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6  structures 5038  species 0  interactions 20676  sequences 102  architectures

Family: HlyD_3 (PF13437)

Summary: HlyD family secretion protein

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.

HlyD family secretion protein Provide feedback

This is a family of largely bacterial haemolysin translocator HlyD proteins.

Internal database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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 26 members:

Apocytochr_F_C Biotin_carb_C Biotin_lipoyl Biotin_lipoyl_2 Complex1_51K CusB_dom_1 DUF2118 DUF2254 GARS_C GCV_H HlyD_2 HlyD_3 HlyD_D23 HlyD_D4 HMBD LAL_C2 NAPRTase_N NQRA OEP Peptidase_M23 PGM1_C PTS_EIIA_1 PurK_C 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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(58)
Full
(20676)
Representative proteomes UniProt
(110075)
RP15
(2350)
RP35
(9283)
RP55
(21472)
RP75
(41261)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(58)
Full
(20676)
Representative proteomes UniProt
(110075)
RP15
(2350)
RP35
(9283)
RP55
(21472)
RP75
(41261)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(58)
Full
(20676)
Representative proteomes UniProt
(110075)
RP15
(2350)
RP35
(9283)
RP55
(21472)
RP75
(41261)
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: Jackhmmer:Q2Y7Y5
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Coggill P
Number in seed: 58
Number in full: 20676
Average length of the domain: 113.8 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 27.78 %

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 22.2 22.2
Trusted cut-off 22.2 22.2
Noise cut-off 22.1 22.1
Model length: 106
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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

Selections

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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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Tree controls

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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_3 domain has been found. There are 6 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0H3GUH7 View 3D Structure Click here
A0A0H3GXQ6 View 3D Structure Click here
A0A0H3H0N0 View 3D Structure Click here
A0A0H3H3P2 View 3D Structure Click here
A0A0H3H4J7 View 3D Structure Click here
A6TBH3 View 3D Structure Click here
A8AQD5 View 3D Structure Click here
A9MNW9 View 3D Structure Click here
B2VGW1 View 3D Structure Click here
B4EY99 View 3D Structure Click here
H9L452 View 3D Structure Click here
O31593 View 3D Structure Click here
P76397 View 3D Structure Click here
Q2G2W5 View 3D Structure Click here
Q32B98 View 3D Structure Click here
Q32J80 View 3D Structure Click here
Q5F679 View 3D Structure Click here
Q5FAA4 View 3D Structure Click here
Q6D2B2 View 3D Structure Click here
Q6DAH5 View 3D Structure Click here
Q7CPM8 View 3D Structure Click here
Q83KI5 View 3D Structure Click here
Q83Q03 View 3D Structure Click here
Q887Q0 View 3D Structure Click here
Q88NC6 View 3D Structure Click here
Q8DQW4 View 3D Structure Click here
Q8DRI1 View 3D Structure Click here
Q8X7J5 View 3D Structure Click here
Q8ZAU9 View 3D Structure Click here
Q8ZCW1 View 3D Structure Click here
Q8ZLD9 View 3D Structure Click here
Q8ZMV7 View 3D Structure Click here
Q8ZNQ3 View 3D Structure Click here
Q9CJB7 View 3D Structure Click here
Q9HTV8 View 3D Structure Click here
Q9HWN9 View 3D Structure Click here
Q9HXC1 View 3D Structure Click here
Q9HY69 View 3D Structure Click here
Q9HYN6 View 3D Structure Click here
Q9HYU0 View 3D Structure Click here