Summary: PAS fold
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This is the Wikipedia entry entitled "PAS domain". More...
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PAS fold Provide feedback
The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya.
Literature references
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Zhulin IB, Taylor BL, Dixon R; , Trends Biochem Sci 1997;22:331-333.: PAS domain S-boxes in archaea, bacteria and sensors for oxygen and redox. PUBMED:9301332 EPMC:9301332
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Borgstahl GE, Williams DR, Getzoff ED; , Biochemistry 1995;34:6278-6287.: 1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore. PUBMED:7756254 EPMC:7756254
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Ponting CP, Aravind L; , Curr Biol 1997;7:674-677.: PAS: a multifunctional domain family comes to light. PUBMED:9382818 EPMC:9382818
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Hefti MH, Francoijs KJ, de Vries SC, Dixon R, Vervoort J; , Eur J Biochem 2004;271:1198-1208.: The PAS fold: a redefination of the PAS domain based upon structural prediction. PUBMED:15009198 EPMC:15009198
Internal database links
SCOOP: | MEKHLA MLTR_LBD PAS_10 PAS_11 PAS_12 PAS_2 PAS_3 PAS_4 PAS_7 PAS_8 PAS_9 sCache_3_3 STAS |
Similarity to PfamA using HHSearch: | PAS_2 PAS_3 PAS_4 PAS_7 PAS_8 PAS_9 PAS_10 PAS_11 |
External database links
HOMSTRAD: | PAS |
SCOP: | 2phy |
SMART: | PAS |
This tab holds annotation information from the InterPro database.
InterPro entry IPR013767
PAS domains are involved in many signalling proteins where they are used as a signal sensor domain [PUBMED:10357859]. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Heme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in:
- Per- period circadian protein
- Arnt- Ah receptor nuclear translocator protein
- Sim- single-minded protein.
PAS domains are often associated with PAC domains INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs [PUBMED:15009198]. In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand [PUBMED:12377121]. Probably the most surprising identification of a PAS domain was that in EAG-like K -channels [PUBMED:9301332].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Biological process | regulation of transcription, DNA-templated (GO:0006355) |
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 PAS_Fold (CL0183), which has the following description:
This clan contains PAS domains that are found in a wide variety of bacterial signaling proteins.
The clan contains the following 17 members:
AbfS_sensor CpxA_peri DUF5593 MEKHLA MLTR_LBD PAS PAS_10 PAS_11 PAS_12 PAS_2 PAS_3 PAS_4 PAS_5 PAS_6 PAS_7 PAS_8 PAS_9Alignments
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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Seed (49) |
Full (40695) |
Representative proteomes | UniProt (164130) |
NCBI (733185) |
Meta (3365) |
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RP15 (5450) |
RP35 (18625) |
RP55 (38714) |
RP75 (64477) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (49) |
Full (40695) |
Representative proteomes | UniProt (164130) |
NCBI (733185) |
Meta (3365) |
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RP15 (5450) |
RP35 (18625) |
RP55 (38714) |
RP75 (64477) |
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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.
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Curation and family details
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Curation
Seed source: | Sequences from SMART alignment |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 49 |
Number in full: | 40695 |
Average length of the domain: | 104.40 aa |
Average identity of full alignment: | 15 % |
Average coverage of the sequence by the domain: | 15.43 % |
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: | 113 | ||||||||||||
Family (HMM) version: | 26 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
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 PAS domain has been found. There are 206 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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