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9  structures 269  species 1  interaction 2143  sequences 23  architectures

Family: T-box (PF00907)

Summary: T-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 "T-box". More...

T-box Edit Wikipedia article

For the computer science term, see Tbox.
T-box
1H6F.png
Crystallographic structure of the TBX3 protein dimer (cyan and green) complexed with DNA (brown) based on the PDB 1h6f coordinates.
Identifiers
Symbol T-box
Pfam PF00907
InterPro IPR001699
PROSITE PS50252
SCOP 1xbr
SUPERFAMILY 1xbr

T-box refers to a group of transcription factors involved in limb and heart development.[1]

In humans and some other animals, defects in the TBX5 gene expression can lead to finger-like thumbs and ventricular septal defects in which there is no separation between the left and right ventricle of the heart and are responsible for Holt-Oram syndrome.

TBX3 is associated with ulnar-mammary syndrome.

Genes encoding T-box proteins include:

See also

References

  1. ^ Wilson V, Conlon FL (2002). "The T-box family". Genome Biol. 3 (6): REVIEWS3008. doi:10.1186/gb-2002-3-6-reviews3008. PMC 139375. PMID 12093383. 

Further reading

External links

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.

T-box Provide feedback

The T-box encodes a 180 amino acid domain that binds to DNA. Genes encoding T-box proteins are found in a wide range of animals, but not in other kingdoms such as plants. Family members are all thought to bind to the DNA consensus sequence TCACACCT. they are found exclusively in the nucleus, and perform DNA-binding and transcriptional activation/repression roles. They are generally required for development of the specific tissues they are expressed in, and mutations in T-box genes are implicated in human conditions such as DiGeorge syndrome and X-linked cleft palate, which feature malformations [2].

Literature references

  1. Muller CW, Herrmann BG; , Nature 1997;389:884-888.: Crystallographic structure of the T domain-DNA complex of the Brachyury transcription factor. PUBMED:9349824 EPMC:9349824

  2. Wilson V, Conlon FL; , Genome Biol 2002;3:REVIEWS3008.: The T-box family. PUBMED:12093383 EPMC:12093383


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001699

Transcription factors of the T-box family are required both for early cell-fate decisions, such as those necessary for formation of the basic vertebrate body plan, and for differentiation and organogenesis [PUBMED:12093383]. The T-box is defined as the minimal region within the T-box protein that is both necessary and sufficient for sequence-specific DNA binding, all members of the family so far examined bind to the DNA consensus sequence TCACACCT. The T-box is a relatively large DNA-binding domain, generally comprising about a third of the entire protein (17-26 kDa).

These genes were uncovered on the basis of similarity to the DNA binding domain [PUBMED:9504043] of Mus musculus (Mouse) Brachyury (T) gene product, which similarity is the defining feature of the family. The Brachyury gene is named for its phenotype, which was identified 70 years ago as a mutant mouse strain with a short blunted tail. The gene, and its paralogues, have become a well-studied model for the family, and hence much of what is known about the T-box family is derived from the murine Brachyury gene.

Consistent with its nuclear location, Brachyury protein has a sequence-specific DNA-binding activity and can act as a transcriptional regulator [PUBMED:9503012]. Homozygous mutants for the gene undergo extensive developmental anomalies, thus rendering the mutation lethal [PUBMED:9395282]. The postulated role of Brachyury is as a transcription factor, regulating the specification and differentiation of posterior mesoderm during gastrulation in a dose-dependent manner [PUBMED:9504043].

T-box proteins tend to be expressed in specific organs or cell types, especially during development, and they are generally required for the development of those tissues, for example, Brachyury is expressed in posterior mesoderm and in the developing notochord, and it is required for the formation of these cells in mice [PUBMED:9196325].

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 P53-like (CL0073), which has the following description:

This clan contains a variety of DNA-binding domains that contain an immunoglobulin-like fold. It includes the DNA-binding domains of NF-kappaB, NFAT, p53, STAT-1, the T-domain and the Runt domain [1].

The clan contains the following 7 members:

CEP1-DNA_bind NDT80_PhoG P53 RHD Runt STAT_bind T-box

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(22)
Full
(2143)
Representative proteomes NCBI
(1755)
Meta
(0)
RP15
(218)
RP35
(311)
RP55
(758)
RP75
(1083)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(22)
Full
(2143)
Representative proteomes NCBI
(1755)
Meta
(0)
RP15
(218)
RP35
(311)
RP55
(758)
RP75
(1083)
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
(22)
Full
(2143)
Representative proteomes NCBI
(1755)
Meta
(0)
RP15
(218)
RP35
(311)
RP55
(758)
RP75
(1083)
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.

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 HMMER3.

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_363 (release 3.0)
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 22
Number in full: 2143
Average length of the domain: 155.30 aa
Average identity of full alignment: 47 %
Average coverage of the sequence by the domain: 35.04 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.5 20.5
Trusted cut-off 20.6 20.6
Noise cut-off 20.1 20.4
Model length: 184
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

T-box

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 T-box domain has been found. There are 9 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 seqence.

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