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0  structures 1931  species 0  interactions 6865  sequences 232  architectures

Family: MHYT (PF03707)

Summary: Bacterial signalling protein N terminal repeat

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Bacterial signalling protein N terminal repeat Provide feedback

Found as an N terminal triplet tandem repeat in bacterial signalling proteins. Family includes CoxC (Q9KX27) and CoxH (Q9KX23) from P.carboxydovorans. Each repeat contains two transmembrane helices. Domain is also described as the MHYT domain [1].

Literature references

  1. Galperin MY, Gaidenko TA, Mulkidjanian AY, Nakano M, Price CW; , FEMS Microbiol Lett 2001;205:17-23.: MHYT, a new integral membrane sensor domain. PUBMED:11728710 EPMC:11728710


This tab holds annotation information from the InterPro database.

InterPro entry IPR005330

The MHYT domain is an about 190-residue domain, which was named after its conserved amino acid pattern. The MHYT domain consists of six predicted transmembrane (TM) segments, connected by short arginine-rich cytoplasmic loops and periplasmic loops that are also rich in charged amino acid residues. Three of its TM segments have a very similar amino acid sequence motif with highly conserved methionine, histidine and tyrosine residues located near the outer face of the cytoplasmic membrane.

The MHYT domain has been found in several phylogenetically distant bacteria, either as a separate, single domain protein, or fused to a LytTR-type DNA-binding helix-turn-helix, or fused to signaling domains, such as histidine kinase, GGDEF, EAL, and PAS. It has been proposed that the MHYT domain serves as a sensor domain in some bacterial two-component signal transduction systems as well as in a variety of other bacterial proteins. A model of the membrane topology of the MHYT domain indicates that its conserved residues could coordinate one or two copper ions, suggesting a role in sensing oxygen, CO or NO [PUBMED:11728710].

Domain organisation

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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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(267)
Full
(6865)
Representative proteomes UniProt
(33584)
NCBI
(58109)
Meta
(132)
RP15
(438)
RP35
(2355)
RP55
(6539)
RP75
(13328)
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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
(267)
Full
(6865)
Representative proteomes UniProt
(33584)
NCBI
(58109)
Meta
(132)
RP15
(438)
RP35
(2355)
RP55
(6539)
RP75
(13328)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(267)
Full
(6865)
Representative proteomes UniProt
(33584)
NCBI
(58109)
Meta
(132)
RP15
(438)
RP35
(2355)
RP55
(6539)
RP75
(13328)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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

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: Yeats C
Previous IDs: SPNTR;
Type: Repeat
Sequence Ontology: SO:0001068
Author: Yeats C
Number in seed: 267
Number in full: 6865
Average length of the domain: 60.20 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 22.82 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 59
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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