Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
2  structures 583  species 0  interactions 766  sequences 18  architectures

Family: AtaL (PF08982)

Summary: Acetylaranotin biosynthesis cluster protein L

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.

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.

Acetylaranotin biosynthesis cluster protein L Provide feedback

This entry includes acetylaranotin biosynthesis cluster protein L (AtaL) from Aspergillus terreus, which is a non-ribosomal peptide synthetase. It is required for the biosynthesis of the toxin acetylaranotin, which is a disulfide bridged cyclic dipeptide [1]. There are a number of steps in the biosyntheis of this epipolythiodioxopiperazine toxin from two phenylananines, but the specific function of AtaL has yet to be determined [1]. Homologues are also known from bacteria.

Literature references

  1. Guo CJ, Yeh HH, Chiang YM, Sanchez JF, Chang SL, Bruno KS, Wang CC;, J Am Chem Soc. 2013;135:7205-7213.: Biosynthetic pathway for the epipolythiodioxopiperazine acetylaranotin in Aspergillus terreus revealed by genome-based deletion analysis. PUBMED:23586797 EPMC:23586797


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015075

This entry includes acetylaranotin biosynthesis cluster protein L (AtaL) from Aspergillus terreus, which is a non-ribosomal peptide synthetase. It is required for the biosynthesis of the toxin acetylaranotin, which is a disulfide bridged cyclic dipeptide [ PUBMED:23586797 ]. There are a number of steps in the biosyntheis of this epipolythiodioxopiperazine toxin from two phenylananines, but the specific function of AtaL has yet to be determined [ PUBMED:23586797 ]. Homologues are also known from bacteria.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Pfam Clan

This family is a member of clan Bet_v_1_like (CL0209), which has the following description:

The Pfam:PF00407 entry is composed of sequences related to the major Birch (Betula verrucose) pollen antigen Bet v 1. This allergen is known to cause hayfever, dermatitis, asthma and occasionally anaphylactic shock. The other families in this clan share the same structure as Bet v 1, which is composed of antiparallel beta sheets and alpha helices. There is a cavity between the beta sheet and a long C terminal helix. The cavity appears to play roles in the binding of lipid molecules [1][2][3] which seems a common feature of the families in this clan.

The clan contains the following 25 members:

AHSA1 Aromatic_hydrox AtaL Bet_v_1 COXG DAPG_hydrolase DUF220 DUF2505 DUF3074 DUF3211 DUF3284 Fungal_KA1 IP_trans KshA_C LigXa_C Lipoprotein_18 PaO Polyketide_cyc Polyketide_cyc2 PRELI Ring_hydroxyl_A START START_2 VanA_C VASt

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
(69)
Full
(766)
Representative proteomes UniProt
(2127)
RP15
(53)
RP35
(291)
RP55
(623)
RP75
(1142)
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
(69)
Full
(766)
Representative proteomes UniProt
(2127)
RP15
(53)
RP35
(291)
RP55
(623)
RP75
(1142)
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
(69)
Full
(766)
Representative proteomes UniProt
(2127)
RP15
(53)
RP35
(291)
RP55
(623)
RP75
(1142)
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_2ffs
Previous IDs: DUF1857;
Type: Family
Sequence Ontology: SO:0100021
Author: Mistry J , Sammut SJ
Number in seed: 69
Number in full: 766
Average length of the domain: 148.9 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 84.83 %

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 27.0 27.0
Trusted cut-off 27.4 27.3
Noise cut-off 25.5 26.6
Model length: 149
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 AtaL 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.

Loading structure mapping...

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
A0A0D2FCU0 View 3D Structure Click here
A0A175VQ28 View 3D Structure Click here
A0A175WII7 View 3D Structure Click here
A0A1C1CDU2 View 3D Structure Click here
Q0CS65 View 3D Structure Click here
Q9I4D2 View 3D Structure Click here
U7PP83 View 3D Structure Click here