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23  structures 484  species 0  interactions 6337  sequences 187  architectures

Family: Agenet (PF05641)

Summary: Agenet domain

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.

Agenet domain Provide feedback

This domain is related to the TUDOR domain PF00567 [1]. The function of the agenet domain is unknown. This family now matches both the two Agenet domains in the FMR proteins [1].

Literature references

  1. Maurer-Stroh S, Dickens NJ, Hughes-Davies L, Kouzarides T, Eisenhaber F, Ponting CP; , Trends Biochem Sci 2003;28:69-74.: The Tudor domain 'Royal Family': Tudor, plant Agenet, Chromo, PWWP and MBT domains. PUBMED:12575993 EPMC:12575993


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008395

Fragile X Mental Retardation Protein (FMRP), and its autosomal paralogues, Fragile X mental Retardation syndrome-related protein 1 and 2 (FXR1 and FXR2), comprise a family of RNA-binding proteins. It is thought that the FRMP family of proteins contributes to the regulation of protein synthesis at sites where mRNAs are locally translated in response to stimuli. These proteins are highly similar to one another and also retain highly conserved domain architecture. The two ribonucleoprotein K homology (KH) domains and the cluster of arginine and glycine residues that constitute the RGG box, comprise a large region that is important for RNA binding and polyribosome association. In addition, two Agenet-like domains exist in tandem within the N-terminal regions of FMRP family proteins. The Agenet-like domain belongs to the "Royal" domain superfamilly which contains also the Tudor, chromo, MBT, PWWP and plant Agenet domains. Biochemical analysis of the tandem Agenet-like domains reveals their ability to preferentially recognise trimethylated peptides in a sequence-specific manner [ PUBMED:12575993 , PUBMED:12950170 , PUBMED:16407062 , PUBMED:21072162 ].

The Agenet-like domain folds into a bent four-stranded antiparallel beta sheet with a fifth strand closing the cavity of the sheet, similar to a thumb across a semiclosed hand [ PUBMED:16407062 , PUBMED:21072162 ].

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 Tudor (CL0049), which has the following description:

This clan covers the Tudor domain 'royal family' [1]. This includes chromo, MBT, PWWP and tudor domains. The chromo domain is a comprised of approximately 50 amino acid residues. There are usually one to three Chromo domains found in a single protein. In some chromo domain containing proteins, a second related chromo domain has been found and is referred to as the Chromo-shadow domain. The structure of the Chromo and Chromo-shadow domains reveal an OB-fold, a fold found in a variety of prokaryotic and eukaryotic nucleic acid binding proteins. More specifically,the chromo-domain structure reveals a three beta strands that are packed against an alpha helix. Interestingly, a similar structure is found in the archaeal chromatin proteins (7kDa DNA-binding domain). These are sequence neutral DNA binding proteins. The DNA binding in these archaeal proteins is mediated through the triple stranded beta sheet. These archaeal domains are though to represent an ancestral chromo domain. Homologs of the chromo domain have been found in fission yeast, ciliated protozoa and all animal species, but appear to be absent in eubacteria, budding yeast and plants [2]. The precise function of the chromo domain is unclear, but the chromo domain is thought to act as a targeting module for chromosomal proteins, although the chromosomal contexts and functional contexts being targeted vary. In all cases studies, the chromo domains are found in proteins that are involved in transcription regulation, positive and negative [2].

The clan contains the following 33 members:

53-BP1_Tudor 7kD_DNA_binding Agenet Chromo Chromo_2 Chromo_shadow Cul7 DUF1325 DUF4537 DUF4819 GEN1_C Hva1_TUDOR LBR_tudor LytTR MBT Mtf2_C ProQ_C PWWP Rad9_Rad53_bind RBB1NT SAWADEE SMN SNase TTD TUDOR Tudor-knot Tudor_1_RapA Tudor_2 Tudor_3 Tudor_4 Tudor_5 Tudor_FRX1 Tudor_RapA

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
(156)
Full
(6337)
Representative proteomes UniProt
(10585)
RP15
(482)
RP35
(2840)
RP55
(5140)
RP75
(7288)
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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
(156)
Full
(6337)
Representative proteomes UniProt
(10585)
RP15
(482)
RP35
(2840)
RP55
(5140)
RP75
(7288)
Alignment:
Format:
Order:
Sequence:
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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
(156)
Full
(6337)
Representative proteomes UniProt
(10585)
RP15
(482)
RP35
(2840)
RP55
(5140)
RP75
(7288)
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_2551 (release 8.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 156
Number in full: 6337
Average length of the domain: 62.70 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 11.41 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 19.0
Trusted cut-off 27.0 19.0
Noise cut-off 26.9 18.9
Model length: 61
Family (HMM) version: 14
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

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 Agenet domain has been found. There are 23 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
A0A0P0V413 View 3D Structure Click here
A0A0P0V413 View 3D Structure Click here
A0A0P0WHJ5 View 3D Structure Click here
A0A0P0WHJ5 View 3D Structure Click here
A0A0P0WI00 View 3D Structure Click here
A0A0P0XM22 View 3D Structure Click here
A0A0P0XTY1 View 3D Structure Click here
A0A0P0Y411 View 3D Structure Click here
A0A0R0EKI3 View 3D Structure Click here
A0A0R0EKI3 View 3D Structure Click here
A0A0R0EKI3 View 3D Structure Click here
A0A0R0EKI3 View 3D Structure Click here
A0A0R0FHX4 View 3D Structure Click here
A0A0R0G0C9 View 3D Structure Click here
A0A0R0HTD5 View 3D Structure Click here
A0A0R0IHC4 View 3D Structure Click here
A0A0R0IST9 View 3D Structure Click here
A0A0R0JPE9 View 3D Structure Click here
A0A0R0LI21 View 3D Structure Click here
A0A1D6E622 View 3D Structure Click here
A0A1D6F0Q0 View 3D Structure Click here
A0A1D6F6N7 View 3D Structure Click here
A0A1D6F6N7 View 3D Structure Click here
A0A1D6F6N8 View 3D Structure Click here
A0A1D6F6N8 View 3D Structure Click here
A0A1D6FYZ4 View 3D Structure Click here
A0A1D6IZB0 View 3D Structure Click here
A0A1D6J4L9 View 3D Structure Click here
A0A1D6JZC0 View 3D Structure Click here
A0A1D6K095 View 3D Structure Click here
A0A1D6K8B6 View 3D Structure Click here
A0A1D6KPB6 View 3D Structure Click here
A0A1D6LSB4 View 3D Structure Click here
A0A1D6NMX3 View 3D Structure Click here
A0A1D6P2J9 View 3D Structure Click here
A0A1D6P6V0 View 3D Structure Click here
A0A1D6QM79 View 3D Structure Click here
A0A1D6QM79 View 3D Structure Click here
A0A2R8RJS5 View 3D Structure Click here
B1H2A6 View 3D Structure Click here
C0P924 View 3D Structure Click here
C0P924 View 3D Structure Click here
C0PEF4 View 3D Structure Click here
C4JC55 View 3D Structure Click here
C4JC55 View 3D Structure Click here
C4JC55 View 3D Structure Click here
F1QLR3 View 3D Structure Click here
F1R159 View 3D Structure Click here
F4I8W1 View 3D Structure Click here
F4I8W1 View 3D Structure Click here
F4I8W1 View 3D Structure Click here
F4JP43 View 3D Structure Click here
F4K315 View 3D Structure Click here
F4KEA4 View 3D Structure Click here
I1JUF7 View 3D Structure Click here
I1JUF7 View 3D Structure Click here
I1KEN6 View 3D Structure Click here
I1LLM4 View 3D Structure Click here
I1LSG0 View 3D Structure Click here
I1MPH0 View 3D Structure Click here
K7K2M6 View 3D Structure Click here
K7K6T0 View 3D Structure Click here
K7KA70 View 3D Structure Click here
K7KN46 View 3D Structure Click here
K7KTK3 View 3D Structure Click here
K7KTK3 View 3D Structure Click here
K7LAA9 View 3D Structure Click here
K7LB84 View 3D Structure Click here
K7LBK6 View 3D Structure Click here
K7LBK6 View 3D Structure Click here
K7LDK7 View 3D Structure Click here
K7LMT6 View 3D Structure Click here
K7LQW1 View 3D Structure Click here
K7LS73 View 3D Structure Click here
K7ML77 View 3D Structure Click here
K7MQK5 View 3D Structure Click here
K7TWB9 View 3D Structure Click here
K7V3C8 View 3D Structure Click here
O22897 View 3D Structure Click here
O22897 View 3D Structure Click here
O22897 View 3D Structure Click here
P35922 View 3D Structure Click here
P51114 View 3D Structure Click here
P51116 View 3D Structure Click here
Q06787 View 3D Structure Click here
Q0IVQ6 View 3D Structure Click here
Q0WP65 View 3D Structure Click here
Q500V5 View 3D Structure Click here
Q500V5 View 3D Structure Click here
Q500V5 View 3D Structure Click here
Q54SY9 View 3D Structure Click here
Q5XI81 View 3D Structure Click here
Q61584 View 3D Structure Click here
Q69J34 View 3D Structure Click here
Q69XL1 View 3D Structure Click here
Q6Z6D8 View 3D Structure Click here
Q6ZKB4 View 3D Structure Click here
Q80WE1 View 3D Structure Click here
Q8H0V4 View 3D Structure Click here
Q8H0V4 View 3D Structure Click here
Q8L7Q0 View 3D Structure Click here
Q8LES5 View 3D Structure Click here
Q8RXR3 View 3D Structure Click here
Q8W109 View 3D Structure Click here
Q9C8Z3 View 3D Structure Click here
Q9C8Z3 View 3D Structure Click here
Q9C8Z3 View 3D Structure Click here
Q9C8Z3 View 3D Structure Click here
Q9FFA0 View 3D Structure Click here
Q9FFA0 View 3D Structure Click here
Q9FFA0 View 3D Structure Click here
Q9FFA2 View 3D Structure Click here
Q9FZD9 View 3D Structure Click here
Q9FZD9 View 3D Structure Click here
Q9LUZ5 View 3D Structure Click here
Q9SLA4 View 3D Structure Click here
Q9WVR4 View 3D Structure Click here
Q9ZVT1 View 3D Structure Click here
Q9ZVT1 View 3D Structure Click here