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0  structures 1727  species 0  interactions 5037  sequences 13  architectures

Family: PucR (PF07905)

Summary: Purine catabolism regulatory protein-like 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.

Purine catabolism regulatory protein-like family Provide feedback

The bacterial proteins found in this family are similar to the purine catabolism regulatory protein expressed by Bacillus subtilis (PucR, O32138). PucR is thought to be a transcriptional activator involved in the induction of the purine degradation pathway, and may contain a LysR-like DNA-binding domain. It is similar to LysR-type regulators in that it represses its own expression [1]. The other members of this family are also annotated as being putative regulatory proteins.

Literature references

  1. Schultz AC, Nygaard P, Saxild HH; , J Bacteriol 2001;183:3293-3302.: Functional analysis of 14 genes that constitute the purine catabolic pathway in Bacillus subtilis and evidence for a novel regulon controlled by the PucR transcription activator. PUBMED:11344136 EPMC:11344136


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR012914

This domain is found in the purine catabolism regulatory protein expressed by Bacillus subtilis (PucR, SWISSPROT ).

PucR is thought to be a transcriptional regulator of genes involved in the purine degradation pathway, and may contain a LysR-like DNA-binding domain [ PUBMED:12029039 ]. It is similar to LysR-type regulators in that it represses its own expression [ PUBMED:11344136 ]. The other members of this family are also putative regulatory proteins.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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
(165)
Full
(5037)
Representative proteomes UniProt
(18438)
RP15
(327)
RP35
(2095)
RP55
(5456)
RP75
(9594)
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
(165)
Full
(5037)
Representative proteomes UniProt
(18438)
RP15
(327)
RP35
(2095)
RP55
(5456)
RP75
(9594)
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
(165)
Full
(5037)
Representative proteomes UniProt
(18438)
RP15
(327)
RP35
(2095)
RP55
(5456)
RP75
(9594)
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: Pfam-B_4388 (release 14.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Fenech M
Number in seed: 165
Number in full: 5037
Average length of the domain: 118.9 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 23.69 %

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 33.5 33.5
Trusted cut-off 33.5 33.5
Noise cut-off 33.3 33.4
Model length: 117
Family (HMM) version: 14
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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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
A0A0H3GLA2 View 3D Structure Click here
K0ERM4 View 3D Structure Click here
K0EVT4 View 3D Structure Click here
K0F2X3 View 3D Structure Click here
K0F3G7 View 3D Structure Click here
O32138 View 3D Structure Click here
Q9I2I9 View 3D Structure Click here