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0  structures 854  species 0  interactions 2495  sequences 530  architectures

Family: ESPR (PF13018)

Summary: Extended Signal Peptide of Type V secretion system

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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.

Extended Signal Peptide of Type V secretion system Provide feedback

This conserved domain is called ESPR for Extended Signal Peptide Region. It is present at the N-terminus of the signal peptides of proteins belonging to the Type V secretion systems, including the autotransporters (T5aSS), TpsA exoproteins of the two-partner system (T5bSS) and trimeric autotransporters (TAAs). So far, the ESPR is present only in Gram-negative bacterial proteins originating from the classes Beta- and Gamma-proteobacteria. ESPR severely impairs inner membrane translocation, suggesting that it adopts a particular conformation or it interacts with a cytoplasmic or inner membrane co-factor, prior to exportation. Deletion of ESPR causes mis-folding of the TAAs passenger domain in the periplasm , substantially impairing its translocation across the outer membrane [3].

Literature references

  1. Desvaux M, Cooper LM, Filenko NA, Scott-Tucker A, Turner SM, Cole JA, Henderson IR;, FEMS Microbiol Lett. 2006;264:22-30.: The unusual extended signal peptide region of the type V secretion system is phylogenetically restricted. PUBMED:17020545 EPMC:17020545

  2. Desvaux M, Scott-Tucker A, Turner SM, Cooper LM, Huber D, Nataro JP, Henderson IR;, Microbiology. 2007;153:59-70.: A conserved extended signal peptide region directs posttranslational protein translocation via a novel mechanism. PUBMED:17185535 EPMC:17185535

  3. Leyton DL, Rossiter AE, Henderson IR;, Nat Rev Microbiol. 2012;10:213-225.: From self sufficiency to dependence: mechanisms and factors important for autotransporter biogenesis. PUBMED:22337167 EPMC:22337167


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR024973

The extended signal peptide region (ESPR) is a highly conserved region found at the N terminus of the signal peptides of proteins belonging to the Type V secretion systems [PUBMED:17020545, PUBMED:17185535]. These proteins include the autotransporters (T5aSS), TpsA exoproteins of the two-partner system (T5bSS) and trimeric autotransporters (T5cSS). ESPR severely impairs inner membrane translocation, suggesting that it adopts a particular conformation or it interacts with a cytoplasmic or inner membrane co-factor, prior to exportation.

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
(290)
Full
(2495)
Representative proteomes NCBI
(2182)
Meta
(23)
RP15
(52)
RP35
(130)
RP55
(207)
RP75
(281)
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Format an alignment

  Seed
(290)
Full
(2495)
Representative proteomes NCBI
(2182)
Meta
(23)
RP15
(52)
RP35
(130)
RP55
(207)
RP75
(281)
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
(290)
Full
(2495)
Representative proteomes NCBI
(2182)
Meta
(23)
RP15
(52)
RP35
(130)
RP55
(207)
RP75
(281)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
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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: Desvaux M
Previous IDs: none
Type: Domain
Author: Coggill P, Desvaux M
Number in seed: 290
Number in full: 2495
Average length of the domain: 24.40 aa
Average identity of full alignment: 44 %
Average coverage of the sequence by the domain: 1.62 %

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 20.0 20.0
Trusted cut-off 20.0 20.0
Noise cut-off 19.9 19.9
Model length: 24
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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