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.
1187  structures 8673  species 0  interactions 11880  sequences 102  architectures

Family: Ribosomal_L14 (PF00238)

Summary: Ribosomal protein L14p/L23e

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

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.

Ribosomal protein L14p/L23e Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000218

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [ PUBMED:11297922 , PUBMED:11290319 ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [ PUBMED:11290319 , PUBMED:11114498 ].

Ribosomal protein L14 is one of the proteins from the large ribosomal subunit. In eubacteria, L14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins, which have been grouped on the basis of sequence similarities. Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins [ PUBMED:15299380 ]. L14 is a protein of 119 to 137 amino-acid residues.

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...

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...

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
(280)
Full
(11880)
Representative proteomes UniProt
(52607)
RP15
(1896)
RP35
(5859)
RP55
(11203)
RP75
(17945)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(280)
Full
(11880)
Representative proteomes UniProt
(52607)
RP15
(1896)
RP35
(5859)
RP55
(11203)
RP75
(17945)
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
(280)
Full
(11880)
Representative proteomes UniProt
(52607)
RP15
(1896)
RP35
(5859)
RP55
(11203)
RP75
(17945)
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: Prosite
Previous IDs: L14;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 280
Number in full: 11880
Average length of the domain: 119.80 aa
Average identity of full alignment: 51 %
Average coverage of the sequence by the domain: 90.04 %

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 23.6 23.6
Trusted cut-off 23.6 23.7
Noise cut-off 23.2 23.5
Model length: 122
Family (HMM) version: 21
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 Ribosomal_L14 domain has been found. There are 1187 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...

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
A0A0N7KGJ7 View 3D Structure Click here
A0A0P0VRI0 View 3D Structure Click here
A0A0R0FA21 View 3D Structure Click here
A0A0R0HSN1 View 3D Structure Click here
A0A0R0L8S6 View 3D Structure Click here
A0A0R0L8S6 View 3D Structure Click here
A0A140KXV7 View 3D Structure Click here
A0A1D6KFN8 View 3D Structure Click here
A0A1D6LSE9 View 3D Structure Click here
A0A1D6QI05 View 3D Structure Click here
A0A1D8PMU5 View 3D Structure Click here
A0A1D8PPT5 View 3D Structure Click here
A0A381MV60 View 3D Structure Click here
A4IAF0 View 3D Structure Click here
B4FGL4 View 3D Structure Click here
B6TKU6 View 3D Structure Click here
C0H4F0 View 3D Structure Click here
C6T0H9 View 3D Structure Click here
I1JZH4 View 3D Structure Click here
I1KY31 View 3D Structure Click here
K7M4L7 View 3D Structure Click here
K7N2C3 View 3D Structure Click here
O21033 View 3D Structure Click here
O94292 View 3D Structure Click here
P08529 View 3D Structure Click here
P0ADY3 View 3D Structure Click here
P0C440 View 3D Structure Click here
P0CT60 View 3D Structure Click here
P0CT61 View 3D Structure Click here
P0CX41 View 3D Structure Click here
P0CX42 View 3D Structure Click here
P35996 View 3D Structure Click here
P48158 View 3D Structure Click here
P48159 View 3D Structure Click here
P49690 View 3D Structure Click here
P54037 View 3D Structure Click here
P56792 View 3D Structure Click here
P62829 View 3D Structure Click here
P62830 View 3D Structure Click here
P62832 View 3D Structure Click here
P9WHD9 View 3D Structure Click here
Q25812 View 3D Structure Click here
Q2FW16 View 3D Structure Click here
Q2PMP9 View 3D Structure Click here
Q2QM60 View 3D Structure Click here
Q4CKV3 View 3D Structure Click here
Q4E4R0 View 3D Structure Click here
Q4E4R1 View 3D Structure Click here
Q54G86 View 3D Structure Click here
Q6P1L8 View 3D Structure Click here
Q6PC14 View 3D Structure Click here
Q7M0E7 View 3D Structure Click here
Q7ZUH5 View 3D Structure Click here
Q84JG5 View 3D Structure Click here
Q8IE09 View 3D Structure Click here
Q93Z17 View 3D Structure Click here
Q9AV77 View 3D Structure Click here
Q9D1I6 View 3D Structure Click here
Q9W4Z2 View 3D Structure Click here