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0  structures 2925  species 0  interactions 3012  sequences 6  architectures

Family: ScpA_ScpB (PF02616)

Summary: ScpA/B protein

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.

ScpA/B protein Provide feedback

ScpA and ScpB participate in chromosomal partition during cell division. It may act via the formation of a condensin-like complex containing smc that pull DNA away from mid-cell into both cell halves. These proteins are part of the Kleisin superfamily.

Literature references

  1. Schleiffer A, Kaitna S, Maurer-Stroh S, Glotzer M, Nasmyth K, Eisenhaber F; , Mol Cell 2003;11:571-575.: Kleisins: a superfamily of bacterial and eukaryotic SMC protein partners. PUBMED:12667442 EPMC:12667442


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003768

This family represents ScpA, which along with ScpB (INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [PUBMED:12065423, PUBMED:12897137]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [PUBMED:10545099], where MukB (INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (INTERPRO) or MukF (INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions.

In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes [PUBMED:12100548].

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 Kleisin (CL0157), which has the following description:

The kleisin superfamily includes ScpA, Scc1, Rec8, and Barren [1]. Scc1 interacts with SMC proteins through N- and C-terminal domains to form a ring-like structure [1].

The clan contains the following 2 members:

Rad21_Rec8 ScpA_ScpB

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
(11)
Full
(3012)
Representative proteomes NCBI
(2298)
Meta
(2016)
RP15
(264)
RP35
(526)
RP55
(667)
RP75
(778)
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PP/heatmap 1 View  View  View  View  View     
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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
(11)
Full
(3012)
Representative proteomes NCBI
(2298)
Meta
(2016)
RP15
(264)
RP35
(526)
RP55
(667)
RP75
(778)
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
(11)
Full
(3012)
Representative proteomes NCBI
(2298)
Meta
(2016)
RP15
(264)
RP35
(526)
RP55
(667)
RP75
(778)
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.

Pfam alignments:

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: COG1354
Previous IDs: DUF173;
Type: Family
Author: Mian N, Bateman A
Number in seed: 11
Number in full: 3012
Average length of the domain: 209.20 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 81.05 %

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 23.7 23.7
Trusted cut-off 23.7 23.7
Noise cut-off 23.4 23.4
Model length: 242
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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