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0  structures 52  species 0  interactions 301  sequences 5  architectures

Family: SVWC (PF15430)

Summary: Single domain von Willebrand factor type C

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Single domain von Willebrand factor type C Provide feedback

SVWC is a family of single-domain von Willebrand factor type C proteins from lower eukaryotes. The canonical pattern of most von Willebrand factor type C (VWC) domains is of ten cysteines, however this family, largely but not exclusively of arthropod proteins, contains only eight. SVWC family proteins respond to environmental challenges, such as bacterial infection and nutritional status. They also are involved in anti-viral immunity, and all of these functions seem linked to SVWC expression being induced by Dicer2.

Literature references

  1. Miyashita M, Otsuki J, Hanai Y, Nakagawa Y, Miyagawa H;, Toxicon. 2007;50:428-437.: Characterization of peptide components in the venom of the scorpion Liocheles australasiae (Hemiscorpiidae). PUBMED:17559900 EPMC:17559900

  2. Schwartz EF, Camargos TS, Zamudio FZ, Silva LP, Bloch C Jr, Caixeta F, Schwartz CA, Possani LD;, Toxicon. 2008;51:1499-1508.: Mass spectrometry analysis, amino acid sequence and biological activity of venom components from the Brazilian scorpion Opisthacanthus cayaporum. PUBMED:18502464 EPMC:18502464

  3. Ribeiro JM, Anderson JM, Manoukis NC, Meng Z, Francischetti IM;, BMC Genomics. 2011;12:136.: A further insight into the sialome of the tropical bont tick, Amblyomma variegatum. PUBMED:21362191 EPMC:21362191

  4. Chen YH, Jia XT, Zhao L, Li CZ, Zhang S, Chen YG, Weng SP, He JG;, Dev Comp Immunol. 2011;35:661-671.: Identification and functional characterization of Dicer2 and five single VWC domain proteins of Litopenaeus vannamei. PUBMED:21256150 EPMC:21256150


External 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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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(127)
Full
(301)
Representative proteomes NCBI
(307)
Meta
(0)
RP15
(34)
RP35
(41)
RP55
(86)
RP75
(121)
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HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(127)
Full
(301)
Representative proteomes NCBI
(307)
Meta
(0)
RP15
(34)
RP35
(41)
RP55
(86)
RP75
(121)
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
(127)
Full
(301)
Representative proteomes NCBI
(307)
Meta
(0)
RP15
(34)
RP35
(41)
RP55
(86)
RP75
(121)
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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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

This family is new in this Pfam release.

Seed source: Jackhmmer:P0C5F3
Previous IDs: none
Type: Family
Author: Coggill P
Number in seed: 127
Number in full: 301
Average length of the domain: 67.30 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 53.12 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.3 27.3
Noise cut-off 26.7 26.7
Model length: 65
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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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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