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30  structures 903  species 0  interactions 3529  sequences 203  architectures

Family: PUB (PF09409)

Summary: PUB 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.

PUB domain Provide feedback

The PUB (also known as PUG) domain is found in peptide N-glycanase where it functions as a AAA ATPase binding domain [1]. This domain is also found on other proteins linked to the ubiquitin-proteasome system.

Literature references

  1. Allen MD, Buchberger A, Bycroft M; , J Biol Chem. 2006;281:25502-25508.: The PUB domain functions as a p97 binding module in human peptide N-glycanase. PUBMED:16807242 EPMC:16807242


This tab holds annotation information from the InterPro database.

InterPro entry IPR018997

The PUB (also known as PUG) domain is found in peptide N-glycanase where it functions as a AAA ATPase binding domain [ PUBMED:16807242 ]. This domain is also found on other proteins linked to the ubiquitin-proteasome system.

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
(82)
Full
(3529)
Representative proteomes UniProt
(5989)
RP15
(844)
RP35
(1727)
RP55
(2824)
RP75
(3651)
Jalview View  View  View  View  View  View  View 
HTML View  View           
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
(82)
Full
(3529)
Representative proteomes UniProt
(5989)
RP15
(844)
RP35
(1727)
RP55
(2824)
RP75
(3651)
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
(82)
Full
(3529)
Representative proteomes UniProt
(5989)
RP15
(844)
RP35
(1727)
RP55
(2824)
RP75
(3651)
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: pdb_2cm0
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mistry J
Number in seed: 82
Number in full: 3529
Average length of the domain: 80.9 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 14.26 %

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 23.0 23.0
Trusted cut-off 23.0 23.0
Noise cut-off 22.9 22.9
Model length: 82
Family (HMM) version: 13
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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The tree shows the occurrence of this domain across different species. 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 PUB domain has been found. There are 30 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
A0A044TR68 View 3D Structure Click here
A0A077Z6G1 View 3D Structure Click here
A0A0D2DZI0 View 3D Structure Click here
A0A0G2K012 View 3D Structure Click here
A0A0N4UIS4 View 3D Structure Click here
A0A144A1D9 View 3D Structure Click here
A0A1C1CJQ5 View 3D Structure Click here
A0A1D6EPM5 View 3D Structure Click here
A0A1D6H8V0 View 3D Structure Click here
A0A1D6I411 View 3D Structure Click here
A0A1D6KID7 View 3D Structure Click here
A0A1D6Q270 View 3D Structure Click here
A0A1D6QR86 View 3D Structure Click here
A0A3P7DLS3 View 3D Structure Click here
A0A3Q0KD47 View 3D Structure Click here
A0A3Q0KE68 View 3D Structure Click here
A0A5K4EAY8 View 3D Structure Click here
A0A7I4KIU7 View 3D Structure Click here
A0A7I4KJE2 View 3D Structure Click here
A4HU22 View 3D Structure Click here
A4HV01 View 3D Structure Click here
A4ICX4 View 3D Structure Click here
C0H579 View 3D Structure Click here
E7F0V6 View 3D Structure Click here
E9AHP5 View 3D Structure Click here
E9PU29 View 3D Structure Click here
I1K3U6 View 3D Structure Click here
I1K5Q4 View 3D Structure Click here
I1KQ73 View 3D Structure Click here
I1KS98 View 3D Structure Click here
K7MGG0 View 3D Structure Click here
K7N1U8 View 3D Structure Click here
K7USU9 View 3D Structure Click here
Q1LYI0 View 3D Structure Click here
Q28YQ7 View 3D Structure Click here
Q2KIJ6 View 3D Structure Click here
Q382M4 View 3D Structure Click here
Q385D5 View 3D Structure Click here
Q38BF0 View 3D Structure Click here
Q38FI8 View 3D Structure Click here