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0  structures 179  species 0  interactions 196  sequences 3  architectures

Family: Ribosomal_L50 (PF10501)

Summary: Ribosomal subunit 39S

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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 subunit 39S Provide feedback

The 39S ribosomal protein appears to be a subunit of one of the larger mitochondrial 66S or 70S units [1]. Under conditions of ethanol-stress in rats the larger subunit is largely dissociated into its smaller components [2]. In E. coli, in the absence of the enzyme pseudouridine synthase (RluD) synthase, there is an accumulation of 50S and 30S subunits and the appearance of abnormal particles (62S and 39S), with concomitant loss of 70S ribosomes [2].

Literature references

  1. Cahill A, Baio DL, Ivester P, Cunningham CC; , Alcohol Clin Exp Res. 1996;20:1362-1367.: Differential effects of chronic ethanol consumption on hepatic mitochondrial and cytoplasmic ribosomes. PUBMED:8947311 EPMC:8947311

  2. Gutgsell NS, Deutscher MP, Ofengand J; , RNA. 2005;11:1141-1152.: The pseudouridine synthase RluD is required for normal ribosome assembly and function in Escherichia coli. PUBMED:15928344 EPMC:15928344


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR018305

This entry represents the L50 protein from the mitochondrial 39S ribosomal subunit. L50 appears to be a secondary RNA-binding protein [PUBMED:3129699]. The 39S ribosomal protein appears to be a subunit of one of the larger mitochondrial 66S or 70S units [PUBMED:8947311]. Under conditions of ethanol-stress in rats the larger subunit is largely dissociated into its smaller components [PUBMED:15928344].

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...

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Pfam Clan

This family is a member of clan PP-binding (CL0314), which has the following description:

The clan contains the following 4 members:

DUF1493 PP-binding PP-binding_2 Ribosomal_L50

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
(30)
Full
(196)
Representative proteomes NCBI
(199)
Meta
(2)
RP15
(28)
RP35
(59)
RP55
(106)
RP75
(144)
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PP/heatmap 1 View  View  View  View  View     
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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
(30)
Full
(196)
Representative proteomes NCBI
(199)
Meta
(2)
RP15
(28)
RP35
(59)
RP55
(106)
RP75
(144)
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
(30)
Full
(196)
Representative proteomes NCBI
(199)
Meta
(2)
RP15
(28)
RP35
(59)
RP55
(106)
RP75
(144)
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.

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: TreeFam_TF105895
Previous IDs: Ribosomal_S39;
Type: Domain
Author: Buljan M, Coggill P
Number in seed: 30
Number in full: 196
Average length of the domain: 108.30 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 36.59 %

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 25.1 25.1
Trusted cut-off 25.1 25.3
Noise cut-off 24.9 24.9
Model length: 112
Family (HMM) version: 4
Download: download the raw HMM for this family

Species distribution

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