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138  structures 8763  species 0  interactions 128752  sequences 714  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.

This is the Wikipedia entry entitled "Radical SAM". More...

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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 (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
(491)
Full
(128752)
Representative proteomes UniProt
(616456)
RP15
(20575)
RP35
(66542)
RP55
(129255)
RP75
(213782)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(491)
Full
(128752)
Representative proteomes UniProt
(616456)
RP15
(20575)
RP35
(66542)
RP55
(129255)
RP75
(213782)
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
(491)
Full
(128752)
Representative proteomes UniProt
(616456)
RP15
(20575)
RP35
(66542)
RP55
(129255)
RP75
(213782)
Raw Stockholm Download   Download   Download   Download   Download      
Gzipped 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: Bateman A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 491
Number in full: 128752
Average length of the domain: 169.40 aa
Average identity of full alignment: 14 %
Average coverage of the sequence by the domain: 41.80 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 29.5 29.5
Trusted cut-off 29.5 29.5
Noise cut-off 29.4 29.4
Model length: 167
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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 Radical_SAM domain has been found. There are 138 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
A0A0P0XTB0 View 3D Structure Click here
A0A0R0FIC1 View 3D Structure Click here
A0A0R0G6E6 View 3D Structure Click here
A0A0R0GA97 View 3D Structure Click here
A0A0R0GAG6 View 3D Structure Click here
A0A0R0HEM4 View 3D Structure Click here
A0A0R0I032 View 3D Structure Click here
A0A0R0IRV7 View 3D Structure Click here
A0A0R4J536 View 3D Structure Click here
A0A0R4J646 View 3D Structure Click here
A0A1D6F795 View 3D Structure Click here
A0A1D6G0E0 View 3D Structure Click here
A0A1D6G3V2 View 3D Structure Click here
A0A1D6GAM0 View 3D Structure Click here
A0A1D6HAY1 View 3D Structure Click here
A0A1D6JM25 View 3D Structure Click here
A0A1D6JS18 View 3D Structure Click here
A0A1D6KKP7 View 3D Structure Click here
A0A1D6L6E5 View 3D Structure Click here
A0A1D6MYU6 View 3D Structure Click here
A0A1D8PKD5 View 3D Structure Click here
A0A1D8PPU8 View 3D Structure Click here
A0A1D8PS33 View 3D Structure Click here
A0A2R8PX77 View 3D Structure Click here
A4HSJ7 View 3D Structure Click here
A4HWP3 View 3D Structure Click here
A4HWS3 View 3D Structure Click here
A4HY57 View 3D Structure Click here
A4I0J4 View 3D Structure Click here
A4IGH2 View 3D Structure Click here
B4FFP5 View 3D Structure Click here
B4FJY4 View 3D Structure Click here
B5DF48 View 3D Structure Click here
B6TM42 View 3D Structure Click here
B6TN12 View 3D Structure Click here
B8A031 View 3D Structure Click here
C0PGU3 View 3D Structure Click here
C0PN26 View 3D Structure Click here
C6KT59 View 3D Structure Click here
D3ZVG1 View 3D Structure Click here
D4ACM1 View 3D Structure Click here
F1LV76 View 3D Structure Click here
F1R905 View 3D Structure Click here
F4IVY6 View 3D Structure Click here
I1JHY9 View 3D Structure Click here
I1JXG4 View 3D Structure Click here
I1JXG5 View 3D Structure Click here
I1KC74 View 3D Structure Click here
I1KTQ5 View 3D Structure Click here
I1KXG4 View 3D Structure Click here
I1LFP7 View 3D Structure Click here
I1LIK7 View 3D Structure Click here
I1LNN6 View 3D Structure Click here
I1LPC2 View 3D Structure Click here
K7K4A9 View 3D Structure Click here
K7LNH5 View 3D Structure Click here
O13642 View 3D Structure Click here
O14023 View 3D Structure Click here
O33183 View 3D Structure Click here
O43766 View 3D Structure Click here
O59761 View 3D Structure Click here
O59778 View 3D Structure Click here
O69696 View 3D Structure Click here
O70600 View 3D Structure Click here
P0A9N4 View 3D Structure Click here
P0ADW6 View 3D Structure Click here
P0AEI1 View 3D Structure Click here
P0AEI4 View 3D Structure Click here
P0CH67 View 3D Structure Click here
P12996 View 3D Structure Click here
P25550 View 3D Structure Click here
P30140 View 3D Structure Click here
P30745 View 3D Structure Click here
P32131 View 3D Structure Click here
P32451 View 3D Structure Click here
P32675 View 3D Structure Click here
P32875 View 3D Structure Click here
P36979 View 3D Structure Click here
P39280 View 3D Structure Click here
P39409 View 3D Structure Click here
P52062 View 3D Structure Click here
P54967 View 3D Structure Click here
P60716 View 3D Structure Click here
P64554 View 3D Structure Click here
P69848 View 3D Structure Click here
P75794 View 3D Structure Click here
P76134 View 3D Structure Click here
P95188 View 3D Structure Click here
P96395 View 3D Structure Click here
P9WH15 View 3D Structure Click here
P9WJ79 View 3D Structure Click here
P9WJS1 View 3D Structure Click here
P9WJS3 View 3D Structure Click here
P9WK05 View 3D Structure Click here
P9WK91 View 3D Structure Click here
P9WL79 View 3D Structure Click here
P9WP73 View 3D Structure Click here
P9WP77 View 3D Structure Click here
P9WP77 View 3D Structure Click here
P9WPQ7 View 3D Structure Click here
Q02908 View 3D Structure Click here
Q08960 View 3D Structure Click here
Q08C92 View 3D Structure Click here
Q09316 View 3D Structure Click here
Q0E297 View 3D Structure Click here
Q0JD33 View 3D Structure Click here
Q0JKY3 View 3D Structure Click here
Q10QB5 View 3D Structure Click here
Q1ZXC6 View 3D Structure Click here
Q20624 View 3D Structure Click here
Q21452 View 3D Structure Click here
Q23651 View 3D Structure Click here
Q2FV03 View 3D Structure Click here
Q2FVJ7 View 3D Structure Click here
Q2FX16 View 3D Structure Click here
Q2FXH0 View 3D Structure Click here
Q2FXY9 View 3D Structure Click here
Q2FXZ6 View 3D Structure Click here
Q2FZ02 View 3D Structure Click here
Q2FZ66 View 3D Structure Click here
Q2FZX4 View 3D Structure Click here
Q2G1D7 View 3D Structure Click here
Q2G1X7 View 3D Structure Click here
Q2QQ49 View 3D Structure Click here
Q2QU90 View 3D Structure Click here
Q2R1U4 View 3D Structure Click here
Q39055 View 3D Structure Click here
Q46861 View 3D Structure Click here
Q4CKR7 View 3D Structure Click here
Q4CUJ9 View 3D Structure Click here
Q4CXG8 View 3D Structure Click here
Q4DC43 View 3D Structure Click here
Q4DKU2 View 3D Structure Click here
Q4DPP3 View 3D Structure Click here
Q4DT80 View 3D Structure Click here
Q4DXJ3 View 3D Structure Click here
Q4DYL7 View 3D Structure Click here
Q4E0Z1 View 3D Structure Click here
Q54J76 View 3D Structure Click here
Q54KV4 View 3D Structure Click here
Q54NM6 View 3D Structure Click here
Q54VE8 View 3D Structure Click here
Q57567 View 3D Structure Click here
Q57705 View 3D Structure Click here
Q57722 View 3D Structure Click here
Q57888 View 3D Structure Click here
Q57910 View 3D Structure Click here
Q57970 View 3D Structure Click here
Q58014 View 3D Structure Click here
Q58036 View 3D Structure Click here
Q58051 View 3D Structure Click here
Q58087 View 3D Structure Click here
Q58096 View 3D Structure Click here
Q58195 View 3D Structure Click here
Q58214 View 3D Structure Click here
Q58218 View 3D Structure Click here
Q58234 View 3D Structure Click here
Q58251 View 3D Structure Click here
Q58275 View 3D Structure Click here
Q58277 View 3D Structure Click here
Q58317 View 3D Structure Click here
Q58376 View 3D Structure Click here
Q58493 View 3D Structure Click here
Q58536 View 3D Structure Click here
Q58555 View 3D Structure Click here
Q58624 View 3D Structure Click here
Q58692 View 3D Structure Click here
Q58708 View 3D Structure Click here
Q58826 View 3D Structure Click here
Q58882 View 3D Structure Click here
Q59015 View 3D Structure Click here
Q59026 View 3D Structure Click here
Q59039 View 3D Structure Click here
Q5JM88 View 3D Structure Click here
Q5RH95 View 3D Structure Click here
Q5RIC0 View 3D Structure Click here
Q5RKZ7 View 3D Structure Click here
Q5SUV1 View 3D Structure Click here
Q5VV42 View 3D Structure Click here
Q5XIH4 View 3D Structure Click here
Q5ZAQ2 View 3D Structure Click here
Q60332 View 3D Structure Click here
Q69U93 View 3D Structure Click here
Q6L534 View 3D Structure Click here
Q6NUM6 View 3D Structure Click here
Q6PG34 View 3D Structure Click here
Q6PHG4 View 3D Structure Click here
Q7JQW6 View 3D Structure Click here
Q7K4W1 View 3D Structure Click here
Q7X7L3 View 3D Structure Click here
Q7XRF1 View 3D Structure Click here
Q84JV6 View 3D Structure Click here
Q8BJM7 View 3D Structure Click here
Q8BTW8 View 3D Structure Click here
Q8CBB9 View 3D Structure Click here
Q8H0V1 View 3D Structure Click here
Q8H8N3 View 3D Structure Click here
Q8I3L6 View 3D Structure Click here
Q8I5E0 View 3D Structure Click here
Q8IDQ0 View 3D Structure Click here
Q8IM25 View 3D Structure Click here
Q8IQF1 View 3D Structure Click here
Q8LEE8 View 3D Structure Click here
Q8MXQ7 View 3D Structure Click here
Q8RXN5 View 3D Structure Click here
Q8WXG1 View 3D Structure Click here
Q91WE6 View 3D Structure Click here
Q93XX3 View 3D Structure Click here
Q93ZR1 View 3D Structure Click here
Q96SZ6 View 3D Structure Click here
Q99M04 View 3D Structure Click here
Q9C7H2 View 3D Structure Click here
Q9CZX0 View 3D Structure Click here
Q9FMJ4 View 3D Structure Click here
Q9H9T3 View 3D Structure Click here
Q9HA92 View 3D Structure Click here
Q9JLH6 View 3D Structure Click here
Q9NV66 View 3D Structure Click here
Q9NZB8 View 3D Structure Click here
Q9VGZ1 View 3D Structure Click here
Q9VQZ6 View 3D Structure Click here
Q9XV04 View 3D Structure Click here
Q9ZWT1 View 3D Structure Click here