!!

Powering down the Pfam website
On October 5th, we will start redirecting the traffic from Pfam (pfam.xfam.org) to InterPro (www.ebi.ac.uk/interpro). The Pfam website will be available at legacy.pfam.xfam.org until January 2023, when it will be decommissioned. You can read more about the sunset period in our blog post.

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.
59  structures 1064  species 0  interactions 1254  sequences 2  architectures

Family: PcrB (PF01884)

Summary: PcrB family

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.

PcrB family Provide feedback

This family contains proteins that are related to PcrB Q53726. The function of these proteins is unknown.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008205

This entry represents geranylgeranylglyceryl phosphate (GGGP) synthase and Heptaprenylglyceryl phosphate (HepGP) synthase.

GGGP synthase is a prenyltransferase that catalyses the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). This reaction is the first ether-bond-formation step in the biosynthesis of archaeal membrane lipids. This entry also matches putative glycerol-1-phosphate prenyltransferases that may catalyse the transfer of a prenyl moiety to sn-glycerol-1-phosphate (G1P) [ PUBMED:18558723 ].

HepGP synthase is a prenyltransferase that catalyses in vivo the transfer of the heptaprenyl moiety of heptaprenyl pyrophosphate (HepPP; 35 carbon atoms) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P), producing heptaprenylglyceryl phosphate (HepGP) [ PUBMED:21761520 ].

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...

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
(4)
Full
(1254)
Representative proteomes UniProt
(6804)
RP15
(140)
RP35
(577)
RP55
(1295)
RP75
(2173)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(4)
Full
(1254)
Representative proteomes UniProt
(6804)
RP15
(140)
RP35
(577)
RP55
(1295)
RP75
(2173)
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
(4)
Full
(1254)
Representative proteomes UniProt
(6804)
RP15
(140)
RP35
(577)
RP55
(1295)
RP75
(2173)
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: Enright A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Enright A , Ouzounis C , Bateman A
Number in seed: 4
Number in full: 1254
Average length of the domain: 228 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 94.6 %

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 23.9 23.9
Trusted cut-off 23.9 23.9
Noise cut-off 23.8 23.8
Model length: 226
Family (HMM) version: 20
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 PcrB domain has been found. There are 59 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
A0B8J3 View 3D Structure Click here
A0RYM1 View 3D Structure Click here
A1RXV6 View 3D Structure Click here
A2BIS8 View 3D Structure Click here
A2SSK1 View 3D Structure Click here
A3DN81 View 3D Structure Click here
A4YJ26 View 3D Structure Click here
A6UW70 View 3D Structure Click here
A7I6L7 View 3D Structure Click here
A8A9K6 View 3D Structure Click here
A8FAP9 View 3D Structure Click here
A8MDA4 View 3D Structure Click here
A9A3Z1 View 3D Structure Click here
B1L6Q8 View 3D Structure Click here
B1YJ15 View 3D Structure Click here
B7GFU9 View 3D Structure Click here
B8GHM9 View 3D Structure Click here
C0Z4C0 View 3D Structure Click here
C5D4J0 View 3D Structure Click here
C6A2A3 View 3D Structure Click here
C7PEQ0 View 3D Structure Click here
O26652 View 3D Structure Click here
O29844 View 3D Structure Click here
O34790 View 3D Structure Click here
Q0W6K5 View 3D Structure Click here
Q12VH4 View 3D Structure Click here
Q18KP6 View 3D Structure Click here
Q2FQM4 View 3D Structure Click here
Q2NET5 View 3D Structure Click here
Q3IT31 View 3D Structure Click here
Q49YV0 View 3D Structure Click here
Q4JAS3 View 3D Structure Click here
Q4L7M1 View 3D Structure Click here
Q53726 View 3D Structure Click here
Q58647 View 3D Structure Click here
Q5HN28 View 3D Structure Click here
Q5JDY1 View 3D Structure Click here
Q5L3C1 View 3D Structure Click here
Q5V1N9 View 3D Structure Click here
Q5WJ32 View 3D Structure Click here