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62  structures 20499  species 9  interactions 37485  sequences 83  architectures

Family: EFG_II (PF14492)

Summary: Elongation Factor G, domain II

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Elongation Factor G, domain II Provide feedback

This domain is found in Elongation Factor G. It shares a similar structure with domain V (PF00679).

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR009022

EF2 (or EFG) participates in the elongation phase of protein synthesis by promoting the GTP-dependent translocation of the peptidyl tRNA of the nascent protein chain from the A-site (acceptor site) to the P-site (peptidyl tRNA site) of the ribosome. EF2 also has a role after the termination phase of translation, where, together with the ribosomal recycling factor, it facilitates the release of tRNA and mRNA from the ribosome, and the splitting of the ribosome into two subunits [PUBMED:12471894]. EF2 is folded into five domains, with domains I and II forming the N-terminal block, domains IV and V forming the C-terminal block, and domain III providing the covalently-linked flexible connection between the two. Domains III and V have the same fold (although they are not completely superimposable and domain III lacks some of the superfamily characteristics), consisting of an alpha/beta sandwich with an antiparallel beta-sheet in a (beta/alpha/beta)x2 topology [PUBMED:11054294]. This double split beta/alpha/beta fold is also seen in a number of ribonucleotide binding proteins. It is the most common motif occurring in the translation system and is referred to as the ribonucleoprotein (RNP) or RNA recognition (RRM) motif.

This domain is found in EF2 proteins from both prokaryotes and eukaryotes, as well as in some tetracycline resistance proteins, peptide chain release factors [PUBMED:8643594], and in the C-terminal region of the bacterial hypothetical protein, YigZ.

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 EF-G_C (CL0437), which has the following description:

This superfamily is characterised by being an alpha-beta 2-Layer Sandwich. It is found in EF2 proteins from both prokaryotes and eukaryotes, as well as in some tetracycline resistance proteins, peptide chain release factors ], and in the C-terminal region of the bacterial hypothetical protein, YigZ.

The clan contains the following 7 members:

DUF1949 EFG_C EFG_II Elong_Iki1 ELP6 RF3_C SBDS_C

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(86)
Full
(37485)
Representative proteomes NCBI
(18882)
Meta
(3371)
RP15
(1200)
RP35
(2713)
RP55
(3858)
RP75
(4843)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(86)
Full
(37485)
Representative proteomes NCBI
(18882)
Meta
(3371)
RP15
(1200)
RP35
(2713)
RP55
(3858)
RP75
(4843)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(86)
Full
(37485)
Representative proteomes NCBI
(18882)
Meta
(3371)
RP15
(1200)
RP35
(2713)
RP55
(3858)
RP75
(4843)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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: Jackhmmer:A0YMC3
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 86
Number in full: 37485
Average length of the domain: 72.60 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 10.67 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 75
Family (HMM) version: 2
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 9 interactions for this family. More...

Ribosom_S12_S23 GTP_EFTU_D2 EFG_C RRF GTP_EFTU GTP_EFTU Ribosom_S12_S23 Exotox-A_cataly EFG_IV

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 EFG_II domain has been found. There are 62 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 seqence.

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