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607  structures 1439  species 0  interactions 8894  sequences 176  architectures

Family: JmjN (PF02375)

Summary: jmjN domain

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jmjN domain Provide feedback

No Pfam abstract.

Literature references

  1. Balciunas D, Ronne H; , Trends Biochem Sci 2000;25:274-276.: Evidence of domain swapping within the jumonji family of transcription factors. PUBMED:10838566 EPMC:10838566


This tab holds annotation information from the InterPro database.

InterPro entry IPR003349

The JmjN and JmjC domains are two non-adjacent domains which have been identified in the jumonji family of transcription factors. Although it was originally suggested that the JmjN and JmjC domains always co-occur and might form a single functional unit within the folded protein, the JmjC domain was latter found without the JmjN domain in organisms from bacteria to human [ PUBMED:10838566 , PUBMED:11165500 ].

JmJC domains are predicted to be metalloenzymes that adopt the cupin fold, and are candidates for enzymes that regulate chromatin remodelling. The cupin fold is a flattened beta-barrel structure containing two sheets of five antiparallel beta strands that form the walls of a zinc- binding cleft. JmjC domains were identified in numerous eukaryotic proteins containing domains typical of transcription factors, such as PHD, C2H2, ARID/BRIGHT and zinc fingers [ PUBMED:11165500 , PUBMED:12446723 ]. The JmjC has been shown to function in a histone demethylation mechanism that is conserved from yeast to human [ PUBMED:16362057 ].

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
(281)
Full
(8894)
Representative proteomes UniProt
(13036)
RP15
(1080)
RP35
(3118)
RP55
(6468)
RP75
(9132)
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
(281)
Full
(8894)
Representative proteomes UniProt
(13036)
RP15
(1080)
RP35
(3118)
RP55
(6468)
RP75
(9132)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(281)
Full
(8894)
Representative proteomes UniProt
(13036)
RP15
(1080)
RP35
(3118)
RP55
(6468)
RP75
(9132)
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: [1]
Previous IDs: jmjN;
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 281
Number in full: 8894
Average length of the domain: 34.20 aa
Average identity of full alignment: 46 %
Average coverage of the sequence by the domain: 2.86 %

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 26.0 26.0
Trusted cut-off 26.1 26.2
Noise cut-off 25.9 25.9
Model length: 34
Family (HMM) version: 20
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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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 JmjN domain has been found. There are 607 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 sequence.

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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
A0A0G2JTU9 View 3D Structure Click here
A0A0G2K5I7 View 3D Structure Click here
A0A0G2K6G9 View 3D Structure Click here
A0A0P0X1F1 View 3D Structure Click here
A0A0P0Y7A9 View 3D Structure Click here
A0A0R0IEN8 View 3D Structure Click here
A0A0R0J5F2 View 3D Structure Click here
A0A0R0L547 View 3D Structure Click here
A0A1D6G6Q6 View 3D Structure Click here
A0A1D6GT42 View 3D Structure Click here
A0A1D6GXC6 View 3D Structure Click here
A0A1D6HGP8 View 3D Structure Click here
A0A1D6HR86 View 3D Structure Click here
A0A1D6IVJ9 View 3D Structure Click here
A0A1D6K9X2 View 3D Structure Click here
A0A1D6LWC4 View 3D Structure Click here
A0A1D6M0J5 View 3D Structure Click here
A0A1D6MB23 View 3D Structure Click here
A0A1D6P7I3 View 3D Structure Click here
A0A1D6PJW6 View 3D Structure Click here
A0A1D6QB64 View 3D Structure Click here
A0A1D6QB77 View 3D Structure Click here
A0A1D6QBK5 View 3D Structure Click here
A0A1D8PL24 View 3D Structure Click here
A0A1D8PLL0 View 3D Structure Click here
A0A1D8PLN0 View 3D Structure Click here
A0A1P8AP94 View 3D Structure Click here
A0A1W2PPD8 View 3D Structure Click here
A0A2R8QCF1 View 3D Structure Click here
A0A2R8QQ41 View 3D Structure Click here
A0A368UI23 View 3D Structure Click here
A1A5Q5 View 3D Structure Click here
B0S6L0 View 3D Structure Click here
B2RXH2 View 3D Structure Click here
C0SUT9 View 3D Structure Click here
F1QNG0 View 3D Structure Click here
F1QPD2 View 3D Structure Click here
F4I6G4 View 3D Structure Click here
F4KIX0 View 3D Structure Click here
I1JXF4 View 3D Structure Click here