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0  structures 2950  species 0  interactions 5450  sequences 50  architectures

Family: TraB_PrgY_gumN (PF01963)

Summary: TraB/PrgY/gumN family

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TraB/PrgY/gumN family Provide feedback

This entry includes Tiki1/2 from humans, TraB/PrgY from the gut flora Enterococcusfaecalis and gumN from the plant pathogen Xanthomonas. Tiki1 is homologous to TraB/PrgY. They have a pair of widely spaced GX2H motifs and a conserved glutamate. From the structural study, this group of proteins have been identified as an ancient metalloprotease clan with a common protein architecture (cobbled from the folds of the EreA/ChaN/PMT group) that mediates proteolytic activities [2]. Tiki1 is a membrane-associated protease that inhibits Wnt via the cleavage of its amino terminus, diminishing Wnt's binding to receptors [1,3]. TraB/PrgY is an inhibitor peptide that may act as a protease to inactivate the mating pheromone [2].

Literature references

  1. Zhou P, Lin K, Zhou X, Zhang W, Huang K, Liu L, Guo J, Xu F;, Chemosphere. 2012;88:1375-1382.: Distribution of polybrominated diphenyl ethers in the surface sediments of the Taihu Lake, China. PUBMED:22726422 EPMC:22726422

  2. Bazan JF, Macdonald BT, He X;, Dev Cell. 2013;25:225-227.: The TIKI/TraB/PrgY family: a common protease fold for cell signaling from bacteria to metazoa?. PUBMED:23673329 EPMC:23673329

  3. Zhang X, Abreu JG, Yokota C, MacDonald BT, Singh S, Coburn KL, Cheong SM, Zhang MM, Ye QZ, Hang HC, Steen H, He X;, Cell. 2012;149:1565-1577.: Tiki1 is required for head formation via Wnt cleavage-oxidation and inactivation. PUBMED:22726442 EPMC:22726442


This tab holds annotation information from the InterPro database.

InterPro entry IPR002816

This entry includes Tiki1/2 from humans, TraB/PrgY from the gut flora Enterococcusfaecalis and gumN from the plant pathogen Xanthomonas. Tiki1 is homologous to TraB/PrgY. They have a pair of widely spaced GX2H motifs and a conserved glutamate. From the structural study, this group of proteins have been identified as an ancient metalloprotease clan with a common protein architecture -cobbled from the folds of the EreA/ChaN/PMT group- that mediates proteolytic activities [ PUBMED:23673329 ].

Tiki1 is a membrane-associated protease that inhibits Wnt via the cleavage of its amino terminus, diminishing Wnt's binding to receptors [ PUBMED:22726442 ].

TraB/PrgY is an inhibitor peptide that may act as a protease to inactivate the mating pheromone [ PUBMED:23673329 ].

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 TIKI (CL0572), which has the following description:

TIKI superfamily proteins carry a core fold contributing to the enzymic activity, that ranges from metalloprotease, erythromycin esterase and bacterial toinosis as in the MARTX and dermonecrotic toxin families, amongst others. All superfamily members carry the active site residues of two histidines and two glutamates [1]. Tiki proteins themselves antagonize Wnt activity upstream of its receptor.

The clan contains the following 3 members:

Cofac_haem_bdg Erythro_esteras TraB_PrgY_gumN

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
(193)
Full
(5450)
Representative proteomes UniProt
(20062)
RP15
(786)
RP35
(2470)
RP55
(5332)
RP75
(8512)
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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
(193)
Full
(5450)
Representative proteomes UniProt
(20062)
RP15
(786)
RP35
(2470)
RP55
(5332)
RP75
(8512)
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
(193)
Full
(5450)
Representative proteomes UniProt
(20062)
RP15
(786)
RP35
(2470)
RP55
(5332)
RP75
(8512)
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: Enright A
Previous IDs: TraB;
Type: Family
Sequence Ontology: SO:0100021
Author: Enright A , Ouzounis C , Bateman A
Number in seed: 193
Number in full: 5450
Average length of the domain: 235.40 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 65.83 %

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 26.8 26.8
Trusted cut-off 26.8 26.8
Noise cut-off 26.7 26.6
Model length: 263
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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;