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0  structures 38  species 0  interactions 51  sequences 2  architectures

Family: VD10_N (PF08476)

Summary: Viral D10 N-terminal

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Viral D10 N-terminal Provide feedback

This domain is found on the N-terminus of the viral protein D10 (VD10) and the related MutT motif proteins [2]. The VD10 protein is probably essential for virus replication [1] and is often found to the N-terminus of a PF00293 domain.

Literature references

  1. Binns MM, Britton BS, Mason C, Boursnell ME; , J Gen Virol 1990;71:2873-2881.: Analysis of the fowlpox virus genome region corresponding to the vaccinia virus D6 to A1 region: location of, and variation in, non-essential genes in poxviruses. PUBMED:2177083 EPMC:2177083

  2. Shors T, Keck JG, Moss B; , J Virol 1999;73:791-796.: Down regulation of gene expression by the vaccinia virus D10 protein. PUBMED:9847390 EPMC:9847390


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013683

This domain is found on the N terminus of the viral protein D10 (VD10) and the related MutT motif proteins [PUBMED:9847390]. The VD10 protein is probably essential for virus replication [PUBMED:2177083] and is often found to the N terminus of a NUDIX hydrolase domain.

Previous studies indicated that the vaccinia virus D10 protein, which is conserved in all sequenced poxviruses, participates in the rapid turnover of host and viral mRNAs. D10 contains a motif present in the family of Nudix/MutT enzymes, a subset of which has been shown to enhance mRNA turnover in eukaryotic cells through cleavage of the 5' cap (m7GpppNm-). The D10 protein possesses an intrinsic activity that liberates m7GDP from capped RNA substrates. Furthermore, point mutations in the Nudix/MutT motif abolished decapping activity. D10 has a strong affinity for capped RNA substrates of lengths of 24-309 nt were decapped efficiently. The poxviruses represent the only virus family shown to encode a Nudix hydrolase-decapping enzyme. The activity of the decapping and capping enzymes, accelerate mRNA turnover and helps to eliminate competing host mRNAs allowing stage-specific synthesis of viral proteins [PUBMED:17283339].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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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...

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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.

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(7)
Full
(51)
Representative proteomes NCBI
(39)
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RP55
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RP75
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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
(7)
Full
(51)
Representative proteomes NCBI
(39)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Alignment:
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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
(7)
Full
(51)
Representative proteomes NCBI
(39)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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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.

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_4155 (release 18.0)
Previous IDs: none
Type: Family
Author: Wuster A
Number in seed: 7
Number in full: 51
Average length of the domain: 44.80 aa
Average identity of full alignment: 58 %
Average coverage of the sequence by the domain: 18.60 %

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 25.0 25.0
Trusted cut-off 52.7 52.7
Noise cut-off 21.0 17.7
Model length: 45
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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