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0  structures 337  species 0  interactions 1019  sequences 50  architectures

Family: VIT (PF08487)

Summary: Vault protein inter-alpha-trypsin domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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.

Vault protein inter-alpha-trypsin domain Provide feedback

Inter-alpha-trypsin inhibitors (ITIs) consist of one light chain and a variable set of heavy chains. ITIs play a role in extracellular matrix (ECM) stabilisation and tumour metastasis as well as in plasma protease inhibition [1]. The vault protein inter-alpha-trypsin (VIT) domain described here is found to the N-terminus of a von Willebrand factor type A domain (PF00092) in ITI heavy chains (ITIHs) and their precursors.

Literature references

  1. Himmelfarb M, Klopocki E, Grube S, Staub E, Klaman I, Hinzmann B, Kristiansen G, Rosenthal A, Durst M, Dahl E; , Cancer Lett 2004;204:69-77.: ITIH5, a novel member of the inter-alpha-trypsin inhibitor heavy chain family is downregulated in breast cancer. PUBMED:14744536 EPMC:14744536

  2. Mayne R, Ren ZX, Liu J, Cook T, Carson M, Narayana S;, Biochem Soc Trans. 1999;27:832-835.: VIT-1: the second member of a new branch of the von Willebrand factor A domain superfamily. PUBMED:10830112 EPMC:10830112


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013694

Inter-alpha-trypsin inhibitors (ITIs) consist of one light chain and a variable set of heavy chains. ITIs play a role in extracellular matrix (ECM) stabilisation and tumour metastasis as well as in plasma protease inhibition [PUBMED:14744536]. The vault protein inter-alpha-trypsin (VIT) domain described here is found to the N terminus of a von Willebrand factor type A domain (INTERPRO) in ITI heavy chains (ITIHs) and their precursors.

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 Cupin (CL0029), which has the following description:

This clan represents the conserved barrel domain of the 'cupin' superfamily [1] ('cupa' is the Latin term for a small barrel). The cupin fold is found in a wide variety of enzymes, but notably contains the non-enzymatic seed storage proteins also.

The clan contains the following 53 members:

2OG-Fe_Oxy_2 2OG-FeII_Oxy 2OG-FeII_Oxy_2 2OG-FeII_Oxy_3 2OG-FeII_Oxy_4 2OG-FeII_Oxy_5 3-HAO AraC_binding AraC_binding_2 AraC_N ARD Asp_Arg_Hydrox Auxin_BP CDO_I CENP-C_C CsiD Cupin_1 Cupin_2 Cupin_3 Cupin_4 Cupin_5 Cupin_6 Cupin_7 Cupin_8 dTDP_sugar_isom DUF1255 DUF1479 DUF1498 DUF1637 DUF1971 DUF386 DUF4437 Ectoine_synth EutQ FdtA FTO_NTD GPI HgmA HutD JmjC KduI MannoseP_isomer Ofd1_CTDD Oxygenase-NA PhyH Pirin Pirin_C PMI_typeI Pox_C4_C10 TauD Tet_JBP VIT VIT_2

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
(18)
Full
(1019)
Representative proteomes NCBI
(925)
Meta
(68)
RP15
(184)
RP35
(259)
RP55
(391)
RP75
(559)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(18)
Full
(1019)
Representative proteomes NCBI
(925)
Meta
(68)
RP15
(184)
RP35
(259)
RP55
(391)
RP75
(559)
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
(18)
Full
(1019)
Representative proteomes NCBI
(925)
Meta
(68)
RP15
(184)
RP35
(259)
RP55
(391)
RP75
(559)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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

Seed source: Pfam-B_2015 (release 18.0)
Previous IDs: none
Type: Family
Author: Wuster A
Number in seed: 18
Number in full: 1019
Average length of the domain: 115.20 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 13.23 %

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 21.3 21.3
Trusted cut-off 21.4 21.3
Noise cut-off 21.2 21.1
Model length: 118
Family (HMM) version: 5
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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