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124  structures 1590  species 0  interactions 40204  sequences 570  architectures

Family: HMG_box (PF00505)

Summary: HMG (high mobility group) box

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "HMG-box". More...

HMG-box Edit Wikipedia article

HMG (high mobility group) box
Identifiers
SymbolPF00505
PfamPF00505
InterProIPR009071
SCOP21hsm / SCOPe / SUPFAM

The HMG-box (High Mobility Group box) is a protein domain which is involved in DNA binding. The structure of the HMG-box domain contains three alpha helices separated by loops. HMG-box domains are found in high mobility group proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin.[1]

References

  1. ^ Thomas JO (2001). "HMG1 and 2: architectural DNA-binding proteins". Biochem. Soc. Trans. 29 (Pt 4): 395–401. PMID 11497996. {{cite journal}}: Unknown parameter |month= ignored (help)

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

HMG (high mobility group) box Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR009071

High mobility group (HMG) box domains are involved in binding DNA, and may be involved in protein-protein interactions as well. The structure of the HMG-box domain consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin. Many of these proteins are regulators of gene expression. HMG-box proteins are found in a variety of eukaryotic organisms, and can be broadly divided into two groups, based on sequence-dependent and sequence-independent DNA recognition; the former usually contain one HMG-box motif, while the latter can contain multiple HMG-box motifs.

HMG-box domains can be found in single or multiple copies in the following protein classes: HMG1 and HMG2 non-histone components of chromatin; SRY (sex determining region Y protein) involved in differential gonadogenesis; the SOX family of transcription factors [ PUBMED:12920151 ]; sequence-specific LEF1 (lymphoid enhancer binding factor 1) and TCF-1 (T-cell factor 1) involved in regulation of organogenesis and thymocyte differentiation [ PUBMED:10890911 ]; structure-specific recognition protein SSRP involved in transcription and replication; MTF1 mitochondrial transcription factor; nucleolar transcription factors UBF 1/2 (upstream binding factor) involved in transcription by RNA polymerase I; Abf2 yeast ARS-binding factor [ PUBMED:11779632 ]; yeast transcription factors lxr1, Rox1, Nhp6b and Spp41; mating type proteins (MAT) involved in the sexual reproduction of fungi [ PUBMED:12781674 ]; and the YABBY plant-specific transcription factors.

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 HMG-box (CL0114), which has the following description:

This clan includes the DNA-binding HMG-box proteins as well as the YABBY-like transcription factors.

The clan contains the following 8 members:

Ccdc124 CHDNT HMG_box HMG_box_2 HMG_box_5 MATalpha_HMGbox Protamine_like YABBY

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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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
(40204)
Representative proteomes UniProt
(69729)
RP15
(6770)
RP35
(15568)
RP55
(30826)
RP75
(41044)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(27)
Full
(40204)
Representative proteomes UniProt
(69729)
RP15
(6770)
RP35
(15568)
RP55
(30826)
RP75
(41044)
Alignment:
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Sequence:
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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
(40204)
Representative proteomes UniProt
(69729)
RP15
(6770)
RP35
(15568)
RP55
(30826)
RP75
(41044)
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.

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: Pfam-B_8 (release 1.0)
Previous IDs: HMG_box; MaoC_dehydrat_N;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 27
Number in full: 40204
Average length of the domain: 67.4 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 13.46 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.4 25.4
Trusted cut-off 25.4 25.4
Noise cut-off 25.3 25.3
Model length: 69
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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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Structures

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 HMG_box domain has been found. There are 124 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044RZC6 View 3D Structure Click here
A0A044S6A7 View 3D Structure Click here
A0A044S809 View 3D Structure Click here
A0A044SAX3 View 3D Structure Click here
A0A044SEI2 View 3D Structure Click here
A0A044TG89 View 3D Structure Click here
A0A044TLS8 View 3D Structure Click here
A0A044TUS3 View 3D Structure Click here
A0A044URY0 View 3D Structure Click here
A0A044UTA5 View 3D Structure Click here
A0A044V329 View 3D Structure Click here
A0A044V9D6 View 3D Structure Click here
A0A044V9Q5 View 3D Structure Click here
A0A077YW65 View 3D Structure Click here
A0A077YWU5 View 3D Structure Click here
A0A077YXK4 View 3D Structure Click here
A0A077YXP2 View 3D Structure Click here
A0A077YY68 View 3D Structure Click here
A0A077Z0M3 View 3D Structure Click here
A0A077Z3F8 View 3D Structure Click here
A0A077Z3N6 View 3D Structure Click here
A0A077Z5Y7 View 3D Structure Click here
A0A077ZAP3 View 3D Structure Click here
A0A077ZD10 View 3D Structure Click here
A0A077ZD51 View 3D Structure Click here
A0A077ZHD0 View 3D Structure Click here
A0A077ZKG9 View 3D Structure Click here
A0A077ZM54 View 3D Structure Click here
A0A0A2V2I9 View 3D Structure Click here
A0A0D2E1U5 View 3D Structure Click here
A0A0D2G2Q6 View 3D Structure Click here
A0A0D2GDS5 View 3D Structure Click here
A0A0D2H4T3 View 3D Structure Click here
A0A0D2HF87 View 3D Structure Click here
A0A0D2HFG8 View 3D Structure Click here
A0A0G2JTG6 View 3D Structure Click here
A0A0G2JTZ2 View 3D Structure Click here
A0A0G2JV60 View 3D Structure Click here
A0A0G2JVD1 View 3D Structure Click here
A0A0G2JVM8 View 3D Structure Click here