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19  structures 4675  species 0  interactions 16764  sequences 4154  architectures

Family: PAS_8 (PF13188)

Summary: PAS domain

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 domain Provide feedback

PAS domains are involved in many signalling proteins where they are used as a signal sensor domain [1]. 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. This domain recognises oxygen and CO (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1.

Literature references

  1. Taylor BL, Zhulin IB;, Microbiol Mol Biol Rev. 1999;63:479-506.: PAS domains: internal sensors of oxygen, redox potential, and light. PUBMED:10357859 EPMC:10357859

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000014

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 ].

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_9


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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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.

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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: Jackhmmer:O26558
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 226
Number in full: 16764
Average length of the domain: 67.70 aa
Average identity of full alignment: 15 %
Average coverage of the sequence by the domain: 9.71 %

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 21.8 14.5
Trusted cut-off 21.8 14.5
Noise cut-off 21.7 14.4
Model length: 67
Family (HMM) version: 10
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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The tree shows the occurrence of this domain across different species. 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 PAS_8 domain has been found. There are 19 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
P07604 View 3D Structure Click here
Q46802 View 3D Structure Click here
Q54W36 View 3D Structure Click here
Q54YH4 View 3D Structure Click here
Q55E44 View 3D Structure Click here
Q9P7Q7 View 3D Structure Click here