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0  structures 236  species 0  interactions 402  sequences 13  architectures

Family: DBINO (PF13892)

Summary: DNA-binding domain

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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.

DNA-binding domain Provide feedback

DBINO is a DNA-binding domain found on global transcription activator SNF2L1 proteins and chromatin re-modelling proteins.

Literature references

  1. Okabe I, Bailey LC, Attree O, Srinivasan S, Perkel JM, Laurent BC, Carlson M, Nelson DL, Nussbaum RL;, Nucleic Acids Res. 1992;20:4649-4655.: Cloning of human and bovine homologs of SNF2/SWI2: a global activator of transcription in yeast S. cerevisiae. PUBMED:1408766 EPMC:1408766

  2. Lazzaro MA, Pepin D, Pescador N, Murphy BD, Vanderhyden BC, Picketts DJ;, Mol Endocrinol. 2006;20:2406-2417.: The imitation switch protein SNF2L regulates steroidogenic acute regulatory protein expression during terminal differentiation of ovarian granulosa cells. PUBMED:16740656 EPMC:16740656

  3. Bakshi R, Mehta AK, Sharma R, Maiti S, Pasha S, Brahmachari V;, Biochem Biophys Res Commun. 2006;339:313-320.: Characterization of a human SWI2/SNF2 like protein hINO80: demonstration of catalytic and DNA binding activity. PUBMED:16298340 EPMC:16298340


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR020838

Proteins belonging to the SNF2 family of DNA dependent ATPases are important members of the chromatin remodelling complexes that are implicated in epigenetic control of gene expression. Members of the SNF2 family of proteins have been identified in organisms ranging from Escherichia coli to Homo sapiens (Human). All of them contain the conserved SNF2 domain, which is defined by the existence of seven motifs (I, Ia, and II-VI) with sequences similarity to those motifs found in DNA and RNA helicases (see PROSITEDOC). SNF2-like family members can be further subdivided into several subfamilies according to the presence of protein motifs outside of the ATPase region. The DBINO (DNA binding domain of INO80) domain is characteristic of the INO80 subfamily and is predicted to have DNA-binding function. The DBINO domain is a 126 amino acid long peptide located near the N terminus, approximately 100 residues upstream of the SNF2 helicase domain. The presence of this domain in all the INO80 subfamily proteins from yeast to humans suggests its conserved function in evolution [PUBMED:15207721, PUBMED:16298340].

The most significant feature of DBINO domain is the occurrence of the positive amino acids arginine and lysine in tandem (RK/KR), in multiple positions, which are likely to bind DNA [PUBMED:15207721].

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
(27)
Full
(402)
Representative proteomes NCBI
(411)
Meta
(1)
RP15
(78)
RP35
(133)
RP55
(201)
RP75
(268)
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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
(27)
Full
(402)
Representative proteomes NCBI
(411)
Meta
(1)
RP15
(78)
RP35
(133)
RP55
(201)
RP75
(268)
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
(27)
Full
(402)
Representative proteomes NCBI
(411)
Meta
(1)
RP15
(78)
RP35
(133)
RP55
(201)
RP75
(268)
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: Jackhmmer:P53115
Previous IDs: none
Type: Domain
Author: Coggill P
Number in seed: 27
Number in full: 402
Average length of the domain: 108.90 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 8.46 %

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 21.9 21.9
Trusted cut-off 21.9 21.9
Noise cut-off 21.8 21.8
Model length: 140
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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