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1238  structures 8727  species 0  interactions 10590  sequences 41  architectures

Family: Ribosomal_L29 (PF00831)

Summary: Ribosomal L29 protein

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Ribosomal L29 protein Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001854

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 L29 is one of the proteins from the large ribosomal subunit. L29 belongs to a family of ribosomal proteins of 63 to 138 amino-acid residues which, on the basis of sequence similarities, groups:

  • Red algal L29.
  • Bacterial L29.
  • Mammalian L35
  • Caenorhabditis elegans L35 (ZK652.4).
  • Yeast L35.

L29 is located on the surface of the large ribosomal subunit, where it participates in forming a protein ring that surrounds the polypeptide exit channel, providing structural support for the ribosome [ PUBMED:10937990 ]. L29 is involved in forming the translocon binding site, along with L19, L22, L23, L24, and L31e. In addition, L29 and L23 form the interaction site for trigger factor (TF) on the ribosomal surface, adjacent to the exit tunnel [ PUBMED:12756233 ]. L29 forms numerous interactions with L23 and with the 23S rRNA.

This family includes eubacterial and archaeal L29 and eukariotic L35 ribosomal proteins, which constitute the uL29 family [ PUBMED:24524803 ].

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 Ribo_L29 (CL0346), which has the following description:

Superfamily includes Ribosomal protein L29 family and its corresponding mitochondrial ribosomal family, L47.

The clan contains the following 2 members:

MRP-L47 Ribosomal_L29


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...

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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.

Representative proteomes UniProt
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Representative proteomes UniProt

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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.

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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...


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: Pfam-B_1296 (release 2.1)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 712
Number in full: 10590
Average length of the domain: 56.8 aa
Average identity of full alignment: 40 %
Average coverage of the sequence by the domain: 64.36 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.5 24.5
Trusted cut-off 24.5 24.5
Noise cut-off 24.4 24.3
Model length: 57
Family (HMM) version: 26
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


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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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The tree shows the occurrence of this domain across different species. More...


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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_L29 domain has been found. There are 1238 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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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
A0A077YXU7 View 3D Structure Click here
A0A0D2HMB9 View 3D Structure Click here
A0A0G2JY60 View 3D Structure Click here
A0A0G2K9Q4 View 3D Structure Click here
A0A0H3GWL2 View 3D Structure Click here
A0A0K0EJF7 View 3D Structure Click here
A0A0N4U6I3 View 3D Structure Click here
A0A175WHZ5 View 3D Structure Click here
A0A1C1CT70 View 3D Structure Click here
A0A1D6ED46 View 3D Structure Click here
A0A1D6FDV3 View 3D Structure Click here
A0A1D6HF36 View 3D Structure Click here
A0A1D6HKQ4 View 3D Structure Click here
A0A1D6QQ10 View 3D Structure Click here
A0A1D8PK30 View 3D Structure Click here
A0A2K6VW31 View 3D Structure Click here
A0B9W3 View 3D Structure Click here
A0L5Y1 View 3D Structure Click here
A0LIJ8 View 3D Structure Click here
A0PXV4 View 3D Structure Click here
A0QSD9 View 3D Structure Click here
A0T0I7 View 3D Structure Click here
A1AVK8 View 3D Structure Click here
A1KB19 View 3D Structure Click here
A1S226 View 3D Structure Click here
A1T0D4 View 3D Structure Click here
A1T4P7 View 3D Structure Click here
A1TJ15 View 3D Structure Click here
A1UBP4 View 3D Structure Click here
A1VIQ8 View 3D Structure Click here
A1W2R5 View 3D Structure Click here
A1WHD3 View 3D Structure Click here
A1WVB4 View 3D Structure Click here
A2SLE9 View 3D Structure Click here
A3CK71 View 3D Structure Click here
A3DJI0 View 3D Structure Click here
A3DNB4 View 3D Structure Click here
A3N366 View 3D Structure Click here
A3PF39 View 3D Structure Click here
A3Q990 View 3D Structure Click here