Summary: Purine catabolism regulatory protein-like family
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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
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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
SCOOP: | DRTGG Hpr_kinase_N Peripla_BP_1 Peripla_BP_4 Peripla_BP_6 |
Similarity to PfamA using HHSearch: | Hpr_kinase_N DRTGG |
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...
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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 (165) |
Full (5037) |
Representative proteomes | UniProt (18438) |
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RP15 (327) |
RP35 (2095) |
RP55 (5456) |
RP75 (9594) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (165) |
Full (5037) |
Representative proteomes | UniProt (18438) |
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RP15 (327) |
RP35 (2095) |
RP55 (5456) |
RP75 (9594) |
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Raw Stockholm | |||||||
Gzipped |
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
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
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 117 | ||||||||||||
Family (HMM) version: | 14 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 |
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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 |