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.
313  structures 3378  species 0  interactions 3788  sequences 8  architectures

Family: Hfq (PF17209)

Summary: Hfq protein

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Hfq protein". More...

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Hfq protein Provide feedback

No Pfam abstract.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005001

This entry represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory non-coding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam:RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see PUBMED:8197116). The name Hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.

The Hfq protein is conserved in a wide range of bacteria and varies in length from 70 to 100 amino acids. In all cases, a conserved Sm motif is located in the N-terminal halves of the molecules. The Hfq protein of E. coli is an 11 kDa polypeptide that forms a hexameric ring-shaped structure. Structural studies have suggested that the beta-4 strand in one molecule dimerises with the beta-5 strand of a neighbouring subunit to form the hexamer. These two strands move with a concerted mobility which may explain the stability of the entire structure [PUBMED:12095248].

The architecture of the Hfq-RNA complex suggests two, not mutually exclusive, mechanisms by which Hfq might exert its function as modulator of RNA-RNA interactions. First, when Hfq binds single-stranded RNA, the target site is unwound in a circular manner. This would greatly destabilise surrounding RNA structures that are located several nucleotides on either side of the binding site, thereby permitting new RNA-RNA interactions. Secondly, the repetition of identical BPs on the Hfq hexamer implies that the binding surface can accommodate more than just a single RNA target. This would allow simultaneous binding of two RNA strands and could greatly enhance interaction between the strands [PUBMED:15009882].

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...

Pfam Clan

This family is a member of clan Sm-like (CL0527), which has the following description:

Conserved domain of core RNA-binding proteins of mRNA splicing and rRNA processing complexes, with a SH3-like Beta-barrel

The clan contains the following 5 members:

DUF903 Hfq LSM LSM14 SM-ATX

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, the UniProtKB sequence database, 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
(147)
Full
(3788)
Representative proteomes UniProt
(11826)
NCBI
(9813)
Meta
(280)
RP15
(806)
RP35
(2349)
RP55
(3735)
RP75
(5568)
Jalview View  View  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
(147)
Full
(3788)
Representative proteomes UniProt
(11826)
NCBI
(9813)
Meta
(280)
RP15
(806)
RP35
(2349)
RP55
(3735)
RP75
(5568)
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
(147)
Full
(3788)
Representative proteomes UniProt
(11826)
NCBI
(9813)
Meta
(280)
RP15
(806)
RP35
(2349)
RP55
(3735)
RP75
(5568)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: Bateman A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 147
Number in full: 3788
Average length of the domain: 63.60 aa
Average identity of full alignment: 56 %
Average coverage of the sequence by the domain: 72.96 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.3 21.3
Trusted cut-off 21.3 21.3
Noise cut-off 21.2 21.2
Model length: 64
Family (HMM) version: 3
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 Hfq domain has been found. There are 313 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...