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41  structures 1544  species 0  interactions 12519  sequences 234  architectures

Family: UBX (PF00789)

Summary: UBX 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.

UBX domain Provide feedback

This domain is present in ubiquitin-regulatory proteins and is a general Cdc48-interacting module [2].

Literature references

  1. Hofmann K, Bucher P; , Trends Biochem Sci 1996;21:172-173.: The UBA domain: a sequence motif present in multiple enzyme classes of the ubiquitination pathway. PUBMED:8871400 EPMC:8871400

  2. Hartmann-Petersen R, Wallace M, Hofmann K, Koch G, Johnsen AH, Hendil KB, Gordon C; , Curr Biol 2004;14:824-828.: The Ubx2 and Ubx3 cofactors direct Cdc48 activity to proteolytic and nonproteolytic ubiquitin-dependent processes. PUBMED:15120077 EPMC:15120077


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001012

The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast. The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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
(19)
Full
(12519)
Representative proteomes UniProt
(20884)
RP15
(2320)
RP35
(5382)
RP55
(9706)
RP75
(12983)
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
(19)
Full
(12519)
Representative proteomes UniProt
(20884)
RP15
(2320)
RP35
(5382)
RP55
(9706)
RP75
(12983)
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
(19)
Full
(12519)
Representative proteomes UniProt
(20884)
RP15
(2320)
RP35
(5382)
RP55
(9706)
RP75
(12983)
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: Alignment kindly provided by SMART
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: SMART, Mistry J , Wood V
Number in seed: 19
Number in full: 12519
Average length of the domain: 81.30 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 18.35 %

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 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 81
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
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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 UBX domain has been found. There are 41 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
A0A0G2K012 View 3D Structure Click here
A0A0N7KQR8 View 3D Structure Click here
A0A0P0VJK9 View 3D Structure Click here
A0A0R0FL85 View 3D Structure Click here
A0A0R0G4U2 View 3D Structure Click here
A0A0R0G4U7 View 3D Structure Click here
A0A0R0J0M1 View 3D Structure Click here
A0A0R4IIQ1 View 3D Structure Click here
A0A140LGH8 View 3D Structure Click here
A0A1D6DU17 View 3D Structure Click here
A0A1D6E917 View 3D Structure Click here
A0A1D6ETD0 View 3D Structure Click here
A0A1D6I6R5 View 3D Structure Click here
A0A1D6J8V7 View 3D Structure Click here
A0A1D6JHM3 View 3D Structure Click here
A0A1D8PCP0 View 3D Structure Click here
A0A1D8PS15 View 3D Structure Click here
A4IB95 View 3D Structure Click here
A4IDV8 View 3D Structure Click here
B0UXY9 View 3D Structure Click here
B4FMI4 View 3D Structure Click here
B4FZ01 View 3D Structure Click here
B6TD00 View 3D Structure Click here
C4JAW0 View 3D Structure Click here
D3ZID8 View 3D Structure Click here
D3ZUE3 View 3D Structure Click here
E7EY86 View 3D Structure Click here
E7FGB9 View 3D Structure Click here
F1Q6Z1 View 3D Structure Click here
F1Q8D2 View 3D Structure Click here
F1R1A5 View 3D Structure Click here
F4IXN6 View 3D Structure Click here
F4JPR7 View 3D Structure Click here
F6NPG5 View 3D Structure Click here
G3V606 View 3D Structure Click here
I1JIK8 View 3D Structure Click here
I1K0C8 View 3D Structure Click here
I1K5Q4 View 3D Structure Click here
I1KQ73 View 3D Structure Click here
I1KZW3 View 3D Structure Click here