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5  structures 2453  species 0  interactions 8124  sequences 1381  architectures

Family: PAS_8 (PF13188)

Summary: PAS domain

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This is the Wikipedia entry entitled "PAS domain". More...

PAS domain Edit Wikipedia article

PAS fold
FixL 1y28.png
Crystallographic structure of the PAS domain of the bacterial oxygen sensor protein fixL.[1] The protein is depicted as a rainbow colored cartoon (N-terminus = blue, C-terminus = red while the heme ligand is shown as sticks (carbon = white, nitrogen = blue, oxygen = red, iron = orange).
Identifiers
Symbol PAS
Pfam PF00989
InterPro IPR013767
SMART PAS
PROSITE PDOC50112
SCOP 2phy
SUPERFAMILY 2phy

The PAS domain is a protein domain contained in many signaling proteins where it functions as a signal sensor.[2][3] PAS domains are found in a large number of organisms from bacteria to humans. The PAS domain was named after the three proteins in which it occurs:

Many PAS-domain proteins detect their signal by way of an associated cofactor such as heme.[4] Proteins that contain a PAS domain include Hypoxia-inducible factors.

References[edit]

  1. ^ PDB 1y28; Dunham CM, Dioum EM, Tuckerman JR, Gonzalez G, Scott WG, Gilles-Gonzalez MA (July 2003). "A distal arginine in oxygen-sensing heme-PAS domains is essential to ligand binding, signal transduction, and structure". Biochemistry 42 (25): 7701–8. doi:10.1021/bi0343370. PMID 12820879. 
  2. ^ Ponting CP, Aravind L (November 1997). "PAS: a multi-functional domain family comes to light". Curr. Biol. 7 (11): R674–7. doi:10.1016/S0960-9822(06)00352-6. PMID 9382818. 
  3. ^ Hefti MH, Françoijs KJ, de Vries SC, Dixon R, Vervoort J (March 2004). "The PAS fold. A redefinition of the PAS domain based upon structural prediction". Eur. J. Biochem. 271 (6): 1198–208. doi:10.1111/j.1432-1033.2004.04023.x. PMID 15009198. 
  4. ^ Gilles-Gonzalez MA, Gonzalez G (February 2004). "Signal transduction by heme-containing PAS-domain proteins". J. Appl. Physiol. 96 (2): 774–83. doi:10.1152/japplphysiol.00941.2003. PMID 14715687. 

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PAS domain Provide feedback

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Internal database links

External 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. Haeme, 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...

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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 13 members:

MEKHLA PAS PAS_10 PAS_11 PAS_2 PAS_3 PAS_4 PAS_5 PAS_6 PAS_7 PAS_8 PAS_9 PocR

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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.

  Seed
(488)
Full
(8124)
Representative proteomes NCBI
(38264)
Meta
(3152)
RP15
(951)
RP35
(1890)
RP55
(2360)
RP75
(2746)
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Format an alignment

  Seed
(488)
Full
(8124)
Representative proteomes NCBI
(38264)
Meta
(3152)
RP15
(951)
RP35
(1890)
RP55
(2360)
RP75
(2746)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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.

  Seed
(488)
Full
(8124)
Representative proteomes NCBI
(38264)
Meta
(3152)
RP15
(951)
RP35
(1890)
RP55
(2360)
RP75
(2746)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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: Jackhmmer:O26558
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 488
Number in full: 8124
Average length of the domain: 67.80 aa
Average identity of full alignment: 15 %
Average coverage of the sequence by the domain: 10.70 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 11.0
Trusted cut-off 21.0 11.0
Noise cut-off 20.9 10.9
Model length: 64
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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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 PAS_8 domain has been found. There are 5 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 seqence.

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