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2  structures 1432  species 0  interactions 6116  sequences 121  architectures

Family: V-SNARE_C (PF12352)

Summary: Snare region anchored in the vesicle membrane C-terminus

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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.

Snare region anchored in the vesicle membrane C-terminus Provide feedback

Within the SNARE proteins interactions in the C-terminal half of the SNARE helix are critical to the driving of membrane fusion; whereas interactions in the N-terminal half of the SNARE domain are important for promoting priming or docking of the vesicle PF05008.

Literature references

  1. Yang HJ, Nakanishi H, Liu S, McNew JA, Neiman AM;, J Cell Biol. 2008;183:1089-1100.: Binding interactions control SNARE specificity in vivo. PUBMED:19064671 EPMC:19064671


Internal database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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 Traffic (CL0147), which has the following description:

The members of this clan are involved in protein trafficking. The Sec20 family are integral membrane proteins involved in ER to Golgi transport [1] and V-SNARES are involved in membrane fusion [2].

The clan contains the following 3 members:

Sec20 V-SNARE V-SNARE_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
(20)
Full
(6116)
Representative proteomes UniProt
(11046)
RP15
(1185)
RP35
(2891)
RP55
(4903)
RP75
(6587)
Jalview View  View  View  View  View  View  View 
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
(20)
Full
(6116)
Representative proteomes UniProt
(11046)
RP15
(1185)
RP35
(2891)
RP55
(4903)
RP75
(6587)
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
(20)
Full
(6116)
Representative proteomes UniProt
(11046)
RP15
(1185)
RP35
(2891)
RP55
(4903)
RP75
(6587)
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: manual
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 20
Number in full: 6116
Average length of the domain: 65.10 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 26.56 %

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 27.1 27.1
Trusted cut-off 27.1 27.1
Noise cut-off 27.0 27.0
Model length: 66
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
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 V-SNARE_C domain has been found. There are 2 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
A0A0R0K964 View 3D Structure Click here
A0A0R0L2Z2 View 3D Structure Click here
A0A1D6H9U2 View 3D Structure Click here
A0A1D6NEE8 View 3D Structure Click here
A0A1D8PJW1 View 3D Structure Click here
A0A2R8Q5I2 View 3D Structure Click here
A4HT91 View 3D Structure Click here
A4HY97 View 3D Structure Click here
A4I0L2 View 3D Structure Click here
A4ICZ3 View 3D Structure Click here
B4FC18 View 3D Structure Click here
B4FSS1 View 3D Structure Click here
B6TMP4 View 3D Structure Click here
B6TUE7 View 3D Structure Click here
B6TWQ1 View 3D Structure Click here
B7Z0M0 View 3D Structure Click here
C0PCF2 View 3D Structure Click here
C6T736 View 3D Structure Click here
C6TGN3 View 3D Structure Click here
E9QCD0 View 3D Structure Click here
I1J5U5 View 3D Structure Click here
I1J7S6 View 3D Structure Click here
I1JE83 View 3D Structure Click here
I1JKS2 View 3D Structure Click here
I1KCV4 View 3D Structure Click here
I1KGV3 View 3D Structure Click here
I1KVK0 View 3D Structure Click here
I1KXX2 View 3D Structure Click here
I1N120 View 3D Structure Click here
K7KZ90 View 3D Structure Click here
K7LFP0 View 3D Structure Click here
O14653 View 3D Structure Click here
O18230 View 3D Structure Click here
O22151 View 3D Structure Click here
O35165 View 3D Structure Click here
O35166 View 3D Structure Click here
O88384 View 3D Structure Click here
O88630 View 3D Structure Click here
O89116 View 3D Structure Click here
O95249 View 3D Structure Click here
P25385 View 3D Structure Click here
P38736 View 3D Structure Click here
P41941 View 3D Structure Click here
P58200 View 3D Structure Click here
P78768 View 3D Structure Click here
Q04338 View 3D Structure Click here
Q09835 View 3D Structure Click here
Q1PDQ2 View 3D Structure Click here
Q21499 View 3D Structure Click here
Q4CNX7 View 3D Structure Click here
Q4CVD2 View 3D Structure Click here
Q4D726 View 3D Structure Click here
Q4DSB4 View 3D Structure Click here
Q4DXS9 View 3D Structure Click here
Q4E3T0 View 3D Structure Click here
Q54CK6 View 3D Structure Click here
Q54R67 View 3D Structure Click here
Q553C3 View 3D Structure Click here
Q55FD0 View 3D Structure Click here
Q55GN5 View 3D Structure Click here
Q5AGY7 View 3D Structure Click here
Q5AIB3 View 3D Structure Click here
Q62931 View 3D Structure Click here
Q6AT61 View 3D Structure Click here
Q6EQ07 View 3D Structure Click here
Q6Z2M4 View 3D Structure Click here
Q6Z9I2 View 3D Structure Click here
Q7SY45 View 3D Structure Click here
Q7T366 View 3D Structure Click here
Q8IIP9 View 3D Structure Click here
Q8S0N4 View 3D Structure Click here
Q8S9S2 View 3D Structure Click here
Q95ZW1 View 3D Structure Click here
Q96AJ9 View 3D Structure Click here
Q9FK28 View 3D Structure Click here
Q9JI51 View 3D Structure Click here
Q9LMP7 View 3D Structure Click here
Q9LNH6 View 3D Structure Click here
Q9LRP1 View 3D Structure Click here
Q9LVP9 View 3D Structure Click here
Q9P7G5 View 3D Structure Click here
Q9SEL5 View 3D Structure Click here
Q9SEL6 View 3D Structure Click here
Q9SJL6 View 3D Structure Click here
Q9UEU0 View 3D Structure Click here
Q9VE50 View 3D Structure Click here
Q9VRL2 View 3D Structure Click here
Q9W0N6 View 3D Structure Click here