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0  structures 193  species 0  interactions 200  sequences 2  architectures

Family: MATalpha_HMGbox (PF04769)

Summary: Mating-type protein MAT alpha 1 HMG-box

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Mating-type protein MAT alpha 1 HMG-box Provide feedback

This family includes Saccharomyces cerevisiae mating type protein alpha 1 (P01365). Mat alpha 1 is a transcription activator which activates mating-type alpha-specific genes. MAT alpha 1 and MCM 1 bind cooperatively to PQ elements upstream of alpha-specific genes [1]. Alpha 1 interacts in vivo with STE12, linking expression of alpha-specific genes to the alpha-pheromone (PF04648) response pathway [1]. In silico modelling of the MAT_Alpha1 domain indicates that its best scoring templates were structures of HMG-box proteins [2] and DOI: 10.4236/ojbiphy.2013.31001. Phylogenetic analysis suggests that the MAT_Alpha1 domain diverged from the MATA_HMG-box subfamily [2]. The name of MATalpha_HMG-box was proposed for the MAT_alpha1 domain [2].

Literature references

  1. Sengupta P, Cochran BH; , Genes Dev 1991;5:1924-1934.: MAT alpha 1 can mediate gene activation by a-mating factor. PUBMED:1916267 EPMC:1916267

  2. Martin T, Lu SW, van Tilbeurgh H, Ripoll DR, Dixelius C, Turgeon BG, Debuchy R;, PLoS One. 2010;5:e15199. : Tracing the origin of the fungal alpha1 domain places its ancestor in the HMG-box superfamily: implication for fungal mating-type evolution. PUBMED:21170349 EPMC:21170349


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006856

This entry represents the MAT Alpha1 domain, which is diverged from the MATA HMG-box domain [PUBMED:21170349]. All ascomycete MAT idiomorphs encode proteins with confirmed or putative DNA-binding motifs [PUBMED:11106025, PUBMED:12679880]. The HMG-box domain can be found in a wide variety of DNA-binding proteins.

In S. cerevisiae, there are two copies of Alpha1: one copy is localised at the MAT locus, the other is localised at the HML locus (MAT alpha 1). The HML locus (HML alpha 1) copy is usually silenced by the Sir2 histone deacetylase. MAT alpha 1 is a transcriptional coactivator involved in the regulation of mating-type alpha-specific gene expression. It activates mating-type alpha-specific genes with the help of the MADS-box containing Mcm1 transcription factor, which together bind cooperatively to PQ elements upstream of alpha-specific genes. The MCM1-MATalpha1 complex is required for the proper DNA-bending that is needed for transcriptional activation [PUBMED:15118075]. Alpha 1 interacts in vivo with Ste12, linking expression of alpha-specific genes to the alpha-pheromone (INTERPRO) response pathway [PUBMED:8339934].

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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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

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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.

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Meta
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(27)
RP35
(85)
RP55
(139)
RP75
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

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  Seed
(10)
Full
(200)
Representative proteomes UniProt
(1018)
NCBI
(945)
Meta
(0)
RP15
(27)
RP35
(85)
RP55
(139)
RP75
(197)
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  Seed
(10)
Full
(200)
Representative proteomes UniProt
(1018)
NCBI
(945)
Meta
(0)
RP15
(27)
RP35
(85)
RP55
(139)
RP75
(197)
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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.

HMM logo

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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.

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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: DOMO:DM04990;
Previous IDs: MAT_Alpha1;
Type: Family
Sequence Ontology: SO:0100021
Author: Kerrison ND
Number in seed: 10
Number in full: 200
Average length of the domain: 172.10 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 52.62 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.1 28.1
Trusted cut-off 29.0 28.3
Noise cut-off 28.0 27.6
Model length: 200
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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