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351  structures 6498  species 3  interactions 6790  sequences 7  architectures

Family: Ribosomal_TL5_C (PF14693)

Summary: Ribosomal protein TL5, C-terminal domain

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Ribosomal protein TL5, C-terminal domain Provide feedback

This family contains the C-terminal domain of ribosomal protein TL5. The N-terminal domain, which binds to 5S rRNA, is contained in family Ribosomal_L25p, PF01386. Full length (N- and C-terminal domain) homologues of TL5 are also known as CTC proteins. TL5 or CTC are not found in Eukarya or Archaea. In some Bacteria, including E. coli, this ribosomal subunit occurs as a single domain protein (named Ribosomal subunit L25), where the only domain is homologous to TL5 N-terminal domain (hence included in family PF01386). The function of the C-terminal domain of TLC is at present unknown.

Literature references

  1. Fedorov R, Meshcheryakov V, Gongadze G, Fomenkova N, Nevskaya N, Selmer M, Laurberg M, Kristensen O, Al-Karadaghi S, Liljas A, Garber M, Nikonov S;, Acta Crystallogr D Biol Crystallogr. 2001;57:968-976.: Structure of ribosomal protein TL5 complexed with RNA provides new insights into the CTC family of stress proteins. PUBMED:11418764 EPMC:11418764


This tab holds annotation information from the InterPro database.

InterPro entry IPR020057

The bacterial ribosomal protein L25 is bound to 5S rRNA along with L5 and L18, forming a separate domain of the ribosome [PUBMED:10696113]. The solution structure of protein L25 uncomplexed with RNA shows two significantly disordered loops and a closed beta-barrel domain with a complex topology that has significant structural similarities to the N-terminal domain of the Thermus thermophilus ribosomal protein TL5, to the general stress protein CTC, and to the C-terminal anticodon-binding domain of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) [PUBMED:11418764, PUBMED:12737824]. GlnRS contains a duplication consisting of two L25-like beta-barrels domains with the swapping of N-terminal strands.

This entry represents a domain with a mainly beta-strand structure found in ribosomal L25-like proteins.

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
(727)
Full
(6790)
Representative proteomes UniProt
(17942)
NCBI
(18484)
Meta
(2021)
RP15
(1965)
RP35
(4902)
RP55
(7036)
RP75
(9515)
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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
(727)
Full
(6790)
Representative proteomes UniProt
(17942)
NCBI
(18484)
Meta
(2021)
RP15
(1965)
RP35
(4902)
RP55
(7036)
RP75
(9515)
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
(727)
Full
(6790)
Representative proteomes UniProt
(17942)
NCBI
(18484)
Meta
(2021)
RP15
(1965)
RP35
(4902)
RP55
(7036)
RP75
(9515)
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: CATH:1feu_A_02
Previous IDs: ShortName;
Type: Domain
Sequence Ontology: SO:0000417
Author: Punta M
Number in seed: 727
Number in full: 6790
Average length of the domain: 85.10 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 40.20 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.3
Noise cut-off 26.9 26.7
Model length: 86
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
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 3 interactions for this family. More...

Ribosomal_L11 Ribosomal_L25p Ribosomal_L16

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_TL5_C domain has been found. There are 351 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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