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70  structures 5712  species 2  interactions 20871  sequences 28  architectures

Family: HlyD (PF00529)

Summary: HlyD membrane-fusion protein of T1SS

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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.

HlyD membrane-fusion protein of T1SS Provide feedback

HlyD is a component of the prototypical alpha-haemolysin (HlyA) bacterial type I secretion system, along with the other components HlyB and TolC. HlyD and HlyB are inner-membrane proteins and specific components of the transport apparatus of alpha-haemolysin. HlyD is anchored in the cytoplasmic membrane by a single transmembrane domain and has a large periplasmic domain within the carboxy-terminal 100 amino acids [1] HlyB and HlyD form a stable complex that binds the recombinant protein bearing a C-terminal HlyA signal sequence and ATP in the cytoplasm [2]. HlyD, HlyB and TolC combine to form the three-component ABC transporter complex that forms a trans-membrane channel or pore through which HlyA can be transferred directly to the extracellular medium. Cutinase has been shown to be transported effectively through this pore [3].

Literature references

  1. Gentschev I, Dietrich G, Goebel W;, Trends Microbiol. 2002;10:39-45.: The E. coli alpha-hemolysin secretion system and its use in vaccine development. PUBMED:11755084 EPMC:11755084

  2. Mergulhao FJ, Summers DK, Monteiro GA;, Biotechnol Adv. 2005;23:177-202.: Recombinant protein secretion in Escherichia coli. PUBMED:15763404 EPMC:15763404

  3. Su L, Chen S, Yi L, Woodard RW, Chen J, Wu J;, Microb Cell Fact. 2012;11:8.: Extracellular overexpression of recombinant Thermobifida fusca cutinase by alpha-hemolysin secretion system in E. coli BL21(DE3). PUBMED:22239833 EPMC:22239833

  4. Su CC, Yang F, Long F, Reyon D, Routh MD, Kuo DW, Mokhtari AK, Van Ornam JD, Rabe KL, Hoy JA, Lee YJ, Rajashankar KR, Yu EW;, J Mol Biol. 2009;393:342-355.: Crystal structure of the membrane fusion protein CusB from Escherichia coli. PUBMED:19695261 EPMC:19695261


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006143

This entry represents a large family of polypeptides, the MFP (for membrane fusion protein) family. MFPs are a component of the of the RND family of transporters (RND refers to resistance, nodulation, and cell division). MFPs are proposed to span the periplasm in some way linking the inner and outer membranes [PUBMED:1495479]. However, some members of this family are found in Gram-positive bacteria, where there is no outer membrane. MFPs are involved in the export of a variety of compounds, from drug molecules to large polypeptides, and are united by their similar overall structural organisation, combined with some conserved regions [PUBMED:16237030].

This family includes:

Gene Ontology

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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 Hybrid (CL0105), which has the following description:

This superfamily contains proteins with a hybrid motif [1]. This motif is embedded in structurally diverse proteins.

The clan contains the following 19 members:

Apocytochr_F_C Biotin_lipoyl Biotin_lipoyl_2 Complex1_51K DUF2118 DUF2254 GCV_H HlyD HlyD_2 HlyD_3 HlyD_D23 HlyD_D4 NQRA OEP Peptidase_M23 PTS_EIIA_1 PYNP_C QRPTase_N RnfC_N

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...

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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
(46)
Full
(20871)
Representative proteomes NCBI
(15380)
Meta
(309)
RP15
(69)
RP35
(168)
RP55
(337)
RP75
(603)
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  Seed
(46)
Full
(20871)
Representative proteomes NCBI
(15380)
Meta
(309)
RP15
(69)
RP35
(168)
RP55
(337)
RP75
(603)
Alignment:
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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
(46)
Full
(20871)
Representative proteomes NCBI
(15380)
Meta
(309)
RP15
(69)
RP35
(168)
RP55
(337)
RP75
(603)
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.

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: MRC-LMB Genome group
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 46
Number in full: 20871
Average length of the domain: 322.50 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 84.76 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.2 26.2
Trusted cut-off 26.2 26.2
Noise cut-off 26.1 26.1
Model length: 80
Family (HMM) version: 16
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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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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Interactions

There are 2 interactions for this family. More...

HlyD HlyD_2

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 HlyD domain has been found. There are 70 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 seqence.

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