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0  structures 2872  species 0  interactions 4524  sequences 31  architectures

Family: TraB (PF01963)

Summary: TraB family

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TraB family Provide feedback

pAD1 is a haemolysin/bacteriocin plasmid originally identified in Enterococcus faecalis DS16. It encodes a mating response to a peptide sex pheromone, cAD1, secreted by recipient bacteria. Once the plasmid pAD1 is acquired, production of the pheromone ceases--a trait related in part to a determinant designated traB. However a related protein is found in C. elegans Q94217 suggesting that members of the TraB family have some more general function. This family also includes the bacterial GumN protein. The family has a conserved GXXH motif close to the N-terminus, a conserved glutamate and a conserved arginine that may be catalytic. The family also includes a second conserved GXXH motif near the C-terminus. This family also contains the Tiki proteins that regulate Wnt signalling [3].

Literature references

  1. An FY, Clewell DB; , Plasmid 1994;31:215-221.: Characterization of the determinant (traB) encoding sex pheromone shutdown by the hemolysin/bacteriocin plasmid pAD1 in Enterococcus faecalis. PUBMED:8029329 EPMC:8029329

  2. Clewell DB;, Plasmid. 2007;58:205-227.: Properties of Enterococcus faecalis plasmid pAD1, a member of a widely disseminated family of pheromone-responding, conjugative, virulence elements encoding cytolysin. PUBMED:17590438 EPMC:17590438

  3. 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


This tab holds annotation information from the InterPro database.

InterPro entry IPR002816

In prokaryotes, for example Enterococcus faecalis (Streptococcus faecalis), the conjugative transfer of certain plasmids is controlled by peptide pheromones [PUBMED:15374642]. Plasmid free recipient cells secret plasmid specific oligopeptides, termed sex pheromones. They induce bacterial clumping and specifically activate the conjugative transfer of the corresponding plasmid. Once recipient cells acquire the plasmid they start to produce a pheromone inhibitor to block the activity of the pheromone and to prevent plasmid containing cells from clumping; they also become donor cells able to transfer the plasmid to plasmid free recipient cells. Examples of such plasmid-pheromone systems are bacteriocin plasmid pPD1 [PUBMED:7559344], haemolysin/bacteriocin plasmid, pAD1 [PUBMED:1924555], tetracycline-resistance plasmid, pCF10 [PUBMED:8349565], and the haemolysin/bacteriocin plasmid, pOB1 [PUBMED:7772836].

TraB in combination with another factor contributes to pheromone shutdown in cells that have acquired a plasmid. It exact function has not yet been determined [PUBMED:2158976, PUBMED:10850999]. This entry also contains plant and mammalian proteins, suggesting that these Trab-related proteins may have a somewhat wider or different function in eukaryotes.

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

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
(199)
Full
(4524)
Representative proteomes UniProt
(10705)
NCBI
(16433)
Meta
(257)
RP15
(1023)
RP35
(2699)
RP55
(4388)
RP75
(5951)
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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
(199)
Full
(4524)
Representative proteomes UniProt
(10705)
NCBI
(16433)
Meta
(257)
RP15
(1023)
RP35
(2699)
RP55
(4388)
RP75
(5951)
Alignment:
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Order:
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
(199)
Full
(4524)
Representative proteomes UniProt
(10705)
NCBI
(16433)
Meta
(257)
RP15
(1023)
RP35
(2699)
RP55
(4388)
RP75
(5951)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: none
Type: Family
Sequence Ontology: SO:0100021
Author: Enright A , Ouzounis C , Bateman A
Number in seed: 199
Number in full: 4524
Average length of the domain: 235.30 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 67.16 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -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 26.7
Model length: 263
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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