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0  structures 25  species 0  interactions 216  sequences 8  architectures

Family: Treacle (PF03546)

Summary: Treacher Collins syndrome protein Treacle

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Treacher Collins syndrome protein Treacle Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003993

Treacher Collins Syndrome (TCS) is an autosomal dominant disorder of craniofacial development, the features of which include conductive hearing loss and cleft palate [PUBMED:9096354, PUBMED:9042910]; it is the most common of the human mandibulo-facial dysostosis disorders [PUBMED:9096354]. The TCS locus has been mapped to human chromosome 5q31.3-32 and the mutated gene identified (TCOF1) [PUBMED:9042910]. To date, 35 mutations have been reported in TCOF1, all but one of which result in the introduction of a premature-termination codon into the predicted protein, Treacle. The observed mutational spectrum supports the hypothesis that TCS results from haploinsufficiency.

Treacle is a low complexity protein of 1,411 amino acids whose predicted protein structure contains a set of highly polar repeated motifs [PUBMED:9096354]. These motifs are common to nucleolar trafficking proteins in other species and are predicted to be phosphorylated by casein kinase. In concert with this observation, the full-length TCOF1 protein sequence also contains putative nuclear and nucleolar localisation signals [PUBMED:9096354]. Throughout the open reading frame are found mutations in TCS families and several polymorphisms. It has thus been suggested that TCS results from defects in a nucleolar trafficking protein that is critically required during human craniofacial development.

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 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
(4)
Full
(216)
Representative proteomes NCBI
(246)
Meta
(0)
RP15
(6)
RP35
(6)
RP55
(11)
RP75
(59)
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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
(4)
Full
(216)
Representative proteomes NCBI
(246)
Meta
(0)
RP15
(6)
RP35
(6)
RP55
(11)
RP75
(59)
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
(4)
Full
(216)
Representative proteomes NCBI
(246)
Meta
(0)
RP15
(6)
RP35
(6)
RP55
(11)
RP75
(59)
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.

Pfam alignments:

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: PRINTS
Previous IDs: treacle;
Type: Family
Author: Griffiths-Jones SR
Number in seed: 4
Number in full: 216
Average length of the domain: 175.30 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 51.50 %

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 21.1 21.1
Trusted cut-off 21.7 21.5
Noise cut-off 19.5 20.6
Model length: 519
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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