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2  structures 1516  species 0  interactions 3321  sequences 71  architectures

Family: UFD1 (PF03152)

Summary: Ubiquitin fusion degradation protein UFD1

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Ubiquitin fusion degradation protein UFD1 Provide feedback

Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified [1]. This family includes UFD1, a 40kD protein that is essential for vegetative cell viability [1]. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterised by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400 and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation [2].

Literature references

  1. Johnson ES, Ma PC, Ota IM, Varshavsky A; , J Biol Chem 1995;270:17442-17456.: A proteolytic pathway that recognizes ubiquitin as a degradation signal. PUBMED:7615550 EPMC:7615550

  2. Pizzuti A, Novelli G, Ratti A, Amati F, Mari A, Calabrese G, Nicolis S, Silani V, Marino B, Scarlato G, Ottolenghi S, Dallapiccola B; , Hum Mol Genet 1997;6:259-265.: UFD1L, a developmentally expressed ubiquitination gene, is deleted in CATCH 22 syndrome. PUBMED:9063746 EPMC:9063746

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004854

This entry includes Ubiquitin fusion degradation protein Ufd1 from fungi and Ufd1-like proteins from animals and plants.

Ufd1 is part of the Ufd1-Npl4 complex that functions as the substrate-recruiting cofactor for Cdc48 segregase. The Cdc48-Ufd1-Npl4 complex is involved in degradation of misfolded ER proteins [ PUBMED:20206597 ]. The Ufd1-Npl4 complex has been found to recruit Cdc48 to ubiquitylated CMG (Cdc45-MCM-GINS) helicase at the end of chromosome replication, thereby driving the disassembly reaction [ PUBMED:28355556 ].

In humans, Npl4-Ufd1 acts as a cofactor in reducing antiviral innate immune responses by facilitating proteasomal degradation of RIG-I (a viral RNA sensor) [ PUBMED:26471729 ].

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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Pfam Clan

This family is a member of clan Cdc48_2-like (CL0402), which has the following description:

Superfamily contains C-terminal domains of N-ethylmaleimide sensitive fusion proteins, VCP-like ATPases, membrane fusion ATPase p97 domain 2, peroxisome biogenesis factor 1 (PEX-1), domain 2, and ubiquitin fusion degradation protein UFD1 families.

The clan contains the following 3 members:



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...

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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.

Representative proteomes UniProt
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Representative proteomes UniProt

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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...


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_3272 (release 6.5)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Mifsud W
Number in seed: 99
Number in full: 3321
Average length of the domain: 162.20 aa
Average identity of full alignment: 42 %
Average coverage of the sequence by the domain: 39.55 %

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 35.6 35.6
Trusted cut-off 35.7 35.7
Noise cut-off 35.5 35.4
Model length: 173
Family (HMM) version: 17
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


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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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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 UFD1 domain has been found. There are 2 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
A0A0P0UY76 View 3D Structure Click here
A0A0P0VFH4 View 3D Structure Click here
A0A0P0WDV8 View 3D Structure Click here
A0A0R0HAJ7 View 3D Structure Click here
A0A0R0JJT7 View 3D Structure Click here
A0A1D6FJ38 View 3D Structure Click here
A0A1D6MLI6 View 3D Structure Click here
A0A1D6QRZ2 View 3D Structure Click here
A0A1P8B7F5 View 3D Structure Click here
A4ICA6 View 3D Structure Click here
A8MQW3 View 3D Structure Click here
B6T4L6 View 3D Structure Click here
C0H540 View 3D Structure Click here
I1JIM1 View 3D Structure Click here
I1JSI6 View 3D Structure Click here
I1K5K8 View 3D Structure Click here
I1KQB3 View 3D Structure Click here
I1LK05 View 3D Structure Click here
I1M7E7 View 3D Structure Click here
I1MDD7 View 3D Structure Click here
K7M3G0 View 3D Structure Click here
O42915 View 3D Structure Click here
P53044 View 3D Structure Click here
P70362 View 3D Structure Click here
Q19584 View 3D Structure Click here
Q55BK0 View 3D Structure Click here
Q5A0H8 View 3D Structure Click here
Q5JLH9 View 3D Structure Click here
Q6DRD5 View 3D Structure Click here
Q6NLS0 View 3D Structure Click here
Q8I3L7 View 3D Structure Click here
Q8ILR6 View 3D Structure Click here
Q92890 View 3D Structure Click here
Q9ES53 View 3D Structure Click here
Q9SVK0 View 3D Structure Click here
Q9VTF9 View 3D Structure Click here