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0  structures 306  species 0  interactions 567  sequences 19  architectures

Family: Vps54_N (PF10475)

Summary: Vacuolar-sorting protein 54, of GARP complex

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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.

Vacuolar-sorting protein 54, of GARP complex Provide feedback

This is a family of vacuolar-sorting proteins 54, from eukaryotes. Along with VPS52 and VPS53 this forms the Golgi-associated retrograde protein complex GARP [1]. VPS54 is separated into N- and C-terminal regions each of which has a different function. This N-terminal family of is important for GARP complex assembly and stability, whereas the C-terminal domain, PF07928 brings about localisation to an early endocytic compartment [2].

Literature references

  1. Perez-Victoria FJ, Mardones GA, Bonifacino JS;, Mol Biol Cell. 2008;19:2350-2362.: Requirement of the human GARP complex for mannose 6-phosphate-receptor-dependent sorting of cathepsin D to lysosomes. PUBMED:18367545 EPMC:18367545

  2. Quenneville NR, Chao TY, McCaffery JM, Conibear E;, Mol Biol Cell. 2006;17:1859-1870.: Domains within the GARP subunit Vps54 confer separate functions in complex assembly and early endosome recognition. PUBMED:16452629 EPMC:16452629


This tab holds annotation information from the InterPro database.

InterPro entry IPR019515

This entry represents Vacuolar protein sorting-associated protein 54, and is thought to be involved in retrograde transport from early and late endosomes to late Golgi found in eukaryotes, but its function is not known.

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 Vps51 (CL0295), which has the following description:

This clan includes an N-terminal domain from several vesicle transport proteins that are related to Vps51.

The clan contains the following 17 members:

COG2 COG5 COG6 Dor1 Exo70 Exo84_C Sec15 Sec3_C Sec3_C_2 Sec5 Sec6 Sec8_exocyst Vps51 Vps52 Vps53_N Vps54_N Zw10

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
(10)
Full
(567)
Representative proteomes UniProt
(1066)
NCBI
(2738)
Meta
(7)
RP15
(182)
RP35
(316)
RP55
(441)
RP75
(529)
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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
(10)
Full
(567)
Representative proteomes UniProt
(1066)
NCBI
(2738)
Meta
(7)
RP15
(182)
RP35
(316)
RP55
(441)
RP75
(529)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(10)
Full
(567)
Representative proteomes UniProt
(1066)
NCBI
(2738)
Meta
(7)
RP15
(182)
RP35
(316)
RP55
(441)
RP75
(529)
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: TreeFam_TF106152
Previous IDs: DUF2450;
Type: Family
Author: Buljan M, Coggill P
Number in seed: 10
Number in full: 567
Average length of the domain: 219.90 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 24.54 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 291
Family (HMM) version: 7
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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