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0  structures 67  species 0  interactions 76  sequences 2  architectures

Family: Imm63 (PF15599)

Summary: Immunity protein 63

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.

Immunity protein 63 Provide feedback

A predicted immunity protein with an alpha+beta fold and a conserved E+G and ExxY motifs. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Ntox40, Tox-CdiAC and Tox-ARC families [1]. The protein is also found in poly-immunity loci in polymorphic toxin systems.

Literature references

  1. Zhang D, de Souza RF, Anantharaman V, Iyer LM, Aravind L;, Biol Direct. 2012;7:18.: Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. PUBMED:22731697 EPMC:22731697


This tab holds annotation information from the InterPro database.

InterPro entry IPR028952

This entry represents a predicted immunity protein with an alpha+beta fold and a conserved E+G and ExxY motifs. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Ntox40, Tox-CdiAC and Tox-ARC families [ PUBMED:22731697 ]. The protein is also found in polyimmunity loci in polymorphic toxin systems.

Polymorphic toxins systems consist of secreted toxins, primarily involved in intra-specific conflict between related strains of prokaryotes. These toxins are as a rule multi-domain and tend to vary their toxin domains through a process of recombination that might replace an existing toxin domain by a distinct one encoded by standalone cassettes, therefore their name as polymorphic toxins. A key feature that distinguishes the polymorphic toxins from conventional toxins (whose primary targets are in distantly related organisms) is the presence of immunity proteins.

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 and the UniProtKB 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
(76)
Representative proteomes UniProt
(595)
RP15
(8)
RP35
(39)
RP55
(81)
RP75
(172)
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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
(9)
Full
(76)
Representative proteomes UniProt
(595)
RP15
(8)
RP35
(39)
RP55
(81)
RP75
(172)
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
(9)
Full
(76)
Representative proteomes UniProt
(595)
RP15
(8)
RP35
(39)
RP55
(81)
RP75
(172)
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: [1]
Previous IDs: Imm38;
Type: Family
Sequence Ontology: SO:0100021
Author: Zhang D , de Souza RF , Anantharaman V , Iyer LM , Aravind L , Finn RD
Number in seed: 9
Number in full: 76
Average length of the domain: 83.9 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 53.77 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.7 26.7
Trusted cut-off 28.4 27.6
Noise cut-off 26.6 25.3
Model length: 83
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
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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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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