Summary: UBX 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.
UBX domain Provide feedback
This domain is present in ubiquitin-regulatory proteins and is a general Cdc48-interacting module [2].
Literature references
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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
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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
External database links
HOMSTRAD: | UBX |
SCOP: | 1i42 |
SMART: | UBX |
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.
Molecular function | protein binding (GO:0005515) |
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 Ubiquitin (CL0072), which has the following description:
This family includes proteins that share the ubiquitin fold. It currently unites four SCOP superfamilies.
The clan contains the following 76 members:
APG12 APG5 Atg8 AUX_IAA B1 BILBO1_N Blt1 Caps_synth_GfcC CHIPS CIDE-N Cobl CRIM DCX DIX DUF2407 DUF348 DUF4430 DWNN FERM_f0 FERM_N FERM_N_2 Flg_new Flg_new_2 Formin_GBD_N GABP-alpha IgG_binding_B Kindlin_2_N Lambda_tail_I Mub_B2 MucBP MucBP_2 Multi_ubiq NLE NQRA_SLBB Oxidored_molyb Par3_HAL_N_term PB1 Phenol_monoox PI3K_p85B PI3K_rbd Prok_Ub RA Rad60-SLD Rad60-SLD_2 Ras_bdg_2 RAWUL RBD SAP18 Sde2_N_Ubi SHIRT SLBB SSSPR-51 Staphylokinase TBK1_ULD TGS ThiS ThiS-like TmoB TUG-UBL1 Tugs Ub-Mut7C Ub-RnfH ubiquitin Ubiquitin_2 Ubiquitin_3 Ubiquitin_4 Ubiquitin_5 UBX Ufm1 ULD UN_NPL4 Urm1 USP7_C2 USP7_ICP0_bdg YchF-GTPase_C YukDAlignments
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...
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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 (8884) |
Representative proteomes | UniProt (14243) |
NCBI (18975) |
Meta (21) |
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RP15 (1472) |
RP35 (3713) |
RP55 (6242) |
RP75 (8936) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (8884) |
Representative proteomes | UniProt (14243) |
NCBI (18975) |
Meta (21) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (1472) |
RP35 (3713) |
RP55 (6242) |
RP75 (8936) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Alignment kindly provided by SMART |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
SMART, Mistry J |
Number in seed: | 19 |
Number in full: | 8884 |
Average length of the domain: | 81.60 aa |
Average identity of full alignment: | 21 % |
Average coverage of the sequence by the domain: | 18.45 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 81 | ||||||||||||
Family (HMM) version: | 21 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 38 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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