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73  structures 1579  species 0  interactions 2117  sequences 29  architectures

Family: EMG1 (PF03587)

Summary: EMG1/NEP1 methyltransferase

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.

EMG1/NEP1 methyltransferase Provide feedback

Members of this family are essential for 40S ribosomal biogenesis. The structure of EMG1 has revealed that it is a novel member of the superfamily of alpha/beta knot fold methyltransferases [2].

Literature references

  1. Eschrich D, Buchhaupt M, Kotter P, Entian KD; , Curr Genet 2002;40:326-338.: Nep1p (Emg1p), a novel protein conserved in eukaryotes and archaea, is involved in ribosome biogenesis. PUBMED:11935223 EPMC:11935223

  2. Leulliot N, Bohnsack MT, Graille M, Tollervey D, Van Tilbeurgh H; , Nucleic Acids Res. 2008;36:629-639.: The yeast ribosome synthesis factor Emg1 is a novel member of the superfamily of alpha/beta knot fold methyltransferases. PUBMED:18063569 EPMC:18063569


This tab holds annotation information from the InterPro database.

InterPro entry IPR005304

8S rRNA (pseudouridine(1248)-N1)-methyltransferase Nep1 (also known as EMG1) methylates pseudouridine at position1248 (Psi1248) in 18S rRNA and is required for small subunit (SSU) ribosomal RNA (rRNA) maturation [ PUBMED:11935223 ]. Mutations in the human homologue cause Bowen-Conradi Syndrome [ PUBMED:20047967 ]. Nep1 is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot [ PUBMED:18063569 , PUBMED:21087996 ].

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 SPOUT (CL0098), which has the following description:

A distinct class of methylases that includes the SpoU and TrmD superfamilies and two superfamilies of predicted methylases defined by the YbeA and MJ0421 proteins in bacteria and archaea, respectively [1] (PFAM:PF00588 PFAM:PF01746). SPOUT is structurally distinct compared to more classical methyltransferases [1]. More specifically, the members of this clan form alpha/beta knots. Knots are extremely rare in protein structures as they pose a folding problem. The mechanism that allow a domain to be folded as a knot are unclear, but are discussed in [2] and reference therein. All members with known structure form homodimers.

The clan contains the following 14 members:

DUF2122 DUF531 EMG1 Methyltrans_RNA Methyltrn_RNA_2 Methyltrn_RNA_3 Methyltrn_RNA_4 RNA_Me_trans SpoU_methylas_C SpoU_methylase SPOUT_MTase SPOUT_MTase_2 Trm56 tRNA_m1G_MT

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 and the UniProtKB 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
(119)
Full
(2117)
Representative proteomes UniProt
(4300)
RP15
(480)
RP35
(1058)
RP55
(1690)
RP75
(2294)
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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
(119)
Full
(2117)
Representative proteomes UniProt
(4300)
RP15
(480)
RP35
(1058)
RP55
(1690)
RP75
(2294)
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
(119)
Full
(2117)
Representative proteomes UniProt
(4300)
RP15
(480)
RP35
(1058)
RP55
(1690)
RP75
(2294)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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: Pfam-B_3290 (release 7.0)
Previous IDs: Mra1; Nep1;
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Mistry J , Wood V
Number in seed: 119
Number in full: 2117
Average length of the domain: 189.8 aa
Average identity of full alignment: 47 %
Average coverage of the sequence by the domain: 73.14 %

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 28.2 28.2
Trusted cut-off 28.2 28.3
Noise cut-off 26.0 28.0
Model length: 206
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

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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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 EMG1 domain has been found. There are 73 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
A0A077ZPQ5 View 3D Structure Click here
A0A0D2GSG4 View 3D Structure Click here
A0A0K0DUX0 View 3D Structure Click here
A0A0K0JN70 View 3D Structure Click here
A0A0N4UM75 View 3D Structure Click here
A0A175VT15 View 3D Structure Click here
A0A1C1CEQ3 View 3D Structure Click here
A0A1D8PF50 View 3D Structure Click here
A0A2K6VE74 View 3D Structure Click here
A0A5S6PSH4 View 3D Structure Click here
A0B5L3 View 3D Structure Click here
A3DNG9 View 3D Structure Click here
A4HX36 View 3D Structure Click here
A4I321 View 3D Structure Click here
B6T8Z1 View 3D Structure Click here
C0NXT6 View 3D Structure Click here
C1H5D7 View 3D Structure Click here
C6A116 View 3D Structure Click here
C6TAF1 View 3D Structure Click here
D3ZDS4 View 3D Structure Click here
F1QQ17 View 3D Structure Click here
G4VLH6 View 3D Structure Click here
I1LPH7 View 3D Structure Click here
J9EPN8 View 3D Structure Click here
K7LDE2 View 3D Structure Click here
K7LZ35 View 3D Structure Click here
K7MJZ0 View 3D Structure Click here
O29524 View 3D Structure Click here
O35130 View 3D Structure Click here
Q06287 View 3D Structure Click here
Q10107 View 3D Structure Click here
Q4CKB4 View 3D Structure Click here
Q4D0P1 View 3D Structure Click here
Q4D5L2 View 3D Structure Click here
Q4DT40 View 3D Structure Click here
Q4DTT4 View 3D Structure Click here
Q57977 View 3D Structure Click here
Q57UH6 View 3D Structure Click here
Q586T6 View 3D Structure Click here
Q5JI44 View 3D Structure Click here