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7  structures 1071  species 0  interactions 1580  sequences 2  architectures

Family: ProQ (PF04352)

Summary: ProQ/FINO family

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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.

ProQ/FINO family Provide feedback

This family includes ProQ, which is required for full activation of the osmoprotectant transporter, ProQ, 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].

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


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 in 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 entry also includes ProQ, which is 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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(46)
Full
(1580)
Representative proteomes NCBI
(857)
Meta
(21)
RP15
(25)
RP35
(76)
RP55
(133)
RP75
(186)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(46)
Full
(1580)
Representative proteomes NCBI
(857)
Meta
(21)
RP15
(25)
RP35
(76)
RP55
(133)
RP75
(186)
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
(46)
Full
(1580)
Representative proteomes NCBI
(857)
Meta
(21)
RP15
(25)
RP35
(76)
RP55
(133)
RP75
(186)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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
Author: Mifsud W, Moxon SJ, Bateman A
Number in seed: 46
Number in full: 1580
Average length of the domain: 115.00 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 57.46 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.7 21.7
Trusted cut-off 21.8 22.0
Noise cut-off 21.0 21.6
Model length: 115
Family (HMM) version: 8
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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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 7 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 seqence.

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