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0  structures 2271  species 0  interactions 4320  sequences 60  architectures

Family: SPASM (PF13186)

Summary: Iron-sulfur cluster-binding domain

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.

Iron-sulfur cluster-binding domain Provide feedback

This domain occurs as an additional C-terminal iron-sulfur cluster binding domain in many radical SAM domain, PF04055 proteins. The domain occurs in a number of proteins that modify a protein to become an active enzyme, or a peptide to become a ribosomal natural product. The domain is named SPASM because it occurs in the maturases of Subilitosin, PQQ, Anaerobic Sulfatases, and Mycofactocin.

Literature references

  1. Haft DH, Basu MK;, J Bacteriol. 2011;193:2745-2755.: Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification. PUBMED:21478363 EPMC:21478363


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR023885

This domain contains regions binding additional 4Fe4S clusters found in various radical SAM proteins C-terminal to the domain described by . Radical SAM enzymes with this domain tend to be involved in protein modification, including anaerobic sulphatase maturation proteins, a quinohemoprotein amine dehydrogenase biogenesis protein, the Pep1357-cyclizing radical SAM enzyme, and various bacteriocin biosynthesis proteins [PUBMED:21478363, PUBMED:21223593]. The motif CxxCxxxxxCxxxC is nearly invariant for members of this family, although PqqE has a variant form. This domain has been named SPASM for Subtilosin, PQQ, Anaerobic Sulphatase, and Mycofactocin.

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
(441)
Full
(4320)
Representative proteomes NCBI
(3391)
Meta
(1345)
RP15
(484)
RP35
(821)
RP55
(978)
RP75
(1134)
Jalview View  View  View  View  View  View  View  View 
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
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
(441)
Full
(4320)
Representative proteomes NCBI
(3391)
Meta
(1345)
RP15
(484)
RP35
(821)
RP55
(978)
RP75
(1134)
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
(441)
Full
(4320)
Representative proteomes NCBI
(3391)
Meta
(1345)
RP15
(484)
RP35
(821)
RP55
(978)
RP75
(1134)
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:O26216
Previous IDs: DUF4008;
Type: Domain
Author: Bateman A
Number in seed: 441
Number in full: 4320
Average length of the domain: 67.60 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 17.48 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.5 21.5
Trusted cut-off 21.5 21.5
Noise cut-off 21.4 21.4
Model length: 64
Family (HMM) version: 1
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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Tree controls

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