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0  structures 239  species 0  interactions 5335  sequences 154  architectures

Family: DBD_Tnp_Mut (PF03108)

Summary: MuDR family transposase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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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.

MuDR family transposase Provide feedback

This region is found in plant proteins that are presumed to be the transposases for Mutator transposable elements [1,2]. These transposons contain two ORFs. The molecular function of this region is unknown.

Literature references

  1. Hershberger RJ, Benito MI, Hardeman KJ, Warren C, Chandler VL, Walbot V; , Genetics 1995;140:1087-1098.: Characterization of the major transcripts encoded by the regulatory MuDR transposable element of maize. PUBMED:7672579 EPMC:7672579

  2. Qin MM, Robertson DS, Ellingboe AH; , Genetics 1991;129:845-854.: Cloning of the Mutator transposable element MuA2, a putative regulator of somatic mutability of the a1-Mum2 allele in maize. PUBMED:1661256 EPMC:1661256


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004332

The plant MuDR transposase domain is present in plant (and some fungal) proteins that are presumed to be the transposases for Mutator transposable elements [ PUBMED:7672579 , PUBMED:1661256 ]. The function of these proteins is unknown.

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 WRKY-GCM1 (CL0274), which has the following description:

WRKY and GCM1 are metal chelating DNA-binding domains (DBD) which share a four stranded fold [1]. We present evidence that they share a stabilising core, which suggests a possible origin from a BED finger-like intermediate that was in turn ultimately derived from a C2H2 Zn-finger domain [1].

The clan contains the following 7 members:

AFT DBD_Tnp_Mut FAR1 FLYWCH GCM Gti1_Pac2 WRKY

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
(5)
Full
(5335)
Representative proteomes UniProt
(7755)
RP15
(451)
RP35
(2187)
RP55
(4883)
RP75
(5790)
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
(5)
Full
(5335)
Representative proteomes UniProt
(7755)
RP15
(451)
RP35
(2187)
RP55
(4883)
RP75
(5790)
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
(5)
Full
(5335)
Representative proteomes UniProt
(7755)
RP15
(451)
RP35
(2187)
RP55
(4883)
RP75
(5790)
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_271 (release 6.5)
Previous IDs: MuDR;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 5
Number in full: 5335
Average length of the domain: 65.5 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 12.19 %

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 25.0 25.0
Trusted cut-off 25.0 25.0
Noise cut-off 24.9 24.9
Model length: 67
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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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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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
A0A096QBS7 View 3D Structure Click here
A0A0N7KD41 View 3D Structure Click here
A0A0N7KL01 View 3D Structure Click here
A0A0P0V1Y9 View 3D Structure Click here
A0A0P0V3Z6 View 3D Structure Click here
A0A0P0VJD7 View 3D Structure Click here
A0A0P0VKK1 View 3D Structure Click here
A0A0P0W3R6 View 3D Structure Click here
A0A0P0WJG3 View 3D Structure Click here
A0A0P0X2B9 View 3D Structure Click here
A0A0P0XEI9 View 3D Structure Click here
A0A0P0XKK2 View 3D Structure Click here
A0A0P0YCI4 View 3D Structure Click here
A0A0R0GWJ1 View 3D Structure Click here
A0A0R0KPI3 View 3D Structure Click here
A0A1D6GDZ6 View 3D Structure Click here
A0A1D6GG53 View 3D Structure Click here
A0A1D6L4A8 View 3D Structure Click here
B9G5G8 View 3D Structure Click here
F4I6P0 View 3D Structure Click here
K7K378 View 3D Structure Click here
K7KH11 View 3D Structure Click here
K7L2J4 View 3D Structure Click here
K7L584 View 3D Structure Click here
K7LJE7 View 3D Structure Click here
K7LJS6 View 3D Structure Click here
K7MJV8 View 3D Structure Click here
K7N051 View 3D Structure Click here
K7N084 View 3D Structure Click here
K7N2H4 View 3D Structure Click here
K7N523 View 3D Structure Click here
K7VFE6 View 3D Structure Click here
Q0D9Q1 View 3D Structure Click here
Q0DAT1 View 3D Structure Click here
Q0E362 View 3D Structure Click here
Q0IZD0 View 3D Structure Click here
Q0JLJ6 View 3D Structure Click here
Q2QMP0 View 3D Structure Click here
Q9C702 View 3D Structure Click here
Q9C7V1 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;