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0  structures 102  species 0  interactions 192  sequences 7  architectures

Family: Myf5 (PF12232)

Summary: Myogenic determination factor 5

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This is the Wikipedia entry entitled "Myogenic determination factor 5". More...

Myogenic determination factor 5 Edit Wikipedia article

Myf5 domain
Identifiers
Symbol Myf5
Pfam PF12232
InterPro IPR022032
Basic domain
PDB 1mdy EBI.jpg
crystal structure of myod bhlh domain bound to dna: perspectives on dna recognition and implications for transcriptional activation
Identifiers
Symbol Basic
Pfam PF01586
InterPro IPR002546
PROSITE PDOC00038
SCOP 1mdy
SUPERFAMILY 1mdy

In molecular biology, the myogenic determination factor 5 proteins are a family of proteins found in eukaryotes. This family includes the Myf5 protein, which is responsible for directing cells to the skeletal myocyte lineage during development. Myf5 is likely to act in a similar way to the other MRF4 proteins such as MyoD which perform the same function. These are histone acetyltransferases and histone deacetylases which activate and repress genes involved in the myocyte lineage.

Myogenic determination factor 5 proteins contain three conserved protein domains. A C-terminal Myf5 domain, a central basic helix-loop-helix (bHLH) domain and an N-terminal basic domain. The bHLH region mediates specific DNA binding.[1] With 12 residues of the basic domain involved in DNA binding.[2] The basic domain forms an extended alpha helix in the structure.

References

This article incorporates text from the public domain Pfam and InterPro IPR022032

This article incorporates text from the public domain Pfam and InterPro IPR002546

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.

Myogenic determination factor 5 Provide feedback

This domain family is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with PF00010 PF01586. There is a conserved CSD sequence motif. Myf5 is responsible for directing cells to the skeletal myocyte lineage during development. Myf5 is likely to act in a similar way to the other MRF4 proteins such as MyoD which perform the same function. These are histone acetyltransferases and histone deacetylases which activate and repress genes involved in the myocyte lineage.

Literature references

  1. Ye HQ, Chen SL, Xu JY;, Comp Biochem Physiol B Biochem Mol Biol. 2007;147:452-459.: Molecular cloning and characterization of the Myf5 gene in sea perch (Lateolabrax japonicus). PUBMED:17395511 EPMC:17395511

  2. McKinsey TA, Zhang CL, Olson EN;, Curr Opin Genet Dev. 2001;11:497-504.: Control of muscle development by dueling HATs and HDACs. PUBMED:11532390 EPMC:11532390


This tab holds annotation information from the InterPro database.

InterPro entry IPR022032

This domain is found in eukaryotes, is approximately 70 amino acids in length, and contains a conserved CSD sequence motif. It is found in association with , . This domain is found in Myogenic factor 5 (Myf5) and Myoblast determination protein 1 (MyoD1). Myf5 is responsible for directing cells to the skeletal myocyte lineage during development [PUBMED:17395511]. Myf5 is likely to act in a similar way to the other MRF4 proteins such as MyoD which perform the same function [PUBMED:21798092].

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
(27)
Full
(192)
Representative proteomes UniProt
(379)
NCBI
(691)
Meta
(0)
RP15
(31)
RP35
(66)
RP55
(134)
RP75
(175)
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Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(27)
Full
(192)
Representative proteomes UniProt
(379)
NCBI
(691)
Meta
(0)
RP15
(31)
RP35
(66)
RP55
(134)
RP75
(175)
Alignment:
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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
(192)
Representative proteomes UniProt
(379)
NCBI
(691)
Meta
(0)
RP15
(31)
RP35
(66)
RP55
(134)
RP75
(175)
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.

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.

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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: PFAM-B_2654 (release 23.0)
Previous IDs: none
Type: Family
Author: Assefa S
Number in seed: 27
Number in full: 192
Average length of the domain: 64.40 aa
Average identity of full alignment: 48 %
Average coverage of the sequence by the domain: 22.14 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.7 21.7
Trusted cut-off 21.9 22.1
Noise cut-off 21.6 21.6
Model length: 71
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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