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0  structures 216  species 0  interactions 281  sequences 7  architectures

Family: SPT2 (PF08243)

Summary: SPT2 chromatin 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.

SPT2 chromatin protein Provide feedback

This family includes the Saccharomyces cerevisiae protein SPT2 which is a chromatin protein involved in transcriptional regulation [1].

Literature references

  1. Novoseler M, Hershkovits G, Katcoff DJ; , J Biol Chem 2005;280:5169-5177.: Functional domains of the yeast chromatin protein Sin1p/Spt2p can bind four-way junction and crossing DNA structures. PUBMED:15563464 EPMC:15563464


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013256

This entry includes the Saccharomyces cerevisiae (Baker's yeast) protein SPT2 which is a chromatin protein involved in transcriptional regulation [PUBMED:15563464].

These proteins shows conservation of several domains across numerous species, including having a cluster of positively charged amino acids. This cluster probably functions in the binding properties of the proteins [PUBMED:15563464]. Sin1p/Spt2p probably modulates the local chromatin structure by binding two strands of double-stranded DNA at their crossover point.

Sin1p/Spt2p has sequence similarity to HMG1 and serves as a negative transcriptional regulator of a small family of genes that are activated by the SWI/SNF chromatin-remodelling complex. It is also involved in maintaining the integrity of chromatin during transcription elongation. Sin1p/Spt2 is required for, and is directly involved in, the efficient recruitment of the mRNA cleavage/polyadenylation complex [PUBMED:16788068]. Spt2 is also involved in regulating levels of histone H3 over transcribed regions [PUBMED:16449659].

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
(7)
Full
(281)
Representative proteomes NCBI
(268)
Meta
(0)
RP15
(57)
RP35
(95)
RP55
(152)
RP75
(195)
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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
(7)
Full
(281)
Representative proteomes NCBI
(268)
Meta
(0)
RP15
(57)
RP35
(95)
RP55
(152)
RP75
(195)
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
(7)
Full
(281)
Representative proteomes NCBI
(268)
Meta
(0)
RP15
(57)
RP35
(95)
RP55
(152)
RP75
(195)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download    
Gzipped 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: manual
Previous IDs: none
Type: Domain
Author: Mistry J, Wood V
Number in seed: 7
Number in full: 281
Average length of the domain: 106.40 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 22.63 %

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 20.9 20.9
Trusted cut-off 20.9 22.1
Noise cut-off 20.3 20.0
Model length: 116
Family (HMM) version: 6
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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