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40  structures 2186  species 1  interaction 5614  sequences 33  architectures

Family: Y1_Tnp (PF01797)

Summary: Transposase IS200 like

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.

Transposase IS200 like Provide feedback

Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS200 from E. coli.

Literature references

  1. Brynestad S, Synstad B, Granum PE; , Microbiology 1997;143:2109-2115.: The Clostridium perfringens enterotoxin gene is on a transposable element in type A human food poisoning strains. PUBMED:9245800 EPMC:9245800

  2. Ronning DR, Guynet C, Ton-Hoang B, Perez ZN, Ghirlando R, Chandler M, Dyda F;, Mol Cell. 2005;20:143-154.: Active site sharing and subterminal hairpin recognition in a new class of DNA transposases. PUBMED:16209952 EPMC:16209952


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002686

Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This entry represents a domain found in transposases for IS200 from Escherichia coli [PUBMED:10471738].

More information about these proteins can be found at Protein of the Month: Transposase [PUBMED:].

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 HUH (CL0481), which has the following description:

This superfamily consists of families of transposases that use tyrosine as nucleophiles and contain a conserved HUH motif where U is a non-conserved hydrophobic residue. Particular examples are the Y1 and Y2 transposases. Y1 transposases come from the IS608 group and the Y2 from the IS91 group. These transposases are nucleases involved in initiating rolling-circle plasmid replication, in initiating replication of certain single-strand (ss) DNA viruses (Rep proteins), and in initiation of conjugative plasmid transfer (relaxases). The IS91 transposase contains two of the three conserved protein sequence motifs identified in RCR proteins, a His-hydrophobic-His (HUH) motif required for metal ion binding, and a YxxxY motif containing two conserved catalytic tyrosine residues. The HUH motif participates in coordinating divalent metal ions essential for catalysis. This clan is also known as the Transposase IS200-like whose members contain extra N-terminal hairpin and C-terminal helix, both or which are involved in dimerisation; there can be helix-swapping in the dimer.

The clan contains the following 2 members:

Y1_Tnp Y2_Tnp

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
(178)
Full
(5614)
Representative proteomes NCBI
(4727)
Meta
(578)
RP15
(388)
RP35
(819)
RP55
(1034)
RP75
(1185)
Jalview View  View  View  View  View  View  View  View 
HTML View    View  View  View  View     
PP/heatmap 1   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
(178)
Full
(5614)
Representative proteomes NCBI
(4727)
Meta
(578)
RP15
(388)
RP35
(819)
RP55
(1034)
RP75
(1185)
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
(178)
Full
(5614)
Representative proteomes NCBI
(4727)
Meta
(578)
RP15
(388)
RP35
(819)
RP55
(1034)
RP75
(1185)
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_1347 (release 4.2)
Previous IDs: Transposase_17;
Type: Family
Author: Bashton M, Bateman A
Number in seed: 178
Number in full: 5614
Average length of the domain: 98.60 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 68.64 %

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 20.6 20.6
Trusted cut-off 20.6 20.6
Noise cut-off 20.5 20.5
Model length: 121
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

Sunburst controls

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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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Interactions

There is 1 interaction for this family. More...

Y1_Tnp

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 Y1_Tnp domain has been found. There are 40 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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