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37  structures 5136  species 4  interactions 65493  sequences 316  architectures

Family: Radical_SAM (PF04055)

Summary: Radical SAM superfamily

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.

Radical SAM superfamily Provide feedback

Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.

Literature references

  1. Sofia HJ, Chen G, Hetzler BG, Reyes-Spindola JF, Miller NE; , Nucleic Acids Res 2001;29:1097-1106.: Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. PUBMED:11222759 EPMC:11222759

  2. Benjdia A, Leprince J, Guillot A, Vaudry H, Rabot S, Berteau O; , J Am Chem Soc. 2007;129:3462-3463.: Anaerobic sulfatase-maturating enzymes: radical SAM enzymes able to catalyze in vitro sulfatase post-translational modification. PUBMED:17335281 EPMC:17335281

  3. Berteau O, Guillot A, Benjdia A, Rabot S; , J Biol Chem. 2006;281:22464-22470.: A new type of bacterial sulfatase reveals a novel maturation pathway in prokaryotes. PUBMED:16766528 EPMC:16766528


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007197

Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation. Evidence exists that these proteins generate a radical species by reductive cleavage of S:-adenosylmethionine (SAM) through an unusual Fe-S centre [PUBMED:11222759, PUBMED:15317939].

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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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
(628)
Full
(65493)
Representative proteomes NCBI
(49841)
Meta
(14153)
RP15
(6768)
RP35
(12613)
RP55
(16003)
RP75
(18526)
Jalview View  View  View  View  View  View  View  View 
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PP/heatmap 1              
Pfam viewer View  View             

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(628)
Full
(65493)
Representative proteomes NCBI
(49841)
Meta
(14153)
RP15
(6768)
RP35
(12613)
RP55
(16003)
RP75
(18526)
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
(628)
Full
(65493)
Representative proteomes NCBI
(49841)
Meta
(14153)
RP15
(6768)
RP35
(12613)
RP55
(16003)
RP75
(18526)
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: Bateman A
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 628
Number in full: 65493
Average length of the domain: 169.40 aa
Average identity of full alignment: 14 %
Average coverage of the sequence by the domain: 43.97 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 29.4 29.4
Trusted cut-off 29.4 29.4
Noise cut-off 29.3 29.3
Model length: 166
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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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 4 interactions for this family. More...

HemN_C Mob_synth_C BATS Wyosine_form

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 Radical_SAM domain has been found. There are 37 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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