Summary: Vps16, C-terminal region
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Vps16, C-terminal region Provide feedback
This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast [1]. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport [2]. The role of VPS16 in this complex is not known.
Literature references
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Rojo E, Gillmor CS, Kovaleva V, Somerville CR, Raikhel NV; , Dev Cell 2001;1:303-310.: VACUOLELESS1 is an essential gene required for vacuole formation and morphogenesis in Arabidopsis. PUBMED:11702788 EPMC:11702788
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Peterson MR, Emr SD; , Traffic 2001;2:476-486.: The class C Vps complex functions at multiple stages of the vacuolar transport pathway. PUBMED:11422941 EPMC:11422941
Internal database links
SCOOP: | Clathrin |
This tab holds annotation information from the InterPro database.
InterPro entry IPR006925
Vps16 forms part of the Class C vacuolar protein sorting (Vps) complex. It is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast [PUBMED:11702788]. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport [PUBMED:11422941]. The role of VPS16 in this complex is not known.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | cytoplasm (GO:0005737) |
Biological process | intracellular protein transport (GO:0006886) |
Domain organisation
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Alignments
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Seed (4) |
Full (1771) |
Representative proteomes | UniProt (3208) |
NCBI (3586) |
Meta (3) |
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RP15 (315) |
RP35 (763) |
RP55 (1218) |
RP75 (1788) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (4) |
Full (1771) |
Representative proteomes | UniProt (3208) |
NCBI (3586) |
Meta (3) |
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RP15 (315) |
RP35 (763) |
RP55 (1218) |
RP75 (1788) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
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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
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Curation
Seed source: | Pfam-B_6003 (release 7.6) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Kerrison ND |
Number in seed: | 4 |
Number in full: | 1771 |
Average length of the domain: | 257.10 aa |
Average identity of full alignment: | 28 % |
Average coverage of the sequence by the domain: | 37.39 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 320 | ||||||||||||
Family (HMM) version: | 13 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There is 1 interaction for this family. More...
Sec1Structures
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 Vps16_C domain has been found. There are 7 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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