Summary
Bacterial DNA-binding protein
No Pfam abstract.
Literature references
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Vis H, Mariani M, Vorgias CE, Wilson KS, Kaptein R, Boelens R; , J Mol Biol 1995;254:692-703.: Solution structure of the HU protein from Bacillus stearothermophilus. PUBMED:7500343
InterPro entry IPR000119
Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins PUBMED:3118156, PUBMED:3047111. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae PUBMED:1961745. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control PUBMED:2972385 is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) PUBMED:8464748.
The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins PUBMED:6540370. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA.
Gene Ontology
| Molecular function | DNA binding (GO:0003677) |
Internal database links
| SCOOP: | Glycos_trans_3N Ribosomal_L12 Pedibin |
External database links
| HOMSTRAD: | Bac_DNA_binding |
| PANDIT: | PF00216 |
| PROSITE: | PDOC00044 |
| SCOP: | 1hue |
| SYSTERS: | Bac_DNA_binding |
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
There are various ways to view or download the sequence alignments that we store. You can use a sequence viewer to look at either the seed or full alignment for the family, or you can look at a plain text version of the sequence in a variety of different formats. More...
View options
Formatting options
Download options
Very large alignments can often cause problems for the formatting tool above. If you find that downloading or viewing a large alignment is problematic, you can also download a gzip-compressed, Stockholm-format file containing the seed or full alignment for this family.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
The main seed and full alignments are generated using sequences from the UniProt sequence database. However, we also generate alignments using sequences from the NCBI sequence database and the "metaseq" metagenomics dataset.
You can view alignments from these two additional datasets using the form above, or you can download alignments of NCBI or metagenomics sequences, as gzip-compressed files.
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 HMMER2.
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. 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 or full alignments.
Note: You can also download the data files for the seed, full, NCBI or metagenomics trees.
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
| Seed source: | Prosite |
| Previous IDs: | none |
| Type: | Domain |
| Author: | Finn RD |
| Number in seed: | 158 |
| Number in full: | 4339 |
| Average length of the domain: | 89.60 aa |
| Average identity of full alignment: | 35 % |
| Average coverage of the sequence by the domain: | 84.35 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 9421015 -E 1000 HMM pfamseq
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| Model details: |
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| Model length: | 90 | ||||||||||||
| Family (HMM) version: | 14 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
Tree controls
HideThe tree shows the occurrence of this domain across different species. More...
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Interactions
There is 1 interaction for this family. More...
Bac_DNA_bindingStructures
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 Bac_DNA_binding domain has been found.
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