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3  structures 2033  species 0  interactions 2424  sequences 9  architectures

Family: DUF493 (PF04359)

Summary: Protein of unknown function (DUF493)

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Domain of unknown function". More...

Domain of unknown function Edit Wikipedia article

A Domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF188 and DUF1000. There are now over 3,000 DUF families within the Pfam database representing over 20% of known families.

History

The DUF naming scheme was introduced by Chris Ponting, through the addition of DUF1 and DUF2 to the SMART database.[1] These two domains were found to be widely distributed in bacterial signaling proteins. Subsequently, the functions of these domains were identified and they have since been renamed as the GGDEF domain and EAL domain respectively.

Structure

Structural genomics programmes have attempted to understand the function of DUFs through structure determination. The structures of over 250 DUF families have been solved.[2]

External Links

List of Pfam familes beginning with the letter D, including DUF families

References

  1. ^ Schultz J, Milpetz F, Bork P, Ponting CP (1998). "SMART, a simple modular architecture research tool: identification of signaling domains". Proc. Natl. Acad. Sci. U.S.A. 95 (11): 5857–64. PMC 34487. PMID 9600884. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  2. ^ Jaroszewski L, Li Z, Krishna SS; et al. (2009). "Exploration of uncharted regions of the protein universe". PLoS Biol. 7 (9): e1000205. doi:10.1371/journal.pbio.1000205. PMC 2744874. PMID 19787035. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

"DUF" families are annotated with the Domain of unknown function Wikipedia article. This is a general article, with no specific information about individual Pfam DUFs. If you have information about this particular DUF, please let us know using the "Add annotation" button below.

Protein of unknown function (DUF493) Provide feedback

This domain is likely to act in a regulatory capacity like PF01842 domains. This domain has a remarkable property in that the C-terminal residue of every protein in the family lies up in the alignment. This suggests that the C-terminal residue plays some important functional role (Bateman A pers obs).

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007454

This family includes several proteins of uncharacterised function.

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 ACT (CL0070), which has the following description:

These domains are involved in binding to amino-acids and causing allosteric regulation of linked enzyme domains [1]. The relationship between these two families was first noticed in [2].

The clan contains the following 12 members:

ACT ACT_3 ACT_4 ACT_5 ACT_6 ACT_7 ACT_8 ALS_ss_C DUF493 NikR_C NIL Thr_dehydrat_C

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
(162)
Full
(2424)
Representative proteomes UniProt
(12257)
RP15
(357)
RP35
(1116)
RP55
(2434)
RP75
(4651)
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
(162)
Full
(2424)
Representative proteomes UniProt
(12257)
RP15
(357)
RP35
(1116)
RP55
(2434)
RP75
(4651)
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
(162)
Full
(2424)
Representative proteomes UniProt
(12257)
RP15
(357)
RP35
(1116)
RP55
(2434)
RP75
(4651)
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: COG2921
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Kerrison ND , Bateman A
Number in seed: 162
Number in full: 2424
Average length of the domain: 82.2 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 74.81 %

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 24.0 24.0
Trusted cut-off 24.0 24.0
Noise cut-off 23.9 23.9
Model length: 84
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

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 DUF493 domain has been found. There are 3 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
A0A0H3GJY1 View 3D Structure Click here
A0A0P0W9X9 View 3D Structure Click here
A1AWI6 View 3D Structure Click here
A1S8T9 View 3D Structure Click here
A3QH58 View 3D Structure Click here
A4XYX5 View 3D Structure Click here
A6T692 View 3D Structure Click here
A8AJH3 View 3D Structure Click here
A8H7D3 View 3D Structure Click here
A9MKE1 View 3D Structure Click here
B1KDX1 View 3D Structure Click here
B1XYQ4 View 3D Structure Click here
B2FUT0 View 3D Structure Click here
B2JC42 View 3D Structure Click here
B2VBJ9 View 3D Structure Click here
B4FA95 View 3D Structure Click here
B4FC01 View 3D Structure Click here
C3K2M0 View 3D Structure Click here
C5BGD7 View 3D Structure Click here
C6TJY5 View 3D Structure Click here
F4HSW0 View 3D Structure Click here
I1KS22 View 3D Structure Click here
I1LN76 View 3D Structure Click here
O25237 View 3D Structure Click here
P0A8J4 View 3D Structure Click here
P0A8J6 View 3D Structure Click here
P0A8J7 View 3D Structure Click here
P44465 View 3D Structure Click here
P57559 View 3D Structure Click here
P67536 View 3D Structure Click here
P67537 View 3D Structure Click here
Q057D5 View 3D Structure Click here
Q05I79 View 3D Structure Click here
Q087L3 View 3D Structure Click here
Q2SA36 View 3D Structure Click here
Q32IU9 View 3D Structure Click here
Q3IJ79 View 3D Structure Click here
Q5F8I2 View 3D Structure Click here
Q5QYE7 View 3D Structure Click here
Q6D7M6 View 3D Structure Click here