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12  structures 183  species 0  interactions 1637  sequences 31  architectures

Family: PE (PF00934)

Summary: PE family

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

PE family Provide feedback

This family named after a PE motif near to the amino terminus of the domain. The PE family of proteins all contain an amino-terminal region of about 110 amino acids. The carboxyl terminus of this family are variable and fall into several classes. The largest class of PE proteins is the highly repetitive PGRS class which have a high glycine content. The function of these proteins is uncertain but it has been suggested that they may be related to antigenic variation of Mycobacterium tuberculosis [1]. The C-terminus of this domain contains the type VII secretion signal that has a YXXXD/E motif.

Literature references

  1. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE 3rd, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jage, Nature 1998;393:537-544.: Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. PUBMED:9634230 EPMC:9634230

  2. Strong M, Sawaya MR, Wang S, Phillips M, Cascio D, Eisenberg D; , Proc Natl Acad Sci U S A. 2006;103:8060-8065.: Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis. PUBMED:16690741 EPMC:16690741


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000084

This family is named after a PE motif near to the amino terminus. The carboxyl terminus of this family are variable and fall into several classes. The largest class of PE proteins is the highly repetitive PGRS class which have a high glycine content. The function of these proteins is uncertain but it has been suggested that they may be related to antigenic variation of Mycobacterium tuberculosis [ PUBMED:9634230 ] and also immune modulation [ PUBMED:31662454 ].

The human pathogen Mycobacterium tuberculosis harbours a large number of genes that encode proteins whose N-termini contain the characteristic motifs Pro-Glu (PE) or Pro-Pro-Glu (PPE). A subgroup of the PE proteins contains polymorphic GC-rich sequences (PGRS), while a subgroup of the PPE proteins contains major polymorphic tandem repeats (MPTR). The function of most of these proteins remains unknown [ PUBMED:19602151 ]. However, the PE_PGRS proteins from Mycobacterium marinum are secreted by components of the ESX-5 system that belongs to the recently defined type VII secretion systems [ PUBMED:18981138 ]. It has also been reported that the PE_PGRS family of proteins contains multiple calcium-binding and glycine-rich sequence motifs GGXGXD/NXUX. This sequence repeat constitutes a calcium-binding parallel beta-roll or parallel beta-helix structure and is found in RTX toxins secreted by many Gram-negative bacteria [ PUBMED:18267304 ].

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 EsxAB (CL0352), which has the following description:

The WXG100 protein secretion system (Wss) is responsible for the secretion of WXG100 proteins (PF06013), such as ESAT-10 (6 kDa early secreted antigenic target) and CFP-10 (10 kDa culture filtrate protein) in Mycobacterium tuberculosis or EsxA (ESAT-6-like extracellularly secreted protein A) and EsxB in Staphylococcus aureus. These two proteins, generally encoded in the same gene cluster, form a 1:1 heterodimeric complex. These proteins are virulence factors involved in host-pathogen interaction [1], as demonstrated in Mycobacterium tuberculosis, Staphylococcus aureus or Bacillus anthracis. The Wss is encoded in many other Gram-positive (monoderm) bacteria. This superfamily contains a number of DUFs which are closely related and may or may not represent the same family of proteins.

The clan contains the following 10 members:

DUF2563 DUF3130 DUF4226 DUF5344 EspA_EspE LXG PE PPE T7SS_ESX_EspC WXG100

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...

View options

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
(249)
Full
(1637)
Representative proteomes UniProt
(12995)
RP15
(119)
RP35
(432)
RP55
(1644)
RP75
(4230)
Jalview View  View  View  View  View  View  View 
HTML View  View           
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
(249)
Full
(1637)
Representative proteomes UniProt
(12995)
RP15
(119)
RP35
(432)
RP55
(1644)
RP75
(4230)
Alignment:
Format:
Order:
Sequence:
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Download options

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
(249)
Full
(1637)
Representative proteomes UniProt
(12995)
RP15
(119)
RP35
(432)
RP55
(1644)
RP75
(4230)
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: Pfam-B_253 (release 3.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 249
Number in full: 1637
Average length of the domain: 88.40 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 25.75 %

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 21.3 21.3
Trusted cut-off 21.3 21.3
Noise cut-off 21.2 21.2
Model length: 91
Family (HMM) version: 22
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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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 PE domain has been found. There are 12 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
I6X486 View 3D Structure Click here
I6X7Z8 View 3D Structure Click here
I6XEF1 View 3D Structure Click here
I6XHM5 View 3D Structure Click here
I6Y2J4 View 3D Structure Click here
I6Y8K5 View 3D Structure Click here
I6Y936 View 3D Structure Click here
I6YG87 View 3D Structure Click here
I6YGS7 View 3D Structure Click here
L0T2H7 View 3D Structure Click here
L0T3X8 View 3D Structure Click here
L0T4W6 View 3D Structure Click here
L0TCB8 View 3D Structure Click here
L7N648 View 3D Structure Click here
L7N649 View 3D Structure Click here
L7N656 View 3D Structure Click here
L7N659 View 3D Structure Click here
L7N660 View 3D Structure Click here
L7N661 View 3D Structure Click here
L7N667 View 3D Structure Click here
L7N680 View 3D Structure Click here
L7N681 View 3D Structure Click here
L7N693 View 3D Structure Click here
L7N695 View 3D Structure Click here
L7N697 View 3D Structure Click here
L7N6A1 View 3D Structure Click here
L7N6A7 View 3D Structure Click here
L7N6B5 View 3D Structure Click here
O53553 View 3D Structure Click here
P71664 View 3D Structure Click here
P9WIE7 View 3D Structure Click here
P9WIE9 View 3D Structure Click here
P9WIF1 View 3D Structure Click here
P9WIF3 View 3D Structure Click here
P9WIF5 View 3D Structure Click here
P9WIF7 View 3D Structure Click here
P9WIF9 View 3D Structure Click here
P9WIG1 View 3D Structure Click here
P9WIG3 View 3D Structure Click here
P9WIG5 View 3D Structure Click here
P9WIG7 View 3D Structure Click here
P9WIG9 View 3D Structure Click here
P9WIH1 View 3D Structure Click here
Q6MWV1 View 3D Structure Click here
Q6MWV6 View 3D Structure Click here
Q6MWW6 View 3D Structure Click here
Q6MWW8 View 3D Structure Click here
Q6MWW9 View 3D Structure Click here
Q6MWX5 View 3D Structure Click here
Q6MWY0 View 3D Structure Click here
Q6MX17 View 3D Structure Click here
Q6MX26 View 3D Structure Click here
Q6MX28 View 3D Structure Click here
Q6MX50 View 3D Structure Click here
Q79FA1 View 3D Structure Click here
Q79FA8 View 3D Structure Click here
Q79FB3 View 3D Structure Click here
Q79FC3 View 3D Structure Click here
Q79FD3 View 3D Structure Click here
Q79FD4 View 3D Structure Click here
Q79FE3 View 3D Structure Click here
Q79FE6 View 3D Structure Click here
Q79FE9 View 3D Structure Click here
Q79FJ9 View 3D Structure Click here
Q79FK4 View 3D Structure Click here
Q79FK9 View 3D Structure Click here
Q79FL8 View 3D Structure Click here
Q79FP0 View 3D Structure Click here
Q79FP1 View 3D Structure Click here
Q79FP2 View 3D Structure Click here
Q79FP3 View 3D Structure Click here
Q79FQ7 View 3D Structure Click here
Q79FR3 View 3D Structure Click here
Q79FR5 View 3D Structure Click here
Q79FS5 View 3D Structure Click here
Q79FS8 View 3D Structure Click here
Q79FT0 View 3D Structure Click here
Q79FT3 View 3D Structure Click here
Q79FU0 View 3D Structure Click here
Q79FU2 View 3D Structure Click here
Q79FU3 View 3D Structure Click here
Q79FV3 View 3D Structure Click here
Q79FV6 View 3D Structure Click here
Q79FV8 View 3D Structure Click here
Q79FW5 View 3D Structure Click here
Q79FW8 View 3D Structure Click here
Q79G04 View 3D Structure Click here
Q79G06 View 3D Structure Click here
Q79G08 View 3D Structure Click here