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0  structures 830  species 0  interactions 1694  sequences 26  architectures

Family: T5orf172 (PF10544)

Summary: T5orf172 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.

T5orf172 domain Provide feedback

This domain was identified by Iyer and colleagues [1].

Literature references

  1. Iyer LM, Koonin EV, Aravind L; , Genome Biol 2002;3:RESEARCH0012.: Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors. PUBMED:11897024 EPMC:11897024


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR018306

This entry represents a DNA-binding domain found in bacteriophage T5, ORF172 [PUBMED:11897024]. The domain is related to the Bro-N and KilA-N domains that are widespread in large-DNA viruses infecting bacteria and eukaryotes [PUBMED:11897024].

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 GIY-YIG (CL0418), which has the following description:

Based on the analysis of genomic distribution, patterns of domain fusions and phylogenetic considerations for individual families, an evolutionary scenario is proposed that explains the emergence and development of the major branches of the GIY-YIG superfamily that links the Slx-type with the UvrC-like endonucleases. Most families appear to target DNA. The GIY-YIG domain has been quite successful in forming monomeric nucleases that utilise additional domains to recognise its DNA targets; this collection of domains can range from extremely simple DNA-binding elements (as in the case of I-TevI) to modules with independent enzymatic activities (as in the case of UvrC or the Penelope elements) [1].

The clan contains the following 4 members:

DUF123 GIY-YIG MUG113 T5orf172

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
(204)
Full
(1694)
Representative proteomes NCBI
(1844)
Meta
(598)
RP15
(747)
RP35
(823)
RP55
(896)
RP75
(930)
Jalview View  View  View  View  View  View  View  View 
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
(204)
Full
(1694)
Representative proteomes NCBI
(1844)
Meta
(598)
RP15
(747)
RP35
(823)
RP55
(896)
RP75
(930)
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
(204)
Full
(1694)
Representative proteomes NCBI
(1844)
Meta
(598)
RP15
(747)
RP35
(823)
RP55
(896)
RP75
(930)
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: Iyer LM
Previous IDs: none
Type: Domain
Author: Iyer LM, Bateman A
Number in seed: 204
Number in full: 1694
Average length of the domain: 92.50 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 29.87 %

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 20.0 20.0
Trusted cut-off 20.0 20.0
Noise cut-off 19.9 19.9
Model length: 100
Family (HMM) version: 4
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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Tree controls

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