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1  structure 2421  species 0  interactions 2465  sequences 3  architectures

Family: YqeY (PF09424)

Summary: Yqey-like 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 "Yqey protein domain". More...

Yqey protein domain Edit Wikipedia article

YqeY
PDB 1ng6 EBI.jpg
structure of cytosolic protein of unknown function yqey from bacillus subtilis
Identifiers
Symbol YqeY
Pfam PF09424
Pfam clan CL0279
InterPro IPR019004
SCOP 1ng5
SUPERFAMILY 1ng5

In molecular biology, the protein domain Yqey is a putative protein of unknown function. It is thought to possibly have a role in protein synthesis, by aiding a molecule named, tRNA, to translate of mRNA into protein. This hypothetical explanation is further supported by structural homology to other tRNA binding proteins.

Function[edit]

The Yqey domain has been found to be involved in the recognition of transfer RNA charged with Glutamine (tRNAGln) recognition. It has also been demonstrated that Yqey plays the role of an affinity enhancer of GlnRS for tRNAGln acting only in cis. However, the presence of Yqey in free state in organisms lacking GlnRS, suggests that this domain may exert additional cellular functions. [1] The function of the Yqey protein domain still remains to be full elucidated, however, sequence homology, may provide a clue.

Homology[edit]

This protein domain shares sequence homology with the C-terminal domain of GatB and GatE, the tRNA-binding subunits of bacterial and archaeal AdTs.[1]

References[edit]

  1. ^ a b Deniziak M, Sauter C, Becker HD, Paulus CA, Giegé R, Kern D (2007). "Deinococcus glutaminyl-tRNA synthetase is a chimer between proteins from an ancient and the modern pathways of aminoacyl-tRNA formation.". Nucleic Acids Res 35 (5): 1421–31. doi:10.1093/nar/gkl1164. PMC 1865053. PMID 17284460. 

This article incorporates text from the public domain Pfam and InterPro IPR019004

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.

Yqey-like protein Provide feedback

The function of this domain found in the YqeY protein is uncertain.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR019004

Putative protein of unknown function; the authentic protein is detected in highly purified mitochondria in high-throughput studies; YOR215C is not an essential gene.

Domain organisation

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

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Pfam Clan

This family is a member of clan GatB_YqeY (CL0279), which contains the following 2 members:

GatB_Yqey YqeY

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
(42)
Full
(2465)
Representative proteomes NCBI
(1873)
Meta
(2150)
RP15
(253)
RP35
(495)
RP55
(623)
RP75
(718)
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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
(42)
Full
(2465)
Representative proteomes NCBI
(1873)
Meta
(2150)
RP15
(253)
RP35
(495)
RP55
(623)
RP75
(718)
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
(42)
Full
(2465)
Representative proteomes NCBI
(1873)
Meta
(2150)
RP15
(253)
RP35
(495)
RP55
(623)
RP75
(718)
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: Bateman A
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 42
Number in full: 2465
Average length of the domain: 142.00 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 94.47 %

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 20.8 20.8
Trusted cut-off 20.8 20.8
Noise cut-off 20.7 20.6
Model length: 143
Family (HMM) version: 5
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 YqeY domain has been found. There are 1 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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