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16  structures 60  species 4  interactions 65  sequences 1  architecture

Family: T3SS_needle_E (PF08988)

Summary: Type III secretion system, cytoplasmic E component of needle

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This is the Wikipedia entry entitled "Type III secretion". More...

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Type III secretion system, cytoplasmic E component of needle Provide feedback

T3SS_needle_E is a family of proteins from the operon that builds and controls the needle of the injection system of type III secretion. The YscE protein, produced by the pathogen Yersinia, assumes a secondary structure composed of two anti-parallel alpha-helices separated by a flexible loop [1]. The family is cytoplasmic and may help to stabilise and prevent early polymerisation of the needle-protein F [2,3].

Literature references

  1. Quinaud M, Chabert J, Faudry E, Neumann E, Lemaire D, Pastor A, Elsen S, Dessen A, Attree I;, J Biol Chem. 2005;280:36293-36300.: The PscE-PscF-PscG complex controls type III secretion needle biogenesis in Pseudomonas aeruginosa. PUBMED:16115870 EPMC:16115870

  2. Sun P, Tropea JE, Austin BP, Cherry S, Waugh DS;, J Mol Biol. 2008;377:819-830.: Structural characterization of the Yersinia pestis type III secretion system needle protein YscF in complex with its heterodimeric chaperone YscE/YscG. PUBMED:18281060 EPMC:18281060

  3. Galle M, Jin S, Bogaert P, Haegman M, Vandenabeele P, Beyaert R;, PLoS One. 2012;7:e41547.: The Pseudomonas aeruginosa type III secretion system has an exotoxin S/T/Y independent pathogenic role during acute lung infection. PUBMED:22844497 EPMC:22844497


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR012671

Members of this family are found exclusively in type III secretion apparatus gene clusters in bacteria. Those bacteria with a protein from this family tend to target animal cells, as does Yersinia pestis [PUBMED:1860816]. This protein is small (about 70 amino acids) and not well characterised.

Gene Ontology

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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, 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
(9)
Full
(65)
Representative proteomes UniProt
(724)
NCBI
(826)
Meta
(5)
RP15
(0)
RP35
(1)
RP55
(3)
RP75
(6)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(9)
Full
(65)
Representative proteomes UniProt
(724)
NCBI
(826)
Meta
(5)
RP15
(0)
RP35
(1)
RP55
(3)
RP75
(6)
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
(9)
Full
(65)
Representative proteomes UniProt
(724)
NCBI
(826)
Meta
(5)
RP15
(0)
RP35
(1)
RP55
(3)
RP75
(6)
Raw Stockholm Download   Download     Download   Download   Download   Download   Download   Download  
Gzipped 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: pdb_1zw0
Previous IDs: DUF1895;
Type: Family
Sequence Ontology: SO:0100021
Author: Mistry J , Sammut SJ
Number in seed: 9
Number in full: 65
Average length of the domain: 65.00 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 83.94 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.8 21.8
Trusted cut-off 22.0 22.4
Noise cut-off 21.7 21.5
Model length: 66
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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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Interactions

There are 4 interactions for this family. More...

T3SS_needle_E Type_III_YscG Type_III_YscG T3SS_needle_F

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the T3SS_needle_E domain has been found. There are 16 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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