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9  structures 813  species 0  interactions 1020  sequences 8  architectures

Family: ProQ (PF04352)

Summary: ProQ/FINO family

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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.

ProQ/FINO family Provide feedback

This family includes ProQ, which is required for full activation of the osmoprotectant transporter, ProP, in Escherichia coli. This family includes several bacterial fertility inhibition (FINO) proteins. The conjugative transfer of F-like plasmids is repressed by FinO, an RNA binding protein. FinO interacts with the F-plasmid encoded traJ mRNA and its antisense RNA, FinP, stabilising FinP against endonucleolytic degradation and facilitating sense-antisense RNA recognition [2]. ProQ operates as an RNA-chaperone, binding RNA and bringing about both RNA strand-exchange and RNA duplexing. This suggests that in fact it does not regulate ProP transcription but rather regulates ProP translation through activity as an RNA-binding protein [3].

Literature references

  1. Kunte HJ, Crane RA, Culham DE, Richmond D, Wood JM; , J Bacteriol 1999;181:1537-1543.: Protein ProQ influences osmotic activation of compatible solute transporter ProP in Escherichia coli K-12. PUBMED:10049386 EPMC:10049386

  2. Ghetu AF, Gubbins MJ, Frost LS, Glover JN; , Nat Struct Biol 2000;7:565-569.: Crystal structure of the bacterial conjugation repressor finO. PUBMED:10876242 EPMC:10876242

  3. Chaulk SG, Smith Frieday MN, Arthur DC, Culham DE, Edwards RA, Soo P, Frost LS, Keates RA, Glover JN, Wood JM;, Biochemistry. 2011;50:3095-3106.: ProQ is an RNA chaperone that controls ProP levels in Escherichia coli. PUBMED:21381725 EPMC:21381725


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR016103

This entry represents a structural domain consisting of six helices in an irregular non-globular array; it also contains two small beta-hairpins. This domain is found at the C terminus of the RNA-binding fertility inhibitor FinO that represses the conjugative transfer of F-like plasmids in Escherichia coli. FinO blocks the translation of TraJ, a positive activator of transcription of gene thereby protecting it from degradation, and catalyses FinP-TraJ mRNA hybridization. Interactions between these two RNAs are predicted to block the TraJ ribosomal binding site. FinO is largely helical, binds to its highest affinity binding site within FinP as a monomer, and contains two distinct RNA binding regions [ PUBMED:10876242 ].

This domain is also found as an N-terminal domain in ProQ, a protein required for full activation of the osmoprotectant transporter ProP in Escherichia coli [ PUBMED:10049386 ].

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
(51)
Full
(1020)
Representative proteomes UniProt
(8516)
RP15
(102)
RP35
(406)
RP55
(1040)
RP75
(2179)
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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
(51)
Full
(1020)
Representative proteomes UniProt
(8516)
RP15
(102)
RP35
(406)
RP55
(1040)
RP75
(2179)
Alignment:
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Sequence:
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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
(51)
Full
(1020)
Representative proteomes UniProt
(8516)
RP15
(102)
RP35
(406)
RP55
(1040)
RP75
(2179)
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: COG3109 & Pfam-B_7673 (release 7.7)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mifsud W , Moxon SJ , Bateman A
Number in seed: 51
Number in full: 1020
Average length of the domain: 107.20 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 51.23 %

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 21.7 21.7
Trusted cut-off 22.1 22.6
Noise cut-off 21.2 21.5
Model length: 110
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Viroids Viroids Unclassified sequence Unclassified sequence

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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 ProQ domain has been found. There are 9 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
P45577 View 3D Structure Click here