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0  structures 178  species 0  interactions 220  sequences 1  architecture

Family: Phage_holin_3_3 (PF16083)

Summary: LydA holin phage, holin superfamily III

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LydA holin phage, holin superfamily III Provide feedback

Phage_holin_3_3 is a family of small hydrophobic holin proteins with one or more transmembrane domains. Holins are encoded within the genomes of Gram-positive and Gram-negative bacteria as well as those of the bacteriophages of these organisms. Their primary function appears to be transport of murein hydrolases across the cytoplasmic membrane to the cell wall where these enzymes hydrolyse the cell wall polymer as a prelude to cell lysis. When chromosomally encoded, these enzymes are therefore autolysins. Holins may also facilitate leakage of electrolytes and nutrients from the cell cytoplasm, thereby promoting cell death. Some may catalyse export of nucleases. LydA and lydB are encoded on the dar operon. The phenotype of a rapid lysis in the absence of active LydB suggests that this protein might be an antagonist of the holin LydA [1].

Literature references

  1. Schmidt C, Velleman M, Arber W;, J Bacteriol. 1996;178:1099-1104.: Three functions of bacteriophage P1 involved in cell lysis. PUBMED:8576044 EPMC:8576044


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR032126

This is a family of small hydrophobic holin proteins with one or more transmembrane domains. Holins are encoded within the genomes of Gram-positive and Gram-negative bacteria as well as those of the bacteriophages of these organisms. Their primary function appears to be transport of murein hydrolases across the cytoplasmic membrane to the cell wall where these enzymes hydrolyse the cell wall polymer as a prelude to cell lysis. When chromosomally encoded, these enzymes are therefore autolysins. Holins may also facilitate leakage of electrolytes and nutrients from the cell cytoplasm, thereby promoting cell death. Some may catalyse export of nucleases. LydA and lydB are encoded on the dar operon. The phenotype of a rapid lysis in the absence of active LydB suggests that this protein might be an antagonist of the holin LydA [PUBMED:8576044].

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-III (CL0564), which has the following description:

This superfamily is characterised by one to three-pass transmembrane proteins from Lambda S, P2, LydA, P35, Hol, Holin-X, D/T-Hol holin families.

The clan contains the following 3 members:

Phage_holin_3_1 Phage_holin_3_3 Phage_holin_3_5

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...

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
(42)
Full
(220)
Representative proteomes UniProt
(940)
NCBI
(2144)
Meta
(7)
RP15
(60)
RP35
(130)
RP55
(224)
RP75
(366)
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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
(42)
Full
(220)
Representative proteomes UniProt
(940)
NCBI
(2144)
Meta
(7)
RP15
(60)
RP35
(130)
RP55
(224)
RP75
(366)
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
(42)
Full
(220)
Representative proteomes UniProt
(940)
NCBI
(2144)
Meta
(7)
RP15
(60)
RP35
(130)
RP55
(224)
RP75
(366)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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: Jackhmmer:Q47424
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Coggill P
Number in seed: 42
Number in full: 220
Average length of the domain: 78.00 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 71.31 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.4 28.4
Trusted cut-off 28.4 28.4
Noise cut-off 28.2 28.2
Model length: 78
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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