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1  structure 194  species 0  interactions 229  sequences 10  architectures

Family: AnkUBD (PF18418)

Summary: Ankyrin ubiquitin-binding domain

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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.

Ankyrin ubiquitin-binding domain Provide feedback

This is an Ankyrin repeat domain found in TRABID (also known as Ubiquitin thioesterase ZRANB1) ( EC:3.4.19.12). In TRABID, the first ankyrin repeat spans residues 260-290 and is connected to the second repeat residues 313-340 by a long linker that packs against what would correspond to the concave surface in an extended ankyrin-repeat structure. Ankyrin-repeat domains mediate protein interactions through a variety of surfaces. The ankyrin domain of TRABID interacts with ubiquitin, hence it is referred to as the ankyrin ubiquitin-binding domain, or AnkUBD [1].

Literature references

  1. Licchesi JD, Mieszczanek J, Mevissen TE, Rutherford TJ, Akutsu M, Virdee S, El Oualid F, Chin JW, Ovaa H, Bienz M, Komander D;, Nat Struct Mol Biol. 2011;19:62-71.: An ankyrin-repeat ubiquitin-binding domain determines TRABID's specificity for atypical ubiquitin chains. PUBMED:22157957 EPMC:22157957


Internal database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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 Ank (CL0465), which has the following description:

The ankyrin repeat is a short sequence region that is about 30-34 amino-acids in length. Multiple copies of the repeat composed of two beta strands and two alpha helices combine to form long arrays. In general these repeats are involved in protein-protein interactions. This superfamily also includes some families that are arrays of several repeats.

The clan contains the following 8 members:

Ank Ank_2 Ank_3 Ank_4 Ank_5 AnkUBD DUF3420 DUF3447

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, the UniProtKB sequence database, 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
(2)
Full
(229)
Representative proteomes UniProt
(370)
NCBI
(614)
Meta
(0)
RP15
(47)
RP35
(104)
RP55
(185)
RP75
(222)
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PP/heatmap 1 View               

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

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(2)
Full
(229)
Representative proteomes UniProt
(370)
NCBI
(614)
Meta
(0)
RP15
(47)
RP35
(104)
RP55
(185)
RP75
(222)
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
(2)
Full
(229)
Representative proteomes UniProt
(370)
NCBI
(614)
Meta
(0)
RP15
(47)
RP35
(104)
RP55
(185)
RP75
(222)
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.

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

This family is new in this Pfam release.

Seed source: ECOD:EUF01021
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: El-Gebali S
Number in seed: 2
Number in full: 229
Average length of the domain: 92.30 aa
Average identity of full alignment: 64 %
Average coverage of the sequence by the domain: 13.23 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.1 26.1
Trusted cut-off 26.1 36.5
Noise cut-off 25.7 25.6
Model length: 97
Family (HMM) version: 1
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 AnkUBD domain has been found. There are 1 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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