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0  structures 16  species 0  interactions 122  sequences 7  architectures

Family: TYA (PF01021)

Summary: Ty transposon capsid protein

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Ty transposon capsid protein Provide feedback

Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion protein of TYA and TYB. The TYA protein is analogous to the gag protein of retroviruses. TYA a is cleaved to form 46kd protein which can form mature virion like particles [1]. This entry corresponds to the capsid protein from Ty1 and Ty2 transposons.

Literature references

  1. Palmer KJ, Tichelaar W, Myers N, Burns NR, Butcher SJ, Kingsman AJ, Fuller SD, Saibil HR; , J Virol 1997;71:6863-6868.: Cryo-electron microscopy structure of yeast Ty retrotransposon virus-like particles. PUBMED:9261411 EPMC:9261411


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015820

Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion protein of TYA and TYB. The TYA protein is analogous to the gag protein of retroviruses. This signature defines TYA, found at the N terminus of the gag and gag-pol polyproteins of approximately 440 amino acids and 1755 amino acids in length respectively.

Yeast retrotransposon Ty1 produces its proteins as precursors that are subsequently cleaved by an aspartic protease encoded by the element. Cleavage of the gag and gag-Pol polyprotein precursors is a critical step in proliferation of retroviruses and retroelements. These cleavage events are essential for transposition as they release the active reverse transcriptase and integrase and they modify the structure of the virus-like particles in a way that is analogous to the morphological changes that occur during retrovirus core maturation [ PUBMED:9261411 , PUBMED:8971723 , PUBMED:8764068 ].

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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Pfam Clan

This family is a member of clan GAG-polyprotein (CL0523), which has the following description:

This superfamily is characterised by family members that are derived from retrotransposons of the copia-type.

The clan contains the following 10 members:

DUF1759 DUF4219 DUF4939 PNMA Retrotran_gag_2 Retrotran_gag_3 Retrotran_gag_4 Retrotrans_gag Ty3_capsid TYA

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...

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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
(6)
Full
(122)
Representative proteomes UniProt
(221)
RP15
(86)
RP35
(90)
RP55
(105)
RP75
(124)
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PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(6)
Full
(122)
Representative proteomes UniProt
(221)
RP15
(86)
RP35
(90)
RP55
(105)
RP75
(124)
Alignment:
Format:
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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
(6)
Full
(122)
Representative proteomes UniProt
(221)
RP15
(86)
RP35
(90)
RP55
(105)
RP75
(124)
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: Pfam-B_90 (release 3.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 6
Number in full: 122
Average length of the domain: 343.70 aa
Average identity of full alignment: 52 %
Average coverage of the sequence by the domain: 37.62 %

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 22.9 22.9
Trusted cut-off 22.9 22.9
Noise cut-off 22.8 22.8
Model length: 384
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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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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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
O13535 View 3D Structure Click here
O74302 View 3D Structure Click here
P0C2I2 View 3D Structure Click here
P0C2I3 View 3D Structure Click here
P0C2I4 View 3D Structure Click here
P0C2I5 View 3D Structure Click here
P0C2I6 View 3D Structure Click here
P0C2I8 View 3D Structure Click here
P0C2I9 View 3D Structure Click here
P0C2J0 View 3D Structure Click here
P0C2J1 View 3D Structure Click here
P0C2J3 View 3D Structure Click here
P0C2J4 View 3D Structure Click here
P0CX57 View 3D Structure Click here
P0CX58 View 3D Structure Click here
P0CX59 View 3D Structure Click here
P0CX60 View 3D Structure Click here
P0CX61 View 3D Structure Click here
P0CX62 View 3D Structure Click here
P0CX63 View 3D Structure Click here
P0CX64 View 3D Structure Click here
P0CX65 View 3D Structure Click here
P0CX66 View 3D Structure Click here
P0CX67 View 3D Structure Click here
P0CX68 View 3D Structure Click here
P0CX69 View 3D Structure Click here
P0CX70 View 3D Structure Click here
P0CX71 View 3D Structure Click here
P0CX72 View 3D Structure Click here
P0CX73 View 3D Structure Click here
P0CX74 View 3D Structure Click here
P0CX75 View 3D Structure Click here
P0CX76 View 3D Structure Click here
P25383 View 3D Structure Click here
P25384 View 3D Structure Click here
P47098 View 3D Structure Click here
P47099 View 3D Structure Click here
P47100 View 3D Structure Click here
Q03434 View 3D Structure Click here
Q03483 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;