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414  structures 2175  species 4  interactions 2334  sequences 4  architectures

Family: Ribosomal_L25p (PF01386)

Summary: Ribosomal L25p family

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 L25p family Provide feedback

Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. This family includes Ctc from B. subtilis P14194 which is induced by stress.

Literature references

  1. Stoldt M, Wohnert J, Gorlach M, Brown LR; , EMBO J 1998;17:6377-6384.: The NMR structure of Escherichia coli ribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases. PUBMED:9799245 EPMC:9799245

  2. Stoldt M, Wohnert J, Ohlenschlager O, Gorlach M, Brown LR; , EMBO J 1999;18:6508-6521.: The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition. PUBMED:10562563 EPMC:10562563


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR029751

Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA [PUBMED:9799245, PUBMED:10562563]. Ribosomal protein L25 has a long-form and a short-form. The long-form is represented by the general stress protein Ctc of Bacillus subtilis, which has now been localised to ribosomes [PUBMED:12432960], and ribosomal protein TL5 of Thermus thermophilus. Ribosomal protein L25 of Escherichia coli and Haemophilus influenzae appear to be orthologous, but consist only of the N-terminal half of Ctc and TL5. Both short (L25-like) and full-length (CTC-like) members of this family bind the E-loop of bacterial 5S rRNA [PUBMED:15236599, PUBMED:17198710].

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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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
(757)
Full
(2334)
Representative proteomes UniProt
(9032)
NCBI
(9724)
Meta
(2020)
RP15
(670)
RP35
(1816)
RP55
(3091)
RP75
(4772)
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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
(757)
Full
(2334)
Representative proteomes UniProt
(9032)
NCBI
(9724)
Meta
(2020)
RP15
(670)
RP35
(1816)
RP55
(3091)
RP75
(4772)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(757)
Full
(2334)
Representative proteomes UniProt
(9032)
NCBI
(9724)
Meta
(2020)
RP15
(670)
RP35
(1816)
RP55
(3091)
RP75
(4772)
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: [1]
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 757
Number in full: 2334
Average length of the domain: 87.70 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 43.41 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.5 23.5
Trusted cut-off 23.5 23.5
Noise cut-off 23.3 23.4
Model length: 81
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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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Interactions

There are 4 interactions for this family. More...

Ribosomal_L16 Ribosomal_TL5_C Ribosomal_L16 Ribosomal_S19

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_L25p domain has been found. There are 414 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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