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.
1223  structures 8673  species 0  interactions 11738  sequences 64  architectures

Family: Ribosomal_S9 (PF00380)

Summary: Ribosomal protein S9/S16

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 S9/S16 Provide feedback

This family includes small ribosomal subunit S9 from prokaryotes and S16 from eukaryotes.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000754

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 S9 is one of the proteins from the small ribosomal subunit. It belongs to the S9P family of ribosomal proteins which, on the basis of sequence similarities [ PUBMED:2332055 ], groups bacterial; algal chloroplast; cyanelle and archaeal S9 proteins; and mammalian, plant, and yeast mitochondrial ribosomal S9 proteins. These proteins adopt a beta-alpha-beta fold similar to that found in numerous RNA/DNA-binding proteins, as well as in kinases from the GHMP kinase family [ PUBMED:8722013 ].

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 S5 (CL0329), which has the following description:

This superfamily contains a wide range of families that possess a structure similar to the second domain of ribosomal S5 protein.

The clan contains the following 18 members:

ChlI DNA_gyraseB DNA_mis_repair EFG_IV Fae GalKase_gal_bdg GHMP_kinases_N IGPD Lon_C LpxC Morc6_S5 Ribonuclease_P Ribosomal_S5_C Ribosomal_S9 RNase_PH Topo-VIb_trans UPF0029 Xol-1_N

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
(622)
Full
(11738)
Representative proteomes UniProt
(44611)
RP15
(1954)
RP35
(5828)
RP55
(11129)
RP75
(17846)
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
(622)
Full
(11738)
Representative proteomes UniProt
(44611)
RP15
(1954)
RP35
(5828)
RP55
(11129)
RP75
(17846)
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
(622)
Full
(11738)
Representative proteomes UniProt
(44611)
RP15
(1954)
RP35
(5828)
RP55
(11129)
RP75
(17846)
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: S9;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD
Number in seed: 622
Number in full: 11738
Average length of the domain: 122.10 aa
Average identity of full alignment: 45 %
Average coverage of the sequence by the domain: 69.53 %

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 22.5 22.5
Trusted cut-off 22.5 22.6
Noise cut-off 22.4 22.4
Model length: 121
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_S9 domain has been found. There are 1223 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
A0A1D6ILX8 View 3D Structure Click here
A0A1D8PCW6 View 3D Structure Click here
A4I218 View 3D Structure Click here
B0BN68 View 3D Structure Click here
B4FR40 View 3D Structure Click here
B6SNQ7 View 3D Structure Click here
B6TG61 View 3D Structure Click here
B6TVN0 View 3D Structure Click here
C6SXF0 View 3D Structure Click here
C6T5U0 View 3D Structure Click here
F1QP17 View 3D Structure Click here
I1JE09 View 3D Structure Click here
I1KM19 View 3D Structure Click here
I1KQE3 View 3D Structure Click here
I1LIK9 View 3D Structure Click here
I1LPC4 View 3D Structure Click here
I1M8G8 View 3D Structure Click here
M0R4I3 View 3D Structure Click here
M0R8S7 View 3D Structure Click here
O14006 View 3D Structure Click here
O94150 View 3D Structure Click here
P0A7X3 View 3D Structure Click here
P0CT64 View 3D Structure Click here
P0CT65 View 3D Structure Click here
P0CX51 View 3D Structure Click here
P0CX52 View 3D Structure Click here
P14131 View 3D Structure Click here
P34388 View 3D Structure Click here
P38120 View 3D Structure Click here
P54024 View 3D Structure Click here
P62249 View 3D Structure Click here
P62250 View 3D Structure Click here
P82933 View 3D Structure Click here
P9WH25 View 3D Structure Click here
Q0IQF7 View 3D Structure Click here
Q1LWH1 View 3D Structure Click here
Q22054 View 3D Structure Click here
Q2FW39 View 3D Structure Click here
Q42340 View 3D Structure Click here
Q4D1L2 View 3D Structure Click here
Q4D916 View 3D Structure Click here
Q4DEK4 View 3D Structure Click here
Q4DEW9 View 3D Structure Click here
Q54CK4 View 3D Structure Click here
Q54Q51 View 3D Structure Click here
Q7XAM9 View 3D Structure Click here
Q8IAX5 View 3D Structure Click here
Q8IHZ4 View 3D Structure Click here
Q8ILW1 View 3D Structure Click here
Q8L6Z4 View 3D Structure Click here
Q8SXF0 View 3D Structure Click here
Q9D7N3 View 3D Structure Click here
Q9M8X9 View 3D Structure Click here
Q9SK22 View 3D Structure Click here
Q9W237 View 3D Structure Click here
Q9XJ27 View 3D Structure Click here
Q9XJ28 View 3D Structure Click here