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0  structures 2739  species 0  interactions 6878  sequences 23  architectures

Family: AI-2E_transport (PF01594)

Summary: AI-2E family transporter

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AI-2E family transporter Provide feedback

This family includes four different proteins from E. coli alone. One of them, YdgG or TqsA, has been shown to mediate transport of the quorum-sensing signal autoinducer 2 (AI-2). It is not clear if TqsA enhances secretion of AI-2 or inhibits AI-2 uptake. By altering the intracellular concentration of AI-2, TqsA affects gene expression in biofilms and biofilm formation [1]. TsqA belongs to the AI-2 exporter (AI-2E) superfamily [2].

Literature references

  1. Herzberg M, Kaye IK, Peti W, Wood TK;, J Bacteriol. 2006;188:587-598.: YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport. PUBMED:16385049 EPMC:16385049

  2. Rettner RE, Saier MH Jr;, J Mol Microbiol Biotechnol. 2010;18:195-205.: The autoinducer-2 exporter superfamily. PUBMED:20559013 EPMC:20559013


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002549

This entry includes Escherichia coli AI-2 transport protein TqsA (YdgG), which controls the transport of the quorum-sensing signal AI-2 either by enhancing its secretion or inhibiting its uptake and consequently represses biofilm formation and motility and affects the global gene expression in biofilms [PUBMED:16385049]. TqsA exhibit a uniform topology with 8 putative transmembrane segments (TMSs), a structure shared by proteins in this family. The function of proteins in this family are mostly unknown, however, it has been suggested that they may transport a variety of compounds, possibly all related in structure [PUBMED:20559013].

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 (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
(29)
Full
(6878)
Representative proteomes UniProt
(30834)
NCBI
(41595)
Meta
(2234)
RP15
(1711)
RP35
(5435)
RP55
(9670)
RP75
(15712)
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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
(29)
Full
(6878)
Representative proteomes UniProt
(30834)
NCBI
(41595)
Meta
(2234)
RP15
(1711)
RP35
(5435)
RP55
(9670)
RP75
(15712)
Alignment:
Format:
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
(29)
Full
(6878)
Representative proteomes UniProt
(30834)
NCBI
(41595)
Meta
(2234)
RP15
(1711)
RP35
(5435)
RP55
(9670)
RP75
(15712)
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: Pfam-B_495 (release 4.1)
Previous IDs: DUF20; UPF0118; AI-2_TqsA;
Type: Family
Author: Bashton M, Bateman A
Number in seed: 29
Number in full: 6878
Average length of the domain: 318.20 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 84.02 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.2 27.2
Trusted cut-off 27.4 27.2
Noise cut-off 27.1 27.1
Model length: 327
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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