Summary: Vacuolar-sorting protein 54, of GARP complex
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 . 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 .
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
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
Internal database links
|SCOOP:||COG2 COG5 Dor1 Sec5 Sec8_exocyst Spc7 Vps51 Vps53_N Zw10|
|Similarity to PfamA using HHSearch:||Vps53_N|
This tab holds annotation information from the InterPro database.
InterPro entry IPR019515
This entry represents a domain found in vacuolar protein sorting-associated protein 54 (VPS54), which acts as component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN). VPS54 is required to tether the complex to the TGN. However, it is not involved in endocytic recycling [PUBMED:25799061].
Proteins containing this domain also includes VPS50 (also known as Syndetin), which is a component of the EARP complex that is involved in endocytic recycling. It is required to tether the EARP complex to recycling endosomes. Nevertheless, it is involved in retrograde transport from early and late endosomes to the TGN [PUBMED:25799061].
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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This clan includes an N-terminal domain from several vesicle transport proteins that are related to Vps51.
The clan contains the following 18 members:COG2 COG5 COG6 Dor1 Dsl1_N Exo70 Exo84_C Sec15 Sec3_C Sec3_C_2 Sec5 Sec6 Sec8_exocyst Vps51 Vps52 Vps53_N Vps54_N Zw10
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Author:||Buljan M, Coggill P|
|Number in seed:||10|
|Number in full:||794|
|Average length of the domain:||220.40 aa|
|Average identity of full alignment:||22 %|
|Average coverage of the sequence by the domain:||24.82 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
|Download:||download the raw HMM for this family|
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