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154  structures 5253  species 0  interactions 11402  sequences 109  architectures

Family: SQS_PSY (PF00494)

Summary: Squalene/phytoene synthase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Squalene/phytoene synthase Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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 Terp_synthase (CL0613), which has the following description:

This superfamily includes a diverse range of terpene synthase enzymes which share an alpha helical core.

The clan contains the following 7 members:

HEPPP_synt_1 polyprenyl_synt SQS_PSY Terpene_syn_C_2 Terpene_synth_C TRI5 UbiA

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
(88)
Full
(11402)
Representative proteomes UniProt
(38377)
RP15
(1483)
RP35
(5141)
RP55
(10631)
RP75
(17065)
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
(88)
Full
(11402)
Representative proteomes UniProt
(38377)
RP15
(1483)
RP35
(5141)
RP55
(10631)
RP75
(17065)
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
(88)
Full
(11402)
Representative proteomes UniProt
(38377)
RP15
(1483)
RP35
(5141)
RP55
(10631)
RP75
(17065)
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: Prosite
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 88
Number in full: 11402
Average length of the domain: 252.80 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 74.27 %

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 26.0 26.0
Trusted cut-off 26.0 26.0
Noise cut-off 25.8 25.9
Model length: 263
Family (HMM) version: 21
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

Align selected sequences to HMM

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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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Tree controls

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The tree shows the occurrence of this domain across different species. More...

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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 SQS_PSY domain has been found. There are 154 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
A0A0R0HM78 View 3D Structure Click here
A0A0R4IVV5 View 3D Structure Click here
A0A0R4J4H6 View 3D Structure Click here
A0A1D6IAQ5 View 3D Structure Click here
A0A1D6L8A5 View 3D Structure Click here
A0A1D6LJ95 View 3D Structure Click here
A0A1D6LKM3 View 3D Structure Click here
A0A1D6LKM3 View 3D Structure Click here
A0A1D8PI71 View 3D Structure Click here
A0A1D8PJ15 View 3D Structure Click here
A2AIL4 View 3D Structure Click here
A4I799 View 3D Structure Click here
A4ID42 View 3D Structure Click here
B0KZ40 View 3D Structure Click here
B4FE64 View 3D Structure Click here
B4FPS7 View 3D Structure Click here
B6UV92 View 3D Structure Click here
C6T9N7 View 3D Structure Click here
D3ZN43 View 3D Structure Click here
F1QP26 View 3D Structure Click here
I1JJ15 View 3D Structure Click here
I1LJ81 View 3D Structure Click here
I1LWA3 View 3D Structure Click here
I1M704 View 3D Structure Click here
I1MY84 View 3D Structure Click here
K7KAF9 View 3D Structure Click here
K7L9Y2 View 3D Structure Click here
K7M8C2 View 3D Structure Click here
K7MRJ6 View 3D Structure Click here
O22105 View 3D Structure Click here
O22106 View 3D Structure Click here
O65688 View 3D Structure Click here
P29704 View 3D Structure Click here
P36596 View 3D Structure Click here
P37268 View 3D Structure Click here
P37271 View 3D Structure Click here
P49085 View 3D Structure Click here
P53798 View 3D Structure Click here
P53799 View 3D Structure Click here
P9WHP3 View 3D Structure Click here
Q02769 View 3D Structure Click here
Q17477 View 3D Structure Click here
Q2FV59 View 3D Structure Click here
Q2QLV9 View 3D Structure Click here
Q330K2 View 3D Structure Click here
Q4CWB4 View 3D Structure Click here
Q4CXF7 View 3D Structure Click here
Q4DKX1 View 3D Structure Click here
Q54DR1 View 3D Structure Click here
Q54E48 View 3D Structure Click here
Q5Z5B7 View 3D Structure Click here
Q6EI12 View 3D Structure Click here
Q6Z368 View 3D Structure Click here
Q8H625 View 3D Structure Click here
Q9SI77 View 3D Structure Click here
Q9VYS5 View 3D Structure Click here