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.
207  structures 6493  species 0  interactions 50834  sequences 7224  architectures

Family: PAS (PF00989)

Summary: PAS fold

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 "PAS domain". More...

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.

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

  1. 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

  2. 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

  3. Ponting CP, Aravind L; , Curr Biol 1997;7:674-677.: PAS: a multifunctional domain family comes to light. PUBMED:9382818 EPMC:9382818

  4. 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

External database links

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.

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 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_9

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
(49)
Full
(50834)
Representative proteomes UniProt
(211000)
RP15
(6635)
RP35
(23824)
RP55
(49960)
RP75
(81029)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(49)
Full
(50834)
Representative proteomes UniProt
(211000)
RP15
(6635)
RP35
(23824)
RP55
(49960)
RP75
(81029)
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
(49)
Full
(50834)
Representative proteomes UniProt
(211000)
RP15
(6635)
RP35
(23824)
RP55
(49960)
RP75
(81029)
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: Sequences from SMART alignment
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 49
Number in full: 50834
Average length of the domain: 104.40 aa
Average identity of full alignment: 15 %
Average coverage of the sequence by the domain: 15.49 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.6 22.6
Trusted cut-off 22.6 22.6
Noise cut-off 22.5 22.5
Model length: 113
Family (HMM) version: 27
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 PAS domain has been found. There are 207 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
A0A0P0Y5C3 View 3D Structure Click here
A0A0R0GET9 View 3D Structure Click here
A0A0R0GET9 View 3D Structure Click here
A0A0R0HSY5 View 3D Structure Click here
A0A0R0HSY5 View 3D Structure Click here
A0A0R0KN47 View 3D Structure Click here
A0A0R0KN47 View 3D Structure Click here
A0A0R4IBR4 View 3D Structure Click here
A0A0R4IH97 View 3D Structure Click here
A0A0R4IY58 View 3D Structure Click here
A0A1D6G6Q3 View 3D Structure Click here
A0A1D6GGX9 View 3D Structure Click here
A0A1D6GGX9 View 3D Structure Click here
A0A1D6HRS3 View 3D Structure Click here
A0A1D6INR5 View 3D Structure Click here
A0A1D6KD94 View 3D Structure Click here
A0A1D6MX83 View 3D Structure Click here
A0A1D6Q065 View 3D Structure Click here
A0A1D8PSC7 View 3D Structure Click here
A0A1I9LPU6 View 3D Structure Click here
A0A2R8PV59 View 3D Structure Click here
A0A2R8Q2I0 View 3D Structure Click here
A0A2R8QI31 View 3D Structure Click here
A0A2R8QNG8 View 3D Structure Click here
A4I2A5 View 3D Structure Click here
A4I628 View 3D Structure Click here
A4IG25 View 3D Structure Click here
A9YTQ3 View 3D Structure Click here
B4YB07 View 3D Structure Click here
B4YB07 View 3D Structure Click here
B4YB10 View 3D Structure Click here
B4YB10 View 3D Structure Click here
C1JIE2 View 3D Structure Click here
C1PHB8 View 3D Structure Click here
C1PHB8 View 3D Structure Click here
D3ZJ66 View 3D Structure Click here
D3ZMU8 View 3D Structure Click here
D4A3Q3 View 3D Structure Click here
D4AA36 View 3D Structure Click here
E1JIM6 View 3D Structure Click here
E7FAJ1 View 3D Structure Click here
E7FDK6 View 3D Structure Click here
E9AGM0 View 3D Structure Click here
F1MAG2 View 3D Structure Click here
F1QNB9 View 3D Structure Click here
F1QQQ1 View 3D Structure Click here
F1QXX7 View 3D Structure Click here
F1RBN7 View 3D Structure Click here
F4HVH9 View 3D Structure Click here
F4JC18 View 3D Structure Click here
F4K645 View 3D Structure Click here
G5EGD2 View 3D Structure Click here
I1L0Q6 View 3D Structure Click here
I1L257 View 3D Structure Click here
I1L257 View 3D Structure Click here
I1MGE5 View 3D Structure Click here
I1MGE5 View 3D Structure Click here
O00327 View 3D Structure Click here
O02219 View 3D Structure Click here
O08785 View 3D Structure Click here
O09000 View 3D Structure Click here
O15516 View 3D Structure Click here
O15945 View 3D Structure Click here
O44712 View 3D Structure Click here
O60658 View 3D Structure Click here
O61734 View 3D Structure Click here
O82754 View 3D Structure Click here
O88502 View 3D Structure Click here
P05709 View 3D Structure Click here
P07663 View 3D Structure Click here
P08400 View 3D Structure Click here
P0AEC3 View 3D Structure Click here
P0AEC8 View 3D Structure Click here
P0AFB5 View 3D Structure Click here
P14712 View 3D Structure Click here
P14712 View 3D Structure Click here
P14713 View 3D Structure Click here
P14713 View 3D Structure Click here
P14714 View 3D Structure Click here
P14714 View 3D Structure Click here
P19862 View 3D Structure Click here
P19862 View 3D Structure Click here
P27540 View 3D Structure Click here
P30561 View 3D Structure Click here
P35869 View 3D Structure Click here
P38140 View 3D Structure Click here
P41738 View 3D Structure Click here
P41739 View 3D Structure Click here
P42497 View 3D Structure Click here
P42497 View 3D Structure Click here
P42498 View 3D Structure Click here
P42498 View 3D Structure Click here
P42499 View 3D Structure Click here
P42499 View 3D Structure Click here
P42500 View 3D Structure Click here
P42500 View 3D Structure Click here
P53762 View 3D Structure Click here
P70365 View 3D Structure Click here
P76016 View 3D Structure Click here
P77510 View 3D Structure Click here
P81133 View 3D Structure Click here
P90953 View 3D Structure Click here
P97459 View 3D Structure Click here
P97460 View 3D Structure Click here
P97481 View 3D Structure Click here
Q06067 View 3D Structure Click here
Q0IML7 View 3D Structure Click here
Q0VBL6 View 3D Structure Click here
Q10CQ8 View 3D Structure Click here
Q10CQ8 View 3D Structure Click here
Q10DU0 View 3D Structure Click here
Q10DU0 View 3D Structure Click here
Q10MG9 View 3D Structure Click here
Q10MG9 View 3D Structure Click here
Q14190 View 3D Structure Click here
Q15596 View 3D Structure Click here
Q15788 View 3D Structure Click here
Q16665 View 3D Structure Click here
Q1LV27 View 3D Structure Click here
Q24167 View 3D Structure Click here
Q2VPD4 View 3D Structure Click here
Q3U1U7 View 3D Structure Click here
Q4CSS9 View 3D Structure Click here
Q4D211 View 3D Structure Click here
Q4D5Q9 View 3D Structure Click here
Q4D9R4 View 3D Structure Click here
Q4DGP8 View 3D Structure Click here
Q4DPG2 View 3D Structure Click here
Q4DX96 View 3D Structure Click here
Q4U3K9 View 3D Structure Click here
Q54VU4 View 3D Structure Click here
Q54VU4 View 3D Structure Click here
Q5RIG3 View 3D Structure Click here
Q5RIV1 View 3D Structure Click here
Q61026 View 3D Structure Click here
Q61045 View 3D Structure Click here
Q61079 View 3D Structure Click here
Q61221 View 3D Structure Click here
Q61324 View 3D Structure Click here
Q6XFQ1 View 3D Structure Click here
Q6XFQ1 View 3D Structure Click here
Q6XFQ2 View 3D Structure Click here
Q6XFQ2 View 3D Structure Click here
Q6XFQ3 View 3D Structure Click here
Q6XFQ3 View 3D Structure Click here
Q6XFQ4 View 3D Structure Click here
Q6XFQ4 View 3D Structure Click here
Q75NT5 View 3D Structure Click here
Q78E60 View 3D Structure Click here
Q8IXF0 View 3D Structure Click here
Q8JIG3 View 3D Structure Click here
Q8WYA1 View 3D Structure Click here
Q98SJ5 View 3D Structure Click here
Q98TW1 View 3D Structure Click here
Q99742 View 3D Structure Click here
Q99743 View 3D Structure Click here
Q99814 View 3D Structure Click here
Q9C902 View 3D Structure Click here
Q9DG12 View 3D Structure Click here
Q9EPW1 View 3D Structure Click here
Q9HBZ2 View 3D Structure Click here
Q9I879 View 3D Structure Click here
Q9JHS2 View 3D Structure Click here
Q9QZQ0 View 3D Structure Click here
Q9WTL8 View 3D Structure Click here
Q9WUI9 View 3D Structure Click here
Q9WVS9 View 3D Structure Click here
Q9Y2N7 View 3D Structure Click here
Q9Y6Q9 View 3D Structure Click here