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0  structures 478  species 0  interactions 6888  sequences 223  architectures

Family: Helitron_like_N (PF14214)

Summary: Helitron helicase-like domain at N-terminus

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.

Helitron helicase-like domain at N-terminus Provide feedback

This family is found in Helitrons, recently recognised eukaryotic transposons that are predicted to amplify by a rolling-circle mechanism. In many instances a protein-coding gene is disrupted by their insertion.

Literature references

  1. Yang L, Bennetzen JL;, Proc Natl Acad Sci U S A. 2009;106:12832-12837.: Structure-based discovery and description of plant and animal Helitrons. PUBMED:19622734 EPMC:19622734


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR025476

This domain is found in Helitrons, recently recognised eukaryotic transposons that are predicted to amplify by a rolling-circle mechanism [ PUBMED:19622734 ]. In many instances a protein-coding gene is disrupted by their insertion.

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(79)
Full
(6888)
Representative proteomes UniProt
(11107)
RP15
(3609)
RP35
(5896)
RP55
(7603)
RP75
(8449)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(79)
Full
(6888)
Representative proteomes UniProt
(11107)
RP15
(3609)
RP35
(5896)
RP55
(7603)
RP75
(8449)
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
(79)
Full
(6888)
Representative proteomes UniProt
(11107)
RP15
(3609)
RP35
(5896)
RP55
(7603)
RP75
(8449)
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.

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: Jackhmmer:Q9S9S3
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Coggill P
Number in seed: 79
Number in full: 6888
Average length of the domain: 148.80 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 17.98 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.9 28.9
Trusted cut-off 28.9 28.9
Noise cut-off 28.8 28.8
Model length: 190
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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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The tree shows the occurrence of this domain across different species. More...

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0P0YAU8 View 3D Structure Click here
A0A0R0E6I2 View 3D Structure Click here
A0A0R0E7A5 View 3D Structure Click here
A0A0R0E7S8 View 3D Structure Click here
A0A0R0E8L7 View 3D Structure Click here
A0A0R0EDW2 View 3D Structure Click here
A0A0R0EEV0 View 3D Structure Click here
A0A0R0EF43 View 3D Structure Click here
A0A0R0EHY4 View 3D Structure Click here
A0A0R0EHZ1 View 3D Structure Click here
A0A0R0EJ52 View 3D Structure Click here
A0A0R0EJ90 View 3D Structure Click here
A0A0R0EJS1 View 3D Structure Click here
A0A0R0EJT3 View 3D Structure Click here
A0A0R0EUW0 View 3D Structure Click here
A0A0R0EW12 View 3D Structure Click here
A0A0R0EYP8 View 3D Structure Click here
A0A0R0EZF3 View 3D Structure Click here
A0A0R0EZH4 View 3D Structure Click here
A0A0R0F728 View 3D Structure Click here
A0A0R0F7N8 View 3D Structure Click here
A0A0R0F7Y8 View 3D Structure Click here
A0A0R0F962 View 3D Structure Click here
A0A0R0FB23 View 3D Structure Click here
A0A0R0FE33 View 3D Structure Click here
A0A0R0FF63 View 3D Structure Click here
A0A0R0FF69 View 3D Structure Click here
A0A0R0FFC7 View 3D Structure Click here
A0A0R0FFG3 View 3D Structure Click here
A0A0R0FFJ9 View 3D Structure Click here
A0A0R0FGN6 View 3D Structure Click here
A0A0R0FQD5 View 3D Structure Click here
A0A0R0FZX5 View 3D Structure Click here
A0A0R0G1Y7 View 3D Structure Click here
A0A0R0G348 View 3D Structure Click here
A0A0R0G3U0 View 3D Structure Click here
A0A0R0G4H1 View 3D Structure Click here
A0A0R0G5D7 View 3D Structure Click here
A0A0R0G5M5 View 3D Structure Click here
A0A0R0G9I6 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;