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0  structures 53  species 0  interactions 718  sequences 4  architectures

Family: US22 (PF02393)

Summary: US22 like

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US22 like Provide feedback

US22 proteins have been found across many animal DNA viruses and some vertebrates [3]. The name sake of this family US22 P09722 is an early nuclear protein that is secreted from cells [2]. The US22 family may have a role in virus replication and pathogenesis [1]. Domain analysis showed that US22 proteins usually contain two copies of conserved modules which is homologous to several other families like SMI1 and SYD (commonly called SUKH superfamily) [3]. Bacterial operon analysis revealed that all bacterial SUKH members function as immunity proteins against various toxins. Thus US22 family is predicted to counter diverse anti-viral responses by interacting with specific host proteins [3].

Literature references

  1. Hanson LK, Dalton BL, Karabekian Z, Farrell HE, Rawlinson WD, Stenberg RM, Campbell AE; , Virology 1999;260:156-164.: Transcriptional analysis of the murine cytomegalovirus HindIII-I region: identification of a novel immediate-early gene region. PUBMED:10405367 EPMC:10405367

  2. Efstathiou S, Lawrence GL, Brown CM, Barrell BG; , J Gen Virol 1992;73:1661-1671.: Identification of homologues to the human cytomegalovirus US22 gene family in human herpesvirus 6. PUBMED:1321206 EPMC:1321206

  3. Zhang D, Iyer LM, Aravind L;, Nucleic Acids Res. 2011;39:4532-4552.: A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. PUBMED:21306995 EPMC:21306995


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003360

Herpesviruses are large and complex DNA viruses, widely found in nature. Human cytomegalovirus (HCMV), an important human pathogen, defines the betaherpesvirus family. Mouse cytomegalovirus (MCMV) and rat cytomegalovirus serve as biological model systems for HCMV. HCMV, MCMV, and rat CMV display the largest genomes among the herpesviruses and are essentially co-linear over the central 180 kb of the 230-kb genomes. Betaherpesviruses, which include the CMVs as well as human herpesviruses 6 and 7, differ from alpha- and gammaherpesviruses by the presence of additional gene families such as the US22 gene family, which are mainly clustered at the ends of the genome. The US22 family was first described in HCMV. This gene family comprises 12 members in both HCMV and MCMV and 11 in rat CMV [PUBMED:12719548].

Members of the US22 gene family are characterised by stretches of hydrophobic and charged residues as well as up to four conserved sequence motifs which are specific for betaherpesviruses. Motif I differs between the HCMV US and UL family members [PUBMED:8709220]. Motifs I and II have consensus sequences, while motifs III and IV are less well defined but have stretches of non-polar residues [PUBMED:10405367, PUBMED:8523552]. Members of this gene family are widely divergent in function and their involvement in viral replication [PUBMED:12719548].

This entry contains US22 family members from the Cytomegalovirus, Muromegalovirus and the Roseolovirus taxonomic groups.

The name sake of this family US22 is an early nuclear protein that is secreted from cells [PUBMED:1321206]. The US22 family may have a role in virus replication and pathogenesis [PUBMED:10405367].

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 SUKH (CL0526), which has the following description:

SUKH superfamily unites a diverse group of proteins including Smi1/Knr4, PGs2, Fbxo3, Skip16, Syd, herpesviral US22, IRS1 and TRS1, and their bacterial homologs [1].

The clan contains the following 7 members:

SMI1_KNR4 SUKH-3 SUKH-4 SUKH_5 SUKH_6 Syd US22

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.

  Seed
(36)
Full
(718)
Representative proteomes NCBI
(635)
Meta
(0)
RP15
(3)
RP35
(3)
RP55
(8)
RP75
(8)
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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
(36)
Full
(718)
Representative proteomes NCBI
(635)
Meta
(0)
RP15
(3)
RP35
(3)
RP55
(8)
RP75
(8)
Alignment:
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Sequence:
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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
(36)
Full
(718)
Representative proteomes NCBI
(635)
Meta
(0)
RP15
(3)
RP35
(3)
RP55
(8)
RP75
(8)
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.

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_1016 (release 5.2)
Previous IDs: none
Type: Family
Author: Bashton M, Bateman A, Zhang D, Aravind L
Number in seed: 36
Number in full: 718
Average length of the domain: 131.60 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 44.51 %

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 35.0 35.0
Trusted cut-off 35.1 35.0
Noise cut-off 33.5 34.8
Model length: 125
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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