure Click here
Q9UN37 View 3D Structure Click here
Q9WV86 View 3D Structure Click here
Q9Y162 View 3D Structure Click here
Q9ZNT0 View 3D Structure Click here