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0  structures 2009  species 0  interactions 5913  sequences 6  architectures

Family: Phage_holin_2_1 (PF04971)

Summary: Bacteriophage P21 holin S

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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.

Bacteriophage P21 holin S Provide feedback

Phage_holin_2_1 is a family of small hydrophobic holin proteins with one or more transmembrane domains. Members of this family fall into the holin superfamily II, and Phage 21 S holin is the prototype for this superfamily. It has two transmembrane segments with both the N- and C-termini on the cytoplasmic side of the inner membrane in E. coli. Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis. It is thought that the temporal precision of holin-mediated lysis may occur through the build up of a holin oligomer which causes the lysis [1,2].

Literature references

  1. Rietsch A, Blasi U; , FEMS Microbiol Lett 1993;107:101-105.: Non-specific hole formation in the Escherichia coli inner membrane by lambda S proteins in independent of cellular secY and secA functions and of the proportion of membrane acidic phospholipids. PUBMED:8467992 EPMC:8467992

  2. Park T, Struck DK, Dankenbring CA, Young R;, J Bacteriol. 2007;189:9135-9139.: The pinholin of lambdoid phage 21: control of lysis by membrane depolarization. PUBMED:17827300 EPMC:17827300


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007054

The lysis S protein is a cytotoxic protein forming holes in membranes causing cell lysis. The action of Lysis S is independent of the proportion of acidic phospholipids in the membrane [PUBMED:8467992].

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 Holin-II (CL0563), which has the following description:

This superfamily is characterised by phage holins of one or two transmembrane domains. It includes the P21 Holin S, the T7 Holin, the HP1 Holin and the Pseudomonas phage F116 Holin families.

The clan contains the following 4 members:

Phage_holin_2_1 Phage_holin_2_2 Phage_holin_2_3 Phage_holin_2_4

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...

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
(1)
Full
(5913)
Representative proteomes NCBI
(891)
Meta
(0)
RP15
(2)
RP35
(5)
RP55
(9)
RP75
(40)
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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
(1)
Full
(5913)
Representative proteomes NCBI
(891)
Meta
(0)
RP15
(2)
RP35
(5)
RP55
(9)
RP75
(40)
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
(1)
Full
(5913)
Representative proteomes NCBI
(891)
Meta
(0)
RP15
(2)
RP35
(5)
RP55
(9)
RP75
(40)
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.

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.

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_7633 (release 7.0)
Previous IDs: Lysis_S;
Type: Family
Author: Finn RD
Number in seed: 1
Number in full: 5913
Average length of the domain: 65.50 aa
Average identity of full alignment: 82 %
Average coverage of the sequence by the domain: 94.50 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.6 22.6
Trusted cut-off 22.7 22.9
Noise cut-off 22.5 22.5
Model length: 68
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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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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