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0  structures 198  species 0  interactions 606  sequences 11  architectures

Family: TALPID3 (PF15324)

Summary: Hedgehog signalling target

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Hedgehog signalling target Provide feedback

TALPID3 is a family of eukaryotic proteins that are targets for Hedgehog signalling. Mutations in this gene noticed first in chickens lead to multiple abnormalities of development.

Literature references

  1. Davey MG, Paton IR, Yin Y, Schmidt M, Bangs FK, Morrice DR, Smith TG, Buxton P, Stamataki D, Tanaka M, Munsterberg AE, Briscoe J, Tickle C, Burt DW;, Genes Dev. 2006;20:1365-1377.: The chicken talpid3 gene encodes a novel protein essential for Hedgehog signaling. PUBMED:16702409 EPMC:16702409

  2. Yin Y, Bangs F, Paton IR, Prescott A, James J, Davey MG, Whitley P, Genikhovich G, Technau U, Burt DW, Tickle C;, Development. 2009;136:655-664.: The Talpid3 gene (KIAA0586) encodes a centrosomal protein that is essential for primary cilia formation. PUBMED:19144723 EPMC:19144723

  3. Ben J, Elworthy S, Ng AS, van Eeden F, Ingham PW;, Development. 2011;138:4969-4978.: Targeted mutation of the talpid3 gene in zebrafish reveals its conserved requirement for ciliogenesis and Hedgehog signalling across the vertebrates. PUBMED:22028029 EPMC:22028029


This tab holds annotation information from the InterPro database.

InterPro entry IPR029246

TALPID3 is the name of a classical chicken mutant with abnormal limb patterning and malformations in other regions of the embryo. It was so called because their paddle-shaped limbs resemble those of the mole (Talpa) [ PUBMED:16702409 ]. Besides the limbs, there is a set of malformations including face, skeleton, and vascular defects [ PUBMED:16702409 ]. TALPID3 gene was then identified and found to be a target for Hedgehog signalling [ PUBMED:11731473 ]. In chickens, TALPID3 protein is a centrosomal protein required for the function of both Gli repressor and activator in the intracellular Hedgehog pathway [ PUBMED:16702409 ]. Similar to the chicken TALPID3 mutants, the mouse mutants also lack primary cilia and have face and neural tube defects. Moreover, it has defects in left/right asymmetry [ PUBMED:21750036 ].

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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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 and the UniProtKB 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
(8)
Full
(606)
Representative proteomes UniProt
(976)
RP15
(61)
RP35
(184)
RP55
(516)
RP75
(701)
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PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(8)
Full
(606)
Representative proteomes UniProt
(976)
RP15
(61)
RP35
(184)
RP55
(516)
RP75
(701)
Alignment:
Format:
Order:
Sequence:
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Download options

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
(8)
Full
(606)
Representative proteomes UniProt
(976)
RP15
(61)
RP35
(184)
RP55
(516)
RP75
(701)
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.

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: Jackhmmer:Q9BVV6
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Eberhardt R , Coggill P , Hetherington K
Number in seed: 8
Number in full: 606
Average length of the domain: 673.30 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 79.42 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.4 27.0
Noise cut-off 26.8 26.7
Model length: 1287
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
E9PV87 View 3D Structure Click here
F1LZT2 View 3D Structure Click here
H6D7E6 View 3D Structure Click here
Q9BVV6 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;