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11  structures 1655  species 0  interactions 3428  sequences 68  architectures

Family: Gar1 (PF04410)

Summary: Gar1/Naf1 RNA binding region

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Gar1/Naf1 RNA binding region Provide feedback

Gar1 is a small nucleolar RNP that is required for pre-mRNA processing and pseudouridylation [1]. It is co-immunoprecipitated with the H/ACA families of snoRNAs. This family represents the conserved central region of Gar1. This region is necessary and sufficient for normal cell growth, and specifically binds two snoRNAs snR10 and snR30. This region is also necessary for nucleolar targeting, and it is thought that the protein is co-transported to the nucleolus as part of a nucleoprotein complex [2]. In humans, Gar1 is also component of telomerase in vivo [3]. Naf1 is an essential protein that plays a role in ribosome biogenesis, modification of spliceosomal small nuclear RNAs and telomere synthesis, and is homologous to Gar1 [4].

Literature references

  1. Venema J, Tollervey D; , Annu Rev Genet 1999;33:261-311.: Ribosome synthesis in Saccharomyces cerevisiae. PUBMED:10690410 EPMC:10690410

  2. Bagni C, Lapeyre B; , J Biol Chem 1998;273:10868-10873.: Gar1p binds to the small nucleolar RNAs snR10 and snR30 in vitro through a nontypical RNA binding element. PUBMED:9556561 EPMC:9556561

  3. Dragon F, Pogacic V, Filipowicz W; , Mol Cell Biol 2000;20:3037-3048.: In vitro assembly of human H/ACA small nucleolar RNPs reveals unique features of U17 and telomerase RNAs. PUBMED:10757788 EPMC:10757788

  4. Leulliot N, Godin KS, Hoareau-Aveilla C, Quevillon-Cheruel S, Varani G, Henry Y, Van Tilbeurgh H;, J Mol Biol. 2007;371:1338-1353.: The box H/ACA RNP assembly factor Naf1p contains a domain homologous to Gar1p mediating its interaction with Cbf5p. PUBMED:17612558 EPMC:17612558

This tab holds annotation information from the InterPro database.

InterPro entry IPR007504

H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes [ PUBMED:16647858 ]. All H/ACA RNPs contain a specific RNA component (snoRNA or scaRNA) and at least four proteins common to all such particles: Cbf5, Gar1, Nhp2 and Nop10. These proteins are highly conserved from yeast to mammals and homologues are also present in archaea [ PUBMED:10871366 ]. The H/ACA protein complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind [ PUBMED:19917616 ].

Naf1 is an RNA-binding protein required for the maturation of box H/ACA snoRNPs complex and ribosome biogenesis. During assembly of the H/ACA snoRNPs complex, it associates with the complex, disappearing during maturation of the complex and being replaced by Gar1 to yield mature H/ACA snoRNPs complex. The core domain of Naf1 is homologous to the core domain of Gar1, suggesting that they share a common Cbf5 binding surface [ PUBMED:17612558 ].

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 EFTPs (CL0575), which has the following description:

This superfamily is characterised ba a barrel that is formed as a greek-key. It is found as the second domain in many elongation factor proteins, as well as in an elaborated from in two ribosomal proteins and in some other N-terminal domains, eg of AlaX and Gar1 and RimM protein famlies.

The clan contains the following 7 members:

Gar1 GTP_EFTU_D2 NSP2_assoc RIBIOP_C Ribosomal_L3 Ribosomal_L35Ae RimM


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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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.

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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: DOMO:DM04007;
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Kerrison ND
Number in seed: 205
Number in full: 3428
Average length of the domain: 86.5 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 22.71 %

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 29.3 29.3
Trusted cut-off 29.4 29.3
Noise cut-off 29.2 29.2
Model length: 92
Family (HMM) version: 17
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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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 Gar1 domain has been found. There are 11 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
A0A044SWP0 View 3D Structure Click here
A0A077Z1J6 View 3D Structure Click here
A0A0D2G1R3 View 3D Structure Click here
A0A0D2HHQ6 View 3D Structure Click here
A0A0H5SCX0 View 3D Structure Click here
A0A0K0DTX9 View 3D Structure Click here
A0A0K0EFG1 View 3D Structure Click here
A0A0N4U8B3 View 3D Structure Click here
A0A0N4U8B4 View 3D Structure Click here
A0A175VY46 View 3D Structure Click here
A0A1C1C698 View 3D Structure Click here
A0A1C1CEN7 View 3D Structure Click here
A0A1D6LQ26 View 3D Structure Click here
A0A1D6M7L3 View 3D Structure Click here
A0A1D6QL43 View 3D Structure Click here
A0A1D8PF56 View 3D Structure Click here
A0A1D8PSP5 View 3D Structure Click here
A0A2K6W3G9 View 3D Structure Click here
A0A3P7DYF9 View 3D Structure Click here
A0A3Q0KU27 View 3D Structure Click here
A0A5K4FA87 View 3D Structure Click here
A1CVY3 View 3D Structure Click here
A3GHP2 View 3D Structure Click here
A4I8L6 View 3D Structure Click here
A4IAK0 View 3D Structure Click here
B4FGF0 View 3D Structure Click here
C0NH00 View 3D Structure Click here
C0NL51 View 3D Structure Click here
C1GUK4 View 3D Structure Click here
C1H2V9 View 3D Structure Click here
F1QXL6 View 3D Structure Click here
I1ML28 View 3D Structure Click here
I1N877 View 3D Structure Click here
K7KY63 View 3D Structure Click here
K7LU49 View 3D Structure Click here
O14360 View 3D Structure Click here
O26972 View 3D Structure Click here
O96722 View 3D Structure Click here
P0CN78 View 3D Structure Click here
P28007 View 3D Structure Click here