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0  structures 2419  species 0  interactions 7299  sequences 55  architectures

Family: DDE_Tnp_ISL3 (PF01610)

Summary: Transposase

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Transposase Provide feedback

Transposase proteins are necessary for efficient DNA transposition. Contains transposases for IS204 (Q50911) [1] IS1001 (Q06126) [2] IS1096 (Q50440) [3] and IS1165 Q48788 [4].

Literature references

  1. Vertes AA, Inui M, Kobayashi M, Kurusu Y, Yukawa H; , Mol Microbiol 1994;11:739-746.: Isolation and characterization of IS31831, a transposable element from Corynebacterium glutamicum. PUBMED:8196545 EPMC:8196545

  2. van der Zee A, Agterberg C, van Agterveld M, Peeters M, Mooi FR; , J Bacteriol 1993;175:141-147.: Characterization of IS1001, an insertion sequence element of Bordetella parapertussis. PUBMED:8093238 EPMC:8093238

  3. Cirillo JD, Barletta RG, Bloom BR, Jacobs WR Jr; , J Bacteriol 1991;173:7772-7780.: A novel transposon trap for mycobacteria: isolation and characterization of IS1096. PUBMED:1660454 EPMC:1660454

  4. Johansen E, Kibenich A; , Plasmid 1992;27:200-206.: Isolation and characterization of IS1165, an insertion sequence of Leuconostoc mesenteroides subsp. cremoris and other lactic acid bacteria. PUBMED:1325060 EPMC:1325060

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002560

This entry represents the DDE domain found in the IS204/IS1001/IS1096/IS116 transposases. Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [ PUBMED:8041625 , PUBMED:1310791 , PUBMED:1718819 ]. This family includes the IS204 [ PUBMED:8196545 ], IS1001 [ PUBMED:8093238 ], IS1096 [ PUBMED:1660454 ] and IS1165 [ PUBMED:1325060 ] transposases.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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.

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

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Representative proteomes UniProt

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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.

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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...


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_1015 (release 4.1)
Previous IDs: Transposase_12;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 56
Number in full: 7299
Average length of the domain: 166.20 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 59.16 %

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 23.0 23.0
Trusted cut-off 23.0 23.0
Noise cut-off 22.9 22.9
Model length: 240
Family (HMM) version: 20
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


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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
I6X9N4 View 3D Structure Click here
P71641 View 3D Structure Click here
P9WKH7 View 3D Structure Click here
Q2FW90 View 3D Structure Click here
V5QQS8 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;