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282  structures 6244  species 0  interactions 53379  sequences 9383  architectures

Family: PAS_9 (PF13426)

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

No Pfam abstract.

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

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
(119)
Full
(53379)
Representative proteomes UniProt
(225176)
RP15
(7938)
RP35
(26616)
RP55
(52772)
RP75
(85914)
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
(119)
Full
(53379)
Representative proteomes UniProt
(225176)
RP15
(7938)
RP35
(26616)
RP55
(52772)
RP75
(85914)
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
(119)
Full
(53379)
Representative proteomes UniProt
(225176)
RP15
(7938)
RP35
(26616)
RP55
(52772)
RP75
(85914)
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: Jackhmmer:A3PI49
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 119
Number in full: 53379
Average length of the domain: 103.10 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 15.94 %

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 27.0 9.5
Trusted cut-off 27.0 9.5
Noise cut-off 26.9 9.4
Model length: 104
Family (HMM) version: 9
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

Selections

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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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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_9 domain has been found. There are 282 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
A0A0K3AVF4 View 3D Structure Click here
A0A0R0JTJ5 View 3D Structure Click here
A0A0R0KYL2 View 3D Structure Click here
A0A0R0KYL2 View 3D Structure Click here
A0A0R4IEI6 View 3D Structure Click here
A0A142J9E8 View 3D Structure Click here
A0A1D6EJ16 View 3D Structure Click here
A0A1D6F6I1 View 3D Structure Click here
A0A1D6GUE9 View 3D Structure Click here
A0A1D6H122 View 3D Structure Click here
A0A1D6KQ74 View 3D Structure Click here
A0A1D6KQ74 View 3D Structure Click here
A0A1D6LP15 View 3D Structure Click here
A0A1D6NP39 View 3D Structure Click here
A0A1D6NP39 View 3D Structure Click here
A0A2R8QJW8 View 3D Structure Click here
A0A368UHU4 View 3D Structure Click here
A0A368UHU4 View 3D Structure Click here
A1ZB14 View 3D Structure Click here
A2A5F7 View 3D Structure Click here
A8WHX9 View 3D Structure Click here
B0S5Z9 View 3D Structure Click here
B0S5Z9 View 3D Structure Click here
B0V138 View 3D Structure Click here
B3DJX4 View 3D Structure Click here
B4FVE0 View 3D Structure Click here
B4FVE0 View 3D Structure Click here
B9MST0 View 3D Structure Click here
C0PGG9 View 3D Structure Click here
E7FB36 View 3D Structure Click here
E9Q4S1 View 3D Structure Click here
F1QNK9 View 3D Structure Click here
F1QTV6 View 3D Structure Click here
F1RBF8 View 3D Structure Click here
I1J5K5 View 3D Structure Click here
I1J5K5 View 3D Structure Click here
I1K5J7 View 3D Structure Click here
I1KMQ9 View 3D Structure Click here
I1KQC3 View 3D Structure Click here
I1L1A1 View 3D Structure Click here
I1LR23 View 3D Structure Click here
I1LR23 View 3D Structure Click here
I1M4Q3 View 3D Structure Click here
I1M4Q3 View 3D Structure Click here
I1MDL2 View 3D Structure Click here
I1MDL2 View 3D Structure Click here
I1MGY9 View 3D Structure Click here
I1MRR0 View 3D Structure Click here
I1MSP6 View 3D Structure Click here
I3ITL7 View 3D Structure Click here
K7K556 View 3D Structure Click here
K7MGJ3 View 3D Structure Click here
K7MGJ3 View 3D Structure Click here
O08962 View 3D Structure Click here
O35219 View 3D Structure Click here
O35800 View 3D Structure Click here
O48963 View 3D Structure Click here
O48963 View 3D Structure Click here
O54852 View 3D Structure Click here
O54853 View 3D Structure Click here
O64511 View 3D Structure Click here
O64511 View 3D Structure Click here
O89047 View 3D Structure Click here
O95259 View 3D Structure Click here
O95263 View 3D Structure Click here
P38097 View 3D Structure Click here
P59111 View 3D Structure Click here
P76129 View 3D Structure Click here
P76129 View 3D Structure Click here
P77334 View 3D Structure Click here
P93025 View 3D Structure Click here
P93025 View 3D Structure Click here
Q02280 View 3D Structure Click here
Q12809 View 3D Structure Click here
Q2G2U4 View 3D Structure Click here
Q2QYY8 View 3D Structure Click here
Q2QYY8 View 3D Structure Click here
Q2R2W1 View 3D Structure Click here
Q2RBR1 View 3D Structure Click here
Q2RBR1 View 3D Structure Click here
Q32ME0 View 3D Structure Click here
Q54RP6 View 3D Structure Click here
Q54VU4 View 3D Structure Click here
Q5PQT0 View 3D Structure Click here
Q5PQT0 View 3D Structure Click here
Q5VRX2 View 3D Structure Click here
Q5VRX2 View 3D Structure Click here
Q5Z8K3 View 3D Structure Click here
Q60603 View 3D Structure Click here
Q63472 View 3D Structure Click here
Q67UX0 View 3D Structure Click here
Q6NNF2 View 3D Structure Click here
Q76KC5 View 3D Structure Click here
Q76KC6 View 3D Structure Click here
Q869S5 View 3D Structure Click here
Q8CEE6 View 3D Structure Click here
Q8CEE6 View 3D Structure Click here
Q8NCM2 View 3D Structure Click here
Q8W420 View 3D Structure Click here
Q920E3 View 3D Structure Click here
Q94BT6 View 3D Structure Click here
Q95SH0 View 3D Structure Click here
Q95SH0 View 3D Structure Click here
Q96L42 View 3D Structure Click here
Q96RG2 View 3D Structure Click here
Q96RG2 View 3D Structure Click here
Q9C9W9 View 3D Structure Click here
Q9EPI9 View 3D Structure Click here
Q9ER47 View 3D Structure Click here
Q9H252 View 3D Structure Click here
Q9JHS1 View 3D Structure Click here
Q9NS40 View 3D Structure Click here
Q9QWS8 View 3D Structure Click here
Q9R1T9 View 3D Structure Click here
Q9ST27 View 3D Structure Click here
Q9ST27 View 3D Structure Click here
Q9ULD8 View 3D Structure Click here
Q9UQ05 View 3D Structure Click here
Q9UTH3 View 3D Structure Click here
Q9WVJ0 View 3D Structure Click here