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0  structures 31  species 0  interactions 793  sequences 8  architectures

Family: PPE-SVP (PF12484)

Summary: PPE-SVP subfamily C-terminal region

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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.

PPE-SVP subfamily C-terminal region Provide feedback

This domain family is found in bacteria, and is approximately 90 amino acids in length. The family is found to the C-terminus of PF00823. There is a conserved SVP sequence motif which is diagnostic of this subfamily [2]. There is a single completely conserved residue W that may be functionally important. The proteins in this family are PPE proteins implicated in immunostimulation and virulence.

Literature references

  1. Mackenzie N, Alexander DC, Turenne CY, Behr MA, De Buck JM;, J Clin Microbiol. 2009;47:1002-1011.: Genomic comparison of PE and PPE genes in the Mycobacterium avium complex. PUBMED:19144814 EPMC:19144814

  2. Gey van Pittius NC, Sampson SL, Lee H, Kim Y, van Helden PD, Warren RM;, BMC Evol Biol. 2006;6:95.: Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions. PUBMED:17105670 EPMC:17105670


This tab holds annotation information from the InterPro database.

InterPro entry IPR022171

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].

This domain family is found in bacteria, and is approximately 90 amino acids in length. The family is found in association with . There is a conserved SVP sequence motif. There is a single completely conserved residue W that may be functionally important. The proteins in this family are PE/PPE proteins implicated in immunostimulation and virulence.

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
(89)
Full
(793)
Representative proteomes UniProt
(6391)
NCBI
(17110)
Meta
(0)
RP15
(33)
RP35
(96)
RP55
(641)
RP75
(2460)
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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
(89)
Full
(793)
Representative proteomes UniProt
(6391)
NCBI
(17110)
Meta
(0)
RP15
(33)
RP35
(96)
RP55
(641)
RP75
(2460)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(89)
Full
(793)
Representative proteomes UniProt
(6391)
NCBI
(17110)
Meta
(0)
RP15
(33)
RP35
(96)
RP55
(641)
RP75
(2460)
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: Prosite
Previous IDs: PE_PPE_C;
Type: Family
Sequence Ontology: SO:0100021
Author: Gavin OL, Bateman A
Number in seed: 89
Number in full: 793
Average length of the domain: 83.20 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 21.93 %

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 21.8 21.8
Noise cut-off 21.7 21.7
Model length: 80
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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

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