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6  structures 154  species 0  interactions 226  sequences 6  architectures

Family: Herpes_alk_exo (PF01771)

Summary: Herpesvirus alkaline exonuclease

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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.

Herpesvirus alkaline exonuclease Provide feedback

This family includes various alkaline exonucleases from members of the herpesviridae. Alkaline exonuclease appears to have an important role in the replication of herpes simplex virus [1].

Literature references

  1. Banks LM, Halliburton IW, Purifoy DJ, Killington RA, Powell KL; , J Gen Virol 1985;66:1-14.: Studies on the herpes simplex virus alkaline nuclease: detection of type-common and type-specific epitopes on the enzyme. PUBMED:2578550 EPMC:2578550


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001616

Equid herpesvirus 1 (Equine herpesvirus 1) is a respiratory virus capable of causing abortion and neurological disease. Its complete DNA sequence has been determined [PUBMED:1318606] and the constituent genes found to be arranged co-linearly with those in the genomes of other alphaherpesviruses, namely Human herpesvirus 3 (HHV-3) and Human herpesvirus 1 (HHV-1) [PUBMED:1318606]. Comparisons of the predicted amino acid sequences have allowed functions of many EHV-1 proteins to be inferred.

For example, detailed analysis of HHV-1 and Human herpesvirus 2 (HHV-2) DNA has revealed an open reading frame sufficient to encode 626 amino acids for the HHV-1 alkaline exonuclease (620 amino acids for HHV-2) [PUBMED:3005609]. Comparison of the predicted amino acid sequences of the viral enzymes has revealed significant differences in the N-terminal portions of the proteins; nevertheless, their three-dimensional structures are believed to be similar.

Gene Ontology

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

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
(14)
Full
(226)
Representative proteomes NCBI
(307)
Meta
(11)
RP15
(14)
RP35
(14)
RP55
(18)
RP75
(18)
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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
(14)
Full
(226)
Representative proteomes NCBI
(307)
Meta
(11)
RP15
(14)
RP35
(14)
RP55
(18)
RP75
(18)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(14)
Full
(226)
Representative proteomes NCBI
(307)
Meta
(11)
RP15
(14)
RP35
(14)
RP55
(18)
RP75
(18)
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.

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_822 (release 4.2)
Previous IDs: none
Type: Family
Author: Bashton M, Bateman A
Number in seed: 14
Number in full: 226
Average length of the domain: 373.60 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 77.26 %

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 19.7 19.7
Trusted cut-off 19.7 19.7
Noise cut-off 19.6 19.6
Model length: 466
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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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 Herpes_alk_exo domain has been found. There are 6 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 seqence.

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