Summary: Ribosomal L25p family
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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
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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
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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
SCOP: | 1dfu |
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]. Eukaryotes contain a protein called L25, which is not homologous to bacterial L25, but rather to bacterial L23.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | ribosome (GO:0005840) |
Molecular function | 5S rRNA binding (GO:0008097) |
structural constituent of ribosome (GO:0003735) | |
Biological process | translation (GO:0006412) |
Domain organisation
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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...
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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 (740) |
Full (7203) |
Representative proteomes | UniProt (19897) |
NCBI (19844) |
Meta (2019) |
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RP15 (2020) |
RP35 (5086) |
RP55 (7441) |
RP75 (10329) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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not generated,
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Seed (740) |
Full (7203) |
Representative proteomes | UniProt (19897) |
NCBI (19844) |
Meta (2019) |
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RP15 (2020) |
RP35 (5086) |
RP55 (7441) |
RP75 (10329) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | [1] |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 740 |
Number in full: | 7203 |
Average length of the domain: | 87.40 aa |
Average identity of full alignment: | 31 % |
Average coverage of the sequence by the domain: | 42.84 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 81 | ||||||||||||
Family (HMM) version: | 19 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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_S19 Ribosomal_L16 Ribosomal_TL5_C Ribosomal_L16Structures
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 568 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.
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